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  • 2020-2024  (4)
  • 2020-2022  (5)
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  • 1
    Publication Date: 2024-04-17
    Description: I attach here 2 excel files: The 1st one is entitled "KAZANIDIS ET AL_ATLAS MINGULAY REEF COMPLEX_MACROBENTHOS DATA". This file contains a presence-absence matrix for macrobenthic fauna that has been collected in Mingulay Reef Complex (Scotland, UK) across 79 stations over the years 2003, 2005, 2009, 2010 and 2011. The 2nd one is entitled "KAZANIDIS ET AL_MINGULAY REEF COMPLEX_ENVIRONMENTAL DATA". This files contains information about coordinates and environmental settings at stations where macrobenthic samples mentioned above, were collected. Please mention that it is quite important that these two excel files stay together
    Keywords: Abra alba; Abyssoninoe hibernica; Acanthicolepis asperrima; Actiniaria spp.; Actiniidae spp.; Aetea sp.; Alcyonium digitatum; Alderina imbellis; Alentia gelatinosa; Alvania beanii; Amaeana trilobata; Ampharetidae spp.; Amphiblestrum auritum; Amphiblestrum flemingii; Amphiblestrum solidum; Amphiblestrum sp.; Amphiglena sp.; Amphilochus manudens; Amphipholis squamata; Amphipoda spp.; Amphiura chiajei; Anarthropora monodon; Annectocyma major; Anomia ephippium; Anthopleura sp.; Anthozoa sp.; Aphroditidae sp.; Aplacophora sp.; Apomatus similis; Aquiloniella scabra; Arca tetragona; Arcopagia crassa; Arcturidae sp.; Aristias neglectus; Aristias sp.; Ascidia conchilega; Ascidia mentula; Ascidiella aspersa; Ascidiella scabra; Asclerocheilus intermedius; Aspidosiphon (Aspidosiphon) muelleri muelleri; Astarte sulcata; Asteroidea sp.; Atlantopandalus propinqvus; ATLAS; A Trans-Atlantic assessment and deep-water ecosystem-based spatial management plan for Europe; Atylus spp.; Aurospio banyulensis; Bicellariella ciliata; Bispira volutacornis; Bivalvia spp.; Boreotrophon truncatus; Brachyura spp.; Branchiomma bombyx; Buskea dichotoma; Buskea nitida; Buskea sp.; Buskia sp.; Caberea ellisii; Callopora dumerilii; Capitellidae sp.; Caprellidae sp.; Capulus ungaricus; Celleporina caliciformis; Celleporina pygmaea; Celleporina sp.; Cerithiopsis tubercularis; Chaetopterus sp.; Chaetopterus variopedatus; Cheilostomatida sp.; Chirona hameri; Chone sp.; Chorizopora sp.; Ciona intestinalis; Cirolanidae sp.; Cirratulidae spp.; Climate change; continental shelf; Copepoda sp.; coral reefs; Crinoid sp.; Crisia denticulata; Crisia eburnea; Crisia spp.; Crustacea spp.; Cyclostomata spp.; DATE/TIME; Deep sea; Diastylidae spp.; Diastylis rugosa; Diplosolen obelium; Disporella hispida; Ditrupa arietina; Donax vittatus; Dorvillea rubrovittata; Dorvilleidae spp.; Dyspanopeus sayi; Ebalia cranchii; Echinocyamus pusillus; Echiura spp.; Edwardsiella carnea; Emarginula fissura; Entalophoroecia deflexa; Entoprocta sp.; Ericthonius difformis; Escharella immersa; Escharella klugei; Escharella octodentata; Escharella ventricosa; Escharina johnstoni; Escharina vulgaris; Eucalathis tuberata; Euchone spp.; Euclymene sp.; Eulalia bilineata; Eulalia tjalfiensis; Eunice dubitata; Eunice norvegica; Eunicidae spp.; Eunoe nodosa; Eunoe sp.; Euphrosine borealis; Euphrosine sp.; Euphrosinidae spp.; Eusyllis blomstrandi; Exidmonea atlantica; Exogone naidina; Exogone verugera; Falcidens crossotus; Filicrisia geniculata; Fimbriosthenelais zetlandica; Flabelligera sp.; Flabelligeridae sp.; Galathea intermedia; Galathea nexa; Galathea sp.; Galathea strigosa; Galatheidae sp.; Gammaridae spp.; Gastropoda spp.; Glycera lapidum; Glycera sp.; Glyceridae spp.; Gnathia dentata; Gnathia sp.; Gnathia vorax; Gnathiidae sp.; Goniadidae spp.; Hanleya hanleyi; Haploploma sciaphilum; Haplopoma graniferum; Haplopoma planum; Haplosyllis spongicola; Harmothoe fraserthomsoni; Harmothoe oculinarum; Harmothoe sp.; Hemicyclopora multispinata; Hemicyclopora polita; Henricia oculata; Herentia hyndmanni; Hesionidae spp.; Heteranomia squamula; Heteromysis (Heteromysis) formosa; Heteromysis (Heteromysis) norvegica; Hexacorallia sp.; Hiatella arctica; Hippoporella hippopus; Hippothoa flagellum; Hippothoa sp.; Holothuroidea spp.; Hydroides norvegica; Hydroides sp.; iAtlantic; Integrated Assessment of Atlantic Marine Ecosystems in Space and Time; Janira maculosa; Jassa falcata; Kellia suborbicularis; Lanassa venusta; Laonice bahusiensis; Lepidonotus squamatus; Leptocheirus aff. pectinatus; Leptochiton cancellatus; Leptometra celtica; Leptoplana tremellaris; Leucothoe spinicarpa; Lichenopora sp.; Lumbrineridae spp.; Lumbrineris futilis; Lumbrineris spp.; Lysianassidae spp.; Lysidice unicornis; Macrofauna; Maldanidae spp.; Marphysa sp.; Maxmuelleria lankesteri; Melinna cristata; Metavermilia multicristata; Metopa pusilla; Metopa sp.; Microporella sp.; Mingulay_Reef_Complex; Modiolula phaseolina; Modiolus modiolus; MRC; MULT; Multiple investigations; Munida rugosa; Munida sarsi; Munna kroyeri; Munna minuta; Munna sp.; Munnidae sp.; Nemertea spp.; Neohololepidella sp.; Neolagisca jeffreysi; Nephtyidae sp.; Nereicolidae spp.; Nereididae sp.; Nereimyra punctata; Notomastus spp.; Notophyllum foliosum; Novocrania anomala; Octocorallia sp.; Oligochaeta sp.; Omalosecosa ramulosa; Oncousoecia diastoporides; Oncousoecia dilatans; Onoba semicostata; Opheliidae sp.; Ophiacantha aculeata; Ophiactis balli; Ophiopholis aculeata; Ophiothrix fragilis; Ophiothrix sp.; Ophiura ophiura; Ophiuroidea spp.; Orbinia sp.; Paguridae spp.; Pagurus forbesii; Palliolum striatum; Palmicellaria elegans; Palmiskenea skenei; Pandalina brevirostris; Parasabella cambrensis; Parasabella saxicola; Parasmittina trispinosa; Parazoanthus anguicomus; Parexogone hebes; Parvicardium cf scabrum; Patinella verrucaria; Pectinariidae spp.; Pectinidae sp.; Pedicellina hispida; Pencilletta penicillata; Pentapora sp.; Peringia ulvae; Phascolosoma (Phascolosoma) granulatum; Pholoe inornata; Pholoe sp.; Pholoidae spp.; Phyllodoce sp.; Phyllodocidae spp.; Placostegus tridentatus; Plagioecia patina; Plagioecia sp.; Pododesmus patelliformis; Pododesmus squama; Polycarpa pomaria; Polychaeta sp.; Polycirrus arcticus; Polycirrus spp.; Polydora sp.; Polynoidae spp.; Polyplacophora sp.; Porania (Porania) pulvillus; Porella compressa; Prenantia cheilostoma; Priapulida sp.; Priapulus caudatus; Propebela rufa; Proscalibregma sp.; Protula sp.; Pseudoparatanais batei; Pseudopotamilla reniformis; Pseudopotamilla sp.; Pyripora catenularia; Pyura tessellata; Ramphonotus minax; Reteporella beaniana; Sabella discifera; Sabella pavonina; Sabellaria spinulosa; Sabellariidae spp.; Sabellidae spp.; Sample code/label; Sample ID; Scalibregmatidae sp.; Schizomavella (Calvetomavella) discoidea; Schizomavella (Schizomavella) hastata; Schizomavella (Schizomavella) linearis; Schizomavella sp.; Scionella sp.; Scolelepis sp.; Scotland Sea; Scrupocellaria scrupea; Scrupocellaria sp.; Serpula planorbis; Serpula vermicularis; Serpulidae spp.; Sigalionidae spp.; Sigalion mathildae; Sigalion sp.; Sipuncula spp.; Smittina affinis; Smittina crystallina; Smittoidea reticulata; Sphaerodoridae spp.; Sphaerosyllis cf. taylori; Sphaerosyllis hystrix; Sphaerosyllis spp.; Spionidae spp.; Spiophanes kroyeri; Spirobranchus lamarcki; Spirobranchus spp.; Spirobranchus triqueter; Station label; Stenopleustes latipes; Stenothoidae spp.; Stomacrustula sinuosa; Stomatopora gingrina; Stomatoporina incurvata; Swiftia pallida; Syllidae spp.; Syllides sp.; Syllis armillaris; Syllis columbretensis; Syllis cornuta; Syllis hyalina; Syllis spp.; Syllis variegata; Terebellidae spp.; Terebellides spp.; Terebellides stroemii; Terebratulina retusa; Terminoflustra barleei; Tessaradoma boreale; Thyasira spp.; Tmetonyx sp.; Tonicella marmorea; Trypanosyllis (Trypanosyllis) coeliaca; Trypanosyllis zebra; Tubulipora flabellaris; Tubulipora lobifera; Tubulipora spp.; Tunicata spp.; Turbicellepora avicularis; Uromunna petiti; Venus verrucosa; Verruca stroemia; vulnerable marine ecosystems; Xantho hydrophilus
    Type: Dataset
    Format: text/tab-separated-values, 27237 data points
    Location Call Number Expected Availability
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  • 2
    Publication Date: 2024-05-29
    Keywords: -; ATLAS; A Trans-Atlantic assessment and deep-water ecosystem-based spatial management plan for Europe; Bathymetric positioning index; Bottom water temperature; Climate change; continental shelf; coral reefs; Current speed; Deep sea; DEPTH, water; Habitat; iAtlantic; Integrated Assessment of Atlantic Marine Ecosystems in Space and Time; Macrofauna; Mingulay_Reef_Complex; MRC; MULT; Multiple investigations; North Atlantic Oscillation index; Reconstructed; Ruggedness; Salinity; Sample code/label; Scotland Sea; Slope; Station label; vulnerable marine ecosystems
    Type: Dataset
    Format: text/tab-separated-values, 1185 data points
    Location Call Number Expected Availability
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  • 3
    Publication Date: 2024-05-29
    Description: The presence-absence data for macrobenthic fauna that has been collected in Mingulay Reef Complex (Scotland, UK) across 79 stations over the years 2003, 2005, 2009, 2010 and 2011. The collection of the benthic samples has been carried out using a Van-Veen grab, mainly from hard habitats (e.g. live and dead coral framework). About 60% of the macrofaunal specimens have been identified at species level using high quality taxonomic keys and advice from taxonomy experts. Most common taxonomic groups analysed here are molluscs, polychaetes, arthropods, bryozoans, anthozoans, tunicates and brachiopods. The collection of the specimens is now deposited at the National Museums of Scotland (see the attached excel file for details). The enviromental data contains information about coordinates and environmental settings at stations where macrobenthic samples mentioned above, were collected. The environmental settings that are included in the file refer to the years 2003, 2005, 2009, 2010, 2011. For more information on the environmental variables have a look in Henry et al. 2010 (doi:10.1007/s00338-009-0577-6) and Henry et al. 2013 (doi:10.5194/bg-10-2737-2013). The environmental variables included in the excel file are: type of macrohabitat (i.e. muddy sand, rubble, rock, live coral, dead framework, live & dead framework), depth (m), slope, ruggedness, broad-scale bathymetric position index, fine-scale bathymetric position index, average current speed (m/s), maximum current speed (m/s), northness, eastness, winter North Atlantic Oscillation Index (same year), winter North Atlantic Oscillation Index (previous year), annual average bottom temperature (same year), annual average bottom salinity (same year). Extraction of bathymetric (depth) and topographic data [slope, aspect, northness, eastness, ruggedness, standardised broad-scale bathymetric position index (BPI; with an inner radius of 1 cell and an outer radius of 5 cells), fine-scale BPI (with an inner radius of 1 cell and an outer radius of 3 cells)] was based on multibeam echosounder data, using the Spatial Analyst and Benthic Terrain Modeler toolboxes in ArcGIS v.10.6.1 Average and maximum current speed values (m/s) were extracted by the ArcGIS v. 10.6.1 Spatial Analyst toolbox using data generated by a high-resolution 3D ocean model created for the MRC by Moreno-Navas et al. (2014). Data for the winter NAOI (DJFM) (Hurrell et al., 2003) were downloaded from the National Center for Atmospheric Research/University Corporation for Atmospheric Research website (climatedataguide.ucar.edu; data accessed on 28/02/2019).
    Keywords: ATLAS; A Trans-Atlantic assessment and deep-water ecosystem-based spatial management plan for Europe; Climate change; continental shelf; coral reefs; Deep sea; iAtlantic; Integrated Assessment of Atlantic Marine Ecosystems in Space and Time; Macrofauna; vulnerable marine ecosystems
    Type: Dataset
    Format: application/zip, 2 datasets
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  • 4
  • 5
    Publication Date: 2020-10-15
    Description: The COVID-19 (Coronavirus disease-2019) pandemic, caused by the SARS-CoV-2 coronavirus, is a significant threat to public health and the global economy. SARS-CoV-2 is closely related to the more lethal but less transmissible coronaviruses SARS-CoV-1 and MERS-CoV. Here, we have carried out comparative viral-human protein-protein interaction and viral protein localization analysis for all three viruses. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 Orf9b, an interaction we structurally characterized using cryo-EM. Combining genetically-validated host factors with both COVID-19 patient genetic data and medical billing records identified important molecular mechanisms and potential drug treatments that merit further molecular and clinical study.
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2020-01-23
    Electronic ISSN: 2296-7745
    Topics: Biology
    Published by Frontiers Media
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  • 7
    Publication Date: 2021-02-25
    Description: The recent emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of Coronavirus Disease 2019 (COVID-19), has led to a worldwide pandemic causing substantial morbidity, mortality, and economic devastation. In response, many laboratories have redirected attention to SARS-CoV-2, meaning there is an urgent need for tools that can be used in laboratories unaccustomed to working with coronaviruses. Here we report a range of tools for SARS-CoV-2 research. First, we describe a facile single plasmid SARS-CoV-2 reverse genetics system that is simple to genetically manipulate and can be used to rescue infectious virus through transient transfection (without in vitro transcription or additional expression plasmids). The rescue system is accompanied by our panel of SARS-CoV-2 antibodies (against nearly every viral protein), SARS-CoV-2 clinical isolates, and SARS-CoV-2 permissive cell lines, which are all openly available to the scientific community. Using these tools, we demonstrate here that the controversial ORF10 protein is expressed in infected cells. Furthermore, we show that the promising repurposed antiviral activity of apilimod is dependent on TMPRSS2 expression. Altogether, our SARS-CoV-2 toolkit, which can be directly accessed via our website at https://mrcppu-covid.bio/, constitutes a resource with considerable potential to advance COVID-19 vaccine design, drug testing, and discovery science.
    Print ISSN: 1544-9173
    Electronic ISSN: 1545-7885
    Topics: Biology
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  • 8
  • 9
    Publication Date: 2024-02-07
    Description: Observations of the eastern subpolar North Atlantic in the 2010s show exceptional freshening and cooling of the upper ocean, peaking in 2016 with the lowest salinities recorded for 120 years. Published theories for the mechanisms driving the freshening include: reduced transport of saltier, warmer surface waters northwards from the subtropics associated with reduced meridional overturning; shifts in the pathways of fresher, cooler surface water from the Labrador Sea driven by changing patterns of wind stress; and the eastward expansion of the subpolar gyre. Using output from a high-resolution hindcast model simulation, we propose that the primary cause of the exceptional freshening and cooling is reduced surface heat loss in the Labrador Sea. Tracking virtual fluid particles in the model backwards from the eastern subpolar North Atlantic between 1990 and 2020 shows the major cause of the freshening and cooling to be an increased outflow of relatively fresh and cold surface waters from the Labrador Sea; with a minor contribution from reduced transport of warmer, saltier surface water northward from the subtropics. The cooling, but not the freshening, produced by these changing proportions of waters of subpolar and subtropical origin is mitigated by reduced along-track heat loss to the atmosphere in the North Atlantic Current. We analyse modelled boundary exchanges and water mass transformation in the Labrador Sea to show that since 2000, while inflows of lighter surface waters remain steady, the increasing output of these waters is due to reduced surface heat loss in the Labrador Sea beginning in the early 2000s. Tracking particles further upstream reveals that the primary source of the increased volume of lighter water transported out of the Labrador Sea is increased recirculation of water, and therefore longer residence times, in the upper 500–1000 m of the subpolar gyre.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
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