pinecone/core-2020-05-10-deduplication huggingface dataset:
Regulatory RNA at the root of animals: dynamic expression of developmental lincRNAs in the calcisponge Sycon ciliatum

Long non-coding RNAs (lncRNAs) play important regulatory roles during
animal development, and it has been hypothesized that an RNA-based gene
regulation was important for the evolution of developmental complexity
in animals. However, most studies of lncRNA gene regulation have been performed
using model animal species, and very little is known about this type
of gene regulation in non-bilaterians. We have therefore analysed RNA-Seq
data derived from a comprehensive set of embryogenesis stages in the calcareous
sponge Sycon ciliatum and identified hundreds of developmentally
expressed intergenic lncRNAs (lincRNAs) in this species. In situ hybridization
of selected lincRNAs revealed dynamic spatial and temporal expression
during embryonic development. More than 600 lincRNAs constitute integral
parts of differentially expressed gene modules, which also contain known
developmental regulatory genes, e.g. transcription factors and signalling molecules.
This study provides insights into the non-coding gene repertoire of one
of the earliest evolved animal lineages, and suggests that RNA-based gene
regulation was likely present in the last common ancestor of animals
The Dispositional Genome: Primus Inter Pares

According to the proponents of Developmental Systems Theory and the Causal Parity Thesis, the privileging of the genome as “first among equals” with respect to the development of phenotypic traits is more a reflection of our own heuristic prejudice than of ontology - the underlying causal structures responsible for that specified development no more single out the genome as primary than they do other broadly “environmental” factors. Parting with the methodology of the popular responses to the Thesis, this paper offers a novel criterion for ‘causal primacy’, one that is grounded in the ontology of the unique causal role of dispositional properties. This paper argues that, if the genome is conceptualised as realising dispositional properties that are “directed toward” phenotypic traits, the parity of ‘causal roles’ between genetic and extra-genetic factors is no longer apparent, and further, that the causal primacy of the genome is both plausible and defensible
Clonal dynamics and evolution of dormancy in the leafy hepatic Lophozia silvicola

Dead shoots of colonies of a leafy hepatic species, Lophozia silvicola, are replaced by shoots developing from asexual propagules, the gemmae. Observations of two populations of L. silvicola showed a strong decreasing seasonal trend in germinability of the gemmae. We suggest that the non-germinating gemmae enter dormancy, and that the proportion of gemmae entering dormancy is season-specific. We assume that there are two types of gemmae, dormant and non-dormant and that only the dormant gemmae can survive during winter. Using a stochastic individual-based cellular automaton model, we investigated whether selection on season-specific dormancy fraction would lead to a decreasing proportion of germinating gemmae. Thus the germination schedule is the evolving trait in the model. Parameter estimates for the model were based on data collected from a population of L. silvicola in southern Finland over a three-year study period. In the simulations, the germination schedule shaped by evolutionary change was similar to the observed pattern. Thus the modelling results give support to the dormancy hypothesis. The qualitative pattern of decreasing germinability towards the end of the growing season is robust. Quantitative predictions are influenced by changes in parameters; for example, if winter mortality of shoots increases relative to mortality during the growing season, production of an increased fraction of dormant gemmae is favoured, especially at the end of the season
Nitridation of InP(1 0 0) surface studied by synchrotron radiation

International audienceThe nitridation of InP(1 0 0) surfaces has been studied using synchrotron radiation photoemission. The samples were chemically cleaned and then ion bombarded, which cleaned the surface and also induced the formation of metallic indium droplets. The nitridation with a Glow Discharge Cell (GDS) produced indium nitride by reaction with these indium clusters. We used the In 4d and P 2p core levels to monitor the chemical state of the surface and the coverage of the species present. We observed the creation of In-N and P-N bonds while the In-In metallic bonds decrease which confirm the reaction between indium clusters and nitrogen species. A theoretical model based on stacked layers allows us to assert that almost two monolayers of indium nitride are produced. The effect of annealing on the nitridated layers at 450 °C has also been analysed. It appears that this system is stable up to this temperature, well above the congruent evaporation temperature (370 °C) of clean InP(1 0 0): no increase of metallic indium bonds due to decomposition of the substrate is detected as shown in previous works [L. Bideux, Y. Ould-Metidji, B. Gruzza, V. Matolin, Surf. Interface Anal. 34 (2002) 712] studying the InP(1 0 0) surfaces
Impact of climate change on the hydrogeology of two basins in Northern France

International audienceThis study presents an analysis of climate change impacts on the water resources of two basins located in Northern France, by integrating four sources of uncertainty: climate modelling, hydrological modelling, downscaling methods, and emission scenarios. The analysis focused on the evolution of the water budget, the river discharges and piezometric heads. Seven hydrological models were used, from lumped rainfall-discharge to distributed hydrogeological models, and led to quite different estimates of the water balance components. One of the hydrological models, CLSM, was found to be unable to simulate the increased water stress and was thus considered as an outlier even though it gave fair results for the present day compared to observations. Although there were large differences in the results between the models, there was a marked tendency towards a decrease of the water resource in the rivers and aquifers (on average in 2050 about -14% and -2.5 m, respectively), associated with global warming and a reduction in annual precipitation (on average in 2050 +2.1 K and -3%, respectively). The uncertainty associated to climate models was shown to clearly dominate, while the three others were about the same order of magnitude and 3 to 4 times lower. In terms of impact, the results found in this work are rather different from those obtained in a previous study, even though two of the hydrological models and one of the climate models were used in both studies. This emphasizes the need for a survey of the climatic change impact on the water resourc
Influence of thermal fluctuations on the Nernst signal in superconducting (K,Ba)BiO3 single crystals

International audienceWe report on the Nernst effect, specific heat and transportmeasurements performed in high quality (K,Ba)BiO3 single crystals close to optimal doping (Tc ∼ 31 K). We show that a nonzero Nernst effect remains visible well above the upper critical field unambiguously deduced from the onset of the specific heat anomaly. This finite Nernst signal is attributed to fluctuations of the amplitude of the order parameter in a region where the free energy is smaller than kBT . Despite the absence of any vortex liquid phase (and hence of any significant phase fluctuations), the field and temperature dependence of the Nernst coefficient is very similar to the one obtained in electron-doped cuprates
On massless electron limit for a multispecies kinetic system with external magnetic field

We consider a three-dimensional kinetic model for a two species plasma consisting of electrons and ions confined by an external nonconstant magnetic field. Then we derive a kinetic-fluid model when the mass ratio me/mi tends to zero. Each species initially obeys a Vlasov-type equation and the electrostatic coupling follows from a Poisson equation. In our modeling, ions are assumed non-collisional while a Fokker-Planck collision operator is taken into account in the electron equation. As the mass ratio tends to zero we show convergence to a new system where the macroscopic electron density satisfies an anisotropic drift-diffusion equation. To achieve this task, we overcome some specific technical issues of our model such as the strong effect of the magnetic field on electrons and the lack of regularity at the limit. With methods usually adapted to diffusion limit of collisional kinetic equations and including renormalized solutions, relative entropy dissipation and velocity averages, we establish the rigorous derivation of the limit model
Self-Radiolysis of Tritiated Water Stored in Zeolites 4A: Production and Behavior of H 2 and O 2

International audienceRadiolysis of confined water and self-radiolysis of tritiated water give rise to several unanswered questions. To take into account this double specificity, we studied systems of zeolites 4A containing tritiated water at different water loading ratios. Two tritiated waters were synthesized at the volumetric activities of 27 and 60 TBq L −1. For each one, five samples were prepared, differentiated by their water loading ratios, expressed in percentage, close to 4%, 7%, 11%, 14%, and 19%. The study of the radiolysis in those systems revealed a double role of zeolites 4A: first, they increase the decomposition of water. Then they enhance the recombination of the major stable radiolytic products detected. We actually evidenced a total recombi-nation between H 2 and O 2 , which is catalyzed by the zeolites
Origins and processes of groundwater salinization in the urban coastal aquifers of Recife (Pernambuco, Brazil): a multi-isotope approach

International audienceIn the coastal multilayer aquifer system of a highly urbanized southern city (Recife, Brazil), where groundwaters are affected by salinization, a multi-isotope approach (Sr, B, O, H) was used to investigate the sources and processes of salinization. The high diversity of the geological bodies, built since the Atlantic opening during the Cretaceous, highly constrains the heterogeneity of the groundwater chemistry, e.g. Sr isotope ratios, and needs to be integrated to explain the salinization processes and groundwater pathways. A palaeoseawater intrusion, most probably the 120 ky B.P. Pleistocene marine transgression, and cationic exchange are clearly evidenced in the most salinized parts of the Cabo and Beberibe aquifers. All 87Sr/86Sr values are above the past and present-day seawater signatures, meaning that the Sr isotopic signature is altered due to additional Sr inputs from dilution with different freshwaters, and water-rock interactions. Only the Cabo aquifer presents a well-delimitated area of Na-HCO3 water typical of a freshening process. The two deep aquifers also display a broad range of B concentrations and B isotope ratios with values among the highest known to date (63-68.5‰). This suggests multiple sources and processes affecting B behaviour, among which mixing with saline water, B sorption on clays and mixing with wastewater. The highly fractionated B isotopic values were explained by infiltration of relatively salty water with B interacting with clays, pointing out the major role played by (palaeo)-channels for the deep Beberibe aquifer recharge. Based on an increase of salinity at end of the dry season, a present-day seawater intrusion is identified in the surficial Boa Viagem aquifer. Our conceptual model presents a comprehensive understanding of the major groundwater salinization pathways and processes, and should be of benefit for other southern Atlantic coastal aquifers to better address groundwater management issues
Infra-red collision-induced and far-line absorption in dense CO atmospheres

International audienceCollision-induced absorption is of great importance to the overall radiative budget in dense CO-rich atmospheres, but its representation in climate models remains uncertain, mainly due to a lack of accurate experimental and theoretical data. Here we compare several parameterisations of the effect, including a new one that makes use of previously unused measurements in the 1200 to 1800 cm spectral range. We find that a widely used parameterisation strongly overestimates absorption in pure CO atmospheres compared to later results, and propose a new approach that we believe is the most accurate possible given currently available data
Thermal inertia of main belt asteroids smaller than 100 km from IRAS data

International audienceRecent works have shown that the thermal inertia of km-sized near-Earth asteroids (NEAs) is more than two orders of magnitude higher than that of main belt asteroids (MBAs) with sizes (diameters) between 200 and 1,000 km. This confirms the idea that large MBAs, over hundreds millions of years,have developed a fine and thick thermally insulating regolith layer, responsible for the low values of their thermal inertia, whereas km-sized asteroids, having collisional lifetimes of only some millions years, have less regolith, and consequently a larger surface thermal inertia. Because it is believed that regolith on asteroids forms as a result of impact processes, a better knowledge of asteroid thermal inertia values and its correlation with size, taxonomic type, and density can be used as an important constraintfor modeling of impact processes on asteroids. However, our knowledge of asteroids' thermal inertia values is still based on few data points with NEAs covering the size range 0.1-20 km and MBAs that >100 km. Here, we use IRAS infrared measurements to estimate the thermal inertias of MBAs with diameters 100 km and known shapes and spin vector: filling an important size gap between the largest MBAs and the km-sized NEAs. An update to the inverse correlation between thermal inertia and diameter is presented. For some asteroids thermophysical modelling allowed us to discriminate between the two still possible spin vector solutions derived from optical lightcurve inversion. This is important for (720) Bohlinia: our preferred solution was predicted to be the correct one by Vokrouhlicky et al. (2003, Nature 425, 147) just on theoretical grounds
Nutrient dynamics at the sediment-water interface in a Mediterranean lagoon (Thau, France): Influence of biodeposition by shellfish farming activities

International audienceThe Thau Lagoon, a French Mediterranean shallow lagoon, is a site where extensive shellfish farming occurs. The aim of the present work is to evaluate the role of this activity on nutrient exchange at the sediment-water interface in relation to organic matter (OM) sedimentation and degradation. Two stations inside (C5) and outside (C4) of the shellfish farming areas were sampled at three seasons. Porewater chemistry surveys and calculated diffusive fluxes were used to evaluate the trophic status of the Thau lagoon. Quantitative (Particulate Organic Carbon) as well as qualitative OM (Hydrogen Index, Carbohydrates) analyses were performed on sediments to assess OM characteristics. Results emphasized that surficial sediments at C5 are always more enriched in OM. Porewater nutrient concentrations are 10-20 times higher at C5 than at C4. In June 2003, the porewater profiles exhibit a sharp gradient at the bottom waters, indicating a hypereutrophic status, leading to an anoxic crisis
Distributed Authentication in GRID5000

International audienceBetween high-performance clusters and grids appears an inter- mediate infrastructure called cluster grid that corresponds to the interconnection of clusters through the Internet. Cluster grids are not only dedicated to specific applications but should allow the users to execute programs of different natures. This kind of architecture also imposes additional constraints as the geographic extension raises availability and security issues. In this context, authentication is one of the key stone by providing access to the resources. Grid5000 is a french project based on a cluster grid topology. This article expounds and justifies the authentication system used in Grid5000. We first show the limits of classical approaches that are local files and NIS in such configurations. We then propose a scalable alternative based on the LDAP protocol allowing to meet the needs of cluster grids, either in terms of availability, security and performances. Finally, among the various applications that can be executed in the Grid5000 platform, we present μgrid, a minimal middleware used for medical data processing
Impact of gneissic layering and localized incipient melting upon melt flow during experimental deformation of migmatites

International audienceIn this study, we test experimentally the role of compositional layering as a key parameter for controlling melt flow in a natural migmatite during coaxial deformation. We performed in – situ pure-shear experiments on two natural gneisses. The first gneiss is weakly foliated with minerals homogenously distributed. The second gneiss shows a pronounced compositional layering of alternating quartz – feldspar – rich and biotite – muscovite – rich layers. Experimental conditions were selected to obtain homogeneous melt distribution in the homogeneous gneiss and heterogeneous melt distribution in the layered gneiss. Initial melt distribution is not modified by deformation in experiments on the homogeneous gneiss, implying that melting products did not migrate from their initiation sites. In contrast, melt flowed in shear zones or in inter-boudin positions during experimental deformation of the heterogeneous gneiss. These experiments attest to the strong influence of initial gneissic layering on melting pattern, melt segregation and flow during deformation of partially molten rocks
Multi-Step Optimization Strategy for Fuel-Optimal Orbital Transfer of Low-Thrust Spacecraft

An effective method for the design of fuel-optimal transfers in two- and three-body dynamics is presented. The optimal control problem is formulated using calculus of variation and primer vector theory. This leads to a multi-point boundary value problem (MPBVP), characterized by complex inner constraints and a discontinuous thrust profile. The first issue is addressed by embedding the MPBVP in a parametric optimization problem, thus allowing a simplification of the set of transversality constraints. The second problem is solved by representing the discontinuous control function by a smooth function depending on a continuation parameter. The resulting trajectory optimization method can deal with different intermediate conditions, and no a priori knowledge of the control structure is required. Test cases in both the two- and three-body dynamics show the capability of the method in solving complex trajectory design problems
Naphthalene diimide carrying two cysteine termini at both imide linkers as a molecular staple

Naphthalene diimide (1) carrying cysteines at the termini of amide substituents were synthesized to act as a molecular staple of double stranded DNA. Since 1 is able to bind to double stranded DNA with threading intercalation, the complex of 1 with double stranded DNA can be topologically immobilized on a gold surface through the S[BOND]Au linkage as confirmed by cyclic voltammetric experiment. Ferrocenyl-double stranded 23-mertic oligonucleotide, dsFcODN, was immobilized on gold electrode with 1.0×1012 molecules cm−2 when electrode was treated with 2.0 µM dsFcODN and 4.0 µM 1 for 1 h at room temperature. The coverage density was similar to that obtained for the terminal thiol-modified oligonucleotide. Compound 1 was applied to detect the 321-meric PCR product of P. gingivalis, which is important in the diagnosis of periodontal disease. This experiment, coupled with the use of ferrocenylnaphthalene diimide, FND as electrochemical indicator for double stranded DNA, resulted in quantitative detection of PCR product within the range of 10 pg µL−1–10 ng µL−1 (15 nM–15 µM). The 1 and FND established a simple and rapid detection method of double stranded PCR product with a detection limit of 10 pg µL−1 (15 nM)
Multifrequency channel microwave reflectometer with frequency hopping operation for density fluctuation measurements in Large Helical Device

In order to measure the internal structure of density fluctuations using a microwave reflectometer, the broadband frequency tunable system, which has the ability of fast and stable hopping operation, has been improved in the Large Helical Device. Simultaneous multipoint measurement is the key issue of this development. For accurate phase measurement, the system utilizes a single sideband modulation technique. Currently, a dual channel heterodyne frequency hopping reflectometer system has been constructed and applied to the Alfv?n eigenmode measurements
Assessment of experimental optical techniques for characterizing heat transfer using numerical simulations

This manuscript addresses the application of numerical simulations for assessing the error in the measurement of the bulk temperature along the laser beam of a 3D flow using a 2D Moiré deflectometry analysis. To analyze the effect of different flow parameters on the error, a 3D computational model of an experimental system was developed. The simulated domain represents the well-known solution of the backward facing step in a rectangular channel but includes a hot-plate at the bottom of the step to enhance the heat transfer effects. The geometry resembles that found in a general heat exchanger. The difference between the computed bulk temperature of the flow and the average temperature obtained via the 2D Moiré is analytically evaluated for various assumed general temperature profiles; the numerically computed profiles of temperature indicates that the error decreases with the channel aspect ratio. The use of CFD enables the determination of the flow topology and thus an evaluation of the 3D flow behavior that will cause the measurement error. A parametric study was performed for different flow conditions, namely, the aspect ratio of the channel, the inflow conditions (flow velocity or Reynolds number), and the temperature of the hot wall. The results indicate that the Moiré technique is suitable for evaluating the bulk temperature in typical heat exchange devices and flow conditions
Survivin: A Dual Player in Healthy and Diseased Skin

Survivin belongs to the inhibitor of apoptosis (IAP) protein family, and, in addition to the antiapoptotic functions, it also regulates the cell cycle. The survivin gene generates five major isoforms with diverse and opposite functions. Survivin is highly expressed in cancer and in few normal adult tissues, including skin. It is mostly detected in the nucleus of keratinocyte stem cells (KSCs), but it is also expressed in melanocytes and fibroblasts. Survivin isoforms are differentially detected in subpopulations of human keratinocytes, exerting contrasting activities. Survivin has an important role in the regulation of cell cycle in keratinocytes, and it protects these cells from anoikis and UV-induced apoptosis. In melanoma, survivin is abundantly expressed, and its subcellular localization varies depending upon tumor thickness and invasiveness. Survivin overexpression has been shown in squamous cell carcinoma (SCC), and it is also involved in UVB-induced carcinogenesis. The presence of survivin both in the nucleus and in the cytoplasm throughout the epidermal layers of psoriatic lesions suggests the involvement of this protein in the keratinocyte alterations typical of this disease. Additional studies on the expression of survivin isoforms and their subcellular localization in relation to function will confirm the key role of survivin in the skin and will open the field to new therapeutic strategies for many cutaneous conditions