Sea surface dynamic height topography and the North Equatorial countercurrent as inferred from a linear model

Hellerman and Rosenstein's (1983) climatological winds are used to force a linear, continuously stratified model of the tropical Atlantic. The dynamic height topography relative to 500 meters is compared with available data. Special attention is paid to the computed North Equatorial countercurrent. We conclude that most of the observed seasonal variations can be explained using simple linear theory. (Résumé d'auteur

Dispersion of wind-induced inertial waves by a barotropic jet

This note attempts to reinterpret previous results on the dispersion of wind-induced inertial waves by a geostrophic barotropic jet in the ocean. The approach is to consider the jet vorticity influence on the different baroclinic modes using a vertical normal mode expansion. Numerical and analytical analysis of the linear equations shows that vorticity effects on a single baroclinic mode strongly depend on the ratio of its Rossby radius and the length scale of the geostrophic vorticity: trapping of the near-inertial energy occurs when this ratio is small. When this ratio is of order one, inertial waves are almost unaffected by the geostrophic vorticity because dispersion efficiently overcomes the jet vorticity effects. A 2-D primitive-equation model is used to examine the scattering of wind-induced inertial waves in realistic situations. Results indicate that contribution of the lowest baroclinic modes, unaffected by the jet vorticity, explain some striking features reported in previous studies as the downward phase propagation of near-inertial waves in the positive vorticity region

Implementation strategies for hyperspectral unmixing using Bayesian source separation

Bayesian Positive Source Separation (BPSS) is a useful unsupervised approach for hyperspectral data unmixing, where numerical non-negativity of spectra and abundances has to be ensured, such in remote sensing. Moreover, it is sensible to impose a sum-to-one (full additivity) constraint to the estimated source abundances in each pixel. Even though non-negativity and full additivity are two necessary properties to get physically interpretable results, the use of BPSS algorithms has been so far limited by high computation time and large memory requirements due to the Markov chain Monte Carlo calculations. An implementation strategy which allows one to apply these algorithms on a full hyperspectral image, as typical in Earth and Planetary Science, is introduced. Effects of pixel selection, the impact of such sampling on the relevance of the estimated component spectra and abundance maps, as well as on the computation times, are discussed. For that purpose, two different dataset have been used: a synthetic one and a real hyperspectral image from Mars.Comment: 10 pages, 6 figures, submitted to IEEE Transactions on Geoscience and Remote Sensing in the special issue on Hyperspectral Image and Signal Processing (WHISPERS

Three-dimensional stirring of thermohaline fronts

This study investigates the stirring of the thermohaline anomalies in a fully turbulent quasigeostrophic stratified flow. Temperature and salinity fields are permanently forced at large scales and are related to density by a linear equation of state. We show, using some inherent properties of quasi-geostrophic turbulence, that the 3-D ageostrophic circulation is the key dynamical characteristic that governs the strength and the spatial distribution of small-scale thermohaline fronts that are strongly density compensated. The numerical simulations well illustrate the formation by the mesoscale eddy field of sharp thermohaline fronts that are mainly located in the saddle regions and around the eddy cores and have a weak signature on the density field. One important aspect revealed by the numerical results is that the thermohaline anomalies experience not only a direct horizontal cascade but also a significant vertical cascade. One consequence of this 3-D cascade is that the ultimate mixing of the thermohaline anomalies will not be necessarily maximum at the depth where the large-scale temperature and salinity anomalies are maximum. Some analytical arguments allow us to identify some of the mechanisms that drive this 3-D cascade

La spectroscopie comme outil de caractérisation des microorganismes : application à la microbiologie du sol et des produits laitiers

Les bactéries sont des microorganismes unicellulaires participant à de nombreux processus biologiques. Les espèces impliquées dans la fermentation lactique et la croissance des plantes suscitent un intérêt particulier en agro-industrie. L’identification de souches bactériennes est essentielle pour concevoir des ferments lactiques pour les produits laitiers et des biofertilisants pour les sols. Les techniques actuelles d’identification des bactéries sont destructives, et nécessitent donc de préparer des échantillons dédiés aux analyses. L’objectif de ce travail est de développer une méthode de criblage par spectroscopie UV-Vis-NIR de bactéries inoculées sur boîtes de Pétri, afin d’en évaluer le potentiel en tant qu’alternative simple, rapide et non destructive aux outils de diagnostic conventionnels. Un protocole de mesure a tout d’abord été établi sur un nombre restreint de souches bactériennes pour un spectromètre NIR et un spectromètre UV-Vis-NIR. 142 souches de bactéries lactiques et 76 souches de rhizobactéries favorisant la croissance des plantes ont ensuite été inoculées sur milieu gélosé puis analysées avec les deux instruments au cours de plusieurs expérimentations. Un biais associé à ces séries d’inoculations et de mesures était présent sur les spectres bruts. Une réduction de ce biais a été possible en corrigeant les acquisitions par rapport aux spectres de boîtes de gélose pure réalisées à chaque expérimentation. Une analyse exploratoire des données spectrales a mis en évidence des différences entre les genres et les espèces des bactéries. Elles ont majoritairement été attribuées aux polysaccharides contenus dans les parois cellulaires, constituants la capsule bactérienne ou sécrétés dans l’environnement extracellulaire. Des modèles de classification ont été développés avec les données spectrales par PLS-DA et réseaux de neurones artificiels. Leurs performances ont été comparées en prédiction sur 84 souches de bactéries lactiques isolées de laits crus et 19 souches de rhizobactéries supplémentaires. Les taux de classification correct des meilleurs modèles obtenus sont respectivement de 70% et 63% pour le genre et l’espèce des bactéries lactiques, et de 66% pour le genre des rhizobactéries. Des pistes d’amélioration ont été proposées pour améliorer les performances et étendre les applications de la méthod

SEA SURFACE DYNAMIC HEIGHT TOPOGRAPHY AND THE NORTH EQUATORIAL COUNTERCURRENT AS INFERRED FROM A LINEAR MODEL

Abstract. Special attention is paid to the computed North Equatorial Countercurrent. We conclude that most of the observed seasonal variations can be explained using simple linear theory

NRL^{-/-} gene edited human embryonic stem cells generate rod-deficient retinal organoids enriched in S-cone-like photoreceptors

Organoid cultures represent a unique tool to investigate the developmental complexity of tissues like the human retina. NRL is a transcription factor required for the specification and homeostasis of mammalian rod photoreceptors. In Nrl‐deficient mice, photoreceptor precursor cells do not differentiate into rods, and instead follow a default photoreceptor specification pathway to generate S‐cone‐like cells. To investigate whether this genetic switch mechanism is conserved in humans, we used CRISPR/Cas9 gene editing to engineer an NRL‐deficient embryonic stem cell (ESC) line (NRL^{−/−}), and differentiated it into retinal organoids. Retinal organoids self‐organize and resemble embryonic optic vesicles (OVs) that recapitulate the natural histogenesis of rods and cone photoreceptors. NRL−/− OVs develop comparably to controls, and exhibit a laminated, organized retinal structure with markers of photoreceptor synaptogenesis. Using immunohistochemistry and quantitative polymerase chain reaction (qPCR), we observed that NRL^{−/−} OVs do not express NRL, or other rod photoreceptor markers directly or indirectly regulated by NRL. On the contrary, they show an abnormal number of photoreceptors positive for S‐OPSIN, which define a primordial subtype of cone, and overexpress other cone genes indicating a conserved molecular switch in mammals. This study represents the first evidence in a human in vitro ESC‐derived organoid system that NRL is required to define rod identity, and that in its absence S‐cone‐like cells develop as the default photoreceptor cell type. It shows how gene edited retinal organoids provide a useful system to investigate human photoreceptor specification, relevant for efforts to generate cells for transplantation in retinal degenerative diseases

Modeling the Nd isotopic composition in the North Atlantic basin using an eddy-permitting model

International audienceBoundary Exchange (BE – exchange of elementsbetween continental margins and the open ocean) hasbeen emphasized as a key process in the oceanic cycle ofneodymium (Nd) (Lacan and Jeandel, 2005a). Here, we usea regional eddy-permitting resolution Ocean General CirculationModel (1/4) of the North Atlantic basin to simulatethe distribution of the Nd isotopic composition, consideringBE as the only source. Results show good agreementwith the data, confirming previous results obtained using thesame parameterization of the source in a coarse resolutionglobal model (Arsouze et al., 2007), and therefore the majorcontrol played by the BE processes in the Nd cycle onthe regional scale. We quantified the exchange rate of theBE, and found that the time needed for the continental marginsto significantly imprint the chemical composition of thesurrounding seawater (further referred as characteristic exchangetime) is of the order of 0.2 years. However, thetimescale of the BE may be subject to large variations as avery short exchange time (a few days) is needed to reproducethe highly negative values of surface waters in the LabradorSea, whereas a longer one (up to 0.5 years) is required tosimulate the radiogenic influence of basaltic margins and distinguishthe negative isotopic signatures of North AtlanticDeep Water from the more radiogenic southern origin watermasses. This likely represents geographical variations inerosion fluxes and the subsequent particle load onto the continentalmargins. Although the parameterization of the BEis the same in both configurations of the model, the characteristicexchange time in the eddy-permitting configuration issignificantly lower than the previous evaluations using a lowresolution configuration (6 months to 10 years), but howeverin agreement with the available seawater Nd isotope data.This results highlights the importance of the model dynamicsin simulating the BE proces

The North Atlantic subpolar gyre in four high resolution models

The authors present the first quantitative comparison between new velocity datasets and high-resolution models in the North Atlantic subpolar gyre [1/10° Parallel Ocean Program model (POPNA10), Miami Isopycnic Coordinate Ocean Model (MICOM), ° Atlantic model (ATL6), and Family of Linked Atlantic Ocean Model Experiments (FLAME)]. At the surface, the model velocities agree generally well with World Ocean Circulation Experiment (WOCE) drifter data. Two noticeable exceptions are the weakness of the East Greenland coastal current in models and the presence in the surface layers of a strong southwestward East Reykjanes Ridge Current. At depths, the most prominent feature of the circulation is the boundary current following the continental slope. In this narrow flow, it is found that gridded float datasets cannot be used for a quantitative comparison with models. The models have very different patterns of deep convection, and it is suggested that this could be related to the differences in their barotropic transport at Cape Farewell. Models show a large drift in watermass properties with a salinization of the Labrador Sea Water. The authors believe that the main cause is related to horizontal transports of salt because models with different forcing and vertical mixing share the same salinization problem. A remarkable feature of the model solutions is the large westward transport over Reykjanes Ridge [10 Sv (Sv ≡ 106 m3 s−1) or more