Predictable hydrodynamic conditions explain temporal variations in the density of benthic foraging seabirds in a tidal stream environment

VC International Council for the Exploration of the Sea 2016. James J. Waggitt was funded by a NERC Case studentship supported by OpenHydro Ltd and Marine Scotland Science (NE/J500148/1). Shore-based surveys were funded by a NERC (NE/J004340/1) and a Scottish National Heritage (SNH) grant. FVCOM was funded by a NERC grant (NE/J004316/1). The bathymetry data used in hydrodynamic models (HI 1122 Sanday Sound to Westray Firth) was collected by the Maritime and Coastguard Agency (MCA) as part of the UK Civil Hydrography Programme. We wish to thank Christina Bristow, Matthew Finn and Jennifer Norris at the European Marine Energy Centre (EMEC); Ian Davies at Marine Scotland Science; Gail Davoren, Shaun Fraser, Pauline Goulet, Alex Robbins and Helen Wade for invaluable discussions; Thomas Cornulier, Alex Douglas, James Grecian and Samantha Patrick for their help with statistical analysis; and Jenny Campbell and the Cockram family for assistance during fieldwork.Peer reviewedPublisher PD

Quantifying pursuit-diving seabirds’ associations with fine-scale physical features in tidal stream environments

Acknowledgements: James J. Waggitt was funded by a NERC Case studentship supported by OpenHydro Ltd and Marine Scotland Science (NE/J500148/1). Vessel-based transects were funded by a NERC (NE/J004340/1) and a Scottish National Heritage (SNH) grant. FVCOM modelling was funded by a NERC grant (NE/J004316/1). Marine Scotland Science provided time on the FRV Alba-na-Mara as part as the Marine Collaboration Research Forum (MarCRF). The bathymetry data used in hydrodynamic models (HI 1122 Sanday Sound to Westray Firth) was collected by the Maritime & Coastguard Agency (MCA) as part of the UK Civil Hydrography Programme. We wish to thank Christina Bristow, Matthew Finn and Jennifer Norris at the European Marine Energy Centre (EMEC); Marianna Chimienti, Ciaran Cronin, Tim Sykes and Stuart Thomas for performing vessel-based transects; Marine Scotland Science staff Eric Armstrong, Ian Davies, Mike Robertson, Robert Watret and Michael Stewart for their assistance; Shaun Fraser, Pauline Goulet, Alex Robbins, Helen Wade and Jared Wilson for invaluable discussions; Thomas Cornulier, Alex Douglas, James Grecian and Samantha Patrick for their help with statistical analysis; and Gavin Siriwardena, Leigh Torres, Mark Whittingham and Russell Wynn for their constructive comments on earlier versions of this manuscript. APC paid through institutional prepayment schemePeer reviewedPublisher PD

A new ELISA kit which uses a combination of Plasmodium falciparum extract and recombinant Plasmodium vivax antigens as an alternative to IFAT for detection of malaria antibodies

BACKGROUND: The methods most commonly used to measure malarial antibody titres are the Indirect Fluorescence Antibody Test (IFAT), regarded as the gold standard, and the Enzyme-Linked ImmunoSorbent Assay (ELISA). The objective here was to assess the diagnostic performance, i.e. the sensitivity and specificity, of a new malaria antibody ELISA kit in comparison to IFAT. This new ELISA kit, the ELISA malaria antibody test (DiaMed), uses a combination of crude soluble Plasmodium falciparum extract and recombinant Plasmodium vivax antigens. METHODS: Two groups were used: 95 samples from malaria patients to assess the clinical sensitivity and 2,152 samples from blood donors, who had not been exposed to malaria, to assess the clinical specificity. RESULTS: The DiaMed ELISA test kit had a clinical sensitivity of 84.2% and a clinical specificity of 99.6% as compared with 70.5% and 99.6% respectively, using the IFAT method. The ELISA method was more sensitive than the IFAT method for P. vivax infections (75% vs. 25%). However, in 923 malaria risk donors the analytical sensitivity of the ELISA test was 40% and its specificity 98.3%, performances impaired by large numbers of equivocal results non-concordant between ELISA and IFAT. When the overall analytical performances of ELISA was compared to IFAT, the ELISA efficiency J index was 0.84 versus 0.71 for IFAT. Overall analytical sensitivity was 93.1% and the analytical specificity 96.7%. Overall agreement between the two methods reached 0.97 with a reliability k index of 0.64. CONCLUSION: The DiaMed ELISA test kit shows a good correlation with IFAT for analytical and clinical parameters. It may be an interesting method to replace the IFAT especially in blood banks, but further extensive investigations are needed to examine the analytical performance of the assay, especially in a blood bank setting

Towards comprehensive observing and modeling systems for monitoring and predicting regional to coastal sea level

A major challenge for managing impacts and implementing effective mitigation measures and adaptation strategies for coastal zones affected by future sea level (SL) rise is our limited capacity to predict SL change at the coast on relevant spatial and temporal scales. Predicting coastal SL requires the ability to monitor and simulate a multitude of physical processes affecting SL, from local effects of wind waves and river runoff to remote influences of the large-scale ocean circulation on the coast. Here we assess our current understanding of the causes of coastal SL variability on monthly to multi-decadal timescales, including geodetic, oceanographic and atmospheric aspects of the problem, and review available observing systems informing on coastal SL. We also review the ability of existing models and data assimilation systems to estimate coastal SL variations and of atmosphere-ocean global coupled models and related regional downscaling efforts to project future SL changes. We discuss (1) observational gaps and uncertainties, and priorities for the development of an optimal and integrated coastal SL observing system, (2) strategies for advancing model capabilities in forecasting short-term processes and projecting long-term changes affecting coastal SL, and (3) possible future developments of sea level services enabling better connection of scientists and user communities and facilitating assessment and decision making for adaptation to future coastal SL change.RP was funded by NASA grant NNH16CT00C. CD was supported by the Australian Research Council (FT130101532 and DP 160103130), the Scientific Committee on Oceanic Research (SCOR) Working Group 148, funded by national SCOR committees and a grant to SCOR from the U.S. National Science Foundation (Grant OCE-1546580), and the Intergovernmental Oceanographic Commission of UNESCO/International Oceanographic Data and Information Exchange (IOC/IODE) IQuOD Steering Group. SJ was supported by the Natural Environmental Research Council under Grant Agreement No. NE/P01517/1 and by the EPSRC NEWTON Fund Sustainable Deltas Programme, Grant Number EP/R024537/1. RvdW received funding from NWO, Grant 866.13.001. WH was supported by NASA (NNX17AI63G and NNX17AH25G). CL was supported by NASA Grant NNH16CT01C. This work is a contribution to the PIRATE project funded by CNES (to TP). PT was supported by the NOAA Research Global Ocean Monitoring and Observing Program through its sponsorship of UHSLC (NA16NMF4320058). JS was supported by EU contract 730030 (call H2020-EO-2016, “CEASELESS”). JW was supported by EU Horizon 2020 Grant 633211, Atlantos

orkney_fallofwarness_seabirdenvironment

Concurrent information on seabird distributions and environmental variables at 500m and 15min resolution in the Fall Of Warness, Orkney, UK

Data from: Quantifying pursuit-diving seabirds' associations with fine-scale physical features in tidal stream environments

The rapid increase in the number of tidal stream turbine arrays will create novel and unprecedented levels of anthropogenic activity within habitats characterized by horizontal current speeds exceeding 2 ms−1. However, the potential impacts on pursuit-diving seabirds exploiting these tidal stream environments remain largely unknown. Identifying similarities between the fine-scale physical features (100s of metres) suitable for array installations, and those associated with foraging pursuit-diving seabirds, could identify which species are most vulnerable to either collisions with moving components, or displacement from these installations. A combination of vessel-based observational surveys, Finite Volume Community Ocean Model outputs and hydroacoustic seabed surveys provided concurrent measures of foraging distributions and physical characteristics at a fine temporal (15 min) and spatial (500 m) resolution across a tidal stream environment suitable for array installations, during both breeding and non-breeding seasons. These data sets were then used to test for associations between foraging pursuit-diving seabirds (Atlantic puffins Fratercula arctica, black guillemots Cepphus grylle, common guillemots Uria aalge, European shags Phalacrocorax aristotelis) and physical features. These species were associated with areas of fast horizontal currents, slow horizontal currents, high turbulence, downward vertical currents and also hard–rough seabeds. The identity and strength of associations differed among species, and also within species between seasons, indicative of interspecific and intraspecific variations in habitat use. However, Atlantic puffins were associated particularly strongly with areas of fast horizontal currents during breeding seasons, and European shags with areas of rough–hard seabeds and downward vertical currents during non-breeding seasons. Synthesis and applications. Atlantic puffins’ strong association with fast horizontal current speeds indicates that they are particularly likely to interact with installations during breeding seasons. Any post-installation monitoring and mitigation measures should therefore focus on this species and season. The multi-species associations with high turbulence and downward vertical currents, which often coincide with fast horizontal current speeds, also highlight useful pre-installation mitigation measures via the omission of devices from these areas, reducing the overall likelihood of interactions. Environmental impact assessments (EIA) generally involve once-a-month surveys across 2-year periods. However, the approaches used in this study show that more focussed surveys can greatly benefit management strategies aiming to reduce the likelihood of negative impacts by facilitating the development of targeted mitigation measures. It is therefore recommended that these approaches contribute towards EIA within development sites

What Controls the Flushing Efficiency and Particle Transport Pathways in a Tropical Estuary? Cochin Estuary, Southwest Coast of India

Estuaries with poor flushing and longer residence time retain effluents and pollutants, ultimately resulting in eutrophication, a decline in biodiversity and, finally, deterioration of water quality. Cochin Estuary (CE), southwest coast of India, is under the threat of nutrient enrichment by the anthropogenic interventions and terrestrial inputs through land runoff. The present study used the FVCOM hydrodynamic model coupled with the Lagrangian particle module (passive) to estimate the residence time and to delineate site-specific transport pathways in the CE. The back and forth movements and residence time of particles was elucidated by using metrics such as path length, net displacement and tortuosity. Spatio-temporal patterns of the particle distribution in the CE showed a similar trend during monsoon and post-monsoon with an average residence time of 25 and 30 days, respectively. During the low river discharge period (pre-monsoon), flood-ebb velocities resulted in a minimum net transport of the water and longer residence time of 90 days compared to that of the high discharge period (monsoon). During the pre-monsoon, particle released at the southern upstream (station 15) traversed a path length of 350 km in 90 days before being flushed out through the Fortkochi inlet, where the axial distance was only 35 km. This indicates that the retention capacity of pollutants within the system is very high and can adversely affect the water quality of the ecosystem. However, path length (120 km) and residence time (7.5 days) of CE were considerably reduced during the high discharge period. Thus the reduced path length and the lower residence time can effectively transport the pollutants reaching the system, which will ultimately restore the healthy ecosystem. This is a pioneer attempt to estimate the flushing characteristics and residence time of the CE by integrating the hydrodynamics and Lagrangian particle tracking module of FVCOM. This information is vital for the sustainable management of sensitive ecosystems