Quantifying the frequency and volume of urine deposition by grazing sheep using tri-axial accelerometers.

Urine patches deposited in pasture by grazing animals are sites of reactive nitrogen (N) loss to the environment due to high concentrations of N exceeding pasture uptake requirements. In order to upscale N losses from the urine patch, several urination parameters are required, including where, when and how often urination events occur as well as the volume and chemical composition. There are limited data available in this respect, especially for sheep. Here, we seek to address this knowledge gap by using non-invasive sensor-based technology (accelerometers) on ewes grazing in situ, using a Boolean algorithm to detect urination events in the accelerometer signal. We conducted an initial study with penned Welsh Mountain ewes (n = 5), with accelerometers attached to the hind, to derive urine flow rate and to determine whether urine volume could be estimated from ewe squat time. Then accelerometers attached to the hind of Welsh Mountain ewes (n = 30 at each site) were used to investigate the frequency of sheep urination events (n = 35 946) whilst grazing two extensively managed upland pastures (semi-improved and unimproved) across two seasons (spring and autumn) at each site (35-40 days each). Sheep urinated at a frequency of 10.2 ± 0.2 and 8.1 ± 0.3 times per day in the spring and autumn, respectively, while grazing the semi-improved pasture. Urination frequency was greater (19.0 ± 0.4 and 15.3 ± 0.3 times per day in the spring and autumn, respectively) in the unimproved pasture. Ewe squat duration could be reliably used to predict the volume of urine deposited per event and was thus used to estimate mean daily urine production volumes. Sheep urinated at a rate of 16.6 mL/s and, across the entire dataset, sheep squatted for an average of 9.62 ± 0.03 s per squatting event, producing an estimated average individual urine event volume of 159 ± 1 mL (n = 35 946 events), ranging between 17 and 745 mL (for squat durations of 1 to 45 s). The estimated mean daily urine volume was 2.15 ± 0.04 L (n = 2 669 days) across the entire dataset. The data will be useful for modelling studies estimating N losses (e.g. ammonia (NH3) volatilisation, nitrous oxide (N2O) emission via nitrification and denitrification and nitrate (NO3-) leaching) from urine patches.

Microbial diversity dynamics during the self-acidification of dairy slurry.

Slurry acidification has been shown to be effective in reducing environmentally damaging gases. However, this involved the use of concentrated acids on farms. Therefore, due to the health and safety concerns, there is an interest in self-acidification of slurry technique. This study was designed to determine the microbial dynamics leading to self-acidification of slurry. A fresh cattle slurry was amended 10% brewing sugar and stored over 30 days. This fermentable carbon source promoted self-acidification of the slurry from pH 7.0 to 4.7 within four days, and was associated with the accumulation of lactic acid and a reduction in methane and relative ammonia emissions. A metagenomics approach through next generation sequencing (NGS) using an Illumina MiSeq platform was used to determine the microbial diversity and dynamics (bacteria and archaea) in the stored amended slurry. 16S ribosomal ribonucleic acid (rRNA) sequence data revealed the presence of the Order of Lactobacillales was associated with the lactic acid production. The operational taxonomic units (OTUs) abundance indicates that the methanogenic community was dominated by hydrogenotrophic methanogens from the member Order of Methanobacteriales, Methanomicrobiales, and Methanosarcinales. The decrease in tolerance by the methanogens in the self-acidified slurry was probably the main reason for the reduced methane emission. These results confirm, at the microbial level, the mechanism of inhibiting methane production via self-acidification during storage period.

Precipitation-optimised targeting of nitrogen fertilisers in a model maize cropping system.

Typically, half of the nitrogen (N) fertiliser applied to agricultural fields is lost to the wider environment. This inefficiency is driven by soil processes such as denitrification, volatilisation, surface run-off and leaching. Rainfall plays an important role in regulating these processes, ultimately governing when and where N fertiliser moves in soil and its susceptibility to gaseous loss. The interaction between rainfall, plant N uptake and N losses, however, remains poorly understood. In this study we use numerical modelling to predict the optimal N fertilisation strategy with respect to rainfall patterns and offer mechanistic explanations to the resultant differences in optimal times of fertiliser application. We developed a modelling framework that describes water and N transport in soil over a growing season and assesses nitrogen use efficiency (NUE) of split fertilisations within the context of different rainfall patterns. We used ninety rainfall patterns to determine their impact on optimal N fertilisation times. We considered the effects of root growth, root N uptake, microbial transformation of N and the effect of soil water saturation and flow on N movement in the soil profile. On average, we show that weather-optimised fertilisation strategies could improve crop N uptake by 20% compared to the mean uptake. In drier years, weather-optimising N applications improved the efficiency of crop N recovery by 35%. Further analysis shows that maximum plant N uptake is greatest under drier conditions due to reduced leaching, but it is harder to find the maximum due to low N mobility. The model could capture contrasting trends in NUE seen in previous arable cropping field trials. Furthermore, the model predicted that the variability in NUE seen in the field could be associated with precipitation-driven differences in N leaching and mobility. In conclusion, our results show that NUE in cropping systems could be significantly enhanced by synchronising fertiliser timings with both crop N demand and local weather patterns.

Image-based quantification of soil microbial dead zones induced by nitrogen fertilization.

Microbial communities in agricultural soils underpin many ecosystem services including the maintenance of soil structure, food production, water purification and carbon storage. However, the impact of fertilization on the health of microbial communities is not well understood. This study investigates the spatial and temporal dynamics of nitrogen (N) transport away from a fertilizer granule with pore scale resolution. Specifically, we examined how soil structure and moisture content influence fertilizer derived N movement through the soil pore network and the subsequent impact of on soil microbial communities. We develop a mathematical model to describe N transport and reactions in soil at the pore-scale. Using X-ray Computed Tomography scans, we reconstructed a microscale description of a soil-pore geometry as a computational mesh. Solving two-phase water/air model produced pore-scale water distributions at 15, 30 and 70% water-filled pore volume. The N-speciation model considered ammonium (NH4+), nitrate (NO3-) and dissolved organic N (DON), and included N immobilization, ammonification and nitrification processes, as well as diffusion in soil solution. We simulated the dissolution of a fertilizer pellet and a pore scale N cycle at three different water saturations. To aid interpretation of the model results, microbial activity at a range of N concentrations was measured. The model showed that the diffusion and concentration of N in water films is critically dependent upon soil moisture and N species. We predict that the maximum NH4+ and NO3- concentrations in soil solution around the pellet under dry conditions are in the order of 1 × 103 and 1 × 104 mol m-3 respectively, and under wet conditions 2 × 102 and 1 × 103 mol m-3, respectively. Supporting experimental evidence suggests that these concentrations would be sufficient to reduce microbial activity in the short-term in the zone immediately around the fertilizer pellet (ranging from 0.9 to 3.8 mm), causing a major loss of soil biological functioning. This model demonstrates the importance of pore-scale processes in regulating N movement and their interactions with the soil microbiome.

Application of Bayesian statistics to estimate nitrous oxide emission factors of three nitrogen fertilisers on UK grasslands.

Trapezoidal integration by linear interpolation of data points is by far the most commonly used method of cumulative flux calculations of nitrous oxide (N2O) in studies that use flux chambers; however, this method is incapable of providing accurate uncertainty estimates. A Bayesian approach was used to calculate N2O emission factors (EFs) and their associated uncertainties from flux chamber measurements made after the application of nitrogen fertilisers, in the form of ammonium nitrate (AN), urea (Ur) and urea treated with Agrotain® urease inhibitor (UI) at four grassland sites in the UK. The comparison between the cumulative fluxes estimated using the Bayesian and linear interpolation methods were broadly similar (R2 = 0.79); however, the Bayesian method was capable of providing realistic uncertainties when a limited number of data points is available. The study reports mean EF values (and 95% confidence intervals) of 0.60 ±â€¯0.63, 0.29 ±â€¯0.22 and 0.26 ±â€¯0.17% of applied N emitted as N2O for the AN, Ur and UI treatments, respectively. There was no significant difference between N2O emissions from the Ur and UI treatments. In the case of the automatic chamber data collected at one site in this study, the data did not fit the log-normal model, implying that more complex models may be needed, particularly for measurement data with high temporal resolution.

Nitrogen use efficiency and nitrous oxide emissions from five UK fertilised grasslands.

Intensification of grasslands is necessary to meet the increasing demand of livestock products. The application of nitrogen (N) on grasslands affects the N balance therefore the nitrogen use efficiency (NUE). Emissions of nitrous oxide (N2O) are produced due to N fertilisation and low NUE. These emissions depend on the type and rates of N applied. In this study we have compiled data from 5 UK N fertilised grassland sites (Crichton, Drayton, North Wyke, Hillsborough and Pwllpeiran) covering a range of soil types and climates. The experiments evaluated the effect of increasing rates of inorganic N fertiliser provided as ammonium nitrate (AN) or calcium ammonium nitrate (CAN). The following fertiliser strategies were also explored for a rate of 320 kg N ha-1: using the nitrification inhibitor dicyandiamide (DCD), changing to urea as an N source and splitting fertiliser applications. We measured N2O emissions for a full year in each experiment, as well as soil mineral N, climate data, pasture yield and N offtake. N2O emissions were greater at Crichton and North Wyke whereas Drayton, Hillsborough and Pwllpeiran had the smallest emissions. The resulting average emission factor (EF) of 1.12% total N applied showed a range of values for all the sites between 0.6 and 2.08%. NUE depended on the site and for an application rate of 320 kg N ha-1, N surplus was on average higher than 80 kg N ha-1, which is proposed as a maximum by the EU Nitrogen Expert Panel. N2O emissions tended to be lower when urea was applied instead of AN or CAN, and were particularly reduced when using urea with DCD. Finally, correlations between the factors studied showed that total N input was related to Nofftake and Nexcess; while cumulative emissions and EF were related to yield scaled emissions.

Evaluation of a vaccine passport to improve vaccine coverage in people living with HIV.

An increased risk of vaccine-preventable infections (VPIs) is seen in people living with HIV (PLWH), and current vaccine coverage and immunity is variable. Vaccine passports have the potential to improve vaccine coverage. The objective was to assess how successful a vaccine passport was in improving vaccine coverage in PLWH. Baseline immunity to VPIs was established in PLWH attending a single HIV clinic and vaccinations required were determined based on the BHIVA Vaccination Guidelines (2015). The passport was completed and the PLWH informed about additional vaccines they should obtain from primary care. After 6-9 months the passport was reviewed including confirmation if vaccines were given. PLWH satisfaction with the system was evaluated by a survey. Seventy-three PLWH provided sufficient data for analysis. At baseline significant proportions of PLWH were not immune/unvaccinated to the main VPIs, especially human papillomavirus, pneumococcus and measles. After the passport was applied immunity improved significantly (56% overall, p < 0.01) for most VPIs; however, full coverage was not achieved. The system was popular with PLWH. The passport was successful in increasing vaccination coverage although full or near-full coverage was not achieved. A more successful service would probably be achieved by commissioning English HIV clinics to provide all vaccines.

The contribution of cattle urine and dung to nitrous oxide emissions: Quantification of country specific emission factors and implications for national inventories.

Urine patches and dung pats from grazing livestock create hotspots for production and emission of the greenhouse gas, nitrous oxide (N2O), and represent a large proportion of total N2O emissions in many national agricultural greenhouse gas inventories. As such, there is much interest in developing country specific N2O emission factors (EFs) for excretal nitrogen (EF3, pasture, range and paddock) deposited during gazing. The aims of this study were to generate separate N2O emissions data for cattle derived urine and dung, to provide an evidence base for the generation of a country specific EF for the UK from this nitrogen source. The experiments were also designed to determine the effects of site and timing of application on emissions, and the efficacy of the nitrification inhibitor, dicyandiamide (DCD) on N2O losses. This co-ordinated set of 15 plot-scale, year-long field experiments using static chambers was conducted at five grassland sites, typical of the soil and climatic zones of grazed grassland in the UK. We show that the average urine and dung N2O EFs were 0.69% and 0.19%, respectively, resulting in a combined excretal N2O EF (EF3), of 0.49%, which is <25% of the IPCC default EF3 for excretal returns from grazing cattle. Regression analysis suggests that urine N2O EFs were controlled more by composition than was the case for dung, whilst dung N2O EFs were more related to soil and environmental factors. The urine N2O EF was significantly greater from the site in SW England, and significantly greater from the early grazing season urine application than later applications. Dycandiamide reduced the N2O EF from urine patches by an average of 46%. The significantly lower excretal EF3 than the IPCC default has implications for the UK's national inventory and for subsequent carbon footprinting of UK ruminant livestock products.

Critical review of the impacts of grazing intensity on soil organic carbon storage and other soil quality indicators in extensively managed grasslands.

Livestock grazing intensity (GI) is thought to have a major impact on soil organic carbon (SOC) storage and soil quality indicators in grassland agroecosystems. To critically investigate this, we conducted a global review and meta-analysis of 83 studies of extensive grazing, covering 164 sites across different countries and climatic zones. Unlike previous published reviews we normalized the SOC and total nitrogen (TN) data to a 30 cm depth to be compatible with IPCC guidelines. We also calculated a normalized GI and divided the data into four main groups depending on the regional climate (dry warm, DW; dry cool, DC; moist warm, MW; moist cool, MC). Our results show that taken across all climatic zones and GIs, grazing (below the carrying capacity of the systems) results in a decrease in SOC storage, although its impact on SOC is climate-dependent. When assessed for different regional climates, all GI levels increased SOC stocks under the MW climate (+7.6%) whilst there were reductions under the MC climate (-19%). Under the DW and DC climates, only the low (+5.8%) and low to medium (+16.1%) grazing intensities, respectively, were associated with increased SOC stocks. High GI significantly increased SOC for C4-dominated grassland compared to C3-dominated grassland and C3-C4 mixed grasslands. It was also associated with significant increases in TN and bulk density but had no effect on soil pH. To protect grassland soils from degradation, we recommend that GI and management practices should be optimized according to climate region and grassland type (C3, C4 or C3-C4 mixed).

Treatment-limiting renal tubulopathy in patients treated with tenofovir disoproxil fumarate.

OBJECTIVES: Tenofovir disoproxil fumarate (TDF) is widely used in the treatment or prevention of HIV and hepatitis B infection. TDF may cause renal tubulopathy in a small proportion of recipients. We aimed to study the risk factors for developing severe renal tubulopathy. METHODS: We conducted an observational cohort study with retrospective identification of cases of treatment-limiting tubulopathy during TDF exposure. We used multivariate Poisson regression analysis to identify risk factors for tubulopathy, and mixed effects models to analyse adjusted estimated glomerular filtration rate (eGFR) slopes. RESULTS: Between October 2002 and June 2013, 60 (0.4%) of 15,983 patients who had received TDF developed tubulopathy after a median exposure of 44.1 (IQR 20.4, 64.4) months. Tubulopathy cases were predominantly male (92%), of white ethnicity (93%), and exposed to antiretroviral regimens that contained boosted protease inhibitors (PI, 90%). In multivariate analysis, age, ethnicity, CD4 cell count and use of didanosine or PI were significantly associated with tubulopathy. Tubulopathy cases experienced significantly greater eGFR decline while receiving TDF than the comparator group (-6.60 [-7.70, -5.50] vs. -0.34 [-0.43, -0.26] mL/min/1.73 m2/year, p < 0.0001). CONCLUSIONS: Older age, white ethnicity, immunodeficiency and co-administration of ddI and PI were risk factors for tubulopathy in patients who received TDF-containing antiretroviral therapy. The presence of rapid eGFR decline identified TDF recipients at increased risk of tubulopathy.

Obesity in the HIV-infected population in Northeast England: a particular issue in Black-African women.

People living with HIV are surviving longer on successful antiretroviral therapy and obesity rates are increasing. We sought to determine the prevalence of being overweight or obese in a regional population of people living with HIV and to explore the demographic and clinical characteristics associated with obesity or being overweight. Data on patients attending three Northeast England clinics were collected including body mass index and demographics. The prevalence of being overweight (body mass index ≥ 25 kg/m2) or obese (body mass index ≥ 30 kg/m2) was determined and compared with regional population data. Associations between being overweight or obese and demographic and other data were further explored using logistic regression models. In 560 patients studied (median age 45 years, 26% Black-African and 69% male), 65% were overweight/obese and 26% obese, which is similar to the local population. However, 83% and 48% of Black-African women were overweight/obese or obese, respectively, with 11% being morbidly obese (body mass index > 40 kg/m2). In the multivariate analyses, the only factors significantly associated with obesity were Black-African race (adjusted odds ratio 2.78, 95% confidence interval 1.60-4.85) and type 2 diabetes (adjusted odds ratio 4.23, 95% confidence interval 1.81-9.91). Levels of obesity and overweight in people living with HIV are now comparable to the levels in the local population of Northeast England; however, the prevalence is significantly higher in Black-African women. Given the additional risk factors for cardiovascular disease inherent in people living with HIV, better strategies to prevent, identify and manage obesity in this population are needed.

A feasibility study for a clinical decision support system prompting HIV testing.

OBJECTIVES: Levels of undiagnosed HIV infection and late presentation remain high globally despite attempts to increase testing. The objective of this study was to evaluate a risk-based prototype application to prompt HIV testing when patients undergo routine blood tests. METHODS: Two computer physician order entry (CPOE) systems were modified using the application to prompt health care workers (HCWs) to add an HIV test when other tests selected suggested that the patient was at higher risk of HIV infection. The application was applied for a 3-month period in two areas, in a large London hospital and in general practices in Teesside/North Yorkshire. At the end of the evaluation period, HCWs were interviewed to assess the usability and acceptability of the prompt. Numbers of HIV tests ordered in the general practice areas were also compared before and after the prompt's introduction. RESULTS: The system was found to be both useable and generally acceptable to hospital doctors, general practitioners and nurse practitioners, with little evidence of prompt/alert fatigue. The issue of the prompt appearing late in the patient consultation did lead to some difficulties, particularly around discussion of the test and consent. In the general practices, around 1 in 10 prompts were accepted and there was a 6% increase in testing rates over the 3-month study period (P = 0.169). CONCLUSIONS: Using a CPOE-based clinical decision support application to prompt HIV testing appears both feasible and acceptable to HCWs. Refining the application to provide more accurate risk stratification is likely to make it more effective.

Nitrous oxide emissions from cattle excreta applied to a Scottish grassland: effects of soil and climatic conditions and a nitrification inhibitor.

Dung and urine excreted onto grasslands are a major source of nitrous oxide (N2O). These N2O emissions stem from inefficient utilisation of nitrogen (N) ingested by ruminants, and the inability of pasture to utilise the deposited N. Predicted growth in dairy and meat consumption means that there is a requirement to quantify N2O emissions, and investigate emission reduction mechanisms. Three 12 month 'seasonal' experiments were undertaken at Crichton, SW Scotland, where N2O emissions were measured from applications of cattle urine, dung, artificial urine and urine+a nitrification inhibitor (NI), dicyandiamide (DCD). The three application timings were 'spring', 'summer' and 'autumn', representative of early-, mid- and late grazing seasons. N2O emissions were measured from static chambers for 12 months. The aim was to quantify emissions from cattle excreta, and determine their dependence on the season of application, and the respective contribution of dung and urine to total excreta emissions. Measurement from NI amended urine was made to assess DCD's potential as an emission mitigation tool. Emissions were compared to the IPCC's default emission factor (EF) of 2% for cattle excreted N. Mean annual cumulative emissions from urine were the highest when applied in summer (5034 g N2O-N ha(-1)), with lower emissions from spring (1903 g N2O-N ha(-1)) and autumn (2014 g N2O-N ha(-1)) application, most likely due to higher temperatures and soil moisture conducive to both nitrification and denitrification in the summer months. Calculated EFs were significantly greater from urine (1.1%) than dung (0.2%) when excreta was applied in summer, and EFs varied with season of application, but in all experiments were lower than the IPCC default of 2%. These results support both lowering and disaggregating this EF into individual EFs for dung and urine. Addition of DCD to urine caused no significant reduction in emissions, suggesting that more research is required into its use as a mitigation option.

Modelling the cost-effectiveness of mitigation methods for multiple pollutants at farm scale.

Reductions in agricultural pollution are essential for meeting nationally and internationally agreed policy targets for losses to both air and water. Numerous studies quantify the impact of relevant mitigation methods by field experimentation or computer modelling. The majority of these studies have addressed individual methods and frequently also individual pollutants. This paper presents a conceptual model for the synthesis of the evidence base to calculate the impact of multiple methods addressing multiple pollutants in order to identify least cost solutions for multiple policy objectives. The model is implemented as a farm scale decision support tool that quantifies baseline pollutant losses for identifiable sources, areas and pathways and incorporates a genetic algorithm based multi-objective procedure for determining optimal suites of mitigation methods. The tool is generic as baseline losses can be replaced with measured data and the default library of mitigation methods can be edited and expanded. The tool is demonstrated through application to two contrasting farm systems, using survey data on agricultural practices typical of England and Wales. These examples show how the tool could be used to help target the adoption of mitigation options for the control of diffuse pollution from agriculture. The feedback from workshops where Farmscoper was demonstrated is included to highlight the potential role of Farmscoper as part of the farm advisory process.

Systematic review of intravenous methylene blue in parathyroid surgery.

BACKGROUND: Methylene blue is an intraoperative adjunct for localization of enlarged parathyroid glands. The availability of preoperative and other intraoperative localization methods, and the reported adverse effects of methylene blue make its routine use debatable. The aim of this study was to perform a systematic review of the use of methylene blue in parathyroidectomy. METHODS: A systematic review of English-language literature in MEDLINE and Scopus databases on the use of intravenous methylene blue in parathyroid surgery was carried out. RESULTS: There were no randomized clinical trials. Thirty-nine observational studies were identified, of which 33 did not have a control arm. The overall median staining rate for abnormal parathyroid glands was 100 per cent. The median cure rates in the methylene blue and no-methylene blue arms were 100 and 98 per cent respectively. Neurotoxicity was reported in 25 patients, all of whom were taking serotonergic medication. CONCLUSION: Observational evidence suggests that methylene blue is efficacious in identifying enlarged parathyroid glands. Toxicity appears to be mild in the absence of concomitant use of serotonin reuptake inhibitors. The effectiveness of methylene blue in the context of currently used preoperative and intraoperative localization techniques has yet to be shown.

Parathyroidectomy in a district general hospital: outcomes and evolution in the era of minimally invasive surgery.

AIM: To determine the outcomes of bilateral neck exploration (BNE) and uptake as well as outcomes of minimally invasive parathyroidectomy (MIP) for primary hyperparathyroidism in a district general hospital (DGH). METHODS: Patients who underwent first-time parathyroidectomy for primary hyperparathyroidism between August 1999 and December 2010 were identified from a prospectively maintained database of a single surgeon and were analysed for outcomes of MIP and BNE. MIP was adopted in 2006 and prior to that all patients underwent BNE. Results were analysed on an intention-to-treat basis. RESULTS: A total of 368 patients underwent parathyroid surgery; BNE (n = 314) and MIP (n = 54). Overall cure rate was 97%. Intention-to-treat analysis, based on surgical approach, showed cure rates of 96.5% with BNE and 96.3% with MIP (p = 1.0). Of the 92 patients assessed for MIP, localisation by ultrasound and sestamibi were noted in 60 (65%) and 65 (71%) patients respectively; however, concordance between the scans was noted in only 54 (59%) patients. Of the 54 patients who underwent MIP, 5 (9.2%) were converted to BNE. Intention-to-treat analysis, based on preoperative imaging, showed cure rates of 96% with BNE and 98% with MIP (p = 0.53). CONCLUSIONS: Satisfactory cure rates for parathyroidectomy are achievable in a 'medium-volume' endocrine unit within a DGH. Preoperative localisation studies with USS and MIBI have a positive concordance rate in only 60% of those considered for MIP, thereby limiting the use of MIP and reinforcing the role of BNE in this era of minimally invasive surgery.

Plasma cell granuloma of the thyroid: a conservative approach to a rare condition and review of the literature.

Introduction. We present a case of an 89-year-old female who attended our surgical endocrine clinic with a 3-month history of a left-sided neck lump. There was no past medical history of thyroid disease. Methods. Following examination and further investigation, including core biopsy, a diagnosis of plasma cell granuloma of the thyroid was made. Biochemical testing of thyroid function and Thyroid Peroxidase Antibody was in-keeping with an associated Hashimoto's thyroiditis. Results. The patient was treated conservatively with thyroxine and regularly seen in clinic. TSH levels improved and the lump showed signs of regression. Conclusion. Plasma cell granuloma of the thyroid is rare with only 16 previously reported cases. We present a new approach to management without the use of surgery or steroids. The literature is reviewed comparing clinico-pathological features and management of other reported cases.