09141 Abstracts Collection -- Web Application Security

From 29th March to 3rd April 2009 the Dagstuhl Seminar 09141 Web Application Security was held in Schloss Dagstuhl -- Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar are put together in this paper. Links to full papers (if available) are provided in the corresponding seminar summary document

Achieving the WHO/UNAIDS antiretroviral treatment 3 by 5 goal: what will it cost?

The "3 by 5" goal to have 3 million people in low and middle income countries on antiretroviral therapy (ART) by the end of 2005 is ambitious. Estimates of the necessary resources are needed to facilitate resource mobilisation and rapid channelling of funds to where they are required. We estimated the financial costs needed to implement treatment protocols, by use of country-specific estimates for 34 countries that account for 90% of the need for ART in resource-poor settings. We first estimated the number of people needing ART and supporting programmes for each country. We then estimated the cost per patient for each programme by country to derive total costs. We estimate that between US5.1 billion dollars and US5.9 billion dollars will be needed by the end of 2005 to provide ART, support programmes, and cover country-level administrative and logistic costs for 3 by 5

Phenotypic and genotypic characteristics of small colony variants and their role in chronic infection

Small colony variant (SCV) bacteria arise spontaneously within apparently homogeneous microbial populations, largely in response to environmental stresses, such as antimicrobial treatment. They display unique phenotypic characteristics conferred in part by heritable genetic changes. Characteristically slow growing, SCVs comprise a minor proportion of the population from which they arise but persist by virtue of their inherent resilience and host adaptability. Consequently, SCVs are problematic in chronic infection, where antimicrobial treatment is administered during the acute phase of infection but fails to eradicate SCVs, which remain within the host causing recurrent or chronic infection. This review discusses some of the phenotypic and genotypic changes that enable SCVs to successfully proliferate within the host environment as potential pathogens and strategies that could ameliorate the resolution of infection where SCVs are present

Draft genome sequence of Pseudomonas aeruginosa ATCC 9027, originally isolated from an outer ear infection

Pseudomonas aeruginosa ATCC 9027 was isolated in 1943 from a case of otitis externa and is commonly employed as a quality control strain for sterility, assessment of antibiofilm agents, and in vitro study of wound infection. Here, we present the 6.34-Mb draft genome sequence and highlight some pertinent genes that are associated with virulence

Effective Temperatures of Low-Mass Stars from High-Resolution H-band Spectroscopy

High-resolution, near-infrared spectra will be the primary tool for finding and characterizing Earth-like planets around low-mass stars. Yet, the properties of exoplanets can not be precisely determined without accurate and precise measurements of the host star. Spectra obtained with the Immersion GRating INfrared Spectrometer (IGRINS) simultaneously provide diagnostics for most stellar parameters, but the first step in any analysis is the determination of the effective temperature. Here we report the calibration of high-resolution H-band spectra to accurately determine effective temperature for stars between 4000-3000 K ($\sim$K8--M5) using absorption line depths of Fe I, OH, and Al I. The field star sample used here contains 254 K and M stars with temperatures derived using BT-Settl synthetic spectra. We use 106 stars with precise temperatures in the literature to calibrate our method with typical errors of about 140 K, and systematic uncertainties less than $\sim$120 K. For the broadest applicability, we present T$_{\rm eff}$--line-depth-ratio relationships, which we test on 12 members of the TW Hydrae Association and at spectral resolving powers between $\sim$10,000--120,000. These ratios offer a simple but accurate measure of effective temperature in cool stars that is distance and reddening independent.Comment: 19 pages, 11 figures and 3 tables. Accepted in Ap

The mutual interplay between calcification and coccolithovirus infection

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johns, C. T., Grubb, A. R., Nissimov, J. I., Natale, F., Knapp, V., Mui, A., Fredricks, H. F., Van Mooy, B. A. S., & Bidle, K. D. The mutual interplay between calcification and coccolithovirus infection. Environmental Microbiology, 21(6), (2019): 1896-1915, doi:10.1111/1462-2920.14362.Two prominent characteristics of marine coccolithophores are their secretion of coccoliths and their susceptibility to infection by coccolithoviruses (EhVs), both of which display variation among cells in culture and in natural populations. We examined the impact of calcification on infection by challenging a variety of Emiliania huxleyi strains at different calcification states with EhVs of different virulence. Reduced cellular calcification was associated with increased infection and EhV production, even though calcified cells and associated coccoliths had significantly higher adsorption coefficients than non‐calcified (naked) cells. Sialic acid glycosphingolipids, molecules thought to mediate EhV infection, were generally more abundant in calcified cells and enriched in purified, sorted coccoliths, suggesting a biochemical link between calcification and adsorption rates. In turn, viable EhVs impacted cellular calcification absent of lysis by inducing dramatic shifts in optical side scatter signals and a massive release of detached coccoliths in a subpopulation of cells, which could be triggered by resuspension of healthy, calcified host cells in an EhV‐free, ‘induced media’. Our findings show that calcification is a key component of the E. huxleyi‐EhV arms race and an aspect that is critical both to the modelling of these host–virus interactions in the ocean and interpreting their impact on the global carbon cycle.We thank Liti Haramaty for her guidance and assistance in culturing and infection experiments. This research was funded by the Gordon and Betty Moore Foundation (GBMF3301 to BVM and KDB and GBMF3789 to KDB) and the National Science Foundation (OCE‐1537951 and OCE‐1559179 to KDB)

Programme costs in the economic evaluation of health interventions

Estimating the costs of health interventions is important to policy-makers for a number of reasons including the fact that the results can be used as a component in the assessment and improvement of their health system performance. Costs can, for example, be used to assess if scarce resources are being used efficiently or whether there is scope to reallocate them in a way that would lead to improvements in population health. As part of its WHO-CHOICE project, WHO has been developing a database on the overall costs of health interventions in different parts of the world as an input to discussions about priority setting. Programme costs, defined as costs incurred at the administrative levels outside the point of delivery of health care to beneficiaries, may comprise an important component of total costs. Cost-effectiveness analysis has sometimes omitted them if the main focus has been on personal curative interventions or on the costs of making small changes within the existing administrative set-up. However, this is not appropriate for non-personal interventions where programme costs are likely to comprise a substantial proportion of total costs, or for sectoral analysis where questions of how best to reallocate all existing health resources, including administrative resources, are being considered. This paper presents a first effort to systematically estimate programme costs for many health interventions in different regions of the world. The approach includes the quantification of resource inputs, choice of resource prices, and accounts for different levels of population coverage. By using an ingredients approach, and making tools available on the World Wide Web, analysts can adapt the programme costs reported here to their local settings. We report results for a selected number of health interventions and show that programme costs vary considerably across interventions and across regions, and that they can contribute substantially to the overall costs of interventions

The costs of a sexually transmitted infection outreach and treatment programme targeting most at risk youth in Tajikistan

<p>Abstract</p> <p>Background</p> <p>Targeted outreach, counselling, and treatment of sexually transmitted infections (STIs) are among the most cost-effective interventions aimed at ameliorating the burden of HIV/STIs. Since many new HIV infections occur in people under the age of 25, youth, and especially most at risk adolescents (MARA), need to be able to access HIV/STI services. Starting in 2006, a programme targeting MARA including outreach, confidential and voluntary counselling and testing, and STI diagnosis and treatment was piloted in three cities in Tajikistan. This study uses data from these pilot sites to estimate the costs of a national programme.</p> <p>Methods</p> <p>Cost data were collected from the three pilot sites. Then, the target population and the number of patients receiving specific types of services are calculated for other areas. The unit costs from the pilot sites are multiplied by usage rates to determine the total costs of a national programme. Scenarios were developed to reflect data uncertainty. The government's ability to finance the programme was estimated using Ministry of Health budget data. Further analyses were done for one of the pilot cities where more detailed data were available.</p> <p>Results</p> <p>In total, costs were projected for eight programme sites, covering an estimated 8,020 MARA. Operational and variable cost for the programme are projected to be US$119,159 (range US$ 104,953 to 151,524) per year. Including annual equivalent cost for capital and start-up items raises this to US$137,082 (range: US$ 123,022 to 169,597) per year. The analyses of potential sources of financing for the programme remain inconclusive, but it may take multiple sources of financing to fund the programme.</p> <p>Conclusion</p> <p>While the cost-effectiveness of similar programmes have been previously assessed using modelled data, more work needs to be done to assess the costs of new programmes in relation to financial resources available. Full costing should consider cost-savings as well as expenditures. If feasible, the impact of the programme should be monitored over time.</p

Association between malaria control and paediatric blood transfusions in rural Zambia: an interrupted time-series analysis

BACKGROUND: Blood transfusions can reduce mortality among children with severe malarial anaemia, but there is limited evidence quantifying the relationship between paediatric malaria and blood transfusions. This study explores the extent to which the use of paediatric blood transfusions is affected by the number of paediatric malaria visits and admissions. It assesses whether the scale-up of malaria control interventions in a facility catchment area explains the use of paediatric blood transfusions. METHODS: The study was conducted at a referral hospital for 13 rural health centres in rural Zambia. Data were used from facility and patient records covering all paediatric malaria admissions from 2000 to 2008. An interrupted time series analysis using an autoregression-moving-average model was conducted to assess the relationship between paediatric malaria outpatient visits and admissions and the use of paediatric blood transfusions. Further investigation explored whether the use of paediatric blood transfusions over time was consistent with the roll out of malaria control interventions in the hospital catchment area. RESULTS: For each additional paediatric malaria outpatient visit, there were 0.07 additional paediatric blood transfusions (95% CI 0.01-0.13; p < 0.05). For each additional paediatric admission for severe malarial anaemia, there were 1.09 additional paediatric blood transfusions (95% CI 0.95-1.23; p < 0.01). There were 19.1 fewer paediatric blood transfusions per month during the 2004–2006 malaria control period (95% CI 12.1-26.0; p < 0.01), a 50% reduction compared to the preceding period when malaria control was relatively limited. During the 2007–2008 malaria control period, there were 27.5 fewer paediatric blood transfusions per month (95% CI 14.6-40.3; p < 0.01), representing a 72% decline compared to the period with limited malaria control. CONCLUSIONS: Paediatric admissions for severe malarial anaemia largely explain total use of paediatric blood transfusions. The reduction in paediatric blood transfusions is consistent with the timing of the malaria control interventions. Malaria control seems to influence the use of paediatric blood transfusions by reducing the number of paediatric admissions for severe malarial anaemia. Reduced use of blood transfusions could benefit other areas of the health system through greater blood availability, particularly where supply is limited