pinecone/core-2020-05-10-deduplication huggingface dataset:
Specificity determinants for the two tRNA substrates of the cyclodipeptide synthase AlbC from Streptomyces noursei

International audienceCyclodipeptide synthases (CDPSs) use two aminoacyl-tRNA substrates in a sequential ping-pong mechanism to form a cyclodipeptide. The crystal structures of three CDPSs have been determined and all show a Rossmann-fold domain similar to the catalytic domain of class-I aminoacyl-tRNA synthetases (aaRSs). Structural features and mutational analyses however suggest that CDPSs and aaRSs interact differently with their tRNA substrates. We used AlbC from Streptomyces noursei that mainly produces cyclo(l-Phe-l-Leu) to investigate the interaction of a CDPS with its substrates. We demonstrate that Phe-tRNA Phe is the first substrate accommodated by AlbC. Its binding to AlbC is dependent on basic residues located in the helix ␣4 that form a basic patch at the surface of the protein. AlbC does not use all of the Leu-tRNA Leu isoacceptors as a second substrate. We show that the G 1-C 72 pair of the acceptor stem is essential for the recognition of the second substrate. Substitution of D163 located in the loop ␣6–␣7 or D205 located in the loop ␤6–␣8 affected Leu-tRNA Leu isoacceptors specificity, suggesting the involvement of these residues in the binding of the second substrate. This is the first demonstration that the two substrates of CDPSs are accommodated in different binding sites
Radiative heat transfer from a black body to dielectric nanoparticles

International audienceHeating of dielectric nanoparticles by black-body radiation is investigated by using molecular-dynamics simulation. The thermal interaction with the radiation is modeled by coupling the ions with a random electric field and including a radiation reaction force. This approach shows that the heat is absorbed by the polariton mode. Its subsequent redistribution among other vibration modes strongly depends on the particle size and on temperature.We observe energy trapping in a finite subset of vibrational mode
Intensive thermodynamic parameters in nonequilibrium systems

16 pages (version publiée)International audienceConsidering a broad class of steady-state nonequilibrium systems for which some additive quantities are conserved by the dynamics, we introduce from a statistical approach intensive thermodynamic parameters (ITPs) conjugated to the conserved quantities. This definition does not require any detailed balance relation to be fulfilled. Rather, the system has to satisfy a general additivity property, which holds in most of the models usually considered in the literature, including those described by a matrix product ansatz with finite matrices. The main property of these ITPs is to take equal values in two subsystems, making them a powerful tool to describe nonequilibrium phase coexistence, as illustrated on different models. We finally discuss the issue of the equalization of ITPs when two different systems are put into contact. This issue is closely related to the possibility of measuring the ITPs using a small auxiliary system, in the same way as temperature is measured with a thermometer, and points at one of the major difficulties of nonequilibrium statistical mechanics. In addition, an efficient alternative determination, based on the measure of fluctuations, is also proposed and illustrated
A secondary resonance in Mercury's rotation

International audienceThe resonant rotation of Mercury can be modelised by a kernel model on which we can add perturbations. Our kernel model is a two-degree of freedom one written in Hamiltonian formalism. For this kernel, we consider that Mercury is solid and rotates on a Keplerian orbit. By introducing the perturbations due to the other planets of the Solar System, it appears that, in a particular case, our slow degree of freedom may enter into a 1:1 resonance with the Great Inequality of Jupiter and Saturn. Actually, as the moments of inertia of Mercury are still poorly known, this phenomenon cannot be excluded
LISACode : A scientific simulator of LISA

International audienceA new LISA simulator (LISACode) is presented. Its ambition is to achieve a new degree of sophistication allowing to map, as closely as possible, the impact of the different sub-systems on the measurements. LISACode is not a detailed simulator at the engineering level but rather a tool whose purpose is to bridge the gap between the basic principles of LISA and a future, sophisticated end-to-end simulator. This is achieved by introducing, in a realistic manner, most of the ingredients that will influence LISA's sensitivity as well as the application of TDI combinations. Many user-defined parameters allow the code to study different configurations of LISA thus helping to finalize the definition of the detector. Another important use of LISACode is in generating time series for data analysis developments
The HARPS search for southern extra-solar planets V. A 14 Earth-masses planet orbiting HD 4308

Accepted for publication in A&A (8 pages, 7 figures)International audienceWe present here the discovery and characterisation of a very light planet around HD4308. The planet orbits its star in 15.56 days. The circular radial-velocity variation presents a tiny semi-amplitude of 4.1 m/s that corresponds to a planetary minimum mass m2sin(i)=14.1 Earth masses. The planet was unveiled by high-precision radial-velocity measurements obtained with the HARPS spectrograph on the ESO 3.6-m telescope. The radial-velocity residuals around the Keplerian solution are 1.3 m/s, demonstrating the very high quality of the HARPS measurements. Activity and bisector indicators exclude any significant perturbations of stellar intrinsic origin, which supports the planetary interpretation. Contrary to most planet-host stars, HD4308 has a marked sub-solar metallicity ([Fe/H]=-0.31), raising the possibility that very light planet occurrence might show a different coupling with the parent star\'s metallicity than do giant gaseous extra-solar planets. Together with Neptune-mass planets close to their parent stars, the new planet occupies a position in the mass-separation parameter space that is constraining for planet-formation and evolution theories. The question of whether they can be considered as residuals of evaporated gaseous giant planets, ice giants, or super-earth planets is discussed in the context of the latest core-accretion models
Relaxation and emission of Bragg-mode and cavity-mode polaritons in a ZnO microcavity at room temperature

International audienceThe strong coupling regime in a ZnO microcavity is investigated through room temperature photoluminescence and reflectivity experiments. The simultaneous strong coupling of excitons to the cavity mode and the first Bragg mode is demonstrated at room temperature. The polariton relaxation is followed as a function of the excitation density. A relaxation bottleneck is evidenced in the Bragg-mode polariton branch. It is partly broken under strong excitation density, so that the emission from this branch dominates the one from cavity-mode polaritons
Quantitative textural analysis of Vulcanian pyroclasts (Montserrat) using multi-scale X-ray computed microtomography: comparison with results from 2D image analysis

International audienceX-ray computed microtomography (μCT) was carried out on four pyroclasts from the 1997 Vulcanian explosions of Soufrière Hills Volcano, Montserrat. Three-dimensional data from multiple image stacks with different spatial resolutions (0.37, 4-8, and 17.4 μm px−1) were combined to generate size distributions of vesicles, inter-vesicle throats, crystals, and Fe-Ti oxides over a 3.4-860-μm size range, and to compare the results with those obtained by 2D image analysis on the same samples. Qualitative textural observations are in good agreement with those made in 2D, but μCT provides better resolution of textural features and spatial relationships. Calculation of size distributions requires automated decoalescence of the connected vesicle network. Problems related to this process, in part due to the high porosity of pumice, result in potential artefacts in the calculated size distributions, which are discussed in detail. The main modes of the 3D vesicle volume distributions are systematically shifted to larger sizes compared with those of the 2D distributions. Sample total vesicularities obtained in 3D are within 13 vol.% of those found in 2D, and within 10 vol.% of those measured by He-pycnometry. Total number densities of vesicles and Fe-Ti oxides from the two methods are consistent only to the first order, 3D values ranging from 37% to 309% of those in 2D. Vesicle coalescence, investigated by examining inter-vesicle throat size distributions, occurred in all pyroclasts between neighbouring vesicles of many sizes. The larger the vesicle, the more connected it is
A conservative adaptive wavelet method for the shallow-water equations on staggered grids

International audienceThis article presents the first dynamically adaptive wavelet method for the shallow-water equations (SWEs) on a staggered hexagonal C-grid. Pressure is located at the centres of the primal grid (hexagons) and velocity is located at the edges of the dual grid (triangles). Distinct bi-orthogonal second-generation wavelet transforms are developed for the pressure and the velocity. These wavelet transforms are based on second-order accurate interpolation and restriction operators. Together with compatible restriction operators for the mass flux and Bernoulli function, they ensure that mass is conserved and that there is no numerical generation of vorticity when solving the SWEs. Grid refinement relies on appropriate thresholding of the wavelet coefficients, allowing error control in both the quasi-geostrophic and inertia-gravity wave regimes. The SWEs are discretized on the dynamically adapted multiscale grid using a mass and potential-enstrophy-conserving finite-difference scheme. The conservation and error control properties of the method are verified by applying it to a propagating inertia-gravity wave packet and to rotating shallow-water turbulence. Significant savings in the number of degrees of freedom are achieved even in the case of rotating shallow-water turbulence. The numerical dissipation introduced by the grid adaptation is quantified. The method has been designed so it can be extended easily to the icosahedral subdivision of the sphere. This work provides important building blocks for the development of fully adaptive general circulation models. © 2013 Royal Meteorological Society
Modeling of Venus, Mars, and Titan

International audienceIncreased computer capacity has made it possible to model the global plasma and neutral dynamics near Venus, Mars and Saturn's moon Titan. The plasma interactions at Venus, Mars, and Titan are similar because each possess a substantial atmosphere but lacks a global internally generated magnetic field. In this article three self-consistent plasma models are described: the magnetohydrodynamic (MHD) model, the hybrid model and the fully kinetic plasma model. Chamberlain and Monte Carlo models of the Martian exosphere are also described. In particular, we describe the pros and cons of each model approach. Results from simulations are presented to demonstrate the ability of the models to capture the known plasma and neutral dynamics near the three objects
Agroclimatic conditions in China under climate change scenarios projected from regional climate models

The recent warming trends have led to rising concerns on how the changing climate has been altering and will continue to alter agroclimatic conditions in China. In this study, high resolution climate scenarios from regional climate models (RCMs) are used as input to the agro-ecological zones (AEZ) model for China and to compute a comprehensive set of agroclimatic indicators. Uncertainties in the projected impacts of climate change on agroclimatic conditions are also discussed with respect to (1) RCM outputs for different emission scenarios, and (2) differences in projections obtained from two different RCMs under the same emission scenario. The results indicate a significant extension of the crop growing period in tandem with the rising temperatures during the crop growing season, which may lead to increase in multi-cropping opportunities at high latitudes and thus advance the total potential output per unit of cropland. However, the results show that the Southwest China will experience a significant reduction in the value of humidity index, implying severe challenges for future agricultural development in the region. Spatially explicit patterns of changes in future agroclimatic conditions, as revealed in this study, can be beneficial for policy-makers, farming communities and other stakeholders to assess risk factors, design adaptation and mitigation measures, and improve management practices at the local to regional scales
Predicting experimentally stable allotropes: Instability of penta-graphene

International audienceIn recent years, a plethora of theoretical carbon allotropes have been proposed, none of which has been experimentally isolated. We discuss here criteria that should be met for a new phase to be potentially experimentally viable. We take as examples Haeckelites, 2D networks of sp2-carbon–containing pentagons and heptagons, and “penta-graphene,” consisting of a layer of pentagons constructed from a mixture of sp2- and sp3-coordinated carbon atoms. In 2D projection appearing as the “Cairo pattern,” penta-graphene is elegant and aesthetically pleasing. However, we dispute the author’s claims of its potential stability and experimental relevanc
Large shocks in the volatility of the Dow Jones Industrial Average index: 1928–2013

International audienceWe determine the events that cause large shocks in volatility of the DJIA index over the period 1928–2013, using a new semi-parametric test based on conditional heteroscedasticity models. We find that these large shocks can be associated with particular events (financial crashes, elections, wars, monetary policies, etc.). We show that some shocks are not identified as extraordinary movements by the investors due to their occurring during high volatility episodes, especially the 1929–1934, 1937–1938 and 2007–2011 periods
The rheological transition in plagioclase-bearing magmas

International audienceVolcanological processes, such as melt segregation, ascent and eruption are directly dependent on the rheological behaviour of magmatic suspensions. An increase of the crystal fraction of the suspension leads to the formation of a solid particle network which abruptly increases magma viscosity. The crystal fraction at which this rheological transition occurs depends on parameters such as the strain rate and the size, shape and sorting of particles. To determine the influence of the crystal shape on the rheological transition, suspensions of plagioclase, a representative anisometric crystal, have been investigated at high temperatures and pressures. Synthetic suspensions with crystal fractions (ϕs) ranging from 0.38 to 0.75 were deformed both in compression and torsion in a Paterson apparatus at 300 MPa, 900 and 800 °C, and for strain rates between 1.0 x 10-5 s-1 and 1.0 x 10-3 s-1. All suspensions exhibit a non-Newtonian shear thinning rheological behaviour. The experimental results, coupled with existing data and models at low crystal fractions (ϕs < 0.3), allow several rheological domains to be identified, from steady-state flow to strain weakening, each characterized by a specific microstructure. In particular, a progressive evolution from a pervasive to a strain partitioning fabric is found when increasing the crystal fraction. Our results highlight the influence of both the strain rate and the shape of crystals on the rheological behaviour of magmas. During crystallization, magmatic suspensions of anisometric minerals such as plagioclase would develop a solid particle network earlier (ϕs ~ 0.3) than suspensions of isometric minerals (ϕs ~ 0.5). Our study shows that localization of strain early in the crystallization history of mushy zones in the magma chamber, near the conduit margins and at the base of lava flows would facilitate the mobilisation, the transfer and the final emplacement at the surface of highly viscous, feldspar-rich magmas
Developing cell therapy techniques for respiratory disease: intratracheal delivery of genetically engineered stem cells in a murine model of airway injury.
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Stem cell therapy for respiratory disease.

International audienceInterest has increased in the use of exogenous stem cells to optimize lung repair and serve as carriers of a therapeutic gene for genetic airway diseases such as cystic fibrosis. We investigated the survival and engraftment of exogenous stem cells after intratracheal injection, in a murine model of acute epithelial airway injury already used in gene therapy experiments on cystic fibrosis. Embryonic stem cells and mesenchymal stem cells were intratracheally injected 24 hr after 2% polidocanol administration, when epithelial airway injury was maximal. Stem cells were transfected with reporter genes immediately before administration. Reporter gene expression was analyzed in trachea-lungs and bronchoalveolar lavage, using nonfluorescence, quantitative, and sensitive methods. Enzyme-linked immunosorbent assay quantitative results showed that 0.4 to 5.5% of stem cells survived in the injured airway. Importantly, no stem cells survived in healthy airway or in the epithelial lining fluid. Using 5-bromo-4-chloro-3-indolyl-beta-d-galactopyranoside staining, transduced mesenchymal stem cells were detected in injured trachea and bronchi lumen. When the epithelium was spontaneously regenerated, the in vivo amount of engrafted mesenchymal stem cells from cell lines decreased dramatically. No stem cells from primary culture were located within the lungs at 7 days. This study demonstrated the feasibility of intratracheal cell delivery for airway diseases with acute epithelial injury
Ionic Liquids Made with Dimethylcarbonate: Solvents as well as Boosted Basic Catalysts for the Michael Reaction

Abstract: This article describes 1) a methodology for the green synthesis of a class of methylammonium and methylphosphonium ionic liquids (ILs), 2) how to tune their acid–base properties by anion exchange, 3) complete neat-phase NMR spectroscopic characterisation of these materials and 4) their application as active organocatalysts for base-promoted carbon– carbon bond-forming reactions. Methylation of tertiary amines or phosphines with dimethyl carbonate leads to the formation of the halogen-free methyl-onium methyl carbonate salts, and these can be easily anion-exchanged to yield a range of derivatives with different melting points, solubility, acid–base properties, stability and viscosity. Treatment with water, in particular, yields bicarbonate-exchanged liquid onium salts. These proved strongly basic, enough to efficiently catalyse the Michael reaction; experiments suggest that in these systems the bicarbonate basicity is boosted by two orders of magnitude with respect to inorganic bicarbonate salts. These basic ionic liquids used in catalytic amounts are better even than traditional strong organic bases. The present work also introduces neat NMR spectroscopy of the ionic liquids as a probe for solute– solvent interactions as well as a tool for characterisation. Our studies show that high catalytic efficacy of functional ionic liquids can be achieved by integrating their green synthesis, along with a fine-tuning of their structure. Demonstrating that ionic liquid solvents can be made by a truly green procedure, and that their properties and reactivity can be tailored to the point of bridging the gap between their use as solvents and as catalysts. Keywords: dimethyl carbonate · green chemistry · ionic liquids · Michael addition · NMR spectroscop
Human resource management and productivity in the "Trust Game Corporation"

Contemporary production activity is crucially determined by the performance of complex tasks with the characteristics of corporate trust games. In this paper, we outline a productivity paradox showing that, under reasonable conditions, the non cooperative solution, that yields a suboptimal firm output, is the equilibrium of corporate trust games when relational preferences are not sufficiently high. We show that tournaments and steeper pay for performance schemes may crowd out cooperation in presence of players preferences for relational goods. These findings help to explain firm investment in workers' relationships and the puzzle on the less than expected use of such schemes
Economic growth and poverty traps in sub-Saharan Africa: The role of education and TFP shocks

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Research in Economics\ud
Volume 67, Issue 3, September 2013, Pages 226-242\ud
Economic growth and poverty traps in sub-Saharan Africa: The role of education and TFP shocks  (Article)\ud
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Cazzavillan, G.a , Donadelli, M.b , Persha, L.c   \ud
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a  Department of Economics, Ca' Foscari University of Venice, Venice, Italy\ud
b  Department of Economics and Finance, LUISS Guido Carli, Viale Romania 32, 00197 Rome, Italy\ud
c  Department of Geography, University of North Carolina at Chapel Hill, NC, United States\ud
View references (37)\ud
Abstract\ud
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This paper investigates the ". education-total factor productivity trade-off" in explaining income per worker differences between sub-Saharan (unlucky) and G7 (lucky) economies. First, we examine the dynamics of average years of schooling (i.e. education), capital per worker, income per worker, and total factor productivity (TFP) across sub-Saharan and G7 countries. We confirm that physical capital and education levels partially explain income per worker differences between lucky and unlucky economies. Second, we undertake a novel examination of the impact of technology shocks on income per worker, with the goal of understanding the role of technology variation in causing cross-country income per worker differences, and as a potential contributor to overall slow growth in the sub-Saharan region. In a vector autoregressive (VAR) framework, we show that the impact of ". ad hoc" TFP shocks on income per worker is larger in unlucky economies than in lucky ones. We observe that average TFP volatility in the "unlucky world" is eight times higher than in the "G7 world". We argue that the order of magnitude of the impact heavily depends on the level of the TFP volatility. Last, we suggest that the documented differences in the amount of physical capital and in the productivity of human capital between these two regions add conceptual support for the existence of poverty traps for sub-Saharan Africa