On the application of loss functions for determining hazardous concentrations

The Hazardous Concentration to x% of an assemblage (HCx) of biological species is the environmental concentration which for a randomly selected species from the assemblage yields an x% probability of violating the species’ toxicological endpoint. Probabilistic methods for estimating the HCx appeal to the probabilistic concept of Species Sensitivity Distributions (SSDs) – a statistical proxy description of interspecies variation within the assemblage. A commonly used estimator class, derived by Aldenberg and Jaworska (2000; Ecotoxicol Environ Saf 46: 1-18), appealed to classical sampling theory, but also coincided with a Bayesian estimator. Two popular estimators from the class are the 50% and 95% (one-sided) underestimate of the HCx. However, whilst choice of x can have ecological significance, choice of confidence remains arbitrary. We reduce the problem to a Bayesian decision theoretic one; and show that their estimator class is equivalent to Bayes Rules under a class of (a-) symmetric linear loss functions, parameterised by the relative cost of over-estimation to under-estimation. A loss function in this sense measures the ‘cost’, which needn’t be monetary, of over- and under-estimation of the HCx estimator. Bayes rules are estimators which minimise expected loss with respect to the posterior SSD – updated with respect to the toxicity data. This potentially opens the way for high-stakes realism to be incorporated into risk assessments. We propose an alternative loss function known as Scaled LINear Exponential (LINEX) which is non-linearly asymmetric in a precautionary way, such that overestimation and underestimation are punished at an exponential and linear rate respectively. We use this loss function to derive an alternative class of HCx estimators

A robust Bayesian analysis of the impact of policy decisions on crop rotations.

We analyse the impact of a policy decision on crop rotations, using the imprecise land use model that was developed by the authors in earlier work. A specific challenge in crop rotation models is that farmer’s crop choices are driven by both policy changes and external non-stationary factors, such as rainfall, temperature and agricultural input and output prices. Such dynamics can be modelled by a non-stationary stochastic process, where crop transition probabilities are multinomial logistic functions of such external factors. We use a robust Bayesian approach to estimate the parameters of our model, and validate it by comparing the model response with a non-parametric estimate, as well as by cross validation. Finally, we use the resulting predictions to solve a hypothetical yet realistic policy problem

Species non-exchangeability for ecotoxicological risk assessment [poster spotlight]

In aquatic based chemical risk assessments, there is a wealth of statistical techniques for use in lower tier risk assessment. In particular, we focus on estimation of the hazardous concentration to x% of an ecological community (HCx); a concept based on the idea of Species Sensitivity Distribution (SSD). The SSD is typically assumed to act as a proxy distribution to model the inter-species variation in the biological assemblage. Over time, a number of criticisms have been made of the SSD concept, but we focus on one in particular – species non-exchangeability. The concept was first discussed within a semi-probabilistic setting by an opinion of the European Food Safety Authority (EFSA) Scientific Panel on Plant Production products and their Residues (EFSA Journal, 2005). We build on their findings to demonstrate, statistically, that the Rainbow trout (Oncorhynchus mykiss) is not exchangeable with other species. By this term, we mean that, a priori, before observing the toxicity value of the species, we do not believe it to be a realisation from the same distribution as the other species in the assemblage. In fact, the Rainbow trout is typically more sensitive than the average fish species across a wide range of substances. In addition, we briefly demonstrate how to exploit historical databases of toxicity data featuring the Rainbow trout to quantify this non-exchangeability in order to derive new estimators for the HCx

Species non-exchangeability in probabilistic ecotoxicological risk assessment

Current ecotoxicological risk assessment for chemical substances is based on the assumption that tolerances of all species in a specified ecological community are a priori exchangeable for each new substance. We demonstrate non-exchangeability by using a large database of tolerances to pesticides for fish species and extend the standard statistical model for species tolerances to allow for the presence of a single species which is considered non-exchangeable with others. We show how to estimate parameters and adjust decision rules that are used in ecotoxicological risk management. Effects of parameter uncertainty are explored and our model is compared with a previously published less tractable alternative. We conclude that the model and decision rules that we propose are pragmatic compromises between conflicting needs for more realistic modelling and for straightforwardly applicable decision rules

A robust Bayesian analysis of the impact of policy decisions on crop rotations

We analyse the impact of a policy decision on crop rotations, using the imprecise land use model that was developed by the authors in earlier work. A specific challenge in crop rotation models is that farmer’s crop choices are driven by both policy changes and external non-stationary factors, such as rainfall, temperature and agricultural input and output prices. Such dynamics can be modelled by a non-stationary stochastic process, where crop transition probabilities are multinomial logistic functions of such external factors. We use a robust Bayesian approach to estimate the parameters of our model, and validate it by comparing the model response with a non-parametric estimate, as well as by cross validation. Finally, we use the resulting predictions to solve a hypothetical yet realistic policy problem

Detoxification of Multiple Heavy Metals by a Half-Molecule ABC Transporter, HMT-1, and Coelomocytes of Caenorhabditis elegans

Developing methods for protecting organisms in metal-polluted environments is contingent upon our understanding of cellular detoxification mechanisms. In this regard, half-molecule ATP-binding cassette (ABC) transporters of the HMT-1 subfamily are required for cadmium (Cd) detoxification. HMTs have conserved structural architecture that distinguishes them from other ABC transporters and allows the identification of homologs in genomes of different species including humans. We recently discovered that HMT-1 from the simple, unicellular organism, Schizosaccharomyces pombe, SpHMT1, acts independently of phytochelatin synthase (PCS) and detoxifies Cd, but not other heavy metals. Whether HMTs from multicellular organisms confer tolerance only to Cd or also to other heavy metals is not known.Using molecular genetics approaches and functional in vivo assays we showed that HMT-1 from a multicellular organism, Caenorhabditis elegans, functions distinctly from its S. pombe counterpart in that in addition to Cd it confers tolerance to arsenic (As) and copper (Cu) while acting independently of pcs-1. Further investigation of hmt-1 and pcs-1 revealed that these genes are expressed in different cell types, supporting the notion that hmt-1 and pcs-1 operate in distinct detoxification pathways. Interestingly, pcs-1 and hmt-1 are co-expressed in highly endocytic C. elegans cells with unknown function, the coelomocytes. By analyzing heavy metal and oxidative stress sensitivities of the coelomocyte-deficient C. elegans strain we discovered that coelomocytes are essential mainly for detoxification of heavy metals, but not of oxidative stress, a by-product of heavy metal toxicity.We established that HMT-1 from the multicellular organism confers tolerance to multiple heavy metals and is expressed in liver-like cells, the coelomocytes, as well as head neurons and intestinal cells, which are cell types that are affected by heavy metal poisoning in humans. We also showed that coelomocytes are involved in detoxification of heavy metals. Therefore, the HMT-1-dependent detoxification pathway and coelomocytes of C. elegans emerge as novel models for studies of heavy metal-promoted diseases

Space Use and Relative Habitat Selection for Immature Green Turtles Within a Caribbean Marine Protected Area

Background A better understanding of sea turtle spatial ecology is critical for the continued conservation of imperiled sea turtles and their habitats. For resource managers to develop the most effective conservation strategies, it is especially important to examine how turtles use and select for habitats within their developmental foraging grounds. Here, we examine the space use and relative habitat selection of immature green turtles (Chelonia mydas) using acoustic telemetry within the marine protected area, Buck Island Reef National Monument (BIRNM), St. Croix, United States Virgin Islands. Results Space use by turtles was concentrated on the southern side of Buck Island, but also extended to the northeast and northwest areas of the island, as indicated by minimum convex polygons (MCPs) and 99%, 95%, and 50% kernel density estimations (KDEs). On average space use for all categories was \u3c 3 km2 with mean KDE area overlap ranging from 41.9 to 67.7%. Cumulative monthly MCPs and their proportions to full MCPs began to stabilize 3 to 6 detection months after release, respectively. Resource selection functions (RSFs) were implemented using a generalized linear mixed effects model with turtle ID as the random effect. After model selection, the accuracy of the top model was 77.3% and showed relative habitat selection values were highest at shallow depths, for areas in close proximity to seagrass, and in reef zones for both day and night, and within lagoon zones at night. The top model was also extended to predict across BIRNM at both day and night. Conclusion More traditional acoustic telemetry analyses in combination with RSFs provide novel insights into animal space use and relative resource selection. Here, we demonstrated immature green turtles within the BIRNM have small, specific home ranges and core use areas with temporally varying relative selection strengths across habitat types. We conclude the BIRNM marine protected area is providing sufficient protection for immature green turtles, however, habitat protection could be focused in both areas of high space use and in locations where high relative selection values were determined. Ultimately, the methodologies and results presented here may help to design strategies to expand habitat protection for immature green turtles across their greater distribution

Cumulative dietary risk characterisation of pesticides that have chronic effects on the thyroid

A retrospective chronic cumulative risk assessment of dietary exposure to pesticide residues, supported by an uncertainty analysis based on expert knowledge elicitation, was conducted for two effects on the thyroid, hypothyroidism and parafollicular cell (C‐cell) hypertrophy, hyperplasia and neoplasia. The pesticides considered in this assessment were identified and characterised in the scientific report on the establishment of cumulative assessment groups of pesticides for their effects on the thyroid. Cumulative exposure assessments were conducted through probabilistic modelling by EFSA and the Dutch National Institute for Public Health and the Environment (RIVM) using two different software tools and reported separately. These exposure assessments used monitoring data collected by Member States under their official pesticide monitoring programmes in 2014, 2015 and 2016 and individual consumption data from 10 populations of consumers from different countries and different age groups. This report completes the characterisation of cumulative risk, taking account of the available data and the uncertainties involved. For each of the 10 populations, it is concluded with varying degrees of certainty that cumulative exposure to pesticides that have the chronic effects on the thyroid mentioned above does not exceed the threshold for regulatory consideration established by risk managers