On-line blind unmixing for hyperspectral pushbroom imaging systems

International audienceIn this paper, the on-line hyperspectral image blind unmixing is addressed. Inspired by the Incremental Non-negative Matrix Factorization (INMF) method, we propose an on-line NMF which is adapted to the acquisition scheme of a pushbroom imager. Because of the non-uniqueness of the NMF model, a minimum volume constraint on the endmembers is added allowing to reduce the set of admissible solutions. This results in a stable algorithm yielding results similar to those of standard off-line NMF methods, but drastically reducing the computation time. The algorithm is applied to wood hyperspectral images showing that such a technique is effective for the on-line prediction of wood piece rendering after finishing. Index Terms— Hyperspectral imaging, Pushbroom imager, On-line Non-negative Matrix Factorization, Minimum volume constraint

Démélange d'images hyperspectrales à l'aide de la NMF en-ligne avec contrainte de dispersion minimale

National audienceWe propose a new method for on-line hyperspectral images unmixing based on an ADMM (Alternating Direction Method of Multipliers) approach, particularly well-adapted to pushbroom imaging systems. The proposed algorithm presents a faster convergence and a lower computational complexity compared to the algorithms based on multiplicative update rules. Due to the general ill-posed nature of the unmixing problem, we impose a minimal endmembers dispersion constraint; this constraint can be interpreted as a convex relaxation of the minimal volume constraint. Real data tests illustrate the good performance of the proposed method compared to the state of the art.Nous proposons une nouvelle méthode de démélange en-ligne d'images hyperspectrales fondée sur une approche de type ADMM (Alternating Direction Method of Multipliers), particulièrement bien adaptée aux systèmes d'imagerie pushbroom. L'algorithme proposé présente une convergence plus rapide et une complexité de calcul plus faible par rapport aux algorithmes fondés sur des règles de mise à jour multiplicatives. En raison du caractère généralement mal posé du problème de démélange, nous intégrons dans la méthode une contrainte de dispersion minimale des endmembers ; cette contrainte peut être interprétée comme une relaxation convexe de la contrainte de volume minimal. Des tests sur des données réelles permettent d'illustrer les bonnes performances de la méthode proposée comparées à l'état de l'art

Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomics

<p>Abstract</p> <p>Background</p> <p>Plant growth is a complex process involving cell division and elongation. <it>Arabidopsis thaliana </it>hypocotyls undergo a 100-fold length increase mainly by cell elongation. Cell enlargement implicates significant changes in the composition and structure of the cell wall. In order to understand cell wall biogenesis during cell elongation, mRNA profiling was made on half- (active elongation) and fully-grown (after growth arrest) etiolated hypocotyls.</p> <p>Results</p> <p>Transcriptomic analysis was focused on two sets of genes. The first set of 856 genes named cell wall genes (CWGs) included genes known to be involved in cell wall biogenesis. A significant proportion of them has detectable levels of transcripts (55.5%), suggesting that these processes are important throughout hypocotyl elongation and after growth arrest. Genes encoding proteins involved in substrate generation or in synthesis of polysaccharides, and extracellular proteins were found to have high transcript levels. A second set of 2927 genes labeled secretory pathway genes (SPGs) was studied to search for new genes encoding secreted proteins possibly involved in wall expansion. Based on transcript level, 433 genes were selected. Genes not known to be involved in cell elongation were found to have high levels of transcripts. Encoded proteins were proteases, protease inhibitors, proteins with interacting domains, and proteins involved in lipid metabolism. In addition, 125 of them encoded proteins with yet unknown function. Finally, comparison with results of a cell wall proteomic study on the same material revealed that 48 out of the 137 identified proteins were products of the genes having high or moderate level of transcripts. About 15% of the genes encoding proteins identified by proteomics showed levels of transcripts below background.</p> <p>Conclusion</p> <p>Members of known multigenic families involved in cell wall biogenesis, and new genes that might participate in cell elongation were identified. Significant differences were shown in the expression of such genes in half- and fully-grown hypocotyls. No clear correlation was found between the abundance of transcripts (transcriptomic data) and the presence of the proteins (proteomic data) demonstrating (i) the importance of post-transcriptional events for the regulation of genes during cell elongation and (ii) that transcriptomic and proteomic data are complementary.</p

Structural and functional features and significance of the physical linkage between ER and mitochondria

The role of mitochondria in cell metabolism and survival is controlled by calcium signals that are commonly transmitted at the close associations between mitochondria and endoplasmic reticulum (ER). However, the physical linkage of the ER–mitochondria interface and its relevance for cell function remains elusive. We show by electron tomography that ER and mitochondria are adjoined by tethers that are ∼10 nm at the smooth ER and ∼25 nm at the rough ER. Limited proteolysis separates ER from mitochondria, whereas expression of a short “synthetic linker” (<5 nm) leads to tightening of the associations. Although normal connections are necessary and sufficient for proper propagation of ER-derived calcium signals to the mitochondria, tightened connections, synthetic or naturally observed under apoptosis-inducing conditions, make mitochondria prone to Ca2+ overloading and ensuing permeability transition. These results reveal an unexpected dependence of cell function and survival on the maintenance of proper spacing between the ER and mitochondria

Quand étudier, c’est travailler. Cadres institués des études et perspectives étudiantes

Les travaux portant sur les étudiant.es constituent un domaine investi par la recherche sociologique en France depuis les années 1960 (Bourdieu & Passeron, 1964 ; Molinari, 1992 ; Baudelot, Establet, Benoliel et al., 1981 ; Galland, 1996 ; Erlich, 1998 ; Felouzis, 2001 ; Gruel, Galland & Houzel, 2009) du fait notamment de la hausse significative de leurs effectifs à partir de cette époque. Plusieurs dimensions de la vie étudiante ont ainsi été étudiées : les trajectoires de formation, les res..

Unsupervised processing of hyperspectral images

National audienceThis work is a part of the CNRS project “ALOHA: Analyse en Ligne de dOnnées Hyperspectrales pour l’industrie Agroalimentaire” and of the ANR-OPTIFIN (Agence Nationale de la Recherche-OPTImisation des FINitions). The aim of these projects is to develop analytical tools adapted to the high throughput online analysis of samples by acquisition and processing of hyperspectral images. One output of the ALOHA and ANR OPTIFIN projects consists in the development of sequential algorithms for the deconvolution and on-the-fly unmixing of hyperspectral data. The main goal is to be able to predict and classify the quality of wood pieces renderings

Live imaging of targeted cell ablation in Xenopus:a new model to study demyelination and repair

Live imaging studies of the processes of demyelination and remyelination have so far been technically limited in mammals. We have thus generated a Xenopus laevis transgenic line allowing live imaging and conditional ablation of myelinating oligodendrocytes throughout the central nervous system (CNS). In these transgenic pMBP-eGFP-NTR tadpoles the myelin basic protein (MBP) regulatory sequences, specific to mature oligodendrocytes, are used to drive expression of an eGFP (enhanced green fluorescent protein) reporter fused to the E. coli nitroreductase (NTR) selection enzyme. This enzyme converts the innocuous pro-drug metronidazole (MTZ) to a cytotoxin. Using two-photon imaging in vivo, we show that pMBP-eGFP-NTR tadpoles display a graded oligodendrocyte ablation in response to MTZ, which depends on the exposure time to MTZ. MTZ-induced cell death was restricted to oligodendrocytes, without detectable axonal damage. After cessation of MTZ treatment, remyelination proceeded spontaneously, but was strongly accelerated by retinoic acid. Altogether, these features establish the Xenopus pMBP-eGFP-NTR line as a novel in vivo model for the study of demyelination/remyelination processes and for large-scale screens of therapeutic agents promoting myelin repair

Long-lived T follicular helper cells retain plasticity and help sustain humoral immunity

CD4; +; memory T cells play an important role in protective immunity and are a key target in vaccine development. Many studies have focused on T central memory (T; cm; ) cells, whereas the existence and functional significance of long-lived T follicular helper (T; fh; ) cells are controversial. Here, we show that T; fh; cells are highly susceptible to NAD-induced cell death (NICD) during isolation from tissues, leading to their underrepresentation in prior studies. NICD blockade reveals the persistence of abundant T; fh; cells with high expression of hallmark T; fh; markers to at least 400 days after infection, by which time T; cm; cells are no longer found. Using single-cell RNA-seq, we demonstrate that long-lived T; fh; cells are transcriptionally distinct from T; cm; cells, maintain stemness and self-renewal gene expression, and, in contrast to T; cm; cells, are multipotent after recall. At the protein level, we show that folate receptor 4 (FR4) robustly discriminates long-lived T; fh; cells from T; cm; cells. Unexpectedly, long-lived T; fh; cells concurrently express a distinct glycolytic signature similar to trained immune cells, including elevated expression of mTOR-, HIF-1-, and cAMP-regulated genes. Late disruption of glycolysis/ICOS signaling leads to T; fh; cell depletion concomitant with decreased splenic plasma cells and circulating antibody titers, demonstrating both unique homeostatic regulation of T; fh; and their sustained function during the memory phase of the immune response. These results highlight the metabolic heterogeneity underlying distinct long-lived T cell subsets and establish T; fh; cells as an attractive target for the induction of durable adaptive immunity