Transport of NOX emissions from sugarcane fertilisation into the Great Barrier Reef Lagoon

The Great Barrier Reef World Heritage Area contains highly sensitive ecosystems that are threatened by the effects of anthropogenic activity including eutrophication. The nearby sugarcane plantations of tropical north Queensland are fertilised annually and there has been ongoing concern about the magnitude of the loss of applied nitrogen to the environment. Previous studies have considered the potential of rainwater run-off to deposit reactive nitrogen species into rivers and ultimately into the Great Barrier Reef Lagoon, but have neglected the possibility of transport via the atmosphere. This paper reports the results of a modelling study commissioned by Australia’s National Heritage Trust aimed at assessing whether or not atmospheric deposition of reactive nitrogen from Queensland’s sugarcane plantations posed a potential threat to the Great Barrier Reef Lagoon. Atmospheric dispersion modelling was undertaken using The Air Pollution Model, developed by Australia’s Commonwealth Scientific and Industrial Research Organisation. Despite the predominance of onshore southeasterly winds, the dispersion model results indicate that 9% of the time during the sugarcane fertilization season (in the modeled years 2001–2006) the meteorological conditions resulted in emissions from the coastal regions of north Queensland being transported out over the ocean around the Great Barrier Reef. The results suggest that there may be a greater efficiency for transport out over the reef during October than for November and December. For the 2 months that exhibited the greatest potential for transport of coastal pollution to the Great Barrier Reef, the modeled deposition of nitrogen oxides (NOX) into the Great Barrier Reef lagoon was less than 1% of the total emissions from the sugarcane plantations, but was not zero. Our model has a simple chemical scheme that does not cover the full chemistry of all reactive nitrogen compounds and so the results are only indicative of the potential levels of deposition. Nevertheless, our study shows that small amounts of NOX that originate from sugarcane fertilization may be transported and dry deposited into the Great Barrier Reef lagoon. Other pathways not included in the modeling scheme may provide a more efficient transport mechanism. Whilst modern practices for the application of fertilizer to sugarcane plantations have drastically reduced emissions, the potential efficiency of transport of pollutants via the atmosphere may be of concern for other more highly polluting agricultural industries

Bayesian atmospheric tomography for detection and quantification of methane emissions : application to data from the 2015 Ginninderra release experiment

Detection and quantification of greenhouse-gas emissions is important for both compliance and environment conservation. However, despite several decades of active research, it remains predominantly an open problem, largely due to model errors and assumptions that appear at each stage of the inversion processing chain. In 2015, a controlled-release experiment headed by Geoscience Australia was carried out at the Ginninderra Controlled Release Facility, and a variety of instruments and methods were employed for quantifying the release rates of methane and carbon dioxide from a point source. This paper proposes a fully Bayesian approach to atmospheric tomography for inferring the methane emission rate of this point source using data collected during the experiment from both point-and path-sampling instruments. The Bayesian framework is designed to account for uncertainty in the parameterisations of measurements, the meteorological data, and the atmospheric model itself when performing inversion using Markov chain Monte Carlo (MCMC). We apply our framework to all instrument groups using measurements from two release-rate periods. We show that the inversion framework is robust to instrument type and meteorological conditions. From all the inversions we conducted across the different instrument groups and release-rate periods, our worst-case median emission rate estimate was within 36% of the true emission rate. Further, in the worst case, the closest limit of the 95% credible interval to the true emission rate was within 11% of this true value

Protocol for a mixed methods realist evaluation of a health service user feedback system in Bangladesh

Introduction: Responsiveness to service users’ views is a widely-recognised objective of health systems. A key component of responsive health systems is effective interaction between users and service providers. Despite a growing literature on patient feedback from high-income settings, less is known about effectiveness of such systems in low and middle income countries. Methodology and analysis: This paper disseminates the protocol for an 18-month ‘RESPOND’ project that aims to evaluate the system of collecting and responding to user feedback in Bangladesh. This mixed-method study uses a Realist Evaluation approach to examine user feedback systems at two Upazila Health Complexes in Comilla district of Bangladesh, and comprises three steps: i) initial theory development; ii) theory validation; and iii) theory refinement and development of lessons learned. The project also utilises: i) Process evaluation to understand causal mechanisms and contexts of implementation; ii) Statistical analysis of patient feedback to clarify the nature of issues reported; iii) Social science methods to illuminate feedback processes and user and provider experiences; and iv) Health policy and systems research to clarify issues related to integration of feedback systems with quality assurance and human resource management. During data analysis, qualitative and quantitative findings will be integrated throughout to help achieve study objectives. Analysis of qualitative and quantitative data will be done using a convergent mixed methods model, involving continuous triangulation of multiple datasets to facilitate greater understanding of the context of user feedback systems including the links with relevant policies, practices and programmes. Ethics and dissemination: Ethics approvals were obtained from the University of Leeds and the Bangladesh Medical Research Council. All data collected for this study will be anonymised and identifying characteristics of respondents will not appear in a final manuscript or reports. The study findings will be presented at scientific conferences and published in peer-reviewed journals

The Ginninderra CH4 and CO2 release experiment: An evaluation of gas detection and quantification techniques

A methane (CH4) and carbon dioxide (CO2) release experiment was held from April to June 2015 at the Ginninderra Controlled Release Facility in Canberra, Australia. The experiment provided an opportunity to compare different emission quantification techniques against a simulated CH4 and CO2 point source release, where the actual release rates were unknown to the participants. Eight quantification techniques were assessed: three tracer ratio techniques (two mobile); backwards Lagrangian stochastic modelling; forwards Lagrangian stochastic modelling; Lagrangian stochastic (LS) footprint modelling; atmospheric tomography using point and using integrated line sensors. The majority of CH4 estimates were within 20% of the actual CH4 release rate (5.8 g/min), with the tracer ratio technique providing the closest estimate to both the CH4 and CO2 release rates (100 g/min). Once the release rate was known, the majority of revised estimates were within 10% of the actual release rate. The study illustrates the power of measuring the emission rate using multiple simultaneous methods and obtaining an ensemble median or mean. An ensemble approach to estimating the CH4 emission rate proved successful with the ensemble median estimate within 16% for the actual release rate for the blind release experiment and within 2% once the release rate was known. The release also provided an opportunity to assess the effectiveness of stationary and mobile ground and aerial CH4 detection technologies. Sensor detection limits and sampling rates were found to be significant limitations for CH4 and CO2 detection. A hyperspectral imager\u27s capacity to image the CH4 release from 100 m, and a Boreal CH4 laser sensor\u27s ability to track moving targets suggest the future possibility to map gas plumes using a single laser and mobile aerial reflector

Meta-analysis of individual-patient data from EVAR-1, DREAM, OVER and ACE trials comparing outcomes of endovascular or open repair for abdominal aortic aneurysm over 5 years

Background: The erosion of the early mortality advantage of elective endovascular aneurysm repair (EVAR) compared with open repair of abdominal aortic aneurysm remains without a satisfactory explanation. Methods: An individual-patient data meta-analysis of four multicentre randomized trials of EVAR versus open repair was conducted to a prespecified analysis plan, reporting on mortality, aneurysm-related mortality and reintervention. Results: The analysis included 2783 patients, with 14 245 person-years of follow-up (median 5·5 years). Early (0–6 months after randomization) mortality was lower in the EVAR groups (46 of 1393 versus 73 of 1390 deaths; pooled hazard ratio 0·61, 95 per cent c.i. 0·42 to 0·89; P = 0·010), primarily because 30-day operative mortality was lower in the EVAR groups (16 deaths versus 40 for open repair; pooled odds ratio 0·40, 95 per cent c.i. 0·22 to 0·74). Later (within 3 years) the survival curves converged, remaining converged to 8 years. Beyond 3 years, aneurysm-related mortality was significantly higher in the EVAR groups (19 deaths versus 3 for open repair; pooled hazard ratio 5·16, 1·49 to 17·89; P = 0·010). Patients with moderate renal dysfunction or previous coronary artery disease had no early survival advantage under EVAR. Those with peripheral artery disease had lower mortality under open repair (39 deaths versus 62 for EVAR; P = 0·022) in the period from 6 months to 4 years after randomization. Conclusion: The early survival advantage in the EVAR group, and its subsequent erosion, were confirmed. Over 5 years, patients of marginal fitness had no early survival advantage from EVAR compared with open repair. Aneurysm-related mortality and patients with low ankle : brachial pressure index contributed to the erosion of the early survival advantage for the EVAR group. Trial registration numbers: EVAR-1, ISRCTN55703451; DREAM (Dutch Randomized Endovascular Aneurysm Management), NCT00421330; ACE (Anévrysme de l'aorte abdominale, Chirurgie versus Endoprothèse), NCT00224718; OVER (Open Versus Endovascular Repair Trial for Abdominal Aortic Aneurysms), NCT00094575

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

3D-Sonic Anemometer measurements of trace gases relevant to air quality in Western Sydney, Australia from 06 July 2017 to 14 September 2017

Date of Operation: 6-July 2017 to 14-September-2017 10:00 Location: Roof of 2 storey building at 2 Percy St, Auburn NSW 2144, Australia, -33.85472, 151.0373, 23.6 m above sea level, height mid-sonic above street level = 8.7 m, height mid-sonic above roof top=2.01 m Data collection rate: 10 Hz, average 5 min, timestamp end of collection period Bearing: 266 deg less 8 deg for offset Interruptions: logging program updated 14-July-2017 14:30 Issues: There was difficulty in determining the orientation of the 3D-sonic due to the surrounding infrastructure and nearby high tension electrical power lines. Final orientation was determined using GPS locations, and verified by comparison with wind direction data from the Australian Bureau of Meteorology (BoM), Sydney Olympic Park AWS site (station number 066212, -33.8338, 151.0718). The average difference in measured wind direction to Olympic Park AWS was +8 +/- 20 deg (+/-1s.d.,N=1037, Wind speed > 1m/s) and 8 degrees has been subtracted from the recorded wind directions

DOAS measurements of trace gases relevant to air quality in Western Sydney, Australia from 28 October 2016 to 13 September 2017

Operating dates: 28-October-2016 12:10 to 18 March 2017 8:35; 23-May-2016 13:30 to 13-September-2017 13:50. Location Spectrometer: Roof of 2-storey building at 2 Percy St, Auburn NSW 2144, Australia, -33.85472, 151.0373, 20.6 m above sea level at rooftop, height rooftop above street level = 6.72 m, measurement path above roof-top 1.2 m Location Reflectors: Roof 3-story building, Cumberland City Council Auburn Office, 1 Susan St Auburn 2144, Australia, -33.85311, 151.0335, 40.8 m rooftop above sea level, height roof top above street = 12.8 m, height mirror above rooftop = 2.7 m to centre mirror Distance instrument to reflector = 395.8 m one-way Total return path-length = 793.6 m (includes 2x1 m internal reflection) Measurement Path Slope: 5.3 Degrees; difference in Altitude = 20.9 m Measurement Path Bearing: 295°52'09'' Instrument description: A DOAS 2000 Differential Optical Absorption Spectrometer (DOAS; Thermo Environmental Instruments Inc., Franklin, MA, 02038, USA, Manufactured 1999) consisting of a 150W Xenon arc-lamp mounted in a telescope to act as emitting and receiving optics was used to make measurements in the Ultraviolet (UV) and Visible (VIS) regions. Light emitted from the telescope is returned via a retro reflector array, 150mm diameter, positioned 25-1000m away. Optic fibre is used to couple the telescope to spectrometer for analysis of the returned light. Light entering the spectrometer passes through an aperture and is sorted by wavelength using a grating. A 40nm region is then scanned at 1 angstrom intervals each detected using a photo multiplier tube (PMT). The resulting spectrum is then analysed as described in a following section. The telescope unit was mounted onto a Gibraltar Heavy duty tripod assembly (Quickset International Inc., Illinois, USA), to provide coarse alignment to the retro-reflector. Fine alignment was achieved by built in alignment aids on the telescope unit. The focus was manually adjusted by moving the source position on a slid rail. The measurement system is sensitive to a wavelength range of 200-650nm allowing for the analysis of many UV and VIS active pollutant gases in the atmosphere. Data is reported for Ozone (O3), Sulphur dioxide (SO2), Nitrogen dioxide (NO2), Formaldehyde (HCHO) and Nitrous acid (HONO). The precision for each species reported is; O3 = 3.9-4.8ppb, SO2 = 0.3-0.6ppb, NO2 = 2.4-4.1ppb, HCHO = 1.4ppb, HONO = 0.3ppb. Data for benzene and toluene were recorded for the first measurement period however the data was not of sufficient quality to be included. Data collection is controlled by the manufacturer's software package called DOAS 2000. The software uses user defined method files for operation and in this instance the collection/analysis procedure was NO2 (430nm) -> HONO (355nm) -> HCHO (330nm) -> SO2 (300nm) -> O3 (283nm) -> Benzene/Toluene (262nm). The measurement procedure continuously cycles around until interrupted by user or external factors. Instrument hardware calibrations are also controlled through the DOAS 2000 software. Calibration: Hardware calibrations were performed every month while wavelength correction checks were performed every 4 hrs and stored for use in spectra processing. Hardware calibrations use a mercury lamp located at the end of the optic fibre feeding the spectrometer. Gas species were calibrated using background mole fraction values (O3, SO2 & NO2), determined from a portable air quality monitoring station (Office of Environment and Heritage, NSW), measuring like species and co-located at the DOAS 2000 telescope. The air quality monitoring station instruments are referenced to a standard gas mixture daily to ensure performance and data quality. Wind speed needed to be > 1m/s for the determined background values to be valid. Data were then scaled according to the ratio of the calibrated background v's the DOAS 2000 background. Zero offsets were applied to HCHO and HONO as there wasn't a like measurement for these species. While the absolute accuracy of the measurements from the DOAS 2000 system can't be assured, based on the calibration strategy employed. However the differences have more confidence and are supported by a close match in scale and pattern of hourly averages from the portable air quality monitoring station. Data Collection Rate: Each spectral window is scanned for 2 mins and the resulting spectrum analysed before moving to the next region. A cycle of six spectral windows took 12-15mins to complete while a 5 spectral window cycle took 10-12mins. Spectral analysis: Spectral analysis was performed on-line by the DOAS 2000 software. In any UV-VIS measurement technique the resulting spectrum is dominated by the lamp or light source. To accurately retrieve information from the spectrum the lamp spectrum for the wavelength region needs to be subtracted. Prior to deployment the lamp was changed and new lamp spectra recorded to be used in analysis. The residual spectrum is then compared to a reference spectrum (treated identically) to provide a path averaged mole fraction measurement of the gas of interest. Reference spectra used in this work were those supplied with the instrument in 1999. Data QA: Data were filtered based on spectral fitting parameters that varied for each species but determined the quality of the fit. Restarting the collection procedure caused a reset of the stored wavelength adjustment corrections, therefore the correction was not made until a wavelength adjustment cycle was run on its regular programmed 4 hr interval. Data collected without the required wavelength adjustment correction were removed. This procedure assisted in removing effects due to alignment changes. Interruptions and issues: Maintaining a stable alignment of the optical system in an outdoor environment proved to be a challenge and significant data were lost. Outages due to alignment loss lasted upto 12 hrs. During summer the loss of alignment was rapid and only relatively short periods (hours) experienced a rapid change in signal to noise. During winter the alignment loss was gradual over many hours with more measurements made at a high PMT voltage, introducing more noise and thus lowering the signal to noise. This is noticeably by the increased scatter in the second half of the data set. Reliability of the spectrometer also caused data loss until a component failure on the 23/11/2016. Spectrometer reliability improved after the component replacement. The following extended (> 1day) outages were experienced: 29/10/2016 - 2/11/2016 poor alignment, site visit to correct. 11/11/2016 - 14/11/2016 alternate instrument deployed, signal to noise poor, data deleted. 23/11/2016 - 9/12/2016 component failure. Identical component from spare instrument used. 23/12/2016 - 10/1/2017 holiday period shutdown, site access unavailable. 10/6/2017 - 13/6/2017 instrument access issues 18/8/2017 - 21/8/2017 strong winds Monthly spectrometer hardware calibrations interrupted data collection for ~5 hrs once a month