First upper limit analysis and results from LIGO science data: stochastic background

I describe analysis of correlations in the outputs of the three LIGO interferometers from LIGO's first science run, held over 17 days in August and September of 2002, and the resulting upper limit set on a stochastic background of gravitational waves. By searching for cross-correlations between the LIGO detectors in Livingston, LA and Hanford, WA, we are able to set a 90% confidence level upper limit of h_{100}^2 Omega_0 < 23 +/- 4.6.Comment: 7 pages; 1 eps figures; proceeding from 2003 Edoardo Amaldi Meeting on Gravitational Wave

Microstructure Characterization of RERTR Fuel

A variety of phases have the potential to develop in the irradiated fuels for the reduced enrichment research test reactor (RERTR) program. To study the radiation stability of these potential phases, three depleted uranium alloys were cast. The phases of interest were identified including U(Si,Al)3, (U,Mo)(Si,Al)3, UMo2Al20, UAl4, and U6Mo4Al43. These alloys were irradiated with 2.6 MeV protons at 200ºC up to 3.0 dpa. The microstructure is characterized using SEM and TEM. Microstructural characterization for an archive dispersion fuel plate (U-7Mo fuel particles in Al-2%Si cladding) was also carried out. TEM sample preparation for the irradiated dispersion fuel has been developed

BitterDB: a database of bitter compounds

Basic taste qualities like sour, salty, sweet, bitter and umami serve specific functions in identifying food components found in the diet of humans and animals, and are recognized by proteins in the oral cavity. Recognition of bitter taste and aversion to it are thought to protect the organism against the ingestion of poisonous food compounds, which are often bitter. Interestingly, bitter taste receptors are expressed not only in the mouth but also in extraoral tissues, such as the gastrointestinal tract, indicating that they may play a role in digestive and metabolic processes. BitterDB database, available at http://bitterdb.agri.huji.ac.il/bitterdb/, includes over 550 compounds that were reported to taste bitter to humans. The compounds can be searched by name, chemical structure, similarity to other bitter compounds, association with a particular human bitter taste receptor, and so on. The database also contains information on mutations in bitter taste receptors that were shown to influence receptor activation by bitter compounds. The aim of BitterDB is to facilitate studying the chemical features associated with bitterness. These studies may contribute to predicting bitterness of unknown compounds, predicting ligands for bitter receptors from different species and rational design of bitterness modulators

Four-Year Treatment Outcomes of Adult Patients Enrolled in Mozambique's Rapidly Expanding Antiretroviral Therapy Program

BACKGROUND: In Mozambique during 2004-2007 numbers of adult patients (≥15 years old) enrolled on antiretroviral therapy (ART) increased about 16-fold, from <5,000 to 79,500. All ART patients were eligible for co-trimoxazole. ART program outcomes, and determinants of outcomes, have not yet been reported. METHODOLOGY/PRINCIPAL FINDINGS: In a retrospective cohort study, we investigated rates of mortality, attrition (death, loss to follow-up, or treatment cessation), immunologic treatment failure, and regimen-switch, as well as determinants of selected outcomes, among a nationally representative sample of 2,596 adults initiating ART during 2004-2007. At ART initiation, median age of patients was 34 and 62% were female. Malnutrition and advanced disease were common; 18% of patients weighed <45 kilograms, and 15% were WHO stage IV. Median baseline CD4(+) T-cell count was 153/µL and was lower for males than females (139/µL vs. 159/µL, p<0.01). Stavudine, lamivudine, and nevirapine or efavirenz were prescribed to 88% of patients; only 31% were prescribed co-trimoxazole. Mortality and attrition rates were 3.4 deaths and 19.8 attritions per 100 patient-years overall, and 12.9 deaths and 57.2 attritions per 100 patient-years in the first 90 days. Predictors of attrition included male sex [adjusted hazard ratio (AHR) 1.5; 95% confidence interval (CI), 1.3-1.8], weight <45 kg (AHR 2.1; 95% CI, 1.6-2.9, reference group >60 kg), WHO stage IV (AHR 1.7; 95% CI, 1.3-2.4, reference group WHO stage I/II), lack of co-trimoxazole prescription (AHR 1.4; 95% CI, 1.0-1.8), and later calendar year of ART initiation (AHR 1.5; 95% CI, 1.2-1.8). Rates of immunologic treatment failure and regimen-switch were 14.0 and 0.6 events per 100-patient years, respectively. CONCLUSIONS: ART initiation at earlier disease stages and scale-up of co-trimoxazole among ART patients could improve outcomes. Research to determine reasons for low regimen-switch rates and increasing rates of attrition during program expansion is needed

Evolutionarily Conserved Substrate Substructures for Automated Annotation of Enzyme Superfamilies

The evolution of enzymes affects how well a species can adapt to new environmental conditions. During enzyme evolution, certain aspects of molecular function are conserved while other aspects can vary. Aspects of function that are more difficult to change or that need to be reused in multiple contexts are often conserved, while those that vary may indicate functions that are more easily changed or that are no longer required. In analogy to the study of conservation patterns in enzyme sequences and structures, we have examined the patterns of conservation and variation in enzyme function by analyzing graph isomorphisms among enzyme substrates of a large number of enzyme superfamilies. This systematic analysis of substrate substructures establishes the conservation patterns that typify individual superfamilies. Specifically, we determined the chemical substructures that are conserved among all known substrates of a superfamily and the substructures that are reacting in these substrates and then examined the relationship between the two. Across the 42 superfamilies that were analyzed, substantial variation was found in how much of the conserved substructure is reacting, suggesting that superfamilies may not be easily grouped into discrete and separable categories. Instead, our results suggest that many superfamilies may need to be treated individually for analyses of evolution, function prediction, and guiding enzyme engineering strategies. Annotating superfamilies with these conserved and reacting substructure patterns provides information that is orthogonal to information provided by studies of conservation in superfamily sequences and structures, thereby improving the precision with which we can predict the functions of enzymes of unknown function and direct studies in enzyme engineering. Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized and uncharacterized enzyme superfamilies

Hookworm-Related Anaemia among Pregnant Women: A Systematic Review

Anaemia affects large numbers of pregnant women in developing countries and increases their risk of dying during pregnancy and delivering low birth weight babies, who in turn are at increased risk of dying. Human hookworm infection has long been recognized among the major causes of anaemia in poor communities, but understanding of the benefits of the management of hookworm infection in pregnancy has lagged behind the other major causes of maternal anaemia. Low coverage of anthelmintic treatment in maternal health programmes in many countries has been the result. After systematically reviewing the available literature we observed that increasing hookworm infection intensity is associated with lower haemoglobin levels in pregnant women. We also estimate that between a quarter and a third of pregnant women in sub-Saharan Africa are infected with hookworm and at risk of preventable hookworm-related anaemia. However, all identified intervention studies showed a benefit of deworming for maternal or child health and we argue that increased efforts should be made to increase the coverage of anthelmintic treatment among pregnant women

Pathogenicity factors in group C and G streptococci

Initially recognized zoonoses, streptococci belonging to Lancefield group C (GCS) and G (GGS) were subsequently recognised as human pathogens causing a diverse range of symptoms, from asymptomatic carriage to life threatening diseases. Their taxonomy has changed during the last decade. Asymptomatic carriage is <4% amongst the human population and invasive infections are often in association with chronic diseases such as diabetes, cardiovascular diseases or chronic skin infections. Other clinical manifestations include acute pharyngitis, pneumonia, endocarditis, bacteraemia and toxic-shock syndrome. Post streptococcal sequalae such as rheumatic fever and acute glomerulonephritis have also been described but mainly in developed countries and amongst specific populations. Putative virulence determinants for these organisms include adhesins, toxins, and other factors that are essential for dissemination in human tissues and for interference with the host immune responses. High nucleotide similarities among virulence genes and their association with mobile genetic elements supports the hypothesis of extensive horizontal gene transfer events between the various pyogenic streptococcal species belonging to Lancefield groups A, C and G. A better understanding of the mechanisms of pathogenesis should be apparent by whole-genome sequencing, and this would result in more effective clinical strategies for the pyogenic group in general

Soil-Transmitted Helminth Reinfection after Drug Treatment: A Systematic Review and Meta-Analysis

Infections with soil-transmitted helminths (the roundworm Ascaris lumbricoides, the whipworm Trichuris trichiura, and hookworm) affect over 1 billion people, particularly rural communities in the developing world. The global strategy to control soil-transmitted helminth infections is ‘preventive chemotherapy’, which means large-scale administration of anthelmintic drugs to at-risk populations. However, because reinfection occurs after treatment, ‘preventive chemotherapy’ must be repeated regularly. Our systematic review and meta-analysis found that at 3, 6, and 12 months after treatment, A. lumbricoides prevalence reached 26% (95% confidence interval (CI): 16–43%), 68% (95% CI: 60–76%) and 94% (95% CI: 88–100%) of pretreatment levels, respectively. For T. trichiura, respective reinfection prevalence at these time points were 36% (95% CI: 28–47%), 67% (95% CI: 42–100%), and 82% (95% CI: 62–100%); and for hookworm, 30% (95% CI: 26–34%), 55% (95% CI: 34–87%), and 57% (95% CI: 49–67%). Prevalence and intensity of reinfection were positively correlated with pretreatment infection status. Our results suggest a frequent anthelmintic drug administration to maximize the benefit of preventive chemotherapy. Moreover, an integrated control strategy, consisting of preventive chemotherapy combined with health education and environmental sanitation is needed to interrupt transmission of soil-transmitted helminths