When dunes move together, structure of deserts emerges

Crescent shaped barchan dunes are highly mobile dunes that are usually presented as a prototypical model of sand dunes. Although they have been theoretically shown to be unstable when considered separately, it is well known that they form large assemblies in desert. Collisions of dunes have been proposed as a mechanism to redistribute sand between dunes and prevent the formation of heavily large dunes, resulting in a stabilizing effect in the context of a dense barchan field. Yet, no models are able to explain the spatial structures of dunes observed in deserts. Here, we use an agent-based model with elementary rules of sand redistribution during collisions to access the full dynamics of very large barchan dune fields. Consequently, stationnary, out of equilibrium states emerge. Trigging the dune field density by a sand load/lost ratio, we show that large dune fields exhibit two assymtotic regimes: a dilute regime, where sand dune nucleation is needed to maintain a dune field, and a dense regime, where dune collisions allow to stabilize the whole dune field. In this dense regime, spatial structures form: the dune field is structured in narrow corridors of dunes extending in the wind direction, as observed in dense barchan deserts

Principal Geodesic Analysis of Merge Trees (and Persistence Diagrams)

This paper presents a computational framework for the Principal Geodesic Analysis of merge trees (MT-PGA), a novel adaptation of the celebrated Principal Component Analysis (PCA) framework [87] to the Wasserstein metric space of merge trees [92]. We formulate MT-PGA computation as a constrained optimization problem, aiming at adjusting a basis of orthogonal geodesic axes, while minimizing a fitting energy. We introduce an efficient, iterative algorithm which exploits shared-memory parallelism, as well as an analytic expression of the fitting energy gradient, to ensure fast iterations. Our approach also trivially extends to extremum persistence diagrams. Extensive experiments on public ensembles demonstrate the efficiency of our approach - with MT-PGA computations in the orders of minutes for the largest examples. We show the utility of our contributions by extending to merge trees two typical PCA applications. First, we apply MT-PGA to data reduction and reliably compress merge trees by concisely representing them by their first coordinates in the MT-PGA basis. Second, we present a dimensionality reduction framework exploiting the first two directions of the MT-PGA basis to generate two-dimensional layouts of the ensemble. We augment these layouts with persistence correlation views, enabling global and local visual inspections of the feature variability in the ensemble. In both applications, quantitative experiments assess the relevance of our framework. Finally, we provide a lightweight C++ implementation that can be used to reproduce our results

Determining Eccentricities of Transiting Planets: A Divide in the Mass-Period Plane

The two dominant features in the distribution of orbital parameters for close-in exoplanets are the prevalence of circular orbits for very short periods, and the observation that planets on closer orbits tend to be heavier. The first feature is interpreted as a signature of tidal evolution, while the origin of the second, a "mass-period relation" for hot Jupiters, is not understood. In this paper we re-consider the ensemble properties of transiting exoplanets with well-measured parameters, focussing on orbital eccentricity and the mass-period relation. We recalculate the constraints on eccentricity in a homogeneous way, using new radial-velocity data, with particular attention to statistical biases. We find that planets on circular orbits gather in a well-defined region of the mass-period plane, close to the minimum period for any given mass. Exceptions to this pattern reported in the Literature can be attributed to statistical biases. The ensemble data is compatible with classical tide theory with orbital circularisation caused by tides raised on the planet, and suggest that tidal circularisation and the stopping mechanisms for close-in planets are closely related to each other. The position mass-period relation is compatible with a relation between a planet's Hill radius and its present orbit.Comment: 8 pages, to be published in MNRA

Spatial structuring and size selection as collective behaviours in an agent-based model for barchan fields.

International audienceIn order to test parameters of the peculiar dynamics occurring in barchan fields, and compute statistical analysis over large numbers of dunes, we build and study an agent-based model, which includes the well-known physics of an isolated barchan, and observations of interactions between dunes. We showed in a previous study that such a model, where barchans interact through short-range sand recapture and collisions, reproduces the peculiar behaviours of real fields, namely its spatial structuring along the wind direction, and the size selection by the local density. In this paper we focus on the mechanisms that drives these features. In particular, we show that eolian remote sand transfer between dunes ensures that a dense field structures itself into a very heterogeneous pattern, which alternates dense and diluted stripes in the wind direction. In these very dense clusters of dunes, the accumulation of collisions leads to the local emergence of a new size for the dunes

Antimicrobial activities of novel bipyridine compounds produced by a new strain of Saccharothrix isolated from Saharan soil

The actinobacterium strain ABH26 closely related to Saccharothrix xinjiangensis, isolated from an Algerian Saharan soil sample, exhibited highly antagonist activity against Gram-positive bacteria, yeasts and filamentous fungi. Its ability to produce antimicrobial compounds was investigated using several solid culture media. The highest antimicrobial activity was obtained on Bennett medium. The antibiotics secreted by strain ABH26 on Bennett medium were extracted by methanol and purified by reverse-phase HPLC using a C18 column. The chemical structures of the compounds were determined after spectroscopic (1H NMR, 13C NMR, 1H-1H COSY and 1H-13C HMBC spectra), and spectrometric (mass spectrum) analyses. Two new cyanogriside antibiotics named cyanogriside I (1) and cyanogriside J (2), were characterized along with three known caerulomycins, caerulomycin A (3), caerulomycin F (4) and caerulomycinonitrile (5). This is the first report of cyanogrisides and caerulomycins production by a member of the Saccharothrix genus. The minimum inhibitory concentrations (MIC) of these antibiotics were determined against pathogenic microorganisms

Streptomyces sp. AT37 isolated from a Saharan soil produces a furanone derivative active against multidrug-resistant Staphylococcus aureus

A novel actinobacterium strain, named AT37, showed a strong activity against some multidrug-resistant Staphylococcus aureus, including methicillin-resistant S. aureus MRSA ATCC 43300, other clinical isolates of MRSA and vancomycin resistant S. aureus VRSA S1. The strain AT37 was isolated from a Saharan soil by a dilution agar plating method using chitin-vitamin agar medium supplemented with rifampicin. The morphological and chemical studies indicated that this strain belonged to the genus Streptomyces. Its 16S rRNA gene sequence was determined and a database search indicated that it was closely associated with the type strain of Streptomyces novaecaesareae NBRC 13368T with 99.6% of similarity. However, the comparison of the morphological and the physiological characteristics of the strain with those of the nearest species showed significant differences. The strain AT37 secreted the antibiotic optimally during mid-stationary phase of growth. One active compound (AT37-1) was extracted from the culture broth with dichloromethane, separated on silica gel plates and purified by HPLC. Based on spectroscopic analysis of UV-Visible, infrared, and 1H and 13C NMR spectra and spectrometric analysis, the chemical structure of the compound AT37-1 was identified as 5-[(5E,7E,11E)-2,10-dihydroxy-9,11-dimethyl-5,7,11-tridecatrien-1-yl]-2-hydroxy-2-(1-hydroxyethyl)-4-methyl-3(2H)-furanone. Minimum inhibitory concentrations and minimum biofilm inhibitory concentration (MBIC50) of this compound showed significant activity against multidrug-resistant S. aureus with 15-30 and 10-15 μg/mL, respectively

Oligomycins A and E, major bioactive secondary metabolites produced by Streptomyces sp. strain HG29 isolated from a Saharan soil

An actinobacterial strain, HG29, with potent activity against pathogenic, toxigenic and phytopathogenic fungi was isolated from a Saharan soil sample of Algeria. On the basis of morphological and chemotaxonomic characteristics, the strain was classified in the genus Streptomyces. Analysis of the 16S rRNA gene sequence showed a similarity level of 99.3% with Streptomyces gancidicus NBRC 15412T. The comparison of its cultural and physiological characteristics with this species revealed significant differences. Moreover, the phylogenetic tree showed that strain HG29 forms a distinct phyletic line within the genus Streptomyces. Production of antifungal activity was investigated by following kinetics in shake broth. The highest antifungal activity was obtained after five days of fermentation, and in the dichloromethane extract. Two active compounds, NK1 and NK2, were purified by HPLC using a C18 column. Their chemical structures were identified through nuclear magnetic resonance experiments and mass spectrometry as oligomycins E and A, respectively, which have not been reported to be produced by S. gancidicus. The two bioactive compounds exhibited significant antifungal activity in vitro, showing minimal inhibitory concentrations (MICs) values between 2 and 75μg/mL

New insights into the origin of the B genome of hexaploid wheat: Evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides

<p>Abstract</p> <p>Background</p> <p>Several studies suggested that the diploid ancestor of the B genome of tetraploid and hexaploid wheat species belongs to the <it>Sitopsis </it>section, having <it>Aegilops speltoides </it>(SS, 2n = 14) as the closest identified relative. However molecular relationships based on genomic sequence comparison, including both coding and non-coding DNA, have never been investigated. In an attempt to clarify these relationships, we compared, in this study, sequences of the Storage Protein Activator (SPA) locus region of the S genome of <it>Ae. speltoides </it>(2n = 14) to that of the A, B and D genomes co-resident in the hexaploid wheat species (<it>Triticum aestivum, AABBDD</it>, 2n = 42).</p> <p>Results</p> <p>Four BAC clones, spanning the SPA locus of respectively the A, B, D and S genomes, were isolated and sequenced. Orthologous genomic regions were identified as delimited by shared non-transposable elements and non-coding sequences surrounding the SPA gene and correspond to 35 268, 22 739, 43 397 and 53 919 bp for the A, B, D and S genomes, respectively. Sequence length discrepancies within and outside the SPA orthologous regions are the result of non-shared transposable elements (TE) insertions, all of which inserted after the progenitors of the four genomes divergence.</p> <p>Conclusion</p> <p>On the basis of conserved sequence length as well as identity of the shared non-TE regions and the SPA coding sequence, <it>Ae speltoides </it>appears to be more evolutionary related to the B genome of <it>T. aestivum </it>than the A and D genomes. However, the differential insertions of TEs, none of which are conserved between the two genomes led to the conclusion that the S genome of <it>Ae. speltoides </it>has diverged very early from the progenitor of the B genome which remains to be identified.</p

The SuperCam Instrument Suite on the Mars 2020 Rover: Science Objectives and Mast-Unit Description

On the NASA 2020 rover mission to Jezero crater, the remote determination of the texture, mineralogy and chemistry of rocks is essential to quickly and thoroughly characterize an area and to optimize the selection of samples for return to Earth. As part of the Perseverance payload, SuperCam is a suite of five techniques that provide critical and complementary observations via Laser-Induced Breakdown Spectroscopy (LIBS), Time-Resolved Raman and Luminescence (TRR/L), visible and near-infrared spectroscopy (VISIR), high-resolution color imaging (RMI), and acoustic recording (MIC). SuperCam operates at remote distances, primarily 2-7 m, while providing data at sub-mm to mm scales. We report on SuperCam's science objectives in the context of the Mars 2020 mission goals and ways the different techniques can address these questions. The instrument is made up of three separate subsystems: the Mast Unit is designed and built in France; the Body Unit is provided by the United States; the calibration target holder is contributed by Spain, and the targets themselves by the entire science team. This publication focuses on the design, development, and tests of the Mast Unit; companion papers describe the other units. The goal of this work is to provide an understanding of the technical choices made, the constraints that were imposed, and ultimately the validated performance of the flight model as it leaves Earth, and it will serve as the foundation for Mars operations and future processing of the data.In France was provided by the Centre National d'Etudes Spatiales (CNES). Human resources were provided in part by the Centre National de la Recherche Scientifique (CNRS) and universities. Funding was provided in the US by NASA's Mars Exploration Program. Some funding of data analyses at Los Alamos National Laboratory (LANL) was provided by laboratory-directed research and development funds

Analyse d'ensembles de descripteurs topologiques

Topological Data Analysis (TDA) forms a collection of tools to generically, robustly and efficiently reveal implicit structural patterns hidden in complex datasets. These tools allow to compute a topological representation for each member of an ensemble of datasets by encoding its main features of interest in a concise and informative manner. A major challenge consists then in designing analysis tools for such ensembles of topological descriptors. Several tools have been well studied for persistence diagrams, one of the most used descriptor. However, they suffer from a lack of specificity, which can yield identical data representations for significantly distinct datasets. In this thesis, we aimed at developing more advanced analysis tools for ensembles of topological descriptors, capable of tackling the lack of discriminability of persistence diagrams and going beyond what was already available for these objects. First, we adapt to merge trees, descriptors having a better specificity, the tools already available for persistence diagrams such as distances, geodesics and barycenters. Then, we want to go beyond this notion of average being the barycenter in order to study the variability within an ensemble of topological descriptors. We then adapt the Principal Component Analysis framework to persistence diagrams and merge trees, resulting in a dimensionality reduction method that indicates which structures in the ensemble are most responsible for the variability. However, this framework allows only to detect linear patterns of variability in the ensemble. To tackle this we propose to generalize this framework to Auto-Encoder in order to detect non-linear, i.e. more complex, patterns in an ensemble of merge trees or persistence diagrams. Specifically, we propose a new neural network layer capable of processing natively these objects. We present applications of all this work in feature tracking in a time-varying ensemble, data reduction to compress an ensemble of topological descriptors, clustering to form homogeneous groups in an ensemble, and dimensionality reduction to create a visual map indicating how the data are organized regarding each other in the ensemble.L'analyse topologique de données forme un ensemble d'outils visant à révéler de manière générique, robuste et efficace les caractéristiques structurelles implicites cachées dans des ensembles de données complexes. Ces outils permettent de calculer une représentation topologique pour chaque membre d'un ensemble de données en encodant ses principales caractéristiques d'intérêt de manière concise et informative. Un défi majeur consiste ensuite à concevoir des outils d'analyse pour de tels ensembles de descripteurs topologiques. Plusieurs outils ont été bien étudiées pour les diagrammes de persistance, l'un des descripteurs les plus utilisés. Cependant, ils souffrent d'un manque de spécificité, pouvant donner des représentations de données identiques pour des données significativement différentes. Dans cette thèse, nous avons cherché à développer des outils d'analyse plus avancés pour des ensembles de descripteurs topologiques, capables de résoudre le problème de discriminabilité des diagrammes de persistance et d'aller au-delà de ce qui était déjà disponible pour ces objets. Tout d'abord nous adaptons aux arbres de fusion, descripteurs ayant une meilleur spécificité, les outils déjà disponibles pour les diagrammes de persistance tels que le calcul de distances, géodésiques et barycentres. Ensuite, nous souhaitons aller au-delà de cette simple notion de moyenne qu'est le barycentre pour étudier la variabilité au sein d'un ensemble de descripteurs topologiques. Nous adaptons alors le cadre de l'Analyse en Composantes Principales aux diagrammes de persistance et les arbres de fusion, résultant une méthode de réduction de dimensions qui indique quelles structures dans l'ensemble sont les plus responsables de la variabilité. Cependant, ce cadre permet uniquement de détecter des tendances linéaires de variabilité dans l'ensemble. Pour résoudre ce problème, nous proposons de généraliser ce cadre aux Auto-Encodeurs afin de détecter des motifs non linéaires, i.e. plus complexes, dans un ensembles d'arbres de fusions ou de diagrammes de persistance. Plus précisément, nous proposons une nouvelle couche de réseau de neurones capable de traiter nativement ces objets. Nous présentons des applications de ces travaux pour le suivi de structures dans un ensemble de données variant dans le temps pour la réduction de données pour compresser un ensemble de descripteurs topologiques, dans le partitionnement pour former des groupes homogènes dans un ensemble, et dans la réduction de dimensions pour créer une carte visuelle indiquant comment les données sont organisées les unes par rapport aux autres dans l'ensemble