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Dual-sPLS: une famille de régressions par PLS (moindres carrés partiels) duale parcimonieuse pour la sélection d'attributs et la prédiction, avec parcimonie accordable ; évaluation sur des données simulées et en proche infrarouge (PIR)
No full textRelating a set of variables X to a response y is crucial in chemometrics. A quantitative prediction objective can be enriched by qualitative data interpretation, for instance by locating the most influential features. When high-dimensional problems arise, dimension reduction techniques can be used. Most notable are projections (e.g. Partial Least Squares or PLS ) or variable selections (e.g. lasso). Sparse partial least squares combine both strategies, by blending variable selection into PLS. The variant presented in this paper, Dual-sPLS, generalizes the classical PLS1 algorithm. It provides balance between accurate prediction and efficient interpretation. It is based on penalizations inspired by classical regression methods (lasso, group lasso, least squares, ridge) and uses the dual norm notion. The resulting sparsity is enforced by an intuitive shrinking ratio parameter. Dual-sPLS favorably compares to similar regression methods, on simulated and real chemical data. Code is provided as an open-source package in R: \url{https://CRAN.R-project.org/package=dual.spls}
Implication of VelB in the development, pathogenicity, and secondary metabolism of Penicillium expansum
No full textInternational audiencePenicillium expansum is the main cause of blue mold disease and the main producer of patulin in apple-derived products. This fungus also produces a wide variety of secondary metabolites, including citrinin and chaetoglobosin A. Secondary metabolism is regulated by global transcription factors that are affected by environmental signals. The light-dependent global transcription factor VelB, a member of the velvet complex, plays an important role in the regulation of secondary metabolism and fungal development in many fungal species. However, the specific roles of VelB in P. expansum remain unknown. A Pe∆velB mutant and a complemented Pe∆velB:velB strain were generated to investigate the role of VelB in pathogenicity and secondary metabolism. The Pe∆velB mutant colonized apples, but at a lower rate than the wild type and complemented strains. Conidiation was significantly reduced in the Pe∆velB strain. Under light conditions, the Pe∆velB strain showed a reduced level of spore viability. Deletion of the velB gene strongly inhibited the production of patulin, citrinin, and chaetoglobosin A on synthetic media or in planta, but increased the production of fumarylalanine; these changes were associated with down-regulation or upregulation of the genes involved in their respective biosynthesis. Analysis of the global secondary metabolism of the Pe∆velB strain revealed that 22 backbone genes were modulated. In addition, genes involved in siderophore biosynthesis, ergosterol biosynthesis, and nitrate assimilation were also upregulated in the PeΔvelB strain. Taken together, our results demonstrate that VelB is involved in the development, pathogenicity, and secondary metabolism of P. expansum
Physical limitations induced by a medium based on wheat bran for the production of biopesticides by Bacillus thuringiensis spp kurstaki
No full textInternational audienceBiopesticides, vectors for the development of the bioeconomy, represent a realistic alternative to petroleum-based chemical pesticides and their known harmfulness to humans and the environment. Bacillus thuringiensis is a gram-positive, spore-forming bacterium used for the production of biocontrol agents in agriculture. This insecticidal activity is mainly due to the production of parasporal δ-endotoxins consisting of an assembly of crystalline proteins called Cry. The European project IPM-4-Citrus (MSCA RISE, No. 734921, 2017-2023) aims to optimise these bioproductions from 3 strains of Bacillus thuringiensis subsp kurstaki (Lip, BLB1 and HD1) in a complex medium (wheat bran). The biochemical composition and nutritional limitations induced by the medium were identified. The physical properties of these heterogeneous suspensions are necessary for the definition of operating conditions favourable to scale-up. In this study, the morpho-granulometry of substrates, the ability to separate solid-liquid suspension and to clarify fermentation broth, and their rheological behaviour were studied as a function of substrate concentration and granulometry.Les biopesticides, vecteurs de développement de la bioéconomie, représentent une alternative réaliste aux pesticides chimiques pétro-sourcés et leur méfaits connus (nocivité pour l’Homme et l’Environnement). Bacillus thuringiensis est une bactérie gram positive, sporulante utilisée pour la production d’agent de biocontrôle en agriculture. Cette activité insecticide est principalement due à la production de δ-endotoxines parasporales constituées par un assemblage de protéines cristallines appelées Cry. Le projet européen IPM-4-Citrus (MSCA RISE, n° 734921, 2017-2023) vise à optimiser ces bioproductions à partir de 3 souches de Bacillus thuringiensis subsp kurstaki (Lip, BLB1 et HD1) dans un milieu complexe (son de blé). La composition biochimique et les limitations nutritionnelles induites par le milieu ont été identifiées. Les propriétés physiques de ces suspensions hétérogènes sont nécessaires à la définition de conditions opératoires favorables à un changement d’échelle. Dans cette étude, la morpho-granulométrie, l’aptitude à la séparation solide-liquide des suspensions biologiques et la rhéométrie ont été étudiées en fonction de la concentration et de la granulométrie du substrat
Équations différentielles énergétiques généralisées modélisant le comportement plastique des matériaux
No full textInternational audienceThe classical thermo-mechanical behavior laws which express the Cauchy stress function in terms of instantaneous deformations variables are specific for each material according to its nature, the type of imposed loadings and the scale of deformation being considered on the material. The energetic approach developed to express the stress function in terms of the deformation energy makes it possible to take into account physical transformation mechanism of the material. In this work a new energetic differential constitutive equations systems are proposed. Thus it can be possible to search to unify in a physical sense the materials constitutive behaviors law formulations. Hence, it is used a generalized differential equations system to find energetic behavior law corresponding to a lot of classical rheological models. The coherence between the analytical or numerical solutions obtained from proposed energetic approach lead to develop and valid more consistent and accurate materials mechanical constitutive models.Les lois de comportement thermomécaniques classiques, qui expriment la fonction de contrainte de Cauchy en termes de déformations instantanées, sont spécifiques à chaque matériau selon sa nature, le type de chargements imposés et l'ampleur de la déformation considérée. L'approche énergétique développée pour exprimer la fonction de contrainte en termes d'énergie de déformation permet de prendre en compte les mécanismes de transformation physique du matériau. Ce travail propose un nouveau système d'équations différentielles constitutives énergétiques. Il permet ainsi d'unifier, au sens physique du terme, les formulations des lois de comportement constitutives des matériaux. Un système d'équations différentielles généralisées est ainsi utilisé pour trouver des lois de comportement énergétiques correspondant à de nombreux modèles rhéologiques classiques. La cohérence entre les solutions analytiques et numériques obtenues grâce à l'approche énergétique proposée permet de développer et de valider des modèles constitutifs mécaniques des matériaux plus cohérents et plus précis
Utilizing AI and Nanotechnology Solutions to Propel Progress in Cancer Diagnostics, Therapeutics, and Integrated Theranostics
No full textInternational audienceThis chapter explores the dynamic convergence of nanotechnology and artificial intelligence (AI) in advancing cancer diagnosis and therapy. Nanotechnology employs nanoparticles for theragnostic applications, integrating diagnostic and therapeutic roles. Customized nanoparticles enable precise imaging and targeted treatment, minimizing harm to healthy tissue. Passive and active targeting optimize drug delivery, combat multidrug resistance, and introduce personalized treatment. AI-driven techniques analyze omics data and clinical information, enabling predictive models for immunotherapy and molecular target therapy. Next-gen sequencing reveals mutations and oncogenic pathways, with AI extracting insights from high-dimensional data. AI's integration into medical practice enhances diagnostics, catalyzing healthcare transformation. The synergy of nanotechnology and AI revolutionizes cancer management and reshapes medical practice
Do Anthropogenic Terpenoids mAtter in Atmospheric Chemistry?: highlights from the DATAbASE project
No full textInternational audienceTerpenoids (isoprene and monoterpenes) are highly reactive Volatile Organic Compounds (VOCs) known for decades for their biogenic origin. However, there is some strong evidence of their anthropogenic origin through, for instance, the most recent studies in North American cities investigating their use as Volatile Chemical Products (VCP) in indoor environments.The overall objective of DATAbASE is to investigate the industrial and non-industrial anthropogenic origin of terpenoids in the urban atmosphere and to evaluate their importance on urban pollution. To do so we have compiled and re-analyzed 15 VOC datasets collected over the last decade in contrasting urban areas from mid-latitudes to subtropical regions. In parallel, we have performed 0D box model simulations using the Cloud Explicit Physico-chemical Scheme (CLEPS). CLEPS is coupled to MCM v3.3.1 to evaluate the impact of anthropogenic terpenoids on atmospheric chemistry by establishing scenarios representative of contrasting urban environments.While the systematic presence of anthropogenic terpenoids has been demonstrated in urban atmosphere worldwide, we have pointed out the significant role of road transport emissions and, for the first time, the industrial emissions of a-pinene, one major monoterpene, in the northern harbor city of Dunkirk, France. Emissions Ratios and Positive Matrix Factorization (PMF) were implemented to quantify the anthropogenic emissions of urban terpenoids. In Paris megacity, the emissions of monoterpenes were estimated to be 11.8 tons each year. In Dunkirk, 3.5 tons of industrial a-pinene are emitted per year which is in the same order of magnitude as in Paris. While absolute anthropogenic emissions of terpenoids usually represent less than 3% of other anthropogenic VOC emissions, they dominate the reactivity of anthropogenic VOC emissions by one to three orders of magnitude regarding nighttime oxidation by NO3 and ozonolysis, respectively. The 0D modelling has been developed to test and evaluate those potential effects. This presentation will synthesize the recent findings of DATAbASE and propose future directions
D-alanylation of Teichoic Acids in Bacilli impedes the immune sensing of peptidoglycan in Drosophila
No full textAbstract Modification of cell wall components is a prominent mean for pathogens to hinder host immune defenses. Here, using the Drosophila model, we aimed at characterizing the role of D-alanine esterification of teichoic acids (TAs) in the resistance of Bacillus thuringiensis to host defenses in vivo . We show that, by preventing cationic antimicrobial effectors-mediated bacterial lysis, this cell wall modification also limits the release of peptidoglycan immunostimulatory fragments thus impeding their sensing and the subsequent induction of the IMD- NF-κB pathway. Interestingly, we show that this strategy is also adopted by Lactobacillus plantarum , a bona fide commensal, to fine-tune its immunomodulatory potential in the Drosophila gut. Markedly, we show that the D-alanylation of TAs is essential for the resistance of L. plantarum to gut lysozyme. Altogether our data shed light on the mechanism underlying the persistence and the low immunostimulatory potential of L. plantarum in the Drosophila gut
Reproducible and relocatable regional ocean modelling: fundamentals and practices
No full textInternational audienceAbstract. In response to an increasing demand for bespoke or tailored regional ocean modelling configurations, we outline fundamental principles and practices that can expedite the process to generate new configurations. The paper develops the principle of reproducibility and advocates adherence by presenting benefits to the community and user. The elements of this principle are reproducible workflows and standardised assessment, with additional effort over existing working practices being balanced against the added value generated. The paper then decomposes the complex build process, for a new regional ocean configuration, into stages and presents guidance, advice and insight for each component. This advice is compiled from across the NEMO (Nucleus for European Modelling of the Ocean) user community and sets out principles and practises that encompass regional ocean modelling with any model. With detailed and region-specific worked examples in Sects. 3 and 4, the linked companion repositories and DOIs all target NEMOv4. The aim of this review and perspective paper is to broaden the user community skill base and to accelerate development of new configurations in order to increase the time available for exploiting the configurations
Ubiquity of anthropogenic terpenoids in cities worldwide: Emission ratios, emission quantification and implications for urban atmospheric chemistry
No full textInternational audienceTerpenoids (isoprene and monoterpenes) are highly reactive Volatile Organic Compounds (VOCs) known for decades for their biogenic origin. Here, we discuss the nature and magnitudeof their anthropogenic emissions. We compiled and re-analyzed fourteen datasets of in-situ VOC observations collected over the last decade in contrasting urban areas from mid-latitudesto subtropical regions. We show the systematic presence of anthropogenic terpenoids in urban ambient air with clear covariations with anthropogenic compounds (R2 > 0.50) even duringmid-latitude winters. Despite the emerging importance of monoterpene emissions from consumer products in North American cities, there is some evidence of monoterpene emissionsfrom tailpipe exhaust in cities of the developing world. The traffic-related fraction of monoterpenes is estimated and can account for up to 40% of their ambient levels. The anthropogenic emission ratios (ER) of some terpenoids (isoprene, -pinene and limonene) are estimated and spatially compared. The anthropogenic emissions of terpenoids are indirectly estimated from those ER combined to regional and global emission inventories (CAMS-GLOB-ANT_v4.2) at urban and country scale focusing on France, Lebanon and Vietnam. Those anthropogenic emissions do not represent more than 3% of other anthropogenic VOC emissions. However, they dominate by one to three orders of magnitude the reactivity of other anthropogenic VOCs regarding NO3 oxidation and ozonolysis. This study raises two questions which need further investigations in the future.: i) the significance of terpenoid emissions from traffic, especially in urban areas of the developing world, ii) the role of anthropogenic terpenoids in nighttime and wintertime atmospheric chemistry at mid-latitudes
Intérêts des remplissages des dolines dans l’étude des paléoenvironnements du Mont-Liban : cas des dolines du Jabal Kneisseh et de Faouar Dara
No full textInternational audienceThe scope of this work is to assess the relevance of the detrital formations trapped in the dolines of Mount-Lebanon with the aim to document the paleoenvironments of this long anthropized mountainous area. The coring of two sequences in the upstream parts of the Nahr Beirut catchment, in distinct geomorphological contexts, was studied. The first sequence was retrieved from a solution doline of the high plateau of Jabal Kneisseh (KD2) and the second one from the tectono-karstic doline of Faouar Dara (FD). Sedimentological and geochemical analysis have been conducted on the extracted materials in order to identify and interpret potential proxies of material transport and deposition. The chronological framework has been obtained by 5 AMS radiocarbon dating of charcoal fragments. The results of the KD2 sequence support the hypothesis of the presence of a more developed vegetation and soil cover over the surface of the high plateau, which had been progressively destroyed following various fire episodes during the late-Holocene (~2429–2000 cal. BP). The results of the FD sequence suggest a link between the filling of the doline and the evolution of the landcover and land uses over the upstream areas during the last millennium (~973–795 cal. BP), potentially linked to the migration of agro-pastoral activities to higher altitudes.Ce travail discute l’intérêt des remplissages des dolines dans l’étude des paléoenvironnements du Mont-Liban. Le carottage de deux séquences du bassin versant du Nahr Beyrouth s’inscrivant dans des contextes géomorphologiques distincts ont été étudiées. La première est extraite d’une doline du haut plateau du Jabal Kneisseh (KD2) et la seconde, de la doline tectono-karstique de Faouar Dara (FD). Les analyses sédimentologiques et géochimiques visent à identifier et interpréter les potentiels indicateurs de transport et déposition du matériel jusque dans les dolines. Le cadre chronologique des séquences a été obtenu par datations AMS C14 de fragments de charbons de bois. Les données analysées de la séquence du Jabal Kneisseh soutiennent l’hypothèse de la présence de couverts végétal et pédologique à la surface du haut plateau qui se seraient progressivement érodés suite à divers épisodes d’incendies durant l’Holocène tardif (~2429–2000 cal. BP). Les résultats à FD suggèrent un lien entre le remplissage de la doline et l’évolution de l’occupation du sol en amont durant le dernier millénaire (~973–795 cal. BP), potentiellement en lien avec une migration en altitude des activités agro-pastorales