The Copernicus Marine Environment Monitoring Service Ocean State Report

The Copernicus Marine Environment Monitoring Service (CMEMS) Ocean State Report (OSR) provides an annual report of the state of the global ocean and European regional seas for policy and decision-makers with the additional aim of increasing general public awareness about the status of, and changes in, the marine environment. The CMEMS OSR draws on expert analysis and provides a 3-D view (through reanalysis systems), a view from above (through remote-sensing data) and a direct view of the interior (through in situ measurements) of the global ocean and the European regional seas. The report is based on the unique CMEMS monitoring capabilities of the blue (hydrography, currents), white (sea ice) and green (e.g. Chlorophyll) marine environment. This first issue of the CMEMS OSR provides guidance on Essential Variables, large-scale changes and specific events related to the physical ocean state over the period 1993–2015. Principal findings of this first CMEMS OSR show a significant increase in global and regional sea levels, thermosteric expansion, ocean heat content, sea surface temperature and Antarctic sea ice extent and conversely a decrease in Arctic sea ice extent during the 1993–2015 period. During the year 2015 exceptionally strong large-scale changes were monitored such as, for example, a strong El Niño Southern Oscillation, a high frequency of extreme storms and sea level events in specific regions in addition to areas of high sea level and harmful algae blooms. At the same time, some areas in the Arctic Ocean experienced exceptionally low sea ice extent and temperatures below average were observed in the North Atlantic Ocean

Downscaling from Oceanic Global Circulation Model towards Regional and Coastal Model using spectral nudging techniques: application to the Mediterranean Sea and IBI area models

In order to favour the downstream from the European MyOcean service of large scale ocean forecasts to the national service of coastal ocean forecasts, studies of new methods improving the downscaling between global or regional ocean models and coastal ones are in progress. In the framework of PREVIMER and MyOcean projects respectively, IFREMER and Mercator Ocean studied in parallel the impact of the spectral nudging method. In the present work, the performance of spectral nudging was assessed using two regional hydrodynamic models: one of Mediterranean Sea and one of the Iberia-Biscay-Ireland (IBI) area. They are both forced by a coarser global circulation model (GCM) (PSY2V4/Mercator Ocean). This technique prevents large and unrealistic departures between the global circulation model (GCM) driving fields and the regional model fields at the GCM spatial scales. Regarding the Med Sea application, the model’s temperature T and salinity S are spectrally nudged towards PSY2V4 solution using nudging terms in the model tracer equations: a semi prognostic approach has been chosen. The simulated fields are then compared with those estimated by no-nudged model and confronted to observations. Results show that the spectral nudging is able to constrain error growth in large-scale circulation without significant damping of the meso-scales eddy fields. Regarding the IBI application, T, S as well as current speed U, V have been nudged towards PSY2V4 solution: the increments are directly added as source and sink terms in the model prognostic equations. PSY2V4, nudged IBI and no-nudged IBI models as well as the present operational IBI model weekly restarted by PSY2V4 are compared and confronted to observations. The large scale and meso-scale structures are better represented off the shelf area where IBI is nudged and the bias significantly decreases on the shelf where the high frequency and high resolution physics of free IBI is better resolved than the assimilated PSY2V4 model one

NEMO on the shelf: assessment of the Iberia-Biscay-Ireland configuration.

International audienceThis work describes the design and validation of a high-resolution (1/36°) ocean forecasting model over the "Iberian-Biscay-Irish" (IBI) area. The system has been set-up using the NEMO model (Nucleus for European Modelling of the Ocean). New developments have been incorporated in NEMO to make it suitable to open- as well as coastal-ocean modelling. In this paper, we pursue three main objectives: (1) to give an overview of the model configuration used for the simulations; (2) to give a broad-brush account of one particular aspect of this work, namely consistency verification; this type of validation is conducted upstream of the implementation of the system before it is used for production and routinely validated; it is meant to guide model development in identifying gross deficiencies in the modelling of several key physical processes; and (3) to show that such a regional modelling system has potential as a complement to patchy observations (an integrated approach) to give information on non-observed physical quantities and to provide links between observations by identifying broader-scale patterns and processes. We concentrate on the year 2008. We first provide domain-wide consistency verification results in terms of barotropic tides, transports, sea surface temperature and stratification. We then focus on two dynamical subregions: the Celtic shelves and the Bay of Biscay slope and deep regions. The model-data consistency is checked for variables and processes such as tidal currents, tidal fronts, internal tides and residual elevation. We also examine the representation in the model of a seasonal pattern of the Bay of Biscay circulation: the warm extension of the Iberian Poleward Current along the northern Spanish coast (Navidad event) in the winter of 2007-2008

Recent Progress in Performance Evaluations and Near Real-Time Assessment of Operational Ocean Products

Operational ocean forecast systems provide routine marine products to an ever-widening community of users and stakeholders. The majority of users need information about the quality and reliability of the products to exploit them fully. Hence, forecast centres have been developing improved methods for evaluating and communicating the quality of their products. Global Ocean Data Assimilation Experiment (GODAE) OceanView, along with the Copernicus European Marine Core Service and other national and international programmes, has facilitated the development of coordinated validation activities among these centres. New metrics, assessing a wider range of ocean parameters, have been defined and implemented in real-time. An overview of recent progress and emerging international standards is presented here

One-month humoral response following two or three doses of mRNA Covid-19 vaccines as primary vaccination in specific populations in France: first results from the ANRS0001S COV-POPART cohort

International audienceObjectives: We aimed to investigate the one-month humoral response to two or three doses as primary vaccination in specific populations compared to healthy adults.Methods: ANRS0001S-COV-POPART (NCT04824651) is a French nationwide multicenter prospective observational cohort study assessing the immune response to Covid-19 vaccines routinely administered to 11 subgroups of patients with chronic conditions and two control groups. Patients and controls who had received at least two vaccine doses and whose results at one month after the second dose were available have been included. Humoral response was assessed at 1-month post first dose, post second dose and post third dose (if applicable), through the percentage of responders (positive anti-Spike SARS-CoV-2 IgG antibodies, geometric means of anti-Spike SARS-CoV-2 IgG antibodies (ELISA) and proportion of participants with anti-SARS-CoV-2-specific neutralizing antibodies (in vitro neutralization assay for the original SARS-CoV-2 strain). All analyses were centralized.Results: We included 4091 participants in this analysis: 2979 participants from specific subpopulations and 1112 controls. Only 522 (17.5%) of the specific populations received 3 doses as primary vaccination regimen. Patients living with HIV, cancer and diabetic patients had high rates of responders after two doses while solid organ transplant (SOT), allogeneic hematopoietic stem cell transplant (HSCT) and hypogammaglobulinemic patients had the lowest percentage of responders (35.9% [95%CI: 29.2; 43.0], 57.4% [48.1; 66.3]) and 77.1% [65.6; 86.3] respectively). In those who received a third dose, the rate of responders reached 54.2% [42.9-65.2] (vs. 32.3% (16.7-51.4) after 2 doses) in SOT and 73.9% [58.9-85.7) (vs. 56.1% [46.2-65.7] after 2 doses) in HSCT. Similar results were found with anti-SARS-CoV-2-specific neutralizing antibodies.Conclusions: Lower COVID-19 vaccine humoral response was observed in specific populations compared to controls. A third dose of vaccine in the primary regimen had a positive effect on both percentages of patients who developed anti-Spike IgG antibodies and specific neutralizing antibodies

Gathering users and developers to shape together the next-generation ocean reanalyses: Ocean reanalyses workshop of the European Copernicus Marine Service

International audienc

Copernicus marine service ocean state report

The oceans regulate our weather and climate from global to regional scales. They absorb over 90% of accumulated heat in the climate system (IPCC Citation2013) and over a quarter of the anthropogenic carbon dioxide (Le Quéré et al. Citation2016). They provide nearly half of the world’s oxygen. Most of our rain and drinking water is ultimately regulated by the sea. The oceans provide food and energy and are an important source of the planet's biodiversity and ecosystem services. They are vital conduits for trade and transportation and many economic activities depend on them (OECD Citation2016). Our oceans are, however, under threat due to climate change and other human induced activities and it is vital to develop much better, sustainable and science-based reporting and management approaches (UN Citation2017). Better management of our oceans requires long-term, continuous and state-of-the art monitoring of the oceans from physics to ecosystems and global to local scales. The Copernicus Marine Environment Monitoring Service (CMEMS) has been set up to address these challenges at European level. Mercator Ocean was tasked in 2014 by the European Union under a delegation agreement to implement the operational phase of the service from 2015 to 2021 (CMEMS Citation2014). The CMEMS now provides regular and systematic reference information on the physical state, variability and dynamics of the ocean, ice and marine ecosystems for the global ocean and the European regional seas (Figure 0.1; CMEMS Citation2016). This capacity encompasses the description of the current situation (analysis), the prediction of the situation 10 days ahead (forecast), and the provision of consistent retrospective data records for recent years (reprocessing and reanalysis). CMEMS provides a sustainable response to European user needs in four areas of benefits: (i) maritime safety, (ii) marine resources, (iii) coastal and marine environment and (iv) weather, seasonal forecast and climate. Figure 0.1. CMEMS geographical areas on the map are for: 1 – Global Ocean; 2 – Arctic Ocean from 62°N to North Pole; 3 – Baltic Sea, which includes the whole Baltic Sea including Kattegat at 57.5°N from 10.5°E to 12.0°E; 4 – European North-West Shelf Sea, which includes part of the North East Atlantic Ocean from 48°N to 62°N and from 20°W to 13°E. The border with the Baltic Sea is situated in the Kattegat Strait at 57.5°N from 10.5°E.to 12.0°E; 5 – Iberia-Biscay-Ireland Regional Seas, which includes part of the North East Atlantic Ocean from 26 to 48°N and 20°W to the coast. The border with the Mediterranean Sea is situated in the Gibraltar Strait at 5.61°W; 6 – Mediterranean Sea, which includes the whole Mediterranean Sea until the Gibraltar Strait at 5.61°W and the Dardanelles Strait; 7 – Black Sea, which includes the whole Black Sea until the Bosporus Strait

Copernicus Marine Service Ocean State Report

The Compernicus Marine Environmenta and Monitoring Servic

Copernicus Marine Service Ocean State Report, Issue 4

Editors: Karina von Schuckmann; Pierre-Yves Le Traon.-- Review Editors: Neville Smith (Chair); Ananda Pascual; Samuel Djavidnia; Jean-Pierre Gattuso; Marilaure Grégoire; Glenn Nolan.The authors would like to thank the Institut Cartogràfic i Geològic de Catalunya (ICGC) for providing data. Thanks are due to FCT/MCTES for the financial support to CESAM (UID/AMB/50017/2019), through national funds.Chapter 1: Introduction and the European Environment policy framework.-- CMEMS OSR4, Chapter 2: State, variability and change in the ocean.-- CMEMS OSR4, Chapter 3: Case studies.-- CMEMS OSR4, Chapter 4: Specific events 2018.-

Reproducibility of fluorescent expression from engineered biological constructs in E. coli

We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest promoter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices.Peer reviewe