pinecone/core-2020-05-10-deduplication huggingface dataset:
Triadin deletion induces impaired skeletal muscle function.

International audienceTriadin is a multiple proteins family, some isoforms being involved in muscle excitation-contraction coupling, and some having still unknown functions. To obtain clues on triadin functions, we engineered a triadin knock-out mouse line and characterized the physiological effect of triadin ablation on skeletal muscle function. These mice presented a reduced muscle strength, which seemed not to alter their survival and has been characterized in the present work. We first checked in these mice the expression level of the different proteins involved in calcium homeostasis and observed in fast muscles an increase in expression of dihydropyridine receptor, with a large reduction in calsequestrin expression. Electron microscopy analysis of KO muscles morphology demonstrated the presence of triads in abnormal orientation and a reduction in the sarcoplasmic reticulum terminal cisternae volume. Using calcium imaging on cultured myotubes, we observed a reduction in the total amount of calcium stored in the sarcoplasmic reticulum. Physiological studies have been performed to evaluate the influence of triadin deletion on skeletal muscle function. Muscle strength has been measured both on the whole animal model, using hang test or electrical stimulation combined with NMR analysis and strength measurement, or on isolated muscle using electrical stimulation. All the results obtained demonstrate an important reduction in muscle strength, indicating that triadin plays an essential role in skeletal muscle function and in skeletal muscle structure. These results indicate that triadin alteration leads to the development of a myopathy, which could be studied using this new animal model
CRISPI: a CRISPR Interactive database

This is a pre-copy-editing, author-produced PDF of an article accepted for publication in Bioinformatics following peer review. The definitive publisher-authenticated version [Rousseau, C., Gonnet, M., Le Romancer, M., Nicolas, J. (2009). CRISPI: a CRISPR Interactive database.Bioinformatics. 25(24):3317-3318] is available online at: http://bioinformatics.oxfordjournals.org/.International audienceThe CRISPR genomic structures (Clustered Regularly Interspaced Short Palindromic Repeats) form a family of repeats that is largely present in archaea and frequent in bacteria. On the basis of a formal model of CRISPR using very few parameters, a systematic study of all their occurrences in all available genomes of Archaea and Bacteria has been carried out. This has resulted in a relational database, CRISPI, which also includes a complete repertory of associated CRISPR-associated genes (CAS). A userfriendly web interface with many graphical tools and functions allows users to extract results, find CRISPR in personal sequences or calculate sequence similarity with spacers
On-line monitoring of fluence distributions and imaging of scanning ion beams

Expérience GANILIn this paper we describe the design of an ion beam monitor developed to control irradiations of biological samples with ions at GANIL (Grand Accélérateur National d'Ions Lourds). This device can be used as an on-line monitor to provide transverse fluence distributions for active scanning ion irradiations. It can also be used as an interceptive beam imager to provide beam profiles or fluence depth distributions. A prototype of the monitor has been tested at GANIL with five different ion beams, having intensities from 104 to 109ions per second. Real time transverse fluence distributions have been obtained with a 1mm spatial resolution
The antiferromagnetic transition for the square-lattice Potts model

We solve the antiferromagnetic transition for the Q-state Potts model (defined geometrically for Q generic) on the square lattice. The solution is based on a detailed analysis of the Bethe ansatz equations (which involve staggered source terms) and on extensive numerical diagonalization of transfer matrices. It involves subtle distinctions between the loop/cluster version of the model, and the associated RSOS and (twisted) vertex models. The latter's continuum limit involves two bosons, one which is compact and twisted, and the other which is not, with a total central charge c=2-6/t, for sqrt(Q)=2cos(pi/t). The non-compact boson contributes a continuum component to the spectrum of critical exponents. For Q generic, these properties are shared by the Potts model. For Q a Beraha number [Q = 4 cos^2(pi/n) with n integer] the two-boson theory is truncated and becomes essentially Z_{n-2} parafermions. Moreover, the vertex model, and, for Q generic, the Potts model, exhibit a first-order critical point on the transition line, i.e., the critical point is also the locus of level crossings where the derivatives of the free energy are discontinuous. In that sense, the thermal exponent of the Potts model is generically nu=1/2. Things are profoundly different for Q a Beraha number, where the transition is second order, with nu=(t-2)/2 determined by the psi_1 parafermion. As one enters the adjacant Berker-Kadanoff phase, the model flows, for t odd, to a minimal model of CFT with c=1-6/t(t-1), while for t even it becomes massive. This provides a physical realization of a flow conjectured by Fateev and Zamolodchikov in the context of Z_N integrable perturbations. Finally, we argue that the antiferromagnetic transition occurs as well on other two-dimensional lattices
Nuclear fission time measurements as a function of excitation energy - A crystal blocking experiment

CASFission times of lead and uranium nuclei have been measured at GANIL by the crystal blocking method. The inverse kinematics was used. Fragment atomic numbers and total excitation energies were determined. For data analysis, full Monte-Carlo trajectory calculations were used to simulate the blocking patterns. The effect of post-scission emissions, included in our simulations, is discussed. At high excitation energies, the scissions occur dominantly at times shorter than 10−19 s, whereas at low excitation energies (E∗<250–300 MeV), scissions occurring at much longer times with sizeable probabilities are observed both for uranium and for lead nuclei, leading to average scission times much longer than those inferred from pre-scission emission
Cosmological implications from the observed properties of CMB.

Observations of the cosmic microwave background represent a remarkable source of information for modern cosmology. Besides providing impressive support for the Big Bang model itself, they quantify the overall framework, or background, for the formation of large scale structure. Most exciting, however, is the potential access these observations give to the first moments of cosmic history and to the physics reigning at such exceptionally high energies, which will remain beyond the reach of the laboratory in any foreseeable future. Upcoming experiments, such as the Planck mission, thus offer a window onto the Physics of the Third Millennium
Planetary space weather: scientific aspects and future perspectives

International audienceIn this paper, we review the scientific aspects of planetary space weather at different regions of our Solar System, performing a comparative planetology analysis that includes a direct reference to the circum-terrestrial case. Through an interdisciplinary analysis of existing results based both on observational data and theoretical models, we review the nature of the interactions between the environment of a Solar System body other than the Earth and the impinging plasma/radiation, and we offer some considerations related to the planning of future space observations. We highlight the importance of such comparative studies for data interpretations in the context of future space missions (e.g. ESA JUICE; ESA/JAXA BEPI COLOMBO). Moreover, we discuss how the study of planetary space weather can provide feedback for better understanding the traditional circum-terrestrial space weather. Finally, a strategy for future global investigations related to this thematic is proposed
Impact of the New South Wales fires during October 2013 on regional air quality in eastern Australia

International audienceSmoke plumes from fires contain atmospheric pollutants that can be transported to populated areas and effect regional air quality. In this paper, the characteristics and impact of the fire plumes from a major fire event that occurred in October 2013 (17–26) in the New South Wales (NSW) in Australia, near the populated areas of Sydney and Wollongong, are studied. Measurements from the Fourier Transform InfraRed (FTIR) spectrometer located at the University of Wollongong allowed a calculation of specific emission factors (EFs) in terms of grams per kilogram of dry fuel burned: 1640 g kg−1 of carbon dioxide; 107 g kg−1 of carbon monoxide; 7.8 g kg−1 of methane; and 0.16 g kg−1 of nitrous oxide. These EFs have then been used to calculate daily fire emissions for the NSW fire event using the APIFLAME emissions' model, leading to an increase of 54% of CO emitted compared to calculations with EFs from Akagi et al. (2011), widely used in the literature
Lateral diffusivity coefficients from the dynamics of a SF6 patch in a coastal environment

International audienceThe dispersion of a patch of the tracer sulfur hexafluoride (SF6) is used to assess the lateral diffusivity in the coastal waters of the western part of the Gulf of Lion (GoL), northwestern Mediterranean Sea, during the Latex10 experiment (September 2010). Immediately after the release, the spreading of the patch is associated with a strong decrease of the SF6 concentrations due to the gas exchange from the ocean to the atmosphere. This has been accurately quantified, evidencing the impact of the strong wind conditions during the first days of this campaign. Few days after the release, as the atmospheric loss of SF6 decreased, lateral diffusivity coefficient at spatial scales of 10 km has been computed using two approaches. First, the evolution of the patch with time was combined with a diffusion-strain model to obtain estimates of the strain rate (γ = 2.5 10- 6 s- 1) and of the lateral diffusivity coefficient (Kh = 23.2 m2s− 1). Second, a steady state model was applied, showing Kh values similar to the previous method after a period of adjustment between 2 and 4.5 days. This implies that after such period, our computation of Kh becomes insensitive to the inclusion of further straining of the patch. Analysis of sea surface temperature satellite imagery shows the presence of a strong front in the study area. The front clearly affected the dynamics within the region and thus the temporal evolution of the patch. Our results are consistent with previous studies in open ocean and demonstrate the success and feasibility of those methods also under small-scale, rapidly-evolving dynamics typical of coastal environments
Rotational non-LTE in HCN in the thermosphere of Titan: Implications for the radiative cooling

International audienceContext. The thermal structure of Titan's thermosphere is determined by the balance between several heating and cooling processes. These processes must be accurately modeled to correctly interpret the available measurements and enhance our understanding of the formation and evolution of this atmosphere. One of the most important thermospheric cooling process for Titan is emission in the HCN rotational band. Aims. We aim to determine the validity of local thermodynamic equilibrium (LTE) for the HCN rotational distribution in the thermosphere of Titan and the impact of its breakdown on the HCN radiative cooling rate in the thermosphere. Methods. A general non-LTE radiative transfer code for rotational lines based on the accelerated lambda iteration (ALI) was used to calculate the excitation of HCN rotational levels in Titan's atmosphere. These level populations were then used to calculate the associated cooling rate. Results. We show that the common assumption in the models of Titan's thermospheric energy balance, namely the LTE distribution of rotational lines of HCN, is generally not valid above about 1100 km, or ~0.025 nbar, which will affect the derived thermospheric cooling rates. The effect of non-LTE is to reduce the cooling rate to 15% of the LTE value at around the exobase altitudes depending on the given density of HCN and collisional partners (N2, CH4, H 2, and electrons). Since collision state-to-state quenching rates of HCN rotational levels are poorly known, a sensitivity analysis of our results to these rates is also presented. © 2013 ESO
Representative elementary volume assessment of three-dimensional x-ray microtomography images of heterogeneous materials: Application to limestones

International audienceOver the last 15 years, x-ray microtomography has become a useful technique to obtain morphological, structural, and topological information on materials. Moreover, these three-dimensional (3D) images can be used as input data to assess certain properties (e.g., permeability) or to simulate phenomena (e.g., transfer properties). In order to capture all the features of interest, high spatial resolution is required. This involves imaging small samples, raising the question of the representativity of the data sets. In this article, we (i) present a methodology to analyze the microstructural properties of complex porous media from 3D images, (ii) assess statistical representative elementary volumes (REVs) for such materials; and (iii) establish criteria to delimit these REVs. In the context of cultural heritage conservation, a statistical study was done on 30 quarry samples for three sorts of stones. We first present the principles of x-ray microtomography experiments and emphasize the care that must be taken in the 3D image segmentation steps. Results show that statistical REVs exist for these media and are reached for the image sizes studied (1300×1300×1000 voxels) for two characteristics: porosity and chord length distributions. Furthermore, the estimators used (porosity, autocorrelation function, and chord length distributions) are sufficiently sensitive to quantitatively distinguish these three porous media from each other. Lastly, this study puts forward criteria based on the above-mentioned estimators to evaluate the REVs. These criteria avoid having to repeat the statistical study for each new material studied. This is particularly relevant to quantitatively monitor the modifications in materials (weathering, deformation . . . ) or to determine the smallest 3D volume for simulation in order to reduce computing time
Beam mismatch effects in Cosmic Microwave Background polarization measurements

International audienceMeasurement of cosmic microwave background polarization is today a major goal of observational cosmology. The level of the signal to measure, however, makes it very sensitive to various systematic effects. In the case of Planck, which measures polarization by combining data from various detectors, the beam asymmetry can induce a temperature leakage or a polarization mode mixing. In this paper, we investigate this effect using realistic simulated beams and propose a first-order method to correct the polarization power spectra for the induced systematic effect
Quantitative 3D Characterization of Cellular Materials: Segmentation and Morphology of Foam

International audienceWood, trabecular bone, coral, liquid foams, grains in polycrystals, igneous rock, and even many types of food share many structural similarities and belong to the general class called cellular materials. The visualization of these materials in 3D has been made possible in the last decades through a variety of imaging techniques including magnetic resonance imaging (MRI), micro-computed X-ray tomography ($\mu$CT), and confocal microscopy. Recent advances in synchrotron-based ultra fast tomography have enabled measurements in liquid foams with thousands of bubbles and time resolutions down to 0.5 seconds. Post-processing techniques have, however, not kept pace and extracting useful physical metrics from such measurements is far from trivial. In this manuscript we present and validate a new, fully-automated method for segmenting and labeling the void space in cellular materials where the walls between cells are not visible or present. The individual cell labeling is based on a new tool, the Gradient Guided Watershed, which, while computationally simple, can be robustly scaled to large data-sets. Specifically we demonstrate the utility of this new method on several liquid foams (with varying liquid fraction and polydispersity) composed of thousands of bubbles, and the subsequent quantitative 3D structural characterization of those foams
A fluid dynamics model of the growth of phototrophic biofilms.

19 pagesInternational audienceA system of nonlinear hyperbolic partial differential equations is derived using mixture theory to model the formation of biofilms. In contrast with most of the existing models, our equations have a finite speed of propagation, without using artificial free boundary conditions. Adapted numerical scheme will be described in detail and several simulations will be presented in one and more space dimensions in the particular case of cyanobacteria biofilms. Besides, the numerical scheme we present is able to deal in a natural and effective way with regions where one of the phases is vanishing
Is cold hardiness size-constrained? A comparative approach in land snails

International audienceBody water is a major element of the cold-hardiness strategies observed in ectothermic animals, in particular in freezing avoidant species for which body ice formation is lethal. Here, we investigate the relationships, in terrestrial snails, between the temperature of crystallisation (Tc) and body water (water mass and water content), shell shape, geographic and climatic distribution, taking into account phylogenetic inertia. Phylogenetic relationships among 31 species from 13 different families of terrestrial Gastropods were studied using 28S rRNA nuclear and COI mitochondrial sequence data, together with species-specific traits. Our results provide evidence for clear relationships between Tc and absolute / relative body water: smaller species with lower water content tended to be characterized by colder temperatures of crystallisation, although some exceptions were noticeable. Environmental conditions do not appear to affect Tc significantly, as well as shell shape which is however correlated with water content. This study confirmed that supercooling ability in land snails is size constrained, with consequences on cold-hardiness strategies
Diffusion Matrices from Algebraic-Geometry Codes with Efficient SIMD Implementation

International audienceThis paper investigates large linear mappings with very good diffusion and efficient software implementations, that can be used as part of a block cipher design. The mappings are derived from linear codes over a small field (typically F 2 4) with a high dimension (typically 16) and a high minimum distance. This results in diffusion matrices with equally high dimension and a large branch number. Because we aim for parameters for which no MDS code is known to exist, we propose to use more flexible algebraic-geometry codes. We present two simple yet efficient algorithms for the software implementation of matrix-vector multi-plication in this context, and derive conditions on the generator matrices of the codes to yield efficient encoders. We then specify an appropriate code and use its automorphisms as well as random sampling to find good such matrices. We provide concrete examples of parameters and implementations, and the corresponding assembly code. We also give performance figures in an example of application which show the interest of our ap-proach
Spectroscopic studies of Ti3+ ions speciation inside MgAl2O4 spinels

International audienceAn electron paramagnetic resonance (EPR) investigation on Ti-doped MgAl2O4 spinels has been made in order to study the Ti3+ sites. The study we present here concerns the angular dependencies of the Ti3+ EPR lines and the variations of the EPR spectra due to a modification of the TiO2 content or of the chemical composition from MgAl2O4 to MgAl4O7 and MgAl6O10. In all the studied samples except one, we observe the presence of both Mn2+ and Ti3+ ions. No correlation was observed between Ti3+ amount and TiO2 content; the titanium ions are located in three different sites: the octahedral B site of the spinel structure; the tetrahedral A site and a last site which remains unclear. On the contrary, the major part of the Mn2+ ions is assumed to be in the tetrahedral A site of the spinel structure and a minor part in the octahedral B site. Our work demonstrates the overall interest of EPR spectroscopy in the study of the paramagnetic optically active ions inside optical materials
Bias in bonding behavior among boron, carbon, and nitrogen atoms in ion implanted a-BN, a-BC, and diamond like carbon films

Cataloged from PDF version of article.In this study, we implanted N + and N 2 + ions into sputter deposited amorphous boron carbide (a-BC) and diamond like carbon (DLC) thin films in an effort to understand the chemical bonding involved and investigate possible phase separation routes in boron carbon nitride (BCN) films. In addition, we investigated the effect of implanted C + ions in sputter deposited amorphous boron nitride (a-BN) films. Implanted ion energies for all ion species were set at 40 KeV. Implanted films were then analyzed using x-ray photoelectron spectroscopy (XPS). The changes in the chemical composition and bonding chemistry due to ion-implantation were examined at different depths of the films using sequential ion-beam etching and high resolution XPS analysis cycles. A comparative analysis has been made with the results from sputter deposited BCN films suggesting that implanted nitrogen and carbon atoms behaved very similar to nitrogen and carbon atoms in sputter deposited BCN films. We found that implanted nitrogen atoms would prefer bonding to carbon atoms in the films only if there is no boron atom in the vicinity or after all available boron atoms have been saturated with nitrogen. Implanted carbon atoms also preferred to either bond with available boron atoms or, more likely bonded with other implanted carbon atoms. These results were also supported by ab-initio density functional theory calculations which indicated that carbon-carbon bonds were energetically preferable to carbon-boron and carbon-nitrogen bonds. © 2011 American Institute of Physics
Floating plant dominance as a stable state

Invasion by mats of free-floating plants is among the most important threats to the functioning and biodiversity of freshwater ecosystems ranging from temperate ponds and ditches to tropical lakes. Dark, anoxic conditions under thick floating-plant cover leave little opportunity for animal or plant life, and they can have large negative impacts on fisheries and navigation in tropical lakes. Here, we demonstrate that floating-plant dominance can be a self-stabilizing ecosystem state, which may explain its notorious persistence in many situations. Our results, based on experiments, field data, and models, represent evidence for alternative domains of attraction in ecosystems. An implication of our findings is that nutrient enrichment reduces the resilience of freshwater systems against a shift to floating-plant dominance. On the other hand, our results also suggest that a single drastic harvest of floating plants can induce a permanent shift to an alternative state dominated by rooted, submerged growth forms