Mapping natural habitats using remote sensing and Sparse partial least square discriminant analysis

This work presents a novel approach for mapping the spatial distribution of natural habitats in the "Foothills of Larzac" Natura 2000 listed site located in a French Mediterranean Biogeographical Region. Sparse Partial Least Square Discriminant Analysis was used to analyze two RapidEye datasets (June 2009 and July 2010) with the purpose of choosing the most informative spectral, textural and thematic variables that allow discriminating the classes of habitats. The Sparse Partial Least Square Discriminant Analysis selected relevant and stable variables for the discrimination of habitat classes that could be linked to ecological or biophysical characteristics. It also gave insight into the similarities and the differences between habitats classes with comparable physiognomic characteristics. The highest user accuracy was obtained for dry improved grasslands (u=91.97%) followed by riparian ash woods (u= 88.38%). These results are very encouraging given that these two classes were identified in Annex 1 of the EC Habitats Directive as of community interest. Due to limited data input requirements and to its computational efficiency, the approach developed in this paper is a good alternative to other types of variable selection approaches in a supervised classification framework and can be easily transferred to other Natura 2000 sites

L'intégration du principe de continuité écologique dans les schémas de cohérence territoriale (SCOT) Analyse de 21 expériences de SCOT

Cette étude s'inscrit dans le cadre des travaux du Comité opérationnel Trame verte et bleue mis en place pour réfléchir aux modalités de mise en place d'une Trame verte et bleue en France, mesure inscrite dans le projet de loi Grenelle 2. À travers un recueil d'expériences de vingt et un schémas de cohérence territoriale (SCOT), l'étude analyse les différentes méthodes d'identification des trames vertes et bleues, les modalités d'intégration de cet outil d'aménagement dans les projets de territoire et les démarches participatives mises en place pour faire adhérer les différents acteurs socio-économiques au projet. L'étude est ponctuée de recommandations pour intégrer la Trame verte et bleue dans un SCOT dans le respect des orientations nationales. / This study is part of the work for the operational committee (COMOP) in charge of formulating the rules and recommendations for implementation of the French ecological network created by the "Grenelle II" law. Based on 21 local development plans (SCOT), the study analyses the different methods used to position local ecological networks, how this planning tool is used in the local development plans and how participative approaches have been developed to ensure that local stakeholders support the project. The study has produced recommendations on how to integrate an ecological network in a SCOT in compliance with national guidelines

"Bacchus" Methodological approach for vineyard inventory and management. Chap.4: Textural and structural analysis

Ce chapitre présente les méthodes qui ont été développées dans le projet Bacchus pour la détection et la caractérisation des parcelles de vigne en imagerie aérienne en se basant sur leur structure. Une analyse texturale est d'abord mise en oeuvre, et complétée par l'introduction de contraintes de régularité des contours pour améliorer la segmentation. Finalement, les parcelles issues de ces premières étapes sont vérifiées et caractérisées au moyen d'une analyse de leur spectre de Fourier. Les résultats obtenus sur diverses zones d'étude du projet Bacchus sont présentés et discutés. / This chapter presents the methodologies that have been developed during the Bacchus project concerning the automatic detection and characterisation of vineyard plots in satellite and aerial images, based on their structural properties. First, a textural analysis has been used. Then shape regularity constraints have been introduced to improve the image segmentation. Finally, the vineyard plots issued from these previous steps are checked and characterised using a Fourier spectrum analysis. Results on various study areas of the Bacchus project are presented and discussed

An automatized frequency analysis for vine plot detection and delineation in remote sensing

La mise à disposition d'un outil automatique pour la détection et la caractérisation des parcelles de vigne est un besoin très important d'un point de vue gestion. Un procédé automatique récursif basé sur l'analyse fréquentielle (utilisation de la Transformée de Fourier et des filtres de Gabor) a été développé pour y répondre. Il permet la détermination des contours de parcelle et une estimation précise de leur inter-rang et de leur orientation. Dans l'optique d'une application à grande échelle, les tests et la validation ont été menés à partir de données standard de télédétection à très haute résolution.. Environ 89% des parcelles sont détectées qui correspondent à plus de 84 % de la surface viticole, et 64% d'entre elles avec des contours corrects. L'orientation des rangs et la largeur d'inter-rang sont obtenus avec une précision de 1 degré et 3,3 cm respectivement. / The availability of an automatic tool for vine plot detection, delineation, and characterization would be very useful for management purposes. An automatic and recursive process using frequency analysis (with Fourier transform and Gabor filters) has been developed to meet this need. This results in the determination of vine plot boundary and accurate estimation of interrow width and row orientation. To foster large-scale applications, tests and validation have been carried out on standard very high spatial resolution remotely sensed data. About 89% of vine plots are detected corresponding to more than 84% of vineyard area, and 64% of them have correct boundaries. Compared with precise on-screen measurements, vine row orientation and interrow width are estimated with an accuracy of 1°and 3.3 cm, respectively

Gap, a mycobacterial specific integral membrane protein, is required for glycolipid transport to the cell surface

The cell envelope of mycobacteria is a complex multilaminar structure that protects the cell from stresses encountered in the environment, and plays an important role against the bactericidal activity of immune system cells. The outermost layer of the mycobacterial envelope typically contains species-specific glycolipids. Depending on the mycobacterial species, the major glycolipid localized at the surface can be either a phenolglycolipid or a peptidoglycolipid (GPL). Currently, the mechanism of how these glycolipids are addressed to the cell surface is not understood. In this study, by using a transposon library of Mycobacterium smegmatis and a simple dye assay, six genes involved in GPLs synthesis have been characterized. All of these genes are clustered in a single genomic region of approximately 60 kb. We show by biochemical analyses that two non-ribosomal peptide synthetases, a polyketide synthase, a methyltransferase and a member of the MmpL family are required for the biosynthesis of the GPLs backbone. Furthermore, we demonstrate that a small integral membrane protein of 272 amino acids named Gap (gap: GPL addressing protein) is specifically required for the transport of the GPLs to the cell surface. This protein is predicted to contain six transmembrane segments and possesses homologues across the mycobacterial genus, thus delineating a new protein family. This Gap family represents a new paradigm for the transport of small molecules across the mycobacterial envelope, a critical determinant of mycobacterial virulence

Assessing the role of EO in biodiversity monitoring: options for integrating in-situ observations with EO within the context of the EBONE concept

The European Biodiversity Observation Network (EBONE) is a European contribution on terrestrial monitoring to GEO BON, the Group on Earth Observations Biodiversity Observation Network. EBONE’s aims are to develop a system of biodiversity observation at regional, national and European levels by assessing existing approaches in terms of their validity and applicability starting in Europe, then expanding to regions in Africa. The objective of EBONE is to deliver: 1. A sound scientific basis for the production of statistical estimates of stock and change of key indicators; 2. The development of a system for estimating past changes and forecasting and testing policy options and management strategies for threatened ecosystems and species; 3. A proposal for a cost-effective biodiversity monitoring system. There is a consensus that Earth Observation (EO) has a role to play in monitoring biodiversity. With its capacity to observe detailed spatial patterns and variability across large areas at regular intervals, our instinct suggests that EO could deliver the type of spatial and temporal coverage that is beyond reach with in-situ efforts. Furthermore, when considering the emerging networks of in-situ observations, the prospect of enhancing the quality of the information whilst reducing cost through integration is compelling. This report gives a realistic assessment of the role of EO in biodiversity monitoring and the options for integrating in-situ observations with EO within the context of the EBONE concept (cfr. EBONE-ID1.4). The assessment is mainly based on a set of targeted pilot studies. Building on this assessment, the report then presents a series of recommendations on the best options for using EO in an effective, consistent and sustainable biodiversity monitoring scheme. The issues that we faced were many: 1. Integration can be interpreted in different ways. One possible interpretation is: the combined use of independent data sets to deliver a different but improved data set; another is: the use of one data set to complement another dataset. 2. The targeted improvement will vary with stakeholder group: some will seek for more efficiency, others for more reliable estimates (accuracy and/or precision); others for more detail in space and/or time or more of everything. 3. Integration requires a link between the datasets (EO and in-situ). The strength of the link between reflected electromagnetic radiation and the habitats and their biodiversity observed in-situ is function of many variables, for example: the spatial scale of the observations; timing of the observations; the adopted nomenclature for classification; the complexity of the landscape in terms of composition, spatial structure and the physical environment; the habitat and land cover types under consideration. 4. The type of the EO data available varies (function of e.g. budget, size and location of region, cloudiness, national and/or international investment in airborne campaigns or space technology) which determines its capability to deliver the required output. EO and in-situ could be combined in different ways, depending on the type of integration we wanted to achieve and the targeted improvement. We aimed for an improvement in accuracy (i.e. the reduction in error of our indicator estimate calculated for an environmental zone). Furthermore, EO would also provide the spatial patterns for correlated in-situ data. EBONE in its initial development, focused on three main indicators covering: (i) the extent and change of habitats of European interest in the context of a general habitat assessment; (ii) abundance and distribution of selected species (birds, butterflies and plants); and (iii) fragmentation of natural and semi-natural areas. For habitat extent, we decided that it did not matter how in-situ was integrated with EO as long as we could demonstrate that acceptable accuracies could be achieved and the precision could consistently be improved. The nomenclature used to map habitats in-situ was the General Habitat Classification. We considered the following options where the EO and in-situ play different roles: using in-situ samples to re-calibrate a habitat map independently derived from EO; improving the accuracy of in-situ sampled habitat statistics, by post-stratification with correlated EO data; and using in-situ samples to train the classification of EO data into habitat types where the EO data delivers full coverage or a larger number of samples. For some of the above cases we also considered the impact that the sampling strategy employed to deliver the samples would have on the accuracy and precision achieved. Restricted access to European wide species data prevented work on the indicator ‘abundance and distribution of species’. With respect to the indicator ‘fragmentation’, we investigated ways of delivering EO derived measures of habitat patterns that are meaningful to sampled in-situ observations

Cell surface properties of two differently virulent strains of Acinetobacter baumannii isolated from a patient

The aim of this study was to unravel, by focusing on cell surface properties, the underlying virulence factors contributing to the difference in the pathogenicity observed in two Acinetobacter baumannii strains isolated from the same patient. The two strains were phenotypically different: (i) a mucoid strain (AB-M), highly virulent in a mouse model of pneumonia, and (ii) a nonmucoid strain (AB-NM), moderately virulent in the same model. The study of the cell surface properties included the microbial adhesion to solvents method, the measurement of the electrophoretic mobility of bacteria, the analysis of biofilm formation by calcofluor white staining, the adherence to silicone catheters, and scanning electron microscopy. The AB-NM strain was more hydrophobic, more adherent to silicone catheters, and produced more biofilm than the AB-M strain. Scanning electron microscopy showed bacterial cells with a rough surface and the formation of large cell clusters for AB-NM whereas the AB-M strain had a smooth surfa..., Le but de cette etude était d’étudier, en se focalisant sur les propriétés de surface des bactéries, des caractères potentiellement impliqués dans la différence de pouvoir pathogène de deux souches d’Acinetobacter baumannii isolées chez un même patient. Ces souches étaient phénotypiquement différentes : une souche mucoïde (AB-M) caractérisée par un pouvoir pathogène élevé dans un modèle expérimental murin de pneumopathie, et une souche non mucoïde (AB-NM), plus faiblement pathogène dans le même modèle. L’étude des propriétés de surface a utilisé la méthode d’adhésion des bactéries aux solvants, la mesure de la mobilité électrophorétique des bactéries, l’analyse de la formation de biofilm par marquage au calcofluor, l’adhésion à des cathéters en silicone, et la microscopie électronique à balayage. La souche AB-NM est apparue plus hydrophobe, plus adhérente aux cathéters, et plus productrice de biofilm que la souche AB-M. L’observation en microscopie électronique à balayage a montré des bactéries à surface ..

Tomato protoplast DNA transformation: physical linkage and recombination of exogenous DNA sequences

Tomato protoplasts have been transformed with plasmid DNA's, containing a chimeric kanamycin resistance gene and putative tomato origins of replication. A calcium phosphate-DNA mediated transformation procedure was employed in combination with either polyethylene glycol or polyvinyl alcohol. There were no indications that the tomato DNA inserts conferred autonomous replication on the plasmids. Instead, Southern blot hybridization analysis of seven kanamycin resistant calli revealed the presence of at least one kanamycin resistance locus per transformant integrated in the tomato nuclear DNA. Generally one to three truncated plasmid copies were found integrated into the tomato nuclear DNA, often physically linked to each other. For one transformant we have been able to use the bacterial ampicillin resistance marker of the vector plasmid pUC9 to 'rescue' a recombinant plasmid from the tomato genome. Analysis of the foreign sequences included in the rescued plasmid showed that integration had occurred in a non-repetitive DNA region. Calf-thymus DNA, used as a carrier in transformation procedure, was found to be covalently linked to plasmid DNA sequences in the genomic DNA of one transformant. A model is presented describing the fate of exogenously added DNA during the transformation of a plant cell. The results are discussed in reference to the possibility of isolating DNA sequences responsible for autonomous replication in tomato.

First in-human radiation dosimetry of (68)Ga-NODAGA-RGDyK.

Integrin-targeting radiopharmaceuticals have potential broad applications, spanning from cancer theranostics to cardiovascular diseases. We have previously reported preclinical dosimetry results of (68)Ga-NODAGA-RGDyK in mice. This study presents the first human dosimetry of (68)Ga-NODAGA-RGDyK in the five consecutive patients included in a clinical imaging protocol of carotid atherosclerotic plaques. Five male patients underwent whole-body time-of-flight (TOF) PET/CT scans 10, 60 and 120 min after tracer injection (200 MBq). Quantification of (68)Ga activity concentration was first validated by a phantom study. To be used as input in OLINDA/EXM, time-activity curves were derived from manually drawn regions of interest over the following organs: brain, thyroid, lungs, heart, liver, spleen, stomach, kidneys, red marrow, pancreas, small intestine, colon, urinary bladder and whole body. A separate dosimetric analysis was performed for the choroid plexuses. Female dosimetry was extrapolated from male data. Effective doses (EDs) were estimated according to both ICRP60 and ICRP103 assuming 30-min and 1-h voiding cycles. The body regions receiving the highest dose were urinary bladder, kidneys and choroid plexuses. For a 30-min voiding cycle, the EDs were 15.7 and 16.5 μSv/MBq according to ICRP60 and ICRP103, respectively. The extrapolation to female dosimetry resulted in organ absorbed doses 17% higher than those of male patients, on average. The 1-h voiding cycle extrapolation resulted in EDs of 19.3 and 19.8 μSv/MBq according to ICRP60 and ICRP103, respectively. A comparison is made with previous mouse dosimetry and with other human studies employing different RGD-based radiopharmaceuticals. According to ICRP60/ICRP103 recommendations, an injection of 200 MBq (68)Ga-NODAGA-RGDyK leads to an ED in man of 3.86/3.92 mSv. For future therapeutic applications, specific attention should be directed to delivered dose to kidneys and potentially also to the choroid plexuses. Clinical trial.gov, NCT01608516