Bayesian joint models with INLA exploring marine mobile predator-prey and competitor species habitat overlap

EPSRC grant Ecowatt 2050 EP/K012851/1 ACKNOWLEDGMENTS We would like to thank the associate editor and the anonymous reviewers for their useful and constructive suggestions which led to a considerable improvement of the manuscript. The authors would also like to thank the following people/organizations for making large datasets available for use in this paper: Mark Lewis (Joint Nature Conservation Committee), Philip Hammond (Scottish Oceans Institute, University of St. Andrews), Susan Lusseau (Marine Scotland Science), Darren Stevens (The Sir Alister Hardy Foundation for Ocean Science, PML), and Yuri Artioli (Plymouth Marine Laboratory). This work was supported by the Engineering and Physical Sciences Research Council (EcoWatt250; EPSRC EP/K012851/1).Peer reviewedPublisher PD

Ecological costs of climate change on marine predator-prey population distributions by 2050

ACKNOWLEDGEMENTS We would like to thank the following people/organizations for making large data sets available for use in this paper: Mark Lewis (Joint Nature Conservation Committee), Philip Hammond (Scottish Oceans Institute), Susan Lusseau (Marine Scotland Science) and the ICES Herring Assessment Working Group (HAWG), Darren Stevens (The Sir Alister Hardy Foundation for Ocean Science, PML), and Yuri Artioli (Plymouth Marine Laboratory). We would also like to thank two anonymous reviewers that improved the clarity of this work.This work was supported by the Engineering and Physical Sciences Research Council (EcoWatt2050; EPSRC EP/K012851/1). Work conducted by D. Sadykova was partially supported by a Grant from Science Foundation Ireland (15/IA/2881).Peer reviewedPublisher PD

The effect of uncertain river forcing on the thermohaline properties of the North West European Shelf Seas

Modeling studies and observations show that the thermohaline properties of the North West European Shelf Seas (NWESS) are sensitive to surface wind and heat flux forcing, as well as river outflows that transport fresh water from land to the ocean. In previous studies, it was assumed that the variability of the thermohaline properties in response to river outflow could be adequately sampled with a high-resolution, submesoscale permitting, long-term (i.e., 30-year) deterministic hindcast. In this study, we assume that the statistical distribution of the river forcing, rather than the time series of forcing itself, is adequately constrained by a 28-year history (1991 to 2018) of river forcing created specifically for our domain. In this way, we created an ensemble of 10 lower-resolution ( 7-km), short-term (i.e., 2.5 years) hindcast models that are forced with randomly perturbed river outflows and an ensemble of surface fluxes from the 10-member ECMWF ERA5 reanalysis (the ‘Test’ ensemble) as well with a companion ensemble that is forced with the ERA5 surface forcing fluxes but unperturbed river outflows (the ‘Base’ ensemble) for the June 2016 through December 2018 time period. In both ensembles, the modeled evolution of 25-hour averaged (to partially filter out tides) temperature and salinity is realistic with peaks in summer for sea surface temperature and in winter for salinity, and annual amplitudes that are comparable to those found in other studies of the NWESS. The increased mean and standard deviation of the sea surface and bottom salinity in the Test ensemble are partly an artifact of the assumption that the errors in river forcing have a log-normal distribution that mimics the episodic nature of river outflow with a positive mean and an asymmetrical shape with a long tail towards large values. For surface density, the standard deviation in the Test ensemble was below 0.5 kg/m3, covering an areal extent larger than that for the Base ensemble throughout the year. The annual cycle of the areal extent of density in that range had a peak in summer and minima in winter, in phase with that of the river outflow forcing. Overall, the effect of uncertain river forcing on the thermohaline properties in this study is small. In order to understand the true impact of river forcings, better temporal and spatial observations of river outflow are needed

Quantify the monthly to decadal variability of climate effects on the lower trophic levelse of shelf sea ecosystems

ECOOP WP10, Deliverable no: D10.1.2.1This report describes three studies using multi-decadal simulations of regional coupled hydrodynamics ecosystem models. These models are used to investigate the relationship between lower trophic level marine ecosystems and biogeochemistry, and the physical environment. The models considered here: POLCOMS-ERSEM Atlantic Margin Model run from 1960 to 2003 (NERC and PML) NORWECOM North Sea Model run from 1985-2006 (IMR) ECOSMO (UiB-GFI) North sea and Baltic Sea run 1980-2004 (UiB-GFI) The POLCOMS-ERSEM model is validated using in-situ data from the world ocean data centre and analysed to investigate the potential long term changes in primary production across the period 1960-2004, in the context of model open boundary conditions and drift. The model experiments demonstrate a strong sensitivity of the on-shelf primary production to the oceanic nutrient boundary conditions, suggesting cross-shelf edge nutrient fluxes provide a significant source of variability. The relationship between the model results and the North Atlantic Oscillation are also considered, demonstrating a r~0.65 correlation with on-shelf nutrients and the NAO The NORWECOM model is validated here using time series data from the Dutch coast. Correlations between model variables in a selection of ICES boxes are compared with a number of driving factors. River loads are shown to dominate coastal boxes. The relationships in open-shelf boxes are more ambiguous, although the southerly inflow is demonstrated to have an important role. The validation of the POLCOMS-ERSEM and NORWECOM models both conclude that the simulations have better skill for nutrients than chlorophyll and in open-shelf seas away from the coast. The validation of ECOSMO presented here focuses on zooplankton and comparison with data from the continuous plankton recorder, investigating six different approaches to matching CPR records with model data. Across the North Sea the mean annual cycle shows good agreement between model and CPR. There is also good correlation with along-track variability. EOF and correlation analysis is used to relate the primary production in the North Sea to atmospheric forcing parameters. The EOF patterns tend to match the distribution of summer time stratification, while the wind speed is shows the highest correlation, particularly during the onset and breakdown of stratification. This indicates the strength of cross-thermocline mixing is an important control on primary production variability. The ECOSMO model has been further developed for use in the Baltic by inclusion of nitrogen fixing cyanobacteria. These studies each demonstrate significant control of the inter-annual variability of shelf sea ecosystems through a range of external forcing vectors: oceanic through cross-shelf edge nutrient flux, terrestrial through variations in river nutrient loading, and atmospheric via the wind control of vertical mixing. Each of these vectors potentially mediates climatic variability and climate change

Carbon on the Northwest European Shelf: Contemporary Budget and Future Influences

A carbon budget for the northwest European continental shelf seas (NWES) was synthesized using available estimates for coastal, pelagic and benthic carbon stocks and flows. Key uncertainties were identified and the effect of future impacts on the carbon budget were assessed. The water of the shelf seas contains between 210 and 230 Tmol of carbon and absorbs between 1.3 and 3.3 Tmol from the atmosphere annually. Off-shelf transport and burial in the sediments account for 60–100 and 0–40% of carbon outputs from the NWES, respectively. Both of these fluxes remain poorly constrained by observations and resolving their magnitudes and relative importance is a key research priority. Pelagic and benthic carbon stocks are dominated by inorganic carbon. Shelf sediments contain the largest stock of carbon, with between 520 and 1600 Tmol stored in the top 0.1 m of the sea bed. Coastal habitats such as salt marshes and mud flats contain large amounts of carbon per unit area but their total carbon stocks are small compared to pelagic and benthic stocks due to their smaller spatial extent. The large pelagic stock of carbon will continue to increase due to the rising concentration of atmospheric CO2, with associated pH decrease. Pelagic carbon stocks and flows are also likely to be significantly affected by increasing acidity and temperature, and circulation changes but the net impact is uncertain. Benthic carbon stocks will be affected by increasing temperature and acidity, and decreasing oxygen concentrations, although the net impact of these interrelated changes on carbon stocks is uncertain and a major knowledge gap. The impact of bottom trawling on benthic carbon stocks is unique amongst the impacts we consider in that it is widespread and also directly manageable, although its net effect on the carbon budget is uncertain. Coastal habitats are vulnerable to sea level rise and are strongly impacted by management decisions. Local, national and regional actions have the potential to protect or enhance carbon storage, but ultimately global governance, via controls on emissions, has the greatest potential to influence the long-term fate of carbon stocks in the northwestern European continental shelf

Carbon on the Northwest European Shelf: Contemporary Budget and Future Influences

© Copyright © 2020 Legge, Johnson, Hicks, Jickells, Diesing, Aldridge, Andrews, Artioli, Bakker, Burrows, Carr, Cripps, Felgate, Fernand, Greenwood, Hartman, Kröger, Lessin, Mahaffey, Mayor, Parker, Queirós, Shutler, Silva, Stahl, Tinker, Underwood, Van Der Molen, Wakelin, Weston and Williamson. A carbon budget for the northwest European continental shelf seas (NWES) was synthesized using available estimates for coastal, pelagic and benthic carbon stocks and flows. Key uncertainties were identified and the effect of future impacts on the carbon budget were assessed. The water of the shelf seas contains between 210 and 230 Tmol of carbon and absorbs between 1.3 and 3.3 Tmol from the atmosphere annually. Off-shelf transport and burial in the sediments account for 60–100 and 0–40% of carbon outputs from the NWES, respectively. Both of these fluxes remain poorly constrained by observations and resolving their magnitudes and relative importance is a key research priority. Pelagic and benthic carbon stocks are dominated by inorganic carbon. Shelf sediments contain the largest stock of carbon, with between 520 and 1600 Tmol stored in the top 0.1 m of the sea bed. Coastal habitats such as salt marshes and mud flats contain large amounts of carbon per unit area but their total carbon stocks are small compared to pelagic and benthic stocks due to their smaller spatial extent. The large pelagic stock of carbon will continue to increase due to the rising concentration of atmospheric CO2, with associated pH decrease. Pelagic carbon stocks and flows are also likely to be significantly affected by increasing acidity and temperature, and circulation changes but the net impact is uncertain. Benthic carbon stocks will be affected by increasing temperature and acidity, and decreasing oxygen concentrations, although the net impact of these interrelated changes on carbon stocks is uncertain and a major knowledge gap. The impact of bottom trawling on benthic carbon stocks is unique amongst the impacts we consider in that it is widespread and also directly manageable, although its net effect on the carbon budget is uncertain. Coastal habitats are vulnerable to sea level rise and are strongly impacted by management decisions. Local, national and regional actions have the potential to protect or enhance carbon storage, but ultimately global governance, via controls on emissions, has the greatest potential to influence the long-term fate of carbon stocks in the northwestern European continental shelf

Consensus guidelines for the use and interpretation of angiogenesis assays

The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

The influence of initial conditions and open boundary conditions on shelf circulation in a 3D ocean-shelf model of the North East Atlantic

Data from climatology (World Ocean Atlas) and two large scale operational ocean models (Forecasting Ocean Assimilation Model – FOAM, UK Met. Office) and the Navy Coastal Ocean Model – NCOM, US Naval Research Laboratory) are used to give initial and open boundary conditions for a northeast Atlantic implementation of the Proudman Oceanographic Laboratory Coastal Ocean Model System (POLCOMS). We study the effects of using the different datasets on the temperature fields and the circulation. On the continental shelf, comparisons of POLCOMS output with AVHRR sea surface temperature data suggest that the effect of using different ocean model initial and boundary conditions is small and that, after 15 months of model time, the impact of the different initial conditions is negligible. Stronger evidence of influence is seen in the deeper oceanic regions of the domain. Volume fluxes through sections governing flow into and out of the North Sea, through the Irish Sea and along the shelf edge show that the impact of the different boundary conditions is small on the shelf but significant elsewhere. These results are contrasted with the use of climatology to assess the value of these Global Ocean Data Assimilation Experiment (GODAE) ocean model products