Clay Minerals Mapping from Imaging Spectroscopy

Mapping subsurface clay minerals is an important issue because they have particular behaviors in terms of mechanics and hydrology that directly affects assets laid at the surface such as buildings, houses, etc. They have a direct impact in ground stability due to their swelling capacities, constraining infiltration processes during flooding, especially when moisture is important. So detecting and characterizing clay mineral in soils serve urban planning issues and improve the risk reduction by predicting impacts of subsidence on houses and infrastructures. High-resolution clay maps are thus needed with accurate indications on mineral species and abundances. Clay minerals, known as phyllosilicates, are divided in three main species: smectite, illite, and kaolinite. The smectite group highly contributes to the swelling behavior of soils, and because geotechnical soil analyses are expensive and time-consuming, it is urgent to develop new approaches for mapping clays’ spatial distribution by using new technologies, e.g., ground spectrometer or remote hyperspectral cameras [0.4–2.5 μm]. These technics constitute efficient alternatives to conventional methods. We present in this chapter some recent results we got for characterizing clay species and their abundances from spectrometry, used either from a ground spectrometer or from hyperspectral cameras

Monitoring Crop Evapotranspiration and Crop Coefficients over an Almond and Pistachio Orchard Throughout Remote Sensing

In California, water is a perennial concern. As competition for water resources increases due to growth in population, California’s tree nut farmers are committed to improving the efficiency of water used for food production. There is an imminent need to have reliable methods that provide information about the temporal and spatial variability of crop water requirements, which allow farmers to make irrigation decisions at field scale. This study focuses on estimating the actual evapotranspiration and crop coefficients of an almond and pistachio orchard located in Central Valley (California) during an entire growing season by combining a simple crop evapotranspiration model with remote sensing data. A dataset of the vegetation index NDVI derived from Landsat-8 was used to facilitate the estimation of the basal crop coefficient (Kcb), or potential crop water use. The soil water evaporation coefficient (Ke) was measured from microlysimeters. The water stress coefficient (Ks) was derived from airborne remotely sensed canopy thermal-based methods, using seasonal regressions between the crop water stress index (CWSI) and stem water potential (Ψstem). These regressions were statistically-significant for both crops, indicating clear seasonal differences in pistachios, but not in almonds. In almonds, the estimated maximum Kcb values ranged between 1.05 to 0.90, while for pistachios, it ranged between 0.89 to 0.80. The model indicated a difference of 97 mm in transpiration over the season between both crops. Soil evaporation accounted for an average of 16% and 13% of the total actual evapotranspiration for almonds and pistachios, respectively. Verification of the model-based daily crop evapotranspiration estimates was done using eddy-covariance and surface renewal data collected in the same orchards, yielding an R2 ≥ 0.7 and average root mean square errors (RMSE) of 0.74 and 0.91 mm·day−1 for almond and pistachio, respectively. It is concluded that the combination of crop evapotranspiration models with remotely-sensed data is helpful for upscaling irrigation information from plant to field scale and thus may be used by farmers for making day-to-day irrigation management decisions

Biodisponibilité des polluants du sol : définition, caractérisation et utilisation potentielle dans la gestion des sites et sols pollués

National audienceL'effet toxique d'un polluant du sol vis-à-vis des organismes sera fonction de la concentration totale de ce polluant dans le sol et de sa biodisponibilité. Ce dernier paramètre définit la fraction d'un contaminant qui sera réellement absorbée par un organisme. De nombreux travaux issus de la littérature internationale insistent sur l'importance de considérer la biodisponibilité d'un polluant en vue d'en évaluer l'impact réel sur un organisme. L'essentiel de ces travaux portent sur les végétaux (on parle alors de phytodisponibilité) ou les microorganismes du sol. Ces dernières années, des recherches ont également été menées pour estimer la biodisponibilité des polluants pour l'Homme via l'ingestion de terre contaminée, une des voies d'exposition majeure pour l'évaluation du risque dans ce domaine. Toutefois, en France, l'application de ce concept est relativement limitée. Ceci conduit à une estimation conservatoire de l'exposition humaine aux contaminants pour la voie " ingestion de terre ". L'objectif de cette communication est de définir la notion de biodisponibilité orale d'un polluant pour l'Homme et de présenter les méthodes de mesure disponibles pour caractériser chacun de ces paramètres. Ensuite, les possibilités et les limites d'intégration de ces notions dans la gestion des sites et sols pollués sont abordées

Development of air and dust sampling methods for quantitative measurements of polybromated diphenyl ethers (PBDEs) in offices

International audienc

Monitoring crop evapotranspiration and crop coefficients over an almond and pistachio orchard throughout remote sensing

In California, water is a perennial concern. As competition for water resources increases due to growth in population, California’s tree nut farmers are committed to improving the efficiency of water used for food production. There is an imminent need to have reliable methods that provide information about the temporal and spatial variability of crop water requirements, which allow farmers to make irrigation decisions at field scale. This study focuses on estimating the actual evapotranspiration and crop coefficients of an almond and pistachio orchard located in Central Valley (California) during an entire growing season by combining a simple crop evapotranspiration model with remote sensing data. A dataset of the vegetation index NDVI derived from Landsat-8 was used to facilitate the estimation of the basal crop coefficient (Kcb), or potential crop water use. The soil water evaporation coefficient (Ke) was measured from microlysimeters. The water stress coefficient (Ks) was derived from airborne remotely sensed canopy thermal-based methods, using seasonal regressions between the crop water stress index (CWSI) and stem water potential (Ψstem). These regressions were statistically-significant for both crops, indicating clear seasonal differences in pistachios, but not in almonds. In almonds, the estimated maximum Kcb values ranged between 1.05 to 0.90, while for pistachios, it ranged between 0.89 to 0.80. The model indicated a difference of 97 mm in transpiration over the season between both crops. Soil evaporation accounted for an average of 16% and 13% of the total actual evapotranspiration for almonds and pistachios, respectively. Verification of the model-based daily crop evapotranspiration estimates was done using eddy-covariance and surface renewal data collected in the same orchards, yielding an R2 ≥ 0.7 and average root mean square errors (RMSE) of 0.74 and 0.91 mm·day−1 for almond and pistachio, respectively. It is concluded that the combination of crop evapotranspiration models with remotely-sensed data is helpful for upscaling irrigation information from plant to field scale and thus may be used by farmers for making day-to-day irrigation management decisions.info:eu-repo/semantics/publishedVersio

The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium.

In animals and plants, the H3K9me3 and H3K27me3 chromatin silencing marks are deposited by different protein machineries. H3K9me3 is catalyzed by the SET-domain SU(VAR)3-9 enzymes, while H3K27me3 is catalyzed by the SET-domain Enhancer-of-zeste enzymes, which are the catalytic subunits of Polycomb Repressive Complex 2 (PRC2). Here, we show that the Enhancer-of-zeste-like protein Ezl1 from the unicellular eukaryote Paramecium tetraurelia, which exhibits significant sequence and structural similarities with human EZH2, catalyzes methylation of histone H3 in vitro and in vivo with an apparent specificity toward K9 and K27. We find that H3K9me3 and H3K27me3 co-occur at multiple families of transposable elements in an Ezl1-dependent manner. We demonstrate that loss of these histone marks results in global transcriptional hyperactivation of transposable elements with modest effects on protein-coding gene expression. Our study suggests that although often considered functionally distinct, H3K9me3 and H3K27me3 may share a common evolutionary history as well as a common ancestral role in silencing transposable elements

Detection of individual trees in urban alignment from airborne data and T contextual information: A marked point process approach

With the current expansion of cities, urban trees have an important role for preserving the health of its in- habitants. With their evapotranspiration, they reduce the urban heat island phenomenon, by trapping CO2 emission, improve air quality. In particular, street trees or alignment trees, create shade on the road network, are structuring elements of the cities and decorate the roads. Street trees are also subject to specific conditions as they have little space for growth, are pruned and can be affected by the spread of diseases in single-species plantations. Thus, their detection, identification and monitoring are necessary. In this study, an approach is proposed for mapping these trees that are characteristic of the urban environment. Three areas of the city of Toulouse in the south of France are studied. Airborne hyperspectral data and a Digital Surface Model (DSM) for high vegetation detection are used. Then, contextual information is used to identify the street trees. Indeed, Geographic Information System (GIS) data are considered to detect the vegetation canopies close to the streets. Afterwards, individual street tree crown delineation is carried out by modeling the discriminative contextual features of individual street trees (hypotheses of small angle between the trees and similar heights) based on Marked Point Process (MPP). Compared to a baseline individual tree crown delineation method based on region growing, our method logically provides the best results with F-score values of 91%, 75% and 85% against 70%, 41% and 20% for the three studied areas respectively. Our approach mainly succeeds in identifying the street trees. In addition, the contribution of the angle, the height and the GIS data in the street tree mapping has been studied. The results encourage the use of the angle, the height and the GIS data together. However, with only the angle and the height, the results are similar to those obtained with the inclusion of the GIS data for the first and the second study cases with F-score values of 88%, 79% and 62% against 91%, 75% and 85% for the three study cases respectively. Finally, it is shown that the GIS data only is not sufficient

Clinical and molecular characterisation of KCNT1-related severe early onset epilepsy

Objective: To characterise the phenotypic spectrum, molecular genetic findings and functional consequences of pathogenic variants in early onset KCNT1-epilepsy. Methods: We identified a cohort of 31 patients with epilepsy of infancy with migrating focal seizures (EIMFS) and screened for variants in KCNT1 using direct Sanger sequencing, a multiple gene next generation sequencing panel and whole exome sequencing. Additional patients with non-EIMFS early onset epilepsy in whom we identified KCNT1 variants on local diagnostic multiple gene panel testing were also included. Where possible, we performed homology modelling to predict putative effects of variants on protein structure and function. We undertook electrophysiological assessment of mutant KCNT1 channels in a Xenopus oocyte model system. Results: We identified pathogenic variants in KCNT1 in 12 patients, four of which are novel. Most variants occurred de novo. Ten had a clinical diagnosis of EIMFS and the other two presented with early onset severe nocturnal frontal lobe seizures. Three patients had a trial of quinidine with good clinical response in one. Computational modelling analysis implicates abnormal pore function (F346L) and impaired tetramer formation (F502V) as putative disease mechanisms. All evaluated KCNT1 variants resulted in marked gain-of-function, with significantly increased channel amplitude and variable blockade by quinidine. Conclusions: Gain-of-function KCNT1 pathogenic variants cause a spectrum of severe focal epilepsies with onset in early infancy. Currently, genotype-phenotype correlations are unclear, though clinical outcome is poor for the majority of cases. Further elucidation of disease mechanisms may facilitate the development of targeted treatments, much needed for this pharmacoresistant genetic epilepsy

Symptom-based stratification of patients with primary Sjögren's syndrome: multi-dimensional characterisation of international observational cohorts and reanalyses of randomised clinical trials

Background Heterogeneity is a major obstacle to developing effective treatments for patients with primary Sjögren's syndrome. We aimed to develop a robust method for stratification, exploiting heterogeneity in patient-reported symptoms, and to relate these differences to pathobiology and therapeutic response. Methods We did hierarchical cluster analysis using five common symptoms associated with primary Sjögren's syndrome (pain, fatigue, dryness, anxiety, and depression), followed by multinomial logistic regression to identify subgroups in the UK Primary Sjögren's Syndrome Registry (UKPSSR). We assessed clinical and biological differences between these subgroups, including transcriptional differences in peripheral blood. Patients from two independent validation cohorts in Norway and France were used to confirm patient stratification. Data from two phase 3 clinical trials were similarly stratified to assess the differences between subgroups in treatment response to hydroxychloroquine and rituximab. Findings In the UKPSSR cohort (n=608), we identified four subgroups: Low symptom burden (LSB), high symptom burden (HSB), dryness dominant with fatigue (DDF), and pain dominant with fatigue (PDF). Significant differences in peripheral blood lymphocyte counts, anti-SSA and anti-SSB antibody positivity, as well as serum IgG, κ-free light chain, β2-microglobulin, and CXCL13 concentrations were observed between these subgroups, along with differentially expressed transcriptomic modules in peripheral blood. Similar findings were observed in the independent validation cohorts (n=396). Reanalysis of trial data stratifying patients into these subgroups suggested a treatment effect with hydroxychloroquine in the HSB subgroup and with rituximab in the DDF subgroup compared with placebo. Interpretation Stratification on the basis of patient-reported symptoms of patients with primary Sjögren's syndrome revealed distinct pathobiological endotypes with distinct responses to immunomodulatory treatments. Our data have important implications for clinical management, trial design, and therapeutic development. Similar stratification approaches might be useful for patients with other chronic immune-mediated diseases. Funding UK Medical Research Council, British Sjogren's Syndrome Association, French Ministry of Health, Arthritis Research UK, Foundation for Research in Rheumatology