Growing grass for a green biorefinery - an option for Ireland?

Growing grass for a green biorefinery – an option for Ireland? Mind the gap: deciphering the gap between good intentions and healthy eating behaviour Halting biodiversity loss by 2020 – implications for agriculture A milk processing sector model for Irelan

Persistence of the immune response induced by BCG vaccination.

BACKGROUND: Although BCG vaccination is recommended in most countries of the world, little is known of the persistence of BCG-induced immune responses. As novel TB vaccines may be given to boost the immunity induced by neonatal BCG vaccination, evidence concerning the persistence of the BCG vaccine-induced response would help inform decisions about when such boosting would be most effective. METHODS: A randomised control study of UK adolescents was carried out to investigate persistence of BCG immune responses. Adolescents were tested for interferon-gamma (IFN-gamma) response to Mycobacterium tuberculosis purified protein derivative (M.tb PPD) in a whole blood assay before, 3 months, 12 months (n = 148) and 3 years (n = 19) after receiving teenage BCG vaccination or 14 years after receiving infant BCG vaccination (n = 16). RESULTS: A gradual reduction in magnitude of response was evident from 3 months to 1 year and from 1 year to 3 years following teenage vaccination, but responses 3 years after vaccination were still on average 6 times higher than before vaccination among vaccinees. Some individuals (11/86; 13%) failed to make a detectable antigen-specific response three months after vaccination, or lost the response after 1 (11/86; 13%) or 3 (3/19; 16%) years. IFN-gamma response to Ag85 was measured in a subgroup of adolescents and appeared to be better maintained with no decline from 3 to 12 months. A smaller group of adolescents were tested 14 years after receiving infant BCG vaccination and 13/16 (81%) made a detectable IFN-gamma response to M.tb PPD 14 years after infant vaccination as compared to 6/16 (38%) matched unvaccinated controls (p = 0.012); teenagers vaccinated in infancy were 19 times more likely to make an IFN-gamma response of > 500 pg/ml than unvaccinated teenagers. CONCLUSION: BCG vaccination in infancy and adolescence induces immunological memory to mycobacterial antigens that is still present and measurable for at least 14 years in the majority of vaccinees, although the magnitude of the peripheral blood response wanes from 3 months to 12 months and from 12 months to 3 years post vaccination. The data presented here suggest that because of such waning in the response there may be scope for boosting anti-tuberculous immunity in BCG vaccinated children anytime from 3 months post-vaccination. This supports the prime boost strategies being employed for some new TB vaccines currently under development

Social disorganization and history of child sexual abuse against girls in sub-Saharan Africa : a multilevel analysis

Background: Child sexual abuse (CSA) is a considerable public health problem. Less focus has been paid to the role of community level factors associated with CSA. The aim of this study was to examine the association between neighbourhood-level measures of social disorganization and CSA. Methods: We applied multiple multilevel logistic regression analysis on Demographic and Health Survey data for 6,351 adolescents from six countries in sub-Saharan Africa between 2006 and 2008. Results: The percentage of adolescents that had experienced CSA ranged from 1.04% to 5.84%. There was a significant variation in the odds of reporting CSA across the communities, suggesting 18% of the variation in CSA could be attributed to community level factors. Respondents currently employed were more likely to have reported CSA than those who were unemployed (odds ratio [OR] = 2.05, 95% confidence interval [CI] 1.48 to 2.83). Respondents from communities with a high family disruption rate were 57% more likely to have reported CSA (OR=1.57, 95% CI 1.14 to 2.16). Conclusion: We found that exposure to CSA was associated with high community level of family disruption, thus suggesting that neighbourhoods may indeed have significant important effects on exposure to CSA. Further studies are needed to explore pathways that connect the individual and neighbourhood levels, that is, means through which deleterious neighbourhood effects are transmitted to individuals

H-COAL: Human Correction of AI-Generated Labels for Biomedical Named Entity Recognition

With the rapid advancement of machine learning models for NLP tasks, collecting high-fidelity labels from AI models is a realistic possibility. Firms now make AI available to customers via predictions as a service (PaaS). This includes PaaS products for healthcare. It is unclear whether these labels can be used for training a local model without expensive annotation checking by in-house experts. In this work, we propose a new framework for Human Correction of AI-Generated Labels (H-COAL). By ranking AI-generated outputs, one can selectively correct labels and approach gold standard performance (100% human labeling) with significantly less human effort. We show that correcting 5% of labels can close the AI-human performance gap by up to 64% relative improvement, and correcting 20% of labels can close the performance gap by up to 86% relative improvement.Comment: Presented at Conference on Information Systems and Technology (CIST) 202

Slurry 15NH4-N recovery in herbage and soil: effects of application method and timing

The effects of slurry application method and weather conditions after application on ammonia volatilisation are well documented, however, the effect on slurry N recovery in herbage is less evident due to large variability of results. The objective of this field experiment was to determine the recovery of cattle slurry NH4-N in herbage and soil in the year of application as affected by application method (trailing shoe versus broadcast) and season of application (spring versus summer), using N-15 as a tracer. In 2007 and 2008, N-15 enriched slurry was applied on grassland plots. N recovery in herbage and soil during the year of application was determined. Both spring and trailing shoe application resulted in significantly higher herbage DM yields, N uptake and an increased recovery of (NH4)-N-15-N in herbage. Additionally, the recovery of slurry (NH4)-N-15-N in the soil at the end of the growing season was increased. Spring and trailing shoe application reduced the losses of slurry (NH4)-N-15-N by on average 14 and 18 percentage points, respectively, which corresponded closely to ammonia volatilisation as predicted by the ALFAM model. It was concluded that slurry N recovery in temperate pasture systems can be increased by adjusting the slurry application method or timing.National Development Pla

Analysis of host responses to Mycobacterium tuberculosis antigens in a multi-site study of subjects with different TB and HIV infection states in sub-Saharan Africa.

BACKGROUND: Tuberculosis (TB) remains a global health threat with 9 million new cases and 1.4 million deaths per year. In order to develop a protective vaccine, we need to define the antigens expressed by Mycobacterium tuberculosis (Mtb), which are relevant to protective immunity in high-endemic areas. METHODS: We analysed responses to 23 Mtb antigens in a total of 1247 subjects with different HIV and TB status across 5 geographically diverse sites in Africa (South Africa, The Gambia, Ethiopia, Malawi and Uganda). We used a 7-day whole blood assay followed by IFN-γ ELISA on the supernatants. Antigens included PPD, ESAT-6 and Ag85B (dominant antigens) together with novel resuscitation-promoting factors (rpf), reactivation proteins, latency (Mtb DosR regulon-encoded) antigens, starvation-induced antigens and secreted antigens. RESULTS: There was variation between sites in responses to the antigens, presumably due to underlying genetic and environmental differences. When results from all sites were combined, HIV- subjects with active TB showed significantly lower responses compared to both TST(-) and TST(+) contacts to latency antigens (Rv0569, Rv1733, Rv1735, Rv1737) and the rpf Rv0867; whilst responses to ESAT-6/CFP-10 fusion protein (EC), PPD, Rv2029, TB10.3, and TB10.4 were significantly higher in TST(+) contacts (LTBI) compared to TB and TST(-) contacts fewer differences were seen in subjects with HIV co-infection, with responses to the mitogen PHA significantly lower in subjects with active TB compared to those with LTBI and no difference with any antigen. CONCLUSIONS: Our multi-site study design for testing novel Mtb antigens revealed promising antigens for future vaccine development. The IFN-γ ELISA is a cheap and useful tool for screening potential antigenicity in subjects with different ethnic backgrounds and across a spectrum of TB and HIV infection states. Analysis of cytokines other than IFN-γ is currently on-going to determine correlates of protection, which may be useful for vaccine efficacy trials

Sexuality and Social Justice: What’s Law Got to Do with It? International Symposium Workshop Report

In March 2015, the Sexuality, Poverty and Law programme at the Institute of Development Studies brought together over 60 activists, lawyers, researchers and international advocates to critically assess the scope of law and legal activism for achieving social justice for those marginalised because of their sexual or gender non-conformity. Delegates represented a broad range of expertise in the field of sexuality, gender identity, rights and social justice. They included a number of leading lawyers and activists involved in litigating cases of sexual and gender rights in countries such as Uganda, Malaysia, the United Kingdom, Argentina and Botswana. Lawyers and activists shared their experiences of working within this fast developing area of domestic and international law. Discussions also addressed the wider social and theoretical aspects of recent legal developments, contributing to our understanding of the complex relationship between research, knowledge exchange, activism and law.UK Department for International Developmen

Management, regulation and environmental impacts of nitrogen fertilization in northwestern Europe under the Nitrates Directive; a benchmark study

Implementation of the Nitrates Directive (NiD) and its environmental impacts were compared for member states in the northwest of the European Union (Ireland, United Kingdom, Denmark, the Netherlands, Belgium, Northern France and Germany). The main sources of data were national reports for the third reporting period for the NiD (2004–2007) and results of the MITERRA-EUROPE model. Implementation of the NiD in the considered member states is fairly comparable regarding restrictions for where and when to apply fertilizer and manure, but very different regarding application limits for N fertilization. Issues of concern and improvement of the implementation of the NiD are accounting for the fertilizer value of nitrogen in manure, and relating application limits for total nitrogen (N) to potential crop yield and N removal. The most significant environmental effect of the implementation of the NiD since 1995 is a major contribution to the decrease of the soil N balance (N surplus), particularly in Belgium, Denmark, Ireland, the Netherlands and the United Kingdom. This decrease is accompanied by a modest decrease of nitrate concentrations since 2000 in fresh surface waters in most countries. This decrease is less prominent for groundwater in view of delayed response of nitrate in deep aquifers. In spite of improved fertilization practices, the southeast of the Netherlands, the Flemish Region and Brittany remain to be regions of major concern in view of a combination of a high nitrogen surplus, high leaching fractions to groundwater and tenacious exceedance of the water quality standards. On average the gross N balance in 2008 for the seven member states in EUROSTAT and in national reports was about 20 kg N ha<sup>−1</sup> yr<sup>−1</sup> lower than by MITERRA. The major cause is higher estimates of N removal in national reports which can amount to more than 50 kg N ha<sup>−1</sup> yr<sup>−1</sup>. Differences between procedures in member states to assess nitrogen balances and water quality and a lack of cross-boundary policy evaluations are handicaps when benchmarking the effectiveness of the NiD. This provides a challenge for the European Commission and its member states, as the NiD remains an important piece of legislation for protecting drinking water quality in regions with many private or small public production facilities and controlling aquatic eutrophication from agricultural sources

Fluoroquinolones and isoniazid-resistant tuberculosis: implications for the 2018 WHO guidance.

INTRODUCTION: 2018 World Health Organization (WHO) guidelines for the treatment of isoniazid (H)-resistant (Hr) tuberculosis recommend a four-drug regimen: rifampicin (R), ethambutol (E), pyrazinamide (Z) and levofloxacin (Lfx), with or without H ([H]RZE-Lfx). This is used once Hr is known, such that patients complete 6 months of Lfx (≥6[H]RZE-6Lfx). This cohort study assessed the impact of fluoroquinolones (Fq) on treatment effectiveness, accounting for Hr mutations and degree of phenotypic resistance. METHODS: This was a retrospective cohort study of 626 Hr tuberculosis patients notified in London, 2009-2013. Regimens were described and logistic regression undertaken of the association between regimen and negative regimen-specific outcomes (broadly, death due to tuberculosis, treatment failure or disease recurrence). RESULTS: Of 594 individuals with regimen information, 330 (55.6%) were treated with (H)RfZE (Rf=rifamycins) and 211 (35.5%) with (H)RfZE-Fq. The median overall treatment period was 11.9 months and median Z duration 2.1 months. In a univariable logistic regression model comparing (H)RfZE with and without Fqs, there was no difference in the odds of a negative regimen-specific outcome (baseline (H)RfZE, cluster-specific odds ratio 1.05 (95% CI 0.60-1.82), p=0.87; cluster NHS trust). Results varied minimally in a multivariable model. This odds ratio dropped (0.57, 95% CI 0.14-2.28) when Hr genotype was included, but this analysis lacked power (p=0.42). CONCLUSIONS: In a high-income setting, we found a 12-month (H)RfZE regimen with a short Z duration to be similarly effective for Hr tuberculosis with or without a Fq. This regimen may result in fewer adverse events than the WHO recommendations