Monthly surface thermal forcing in the tropical Pacific from 1980 to 1983

Monthly distributions of surface latent heat flux and solar irradiance in the tropical Pacific were computed from observations of the scanning multichannel microwave radiometer on Nimbus-7 and the visible infrared spin scan radiometer on GOES-W. They are the dominant variable components of the surface heat flux, the sum of which gives the approximate thermal forcing on the ocean. Monthly maps of this sum, from January 1980 to September 1983, and within 20 deg N and 20 deg S, 180 deg and 80 deg W, are presented

Bayesian Methodology for Ocean Color Remote Sensing

66 pagesThe inverse ocean color problem, i.e., the retrieval of marine reflectance from top-of-atmosphere (TOA) reflectance, is examined in a Bayesian context. The solution is expressed as a probability distribution that measures the likelihood of encountering specific values of the marine reflectance given the observed TOA reflectance. This conditional distribution, the posterior distribution, allows the construction of reliable multi-dimensional confidence domains of the retrieved marine reflectance. The expectation and covariance of the posterior distribution are computed, which gives for each pixel an estimate of the marine reflectance and a measure of its uncertainty. Situations for which forward model and observation are incompatible are also identified. Prior distributions of the forward model parameters that are suitable for use at the global scale, as well as a noise model, are determined. Partition-based models are defined and implemented for SeaWiFS, to approximate numerically the expectation and covariance. The ill-posed nature of the inverse problem is illustrated, indicating that a large set of ocean and atmospheric states, or pre-images, may correspond to very close values of the satellite signal. Theoretical performance is good globally, i.e., on average over all the geometric and geophysical situations considered, with negligible biases and standard deviation decreasing from 0.004 at 412 nm to 0.001 at 670 nm. Errors are smaller for geometries that avoid Sun glint and minimize air mass and aerosol influence, and for small aerosol optical thickness and maritime aerosols. The estimated uncertainty is consistent with the inversion error. The theoretical concepts and inverse models are applied to actual SeaWiFS imagery, and comparisons are made with estimates from the SeaDAS standard atmospheric correction algorithm and in situ measurements. The Bayesian and SeaDAS marine reflectance fields exhibit resemblance in patterns of variability, but the Bayesian imagery is less noisy and characterized by different spatial de-correlation scales, with more realistic values in the presence of absorbing aerosols. Experimental errors obtained from match-up data are similar to the theoretical errors determined from simulated data. Regionalization of the inverse models is a natural development to improve retrieval accuracy, for example by including explicit knowledge of the space and time variability of atmospheric variables

Continuation of Nesterov's Smoothing for Regression with Structured Sparsity in High-Dimensional Neuroimaging

Predictive models can be used on high-dimensional brain images for diagnosis of a clinical condition. Spatial regularization through structured sparsity offers new perspectives in this context and reduces the risk of overfitting the model while providing interpretable neuroimaging signatures by forcing the solution to adhere to domain-specific constraints. Total Variation (TV) enforces spatial smoothness of the solution while segmenting predictive regions from the background. We consider the problem of minimizing the sum of a smooth convex loss, a non-smooth convex penalty (whose proximal operator is known) and a wide range of possible complex, non-smooth convex structured penalties such as TV or overlapping group Lasso. Existing solvers are either limited in the functions they can minimize or in their practical capacity to scale to high-dimensional imaging data. Nesterov's smoothing technique can be used to minimize a large number of non-smooth convex structured penalties but reasonable precision requires a small smoothing parameter, which slows down the convergence speed. To benefit from the versatility of Nesterov's smoothing technique, we propose a first order continuation algorithm, CONESTA, which automatically generates a sequence of decreasing smoothing parameters. The generated sequence maintains the optimal convergence speed towards any globally desired precision. Our main contributions are: To propose an expression of the duality gap to probe the current distance to the global optimum in order to adapt the smoothing parameter and the convergence speed. We provide a convergence rate, which is an improvement over classical proximal gradient smoothing methods. We demonstrate on both simulated and high-dimensional structural neuroimaging data that CONESTA significantly outperforms many state-of-the-art solvers in regard to convergence speed and precision.Comment: 11 pages, 6 figures, accepted in IEEE TMI, IEEE Transactions on Medical Imaging 201

Comments on the "Spatial variability of coastal surface water temperature during upwelling"

International audienceComments on the article "Spatial variability of coastal surface water temperature during upwelling

Rice root genetic architecture: Meta-analysis from a drought QTL database

During the last 10 years, a large number of quantitative trait loci (QTLs) controlling rice root morphological parameters have been detected in several mapping populations by teams interested in improving drought resistance in rice. Compiling these data could be extremely helpful in identifying candidate genes by positioning consensus QTLs with more precision through meta-QTL analysis. We extracted information from 24 published papers on QTLs controlling 29 root parameters including root number, maximum root length, root thickness, root/ shoot ratio, and root penetration index. A web-accessible database of 675 root QTLs detected in 12 populations was constructed. This database includes also all QTLs for drought resistance traits in rice published between 1995 and 2007. The physical position on the pseudochromosomes of the markers flanking each QTL was determined. An overview of the number of root QTLs in 5-Mb segments covering the whole genome revealed the existence of "hot spots," The 32 trait × chromosome combinations comprising six or more QTLs were subjected to a meta-QTL analysis using the software package MetaQTL. The method enabled us both to determine the likely number of true QTLs in these areas using an Akaike information criterion and to estimate their position. The meta-QTL confidence intervals were notably reduced and, for the smallest ones, encompassed only a few genes. (Résumé d'auteur

Patterns of rice diversity from SNP delineated the origin of the atypical O. sativa group in Madagascar from intermediary forms of the Indian sub-continent

Madagascar Island was one of the last major Old World areas where human settlement was accompanied by the introduction of Oryza sativa. Early studies had reported the presence of a rice group specific to Madagascar. Using 1536 SNP markers, we compared diversity patterns between a panel of 147 Malagasy rice varieties, a reference panel of 370 Asian varieties and representatives of wild relatives of O. sativa. Migration bottleneck has resulted in 30-40% reduction of diversity among the indica and japonica groups in Madagascar. The Malagasy panel showed many fewer indica x japonica recombinations compared to the Asian panel, suggesting that the two groups had undergone much less recombinations when migration to the Island occurred. The existence of the Malagasy-specific group (Gm) was confirmed. Its diversity patterns positioned it halfway from indica and aus groups. Madagascar also hosted cold tolerant tropical japonica varieties, with very long grain. The Gm group most probably arose from founder effect from intermediary forms of rice originated from either India or Sri Lanka that did not belong to the four majors O. sativa groups. It then underwent human selection for cold tolerance. Signs of inter-group recombinations were also observed, but recombinations did not seem to have played a major role in the dynamics of rice adaptation to the Island's agro-ecological constraints. Connections between Gm and O. rufipogon from its putative area of origin reinforce the hypothesis of multiple and diffuse domestication of O. sativa as opposed to two independent domestications occurring in two distinct geographical areas. (Texte intégral

Satellite determination of the mesoscale variability of the sea surface temperature

International audienceSatellite infrared data have been used to investigate the mesoscale variability of the SST (sea surface temperature) field. A statistical analysis of the SST field has been performed by means of the structure function. Results give the equivalent power-law exponent n of the spatial variance density spectrum E(k) ∼ k−h. The exponent n was found to vary from 1.5 to 2,3 with a mean value of 1.8 in the ]range of scales 3–100 km which is in agreement with previous one-dimensional analysis from shipborne and airborne measurements. These observed values of n are discussed and compared with the values predicted by turbulence theories

Sea surface temperature of the coastal zones of France

Thermal gradients in French coastal zones for the period of one year were mapped in order to enable a coherent study of certain oceanic features detectable by the variations in the sea surface temperature field and their evolution in time. The phenomena examined were mesoscale thermal features in the English Channel, the Bay of Biscay, and the northwestern Mediterranean; thermal gradients generated by French estuary systems; and diurnal heating in the sea surface layer. The investigation was based on Heat Capacity Mapping Mission imagery

Phosphorylation of human DNA polymerase λ by the cyclin-dependent kinase Cdk2/cyclin A complex is modulated by its association with proliferating cell nuclear antigen

DNA polymerase (Pol) λ is a member of the Pol X family and possesses four different enzymatic activities, being DNA polymerase, terminal transferase, deoxyribose phosphate lyase and polynucleotide synthetase, all localized in its C-terminal region. On the basis of its biochemical properties, Pol λ has been implicated in various DNA repair pathways, such as abasic site translesion DNA synthesis, base excision repair and non-homologous end joining of double strand breaks. However, its role in vivo has not yet been elucidated. In addition, Pol λ has been shown to interact with the replication clamp proliferating cell nuclear antigen (PCNA) in vitro and in vivo. In this work, we searched by affinity chromatography for novel partners and we identified the cyclin-dependent kinase Cdk2 as novel partner of Pol λ. Pol λ is phosphorylated in vitro by several Cdk/cyclin complexes, including Cdk2/cyclin A, in its proline-serine-rich domain. While the polymerase activity of Pol λ was not affected by Cdk2/cyclin A phosphorylation, phosphorylation of Pol λ was decreased by its interaction with PCNA. Finally, Pol λ is also phosphorylated in vivo in human cells and this phosphorylation is modulated during the cell cycl

Multiblock analysis of omics and imaging data with variable selection

Congrès sous l’égide de la Société Française de Génie Biologique et Médical (SFGBM)National audienceSparse generalized canonical correlation analysis (SGCCA) has been proposed to combine RGCCA with an ℓ 1-penalty in a unified framework. Within this framework, blocks are not necessarily fully connected, which provides flexibility. The versatility and usefulness of SGCCA are illustrated on a 3-block dataset which combine Gene Expression, Comparative Genomic Hybridiza-tion and tumor location, determined on RMI at diagnosis. All data were measured on a cohort of 53 children with High Grade Glioma. SGCCA is available on CRAN as part of the RGCCA package