Showing papers by "University of Nice Sophia Antipolis published in 2015"

Advanced Virgo: a second-generation interferometric gravitational wave detector

Abstract: Advanced Virgo is the project to upgrade the Virgo interferometric detector of gravitational waves, with the aim of increasing the number of observable galaxies (and thus the detection rate) by three orders of magnitude. The project is now in an advanced construction phase and the assembly and integration will be completed by the end of 2015. Advanced Virgo will be part of a network, alongside the two Advanced LIGO detectors in the US and GEO HF in Germany, with the goal of contributing to the early detection of gravitational waves and to opening a new window of observation on the universe. In this paper we describe the main features of the Advanced Virgo detector and outline the status of the construction.

The eleventh and twelfth data releases of the Sloan Digital Sky Survey: final data from SDSS-III

Abstract: The third generation of the Sloan Digital Sky Survey (SDSS-III) took data from 2008 to 2014 using the original SDSS wide-field imager, the original and an upgraded multi-object fiber-fed optical spectrograph, a new near-infrared high-resolution spectrograph, and a novel optical interferometer. All the data from SDSS-III are now made public. In particular, this paper describes Data Release 11 (DR11) including all data acquired through 2013 July, and Data Release 12 (DR12) adding data acquired through 2014 July (including all data included in previous data releases), marking the end of SDSS-III observing. Relative to our previous public release (DR10), DR12 adds one million new spectra of galaxies and quasars from the Baryon Oscillation Spectroscopic Survey (BOSS) over an additional 3000 sq. deg of sky, more than triples the number of H-band spectra of stars as part of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE), and includes repeated accurate radial velocity measurements of 5500 stars from the Multi-Object APO Radial Velocity Exoplanet Large-area Survey (MARVELS). The APOGEE outputs now include measured abundances of 15 different elements for each star. In total, SDSS-III added 2350 sq. deg of ugriz imaging; 155,520 spectra of 138,099 stars as part of the Sloan Exploration of Galactic Understanding and Evolution 2 (SEGUE-2) survey; 2,497,484 BOSS spectra of 1,372,737 galaxies, 294,512 quasars, and 247,216 stars over 9376 sq. deg; 618,080 APOGEE spectra of 156,593 stars; and 197,040 MARVELS spectra of 5,513 stars. Since its first light in 1998, SDSS has imaged over 1/3 of the Celestial sphere in five bands and obtained over five million astronomical spectra.

Modules for experiments in stellar astrophysics (mesa): binaries, pulsations, and explosions

Abstract: We substantially update the capabilities of the open-source software instrument Modules for Experiments in Stellar Astrophysics (MESA). MESA can now simultaneously evolve an interacting pair of differentially rotating stars undergoing transfer and loss of mass and angular momentum, greatly enhancing the prior ability to model binary evolution. New MESA capabilities in fully coupled calculation of nuclear networks with hundreds of isotopes now allow MESA to accurately simulate advanced burning stages needed to construct supernova progenitor models. Implicit hydrodynamics with shocks can now be treated with MESA, enabling modeling of the entire massive star lifecycle, from pre-main sequence evolution to the onset of core collapse and nucleosynthesis from the resulting explosion. Coupling of the GYRE non-adiabatic pulsation instrument with MESA allows for new explorations of the instability strips for massive stars while also accelerating the astrophysical use of asteroseismology data. We improve treatment of mass accretion, giving more accurate and robust near-surface profiles. A new MESA capability to calculate weak reaction rates "on-the-fly" from input nuclear data allows better simulation of accretion induced collapse of massive white dwarfs and the fate of some massive stars. We discuss the ongoing challenge of chemical diffusion in the strongly coupled plasma regime, and exhibit improvements in MESA that now allow for the simulation of radiative levitation of heavy elements in hot stars. We close by noting that the MESA software infrastructure provides bit-for-bit consistency for all results across all the supported platforms, a profound enabling capability for accelerating MESA's development.

Modules for Experiments in Stellar Astrophysics (MESA): Binaries, Pulsations, and Explosions

Abstract: We substantially update the capabilities of the open-source software instrument Modules for Experiments in Stellar Astrophysics (MESA). MESA can now simultaneously evolve an interacting pair of differentially rotating stars undergoing transfer and loss of mass and angular momentum, greatly enhancing the prior ability to model binary evolution. New MESA capabilities in fully coupled calculation of nuclear networks with hundreds of isotopes now allow MESA to accurately simulate advanced burning stages needed to construct supernova progenitor models. Implicit hydrodynamics with shocks can now be treated with MESA, enabling modeling of the entire massive star lifecycle, from pre-main sequence evolution to the onset of core collapse and nucleosynthesis from the resulting explosion. Coupling of the GYRE non-adiabatic pulsation instrument with MESA allows for new explorations of the instability strips for massive stars while also accelerating the astrophysical use of asteroseismology data. We improve treatment of mass accretion, giving more accurate and robust near-surface profiles. A new MESA capability to calculate weak reaction rates "on-the-fly" from input nuclear data allows better simulation of accretion induced collapse of massive white dwarfs and the fate of some massive stars. We discuss the ongoing challenge of chemical diffusion in the strongly coupled plasma regime, and exhibit improvements in MESA that now allow for the simulation of radiative levitation of heavy elements in hot stars. We close by noting that the MESA software infrastructure provides bit-for-bit consistency for all results across all the supported platforms, a profound enabling capability for accelerating MESA's development.

Characterization of the LIGO detectors during their sixth science run

Abstract: In 2009–2010, the Laser Interferometer Gravitational-Wave Observatory (LIGO) operated together with international partners Virgo and GEO600 as a network to search for gravitational waves (GWs) of astrophysical origin. The sensitivity of these detectors was limited by a combination of noise sources inherent to the instrumental design and its environment, often localized in time or frequency, that couple into the GW readout. Here we review the performance of the LIGO instruments during this epoch, the work done to characterize the detectors and their data, and the effect that transient and continuous noise artefacts have on the sensitivity of LIGO to a variety of astrophysical sources.

Invasion biology of spotted wing Drosophila (Drosophila suzukii): a global perspective and future priorities

Abstract: The Asian vinegar fly Drosophila suzukii (spotted wing Drosophila (SWD)) has emerged as a major invasive insect pest of small and stone fruits in both the Americas and Europe since the late 2000s. While research efforts have rapidly progressed in Asia, North America, and Europe over the past 5 years, important new insights may be gained in comparing and contrasting findings across the regions affected by SWD. In this review, we explore common themes in the invasion biology of SWD by examining (1) its biology and current pest status in endemic and recently invaded regions; (2) current efforts and future research needs for the development of predictive models for its geographic expansion; and (3) prospects for both natural and classical (=importation) biological control of SWD in invaded habitats, with emphasis on the role of hymenopteran parasitoids. We conclude that particularly fruitful areas of research should include fundamental studies of its overwintering, host-use, and dispersal capa- bilities; as well as applied studies of alternative, cost-ef- fective management techniques to complement insecticide use within the integrated pest management framework. Finally, we emphasize that outreach efforts are critical to effective SWD management by highlighting successful

The Top 10 oomycete pathogens in molecular plant pathology

Abstract: Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens which threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant-pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. This article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.

CHEMICAL CARTOGRAPHY with APOGEE: METALLICITY DISTRIBUTION FUNCTIONS and the CHEMICAL STRUCTURE of the MILKY WAY DISK

Abstract: Using a sample of 69,919 red giants from the SDSS-III/APOGEE Data Release 12, we measure the distribution of stars in the [/Fe] versus [Fe/H] plane and the metallicity distribution functions (MDFs) across an unprecedented volume of the Milky Way disk, with radius 3 < R < 15 kpc and height kpc. Stars in the inner disk (R < 5 kpc) lie along a single track in [/Fe] versus [Fe/H], starting with -enhanced, metal-poor stars and ending at [/Fe] ∼ 0 and [Fe/H] ∼ +0.4. At larger radii we find two distinct sequences in [/Fe] versus [Fe/H] space, with a roughly solar- sequence that spans a decade in metallicity and a high- sequence that merges with the low- sequence at super-solar [Fe/H]. The location of the high- sequence is nearly constant across the disk.

Seismicity triggered by fluid injection–induced aseismic slip

Abstract: Anthropogenic fluid injections are known to induce earthquakes. The mechanisms involved are poorly understood, and our ability to assess the seismic hazard associated with geothermal energy or unconventional hydrocarbon production remains limited. We directly measure fault slip and seismicity induced by fluid injection into a natural fault. We observe highly dilatant and slow [~4 micrometers per second (μm/s)] aseismic slip associated with a 20-fold increase of permeability, which transitions to faster slip (~10 μm/s) associated with reduced dilatancy and micro-earthquakes. Most aseismic slip occurs within the fluid-pressurized zone and obeys a rate-strengthening friction law μ = 0.67 + 0.045ln(v/v₀) with v₀ = 0.1 μm/s. Fluid injection primarily triggers aseismic slip in this experiment, with micro-earthquakes being an indirect effect mediated by aseismic creep.

Selective enhancement of topologically induced interface states in a dielectric resonator chain

Abstract: The recent realization of topological phases in insulators and superconductors has advanced the search for robust quantum technologies. The prospect to implement the underlying topological features controllably has given incentive to explore optical platforms for analogous realizations. Here we realize a topologically induced defect state in a chain of dielectric microwave resonators and show that the functionality of the system can be enhanced by supplementing topological protection with non-hermitian symmetries that do not have an electronic counterpart. We draw on a characteristic topological feature of the defect state, namely, that it breaks a sublattice symmetry. This isolates the state from losses that respect parity-time symmetry, which enhances its visibility relative to all other states both in the frequency and in the time domain. This mode selection mechanism naturally carries over to a wide range of topological and parity-time symmetric optical platforms, including couplers, rectifiers and lasers.

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

Abstract: Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA-based surveys provided similar relative abundances for most class-level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates (MALV)-I and MALV-II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal Fungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.

Molecular and Translational Classifications of DAMPs in Immunogenic Cell Death

Abstract: The immunogenicity of malignant cells has recently been acknowledged as a critical determinant of efficacy in cancer therapy. Thus, besides developing direct immunostimulatory regimens, including dendritic cell-based vaccines, checkpoint-blocking therapies, and adoptive T-cell transfer, researchers have started to focus on the overall immunobiology of neoplastic cells. It is now clear that cancer cells can succumb to some anticancer therapies by undergoing a peculiar form of cell death that is characterized by an increased immunogenic potential, owing to the emission of the so-called "damage-associated molecular patterns" (DAMPs). The emission of DAMPs and other immunostimulatory factors by cells succumbing to immunogenic cell death (ICD) favors the establishment of a productive interface with the immune system. This results in the elicitation of tumor-targeting immune responses associated with the elimination of residual, treatment-resistant cancer cells, as well as with the establishment of immunological memory. Although ICD has been characterized with increased precision since its discovery, several questions remain to be addressed. Here, we summarize and tabulate the main molecular, immunological, preclinical, and clinical aspects of ICD, in an attempt to capture the essence of this phenomenon, and identify future challenges for this rapidly expanding field of investigation.

Phosphatidylserine transport by ORP/Osh proteins is driven by phosphatidylinositol 4-phosphate

Abstract: In eukaryotic cells, phosphatidylserine (PS) is synthesized in the endoplasmic reticulum (ER) but is highly enriched in the plasma membrane (PM), where it contributes negative charge and to specific recruitment of signaling proteins. This distribution relies on transport mechanisms whose nature remains elusive. Here, we found that the PS transporter Osh6p extracted phosphatidylinositol 4-phosphate (PI4P) and exchanged PS for PI4P between two membranes. We solved the crystal structure of Osh6p:PI4P complex and demonstrated that the transport of PS by Osh6p depends on PI4P recognition in vivo. Finally, we showed that the PI4P-phosphatase Sac1p, by maintaining a PI4P gradient at the ER/PM interface, drove PS transport. Thus, PS transport by oxysterol-binding protein–related protein (ORP)/oxysterol-binding homology (Osh) proteins is fueled by PI4P metabolism through PS/PI4P exchange cycles.

Gaia FGK benchmark stars: Effective temperatures and surface gravities

Abstract: Context. In the era of large Galactic stellar surveys, carefully calibrating and validating the data sets has become an important and integral part of the data analysis. Moreover, new generations of stellar atmosphere models and spectral line formation computations need to be subjected to benchmark tests to assess any progress in predicting stellar properties. Aims. We focus on cool stars and aim at establishing a sample of 34 Gaia FGK benchmark stars with a range of different metallicities. The goal was to determine the effective temperature and the surface gravity independently of spectroscopy and atmospheric models as far as possible. Most of the selected stars have been subjected to frequent spectroscopic investigations in the past, and almost all of them have previously been used as reference, calibration, or test objects. Methods. Fundamental determinations of T eff and log g were obtained in a systematic way from a compilation of angular diameter measurements and bolometric fluxes and from a homogeneous mass determination based on stellar evolution models. The derived parameters were compared to recent spectroscopic and photometric determinations and to gravity estimates based on seismic data. Results. Most of the adopted diameter measurements have formal uncertainties around 1%, which translate into uncertainties in effective temperature of 0.5%. The measurements of bolometric flux seem to be accurate to 5% or better, which contributes about 1% or less to the uncertainties in effective temperature. The comparisons of parameter determinations with the literature in general show good agreements with a few exceptions, most notably for the coolest stars and for metal-poor stars. Conclusions. The sample consists of 29 FGK-type stars and 5 M giants. Among the FGK stars, 21 have reliable parameters suitable for testing, validation, or calibration purposes. For four stars, future adjustments of the fundamental T eff are required, and for five stars the log g determination needs to be improved. Future extensions of the sample of Gaia FGK benchmark stars are required to fill gaps in parameter space, and we include a list of suggested candidates.

ER stress induces NLRP3 inflammasome activation and hepatocyte death.

Abstract: The incidence of chronic liver disease is constantly increasing, owing to the obesity epidemic However, the causes and mechanisms of inflammation-mediated liver damage remain poorly understood Endoplasmic reticulum (ER) stress is an initiator of cell death and inflammatory mechanisms Although obesity induces ER stress, the interplay between hepatic ER stress, NLRP3 inflammasome activation and hepatocyte death signaling has not yet been explored during the etiology of chronic liver diseases Steatosis is a common disorder affecting obese patients; moreover, 25% of these patients develop steatohepatitis with an inherent risk for progression to hepatocarcinoma Increased plasma LPS levels have been detected in the serum of patients with steatohepatitis We hypothesized that, as a consequence of increased plasma LPS, ER stress could be induced and lead to NLRP3 inflammasome activation and hepatocyte death associated with steatohepatitis progression In livers from obese mice, administration of LPS or tunicamycin results in IRE1α and PERK activation, leading to the overexpression of CHOP This, in turn, activates the NLRP3 inflammasome, subsequently initiating hepatocyte pyroptosis (caspase-1, -11, interleukin-1β secretion) and apoptosis (caspase-3, BH3-only proteins) In contrast, the LPS challenge is blocked by the ER stress inhibitor TUDCA, resulting in: CHOP downregulation, reduced caspase-1, caspase-11, caspase-3 activities, lowered interleukin-1β secretion and rescue from cell death The central role of CHOP in mediating the activation of proinflammatory caspases and cell death was characterized by performing knockdown experiments in primary mouse hepatocytes Finally, the analysis of human steatohepatitis liver biopsies showed a correlation between the upregulation of inflammasome and ER stress markers, as well as liver injury We demonstrate here that ER stress leads to hepatic NLRP3 inflammasome pyroptotic death, thus contributing as a novel mechanism of inflammation-mediated liver injury in chronic liver diseases Inhibition of ER-dependent inflammasome activation and cell death pathways may represent a potential therapeutic approach in chronic liver diseases

On the Differential Structure of Metric Measure Spaces and Applications

Abstract: Introduction Preliminaries Differentials and gradients Laplacian Comparison estimates Appendix A. On the duality between cotangent and tangent spaces Appendix B. Remarks about the definition of the Sobolev classes References

Riemannian Ricci curvature lower bounds in metric measure spaces with -finite measure

Abstract: In prior work (4) of the first two authors with Savare, a new Riemannian notion of lower bound for Ricci curvature in the class of metric measure spaces (X,d,m) was introduced, and the corresponding class of spaces denoted by RCD(K,∞). This notion relates the CD(K,N) theory of Sturm and Lott-Villani, in the case N = ∞, to the Bakry-Emery approach. In (4) the RCD(K,∞) property is defined in three equivalent ways and several properties of RCD(K,∞) spaces, including the regularization properties of the heat flow, the connections with the theory of Dirichlet forms and the stability under tensor products, are provided. In (4) only finite reference measures m have been considered. The goal of this paper is twofold: on one side we extend these results to general σ-finite spaces, on the other we remove a technical assumption appeared in (4) concerning a strengthening of the CD(K,∞) condition. This more general class of spaces includes Euclidean spaces endowed with Lebesgue measure, complete noncompact Riemannian manifolds with bounded geometry and the pointed metric measure limits of manifolds with lower Ricci curvature bounds.

Epigenetic switch drives the conversion of fibroblasts into proinvasive cancer-associated fibroblasts

Abstract: Carcinoma-associated fibroblasts (CAF) mediate the onset of a proinvasive tumour microenvironment. The proinflammatory cytokine LIF reprograms fibroblasts into a proinvasive phenotype, which promotes extracellular matrix remodelling and collective invasion of cancer cells. Here we unveil that exposure to LIF initiates an epigenetic switch leading to the constitutive activation of JAK1/STAT3 signalling, which results in sustained proinvasive activity of CAF. Mechanistically, p300-histone acetyltransferase acetylates STAT3, which, in turn, upregulates and activates the DNMT3b DNA methyltransferase. DNMT3b methylates CpG sites of the SHP-1 phosphatase promoter, which abrogates SHP-1 expression, and results in constitutive phosphorylation of JAK1. Sustained JAK1/STAT3 signalling is maintained by DNA methyltransferase DNMT1. Consistently, in human lung and head and neck carcinomas, STAT3 acetylation and phosphorylation are inversely correlated with SHP-1 expression. Combined inhibition of DNMT activities and JAK signalling, in vitro and in vivo, results in long-term reversion of CAF-associated proinvasive activity and restoration of the wild-type fibroblast phenotype.

ERS task force statement: diagnosis and treatment of primary spontaneous pneumothorax.

Abstract: Primary spontaneous pneumothorax (PSP) affects young healthy people with a significant recurrence rate. Recent advances in treatment have been variably implemented in clinical practice. This statement reviews the latest developments and concepts to improve clinical management and stimulate further research.The European Respiratory Society's Scientific Committee established a multidisciplinary team of pulmonologists and surgeons to produce a comprehensive review of available scientific evidence.Smoking remains the main risk factor of PSP. Routine smoking cessation is advised. More prospective data are required to better define the PSP population and incidence of recurrence. In first episodes of PSP, treatment approach is driven by symptoms rather than PSP size. The role of bullae rupture as the cause of air leakage remains unclear, implying that any treatment of PSP recurrence includes pleurodesis. Talc poudrage pleurodesis by thoracoscopy is safe, provided calibrated talc is available. Video-assisted thoracic surgery is preferred to thoracotomy as a surgical approach.In first episodes of PSP, aspiration is required only in symptomatic patients. After a persistent or recurrent PSP, definitive treatment including pleurodesis is undertaken. Future randomised controlled trials comparing different strategies are required.

Emergent vortices in populations of colloidal rollers

Abstract: Coherent vortical motion has been reported in a wide variety of populations including living organisms (bacteria, fishes, human crowds) and synthetic active matter (shaken grains, mixtures of biopolymers), yet a unified description of the formation and structure of this pattern remains lacking. Here we report the self-organization of motile colloids into a macroscopic steadily rotating vortex. Combining physical experiments and numerical simulations, we elucidate this collective behaviour. We demonstrate that the emergent-vortex structure lives on the verge of a phase separation, and single out the very constituents responsible for this state of polar active matter. Building on this observation, we establish a continuum theory and lay out a strong foundation for the description of vortical collective motion in a broad class of motile populations constrained by geometrical boundaries.

Sprint Acceleration Mechanics: The Major Role of Hamstrings in Horizontal Force Production

Abstract: Recent literature supports the importance of horizontal ground reaction force (GRF) production for sprint acceleration performance. Modeling and clinical studies have shown that the hip extensors are very likely contributors to sprint acceleration performance. We experimentally tested the role of the hip extensors in horizontal GRF production during short, maximal, treadmill sprint accelerations. Torque capabilities of the knee and hip extensors and flexors were assessed using an isokinetic dynamometer in 14 males familiar with sprint running. Then, during 6-s sprints on an instrumented motorized treadmill, horizontal and vertical GRF were synchronized with electromyographic (EMG) activity of the vastus lateralis, rectus femoris, biceps femoris, and gluteus maximus averaged over the first half of support, entire support, entire swing and end-of-swing phases. No significant correlations were found between isokinetic or EMG variables and horizontal GRF. Multiple linear regression analysis showed a significant relationship (P = 0.024) between horizontal GRF and the combination of biceps femoris EMG activity during the end of the swing and the knee flexors eccentric peak torque. In conclusion, subjects who produced the greatest amount of horizontal force were both able to highly activate their hamstring muscles just before ground contact and present high eccentric hamstring peak torque capability.