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Any offset between these two halo mass scales will result in offsets in Fig. 9. For example, a number of recent papers have argued that failure of some of the assumptions underlying the standard methods for estimating cluster masses from X-ray data (e. g. , detailed hydrostatic equilibrium or the unimportance of turbul...
10.1051/0004-6361/201220941
article
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Physics and Astronomy
https://openalex.org/fields/31
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This is the lowest mass scale to which an SZ scaling relation has so far been measured. The fact that the signal is close to the self-similar prediction implies that Planckdetected hot gas represents roughly the mean cosmic fraction of the mass even in such low-mass systems. Consistency with their low observed X-ray lu...
10.1051/0004-6361/201220941
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Acknowledgements. The authors from the consortia funded principally by CNES , CNRS , ASI , NASA , and Danish Natural Research Council acknowledge the use of the pipeline-running infrastructures Magique3 at Institut d'Astrophysique de Paris (France) , CPAC at Cambridge (UK) , and USPDC at IPAC (USA). The develo...
10.1051/0004-6361/201220941
article
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Physics and Astronomy
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Spectroscopic data processing, redshift measurement, and reliability flag The multi-slit spectroscopy data processing has been performed using the VIPGI data processing environment (Scodeggio et al. , 2005). It consists of 2D spectra extraction, sky-subtraction, combination of individual 2D spectra, 1D spectra tracing...
10.1051/0004-6361/201322179
article
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Physics and Astronomy
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5 have been observed with SINFONI in a pilot program for MASSIV (Lemoine-Busserolle et al. 2010), including 2 flag 3 and one flag 4 object, their redshifts were all confirmed from at least [OIII]5007Å detection. From the VVDS objects re-observed by VIPERS we derive the velocity difference distribution. The 1-sigma of t...
10.1051/0004-6361/201322179
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Physics and Astronomy
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We contend that they are not of the same nature, and that care must be taken when comparing them. From our VIMOS experience dealing with > 1. 5 × 10 5 spectroscopic redshift measurements from the VVDS, zCOSMOS, and VIPERS surveys, it appears that it is illusory to aim at a classification of galaxy redshifts measurement...
10.1051/0004-6361/201322179
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In the following we call these samples the 'Ultra-Deep', the 'Deep-re-observed', and the 'colour-selected' samples. The VMMPS mask-design software (Bottini et al. , 2005) was first used to force slits on the colour-selected sample (a few per VIMOS quadrant), then to force slits on the Deep-reobserved sample (about 20...
10.1051/0004-6361/201322179
article
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false
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All the multi-wavelength data has been cross-correlated with the VVDS spectroscopic sample and is made available on the VVDS database.
10.1051/0004-6361/201322179
article
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false
Physics and Astronomy
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VVDS complete data release The data produced by the VVDS are all publicly released on a database with open access. A complete information system has been developed with the data embedded in a reliable database environment, as described in Le Brun et al. (in preparation). Queries combining the main survey parameters ca...
10.1051/0004-6361/201322179
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We demonstrate that galaxies with VVDS flags 2, 3, 4 and 9 have a reliability ranging from 83 to 100%, making this the primary sample for science analysis. Galaxies with flag=1 can be used for science analyses after taking into account that they have a ∼50% probability to be correct. We emphasize that this probabilisti...
10.1051/0004-6361/201322179
article
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All the VVDS data in this final release are made publicly available on a dedicated database available at http://cesam. lam. fr/vvds.
10.1051/0004-6361/201322179
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Physics and Astronomy
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VVDS-Deep sample is based solely on I-band selection 17. 5 ≤ I AB ≤ 24. Total integration times of 4. 5h have been obtained with the LRRED grism. The VVDS-Deep observations of the 0226-04 field have been extensively described in Le Fèvre et al. (2005a) and the ECDFS in Le Fèvre et al. (2004a). The VVDS-Deep dataset now...
10.1051/0004-6361/201322179
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Acknowledgements. We thank the referee, N. Padilla for his careful review of the manuscript and suggestions which have significantly improved this paper. We thank ESO staff for their continuous support for the VVDS surveys, particularly the Paranal staff conducting the observations and the ESO user support group ...
10.1051/0004-6361/201322179
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Physics and Astronomy
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Note that any misalignment of those surfaces generates spurious waves in the measured output bar signals. The amplified signal of the strain gages is recorded at a frequency of 1MHz. The recorded strain signals are post-processed with the software package DAVID (Gary, 2005) to reconstruct the time histories of the ax...
10.1007/s11340-013-9712-y
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Materials Science
https://openalex.org/fields/25
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Local displacement measurements A high speed video system (Phantom v7. 3 with 90mm macro lenses) is employed to record pictures of the specimen surface at a frequency of 111kHz (1 frame every 9µs). A resolution of 448x32 pixels is chosen. The camera is positioned at a distance of about 400mm from the specimen surface, ...
10.1007/s11340-013-9712-y
article
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false
Materials Science
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Finite element model The explicit solver of the finite element analysis software Abaqus ( 2007 ) is used to perform the analysis. All parts are meshed with reduced integration 3D solid elements (type C3D8R from the Abaqus element library). The elements of the bar meshes have an edge length of 5mm in the axial directio...
10.1007/s11340-013-9712-y
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Materials Science
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Acknowledgements The partial financial support of the French National Center for Scientific Research (CNRS) and the MIT/Industry fracture consortium is gratefully acknowledged. Professors Tomasz Wierzbicki (MIT) and Bengt Lundberg ( Uppsala University ) are thanked for valuable discussion. Mr. Philippe Chevalier...
10.1007/s11340-013-9712-y
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Materials Science
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Suggested volcanoes and associated stratospheric surface area density follow CCMVal (http://www. pa. op. dlr. de/CCMVal/Forcings/ CCMVal Forcings WMO2010. html), with no volcanic eruptions in the future. The proposed simulation length was 4-10 yr (excluding spinup, see Table 2 ) using prescribed monthly sea surface te...
10.5194/gmd-6-179-2013
article
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Earth and Planetary Sciences
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Emissions and concentration boundary conditions Consistent gridded emissions data from 1850 to 2100 were created in support of CMIP5 and of this activity; the historical portion of this dataset is discussed in Lamarque et al. (2010). The year 2000 dataset was used for harmonization with the future emissions determine...
10.5194/gmd-6-179-2013
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Earth and Planetary Sciences
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, 2005) Constant present-day isoprene, Other VOCs, Oceanic CO, Soil NOx NCAR-CAM3. 5 Interactive, based on model's convection (Price et al. , 1997; Ridley et al. , 2005) , scaled to produce ∼ 3-5 Tg N. Not every model performed all simulations, even the primary ones. The overall availability of results for each model...
10.5194/gmd-6-179-2013
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Earth and Planetary Sciences
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On the other hand, UM-CAM and STOC-HadAM3 share the same dynamical core. A high degree of similarity is also found in GISS-E2-R and GISS-E2-R-TOMAS (different aerosol scheme; we will use the terminology GISS-E2s when common characteristics are discussed) and NCAR-CAM3. 5 and CESM-CAM-Superfast (different chemistry sche...
10.5194/gmd-6-179-2013
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Boundary conditions As mentioned in Sect. Model, also based on ECHAM5, but with differences in resolution and shortwave radiation (Cagnazzo et al. , 2007). Some models used the previous AR4 simulations, applying an approximate correspondence between RCPs and SRES scenarios (GEOSCCM, NCAR-CAM3. 5; see Lamarque et al. ...
10.5194/gmd-6-179-2013
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Earth and Planetary Sciences
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, 2011b). Had-GEM2s, STOC-HadAM3 and UM-CAM input their time-varying stratospheric ozone distribution from the CMIP5 database (Cionni et al. , 2011). Finally, LMDzORINCA uses a constant (for all simulations) climatological values of stratospheric ozone (Li and Shine, 1995). Note that changes in stratospheric ozone do...
10.5194/gmd-6-179-2013
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Earth and Planetary Sciences
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, 2012) , (2) tropospheric ozone changes (Young et al. , 2012) , (3) ozone radiative forcing and attribution (Stevenson et al. , 2012) , (4) comparison of ozone and associated forcing with TES (Bowman et al. , 2012) , (5) black carbon deposition (Lee et al. , 2012) , and (6) OH and methane lifetime in the historica...
10.5194/gmd-6-179-2013
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Earth and Planetary Sciences
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Acknowledgements. ACCMIP is organized under the auspices of Atmospheric Chemistry and Climate (AC&C), a project of International Global Atmospheric Chemistry (IGAC) and Stratospheric Processes And their Role in Climate (SPARC) under the International Geosphere-Biosphere Project ( IGBP ) and World Climate Researc...
10.5194/gmd-6-179-2013
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false
Earth and Planetary Sciences
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The Pacific Northwest National Laboratory (PNNL) is operated for the DOE by Battelle Memorial Institute under contract DE-AC06-76RLO 1830. The work of D. B. and P. C. was funded by the US Dept. of Energy (BER) , performed under the auspices of LLNL under Contract DE-AC52-07NA27344 , and used the supercomputing r...
10.5194/gmd-6-179-2013
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Earth and Planetary Sciences
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The LMDz-OR-INCA simulations were done using computing resources provided by the CCRT/GENCI computer center of the CEA. The MIROC-CHEM calculations were performed on the NIES supercomputer system ( NEC SX-8R ), and supported by the Environment Research and Technology Development Fund ( S-7 ) of the Ministry of the...
10.5194/gmd-6-179-2013
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Earth and Planetary Sciences
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1 CCM 1. 875/2. 5/L30, 3. 5 hPa Prescribed distributions from NCAR-CAM3. 5 STOC-HadAM3 CGCM 5. 0/5. 0/L19, 50 hPa Prescribed globally uniform CH 4 concentrations. Different for each time slice following CMIP5 dataset UM-CAM CGCM 2. 5/3. 75/L19, 4. 6 hPa Prescribed atmospheric concentration with no spatial variation; di...
10.5194/gmd-6-179-2013
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Earth and Planetary Sciences
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Offline stratospheric O 3 from 41 species CMIP5 dataset LMDzORINCA 82 gas species; no aerosols Offline stratospheric O 3 (climatol- ogy from Li and Shine, 1995) MIROC-CHEM 58 gas species; SO 4 , BC, OC, sea salt, dust; AIE in- Full stratospheric chemistry cluded MOCAGE 110 gas species; no aerosols Full stratospheric ch...
10.5194/gmd-6-179-2013
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Earth and Planetary Sciences
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Start-up for a new education on headache disorders after Global Burden of Disease Study 2010 The Global Burden of Disease Study 2010 (GBD 2010), recently published in The Lancet [1], has marked new standards for all scientific societies, NGOs and patients' associations that gravitate towards headache disorders. These s...
10.1186/1129-2377-14-41
editorial
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Medicine
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Start-up for a new education on headache disorders after Global Burden of Disease Study 2010 The Global Burden of Disease Study 2010 (GBD 2010), recently published in The Lancet [1], has marked new standards for all scientific societies, NGOs and patients' associations that gravitate towards headache disorders. These s...
10.1186/1129-2377-14-41
editorial
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2,013
true
false
false
false
Medicine
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Acknowledgments All Authors (except TJS) are Trustees and Directors of the European Headache Federation (EHF). TJS is a founding member and past-President of EHF. The Authors declared no COI related to the contents of this Editorial.
10.1186/1129-2377-14-41
editorial
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false
Medicine
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, 2005). Given the limitations of direct remote sensing and land surface modeling approaches for estimating ET, the objective of this paper is to demonstrate how the two approaches can be combined to create a hybrid which improves ET estimates across Africa. Examples of model hybridization include combining land surfac...
10.5194/hess-17-1079-2013
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Environmental Science
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Data processing and handling The PT-JPL model is run globally at a quasi-0. 05 • resolution daily time step from 2000-2008 for sub-Saharan Africa and is aggregated to a monthly time step for visualization and comparison purposes with field data. The choice of resampling to 0. 05 • resolution assumes that spatial hetero...
10.5194/hess-17-1079-2013
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Environmental Science
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Parameter Description Equation f C Fractional total vegetation cover e -(kLAI) B C Plant coefficient r+ r(1+C h R C )+ β Soil moisture availability 1 -W REF -W f W C Water holding capacity f C P -D -LE C S Maximum water holding capacity Optimized constant Land Information System (LIS) (Kumar et al. , 2006) , compute s...
10.5194/hess-17-1079-2013
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Environmental Science
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GLDAS uses NOAA/GDAS atmospheric fields, Climate Prediction Center Merged Analysis of Precipitation fields, and observation-driven shortwave and longwave radiation using the Air Force Weather Agency's AGRicultural METeorological modeling system. These data are produced at 3-hourly intervals and aggregated to a monthly ...
10.5194/hess-17-1079-2013
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Environmental Science
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The observed data are from three online sources: AMMA (www. amma-international. org), CarboAfrica (www. carboafrica. net) and Fluxnet (www. fluxdata. org). Five of the sites (BW-Ma1, CG-Euc, NE-Waf, NE-Wam, and ZA-Kru) include half-hourly data needed to run the PT-JPL model: surface air temperature ( • C), incoming lon...
10.5194/hess-17-1079-2013
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Environmental Science
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Half-hourly (uncorrected) data from the flux towers are used, because the PT-JPL model computes LE from daytime R N only. Average daily (corrected) data is typically filled using look-up tables (Reichstein et al. , 2005) and/or artificial neural networks (Papale and Valentini, 2003) , however these data are not avai...
10.5194/hess-17-1079-2013
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Statistical analysis The analysis is done in three phases: (1) evaluation of the PT-JPL model using station data to determine the appropriateness of the LE C component, (2) sensitivity analysis of the PT-JPL model to remote sensing and surface reanalysis forcing and comparison of PT-JPL ground inputs with surface reana...
10.5194/hess-17-1079-2013
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Environmental Science
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Some of the relationships are clearly non-linear, however statistics from a linear fit are chosen for comparison purposes between inputs and across sites. It is expected that GLDAS p and q data correlates well with observed RH. Observed q and p are not used for direct comparison, because these data are not available fo...
10.5194/hess-17-1079-2013
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Environmental Science
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Hybrid model Time series of observed LE and modeled LE using PT-JPL, GNOAH, and the combined model (PT-JPL LE C + GNOAH LE I,S ) for six of the eight stations are shown in Fig. 3. Table 9 includes goodness-of-fit statistics for six of the eight stations: ZM-Mon and NE-Wam are omitted, because the former had less than...
10.5194/hess-17-1079-2013
article
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Discussion The study represents an initial attempt to use a suite of new flux tower data in sub-Saharan Africa to improve ET estimation using remote sensing and surface climate reanalysis data for regular near real-time continental scale monitoring. The integration of the evaporation components from GNOAH with the PT-J...
10.5194/hess-17-1079-2013
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Environmental Science
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, 2009). These factors could lead to a drop in LE of nearly 17 W m -2 , assuming a one standard deviation drop in R N from the sensitivity analysis, which still does not account for the underestimation of LE. It is expected that the large positive bias from the reanalysis data would act to improve the correlations at t...
10.5194/hess-17-1079-2013
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Environmental Science
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Acknowledgements. This work was primarily supported by the US Agency for International Development through a US Geological Survey cooperative agreement ( 04HQAG0001 ) and National Aeronautics and Space Administration Precipitation grant ( NNX07AG26G ). The eddy covariance data was acquired by the Fluxnet communi...
10.5194/hess-17-1079-2013
article
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Environmental Science
https://openalex.org/fields/23
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M-and H-waves A bipolar cuff electrode was placed on the peroneal nerve for stimulation (0. 1 ms pulses). The cathode (positive electrode) was oriented proximally. A pair of wire electrodes was placed subcutaneously on the Tibialis anterior muscle for EMG (electromyographic) recording. Ground electrode was implanted in...
10.1042/an20120082
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Medicine
https://openalex.org/fields/27
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Following the frequency series testing, the H-reflex amplitude was confirmed at 0. 3 Hz for consistency. If the amplitude at recheck was less than 90 % of the initial amplitude, data were discarded. The M-and H-waves were only recorded on the left side. The investigator was blind to the experimental groups during recor...
10.1042/an20120082
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Medicine
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ACKNOWLEDGEMENT We thank Dr Eric Pinet ( Aqua Gel Technologies Inc. , Québec, Canada ) for providing the pHPMA hydrogel.
10.1042/an20120082
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Medicine
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Straylight measurements are considered as of good quality (more details can be found in the GOMOS product handbook at http://envisat. esa. int/handbooks/gomos/toc. htm). the GOMOS data used here are obtained with the version 5 of the ESA level 1 operational processor. all the selected spectra are linearly interpolated ...
10.5194/amtd-6-3511-2013
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Earth and Planetary Sciences
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All the cases of bimodal distributions observed in our study are due to measurements done inside and outside the polar vortex. In this case, both modes are studied separately and, after visual inspection, we have selected the one that represents the high latitude band, in other words the one inside the polar vortex wit...
10.5194/amtd-6-3511-2013
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Earth and Planetary Sciences
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Monthly climatology of OClO In Fig. 8 , we show the time series of OClO SCDs in three latitude bands: the equatorial band (10 • S-10 • N, middle panel), the north polar band (60 • N-90 • N, top panel) and the south polar band (60 • S-90 • S, bottom panel). In the equatorial region, the missing data in 2005 are due to a...
10.5194/amtd-6-3511-2013
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Earth and Planetary Sciences
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Acknowledgements. This study was funded by the PRODEX/RADIAL (PEA 4000102793 ) contract under the authority of the Belgian Space Science Office (BELSPO). We thank the AMON and SALOMON science team for giving us the authorization to use their OClO concentration profiles.
10.5194/amtd-6-3511-2013
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Earth and Planetary Sciences
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We present a simulation analysis of weak gravitational lensing flexion and shear measurement using shapelet decomposition, and identify differences between flexion and shear measurement noise in deep survey data. Taking models of galaxies from the Hubble Space Telescope Ultra Deep Field (HUDF) and applying a correction...
10.1093/mnras/stt1353
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Physics and Astronomy
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2005) , the Cosmic Evolution Survey (COSMOS; see, e. g. Scoville et al. 2007; Leauthaud et al. 2007 ) and the Space Telescope A901/902 Galaxy Evolution Survey (STAGES; see, e. g. Gray et al. 2009). The imaging data from these surveys share important characteristics as regards lensing measurement, having a small but non...
10.1093/mnras/stt1353
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Physics and Astronomy
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Image deconvolution using shapelets Within the shapelet framework, there are two possible methods with which to correct galaxy images for the effects of the optical system. Both approaches begin with the construction of a shapelet model of the PSF g(θ) at the location of each galaxy: this model should be as accurate as...
10.1093/mnras/stt1353
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Physics and Astronomy
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2005 Heymans et al. , 2008)) , we choose the V 606 filter image for the construction of the shapelet starter set, as representative of typical lensing source galaxies. A detailed description of the modelling of galaxies in the HUDF can be found in Appendix A. Given the input parameters, postage stamps, and model of the...
10.1093/mnras/stt1353
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Physics and Astronomy
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Performing a shapelet flexion transformation that is accurate to third order therefore increases n max by 9, meaning that a modest n max = 12 shapelet galaxy requires a far more complex n max = 21 model once flexed. The SHAPELETS software suffers extreme memory demands and reductions in speed beyond n max = 20, and so ...
10.1093/mnras/stt1353
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Physics and Astronomy
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Correlated noise The final ingredient in the creation of simulated images is the addition of realistic measurement noise, due to diffuse background light and finite photon number counts. An important consideration for shape measurement is the impact of spatially correlated noise. This is present due to the standard pra...
10.1093/mnras/stt1353
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Physics and Astronomy
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Object detection and shapelet decomposition To test and calibrate shapelet measurements of shear and flexion, we treat the 540 ACS simulation tiles as if they were new telescope data (with properties such as galaxy positions and shapes unknown). The first step is therefore to detect objects in the images from peaks in ...
10.1093/mnras/stt1353
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Physics and Astronomy
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While unrealistic, this simplification will allows any measurement biases to be interpreted cleanly rather than being subject to external factors such as poor PSF modelling. The problem of building accurate PSF models is important enough to be addressed in its own right, and this is increasingly reflected in the litera...
10.1093/mnras/stt1353
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Physics and Astronomy
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A2 Postage stamp image extraction The decomposition of stars and galaxy images into shapelet models must be preceded by the creation of 'postage stamp' images of each object in the catalogue, cropped around the object in question, and masked for neighbours. A postage stamp is also made containing a map of the noise and...
10.1093/mnras/stt1353
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Physics and Astronomy
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We choose NFWHM = 6 in this analysis, the default value of 5 being found to be often insufficiently large to allow the shapelet modelling of the extended outer profiles of deep, space-based images. The initial version of the SHAPELETS software used in this analysis flagged as a modelling failure any objects for which t...
10.1093/mnras/stt1353
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Unlike in the KSB approach, image pixels at a distance from the object centroid are not explicitly down-weighted Downloaded from https://academic. oup. com/mnras/article/435/1/822/1128681 by guest on 30 July 2022 increasing the importance of careful masking. The SHAPELETS software therefore constructs over each object ...
10.1093/mnras/stt1353
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The SHAPELETS software also outputs the diagonal entries of the covariance matrix for all shapelet coefficients, and so these are used to combine the models for each star in an inverse-variance weighted average, giving the resulting PSF model seen in Fig. A2. That this model incorporates no spatial variation across the...
10.1093/mnras/stt1353
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These quantities are chosen by an amoeba-driven optimization process (described by Massey & Refregier 2005; we note that other implementations of the shapelet method do not necessarily allow n max to vary, e. g. Kuijken 2006 ). However, the SHAPELETS software does require the choice of a limiting maximum value of n m...
10.1093/mnras/stt1353
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For n max > 20, the SHAPELETS software therefore calculates these numbers as double-precision floating point numbers, as and when they are required. This leads to significant processing overheads, albeit ones which might plausibly be averted with some changes to the internal processing design of the SHAPELETS software ...
10.1093/mnras/stt1353
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We therefore choose N_MAX=20, which nonetheless allows a high degree of galaxy substructural complexity to be realized (e. g. Fig. 5 ). We choose N_MIN =0 so as to give the SHAPELETS code freedom to model galaxies with a simple circular Gaussian if there is no strong statistical support for a more complex model. The ot...
10.1093/mnras/stt1353
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AC K N OW L E D G E M E N T S The authors would like to thank Dave Goldberg for interesting discussions in the course of the work that led to this paper, and the anonymous referee for many helpful suggestions and improvements. BR and CH acknowledge support from the European Research Council in the form of a Startin...
10.1093/mnras/stt1353
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Acknowledgements GM, JP acknowledge funding from the Engineering and Flow Programme funded by the National Measurement Office. The EMRP is jointly funded by the EMRP participating countries within Euramet and the European Union. © Queen 's Printer and Controller of HMSO, 2013.
10.1051/metrology/201315001
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Engineering
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Issues about monitoring hydrological variability Most of the past studies about hydrological variability rely on ship-based CTD or even bottle sample observations being operated only in specific places and on a monthly (at best) to annual basis. The data available since the beginning of the last century (e. g. Painter ...
10.5194/os-9-301-2013
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Earth and Planetary Sciences
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This is a serious limit, given the importance of intense mesoscale dynamics in these areas, which makes the interpretation of data from monitoring programs even more difficult (Millot and Briand, 2002) , and prevents reliable trend detection from episodic and sparse observations (e. g. Millot and Taupier-Letage, 2005)...
10.5194/os-9-301-2013
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Earth and Planetary Sciences
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This data set presently constitutes one of the longest, uninterrupted Mediterranean time series (along with the Corsica Channel series, the DYFAMED and the CEFREM -Centre de Formation et de Recherche sur l'Environnement Marin-series). These data were of particular relevance in documenting the propagation of the EMT sig...
10.5194/os-9-301-2013
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Earth and Planetary Sciences
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The recorded time series can be used for studies of long-term changes of the Adriatic response to local climatic forcing and the volume of the dense water formed as a function of the winter heat losses (Cardin and Gačić, 2003). The amount of the dense water formed also determines the water exchange between the Adriati...
10.5194/os-9-301-2013
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Earth and Planetary Sciences
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The joining of a new partner to the network is done on a volunteer basis, and interested new mooring managers just need to contact the coordinators. Missing sites that deserve to be monitored to achieve the objectives of the HC Programme could be for instance: (i) the AW flow between WMED and EMED, in the middle of the...
10.5194/os-9-301-2013
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Earth and Planetary Sciences
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Acknowledgements. This is a contribution to the CIESM HY-DROCHANGES Programme (http://www. ciesm. org/marine/programs/hydrochanges. htm),which has been initiated by one of the authors (CM). We thank Frederic Briand , Director General of CIESM (the Mediterranean Science Commission ), for his continuing support given...
10.5194/os-9-301-2013
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Earth and Planetary Sciences
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Small non-coding RNAs (smRNA) participate in the regulation of development, cell differentiation, adaptation to environmental constraints and defense responses in plants. They negatively regulate gene expression by degrading specific mRNA targets, repressing their translation or modifying chromatin conformation through...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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In addition to conserved miRNAs present in other plant species, 229, 179, and 35 novel miRNA families were identified respectively in these 3 legumes, among which several seems legume-specific. New potential functions of several miRNAs in the legume-specific nodulation process are discussed. Furthermore, a new category...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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truncatula available genomic and expressed sequence (EST) databases. In contrast to Arabidopsis, an important gene diversification was observed in the three legume models (for DCL2, AGO4, AGO2, and AGO10) or specifically in soybean for DCL1 and DCL4. Functional significance of these variant isoforms may reflect peculia...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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Even though genome sequences of three model legumes are not yet completely finished, a very large portion is available in genomic and EST databases to permit gene identification and annotation. However, we cannot exclude that the lack of certain sequences in these databases may be due to its low expression and presence...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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LEGUME miRNA DIVERSITY AND FUNCTIONS IN NODULATION DEEP SEQUENCING REVEALED A LARGE DIVERSITY OF CONSERVED AND NOVEL miRNAs Since 2006, most miRNAs from animal and plant species have been registered in the miRNA database, called miRBAse (www. mirbase. org/, Griffiths- Jones et al. , 2006). Taking into account v19. 0 (...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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We thus searched these miRNAs in available L. japonicus genomic data and identified 5 miR395 and one miR530 genes. In contrast, even after deep sequencing of a large variety of tissues and conditions, miR397 was never reported in M. truncatula. Lack of this miRNA was first noticed by Sunkar and Jagadeeswaran (2008) , ...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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truncatula (Table 1 ). This was expected as the large soybean genome size, estimated at ∼1115 Mbp, was associated to remnants of a whole genome duplication event, which occurred approximately ∼13 Mya ago in soybean (Schmutz et al. , 2010). Nevertheless, the ratio between gene numbers in G. max and M. truncatula is ge...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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, 2010). According to miRBase, all, except miR1511, miR1515, miR2111 and miR2118, may be considered as "legume-specific". However, Zhai et al. (2011) showed that variants of miR1507 and miR1509 were present in smRNA libraries of non-leguminous species. For instance, miR1507 was highly abundant in grapes. In addition,...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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japonicus. In miRBAse, M. truncatula and G. max correspond to the first and third plant species in term of total numbers of miRNA genes, with 675 and 506 genes, respectively. This huge diversity, comparable to, e. g. , rice, may be due to the high number of smRNA deep sequencing analyses performed (9 and 10 reports for...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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Even though their genome sequences are not yet completely finished, a very large portion is available in genomic and EST databases for database mining. For this, we carried out TBLASTX analyses to identify the orthologs of Arabidopsis DCL and AGO proteins in the three legumes for which large genomic databases are avail...
10.3389/fpls.2013.00236
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truncatula and L. japonicus, while two GmDCL1 genes are present in soybean. The functional significance (if any) of this specific event of DCL1 duplication in soybean remains to be elucidated. In contrast, like in many angiosperms, a duplication of DCL2 was observed both in L. japonicus and G. max. According to Margis...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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truncatula and L. japonicus genomic databases. For instance, AGO3 and AGO9 are absent both in Lotus and M. truncatula genomic databases (Capitão et al. , 2011; Young et al. , 2011). However, according to its strong similarity with the soybean AGO9, we propose to rename MtAGO11a (Capitão et al. , 2011) in MtAGO9. In ...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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On the other hand, expression analysis suggest that AGO2 and AGO3 are more expressed in seeds than other tissues and accumulation of smRNA species is similar in ago2 and ago3 mutants (Takeda et al. , 2008). These latter experiments support that there is functional redundancy of AGO2 and AGO3 in Arabidopsis, notably in...
10.3389/fpls.2013.00236
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0, March 2011), this TC was split into two contigs (TC188472 and TC194233), which in fact correspond to the so-called MtAGO12a/b genes. Although these AGO12 isoforms fall into the AGO1/AGO10 clade, they are more closely related to AGO10 (Figure 5 ). Thus, the absence of AGO1, but also of AGO5, in M. truncatula databas...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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, 2009; Parker, 2010) ; The PIWI domain is responsible of the catalytic activity of AGO proteins (Baumberger and Baulcombe, 2005) ; the PAZ domain is necessary to recognize the 3 end of the smRNA for loading into the RISC and determines the AGO specificity. Among the identified domains in legume AGOs (Data Sheet 4), o...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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Phylogenetic trees were constructed thanks to T-Coffee software. The phylogenetic tree was generated with MEGA4. 0 software using the Neighbor joining tree (Capitão et al. , 2011). The four AGO clades are indicated in the right part of the figure. and AGO3 may be replaced by Asp (DDD) without affecting their endonucle...
10.3389/fpls.2013.00236
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CONCLUDING REMARKS Since five years, the rapid progress of genomic technologies has allowed the construction and high-throughput sequencing of a very large set of smRNA libraries in model legumes, in particular from M. truncatula and G. max. Compilation of data from miRBase and smRNA deep sequencings revealed the large...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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Phylogenetic tree of AGO proteins in M. truncatula, L. japonicus, G. max, A. thaliana, P. trichocarpa, and O. sativa. Full length sequences of the predicted AGO proteins from A. thaliana, P. trichocarpa and O. sativa were retrieved from Genbank (NCBI). DCL from M. truncatula, soybean (G. max) and L. japonicus were sear...
10.3389/fpls.2013.00236
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ACKNOWLEDGMENTS Pilar Bustos-Sanmamed was the recipient of a Marie Curie Postdoctoral IE Fellowship (European Commision, MEDEPIMIR, N • PIEF-GA-2010-273743 ). Jérémie Bazinwork was supported by a post-doctoral contract from University Paris Diderot Paris 7, France. This work was supported by the program Saclay Pl...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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5| Phylogenetic tree of AGO proteins in M. truncatula, L. japonicus, G. max, A. thaliana, P. trichocarpa, and O. sativa. Full length sequences of the predicted AGO proteins from A. thaliana, P. trichocarpa and O. sativa were retrieved from Genbank (NCBI). DCL from M. truncatula, soybean (G. max) and L. japonicus were s...
10.3389/fpls.2013.00236
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Agricultural and Biological Sciences
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Multi-site observational study Data to support the short form adaptation was collected in a US-based, non-randomized, multi-center, standalone observational study in male and female patients who have MS with and without NDO. MS patients were recruited through neurology practices to complete patient reported outcome ass...
10.1186/1471-2377-13-78
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Medicine
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Acknowledgements The authors would like to acknowledge the following for their help in the development of this manuscript: Vasudha Mukherjee Bal and Marcy Fitzrandolph for managing and overseeing the qualitative design and development of the ABSST. Benjamin Banderas for managing the quantitative phase of the study...
10.1186/1471-2377-13-78
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Medicine
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Acknowledgements. We thank JC Thiers , C Foure , A Matassa-Ohm for excellent technical help and Dr. V Gallet ( SNCF Laboratory, Toulouse, France ) for providing human serum. We are grateful to Dr. F Lezoualc 'h for critical reading of the manuscript. These studies were supported by grants from INSERM and Toulou...
10.1038/cddis.2013.47
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Biochemistry, Genetics and Molecular Biology
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Real data experiments: p»n We propose to test the performance of our method on ARCENE dataset which is one of the five NIPS 2003 feature selection challenge data sets. The data set is obtained from UCI Machine Learning Repository [http://archive. ics. uci. edu/ml]. For this two-class classification problem with continu...
10.46298/arima.1962
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Mathematics
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Acknowledgments -We wish to thank S. Blatt , S. Gopalakrishnan , A. C. Hewson , M. Koehl , Y. Oreg , M. Punk , S. Will , A. Tsvelik , G. Zarand , F. Zhou , and M. Zwierlein for helpful discussions. We would like to thank Martin Zwierlein for pointing out to us the possibility of using Feshbach bound state...
10.1103/physrevlett.111.215304
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Physics and Astronomy
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However, reports suggest that many patients with NMIBC are not optimally managed as per current clinical practice guidelines [9] [10] [11]. The present individual patient data survey (IPDS) was designed to investigate clinical practice patterns in the management of intermediate-and high-risk NMIBC. In particular, the ...
10.1111/bju.12012
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Medicine
https://openalex.org/fields/27