Training neural mapping schemes for satellite altimetry with simulation data

Satellite altimetry combined with data assimilation and optimal interpolation schemes have deeply renewed our ability to monitor sea surface dynamics. Recently, deep learning (DL) schemes have emerged as appealing solutions to address space-time interpolation problems. The scarcity of real altimetry dataset, in terms of space-time coverage of the sea surface, however impedes the training of state-of-the-art neural schemes on real-world case-studies. Here, we leverage both simulations of ocean dynamics and satellite altimeters to train simulation-based neural mapping schemes for the sea surface height and demonstrate their performance for real altimetry datasets. We analyze further how the ocean simulation dataset used during the training phase impacts this performance. This experimental analysis covers both the resolution from eddy-present configurations to eddy-rich ones, forced simulations vs. reanalyses using data assimilation and tide-free vs. tide-resolving simulations. Our benchmarking framework focuses on a Gulf Stream region for a realistic 5-altimeter constellation using NEMO ocean simulations and 4DVarNet mapping schemes. All simulation-based 4DVarNets outperform the operational observation-driven and reanalysis products, namely DUACS and GLORYS. The more realistic the ocean simulation dataset used during the training phase, the better the mapping. The best 4DVarNet mapping was trained from an eddy-rich and tide-free simulation datasets. It improves the resolved longitudinal scale from 151 kilometers for DUACS and 241 kilometers for GLORYS to 98 kilometers and reduces the root mean squared error (RMSE) by 23% and 61%. These results open research avenues for new synergies between ocean modelling and ocean observation using learning-based approaches

Scale-aware neural calibration for wide swath altimetry observations

Sea surface height (SSH) is a key geophysical parameter for monitoring and studying meso-scale surface ocean dynamics. For several decades, the mapping of SSH products at regional and global scales has relied on nadir satellite altimeters, which provide one-dimensional-only along-track satellite observations of the SSH. The Surface Water and Ocean Topography (SWOT) mission deploys a new sensor that acquires for the first time wide-swath two-dimensional observations of the SSH. This provides new means to observe the ocean at previously unresolved spatial scales. A critical challenge for the exploiting of SWOT data is the separation of the SSH from other signals present in the observations. In this paper, we propose a novel learning-based approach for this SWOT calibration problem. It benefits from calibrated nadir altimetry products and a scale-space decomposition adapted to SWOT swath geometry and the structure of the different processes in play. In a supervised setting, our method reaches the state-of-the-art residual error of ~1.4cm while proposing a correction on the entire spectral from 10km to 1000kComment: 8 pages, 7 figures, Preprin

Deciphering the complex signalling systems that regulate intestinal epithelial cell death processes and shedding

Intestinal epithelial cells play a fundamental role in maintaining homeostasis. Shedding of intestinal cells in a controlled manner is critical to maintenance of barrier function. Barrier function is maintained during this shedding process by a redistribution of tight junctional proteins to facilitate closure of the gap left by the shedding cell. However, despite the obvious importance of epithelial cell shedding to gut health a central question is how the extrusion of epithelial cells is achieved, enabling barrier integrity to be maintained in the healthy gut and restored during inflammation remains largely unanswered. Recent studies have provided evidence that excessive epithelial cell shedding and loss of epithelial barrier integrity is triggered by exposure to lipopolysaccharide (LPS) or tumour necrosis factor (TNF). Subsequent studies have provided evidence of the involvement of specific cellular components and signalling mechanisms as well as the functionality of microbiota that can be either detrimental or beneficial for intestinal barrier integrity. This review, will focus on the evidence and decipher how the signalling systems through which the mucosal immune system and microbiota can regulate epithelial cell shedding and how these mechanisms interact to preserve the viability of the epithelium

Apical invasion of intestinal epithelial cells by salmonella typhimurium requires villin to remodel the brush border actin cytoskeleton

Funding Information: We thank R. Friedman, C. Mulet and T. Pedron for technical help. We thank T. Marlovits for antibodies, H.D. Hardt and J. Galan for Salmonella strains, and D. Zhou and V. Koronakis for plasmids. We acknowledge France-BioImaging infrastructure supported by the French National Research Agency (ANR-10-INSB-04-01, «Investments for the future»). This work was supported by the ERC (P.S. Advanced Grant HOMEOEPITH, number 232798). P.J.S. is an HHMI senior foreign scholar. The authors declare no conflict of interest. Publisher Copyright: © 2015 Elsevier Inc.Salmonella invasion of intestinal epithelial cells requires extensive, though transient, actin modifications at the site of bacterial entry. The actin-modifying protein villin is present in the brush border where it participates in the constitution of microvilli and in epithelial restitution after damage through its actin-severing activity. We investigated a possible role for villin in Salmonella invasion. The absence of villin, which is normally located at the bacterial entry site, leads to a decrease in Salmonella invasion. Villin is necessary for early membrane-associated processes and for optimal ruffle assembly by balancing the steady-state level of actin. The severing activity of villin is important for Salmonella invasion in vivo. The bacterial phosphatase SptP tightly regulates villin phosphorylation, while the actin-binding effector SipA protects F-actin and counterbalances villin-severing activity. Thus, villin plays an important role in establishing the balance between actin polymerization and actin severing to facilitate the initial steps of Salmonella entry.publishersversionpublishe

Wind‐driven control of shelf‐sea CO2 sinks

Continental shelf surface waters are considered a variable but increasing sink of atmospheric carbon dioxide (CO2), but the mechanisms controlling these increasing sinks are unclear. We identify that the winter wind-driven surface atmosphere-ocean CO2 gas exchange and wind-driven movement of water onto (or off of) shelf seas are consistent with the atmospheric CO2 uptake tendency of many shelf seas. A 20-year observational-based analysis shows that geostrophic, wind and wave driven currents all contribute to the surface shelf break water velocities, but the dominance of each is location and season dependent. Analyzing these flows for fourteen shelf-seas based on their 20-year long-term gradient in air-sea partial pressure of carbon dioxide (their atmospheric CO2 uptake tendency) identifies significant relationships between uptake tendency and winter (r2 = 0.72 ± 0.03, p < 0.01, n = 14) and autumn (r2 = 0.57 ± 0.05, p < 0.01, n = 14) wind-driven surface flows. These signals are most strong in winter, but the results are consistent at annual scales. Including the wintertime wind-driven air-sea CO2 gas exchange further enhances this result, and collectively they describe 82% of the variance in the atmospheric CO2 uptake tendency data (r2 = 0.82 ± 0.06, p < 0.01, n = 14). These findings identify that long-term wind-driven water flow and surface gas exchange are key mechanisms for controlling their chemical evolution and their status as CO2 sinks. This observational-based evidence highlights the need for these wind-driven processes to be resolved within methods used to predict or understand continental shelf-sea carbonate system state and ocean health

SEASTAR: a mission to study ocean submesoscale dynamics and small-scale atmosphere-ocean processes in coastal, shelf and polar seas

High-resolution satellite images of ocean color and sea surface temperature reveal an abundance of ocean fronts, vortices and filaments at scales below 10 km but measurements of ocean surface dynamics at these scales are rare. There is increasing recognition of the role played by small scale ocean processes in ocean-atmosphere coupling, upper-ocean mixing and ocean vertical transports, with advanced numerical models and in situ observations highlighting fundamental changes in dynamics when scales reach 1 km. Numerous scientific publications highlight the global impact of small oceanic scales on marine ecosystems, operational forecasts and long-term climate projections through strong ageostrophic circulations, large vertical ocean velocities and mixed layer re-stratification. Small-scale processes particularly dominate in coastal, shelf and polar seas where they mediate important exchanges between land, ocean, atmosphere and the cryosphere, e.g., freshwater, pollutants. As numerical models continue to evolve toward finer spatial resolution and increasingly complex coupled atmosphere-wave-ice-ocean systems, modern observing capability lags behind, unable to deliver the high-resolution synoptic measurements of total currents, wind vectors and waves needed to advance understanding, develop better parameterizations and improve model validations, forecasts and projections. SEASTAR is a satellite mission concept that proposes to directly address this critical observational gap with synoptic two-dimensional imaging of total ocean surface current vectors and wind vectors at 1 km resolution and coincident directional wave spectra. Based on major recent advances in squinted along-track Synthetic Aperture Radar interferometry, SEASTAR is an innovative, mature concept with unique demonstrated capabilities, seeking to proceed toward spaceborne implementation within Europe and beyond

Accuracy Assessment of Global Internal-Tide Models Using Satellite Altimetry

Altimeter measurements are corrected for several geophysical parameters in order to access ocean signals of interest, like mesoscale or sub-mesoscale variability. The ocean tide is one of the most critical corrections due to the amplitude of the tidal elevations and to the aliasing phenomena of high-frequency signals into the lower-frequency band, but the internal-tide signatures at the ocean surface are not yet corrected globally. Internal tides can have a signature of several centimeters at the surface with wavelengths of about 50–250 km for the first mode and even smaller scales for higher-order modes. The goals of the upcoming Surface Water Ocean Topography (SWOT) mission and other high-resolution ocean measurements make the correction of these small-scale signals a challenge, as the correction of all tidal variability becomes mandatory to access accurate measurements of other oceanic signals. In this context, several scientific teams are working on the development of new internal-tide models, taking advantage of the very long altimeter time series now available, which represent an unprecedented and valuable global ocean database. The internal-tide models presented here focus on the coherent internal-tide signal and they are of three types: empirical models based upon analysis of existing altimeter missions, an assimilative model and a three-dimensional hydrodynamic model. A detailed comparison and validation of these internal-tide models is proposed using existing satellite altimeter databases. The analysis focuses on the four main tidal constituents: M2, K1, O1 and S2. The validation process is based on a statistical analysis of multi-mission altimetry including Jason-2 and Cryosphere Satellite-2 data. The results show a significant altimeter variance reduction when using internal-tide corrections in all ocean regions where internal tides are generating or propagating. A complementary spectral analysis also gives some estimation of the performance of each model as a function of wavelength and some insight into the residual non-stationary part of internal tides in the different regions of interest. This work led to the implementation of a new internal-tide correction (ZARON\u27one) in the next geophysical data records version-F (GDR-F) standards

Global Observations of Fine-Scale Ocean Surface Topography With the Surface Water and Ocean Topography (SWOT) Mission

The future international Surface Water and Ocean Topography (SWOT) Mission, planned for launch in 2021, will make high-resolution 2D observations of sea-surface height using SAR radar interferometric techniques. SWOT will map the global and coastal oceans up to 77.6 latitude every 21 days over a swath of 120 km (20 km nadir gap). Today’s 2D mapped altimeter data can resolve ocean scales of 150 km wavelength whereas the SWOT measurement will extend our 2D observations down to 15–30 km, depending on sea state. SWOT will offer new opportunities to observe the oceanic dynamic processes at scales that are important in the generation and dissipation of kinetic energy in the ocean, and that facilitate the exchange of energy between the ocean interior and the upper layer. The active vertical exchanges linked to these scales have impacts on the local and global budgets of heat and carbon, and on nutrients for biogeochemical cycles. This review paper highlights the issues being addressed by the SWOT science community to understand SWOT’s very precise sea surface height (SSH)/surface pressure observations, and it explores how SWOT data will be combined with other satellite and in situ data and models to better understand the upper ocean 4D circulation (x, y, z, t) over the next decade. SWOT will provide unprecedented 2D ocean SSH observations down to 15–30 km in wavelength, which encompasses the scales of “balanced” geostrophic eddy motions, high-frequency internal tides and internal waves. Frontiers in Marine Science | www.frontiersin.org 1 May 2019 | Volume 6 | Article 232 Morrow et al. SWOT Fine-Scale Global Ocean Topography This presents both a challenge in reconstructing the 4D upper ocean circulation, or in the assimilation of SSH in models, but also an opportunity to have global observations of the 2D structure of these phenomena, and to learn more about their interactions. At these small scales, ocean dynamics evolve rapidly, and combining SWOT 2D SSH data with other satellite or in situ data with different space-time coverage is also a challenge. SWOT’s new technology will be a forerunner for the future altimetric observing system, and so advancing on these issues today will pave the way for our future

Assessing the potential impact of assimilating total surface current velocities in the Met Office’s global ocean forecasting system

Accurate prediction of ocean surface currents is important for marine safety, ship routing, tracking of pollutants and in coupled forecasting. Presently, velocity observations are not routinely assimilated in global ocean forecasting systems, largely due to the sparsity of the observation network. Several satellite missions are now being proposed with the capability to measure Total Surface Current Velocities (TSCV). If successful, these would substantially increase the coverage of ocean current observations and could improve accuracy of ocean current forecasts through data assimilation. In this paper, Observing System Simulation Experiments (OSSEs) are used to assess the impact of assimilating TSCV in the Met Office’s global ocean forecasting system. Synthetic observations are generated from a high-resolution model run for all standard observation types (sea surface temperature, profiles of temperature and salinity, sea level anomaly and sea ice concentration) as well as TSCV observations from a Sea surface KInematics Multiscale monitoring (SKIM) like satellite. The assimilation of SKIM like TSCV observations is tested over an 11 month period. Preliminary experiments assimilating idealised single TSCV observations demonstrate that ageostrophic velocity corrections are not well retained in the model. We propose a method for improving ageostrophic currents through TSCV assimilation by initialising Near Inertial Oscillations with a rotated incremental analysis update (IAU) scheme. The OSSEs show that TSCV assimilation has the potential to significantly improve the prediction of velocities, particularly in the Western Boundary Currents, Antarctic Circumpolar Current and in the near surface equatorial currents. For global surface velocity the analysis root-mean-square-errors (RMSEs) are reduced by 23% and there is a 4-day gain in forecast RMSE. There are some degradations to the subsurface in the tropics, generally in regions with complex vertical salinity structures. However, outside of the tropics, improvements are seen to velocities throughout the water column. Globally there are also improvements to temperature and sea surface height when TSCV are assimilated. The TSCV assimilation largely corrects the geostrophic ocean currents, but results using the rotated IAU method show that the energy at inertial frequencies can be improved with this method. Overall, the experiments demonstrate significant potential benefit of assimilating TSCV observations in a global ocean forecasting system