The effects of intertidal oyster (Crassostrea gigas) culture on the spatial distribution of waterbirds

Atkins was commissioned by the Marine Institute to provide ornithological services in relation to the appropriate assessment of aquaculture and fisheries activities on coastal Special Protecion Areas for birds (SPA's). Intertidal culture of the Pacific Oyster using oyster trestles is widespread in Ireland and occurs in 16 SPAs and the potential impact of this activity on waterbird populations will be an issue in a number of Appropriate Assessments. Therefore, a research programme was designed by Atkins, in consultation with the Marine Institute, to fill this information gap. This research programme included a review of the distribution of intertidal oyster culture in Ireland in relation to coastal Special Areas, and other areas of importance for waterbirds and extensive and intensive studies of the relationship between waterbird distribution and intertidal oyster culture

The role of hnRNPs in frontotemporal dementia and amyotrophic lateral sclerosis

Dysregulated RNA metabolism is emerging as a crucially important mechanism underpinning the pathogenesis of frontotemporal dementia (FTD) and the clinically, genetically and pathologically overlapping disorder of amyotrophic lateral sclerosis (ALS). Heterogeneous nuclear ribonucleoproteins (hnRNPs) comprise a family of RNA-binding proteins with diverse, multi-functional roles across all aspects of mRNA processing. The role of these proteins in neurodegeneration is far from understood. Here, we review some of the unifying mechanisms by which hnRNPs have been directly or indirectly linked with FTD/ALS pathogenesis, including their incorporation into pathological inclusions and their best-known roles in pre-mRNA splicing regulation. We also discuss the broader functionalities of hnRNPs including their roles in cryptic exon repression, stress granule assembly and in co-ordinating the DNA damage response, which are all emerging pathogenic themes in both diseases. We then present an integrated model that depicts how a broad-ranging network of pathogenic events can arise from declining levels of functional hnRNPs that are inadequately compensated for by autoregulatory means. Finally, we provide a comprehensive overview of the most functionally relevant cellular roles, in the context of FTD/ALS pathogenesis, for hnRNPs A1-U

Resistance training for rehabilitation after burn injury: A systematic literature review and meta-analysis

Background/aim: Resistance training is beneficial for rehabilitation in many clinical conditions, though this has not been systematically reviewed in burns. The objective was to determine the effectiveness of resistance training on muscle strength, lean mass, function, quality of life and pain, in children and adults after burn injury. Methods: Medline & EMBASE, PubMed, CINAHL and CENTRAL were searched from inception to October 2016. Studies were identified that implemented resistance training in rehabilitation. Data were combined and included in meta-analyses for muscle strength and lean mass. Otherwise, narrative analysis was completed. The quality of evidence for each outcome was summarised and rated using the GRADE framework. Results: Eleven studies matched our inclusion criteria. Primary analysis did not demonstrate significant improvements for increasing muscle strength (SMD 0.74, 95% CI _0.02 to 1.50, p=0.06). Sensitivity analysis to correct an apparent anomaly in published data suggested a positive effect (SMD 0.37, 95% CI 0.08–0.65, p=0.01). Psychological quality of life demonstrated benefit from training (MD=25.3, 95% CI 3.94–49.7). All studies were rated as having high risk of bias. The quality of the evidence was rated as low or very low. Conclusion: Further research with robust methodology is recommended to assess the potential benefit suggested in this review

Seasonal phytoplankton blooms in the Gulf of Aden revealed by remote sensing

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.  The Gulf of Aden, situated in the northwest Arabian Sea and linked to the Red Sea, is a relatively unexplored ecosystem. Understanding of large-scale biological dynamics is limited by the lack of adequate datasets. In this study, we analyse 15 years of remotely-sensed chlorophyll-a data (Chl-a, an index of phytoplankton biomass) acquired from the Ocean Colour Climate Change Initiative (OC-CCI) of the European Space Agency (ESA). The improved spatial coverage of OC-CCI data in the Gulf of Aden allows, for the first time, an investigation into the full seasonal succession of phytoplankton biomass. Analysis of indices of phytoplankton phenology (bloom timing) reveals distinct phytoplankton growth periods in different parts of the gulf: a large peak during August (mid-summer) in the western part of the gulf, and a smaller peak during November (mid-autumn) in the lower central gulf and along the southern coastline. The summer bloom develops rapidly at the beginning of July, and its peak is approximately three times higher than that of the autumnal bloom. Remotely-sensed sea-surface temperature (SST), wind-stress curl, vertical nutrient profiles and geostrophic currents inferred from the sea-level anomaly, were analysed to examine the underlying physical mechanisms that control phytoplankton growth. During summer, the prevailing southwesterlies cause upwelling along the northern coastline of the gulf (Yemen), leading to an increase in nutrient availability and enhancing phytoplankton growth along the coastline and in the western part of the gulf. In contrast, in the central region of the gulf, lowest concentrations of Chl-a are observed during summer, due to strong downwelling caused by a mesoscale anticyclonic eddy. During autumn, the prevailing northeasterlies enable upwelling along the southern coastline (Somalia) causing local nutrient enrichment in the euphotic zone, leading to higher levels of phytoplankton biomass along the coastline and in the lower central gulf. The monsoon wind reversal is shown to play a key role in controlling phytoplankton growth in different regions of the Gulf of Aden.European Space Agenc

The response of ground-dwelling spiders (Araneae) and hoverflies (Diptera: Syrphidae) to afforestation assessed using within site tracking

In many countries throughout the world, the area of plantation forests continues to increase and they now dominate many landscapes. In recent decades, forest cover in Ireland has expanded largely due to commercial afforestation with non-native conifers. This study provides the first within-site assessment of the response of two important arthropod groups to afforestation in agricultural grasslands in Ireland. Five sites were studied 1 year before and 7 years after afforestation using pitfall trapping for active ground-dwelling spiders and Malaise trapping for hoverflies. Both species groups were studied in grassland habitat, and spiders were also sampled in field boundary hedgerow habitat. Afforestation within the study sites had a positive effect on ground-dwelling spider diversity over the first 7 years; total species richness increased in afforested grassland and hedgerow habitats, and forest specialist species richness increased in afforested grassland habitat. This was concurrent with, and most likely influenced by, the increase in habitat structure created by the forest vegetation, litter and deadwood layers and the increase in canopy cover. There was no effect of afforestation on hoverfly species richness over the first 7 years, possibly due to confounding effects of hoverfly movements across landscapes. Spider and hoverfly species compositions were also positively affected by afforestation. These results indicated that afforestation in our study sites, set within a predominantly agricultural landscape, benefitted arthropod diversity by increasing habitat diversity. Hedgerow habitats were also an important contributor to biodiversity in these newly planted forests. Ecologically oriented planning and management of afforestation must consider the influence of habitat quality in forest plantations, including the protection of biodiversity rich habitats and the quality of the land being afforested, to improve the contribution to biodiversity enhancement and conservation

Fermionic entanglement in itinerant systems

We study pairwise quantum entanglement in systems of fermions itinerant in a lattice from a second-quantized perspective. Entanglement in the grand-canonical ensemble is studied, both for energy eigenstates and for the thermal state. Relations between entanglement and superconducting correlations are discussed in a BCS-like model and for $\eta$-pair superconductivity.Comment: 8 Pages LaTeX, 5 Figures included. Presentation improved, results and references adde

Ocean Lagrangian Trajectories (OLTraj): Lagrangian analysis for non-expert users

This is the final version. Available on open access from F1000Research via the DOI in this record. Data availability: Underlying data The original Copernicus data (January 1998 - December 2019) is available from: https://resources.marine.copernicus.eu/product-detail/SEALEVEL_GLO_PHY_L4_REP_OBSERVATIONS_008_047/INFORMATION CEDA: Global ocean Lagrangian trajectories based on AVISO velocities, v2.2. http://doi.org/10.5285/5c2b70d069cb467ab73e80b84c3e395a This dataset contains the following underlying data: Daily files from 1998-01-01 to 2019-12-31. This dataset is available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).Software availability: Source code to compute OLTraj available from: https://github.com/grgdll/OLTraj Archived source code at time of publication: https://doi.org/10.5281/zenodo.5082983 The repository for the examples is: https://github.com/grgdll/OLTraj_examples Archived source code at time of publication: https://doi.org/10.5281/zenodo.5518531Lagrangian analysis is becoming increasingly important to better understand the ocean's biological and biogeochemical cycles. Yet, biologists and chemists often lack the technical skills required to set up such analyses. Here, we present a new product of pre-computed ocean Lagrangian trajectories (OLTraj) targeting non-expert users, and demonstrate how to use it by means of worked examples. OLTraj is based on satellite-derived geostrophic currents, which allows one to directly compare it with other in-situ or satellite products. We anticipate that OLTraj will foster a new interest in Lagrangian applications in ocean biology and biogeochemistry.European Union Horizon 2020Natural Environment Research Council (NERC