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

Use of our Future Seas : Relevance of Spatial and Temporal Scale for Physical and Biological Indicators

Funding This work was supported by the Supergen Offshore Renewable Energy (ORE) Hub, funded by the Engineering and Physical Sciences Research Council (EPSRC EP/S000747/1). Acknowledgments The authors would like to thank the following people for providing original images, incorporated in this work: Rory O’Hara Murray (Marine Scotland Science, United Kingdom), Ella-Sophia Benninghaus and Morgane Declerck (University of Aberdeen, United Kingdom).Peer reviewedPublisher PD

MEDSLIK-II, a Lagrangian marine surface oil spill model for short-term forecasting – Part 1: Theory

The processes of transport, diffusion and transformation of surface oil in seawater can be simulated using a Lagrangian model formalism coupled with Eulerian circulation models. This paper describes the formalism and the conceptual assumptions of a Lagrangian marine surface oil slick numerical model and rewrites the constitutive equations in a modern mathematical framework. The Lagrangian numerical representation of the oil slick requires three different state variables: the slick, the particle and the structural state variables. Transformation processes (evaporation, spreading, dispersion and coastal adhesion) act on the slick state variables, while particle variables are used to model the transport and diffusion processes. The slick and particle variables are recombined together to compute the oil concentration in water, a structural state variable. The mathematical and numerical formulation of oil transport, diffusion and transformation processes described in this paper, together with the many simplifying hypothesis and parameterizations, form the basis of a new, open source Lagrangian surface oil spill model, the so-called MEDSLIK-II, based on its precursor MEDSLIK (Lardner et al., 1998, 2006; Zodiatis et al., 2008a). Part 2 of this paper describes the applications of the model to oil spill simulations that allow the validation of the model results and the study of the sensitivity of the simulated oil slick to different model numerical parameterizations

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

Guidance note on the application of coastal modelling for small island developing states

This report is part of the NOC-led project “Climate Change Impact Assessment: Ocean Modelling and Monitoring for the Caribbean CME states”, 2017-2020, under the Commonwealth Marine Economies (CME) Programme in the Caribbean. Small Island Developing States (SIDS) are very diverse, but have something in common: they are all vulnerable to human-induced climate change, but have contributed very little to causing the problem, due to their small size and limited development. Much time has been spent in debating climate change and adaptation strategies for such countries, but little has been done in developing practical tools to assist them in managing the coastal zone. In this report we aim to address that. In April 2017, some senior staff members from the National Oceanography Centre (NOC) visited St Vincent and the Grenadines, as part of the UK Foreign and Commonwealth Office-funded Neptune programme. At that time, some of the issues around coastal erosion on the east coast of St Vincent were identified, as well as some extreme events from which St Vincent and the Grenadines had suffered substantial losses of GDP. This was followed up by a workshop in January 2018 on ‘Implementing and Monitoring the Sustainable Development Goals in the Caribbean: The Role of the Ocean’, which was co-sponsored by the UK Government-funded Commonwealth Marine Economies Programme (CMEP) via the NOC (CMEP being the successor to Neptune). During the period September 2017 to March 2020, the National Oceanography Centre, funded by the CMEP, has been working with St Vincent and the Grenadines to provide knowledge, data and training about data analysis application and software for the use of coastal managers, particularly in order to address the problem of coastal erosion. We held a stakeholder workshop in Kingstown, St Vincent, in March 2018 and a hands-on technical training workshop in January 2019. A final workshop is being held in March 2020. Here we present an overview of coastal modelling methodology for use by Small Island Developing States (SIDS), including references to previous model review studies and guidance on how to access and apply model outputs, which will be presented at the workshop, entitled ‘Applying Knowledge of Coastal Processes for Coastal Zone Management into the Future’. This report seeks to collate the information on Coastal Modelling, which may be relevant to all SIDS, in order to support evidence-based decision-making. The case study is built around work done for St Vincent and the Grenadines. It is not the intention to explain in detail the technical working and development of models, as it is envisaged that SIDS will not want or need to run complex models themselves, but if this is desired, information on further reading and training is provided. Some of the simpler and more accessible models, with particularly useful applications in the coastal zone, which do not require computer resources beyond a laptop computer, are described in more detail for in-house application and their use in decision-making is explained. The way forward in regional collaboration and capacity-building is discussed

Turbulence changes due to a tidal stream turbine operation in the Pentland Firth (Scotland, UK)

The high tidal stream resource in the Pentland Firth (Scotland, UK) has encouraged the development of commercial scale tidal farms. This work is a modelling study primarily focused on how the layout of arrays determines the extractable power and may affect physical processes in the region. Furthermore, the study provides information about submarine turbine maintenance. Tidal dynamics in the Pentland Firth and Orkney Waters (PFOW) have been reproduced by a three-dimensional FVCOM model implementation. The tidal stream turbines were represented in the model as sub grid scale objects by using a momentum sink approach. It has been explored how different turbine location, number and spacing can allow achieving very different amount of power resource, as well as degree of change to flow velocities. It has also been verified that turbulence changes can lead to an increase in bottom currents in the vicinity of the tidal turbines

Tide-surge interaction in the Pearl River Estuary: A case study of Typhoon Hato

In this study, the characteristics and mechanisms of tide-surge interaction in the Pearl River Estuary (PRE) during Typhoon Hato in August 2017 are studied in detail using a 3D nearshore hydrodynamic model. The wind field of Typhoon Hato is firstly reconstructed by merging the Holland parametric tropical cyclone model results with the CFSR reanalysis data, which enables the model to reproduce the pure astronomical tides and storm tides well; in particular, the distinctive oscillation pattern in the measured water levels due to the passage of the typhoon has been captured. Three different types of model runs are conducted in order to separate the water level variations due to the astronomical tide, storm surge, and tide-surge interactions in the Pearl River Estuary. The results show the strong tidal modulation of the surge level, as well as alteration of the phase of surge, which also changes the peak storm tidal level, in addition to the tidal modulation effects. In order to numerically assess the contributions of three non-linear processes in the tide-surge interaction and quantify their relative significance, the widely used “subtraction” approach and a new “addition” approach are tested in this study. The widely used “subtraction” approach is found to be unsuitable for the assessment due to the “rebalance” effect, and thus the new “addition” approach is proposed along with a new indicator to represent the tide-surge interaction, from which more reasonable results are obtained. Detailed analysis using the “addition” approach indicates that the quadratic bottom friction, shallow water effect, and nonlinear advective effect play the first, second, and third most important roles in the tidal-surge interaction in the estuary, respectively

Quantifying processes contributing to marine hazards to inform coastal climate resilience assessments, demonstrated for the Caribbean Sea

Scientific evidence is critical to underpin the decisions associated with shoreline management, to build climate-resilient communities and infrastructure. We explore the role of waves, storm surges and sea level rise for the Caribbean region with a focus on coastal impacts in the eastern Caribbean islands. We simulate past extreme events and a worst-case scenario, modelling the storm surges and waves, suggesting a storm surge might reach 1.5 m, depending on the underwater topography. Coastal wave heights of up to 12 m offshore and up to 5 m near the coast of St Vincent are simulated with a regional wave model. We deliver probabilistic sea level projections for 2100, with a low-probability–high-impact estimate of possible sea level rise up to 2.2 m, exceeding the 1.8 m global estimate for the same scenario. We introduce a combined vulnerability index, which allows for a quantitative assessment of relative risk across the region, showing that sea level rise is the most important risk factor everywhere but wave impacts are important on windward coasts, increasing to the north, towards the main hurricane track. Our work provides quantitative evidence for policy-makers, scientists and local communities to actively prepare for and protect against climate change

Mangrove forests can be an effective coastal defence in the Pearl River Delta, China

Coastal vegetation can reduce extreme water levels during storm events, but the controlling factors and processes in complex estuary or delta systems are still unclear. This limits an effective implementation of nature-based coastal defences in delta mega-cities in low-lying coastal areas. Here we have numerically modelled how mangroves can offer coastal protection to the large coastal cities located in the Pearl River Delta (China), such as Guangzhou and Shenzhen, during strong typhoons, like Hato (2017). Water level attenuation by mangroves is effective during extreme water level conditions and differences in mangrove forests’ properties drive their coastal protection function. The local (within-wetland) attenuation of extreme water levels is more effective with wide vegetation patches and higher vegetation drag. Narrower vegetation patches can still provide non-local (upstream) water level attenuation if located in the upper estuary channels, but their design needs to avoid amplification of water levels in other delta areas

Chest CT Features of COVID-19 in Rome, Italy

Background The standard for diagnosis of SARS-CoV-2 virus is reverse transcription polymerase chain reaction (RT-PCR) test, but chest CT may play a complimentary role in the early detection of COVID-19 pneumonia. Purpose To investigate CT features of patients with COVID-19 in Rome, Italy, and to compare the accuracy of CT with RT-PCR. Methods In this prospective study from March 4, 2020, until March 19, 2020, consecutive patients with suspected COVID-19 infection and respiratory symptoms were enrolled. Exclusion criteria were: chest CT with contrast medium performed for vascular indications, patients who refused chest CT or hospitalization, and severe CT motion artifact. All patients underwent RT-PCR and chest CT. Diagnostic performance of CT was calculated using RT-PCR as reference. Chest CT features were calculated in a subgroup of RT-PCR-positive and CT-positive patients. CT features of hospitalized patients and patient in home isolation were compared by using Pearson chi squared test. Results Our study population comprised 158 consecutive study participants (83 male and 75 female, mean age 57 y ±17). Fever was observed in 97/158 (61%), cough in 88/158 (56%), dyspnea in 52/158 (33%), lymphocytopenia in 95/158 (60%), increased C-reactive protein level in 139/158 (88%), and elevated lactate dehydrogenase in 128/158 (81%) study participants. Sensitivity, specificity, and accuracy of CT were 97% (60/62)[95% IC, 88-99%], 56% (54/96)[95% IC,45-66%] and 72% (114/158)[95% IC 64-78%], respectively. In the subgroup of RT-PCR-positive and CT-positive patients, ground-glass opacities (GGO) were present in 58/58 (100%), multilobe and posterior involvement were both present in 54/58 (93%), bilateral pneumonia in 53/58 (91%), and subsegmental vessel enlargement (> 3 mm) in 52/58 (89%) of study participants. Conclusion The typical pattern of COVID-19 pneumonia in Rome, Italy, was peripherally ground-glass opacities with multilobe and posterior involvement, bilateral distribution, and subsegmental vessel enlargement (> 3 mm). Chest CT sensitivity was high (97%) but with lower specificity (56%)