dataesr/scientific-paragraphs-categorization huggingface dataset:
It is shown that a larger training set is strongly desirable, and it is shown that samples near the center of the compositional phase space could be trained with a smaller set than samples near the edge of the phase space. In anticipation of adding standards to the training set by using spectra obtained on laboratory instruments nearly identical to ChemCam, requirements are determined for matching the wavelength at each channel and for matching ChemCam's spectral resolution. It is shown that errors associated with precision are only a small fraction of the overall uncertainties. We have also shown that, preliminarily and within current uncertainties, the plasma temperature does not appear to change as a function of the distance to the target. Overall, the calibration database obtained with the ChemCam instrument prior to launch has supported the Mars analyses moderately well, but will be enlarged and further optimized for the Mars data that are currently being obtained.
Acknowledgments The ChemCam team is grateful for support from the  NASA   Mars Program Office for ChemCam , and from  CNES. We also gratefully acknowledge the  Los Alamos National Laboratory 's  laboratory-directed research and development exploratory research (LDRD-ER) program  for supporting early MVA studies. Many people supported the ChemCam instrument that was used to carry out these studies, and we are particularly grateful to other ChemCam team members who supported this work. B. Banisadr  is thanked for his contributions to the total emission studies.
The differentiation of H2k mdx and C2C12 cells were monitored by measuring the Troponin T level by 'western blot' (data not shown). Primary cardiomyocytes were isolated from the ventricles of 1-to 2-day-old newborn wild-type C57BL/6 J mice (Charles River) or mdx mice (provided by M. Wood) by enzymatic digestion with type-4 collagenase (Serlabo Technologies) and pancreatin (Sigma-Aldrich), as described previously  (31). Briefly, freshly isolated cells were seeded in T25 flasks to allow selective adhesion of cardiac fibroblasts  (32)  in plating medium: 250 ml DMEM (PAA laboratories), 250 ml M199 (Sigma-Aldrich), 5 ml glutamax (100X, Gibco Õ , Life Technologies), 5 ml PS, 50 ml horse serum (HS, Sigma-Aldrich) and 25 ml FBS (PAA laboratories). Cardiomyocytes remaining in the supernatant were seeded in well culture plates coated with 0.
An EC50 of 183 nM was recorded for Pip6a-PMO in H2k mdx myoblasts (data not shown), which is $6-times lower than in the H2k mdx myotubes. We also monitored exon-23 skipping 48 h post-treatment and a more pronounced exon-skipping activity was achieved compared with 24 h treatment (EC 50 at 48 h = 20 nM) (Supplementary Figure  S1 ). We also verified that the unlabelled Pip6a-PMO conjugate had a similar biological activity profile as compared with the fluorescently labelled conjugate (Supplementary Figure  S2 ). Taken together, these studies show that Pip6a-PMO enables efficient exon skipping at low concentrations (as indicated by EC 50 values) and is completely resistant to interference by serum proteins in line with its ability to restore efficiently dystrophin expression on systemic administration in mdx mice  (28).
H2k mdx myoblasts and myotubes were treated with Pip6a-PMO, and its cellular distribution was analysed by fluorescence microscopy. Strikingly, the intracellular distribution of Pip6a-PMO was rather different in H2k mdx myoblasts and myotubes (Figure  3 ). In myoblasts, Pip6a-PMO had a mostly cytoplasmic punctate distribution pattern reminiscent of association with endocytic vesicles and little fluorescence arose from cell nuclei. Longer incubation periods (6 h or 8 h), as well as 4 h post-treatment timelapse experiments (12 h) clearly demonstrated that this dotted Pip6a-PMO pattern did not change over time (data not shown). Nearly the same internalization pattern was observed in H2k mdx myotubes after a short (1 h) incubation (Figure  3 ). On the contrary, at longer incubation times (4 h), Pip6a-PMO was diffusely distributed in the cytoplasm of myotubes and a strong fluorescent signal was recorded in the nuclei (Figure  3 ).
Fluorescence spectroscopy analysis showed that energy-depletion significantly decreased the uptake of Pip6a-PMO (Figure  4A ), although the exon-skipping activity was completely abolished (Figure  4B ). Similar effects were recorded when the experiments were carried out at 4 C under conditions where energy-dependent processes are greatly slowed down (data not shown). From the pharmacological inhibitors of endocytosis only nystatin, which is specific of caveolae-mediated endocytosis, had a pronounced effect on both uptake (Figure  4A ) and exon 23-skipping efficiency (Figure  4B ) of Pip6a-PMO. The involvement of caveolae-mediated endocytosis was confirmed with additional caveolae inhibitors, such as Filipin III and Genistein that also inhibited both uptake and exon skiping activity of Pip6a-PMO (Supplementary Figure  S6 ).
FUNDING Association Franc¸aise contre les Myopathies (AFM), [14784 to M. J. G. , M. J. A. W. and B. L. ]; The work in the laboratory of M. J. G. was also supported by the  Medical Research Council (MRC)  [ U105178803 ] and in the laboratory of M. J. A. W. by the  Medical Research Council  [ G0900887 ]; Work in the laboratory of B. L. was partly funded by the  Centre National de la Recherche Scientifique (CNRS) ; The  EU-Lifelong Learning Programme (ERASMUS Placements ) supported (to S. G. ). Funding for open access charge: Association Franc¸aise contre les Myopathies (AFM), [14784].
Cell motility Random migration experiments were carried out in primary tumour cells. Cells in plastic six-well plates were imaged over at least 6 h using an inverted fluorescent 2D Leica DM IRB microscope with photometric CoolSNAP fx camera in a chamber with controlled temperature and CO 2 conditions and a moving stage. Dividing cells were excluded from the analysis. To access the effect of Trastuzumab on cell motility, cells where imaged 12 h after treatment with 20 mg/ml of Trastuzumab (Herceptin 1 , Roche). The cell tracking plug-in of ImageJ software (http://rsbweb. nih. gov/ij/plugins/track/track. html) was used to calculate parameters of cell motility.
Flow cytometric analysis For anoikis experiments, 5 Â 10 5 cells were cultured in suspension for 16 h (378C; 5% CO 2 ). Cells were stained with annexin V-FITC and/or propidium iodide (556547, BD Biosciences). Cytometric analysis was performed on FACsCalibur (Becton Dickinson). Fifteen thousand events were analysed using CellQuest (Becton Dickinson) and FlowJo software. To study the levels of ErbB2 at the membrane SkBR3 cells were transfected with different constructs. Twenty-four hours after transfection cells were harvested and stained with HER2-APC antibody according to manufacturer instructions. Cytometric analysis was performed on FACSAriaIII (BD Biosciences), 10,000 events per condition were analysed using FlowJo software. Mean-APC fluorescence levels were quantified in cells expressing either Htt Q23 or Q100 (mCherry positive, gated 10 3 to 10 5 ) and/or dynamin 2 constructs (FITC positive, gated 10 4 to 10 5 ).
Mice FVB/N-Tg(MMTV-PyVT)634Mul/J and FVB-Tg(MMTV-Erbb2)NK1Mul/J mice were obtained from The Jackson Laboratory. Hdh Q111/Q111 mouse line (CD1 background) have been described earlier  (Wheeler et al, 1999). For tumour-free survival assays, mice were surveyed for tumour appearance by palpation. Spontaneous tumours dissected in small pieces (8 mm 3 ) were grafted in the right flank of 6-week-old nude mice (Charles river laboratories: Crl:Nu(Ico)-Foxn1 nu;  Morton & Houghton, 2007). Tumour growth was followed and mice were sacrificed before the largest tumour reached 10% of the body weight. Tumoural progression was determined on mice sacrificed at 6, 8, 12 and 14 weeks of age. Abdominal mammary glands were dissected, stained with carmine aluminium and percentage of tumoural area was evaluated using ImageJ software.
RNA extraction, microarray and real time PCR Total RNA was isolated from frozen mammary tumours using miRNeasy mini kit (Qiagen). One hundred nanograms of total RNA was amplified with Ambion 1 WT Expression Kit. cRNA products were monitored using the Nanodrop (Thermo, France) and the Agilent Bioanalyzer. Affymetrix Mouse Exon 1. 0 ST arrays were hybridized according to Affymetrix (Santa Clara, USA) labelling and hybridization procedures. Microarrays were hybridized, washed and scanned using Affymetrix instruments. Total RNAs RIN values were between 8. 1 and 9. 3. Microarrays were hybridized with 4. 7 mg of labelled DNA. Raw data are controlled with Expression console (Affymetrix). RNA samples were retrotranscribed using the First-Strand cDNA Synthesis Kit (Invitrogen). cDNAs were diluted 1:10 and submitted to RT-PCR with 7900HT Fast real time PCR system (Applied biosystems) using power SYBR Green PCR Master mix (Applied biosystems) with the following htt (5 0 -CTCAGAAGTGCAGGCCTTACCT-3 0 , 5 0 -GATTCCTCCGGTCTTTTGCTT-3 0 and 5 0 -CTCAGAAGTGCAGGCCTTACCT-3 0 , 5 0 -GATTCCTCCGGTCTTTTGCTT-3 0 ;  Benn et al, 2008)  and ErbB2 (5 0 -GAAACCGGACCTCTCCTACA-3 0 , 5 0 -CGGAYCYYCYGTCTCCTTCG-3 0 ;  Landis et al, 2006)  oligonucleotide pairs.
Microarray data analysis Dataset analysis and visualization were made using EASANA 1 (GenoSplice technology, www. genosplice. com), based on the GenoSplice's FAST DB 1 annotations. Exon Array data were normal-ized using quantile normalization. Background correction was made by using the antigenomic probes. Only probes targeting exons annotated from FAST DB 1 transcripts were selected. Among these selected probes, bad-quality probes (e. g. probes labelled by Affymetrix as 'cross-hybridizing') and probes with too low intensity signal compared to antigenomic background probes with the same GC content were removed from the analysis. The p-values were not corrected for multiple comparisons. Probes with a DABG p-value 0. 05 in at least half of the arrays were considered for statistical analysis.
Only genes expressed in at least one compared condition were analysed. To be considered as expressed, the DABG p-value had to be 0. 05 for at least half of the gene probes. Unpaired Student t-test was performed to compare gene intensities in the different biological replicates. Genes were considered significantly regulated when fold-change !1. 5 and p-value 0. 05. GEO accession number: GSE28685.
Acknowledgements We greatly acknowledge:  F. Saudou ,  M. A. Glukhova  and  C. T. Quang  for reagents and/or discussions; L. Thibault for help with experiments; F. P. Cordelieres ( Institut Curie imaging facility ), staff of the  Institut Curie animal facility ,  S. Dodier  ( Institut Curie histology facility ),  C. Lasgi  ( Institut Curie Flow cytometry facility ),  N. Gruel ,  C. Hego ,  C. Jauffret ,  A. Nicolas  and  C. Reyes  for advice and technical help; members of the  Humbert and Saudou's laboratories  for helpful comments. This work was supported by grants from  Agence Nationale pour la Recherche -Maladies Rares  ( ANR-09-BLAN-0080 , S. H. ),  Association pour la Recherche sur le Cancer  (ARC subvention libre n83188, S. H. ),  CNRS ,  INSERM and Institut Curie. C. M. S. was supported by a Fundaca ˜o para a Ciencia e a Tecnologia ( FCT, Portugal) doctoral fellowship  ( SFRH/BD/60728/ 2009 ); J.
Theoretical estimation of the Hill coefficient is determined by the mean of Gnuplot software. The latter own a fitting command based on the nonlinear least-squares Marquardt-Levenberg algorithm to infer the parameters values. The process consists at three mains steps: i) describe a user-defined analytical function with undetermined parameters; ii) provide this function to the fit command and iii) choose the variable parameters of interest. The output of this command gives information about the value of the desired parameter, its standard deviation error and a confidence interval.
Acknowledgments We thank  José A. Rodrigo  and  Tatiana Alieva  for valuable advice and  Paqui, Óscar  and  Juana  for invaluable support. The financial support from the  Spanish Ministerio de Economía y Competividad  under projects  TEC   2011-23629 ,  CTQ2008-02578/BQU ,  CTQ2012-37404-C02-01  and Consolider SAUUL  CSD2007-00013  and from  Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) ,  Brazil , under project  477260/2010-1 , are acknowledged. P. V. acknowledges a PQ fellowship of  CNPq. The publication of this work was supported by  Servicio Nacional de Aprendizagem Industrial (SENAI) -DR/Bahia, Brazil.
For these levels, static absorption measurements are performed to obtain absolute values of the 2 3 S atom density at null polarization. Then, at fixed OP light power (0. 5 W), the three full OP dynamics (build-up and decay) are successively recorded. For the last and strongest discharge, two additional recordings of the polarization build-up are performed at higher power (1 and 2 W) before the discharge is switched off. The data at 0. 5, 1, and 2 W are thus acquired in identical plasma conditions, which are expected to be fairly close to those characterized by the initial static measurements given the generally good reproducibility of the results. 2. 4 2 3 S-2 3 P light absorption measurements.
If the whole set of data is considered, irrespective of cell contents, the changes in Γ OP seem to correlate better with those of the 2 3 S atom density (Fig. 13b ) than with those of the decay rate (Fig. 13c ). Recently a fairly simple approach of MEOP dynamics has been proposed, based on a global angular momentum budget for the atomic system  [24]. In the rate equation describing the time evolution of M , the pumping speed is obtained as the net difference between a driving OP term (the rate at which nuclear orientation is transferred from the OP light to the 1 1 S atoms, through ME collisions with the polarized 2 3 S atoms) and of a loss term (the rate at which orientation is destroyed by relaxation processes). The input rate of angular momentum is determined by the global efficiency of the OP cycles and increasingly sophisticated models have been developed to quantitatively account for all relevant processes: laser-induced 2 3 S-2 3 P transitions, spontaneous emission, redistribution between Zeeman sublevels (by collisions or other interactions), ME exchange with the 1 1 S atom reservoir.
The peaks heights as well as the dip between the two lines are enhanced. These differences in behavior explain the significantly lower sensitivity of the adjustments to the parameter T gas , because the experimental data include a global scaling factor associated with the average 2 3 S atom density n s m and its (unknown) modulation amplitude driven by the rf excitation. For each OP cell, line shape adjustments are performed for all the recordings (MEOP measurements for three rf levels, one test of reproducibility). The data are sometimes too noisy to provide helpful discrimination between adjusted ω L values. However, on average, the uncertainty δω L ranges from ±0. 1 to ±0. 2 GHz for the individual recordings and the results are consistent within δT gas ≃ ±10 K for the whole run (with an individual uncertainty on T gas culminating at ±20 K at high density).
Acknowledgments Financing support from the  European network PHeLINet  ( MRTN-CT-2006-36002 ) and the  Polish Ministry of Science and Higher Education  ( SPUB 547/6. PRUE/2008/07 ) is gratefully acknowledged. Glass work has been carried out at L. K. B. in Paris by  Florence Thibout. Access  to the 4. 7 T magnet has been kindly granted by the  MRI department of the Inst. of Nucl. Phys. in Krakow.
Data Collection The screening procedure included 24 different sampling locations (five samples at each location), 8 in a four bedded medical intensive care unit (MITU) and 16 in a nine bedded surgical intensive care unit (SITU) (Figure  1 ) at the University College London Hospital (UCLH). Ward sampling was carried out with Tryptic Soy Agar (TSA) contact plates (5. 5cm diameter i. e. 24cm 2 ) in order to provide a quantitative measure on a nonselective growth medium, which would enable growth of skin and environmental flora  [11, 12, 13]. Surfaces were sampled at these different locations in each bed space and distant to bed (door pressure panels or handles, nursing station etc). Samples were always taken from the same site on all locations (e. g. the centre panels of doors, the centre of the floor space, the centre of bed rails, centre of the bottom left bed wheel, above the bed head).
Surface types included bed rails, floor, alcohol hand gel pump, bedside table, bed wheels, chair, clinical waste bin, storage trolley and unit top and shelf, top of computer, and surface material (porous and non-porous) are described in Table  S1. Thirdly, samples were taken at the same time at each cross-sectional survey, without alteration to ventilation or cleaning regime, in order to ensure data comparability. Cleaning procedure was undertaken adhering to Department of Health Guidelines  [15] : at UCLH, routine cleaning was undertaken using water and microfibre with no detergent, twice a day (8 am and 3 pm). Samples were taken three hours after routine morning cleaning in an attempt to standardize procedures. In addition, ITU cleaning does take place throughout the day as nurses actively wipe down surfaces with alcohol within bed spaces.
With an incidence ratio significantly higher than 1, a surface type was considered to be at risk of being more contaminated than the reference class, with a higher TVC, whatever the TVC of the reference class. A contrario, with an incidence ratio significantly lower than 1, a surface type was considered to have a lower TVC than the reference class. The statistical analysis was performed using the software R 2. 10. 1 (The R Foundation for statistical computing, Vienna, Austria), and the mgcv 1. 7-22 package developed by Simon Wood  [19]. Maps were performed using the geographic information system ArcGIS (Environmental Systems Research Institute, Redlands, California). All p-values were compared to the classical α-threshold of 0. 05. GAMM for surface types. Associations between bacterial counts and surface types were assessed using a GAMM model including the following risk factors: 'Surface types' and 'Ward' (MITU or SITU).
This study was undertaken with funding provided by the  Health and Care Infrastructure Research Centre  supported by the  Engineering and Physical Sciences Research Council. ECG received salary funding from the  National Institute of Health Research  during the course of this research. NK was supported in part by the  National Institute for Health Research Biomedical Research Centre Funding Scheme at Great Ormond Street Hospital  and the  Institute of Child Health. JG received a research fellowship from the  Association  for the development of research in biology and medicine during his 2012 stay at the  Department of Statistical Science University College London. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
MATERIALS AND METHODS The dietary data and the food database were derived from the INCA French dietary survey. 4 Each food of the food database (n ¼ 597) was allocated to one of two classes, eligible and non-eligible, according to each of the five European nutrient profile systems tested. Their main characteristics can be found in Table  1. Two systems are currently used for food labeling, namely Choices v2. 2  5  and Green Keyhole,  6  two have been proposed to assess food products' eligibility to claim but that are not currently in use, namely the French AFSSA system (Agence Franc¸aise de SecuriteSanitaire des Aliments)  7  and the EC system (European Commission draft),  8  and FoodProfiler, a system in use for self-limiting advertisement to children. 9 Using a previously described diet modeling approach,  3  the feasibility of designing healthy or unhealthy diets with eligible foods only, or with non-eligible foods only, was tested for each nutrient profiling system.
MATERIALS AND METHODS Isolates. The E. coli O104:H4 isolates sequenced in this study were provided by the French National Reference Center for E. coli and Shigella (Institut Pasteur and Hôpital Robert Debré, Paris, France; Table  1 ). These include (i) an isolate from a patient infected in Turkey  (15)  who was among a group of travelers, a number of whom developed bloody and nonbloody diarrhea, and (ii) four sporadic isolates, previously unreported, from children in France with HUS and without known epidemiological links to described outbreaks (Gen-Bank accession no. for Escherichia coli Ec12-0465, AIPQ01000000; Escherichia coli Ec12-0466, AIPR01000000; Escherichia coli Ec11-9450, AGWF01000000; Escherichia coli Ec11-9941, AGWH01000000; Escherichia coli Ec11-9990,AGWG01000000). Besides the genomes of these 5 isolates, we included previously reported E.
Prophages are denoted in bold and plasmids in italic. See text for details and support for hypothetical gain, loss, recombination, and SNP events. Note that not all differences among genomes are represented here; most differences among isolates for which the ancestral state is not certain (for example, phage H on 55989) are not shown. PHAST  (48)  database using an E value cutoff of 1eϪ10. Regions of specific interest were manually annotated to improve the automated gene prediction and annotation. Plasmid analysis. Scaffolds less than 200 kb in size were aligned to reference plasmids by Nucmer  (46)  to determine plasmid content and extent of identity. The plasmids from 01-09591 (also referred to as HUSEC041) were designated pHUSEC41-1 to -4  (20). The set of reference plasmids included pTY1, pTY2, pTY3, p55989, pHUSEC41-1, pHUSEC41-4, pEc09-7901-c, and pEc12-0466-c.
ACKNOWLEDGMENTS This project has been funded in part with federal funds from the  National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services , under contract number  HHSN272200900018C  ( Broad Institute ). M. L. and W. P. H. received support from award number  U54 GM088558  from the  National Institute of General Medical Sciences. Y. H. G. received support from grant number  U54 AI057159. This work was partially supported by the  Institut Pasteur  and by the  Institut de veille sanitaire (Saint-Maurice, France ). The content is solely the responsibility of the authors and does not necessarily represent the official views of the  National Institute of General Medical Sciences  or the  National Institutes of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
We thank all corresponding laboratories of the French National Reference Center for E. coli and  Shigella. We gratefully acknowledge  Charlotte Balière ,  Isabelle Carles ,  Monique Lejay-Colin , and  Corinne Ruckly  for their expert technical assistance. We thank the  Broad Biological Samples Platform  and the  Broad Genomics Platform. We are grateful to  Lucia Alvarado-Balderrama  for GenBank data deposition. We thank  Nick Croucher  and  Bruce Birren  for comments and input on the analyses and  Cheryl Murphy  and  Chad Nusbaum  for their helpful comments on the manuscript.
The absolute value of the imbalance could be affected by the kinematic selection of the trigger pair unrelated to the jet-medium interactions, for example, by the k T effect. To provide quantitative assessment of jet-medium interaction effects and allow discriminating of the theoretical models, the relative di-jet energy imbalance between Au + Au and d + Au data is more informative. Earlier measurement has been previously reported in Ref. [16] ; we use these results here for comparison. The details of new datasets and analysis selections are discussed below. For a more uniform detector acceptance only events with a primary vertex position V Z within 25 cm of the center of the STAR time projection chamber (TPC) along the longitudinal beam direction were used in the analysis. Run 2007 provided 74 × 10 6 Au + Au minimum-bias (MB) events.