Water quality of the Great Barrier Reef : distributions, effects on reef biota and trigger values for the protection of ecosystem health

This Report to the GBMPA provides technical background information and statistical data analysis for defining improved water quality guideline trigger values for the GBR Water Quality Guidelines

A diver-operated hyperspectral imaging and topographic surveying system for automated mapping of benthic habitats

We developed a novel integrated technology for diver-operated surveying of shallow marine ecosystems. The HyperDiver system captures rich multifaceted data in each transect: hyperspectral and color imagery, topographic profiles, incident irradiance and water chemistry at a rate of 15-30 m(2) per minute. From surveys in a coral reef following standard diver protocols, we show how the rich optical detail can be leveraged to generate photopigment abundance and benthic composition maps. We applied machine learning techniques, with a minor annotation effort (<2% of pixels), to automatically generate cm-scale benthic habitat maps of high taxonomic resolution and accuracy (93-97%). The ability to efficiently map benthic composition, photopigment densities and rugosity at reef scales is a compelling contribution to modernize reef monitoring. Seafloor-level hyperspectral images can be used for automated mapping, avoiding operator bias in the analysis and deliver the degree of detail necessary for standardized environmental monitoring. The technique can deliver fast, objective and economic reef survey results, making it a valuable tool for coastal managers and reef ecologists. Underwater hyperspectral surveying shares the vantage point of the high spatial and taxonomic resolution restricted to field surveys, with analytical techniques of remote sensing and provides targeted validation for aerial monitoring

Classifying the biodiversity of the Great Barrier Reef World Heritage Area for the classification phase of the representative areas program

This technical report outlines the methods that the Great Barrier Reef Marine Park Authority used to classify the biodiversity of the marine environs of the Great Barrier Reef World Heritage Area for the Representative Areas Program. Classification was the first step in the multiphase Representative Areas Program that eventuated in a new network of no-take areas, free from extractive activities, in the Great Barrier Reef Marine Park

Development of a 'millimanipulation' device to study the removal of soft solid fouling layers from solid substrates and its application to cooked lard deposits

A mm-scale scraping device was developed to study the removal behaviour of soft solid fouling layers (thickness 0.5 to 10 mm) from solid substrates. A blade is dragged through the circular or rectangular samples at controlled speed and the resistance forces measured. Tests with a viscous liquid (honey) and viscoplastic material (a Vaseline-carbon black paste) indicated that cohesive deformation dominated the measured force. Two model food soils were: (i) unbaked lard, and (ii) lard baked for different times with and without added ovalbumin. The cohesive strength of the baked lard, and its removal behaviour, changed noticeably following autoxidative polymerisation. Ovalbumin delayed the onset of polymerisation.An EPSRC studentship for AA is gratefully acknowledged, as it project support and a summer studentship for JP from Proctor & Gamble.This is the final version. It was first published by Elsevier at http://www.sciencedirect.com/science/article/pii/S0960308514000972

Bayesian Classification and Regression Trees for Predicting Incidence of Cryptosporidiosis

Background Classification and regression tree (CART) models are tree-based exploratory data analysis methods which have been shown to be very useful in identifying and estimating complex hierarchical relationships in ecological and medical contexts. In this paper, a Bayesian CART model is described and applied to the problem of modelling the cryptosporidiosis infection in Queensland, Australia. Methodology/Principal Findings We compared the results of a Bayesian CART model with those obtained using a Bayesian spatial conditional autoregressive (CAR) model. Overall, the analyses indicated that the nature and magnitude of the effect estimates were similar for the two methods in this study, but the CART model more easily accommodated higher order interaction effects. Conclusions/Significance A Bayesian CART model for identification and estimation of the spatial distribution of disease risk is useful in monitoring and assessment of infectious diseases prevention and control

Risk factor analysis and spatiotemporal CART model of cryptosporidiosis in Queensland, Australia

Background: It remains unclear whether it is possible to develop a spatiotemporal epidemic prediction model for cryptosporidiosis disease. This paper examined the impact of social economic and weather factors on cryptosporidiosis and explored the possibility of developing such a model using social economic and weather data in Queensland, Australia.Methods: Data on weather variables, notified cryptosporidiosis cases and social economic factors in Queensland were supplied by the Australian Bureau of Meteorology, Queensland Department of Health, and Australian Bureau of Statistics, respectively. Three-stage spatiotemporal classification and regression tree (CART) models were developed to examine the association between social economic and weather factors and monthly incidence of cryptosporidiosis in Queensland, Australia. The spatiotemporal CART model was used for predicting the outbreak of cryptosporidiosis in Queensland, Australia.Results: The results of the classification tree model (with incidence rates defined as binary presence/absence) showed that there was an 87% chance of an occurrence of cryptosporidiosis in a local government area (LGA) if the socio-economic index for the area (SEIFA) exceeded 1021, while the results of regression tree model (based on non-zero incidence rates) show when SEIFA was between 892 and 945, and temperature exceeded 32°C, the relative risk (RR) of cryptosporidiosis was 3.9 (mean morbidity: 390.6/100,000, standard deviation (SD): 310.5), compared to monthly average incidence of cryptosporidiosis. When SEIFA was less than 892 the RR of cryptosporidiosis was 4.3 (mean morbidity: 426.8/100,000, SD: 319.2). A prediction map for the cryptosporidiosis outbreak was made according to the outputs of spatiotemporal CART models.Conclusions: The results of this study suggest that spatiotemporal CART models based on social economic and weather variables can be used for predicting the outbreak of cryptosporidiosis in Queensland, Australia

Why Are Some Plant Genera More Invasive Than Others?

Determining how biological traits are related to the ability of groups of organisms to become economically damaging when established outside of their native ranges is a major goal of population biology, and important in the management of invasive species. Little is known about why some taxonomic groups are more likely to become pests than others among plants. We investigated traits that discriminate vascular plant genera, a level of taxonomic generality at which risk assessment and screening could be more effectively performed, according to the proportion of naturalized species which are pests. We focused on the United States and Canada, and, because our purpose is ultimately regulatory, considered species classified as weeds or noxious. Using contingency tables, we identified 11 genera of vascular plants that are disproportionately represented by invasive species. Results from boosted regression tree analyses show that these categories reflect biological differences. In summary, approximately 25% of variation in genus proportions of weeds or noxious species was explained by biological covariates. Key explanatory traits included genus means for wetland habitat affinity, chromosome number, and seed mass

Disturbance and the Dynamics of Coral Cover on the Great Barrier Reef (1995–2009)

Coral reef ecosystems worldwide are under pressure from chronic and acute stressors that threaten their continued existence. Most obvious among changes to reefs is loss of hard coral cover, but a precise multi-scale estimate of coral cover dynamics for the Great Barrier Reef (GBR) is currently lacking. Monitoring data collected annually from fixed sites at 47 reefs across 1300 km of the GBR indicate that overall regional coral cover was stable (averaging 29% and ranging from 23% to 33% cover across years) with no net decline between 1995 and 2009. Subregional trends (10–100 km) in hard coral were diverse with some being very dynamic and others changing little. Coral cover increased in six subregions and decreased in seven subregions. Persistent decline of corals occurred in one subregion for hard coral and Acroporidae and in four subregions in non-Acroporidae families. Change in Acroporidae accounted for 68% of change in hard coral. Crown-of-thorns starfish (Acanthaster planci) outbreaks and storm damage were responsible for more coral loss during this period than either bleaching or disease despite two mass bleaching events and an increase in the incidence of coral disease. While the limited data for the GBR prior to the 1980's suggests that coral cover was higher than in our survey, we found no evidence of consistent, system-wide decline in coral cover since 1995. Instead, fluctuations in coral cover at subregional scales (10–100 km), driven mostly by changes in fast-growing Acroporidae, occurred as a result of localized disturbance events and subsequent recovery

Mining social mixing patterns for infectious disease models based on a two-day population survey in Belgium

<p>Abstract</p> <p>Background</p> <p>Until recently, mathematical models of person to person infectious diseases transmission had to make assumptions on transmissions enabled by personal contacts by estimating the so-called WAIFW-matrix. In order to better inform such estimates, a population based contact survey has been carried out in Belgium over the period March-May 2006. In contrast to other European surveys conducted simultaneously, each respondent recorded contacts over two days. Special attention was given to holiday periods, and respondents with large numbers of professional contacts.</p> <p>Methods</p> <p>Participants kept a paper diary with information on their contacts over two different days. A contact was defined as a two-way conversation of at least three words in each others proximity. The contact information included the age of the contact, gender, location, duration, frequency, and whether or not touching was involved.</p> <p>For data analysis, we used association rules and classification trees. Weighted generalized estimating equations were used to analyze contact frequency while accounting for the correlation between contacts reported on the two different days.</p> <p>A contact surface, expressing the average number of contacts between persons of different ages was obtained by a bivariate smoothing approach and the relation to the so-called next-generation matrix was established.</p> <p>Results</p> <p>People mostly mixed with people of similar age, or with their offspring, their parents and their grandparents. By imputing professional contacts, the average number of daily contacts increased from 11.84 to 15.70. The number of reported contacts depended heavily on the household size, class size for children and number of professional contacts for adults. Adults living with children had on average 2 daily contacts more than adults living without children. In the holiday period, the daily contact frequency for children and adolescents decreased with about 19% while a similar observation is made for adults in the weekend. These findings can be used to estimate the impact of school closure.</p> <p>Conclusion</p> <p>We conducted a diary based contact survey in Belgium to gain insights in social interactions relevant to the spread of infectious diseases. The resulting contact patterns are useful to improve estimating crucial parameters for infectious disease transmission models.</p

Phase diagram of calcium at high pressure and high temperature

Resistively heated diamond-anvil cells have been used together with synchrotron x-ray diffraction to investigate the phase diagram of calcium up to 50 GPa and 800 K. The phase boundaries between the Ca-I (fcc), Ca-II (bcc), and Ca-III (simple cubic, sc) phases have been determined at these pressure-temperature conditions, and the ambient temperature equation of state has been generated. The equation of state parameters at ambient temperature have been determined from the experimental compression curve of the observed phases by using third-order Birch-Murnaghan and Vinet equations. A thermal equation of state was also determined for Ca-I and Ca-II by combining the room-temperature Birch-Murnaghan equation of state with a Berman-type thermal expansion model.Part of the research was supported by the Spanish Government MINECO under Grants No. MAT2016-75586-C4-1/4P and No. MAT2015-71070-REDC.Peer reviewe