Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG

The structures of a new crystal form of free Escherichia coli uracil DNA glycosylase (UDG), containing four molecules in the asymmetric unit, and two forms of its complex with the proteinaceous inhibitor Ugi, containing two and four crystallographically independent complexes, have been determined. A comparison of these structures and the already known crystal structures containing UDG shows that the enzyme can be considered to be made up of two independently moving structural entities or domains. A detailed study of free and DNA-bound human enzyme strengthens this conclusion. The domains close upon binding to uracil-containing DNA, whereas they do not appear to do so upon binding to Ugi. The comparative study also shows that the mobility of the molecule involves the rigid-body movement of the domains superposed on flexibility within domains

Rapid UBVRI Follow-up of the Highly Collimated Optical Afterglow of GRB010222

(Abridged) We present the earliest optical observations of the optical counterpart to the GRB 010222, obtained with the FLWO 1.2-m telescope in UBVRI passbands, starting 3.64 hours after the burst. We also present late R-band observations of the afterglow obtained with the 1.8-m VATT ~25 days after the burst. The temporal analysis of our data joined with published data indicates a steepening decay, independent of wavelength, asymptotically approaching t^{-0.80+/-0.05} at early times (t << 1 day) and t^{-1.30+/-0.05} at late times, with a sharp break at t_b=0.72+/-0.1 days. This is the second earliest observed break of any afterglow (after GRB 980519), which clearly indicates the importance of rapid multi-band follow-up for GRB afterglow research. The optical spectral energy distribution, corrected for small Galactic reddening, can be fit fairly well by a single power-law with a slope of -1.07+/-0.09. However, when we fit using our BVRI data only, we obtain a shallower slope of -0.88+/- 0.1, in excellent agreement with the slope derived from our low-resolution spectrum (-0.89 +/- 0.03). The spectral slope and light curve decay slopes we derive are not consistent with a jet model despite the presence of a temporal break. Significant host dust extinction with a star-burst reddening law would flatten the spectral index to match jet predictions and still be consistent with the observed spectral energy distribution. We derive an opening angle of 2.1 deg, smaller than any listed in the recent compilation of Frail et al. The total beamed energy corrected for the jet geometry is 4x10^50 erg, very close to the ``standard'' value of 5x10^50 erg found by Frail et al. for a number of other bursts with light-curve breaks.Comment: revised version (minor changes only) to be published in the ApJ Part 1, 12 pages, 4 figures; all data used for the fits and our CCD frames available at ftp://cfa-ftp.harvard.edu/pub/kstanek/GRB010222/ and through WWW at http://cfa-www.harvard.edu/cfa/oir/Research/GRB

SN 2007uy - metamorphosis of an aspheric Type Ib explosion

The supernovae of Type Ibc are rare and the detailed characteristics of these explosions have been studied only for a few events. Unlike Type II SNe, the progenitors of Type Ibc have never been detected in pre-explosion images. So, to understand the nature of their progenitors and the characteristics of the explosions, investigation of proximate events are necessary. Here we present the results of multi-wavelength observations of Type Ib SN 2007uy in the nearby ($\sim$ 29.5 Mpc) galaxy NGC 2770. Analysis of the photometric observations revealed this explosion as an energetic event with peak absolute R band magnitude $-18.5\pm0.16$, which is about one mag brighter than the mean value ($-17.6\pm0.6$) derived for well observed Type Ibc events. The SN is highly extinguished, E(B-V) = 0.63$\pm$0.15 mag, mainly due to foreground material present in the host galaxy. From optical light curve modeling we determine that about 0.3 M$_{\odot}$ radioactive $^{56}$Ni is produced and roughly 4.4 M$_{\odot}$ material is ejected during this explosion with liberated energy $\sim 15\times10^{51}$ erg, indicating the event to be an energetic one. Through optical spectroscopy, we have noticed a clear aspheric evolution of several line forming regions, but no dependency of asymmetry is seen on the distribution of $^{56}$Ni inside the ejecta. The SN shock interaction with the circumburst material is clearly noticeable in radio follow-up, presenting a Synchrotron Self Absorption (SSA) dominated light curve with a contribution of Free Free Absorption (FFA) during the early phases. Assuming a WR star, with wind velocity \ga 10^3 {\rm km s}^{-1}, as a progenitor, we derive a lower limit to the mass loss rate inferred from the radio data as \dot{M} \ga 2.4\times10^{-5} M$_{\odot}$, yr$^{-1}$, which is consistent with the results obtained for other Type Ibc SNe bright at radio frequencies.Comment: 22 pages, 13 figures, accepted for publication in MNRA

Influenza-A Viruses in Ducks in Northwestern Minnesota: Fine Scale Spatial and Temporal Variation in Prevalence and Subtype Diversity

Waterfowl from northwestern Minnesota were sampled by cloacal swabbing for Avian Influenza Virus (AIV) from July – October in 2007 and 2008. AIV was detected in 222 (9.1%) of 2,441 ducks in 2007 and in 438 (17.9%) of 2,452 ducks in 2008. Prevalence of AIV peaked in late summer. We detected 27 AIV subtypes during 2007 and 31 during 2008. Ten hemagglutinin (HA) subtypes were detected each year (i.e., H1, 3–8, and 10–12 during 2007; H1-8, 10 and 11 during 2008). All neuraminidase (NA) subtypes were detected during each year of the study. Subtype diversity varied between years and increased with prevalence into September. Predominant subtypes during 2007 (comprising ≥5% of subtype diversity) included H1N1, H3N6, H3N8, H4N6, H7N3, H10N7, and H11N9. Predominant subtypes during 2008 included H3N6, H3N8, H4N6, H4N8, H6N1, and H10N7. Additionally, within each HA subtype, the same predominant HA/NA subtype combinations were detected each year and included H1N1, H3N8, H4N6, H5N2, H6N1, H7N3, H8N4, H10N7, and H11N9. The H2N3 and H12N5 viruses also predominated within the H2 and H12 subtypes, respectively, but only were detected during a single year (H2 and H12 viruses were not detected during 2007 and 2008, respectively). Mallards were the predominant species sampled (63.7% of the total), and 531 AIV were isolated from this species (80.5% of the total isolates). Mallard data collected during both years adequately described the observed temporal and spatial prevalence from the total sample and also adequately represented subtype diversity. Juvenile mallards also were adequate in describing the temporal and spatial prevalence of AIV as well as subtype diversity

Technical summary

The Working Group III (WGIII) contribution to the IPCC's Fifth Assessment Report (AR5) assesses literature on the scientific, technological, environmental, economic and social aspects of mitigation of climate change. It builds upon the WGIII contribution to the IPCC's Fourth Assessment Report (AR4), the Special Report on Renewable Energy Sources and Climate Change Mitigation (SRREN) and previous reports and incorporates subsequent new findings and research. Throughout, the focus is on the implications of its findings for policy, without being prescriptive about the particular policies that governments and other important participants in the policy process should adopt. In light of the IPCC's mandate, authors in WGIII were guided by several principles when assembling this assessment: (1) to be explicit about mitigation options, (2) to be explicit about their costs and about their risks and opportunities vis-a-vis other development priorities, (3) and to be explicit about the underlying criteria, concepts, and methods for evaluating alternative policies. This summary offers the main findings of the report

Constraining Present‐Day Anthropogenic Total Iron Emissions Using Model and Observations

Iron emissions from human activities, such as oil combustion and smelting, affect the Earth's climate and marine ecosystems. These emissions are difficult to quantify accurately due to a lack of observations, particularly in remote ocean regions. In this study, we used long‐term, near‐source observations in areas with a dominance of anthropogenic iron emissions in various parts of the world to better estimate the total amount of anthropogenic iron emissions. We also used a statistical source apportionment method to identify the anthropogenic components and their sub‐sources from bulk aerosol observations in the United States. We find that the estimates of anthropogenic iron emissions are within a factor of 3 in most regions compared to previous inventory estimates. Under‐ or overestimation varied by region and depended on the number of sites, interannual variability, and the statistical filter choice. Smelting‐related iron emissions are overestimated by a factor of 1.5 in East Asia compared to previous estimates. More long‐term iron observations and the consideration of the influence of dust and wildfires could help reduce the uncertainty in anthropogenic iron emissions estimates

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Cross-National Analysis of the Associations between Traumatic Events and Suicidal Behavior: Findings from the WHO World Mental Health Surveys

Background Community and clinical data have suggested there is an association between trauma exposure and suicidal behavior (i.e., suicide ideation, plans and attempts). However, few studies have assessed which traumas are uniquely predictive of: the first onset of suicidal behavior, the progression from suicide ideation to plans and attempts, or the persistence of each form of suicidal behavior over time. Moreover, few data are available on such associations in developing countries. The current study addresses each of these issues.Methodology/Principal Findings Data on trauma exposure and subsequent first onset of suicidal behavior were collected via structured interviews conducted in the households of 102,245 (age 18+) respondents from 21 countries participating in the WHO World Mental Health Surveys. Bivariate and multivariate survival models tested the relationship between the type and number of traumatic events and subsequent suicidal behavior. A range of traumatic events are associated with suicidal behavior, with sexual and interpersonal violence consistently showing the strongest effects. There is a dose-response relationship between the number of traumatic events and suicide ideation/attempt; however, there is decay in the strength of the association with more events. Although a range of traumatic events are associated with the onset of suicide ideation, fewer events predict which people with suicide ideation progress to suicide plan and attempt, or the persistence of suicidal behavior over time. Associations generally are consistent across high-, middle-, and low-income countries.Conclusions/Significance This study provides more detailed information than previously available on the relationship between traumatic events and suicidal behavior and indicates that this association is fairly consistent across developed and developing countries. These data reinforce the importance of psychological trauma as a major public health problem, and highlight the significance of screening for the presence and accumulation of traumatic exposures as a risk factor for suicide ideation and attempt.African and African American StudiesPsycholog

Smoking prevalence and attributable disease burden in 195 countries and territories, 1990-2015 : a systematic analysis from the Global Burden of Disease Study 2015

Background The scale-up of tobacco control, especially after the adoption of the Framework Convention for Tobacco Control, is a major public health success story. Nonetheless, smoking remains a leading risk for early death and disability worldwide, and therefore continues to require sustained political commitment. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) offers a robust platform through which global, regional, and national progress toward achieving smoking-related targets can be assessed. Methods We synthesised 2818 data sources with spatiotemporal Gaussian process regression and produced estimates of daily smoking prevalence by sex, age group, and year for 195 countries and territories from 1990 to 2015. We analysed 38 risk-outcome pairs to generate estimates of smoking-attributable mortality and disease burden, as measured by disability-adjusted life-years (DALYs). We then performed a cohort analysis of smoking prevalence by birth-year cohort to better understand temporal age patterns in smoking. We also did a decomposition analysis, in which we parsed out changes in all-cause smoking-attributable DALYs due to changes in population growth, population ageing, smoking prevalence, and risk-deleted DALY rates. Finally, we explored results by level of development using the Socio-demographic Index (SDI). Findings Worldwide, the age-standardised prevalence of daily smoking was 25.0% (95% uncertainty interval [UI] 24.2-25.7) for men and 5.4% (5.1-5.7) for women, representing 28.4% (25.8-31.1) and 34.4% (29.4-38.6) reductions, respectively, since 1990. A greater percentage of countries and territories achieved significant annualised rates of decline in smoking prevalence from 1990 to 2005 than in between 2005 and 2015; however, only four countries had significant annualised increases in smoking prevalence between 2005 and 2015 (Congo [Brazzaville] and Azerbaijan for men and Kuwait and Timor-Leste for women). In 2015, 11.5% of global deaths (6.4 million [95% UI 5.7-7.0 million]) were attributable to smoking worldwide, of which 52.2% took place in four countries (China, India, the USA, and Russia). Smoking was ranked among the five leading risk factors by DALYs in 109 countries and territories in 2015, rising from 88 geographies in 1990. In terms of birth cohorts, male smoking prevalence followed similar age patterns across levels of SDI, whereas much more heterogeneity was found in age patterns for female smokers by level of development. While smoking prevalence and risk-deleted DALY rates mostly decreased by sex and SDI quintile, population growth, population ageing, or a combination of both, drove rises in overall smoking-attributable DALYs in low-SDI to middle-SDI geographies between 2005 and 2015. Interpretation The pace of progress in reducing smoking prevalence has been heterogeneous across geographies, development status, and sex, and as highlighted by more recent trends, maintaining past rates of decline should not be taken for granted, especially in women and in low-SDI to middle-SDI countries. Beyond the effect of the tobacco industry and societal mores, a crucial challenge facing tobacco control initiatives is that demographic forces are poised to heighten smoking's global toll, unless progress in preventing initiation and promoting cessation can be substantially accelerated. Greater success in tobacco control is possible but requires effective, comprehensive, and adequately implemented and enforced policies, which might in turn require global and national levels of political commitment beyond what has been achieved during the past 25 years.Peer reviewe

Global, regional, and national incidence, prevalence, and years lived with disability for 310 diseases and injuries, 1990–2015: a systematic analysis for the Global Burden of Disease Study 2015

Background Non-fatal outcomes of disease and injury increasingly detract from the ability of the world's population to live in full health, a trend largely attributable to an epidemiological transition in many countries from causes affecting children, to non-communicable diseases (NCDs) more common in adults. For the Global Burden of Diseases, Injuries, and Risk Factors Study 2015 (GBD 2015), we estimated the incidence, prevalence, and years lived with disability for diseases and injuries at the global, regional, and national scale over the period of 1990 to 2015. Methods We estimated incidence and prevalence by age, sex, cause, year, and geography with a wide range of updated and standardised analytical procedures. Improvements from GBD 2013 included the addition of new data sources, updates to literature reviews for 85 causes, and the identification and inclusion of additional studies published up to November, 2015, to expand the database used for estimation of non-fatal outcomes to 60 900 unique data sources. Prevalence and incidence by cause and sequelae were determined with DisMod-MR 2.1, an improved version of the DisMod-MR Bayesian meta-regression tool first developed for GBD 2010 and GBD 2013. For some causes, we used alternative modelling strategies where the complexity of the disease was not suited to DisMod-MR 2.1 or where incidence and prevalence needed to be determined from other data. For GBD 2015 we created a summary indicator that combines measures of income per capita, educational attainment, and fertility (the Socio-demographic Index [SDI]) and used it to compare observed patterns of health loss to the expected pattern for countries or locations with similar SDI scores. Findings We generated 9·3 billion estimates from the various combinations of prevalence, incidence, and YLDs for causes, sequelae, and impairments by age, sex, geography, and year. In 2015, two causes had acute incidences in excess of 1 billion: upper respiratory infections (17·2 billion, 95% uncertainty interval [UI] 15·4–19·2 billion) and diarrhoeal diseases (2·39 billion, 2·30–2·50 billion). Eight causes of chronic disease and injury each affected more than 10% of the world's population in 2015: permanent caries, tension-type headache, iron-deficiency anaemia, age-related and other hearing loss, migraine, genital herpes, refraction and accommodation disorders, and ascariasis. The impairment that affected the greatest number of people in 2015 was anaemia, with 2·36 billion (2·35–2·37 billion) individuals affected. The second and third leading impairments by number of individuals affected were hearing loss and vision loss, respectively. Between 2005 and 2015, there was little change in the leading causes of years lived with disability (YLDs) on a global basis. NCDs accounted for 18 of the leading 20 causes of age-standardised YLDs on a global scale. Where rates were decreasing, the rate of decrease for YLDs was slower than that of years of life lost (YLLs) for nearly every cause included in our analysis. For low SDI geographies, Group 1 causes typically accounted for 20–30% of total disability, largely attributable to nutritional deficiencies, malaria, neglected tropical diseases, HIV/AIDS, and tuberculosis. Lower back and neck pain was the leading global cause of disability in 2015 in most countries. The leading cause was sense organ disorders in 22 countries in Asia and Africa and one in central Latin America; diabetes in four countries in Oceania; HIV/AIDS in three southern sub-Saharan African countries; collective violence and legal intervention in two north African and Middle Eastern countries; iron-deficiency anaemia in Somalia and Venezuela; depression in Uganda; onchoceriasis in Liberia; and other neglected tropical diseases in the Democratic Republic of the Congo. Interpretation Ageing of the world's population is increasing the number of people living with sequelae of diseases and injuries. Shifts in the epidemiological profile driven by socioeconomic change also contribute to the continued increase in years lived with disability (YLDs) as well as the rate of increase in YLDs. Despite limitations imposed by gaps in data availability and the variable quality of the data available, the standardised and comprehensive approach of the GBD study provides opportunities to examine broad trends, compare those trends between countries or subnational geographies, benchmark against locations at similar stages of development, and gauge the strength or weakness of the estimates available. Funding Bill &amp; Melinda Gates Foundation