dataesr/scientific-paragraphs-categorization huggingface dataset:
Genotype and K Supply Cause Phenotypic Variation of Root Architecture in Arabidopsis Seedlings of 26 natural accessions of Arabidopsis (Supplemental Table  S1   ; McKhann et al. , 2004)  were grown in two contrasting environments: control ([K] = 2 mM) and low K ([K] = 0. 01 mM). Quantitative analysis of 14 root architectural traits was performed 12 d after germination (DAG) with EZ Rhizo software  (Armengaud et al. , 2009b; Supplemental Data Set S1). For abbreviations and definitions of traits, see Table  I. Across all accessions, low K supply resulted in a reduction of the trait value as compared with the control for 11 of the 14 quantified traits (Table  I ). Only LR path length in the third quartile from the root-shoot junction (LRP 0. 75) and LR densities normalized to the length of the MR (LRdensMR) or branched zone (LRdensBZ) were, on average, increased in low K.
" These findings are backed up by  Prinzenberg et al. (2010) , who measured shoot and root growth traits combined with element profiles in a Ler 3 Kashmir-2 RIL population in three conditions: control, low K, and low phosphorus. They identified among others multielemental loci at CHR1. 3 (K, iron, magnesium), CHR3. 1 (K, phosphorus, magnesium, cobalt, manganese, zinc), CHR3. 2 (K, phosphorus, zinc), and CHR5. 3 (multiple elements). We compared publicly available ionomic data of Col-0 and Ct-1 (Purdue Ionomics Information Management System database;  Baxter et al. , 2007). The accessions show differences in manganese and cobalt content, but all other ions, including K, are present at similar levels. However, these data are derived from shoots of plants grown in (K-sufficient) soil and therefore are mirrored by similar root architectures of Col-0 and Ct-1 in control conditions in our study.
Plant Material and Growth Conditions Arabidopsis (Arabidopsis thaliana) accessions Akita, Alc-0, Bay-0, Bl-1, Bla-1, Bur-0, Blh-0, Col-0, Ct-1, Cvi-0, Edi-0, Ge-0, Gre-0, Jea, Kn-0, Mh-1, Mt-0, N13, Oy-0, Pyl-1, Sakata, Sha, St-0, and Stw-0 were obtained from the Versailles Resource Centre (Institut National de la Recherche Agronomique Versailles; http://dbsgap. versailles. inra. fr/vnat/). Ler and Wassilewskija from seed stocks maintained at the University of Glasgow were also included in the analysis. For QTL analysis, a Col-0 3 Ct-1 core population (7 RV;  Simon et al. , 2008)  of 164 RILs was obtained from the Versailles Resource Centre (Supplemental Table  S1 ). Ten lines were excluded from the analysis due to missing data at some markers  (Simon et al. , 2008). Seeds were surface sterilized with absolute ethanol for 1 min and in 2% sodium hypochlorite containing 0.
Quantification of Root Architecture Plates were scanned at 6, 8, 10 and 12 DAG using a conventional flatbed scanner and a resolution of 200 dpi. All scanned images were stored at Glasgow and can be made available to interested researchers for further analysis. Root phenotypes of different accessions were compared 12 DAG. For QTL analysis, control plants were scored 10 DAG because some lines reached the bottom of the plate before day 12. Image analysis was performed with EZ Rhizo software  (Armengaud et al. , 2009b). In addition to the parameters measured by EZ Rhizo, the mean LR length within MR quartiles was calculated for each root.
QTL Analysis Twelve root architecture traits (Fig. 8 ) were included in the analysis. Outliers were removed from the data set, and genotype averages were calculated for all quantified root parameters. Heritability of traits was estimated as h2 = s2g/(s2g + [s2e/r]), with s 2 g being the genetic variance, s2e the residual variance, and r the number of replicates. LOD scores were computed for each root parameter with Windows QTL Cartographer 2. 5  (Wang et al. , 2011)  using the composite interval mapping function and 1,000 permutations to determine the LOD threshold. QTL effects were subsequently calculated using the multiple interval mapping function.
Identification of the Leishmania Flabarin We previously discovered the involvement of small G proteins in the biogenesis of the Leishmania flagellum  [21] [22] [23] , which led us to try and identify effectors. One of the approaches used was bioinformatics: the L. major genome  [24] , the only available Leishmania genome sequence at the time of the experiments, was searched for homologues of known partners of the human ARF/ ARL small G proteins  [25] [26] [27]. We found LmjF. 27. 1730, an unannotated 340-aa protein, as potential homologue of human HsArfaptin-1 (Genbank U52521), a partner of several ARF/ARL family members  [25, 28]. The Nterminal region of LmjF. 27. 1730 (amino acids 10-231) showed some identity (Fig. S1A ) with the C-terminal region of HsArfaptin-1 (amino acids 61-339 for a total length of 341).
Using the CSS-Palm software  [41] , we found a potential palmitoylation site in the LdFlabarin N-terminus (amino acids 1-7, MPLCASI) with a palmitoylable cysteine at position 4. This site is conserved in Leishmania and Trypanosoma Flabarins, with the exception of T. vivax (Table  S1 ). The cysteine 4 was replaced by a serine (LdFlabarin/C4S-mRed); as a consequence, the potential palmitoylation site was destroyed. Compared to the flagellar wildtype LdFlabarin-mRed (Fig 5C ), the fluorescence was diffuse throughout the cell body (Fig. 5D ). Cell fractionation showed that the mutant protein LdFlabatin/C4S-mRed was not associated with the membrane fraction (Fig 5A  , lane P ) but remained soluble in the 100 000 g supernatant (Fig 5A  , lane S ). Thus, the cysteine 4 was indispensable for the membrane localization as for the flagellar addressing of LdFlabarin.
mexicana sequence (GenBank U45884)  [34]. The LaPFR-2C ORF (submitted to GenBank, accession number JN874564) comprised 1797 bp/591 amino acids (98%/98. 7% identity to LmxPFR2C, respectively  [34] ) with 36 nucleotides/8 amino acids differences. The ORF was cloned into the Acc65 I site of the pNUS-GFPnH vector (pNUS-GFPnH-LaPFR2C). LdCentrin  [31]  (GenBank AF406767) was amplified from L. donovani LV9 genomic DNA with oligonucleotides G446(gatcca-tATGGCTGCGCTGACGGATGAACA)/G447(gatcggtaccCT-TTCCACGCATGTGCAGCA) and cloned into pNUS-GFPcH (pNUS-LdCentrin-GFPcH); its sequence was 100% identical to the GenBank sequence.
Acknowledgments The authors thank  Pr. P. Bastien  for his support and encouragements;  Dr. A. Barral  for the L. amazonensis strains  BA125  and  BA276 ;  Y. Balard ,  N. Biteau ,  L. Crobu ,  C. Giroud ,  L. Talignani  and  Drs. S. Besteiro ,  C. Blaineau ,  M. Page  `s,  D. Robinson ,  Y. Sterkers  and  D. Tareste  for their help;  C. Hubert  ( Sequencing Facility of Bordeaux, France ) for some DNA sequencing;  P. Boutinaud  and  N. Barougier  ( Animal Facility, IRD, Montpellier, France ) for the rabbit immunization and the anti-LdFlabarin antiserum collection; the  Electronic Imaging Pole of Bordeaux Imaging Center. This work was initiated at the  UMR CNRS 5234 (Bordeaux)  and continued at both the UMR CNRS 5290 (formerly 2724, Montpellier) and the  UMR CNRS 5095 (Bordeaux).
Isolation of total RNA, cDNA generation and PCR Total RNA was extracted 24 h after transfection of cells with VCAM-1 constructs using the RNeasy kit (Qiagen, Hilden, Germany) and up to 5 mg of total RNA was applied as template for cDNA synthesis by SuperScript II (Invitrogen, Karlsruhe, Germany). VCAM-1 quantitative real-time PCR was performed using Power SYBR Green (Applied Biosystems) and primer 5 0 -TTCCCTAGA-GATCCAGAAATCGAG-3 0 (sense) and 5 0 -CTTGCAGCTTACAGTGACA-GAGC-3 0 (antisense;  [16] ), on an Applied Biosystems 7500 Fast Real-Time PCR system. Samples were run in duplicates under standard real-time PCR conditions. Relative quantification was calculated using the DDCt method. GAPDH (sense primer 5 0 -CTGCACCACCAACTGCTTAGCAC-3 0 ; antisense primer 5 0 -GTGATGG-CATGGACTGTGGTCATGAG-3 0 ) was used as endogenous control.
Western blot analysis Whole cell lysates were prepared 24 h after transfection with VCAM-1 constructs using RIPA buffer containing "Complete" protease inhibitors (Roche, Mannheim, Germany). After separation by SDS-PAGE, membranes were detected with human VCAM-1 monoclonal antibody (1:1000; Santa Cruz, Sta. Cruz, USA, sc-13160) and anti-mouse secondary antibody (1:2000; GE Healthcare). The open source software ImageJ (http://rsbweb. nih. gov/ij/) was used for band intensity quantification.
Funding  Eva Brand  is supported by a  Heisenberg professorship  from the  Deutsche Forschungsgemeinschaft (DFG ,  Br1589/8-2 ). This study was also supported by a grant from the  European Union-Project Network of Excellence ,  FP6-2005-LIFESCIHEALTH-6 ,  Integrating Genomics, Clinical Research and Care in Hypertension, InGenious HyperCare  (proposal No. 037093  to  Eva Brand  and  Stefan-Martin Brand ) and an  ICT  in the  FP7-ICT-2007-2 , project number  224635 ,  VPH2-Virtual Pathological Heart of the Virtual Physiological Human (supported Boris Schmitz ), to  Stefan-Martin Brand , formerly  Stefan-Martin Brand-Herrmann/Stefan-Martin Herrmann. Adelheid Korb-Pap  was supported by the  Bundesministerium für Bildung und Forschung , grant number  01EC1008D.
Different weight vectors If w k = 1, for all k then minimization determines sets that use the fewest number of pairs. Calculations of networks that maximized a measure of total covariance, while keeping numbers of pairs small, were performed through minimization with the weights w k ~ S S{S k where S S is the integer ceiling of the maximum of all covariance values S. This choice ensures the weights are nonnegative, the minimization will preferentially include pairs with high S, and will penalize the addition of pairs in general. All calculations were performed with Matlab version R2010b (The MathWorks Inc. , USA). The binary integer programming problems were solved using the bintprog routine.
Acknowledgments We thank  F. Abravanel  and  K. Barange  ( CHU Toulouse, France ),  Y. Baazia  and  D. Roulot  ( Hopital Avicenne, Bobigny, France ),  C. Gaudy  and  L. D Alteroche  ( CHU Tours, France ),  C. Henquell  and  A. Abergel  ( CHU Clermont-Ferrand, France ), A-M. Roque-Afonso  and  B. Roche  ( Hopital Paul-Brousse, Villejuif, France ),  V. Thibault  and  P. Lebray  ( Hopital Pitie-Salpe  ˆtriere, Paris, France),  P. Trimoulet  and  V. de Ledinghen  ( CHU de Bordeaux, France ),  S. Vallet  and  JB Nousbaum  ( CHU, Brest, France ) for providing patient serum samples.
This work was supported by the  European Union  ( ERC-2008-AdG-233130-HEPCENT ,  INTERREG-IV-Rhin Superieur-FEDER-Hepato-Regio-Net 2009 ), the chair of excellence program of the  Agence Nationale de la Recherche France  ( ANR-05-CEXC-008 ),  ANRS  ( 2011/132 ,  2011/154 ,  2012/239&319 ,  2012/318 ),  DGOS Inserm   A12027MS , the  University of Strasbourg and Laboratoire d'excellence LabEx HEPSYS  ( ANR-10-LAB-28 ). E. Schvoerer thanks the  Fondation Transplantation (France) ,  Region Alsace (France) ,  Region Lorraine (France) ,  Abbott Molecular (France)  and  Roche (France)  for unrestricted financial support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Western blot We used the same protocol as previously described  (Dourlen et al. , 2012). 100 embryos or 20 wing imaginal discs for each genotype were homogenized in Laemmli buffer (10% glycerol, pH 6. 8 0. 5M Tris, 10% SDS, 1% bromophenol blue, 1% b-mercaptoethanol, 100 mM DTT). Samples were then boiled and loaded onto a 12% acrylamide gel (Biorad), transferred and incubated overnight at 4˚C with a primary antibody. Samples were then incubated with HRP-coupled secondary antibodies, and eventually detected with a chemoluminescent kit (GE Healthcare Life Sciences). The following antibodies were used: ''Calvados'' Anti-Hh (kind gift from P. Therond) and Anti-Tubulin (Sigma). We used the following secondary antibodies: Anti-mouse HRP and Anti-rabbit HRP antibodies (Biorad). We used the ImageJ software to quantify protein bands.
Acknowledgements We thank the  DROSO-TOOLS  and PLATIM facilities of the  UMS3444 ,  Armel Gallet , Pascal Therond, L. S. Shashidara ,  James Skeath ,  Bloomington  and the  Developmental Studies Hybridoma Bank  for reagents. This work was supported by the  Chaire d'excellence Program  from the  CNRS  to S. V. , the  FRM  and ATIP from  CNRS  to B. M.
Flow Cytometry Peripheral venous blood was drawn from a large antecubital vein with a 19-gauge needle and anticoagulated with the direct thrombin inhibitor D-phenylalanine-L-prolyl-L-arginine chloromethyl ketone (PPACK, 75 lmol/L; Cambridge Biosciences, UK). 21 Immediately following venesection, aliquots of whole blood (500 lL) were incubated for 5 minutes in the presence or absence of thrombin receptor-activating peptide (TRAP; 0. 1, 0. 3, and 1. 0 lmol/L) to induce platelet activation. Sample aliquots (60 lL) were then incubated with anti-CD14-PE, anti-CD42a-FITC, and isotype matched controls for 20 minutes at room temperature. Thereafter, samples were fixed and the red cells lysed by the addition of 500 lL of FACS-Lyse solution. Samples were then stored at 4°C and analyzed on a FACS Calibur flow cytometer (Becton Dickinson) using Cell Quest software as described previously.
Statistical Analysis In vitro study data are presented as meanAEstandard error of the mean (SEM) and were analyzed with 2-way analysis of variance (ANOVA) with repeated measures. For the in vivo study, data are presented as meanAEstandard deviation (SD). In this study, the change from baseline values for PMA were analyzed using a mixed-effects analysis of covariance (AN-COVA) that accounts for repeated measures taken within a 2-period crossover design. Baseline values were included in the model as a covariate. Treatment (PSI-697 or placebo), time, period, and sequence as well as the interaction between time and treatment were included in the model as fixed effects. Subject was a random effect in the model. Statistical significance was taken as a 2-sided P value <0. 05.
gave a brief description of the ISL instrument design, its in-flight operation, and data analysis techniques. 14 eran et al. developed a particle in cell (PIC) model to investigate the capabilities of the SLP to diagnose bulk plasma parameters. 15 Their model, however, did not account for the influence of the magnetic field on current collection of the SLP. The goal of the present study is to simulate the current characteristics of the DEMETER SLP. For this purpose, we use PTetra which is capable of simulating the time dependent interaction of satellites with space plasma. 16 The numerical results of our study show some interesting features. These include the angular anisotropy in the current collected by various collectors, the sensitivity of the electron current to the orientation of the magnetic field, and the enhancement in the ion current due to the presence of the minority light H þ ions.
The simulation results obtained for these three cases are compared with in-flight DEMETER satellite measurements. Two sweeps are presented for the measurements: a short duration (fast) and a long duration (slow) sweep. These two sweeps are explained by Lebreton et al. 14  in Sec. III B 5. The data acquisition times for the fast and the slow sweeps are 0. 25 s and 2 s, respectively. Each sweep consists of two parts: an up (negative to positive) and a down scan (positive to negative). In Figures  3  and 4 , the fast up scans (thick solid line) are followed by the fast down scan (broken line), and the slow up scans (thin solid) are followed by slow down scans (broken thin line). It is noted that the up and scans for both sweeps show hysteresis. The difference between the I-V curves for the up and the down sweeps is used to estimate the surface properties of the probe, and in particular to characterize the thin layer due, for example, to surface contamination, or perhaps to a thin dielectric film of unknown origin, which is thought to be responsible for the hysteresis which varies with sweep speed.
ACKNOWLEDGMENTS N. I. and R. M. acknowledge the support by  Natural Sciences and Engineering Research Council of Canada (NSERC). The DEMETER Langmuir probe instrument was developed, and funding provided as part of the Instrument research programme, while J. -P. L. was affiliated with the  Space Science Department of ESA at ESTEC. This work was also supported in part by the  International Space Science Institute in Bern, Switzerland. The simulations presented in this work made use of the WestGrid computing facilities.
Reduction of effective carrier lifetime with a MSM junction The following step is to estimate the reduction of free carrier lifetime that can be obtained when polarizing a lateral MSM junction around the resonator. This implies the knowledge of the free carrier distribution of the illuminated photonic crystal. In that purpose, a 2D Technology Computer Aided Design (TCAD) simulation was performed using the ATLAS software which solves the drift-diffusion, carrier generation and Poisson equations by a finite-element method algorithm. The investigated structure is a triangular lattice air hole photonic crystal with a missing hole row in the ΓK direction (namely a W1 waveguide) and two lateral Schottky electrodes that are symmetrical with respect to the waveguide center. The simulation domain is limited to the active region represented in Fig.
Particle identification (PID) requirements are imposed on all three tracks to suppress combinatorial background and mis-identified charm meson decays. The same Λ + c selection is used for the signal and normalisation modes. The Ξ + cc candidates are formed by combining a Λ + c candidate with two tracks, one identified as a K -and one as a π +. These three particles are required to form a common vertex (χ 2 /ndf < 10) that is displaced from the PV (vertex separation χ 2 > 16). The kaon and pion daughter tracks are also required to not originate at the PV (χ 2 IP > 16) and to have p T > 250 MeV/c. The Ξ + cc candidate is required to point back to the PV and to have p T > 2000 MeV/c. A multivariate selection is applied only to the signal mode to further improve the purity. The selector used is an artificial neural network (ANN) implemented in the TMVA package  [37].
In the present contribution we demonstrate that Medium Energy Ion Scattering (MEIS) measurements and Rutherford Backscattering Spectrometry (RBS), in combination with pertinent data from Transmission Electron Microscopy (TEM) and/or Grazing Incidence Small Angle X-ray Scattering (GISAXS) can indeed provide a rather complete and accurate characterization of buried NP systems. Our studies are performed considering a model case system consisting of planar arrangements of Au NPs containing three distinct Au concentrations embedded in a SiO 2 film. GISAXS and TEM are well-established techniques to investigate microstructural properties of such NP systems  11, 12. Only recently, the potential of MEIS as a tool for the characterization of shape, sizes, local composition.
and stoichiometry of NPs systems has been more systematically explored, but mostly for surface located nanostructures  [13] [14] [15] [16]. For more complex systems the MEIS potentialities can be significantly enhanced with the aid of simulation codes such as the PowerMEIS  17, 18. This code also accounts for multiple scattering effects, which otherwise tend to blur the information extracted from buried NP systems  19. In the present contribution we demonstrate that, it is possible to obtain detailed information not only on the microstructure properties of the Au NPs but also on the dissolved part of the Au content (atomically or as small clusters with a few tens of atoms), which was quantified according to their concentration and the depth distribution.
The total amount of the deposited Au measured by MEIS (and confirmed by RBS measurements) for the 25, 50 and 100 s samples are 1. 8, 3. 1 and 7. 4 3 10 15 Au atoms/cm 2 , respectively. Taking into account the total amount of deposited Au, MEIS simulations were carried out using the PowerMEIS code  22. An analysis without considering the TEM data could lead to unrealistic results since there are many free parameters in the simulation. Therefore the NP sizes and number concentration obtained by TEM were used as an input to the simulations  18. In order to simulate a MEIS spectrum one has to assume a particular geometrical shape, atomic composition and density. In the present case we assumed 2D arrays of spherical NPs with given radius and areal density. Since the total amount of atoms is fixed, only the NP radius was adjusted.
Typical beam current was less than 15 nA. The angle of incidence used was of 10u and backscattered He 1 ions emerging from the target were analyzed using a Toroidal Electrostatic Analyzer (TEA) mounted at 120 degrees with respect to the beam direction. At the top end of the TEA a set of two microchannel plates coupled to a position-sensitive detector allows each ion to be energyand angle-analyzed leading to 2-D spectra. The TEA angular aperture is 24 degrees and each angle bin corresponds to 0. 08 degrees. The overall energy resolution of the system is 600 eV. Details of the data analysis are described in refs. 17-19, 22. The MEIS analysis was performed using the 500 kV electrostatic accelerator from the Ion Implantation Laboratory (LII), IF-UFRGS. The MEIS measurements were analyzed using the PowerMEIS package  22  where the sample is discretized layer by layer using full 3D matrices.
Each one represents a layer, and each element of the matrix stands for specific composition, stoichiometry and density of the material. In this way the set of NPs was generated with specific shapes, size and pair correlation function. The PowerMEIS program can handle any geometric shape, size distribution, and density of the nanostructures. It also accounts for the asymmetry of the energy loss-distribution due to the backscattering collision and to multiple scattering effects. Standard Rutherford backscattering Spectrometry (RBS) experiments were also performed using a 1. 4 MeV He 21 ion beam from the 3 MV tandetrom accelerator from the LII-IF-UFRGS. TEM observations were performed in cross-sectional and plan-view samples prepared by ion milling. The samples were characterized at 200 keV via selected area diffraction measurements (SAD) as well as via diffraction and phase contrast observations modes to determine shape, size, size distribution, spatial order and phase of the NPs using a JEM 2010 microscope from the Center of Electron Microscopy UFRGS.
Additional high-resolution observations were carried out in a Cs-corrected FEI Titan 80/300 microscope from the Brazilian National Institute of Metrology (INMETRO). Z-contrast images were acquired through scanning transmission electron microscopy (STEM) using a high-angle annular dark-field detector  (HAADF). The GISAXS measurements were performed in the Brazilian Synchrotron Light Source LNLS, with 8. 5 keV of X-ray energy. The GISAXS data were analyzed with the FitGISAXS package  24  developed within the IGOR Pro analysis software (WaveMetrics, Inc. ).
The developed code has been validated on several benchma rk tests of natural and forced convection  [20]. At each time-step, a converged solution was supposed to be obtained when the residuals of all transport equations reached the L 2 -norm tolerance of 10 À6 in non-dimensi onal form. The calculations were performed on a shared memory machine (SGI ALTIX), with 20 Itanium2 processors and 40 GBytes memory, using OpenMP instructions for the loops parallelization  [20, 21].