pinecone/core-2020-05-10-deduplication huggingface dataset:
Adenosine triphosphatase pontin is overexpressed in hepatocellular carcinoma and coregulated with reptin through a new posttranslational mechanism.

International audienceReptin and Pontin are related ATPases associated with stoichiometric amounts in several complexes involved in chromatin remodeling, transcriptional regulation, and telomerase activity. We found that Reptin was up-regulated in hepatocellular carcinoma (HCC) and that down-regulation of Reptin led to growth arrest. We show here that Pontin messenger RNA (mRNA) is also up-regulated in human HCC 3.9-fold as compared to nontumor liver (P = 0.0004). Pontin expression was a strong independent factor of poor prognosis in a multivariate analysis. As for Reptin, depletion of Pontin in HuH7 cells with small interfering RNAs (siRNAs) led to growth arrest. Remarkably, Pontin depletion led to down-regulation of Reptin as shown with western blot, and vice versa. Whereas siRNAs induced a decrease of their cognate mRNA targets, they did not affect the transcripts of the partner protein. Translation of Pontin or Reptin was not altered when the partner protein was silenced. However, pulse-chase experiments demonstrated that newly synthesized Pontin or Reptin stability was reduced in Reptin- or Pontin-depleted cells, respectively. This phenomenon was reversed upon inhibition of proteasome or ubiquitin-activating enzyme (E1). In addition, proteasome inhibition could partly restore Pontin steady-state levels in Reptin-depleted cells, as shown by western blot. This restoration was not observed when cells were also treated with cycloheximide, thus confirming that proteasomal degradation in this setting was restricted to newly synthesized Pontin. CONCLUSION: Reptin and Pontin protein levels are strictly controlled by a posttranslational mechanism involving proteasomal degradation of newly synthesized proteins. These data demonstrate a tight regulatory and reciprocal interaction between Reptin and Pontin, which may in turn lead to the maintenance of their 1:1 stoichiometry
Finite-temperature coarse-graining of one-dimensional models: mathematical analysis and computational approaches

Published in "Journal of Nonlinear Science", 2010, vol. 20, no 2, p. 241-275 http://hal-enpc.archives-ouvertes.fr/hal-00625882/fr/International audienceWe present a possible approach for the computation of free energies and ensemble averages of one-dimensional coarse-grained models in materials science. The approach is based upon a thermodynamic limit process, and makes use of ergodic theorems and large deviations theory. In addition to providing a possible efficient computational strategy for ensemble averages, the approach allows for assessing the accuracy of approximations commonly used in practice
Formation of Zn–Ca phyllomanganate nanoparticles in grass roots

International audienceIt is now well established that a number of terrestrial and aquatic microorganisms have the capacity to oxidize and precipitate Mn as phyllomanganate. However, this biomineralization has never been shown to occur in plant tissues, nor has the structure of a natural Mn(IV) biooxide been characterized in detail. We show that the graminaceous plant Festuca rubra (red fescue) produces a Zn-rich phyllomanganate with constant Zn:Mn and Ca:Mn atomic ratios (0.46 and 0.38, respectively) when grown on a contaminated sediment. This new phase is so far the Zn-richest manganate known to form in nature (chalcophanite has a Zn:Mn ratio of 0.33) and has no synthetic equivalent. Visual examination of root fragments under a microscope shows black precipitates about ten to several tens of microns in size, and their imaging with backscattered and secondary electrons demonstrates that they are located in the root epidermis. In situ measurements by Mn and Zn K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy and X-ray diffraction (XRD) with a micro-focused beam can be quantitatively described by a single-phase model consisting of Mn(IV) octahedral layers with 22% vacant sites capped with tetrahedral and octahedral Zn in proportions of 3:1. The layer charge deficit is also partly balanced by interlayer Mn and Ca. Diffracting crystallites have a domain radius of 33 Å in the ab plane and contain only 1.2 layers (not, vert, similar8.6 Å) on average. Since this biogenic Mn oxide consists mostly of isolated layers, basal 00l reflections are essentially absent despite its lamellar structure. Individual Mn layers are probably held together in the Mn–Zn precipitates by stabilizing organic molecules. Zinc biomineralization by plants likely is a defense mechanism against toxicity induced by excess concentrations of this metal in the rhizosphere
Carbon taxation in France: a failure compared with experience elsewhere in Europe? The case of road freight transport

International audienceThe French carbon tax was introduced as part of the 2010 Draft Finance Act in the form of a Climate and Energy Tax (Contribution Climat-Energie - CCE), and was then withdrawn. Without going into the political reasons for its withdrawal, this paper will examine how effective it could have been from the environmental and economic standpoints, in particular as carbon taxation has been successfully introduced in other European countries.Taking the example of road freight transport, which is specifically targeted by the legislation, we shall refer to European examples, forecasts made by experts (on the basis of a variety of simulations using macroeconomic models, or the recommendations of the Rocard Commission), and the statements of French stakeholders (shippers, hauliers, federations,…). Was the abandonment of the carbon tax justified after its rejection by the majority of the stakeholders on the grounds that it would undermine their competitiveness and impose an excessive tax burden on the sector?Keyword
Quantum phenomena in Communities of Practice.

International audienceAlthough Communities of Practice have become a core concept in understanding how knowledge is managed within organizations, there have been few studies of the praxis of formation of Communities of Practice. In this article, we report on a Grounded Theory study of the members of a previously identified Community of Practice within the UK Higher Education Academy Psychology Network. In addition to providing data on the functioning of the community, the study also revealed a hitherto unrecognized form of community that exhibits all of the characteristics of CoPs yet has only a transient existence that seems to nucleate around an existing core community. Drawing on the metaphor of quantum behaviour, we termed these communities Quantum Communities of Practice. We describe a theory to explain this phenomenon that is grounded in the data from the study. We conclude by discussing the value and validity of our findings and methodology and indicating the next steps we will take in our research
Deformation twinning in the full-α″ martensitic Ti–25Ta–20Nb shape memory alloy

International audienceDeformation twinning of the Ti–25Ta–20Nb (mass%) shape memory alloy is characterized using EBSD and TEM. The selfaccommodating α″ microstructure is shown to be first deformed using \111\α″ type I and &lt;211&gt;α″ type II reorientation twinning. Plastic deformation occurs further by plastic twinning with a new \130\&lt;310&gt;α″ twinning system. Maximum lattice deformation calculation is a relevant parameter to predict the variant of martensite that is favored during the reorientation process. Conversely, Schmid factor analysis can be used to predict the selection of \130\&lt;310&gt;α″ twinning variants during deformation. Analogy between \130\&lt;310&gt;α″ and \332\&lt;113&gt;β twinning systems is highlighte
Study of ferroelectric/dielectric multilayers for tunable stub resonator applications at microwaves

International audienceTunable coplanar waveguide stub resonators deposited on various ferroelectric/dielectric heterostructures are studied in the 10-GHz band. A frequency tunability of up to ~ 45% is achieved under a moderate biasing field (Ebias < 100 kV/cm) when the resonator is printed on KTa0.5Nb0.5O3 (KTN) ferroelectric thin film alone: this comes from the large permittivity agility of the KTN material (εr(KTN) varies from ~ 700 to ~ 200). Nevertheless this also leads to significant insertion loss due to the dielectric loss of the ferroelectric material itself (tanδr(KTN) ≈ 0.15-0.30 at 10 GHz). In this paper, an original route has been considered to reduce the device loss while keeping up a high frequency tunability. It consists in associating the KTN film with a dielectric film to elaborate ferroelectric/dielectric multilayers. The Bi1.5Zn0.9Nb1.5O7−δ (BZN) oxide material is selected here for two main reasons, namely its low dielectric loss (tanδr(BZN) ≈ 0.005-0.0075) and its moderate relative permittivity (εr(BZN) ≈ 95-125) at 12.5 GHz. The relevance of this approach is studied numerically and experimentally. We compare numerically two different heterostructures for which the ferroelectric film is grown on the dielectric film (KTN/BZN), or vice versa (BZN/KTN). A stub resonator printed on the most relevant heterostructure has been fabricated, and experimental data are discussed and compared to the numerical results
Double directional characterisation of radio wave propagation through metallic watertight doors on board ships

International audienceThe objective of this Letter is to characterise the electromagnetic wave propagation between adjacent rooms in lower deck areas of ships. A wideband MIMO (Multiple-Input Multiple-Output) channel sounder has been used to realize double directional propagation measurements at 2.2 GHz. The antenna configuration was a linear array at the transmission side and a rectangular one at the reception. The measurement data are first processed with a classic beamforming technique, then with a high resolution algorithm to extract the dominant paths. A ray-tracing based simulation tool is used to understand the measurement results. It is observed that, in spite of the metallic structure of watertight doors, wireless communication remains possible between adjacent rooms after door closure. Results show that electromagnetic waves mainly propagate through door edges openings
Investigation of sheet-flow processes based on novel acoustic high-resolution velocity and concentration measurements

International audienceA new dataset of uniform and steady sheet flow experiments is presented in this paper. An Acoustic Concentration and Velocity Profiler (ACVP) is used to measure time-resolved profiles of collocated 2C velocity (u,w) and sediment concentration and to measure the time evolution of the bed interface position. Ensemble averaging over eleven similar experiment realisations is done to evaluate the mean profiles of streamwise velocity, concentration , sediment flux and Reynolds shear stress. The repeatability, stationarity and uniformity of the flow are carefully checked for a Shields number θ ≈ 0.5 and a suspension number of S = 1.1. The mean profile analysis allows to separate the flow into two distinct layers: a suspension layer dominated by turbulence and a bed layer dominated by granular interactions. The bed layer can be further subdivided into a frictional layer capped by a collisional layer. In the suspension layer, the mixing length profile is linear with a strongly reduced von Karman parameter equal to 0.225. The Schmidt number is found to be constant in this region with a mean value of σ s = 0.44. The present results are then interpreted in terms of existing modelling approaches and the underlying assumptions are discussed. In particular, the well-known Rouse profile is shown to predict the concentration profile adequately in the suspension layer provided that all the required parameters can be evaluated separately. However, the strong intermittency of the flow observed in the bed layer under the impact of turbulent large-scale coherent flow structures suggests the limitations of averaged steady two-phase flow models
When 2D is not enough, go for an extra dimension.

International audienceThe use of an extra SDS separation in a different buffer system provide a technique for deconvoluting 2D gel spots made of several proteins (Colignon et al. Proteomics, 2013, 13, 2077-2082). This technique keeps the quantitative analysis of the protein amounts and combines it with a strongly improved identification process by mass spectrometry, removing identification ambiguities in most cases. In some favorable cases, posttranslational variants can be separated by this procedure. This versatile and easy to use technique is anticipated to be a very valuable addition to the toolbox used in 2D gel-based proteomics
Peptide binding to ochratoxin A mycotoxin: a new approach in conception of biosensors.

International audienceOchratoxin A (OTA) is a widespread and abundant natural carcinogenic mycotoxin produced by several species of Aspergillus and Penicillium fungi. Due to the ubiquitous presence of these fungi in food and potential risk for human health, a rapid and sensitive in vitro detection assay is required. Analytical methods for OTA detection/identification are generally based on liquid-liquid extraction, clean-up using an immunoaffinity column (IAC), and identification by reversed-phase high pressure liquid chromatography with fluorescence detection (HPLC-FLD). However, IACs are costly and have a short lifespan. Therefore, an interesting approach would appear to be the design and chemical synthesis of a mimotope peptide simulating mycotoxin-specific antibodies. We have developed a promising alternative method that is based on the use of peptides which are able to bind to specific chemical functions and/or molecular structures. Accordingly, a number of peptides (derived from the structures of major redox proteins) were selected and produced by chemical solid phase syntheses. The ability of such peptides to bind to ochratoxin A was evaluated by HPLC. The peptide NF04 (structurally derived from an oxidoreductase enzyme), which was found to be the sole potently reactive compound among tested molecules, was further evaluated in a peptide-based enzyme-linked immunosorbent assay (peptide-based ELISA), thus confirming its specific interaction with ochratoxin A
Effects of different modified diets on growth, digestive enzyme activities and muscle compositions in juvenile Siamese fighting fish (Betta splendens Regan, 1910)

The effects of four modified diets (gamma-irradiated, microwave-irradiated, probiotic-supplemented and
carbohydrase-supplemented diets) were studied on digestive enzyme specific activities and growth performance
quality of juvenile Siamese fighting fish (Betta splendens Regan, 1910) during 2 weeks of critical and
intensive rearing period. The modified procedures did not change biochemical compositions and gross energy
of diets, but generally resulted in relatively higher in vitro digestibilities of protein and carbohydrate and
fish survival rate, albeit insignificant. Only gamma irradiation significantly increased in vitro protein digestibility
of the diet, and microwave irradiation increased starch gelatinization and water solubility (Pb0.05).
Fish fed microwave-treated diet showed highest values in all studied growth indicators and digestive
enzyme specific activities (except lipase), with significantly higher amylase specific activity and activity
ratio of amylase to trypsin (A/T ratio). Correlation analysis indicated significant relationships (Pb0.05) among
the levels of total protease, amylase and trypsin, and between SGR and A/T ratio. Muscle and body compositions
of juveniles fed on microwave- or gamma-irradiated diets were similar to the control, while the juveniles fed on
probiotic- or carbohydrase-supplemented diets showed lower protein depositions (Pb0.05). Similar levels of
RNA, RNA/Protein ratio, and Protein/Lipid ratio in body andmuscle in all dietary groups fed ad libitumsuggested
that the improved growth performance in juvenile Siamese fighting fish fed on microwave-irradiated diet may
not be only due to improved physicochemical properties of the diet but also improved fish consumption rate
Liver fibrosis progression at autopsy in injecting drug users infected by hepatitis C: A longitudinal long-term cohort study

-There is a paucity of unbiased data on the natural history of hepatitis C virus (HCV) infection in injecting drug users (IDUs). The purpose of this study was to assess the risk of developing advanced fibrosis associated with chronic hepatitis C (CHC) infection among injecting drug users (IDUs) who underwent an autopsy.
A longitudinal cohort design was applied, in which the stage of liver fibrosis in anti-HCV positive IDUs with or without chronic HCV infection was assessed in liver tissue from autopsies performed up to 35years after HCV exposure. The cohort originated from 864 IDUs consecutively admitted for drug abuse treatment 1970–1984. Stored sera, mostly drawn at the time of admission for drug treatment, were available in 635 subjects. 220 out of 523 anti-HCV positive subjects had died before 2009. Liver tissue from autopsies was available from 102/220 subjects, of which 61 were HCV RNA positive. Liver sections were classified according to METAVIR scores for fibrosis. Two pathologists, both blinded for serologic results, scored sections of liver tissue.
Among HCV RNA positive subjects 16.4% (10/61) had septal fibrosis (F3) or cirrhosis (F4) compared to 2.4% (1/41) among anti HCV positive/HCV RNA negative subjects (p=0.026). Of 18 HCV RNA positive subjects autopsied <15years after HCV exposure none had F3 or F4. Among subjects autopsied >25years after exposure 35% (6/17) had F3–F4.
Among IDUs chronically infected by HCV, 1/3 developed septal fibrosis or cirrhosis 25years or more after exposure
Simultaneous 3D measurement of the translation and rotation of finite-size particles and the flow field in a fully developed turbulent water flow

International audienceWe report a novel experimental technique that measures simultaneously in three dimensions the trajectories, the translation and the rotation of finite-size inertial particles together with the turbulent flow. The flow field is analyzed by tracking the temporal evolution of small fluorescent tracer particles. The inertial particles consist of a super-absorbent polymer that renders them index and density matched with water and thus invisible. The particles are marked by inserting at various locations tracer particles into the polymer. Translation and rotation, as well as the flow field around the particle are recovered dynamically from the analysis of the marker and tracer particle trajectories. We apply this technique to study the dynamics of inertial particles much larger in size (Rp/η ≈ 100) than the Kolmogorov length scale η in a von Kármán swirling water flow (Rλ ≈ 400). We show, using the mixed (particle/fluid) Eulerian second-order velocity structure function, that the interaction zone between the particle and the flow develops in a spherical shell of width 2Rp around the particle of radius Rp. This we interpret as an indication of a wake induced by the particle. This measurement technique has many additional advantages that will make it useful to address other problems such as particle collisions, dynamics of non-spherical solid objects, or even of wet granular matter
Exploiting Diversification in Gossip-Based Recommendation

International audienceIn the context of Web 2.0, the users become massive producers of diverse data that can be stored in a large variety of systems. The fact that the users' data spaces are distributed in many different systems makes data sharing difficult. In this context of large scale distribution of users and data, a general solution to data sharing is offered by distributed search and recommendation. In particular, gossip-based approaches provide scalability, dynamicity, autonomy and decentralized control. Generally, in gossip-based search and recommendation, each user constructs a cluster of "relevant" users that will be employed in the processing of queries. However, considering only relevance introduces a sig-nificant amount of redundancy among users. As a result, when a query is submitted, as the user profiles in each user's cluster are quite similar, the probability of retrieving the same set of relevant items increases, and recall results are limited. In this paper, we propose a gossip-based search and recommendation approach that is based on a new clustering score, called usefulness, that combines relevance and diversity, and we present the corresponding new gossip-based clustering algorithm. We val-idate our proposal with an experimental evaluation using three datasets based on MovieLens, Flickr and LastFM. Compared with state of the art solutions, we obtain major gains with a three order of magnitude recall improvement when using the notion of usefulness regardless of the relevance score between two users used
Physical controls and depth of emplacement of igneous bodies: A review

International audienceThe formation and growth of magma bodies are now recognised as involvingthe amalgamation of successive, discrete pulses such as sills. Sills wouldthus represent the building blocks of larger plutons (sensu lato). Mechanicaland thermal considerations on the incremental development of these plutonsraise the issue of the crustal levels at which magma can stall and accumulateas sills. Reviewing the mechanisms that could a priori explain sill formation,it is shown that principal physical controls include: rigidity contrast,where sills form at the interface between soft strata overlaid by comparativelystiffer strata; rheology anisotropy, where sills form within the weakestductile zones; and rotation of deviatoric stress, where sills form when theminimum compressive stress becomes vertical. Comparatively, the conceptof neutral buoyancy is unlikely to play a leading control in the emplacementof sills, although it could assist their formation. These different controls on sill formation, however, do not necessarily operate on the same length scale.The length scale associated with the presence of interfaces separating upperstiffer layers from lower softer ones determines the depth at which rigiditycontrolledsills will form. On another hand, the emplacement depths for rheology-controlled sills is likely to be determined by the distribution of theweakest ductile zones. Whereas the emplacement depth of stress-controlledsills is determined by a balance between the horizontal maximum compressivestress, which favours sill formation, and the buoyancy of their feeder dykes,which drives magma vertically. Ultimately, the depth at which a sill formsdepends on whether crustal anisotropy or stress rotation is the dominantcontrol, i.e. which of these processes operates at the smallest length scale.Using dimensional analysis, it is shown that sill formation controlled by remotestress rotation would occur on length scales of hundreds of meters orgreater. This therefore suggests that crustal heterogeneities and their associatedanisotropy are likely to play a larger role than remote stress rotation incontrolling sill emplacement, unless these heterogeneities are several hundredmeters or more apart. This also reinforces the role of local stress barriers,owing to interactions between deviatoric stress and crustal heterogeneities,in the formation of sills