Détection de métaux lourds dans les sols par spectroscpoie d'émission sur plasma induit par laser (LIBS)

Dans les domaines de l’analyse, du contrôle et de la mesure physique, le laser constitue un outil métrologique particulièrement puissant et polyvalent, capable d’apporter des réponses concrètes à des problématiques variées, y compris d’ordre sociétal. Parmi ces dernières, la contamination des sites et des sols par les métaux lourds est un enjeu de santé publique important qui requiert de disposer de moyens de mesure adaptés aux réglementations existantes et suffisamment souples d’utilisation. Technique rapide et ne nécessitant pas de préparation de l’échantillon, la spectroscopie sur plasma induit par laser (LIBS) présente des avantages très intéressants pour réaliser des mesures sur site de la teneur en métaux lourds à l’échelle de la dizaine de ppm; la conception d’un appareil portable à moyen terme est envisageable. Dans cette thèse nous montrons d’abord que le régime femtoseconde ne présente pas d’avantages par rapport au régime nanoseconde standard pour notre problématique. Ensuite nous mettons en oeuvre un traitement avancé des spectres LIBS par des méthodes chimiométriques dont les performances améliorent sensiblement les résultats des analyses qualitatives et quantitatives d’échantillons de sols.In the fields of analysis, control and physical measurement, the laser constitutes a particularly powerful and multi-purpose metrological tool, capable to bring concrete solutions to various matters, including of a societal nature. Among the latter, contamination of sites and soils by heavy metals is an important issue of public health which requires to have measurement means adapted to existing regulations and whose use be sufficiently flexible. As a fast technique which does not need any sample preparation, laser-induced breakdown spectroscopy (LIBS) offers very interesting advantages for making on-site measurements of heavy metals content at the 10-ppm level ; the design of a portable system is conceivable in the medium term. In this work we first show that the femtosecond regime presents no advantages with respect to the standard nanosecond regime for our issue. The we implement an advanced treatment of LIBS spectra by chemometric techniques whose performances significantly improve the results of qualitative and quantitative analyses of soils samples

HyperPCA: a Powerful Tool to Extract Elemental Maps from Noisy Data Obtained in LIBS Mapping of Materials

Laser-induced breakdown spectroscopy is a preferred technique for fast and direct multi-elemental mapping of samples under ambient pressure, without any limitation on the targeted element. However, LIBS mapping data have two peculiarities: an intrinsically low signal-to-noise ratio due to single-shot measurements, and a high dimensionality due to the high number of spectra acquired for imaging. This is all the truer as lateral resolution gets higher: in this case, the ablation spot diameter is reduced, as well as the ablated mass and the emission signal, while the number of spectra for a given surface increases. Therefore, efficient extraction of physico-chemical information from a noisy and large dataset is a major issue. Multivariate approaches were introduced by several authors as a means to cope with such data, particularly Principal Component Analysis. Yet, PCA is known to present theoretical constraints for the consistent reconstruction of the dataset, and has therefore limitations to efficient interpretation of LIBS mapping data. In this paper, we introduce HyperPCA, a new analysis tool for hyperspectral images based on a sparse representation of the data using Discrete Wavelet Transform and kernel-based sparse PCA to reduce the impact of noise on the data and to consistently reconstruct the spectroscopic signal, with a particular emphasis on LIBS data. The method is first illustrated using simulated LIBS mapping datasets to emphasize its performances with highly noisy and/or highly interfered spectra. Comparisons to standard PCA and to traditional univariate data analyses are provided. Finally, it is used to process real data in two cases that clearly illustrate the potential of the proposed algorithm. We show that the method presents advantages both in quantity and quality of the information recovered, thus improving the physico-chemical characterisation of analysed surfaces.Comment: 20 pages, 8 pages of supplementary materia

Trustworthiness of Laser-Induced Breakdown Spectroscopy Predictions via Simulation-based Synthetic Data Augmentation and Multitask Learning

We consider quantitative analyses of spectral data using laser-induced breakdown spectroscopy. We address the small size of training data available, and the validation of the predictions during inference on unknown data. For the purpose, we build robust calibration models using deep convolutional multitask learning architectures to predict the concentration of the analyte, alongside additional spectral information as auxiliary outputs. These secondary predictions can be used to validate the trustworthiness of the model by taking advantage of the mutual dependencies of the parameters of the multitask neural networks. Due to the experimental lack of training samples, we introduce a simulation-based data augmentation process to synthesise an arbitrary number of spectra, statistically representative of the experimental data. Given the nature of the deep learning model, no dimensionality reduction or data selection processes are required. The procedure is an end-to-end pipeline including the process of synthetic data augmentation, the construction of a suitable robust, homoscedastic, deep learning model, and the validation of its predictions. In the article, we compare the performance of the multitask model with traditional univariate and multivariate analyses, to highlight the separate contributions of each element introduced in the process.Comment: 35 pages, appendix with supplementary materia

Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea–specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops

Detection of heavy metals in soils by laser-induced breakdown spectroscopy (LIBS)

Dans les domaines de l'analyse, du contrôle et de la mesure physique, le laser constitue un outil métrologique particulièrement puissant et polyvalent, capable d'apporter des réponses concrètes à des problématiques variées, y compris d'ordre sociétal. Parmi ces dernières, la contamination des sites et des sols par les métaux lourds est un enjeu de santé publique important qui requiert de disposer de moyens de mesure adaptés aux réglementations existantes et suffisamment souples d'utilisation. Technique rapide et ne nécessitant pas de préparation de l'échantillon, la spectroscopie sur plasma induit par laser (LIBS) présente des avantages très intéressants pour réaliser des mesures sur site de la teneur en métaux lourds à l'échelle de la dizaine de ppm; la conception d'un appareil portable à moyen terme est envisageable.Dans cette thèse nous montrons d'abord que le régime femtoseconde ne présente pas d'avantages par rapport au régime nanoseconde standard pour notre problématique. Ensuite nous mettons en œuvre un traitement avancé des spectres LIBS par des méthodes chimiométriques dont les performances améliorent sensiblement les résultats des analyses qualitatives et quantitatives d'échantillons de sols.In the fields of analysis, control and physical measurement, the laser constitutes a particularly powerful and multi-purpose metrological tool, capable to bring concrete solutions to various matters, including of a societal nature. Among the latter, contamination of sites and soils by heavy metals is an important issue of public health which requires to have measurement means adapted to existing regulations and whose use be sufficiently flexible. As a fast technique which does not need any sample preparation, laser-induced breakdown spectroscopy (LIBS) offers very interesting advantages for making on-site measurements of heavy metals content at the 10-ppm level; the design of a portable system is conceivable in the medium term.In this work we first show that the femtosecond regime presents no advantages with respect to the standard nanosecond regime for our issue. Then we implement an advanced treatment of LIBS spectra by chemometric techniques whose performances significantly improve the results of qualitative and quantitative analyses of soils samples

Détection de métaux lourds dans les sols par spectroscopie d'émission sur plasma induit par laser (LIBS)

In the fields of analysis, control and physical measurement, the laser constitutes a particularly powerful and multi-purpose metrological tool, capable to bring concrete solutions to various matters, including of a societal nature. Among the latter, contamination of sites and soils by heavy metals is an important issue of public health which requires to have measurement means adapted to existing regulations and whose use be sufficiently flexible. As a fast technique which does not need any sample preparation, laser-induced breakdown spectroscopy (LIBS) offers very interesting advantages for making on-site measurements of heavy metals content at the 10-ppm level; the design of a portable system is conceivable in the medium term.In this work we first show that the femtosecond regime presents no advantages with respect to the standard nanosecond regime for our issue. Then we implement an advanced treatment of LIBS spectra by chemometric techniques whose performances significantly improve the results of qualitative and quantitative analyses of soils samples.Dans les domaines de l'analyse, du contrôle et de la mesure physique, le laser constitue un outil métrologique particulièrement puissant et polyvalent, capable d'apporter des réponses concrètes à des problématiques variées, y compris d'ordre sociétal. Parmi ces dernières, la contamination des sites et des sols par les métaux lourds est un enjeu de santé publique important qui requiert de disposer de moyens de mesure adaptés aux réglementations existantes et suffisamment souples d'utilisation. Technique rapide et ne nécessitant pas de préparation de l'échantillon, la spectroscopie sur plasma induit par laser (LIBS) présente des avantages très intéressants pour réaliser des mesures sur site de la teneur en métaux lourds à l'échelle de la dizaine de ppm; la conception d'un appareil portable à moyen terme est envisageable.Dans cette thèse nous montrons d'abord que le régime femtoseconde ne présente pas d'avantages par rapport au régime nanoseconde standard pour notre problématique. Ensuite nous mettons en œuvre un traitement avancé des spectres LIBS par des méthodes chimiométriques dont les performances améliorent sensiblement les résultats des analyses qualitatives et quantitatives d'échantillons de sols

Détection de métaux lourds dans les sols par spectroscopie d'émission sur plasma induit par laser (LIBS)

In the fields of analysis, control and physical measurement, the laser constitutes a particularly powerful and multi-purpose metrological tool, capable to bring concrete solutions to various matters, including of a societal nature. Among the latter, contamination of sites and soils by heavy metals is an important issue of public health which requires to have measurement means adapted to existing regulations and whose use be sufficiently flexible. As a fast technique which does not need any sample preparation, laser-induced breakdown spectroscopy (LIBS) offers very interesting advantages for making on-site measurements of heavy metals content at the 10-ppm level; the design of a portable system is conceivable in the medium term.In this work we first show that the femtosecond regime presents no advantages with respect to the standard nanosecond regime for our issue. Then we implement an advanced treatment of LIBS spectra by chemometric techniques whose performances significantly improve the results of qualitative and quantitative analyses of soils samples.Dans les domaines de l'analyse, du contrôle et de la mesure physique, le laser constitue un outil métrologique particulièrement puissant et polyvalent, capable d'apporter des réponses concrètes à des problématiques variées, y compris d'ordre sociétal. Parmi ces dernières, la contamination des sites et des sols par les métaux lourds est un enjeu de santé publique important qui requiert de disposer de moyens de mesure adaptés aux réglementations existantes et suffisamment souples d'utilisation. Technique rapide et ne nécessitant pas de préparation de l'échantillon, la spectroscopie sur plasma induit par laser (LIBS) présente des avantages très intéressants pour réaliser des mesures sur site de la teneur en métaux lourds à l'échelle de la dizaine de ppm; la conception d'un appareil portable à moyen terme est envisageable.Dans cette thèse nous montrons d'abord que le régime femtoseconde ne présente pas d'avantages par rapport au régime nanoseconde standard pour notre problématique. Ensuite nous mettons en œuvre un traitement avancé des spectres LIBS par des méthodes chimiométriques dont les performances améliorent sensiblement les résultats des analyses qualitatives et quantitatives d'échantillons de sols