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  • Journal article
    Pirani M, Mason A, Hansell A, Richardson S, Blangiardo Met al., 2020,

    A flexible hierarchical framework for improving inference in area-referenced environmental health studies

    , Biometrical Journal: journal of mathematical methods in biosciences, Vol: 62, Pages: 1650-1669, ISSN: 0323-3847

    Study designs where data have been aggregated by geographical areas are popular in environmental epi-demiology. These studies are commonly based on administrative databases and, providing a completespatial coverage, are particularly appealing to make inference on the entire population. However, the re-sulting estimates are often biased and difficult to interpret due to unmeasured confounders, which typicallyare not available from routinely collected data. We propose a framework to improve inference drawn fromsuch studies exploiting information derived from individual-level survey data. The latter are summarized inan area-level scalar score by mimicking at ecological-level the well-known propensity score methodology.The literature on propensity score for confounding adjustment is mainly based on individual-level studiesand assumes a binary exposure variable. Here we generalize its use to cope with area-referenced stud-ies characterized by a continuous exposure. Our approach is based upon Bayesian hierarchical structuresspecified into a two-stage design: (i) geolocated individual-level data from survey samples are up-scaled atecological-level, then the latter are used to estimate a generalizedecological propensity score(EPS) in thein-sample areas; (ii) the generalized EPS is imputed in the out-of-sample areas under different assumptionsabout the missingness mechanisms, then it is included into the ecological regression, linking the exposureof interest to the health outcome. This delivers area-level risk estimates which allow a fuller adjustment forconfounding than traditional areal studies. The methodology is illustrated by using simulations and a casestudy investigating the risk of lung cancer mortality associated with nitrogen dioxide in England (UK).

  • Journal article
    Paillassa J, Wright I, Prentice IC, Pepin S, Smith N, Ethier G, Westerband A, Lamarque L, Han W, Cornwell W, Marie Vet al., 2020,

    When and where soil is important to modify the carbon and water economy of leaves.

    , New Phytologist, Vol: 228, Pages: 121-135, ISSN: 0028-646X

    Photosynthetic “least‐cost” theory posits that the optimal trait combination for a given environment is that where the summed costs of photosynthetic water and nutrient acquisition/use are minimised. The effects of soil water and nutrient availability on photosynthesis should be stronger as climate‐related costs for both resources increase.Two independent datasets of photosynthetic traits, Globamax (1509 species, 288 sites) and Glob13C (3645 species, 594 sites), were used to quantify biophysical and biochemical limitations of photosynthesis and the key variable Ci/Ca (CO2 drawdown during photosynthesis). Climate and soil variables were associated with both datasets.The biochemical photosynthetic capacity was higher on alkaline soils. This effect was strongest at more arid sites, where water unit‐costs are presumably higher. Higher values of soil silt and depth increased Ci/Ca, likely by providing greater H2O supply, alleviating biophysical photosynthetic limitation when soil water is scarce.Climate is important in controlling the optimal balance of H2O and N costs for photosynthesis, but soil properties change these costs, both directly and indirectly. In total, soil properties modify the climate‐demand driven predictions of Ci/Ca by up to 30% at a global scale.

  • Journal article
    Baker AL, Craighead RM, Jarvis EJ, Stenton HC, Angeloudis A, Mackie L, Avdis A, Piggott MD, Hill Jet al., 2020,

    Modelling the impact of tidal energy on species communities

    , Ocean and Coastal Management, Vol: 193, ISSN: 0964-5691

    Tidal energy has the potential to form a key component of the energy production in a number of countries, including the UK. Nonetheless, the deployment of tidal energy systems is associated with potential environmental impacts as prime resource sites often coincide with unique ecosystems inhabited by sensitive organisms. Previous studies have generally focused on the hydrodynamic impact of tidal energy schemes, i.e. how schemes alter the flow dynamics and sedimentary transport processes. Whilst these efforts are key in understanding environmental impacts, there is no straightforward step for translating sediment to faunal changes. Species distribution models offer methods to quantitatively predict certain possible impacts of tidal energy extraction. The River Severn is a distinguished candidate region for tidal energy in the UK featuring sites under stringent ecological protection regulations. We examine the impact of a proposed Severn tidal barrage on 14 species via the linking of hydrodynamic modelling to species distribution models. Through a selection of species that are linked via a simple food web system we extrapolate changes in prey species to the respective predator species. We show that species at lower trophic levels would be adversely affected by the barrage, but higher trophic level organisms increase in possible habitable area. Once food web relationships are acknowledged this increase in habitat area decreases, but is still net positive. Overall, all 14 species were affected, with most gaining in distribution area, and only four losing distribution area within the Severn Estuary. We conclude that a large-scale tidal barrage may have detrimental and complex impacts on species distribution, altering food web dynamics and altering food availability in the Severn Estuary. The methodology outlined herein can be transferred to the assessment and optimisation of prospective projects globally to aide in the sustainable introduction of the technology.

  • Journal article
    Angeloudis A, Kramer SC, Hawkins N, Piggott MDet al., 2020,

    On the potential of linked-basin tidal power plants: An operational and coastal modelling assessment

    , Renewable Energy, Vol: 155, Pages: 876-888, ISSN: 0960-1481

    Single-basin tidal range power plants have the advantage of predictable energy outputs, but feature non-generation periods in every tidal cycle. Linked-basin tidal power systems can reduce this variability and consistently generate power. However, as a concept the latter are under-studied with limited information on their performance relative to single-basin designs. In addressing this, we outline the basic principles of linked-basin power plant operation and report results from their numerical simulation. Tidal range energy operational models are applied to gauge their capabilities relative to conventional, single-basin tidal power plants. A coastal ocean model (Thetis) is then refined with linked-basin modelling capabilities. Simulations demonstrate that linked-basin systems can reduce non-generation periods at the expense of the extractable energy output relative to conventional tidal lagoons and barrages. As an example, a hypothetical case is considered for a site in the Severn Estuary, UK. The linked-basin system is seen to generate energy 80–100% of the time over a spring-neap cycle, but harnesses at best 30% of the energy of an equivalent-area single-basin design.

  • Journal article
    Paluszny Rodriguez A, Graham CC, Daniels K, Tsaparli V, Xenias D, Salimzadeh S, Whitmarsh L, Harrington J, Zimmerman Ret al., 2020,

    Caprock integrity and public perception studies of carbon storage in depleted hydrocarbon reservoirs

    , International Journal of Greenhouse Gas Control, Vol: 98, ISSN: 1750-5836

    Capture and subsurface storage of CO2 is widely viewed as being a necessary component of any strategy to minimise and control the continued increase in average global temperatures. Existing oil and gas reservoirs can be re-used for carbon storage, providing a substantial fraction of the vast amounts of subsurface storage space that will be required for the implementation of carbon storage at an industrial scale. Carbon capture and storage (CCS) in depleted reservoirs aims to ensure subsurface containment, both to satisfy safety considerations, and to provide confidence that the containment will continue over the necessary timescales. Other technical issues that need to be addressed include the risk of unintended subsurface events, such as induced seismicity. Minimisation of these risks is key to building confidence in CCS technology, both in relation to financing/liability, and the development and maintenance of public acceptance. These factors may be of particular importance with regard to CCS projects involving depleted hydrocarbon reservoirs, where the mechanical effects of production activities must also be considered. Given the importance of caprock behaviour in this context, several previously published geomechanical caprock studies of depleted hydrocarbon reservoirs are identified and reviewed, comprising experimental and numerical studies of fourteen CCS pilot sites in depleted hydrocarbon reservoirs, in seven countries (Algeria, Australia, Finland, France, Germany, Netherlands, Norway, UK). Particular emphasis is placed on the amount and types of data collected, the mathematical methods and codes used to conduct geomechanical analysis, and the relationship between geomechanical aspects and public perception. Sound geomechanical assessment, acting to help minimise operational and financial/liability risks, and the careful recognition of the impact of public perception are two key factors that can contribute to the development of a successful CCS project in a

  • Journal article
    Cai Y, Hansell AL, Granell R, Blangiardo M, Zottoli M, Fecht D, Gulliver J, Henderson AJ, Elliott Pet al., 2020,

    Prenatal, early-life and childhood exposure to air pollution and lung function: the ALSPAC cohort

    , American Journal of Respiratory and Critical Care Medicine, Vol: 202, Pages: 112-123, ISSN: 1073-449X

    RATIONALE: Exposure to air pollution during intrauterine development and through childhood may have lasting effects on respiratory health. OBJECTIVES: To investigate lung function at ages 8 and 15 years in relation to air pollution exposures during pregnancy, infancy and childhood in a UK population-based birth cohort. METHODS: Individual exposures to source-specific particulate matter with diameter ≤10µm (PM10) during each trimester, 0-6 months, 7-12 months (1990-1993) and up to age 15 years (1991-2008) were examined in relation to %predicted Forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) at ages 8(N=5,276) and 15(N=3,446) years, usinglinear regression models adjusted for potential confounders. A profile regression model was used to identify sensitive time periods. MEASUREMENTS AND MAIN RESULTS: We did not find clear evidence for a sensitive exposure period for PM10 from road-traffic: at age 8 years, 1µg/m3 higher exposure during the first trimester was associated with lower %predicted of FEV1(-0.826, 95%CI:-1.357 to -0.296) and FVC(-0.817, 95%CI:-1.357 to -0.276), but similar associations were seen for exposures for other trimesters, 0-6 months, 7-12 months, and 0-7 years. Associations were stronger among boys, children whose mother had a lower education level or smoked during pregnancy. For PM10 from all sources, the third trimester was associated with lower %predicted of FVC (-1.312, 95%CI: -2.100 to -0.525). At age 15 years, no adverse associations were seen with lung function. CONCLUSIONS: Exposure to road-traffic PM10 during pregnancy may result in small but significant reductions in lung function at age 8 years.

  • Journal article
    Pan W, Kramer S, Kärnä T, Piggott Met al., 2020,

    Comparing non-hydrostatic extensions to a discontinuous finite element coastal ocean model

    , Ocean Modelling, Vol: 151, ISSN: 1463-5003

    The unstructured mesh, discontinuous Galerkin finite element discretisation based coastal ocean model, Thetis, has been extended to include non-hydrostatic (buoyancy-driven and free surface) dynamics. Two alternative approaches to achieve this are described in this work. The first (a 3D based algorithm) makes use of prismatic element based meshes and uses a split-step pressure projection method for baroclinic and barotropic modes, while the second (a 2D based algorithm) adopts a novel multi-layer approach to convert a 3D problem into a combination of multiple 2D computations with only 2D triangle meshes required. Model development is carried out at high-level with the Firedrake library, using code generation techniques to automatically produce low-level code for the discretised model equations in an efficient and rapid manner. Through comparisons against several barotropic/baroclinic test cases where non hydrostatic effects are important, the implemented approaches are verified and validated, and the proposed algorithms compared. Depending on whether the problems are dominated by dispersive, baroclinic or barotropic features, recommendation are given over the use of full 3D or multi-layer 2D based approaches to achieve optimal computational accuracy and efficiency. It is demonstrated that while in general the 2D approach is well-suited for barotropic problems and dispersive free surface waves, the 3D approach is more advantageous for simulating baroclinic buoyancy-driven flows due in part to the high vertical resolution typically required to represent the active tracer fields. Keywords: Discontinuous Galerkin, Finite element, Unstructured mesh, Baroclinic flow, Non-hydrostatic, Dispersion, Free surface

  • Journal article
    Paschalis A, Fatichi S, Zscheischler J, Ciais P, Bahn M, Boysen L, Chang J, De Kauwe M, Estiarte M, Goll D, Hanson PJ, Harper AB, Hou E, Kigel J, Knapp AK, Larsen KS, Li W, Lienert S, Luo Y, Meir P, Nabel JEMS, Ogaya R, Parolari AJ, Peng C, Peñuelas J, Pongratz J, Rambal S, Schmidt IK, Shi H, Sternberg M, Tian H, Tschumi E, Ukkola A, Vicca S, Viovy N, Wang Y-P, Wang Z, Williams K, Wu D, Zhu Qet al., 2020,

    Rainfall-manipulation experiments as simulated by terrestrial biosphere models: where do we stand?

    , Global Change Biology, Vol: 26, Pages: 3336-3355, ISSN: 1354-1013

    Changes in rainfall amounts and patterns have been observed and are expected to continue in the near future with potentially significant ecological and societal consequences. Modelling vegetation responses to changes in rainfall is thus crucial to project water and carbon cycles in the future. In this study, we present the results of a new model-data intercomparison project, where we tested the ability of ten terrestrial biosphere models to reproduce observed sensitivity of ecosystem productivity to rainfall changes at ten sites across the globe, in nine of which, rainfall exclusion and/or irrigation experiments had been performed. The key results are: (a) Inter-model variation is generally large and model agreement varies with time scales. In severely water limited sites, models only agree on the interannual variability of evapotranspiration and to a smaller extent gross primary productivity. In more mesic sites model agreement for both water and carbon fluxes is typically higher on fine (daily-monthly) time scales and reduces on longer (seasonal-annual) scales. (b) Models on average overestimate the relationship between ecosystem productivity and mean rainfall amounts across sites (in space) and have a low capacity in reproducing the temporal (interannual) sensitivity of vegetation productivity to annual rainfall at a given site, even though observation uncertainty is comparable to inter-model variability. (c) Most models reproduced the sign of the observed patterns in productivity changes in rainfall manipulation experiments but had a low capacity in reproducing the observed magnitude of productivity changes. Models better reproduced the observed productivity responses due to rainfall exclusion than addition. (d) All models attribute ecosystem productivity changes to the intensity of vegetation stress and peak leaf area, whereas the impact of the change in growing season length is negligible. The relative contribution of the peak leaf area and vegetation stress i

  • Journal article
    Pacey A, Wilkinson JJ, Cooke DR, 2020,

    Chlorite and epidote mineral chemistry in porphyry ore systems: a case study of the Northparkes district, NSW, Australia

    , Economic Geology, Vol: 115, Pages: 701-727, ISSN: 0361-0128

    Propylitic alteration, characterized by the occurrence of chlorite and epidote, is typically the most extensive and peripheral alteration facies developed around porphyry ore deposits. However, exploration within this alteration domain is particularly challenging, commonly owing to weak or nonexistent whole-rock geochemical gradients and the fact that similar assemblages can be developed in other geologic settings, particularly during low-grade metamorphism. We document and interpret systematic spatial trends in the chemistry of chlorite and epidote from propylitic alteration around the E48 and E26 porphyry Cu-Au deposits of the Northparkes district, New South Wales, Australia. These trends vary as a function of both distance from hydrothermal centers and alteration paragenesis.The spatial trends identified in porphyry-related chlorite and epidote at Northparkes include (1) a deposit-proximal increase in Ti, As, Sb, and V in epidote and Ti in chlorite, (2) a deposit-distal increase in Co and Li in chlorite and Ba in epidote, and (3) a pronounced halo around deposits in which Mn and Zn in chlorite, as well as Mn, Zn, Pb, and Mg in epidote, are elevated. Chlorite Al/Si ratios and epidote Al/Fe ratios may show behavior similar to that of Mn-Zn or may simply decrease outward, and V and Ni concentrations in chlorite are lowest in the peak Mn-Zn zone. In comparison to porphyry-related samples, chlorite from the regional metamorphic assemblage in the district contains far higher concentrations of Li, Ca, Ba, Pb, and Cu but much less Ti. Similarly, metamorphic epidote contains higher concentrations of Sr, Pb, As, and Sb but less Bi and Ti.These chlorite and epidote compositional trends are the net result of fluid-mineral partitioning under variable physicochemical conditions within a porphyry magmatic-hydrothermal system. They are most easily explained by the contribution of spent magmatic-derived ore fluid(s) into the propylitic domain. It is envisaged that such fluids exp

  • Journal article
    Peng Y, Bloomfield K, Prentice IC, 2020,

    A theory of plant function helps to explain leaf-trait and productivity responses to elevation

    , New Phytologist, Vol: 226, Pages: 1274-1284, ISSN: 0028-646X

    Several publications have examined leaf‐trait and carbon‐cycling shifts along an Amazon‐Andes transect spanning 3.5 km elevation and 16℃ mean annual temperature. Photosynthetic capacity was previously shown to increase as temperature declines with increasing elevation, counteracting enzyme‐kinetic effects. Primary production declines, nonetheless, due to decreasing light availability. We aimed to predict leaf‐trait and production gradients from first principles, using published data to test an emerging theory whereby photosynthetic traits and primary production depend on optimal acclimation and/or adaptation to environment.We re‐analysed published data for 210 species at 25 sites, fitting linear relationships to elevation for both predicted and observed photosynthetic traits and primary production.Declining leaf‐internal/ambient CO2 ratio (χ) and increasing carboxylation (Vcmax) and electron‐transport (Jmax) capacities with increasing elevation were predicted. Increases in leaf nitrogen content with elevation were explained by increasing Vcmax and leaf mass‐per‐area. Leaf and soil phosphorus covaried, but after controlling for elevation, no nutrient metric accounted for any additional variance in photosynthetic traits. Primary production was predicted to decline with elevation.This analysis unifies leaf and ecosystem observations in a common theoretical framework. The insensitivity of primary production to temperature is shown to emerge as a consequence of the optimization of photosynthetic traits.

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