dataesr/scientific-paragraphs-categorization huggingface dataset:
Features of plasmids associated with copper resistance in xanthomonads Cop genes were plasmid-borne for all the Xanthomonas strains sequenced. Consistent with previous WGS data from Stenotrophomonas maltophilia, these genes were present on the chromosome of the strain of Stenotrophomonas sp. isolated from citrus phyllosphere  (Crossman et al. 2008; Davenport et al. 2014; Pak et al. 2015). A MAUVE comparison suggested that, with the exception of X. euvesicatoria LMG930, all other plasmids bearing cop genes were genetically related (Fig. 2 ). Consequently, the plasmid from the X. citri pv. citri strain LH201 was arbitrarily selected as our reference. MAGE annotation of this plasmid revealed two tRNA and 258 CDS, 176 of which (68%) encoded proteins of unknown function (Fig. 3 ). We identified the plasmid replication initiator gene trfA near a GC-skew switch.
This commonly indicates the origin of replication (oriV)  (Grigoriev 1998) , suggesting that the oriV locus is located nearby. We revealed an 87 amino acid long conserved domain of a putative HigB-like addiction module killer toxin (e-value < 10 -10 )  (Schuessler et al. 2013). A 222 amino acid long putative transcriptional regulator of the xenobiotic response element family, which might serve as an antitoxin protein, was found downstream and antisense to the toxin (evalue < 10 -8 ). The pLH201. 1 encodes for all the apparatus required for conjugation with 16 Tra proteins, located at two different regions of the plasmid (region 1: 69 675 -74 152; region 2: 182 783 -205 787) and organized in at least three operons (Fig. 3 ). Using the NCBI plasmid and the ICEberg ICE databases, we conducted a search at the amino acid level, keeping only sequences that matched at least one Tra protein from each of the three pLH201.
Networks of gene sharing As the clues indicated a mosaic structure for the Cu R plasmid, we searched for pLH201. 1 homologues in the public NCBI databases NR and WGS. Networks of gene sharing (Fig. 4 ) revealed that pLH201. 1 homologues present in X. citri pv. citri could only be identified from X. gardneri and X. vesicatoria, consistent with data produced in this paper. In contrast, genes homologous to TnpLH201. 1 were detected from 14 species included in five genera (Xanthomonas, Stenotrophomonas Pseudoxanthomonas, Pelomonas and Pseudomonas). Globally, Cu R gene homologues were found further apart in the taxonomy than plasmid backbone homologues. 30% of the genomes represented on the network only shared one or two genes with pLH201. 1, 86% of which (26% of the total) only matched known insertion sequences.
2011). In 12 out of 13 Cu R sequenced strains, we identified an additional gene cluster that could be involved in copper resistance and may explain the partial phenotype restoration observed by  Behlau et al. (2011). The HME-RND system, which is also present in S. maltophilia  (Crossman et al. 2008 ) and forms a channel through the periplasm, is composed of an inner membrane pump (here CusA), a periplasmic protein (CusB) and an outer membrane protein (SmmD)  (Routh et al. 2011). The cusAB/smmD is not widespread among xanthomonads. It is not present in the draft genome of the strain complemented with copLAB by  Behlau et al. for their functional analysis (data not shown) and, to date, has solely been detected from the draft genome of the Cu R X. vesicatoria ATCC 35937 and mentioned in the NR database in S.
Acknowledgements We would like to thank  B. Barrès ,  B. Doublet  and  P. Roumagnac  for their helpful contribution to discussions, as well as all those who provided help during field prospection. The  European Regional Development Fund (ERDF)  and  European Agricultural Fund for Rural Development (EAFRD) ,  Conseil Départemental de la Réunion ,  Région Réunion , État français, the  French Agropolis Foundation  ( Labex Agro -Montpellier, E-SPACE  project number  1504-004 ),  ANSES  and  CIRAD  provided financial support.
Acknowledgements We acknowledge the departments of Life and Material Sciences of the french  Centre National d'Etudes Spatiales (CNES)  for financial support. We are grateful to the  Research Center for Obstetrics, Gynecology and Perinatology (Moscow)  and to  Mikhail Vysokikh  for collaboration and for providing DT with the opportunity of long-term stays at LIPhy and IAB. Confocal facility of the IAB platform was cofunded thanks to grants of " Association pour la Recherche sur le Cancer" (ARC, Villejuif, France) ,  "Ligue Contre le Cancer" (LCC Isère/Ardèche) , and the  CPER program. We thank  Dr. Salima Rafai  ( LIPhy ) for her help with particle tracking velocimetry,  Pr. Marc-Antoine Custaud  ( Univ. of Angers, France ),  Dr. Abdul Barakat  and  Avin Babataheri  ( LadhyX laboratory, Palaiseau, France ) for stimulating discussions and suggestions at the early stage of the project.
Minerals were identified using the PDF-2 database cards from the ICDD (International Centre for Diffraction Data, http://www. icdd. com). The temperature at which primary mineral peaks began decreasing in intensity marked the onset of phase instability and the temperature at which these peaks became indistinguishable from background defined the phase-out point. Differential scanning calorimetry was performed using a Netzsch Pegasus 404 simultaneous thermal analyser. 30-70 mg of rock material, gently hand-crushed in an agate mortar, was loaded into lidded platinum crucibles. The experiments were performed in a 20 ml. min -1 argon flow. The mass and unconverted DSC signal (μ V. mg -1 ) were measured continuously at high resolution 200 pts. K -1. Baseline empty-crucible runs were subtracted from the resultant data.
Acknowledgements This work could not have been achieved without the impetus from  Rebecca L. Hearne  and was benefited by three anonymous reviewers, internal review by  Diane Moore , and editorial handling by  Philip Benson. Funding was provided by the  European Research Council  grant EVOKES and a  Partenariats Hubert Curien Procope grant  (grant number  332065SG ). We are grateful to the  British Geological Survey  for providing the open-access map data used in Fig. 4 (license available here: http://www. nationalarchives. gov. uk/doc/open-government-licence/version/3/).
Data collection The data included demographics, cardiovascular risk factors (history of hypertension or treated hypertension, diabetes, history of hypercholesterolemia or treated hypercholesterolemia, current smoking), admission characteristics and hemodynamic parameters. Patients' BMI (weight (kg)/height (m 2 )) was measured within 48 hours of admission. Ischemic time was the time between symptom onset and crossing the culprit lesion with the floppy guide wire. We recorded anterior wall infarction, and coronary angiograms before intervention, after aspiration thrombectomy, and at the end of the procedure were analyzed. We evaluated baseline, post-thrombectomy, and final antegrade coronary flow according to the TIMI (Thrombolysis In Myocardial Infarction) criteria, together with the final myocardial blush grades.
CMR data analysis Prospective image analyses were performed using QIR 1 software (Universitede Bourgogne, Dijon, France). Left ventricular End-Diastolic Volume (EDV) and End-Systolic Volume (ESV) were calculated from short-axis views. The Left Ventricular Ejection Fraction (LVEF) was calculated with the following formula: LVEF = (EDV-ESV)/EDV. Reverse remodeling was defined as a decrease in LVESV >10% on the cardiac MR images obtained one week and 6 months after STEMI  [16]. For the detection and quantification of the infarct zone and microvascular obstruction, an automatic method was used. First, the endocardial and epicardial contours were manually traced on each short-axis LGE image. The myocardium area was segmented as normal and pathological areas using a Gaussian mixture model (GMM).
Microvascular obstruction was defined as a dark area surrounded by the MI area. Infarct size (IS) was determined for each patient by summing the results for each slice multiplied by the gap between slices, and was expressed as a percentage of total myocardial volume. In addition, delayed enhancement images were visually analyzed according to a 17-segment model. Images were analyzed by the consensus of 2 expert observers, blinded to patient data and the results of other examinations. The inter-observer variability was less than 5%. In cases of disagreement, the final decision was taken by consensus.
MPO, MO and infarct size Microvascular obstruction as assessed by CMR at day 3 was observed in the same proportion (50 vs. 65%, p = 0. 728) between the low vs. high MPO group levels. However, the extent of the microvascular obstruction was significantly greater in the high-MPO group (6 (0-9) vs. 16. 5 (0-31), p = 0. 027) (Table  2 ), together with a greater infarct size, and a trend towards a lower left ventricular ejection fraction (LVEF) (p = 0. 054) at one week. CMR data at 6 months showed that reverse systolic remodeling was two fold more present in the low-MPO group (p = 0. 058). Interestingly, the extent of MO (8. 5 (6. 5-31) vs. 4. 1 (3-11. 55), p = 0. 042) and IS remained significantly greater (24. 5 (9. 75-35) vs. 7. 5 (2. 5-18. 75), p = 0. 022) (Fig  1 ) in the high-MPO group. Plasma MPO levels at the culprit artery positively correlated with the IS at the acute phase but also at 6-months (respectively r = 0.
The coming era of large photometric wide-field surveys will increase the detection rate of supernovae by orders of magnitude. Such numbers will restrict spectroscopic follow-up in the vast majority of cases, and hence new methods based solely on photometric data must be developed. Here, we construct a complete Hubble diagram of Type II supernovae combining data from three different samples: the Carnegie Supernova Project-I, the Sloan Digital Sky Survey-II SN, and the Supernova Legacy Survey. Applying the Photometric Colour Method (PCM) to 73 Type II supernovae (SNe II) with a redshift range of 0. 01-0. 5 and with no spectral information, we derive an intrinsic dispersion of 0. 35 mag. A comparison with the Standard Candle Method (SCM) using 61 SNe II is also performed and an intrinsic dispersion in the Hubble diagram of 0.
Carnegie Supernova Project-I The CSP-I had guaranteed access to ∼ 300 nights per year between 2004-2009 on the Swope 1-m and the du Pont 2. 5-m telescopes at the Las Campanas Observatory (LCO), both equipped with high-performance CCD and IR cameras and CCD spectrographs. This observation time allowed the CSP-I to obtain optical-band light-curves 67 SNe II (with z ≤ 0. 04) with good temporal coverage and more than 500 visual-wavelength spectra for these same objects. The optical photometry (u, g, r, i) was obtained after data processing via standard reduction techniques. The final magnitudes were derived relative to local sequence stars and calibrated from observations of standard stars  (Smith et al. 2002)  and are expressed in the natural photometric system of the Swope+CSP-I bands. The spectra were also reduced and calibrated in a standard manner using IRAF.
Sloan Digital Sky Survey-II SN Survey The SDSS-II SN Survey was operated during 3-years, from September 2005 to November 2007. Using the 2. 5-m telescope at Apache Point Observatory in New Mexico  (Gunn et al. 2006) , repeatedly imaged the same region of the sky around the Southern equatorial stripe 82  (Stoughton et al. 2002). This survey observed about 80 spectroscopically confirmed core-collapse SNe but the main driver of this project was the study of SNe Ia, involving the acquisition of only one or two spectra per SNe II. The images were obtained using the wide-field SDSS-II CCD camera  (Gunn et al. 1998) , and the photometry was computed using the five ugriz filters defined in  Fukugita et al. (1996). More information about the data reduction can be found in  York et al. (2000) ,  Ivezić et al.
2006) , to constrain SN II rise-times  (González-Gaitán et al. 2015) , and to derive a precise measurement of the core-collapse SN rate  (Bazin et al. 2009). Photometry was obtained in four pass-bands (g, r, i, z) similar to those used by the SDSS-II and CSP-I  (Regnault et al. 2009 ). After each run, the images are pre-processed using the Elixir pipeline  (Magnier & Cuillandre 2004 ) and then, sky background subtraction, astrometry, and photometric correction have been performed using two different and independent pipelines. The description of all the data reduction steps can be found in  Astier et al. (2006) ,  Baumont et al. (2008) ,  Regnault et al. (2009) ,  Guy et al. (2010) ,  Perrett et al. (2010) , and  Conley et al. (2011). Due to the redshift of the SNe, and their faintness, spectroscopy was obtained using different large telescopes.
2002). In the following we describe how we account for these factors and place all of the photometry on a common photometric system. Correcting for AvG is straightforward using the value derived by  Schlafly & Finkbeiner (2011)  and gathered in the NASA/IPAC Extragalactic Database (NED 7  ). Correcting for Avh is more complicated. To date, no accurate methods exist. For example, the equivalent width of the Na I doublet lines  (Turatto et al. 2003 ) is a bad proxy for extinction  (Poznanski et al. 2011). For the colour-colour diagram, and multi-band fit methods  (Folatelli et al. 2013; Rodríguez et al. 2014 ) a better understanding and estimation of the SNe II intrinsic colour is necessary to derive a good approximation of Avh. To take into account the host-galaxy extinction, similarly to what it has been done in SNe Ia cosmology, we add a colour term correction in the standardisation method which takes care of the magnitude-colour variations independently of their origin.
Support for T. D. , S. G. , M. H. , H. K. , C. G, is provided by the  Ministry of Economy, Development, and Tourism's Millennium Science Initiative  through grant  IC120009 , awarded to  The Millennium Institute of Astrophysics, MAS. S. G. acknowledges support from  Basal  Project  PFB03. H. K. also acknowledge support by  CONICYT  through  FONDECYT  grants  3140566  and 3140563 respectively. L. G. was supported in part by the  US National Science Foundation  under Grant  AST-1311862. M. D. S. gratefully acknowledge generous support provided by the  Danish Agency for Science and Technology and Innovation realized  through a  Sapere Aude Level 2 grant. M. S. acknowledges support from  EU/FP7-ERC  grant  615929. The work of the  CSP-I  has been supported by the  National Science Foundation  under grants  AST0306969 ,  AST0607438 , and  AST1008343.
This research has made use of the NASA/IPAC Extragalactic Database (NED) which is operated by the  Jet Propulsion Laboratory, California Institute of Technology , under contract with the  National Aeronautics and Space Administration  and of data provided by the  Central Bureau for Astronomical Telegrams. This work is based in part on data produced at the  Canadian Astronomy Data Centre  as part of the  CFHT Legacy Survey , a collaborative project of the  National Research Council of Canada  and the  French Centre National de la Recherche Scientifique. The Work is also based on observations obtained at the  Gemini Observatory , which is operated by the  Association of Universities for Research in Astronomy, Inc. , under a cooperative agreement with the NSF on behalf of the Gemini partnership: the  National Science Foundation  ( United States ), the  STFC  ( United Kingdom ), the  National Research Council (Canada) ,  CONICYT (Chile) , the  Australian Research Council (Australia) ,  CNPq (Brazil)  and  CONICET (Argentina).
CSP-I=Carnegie Supernova Project-I, SDSS-II=Sloan Digital Sky Survey II SN, SNLS= Supernova Legacy Survey. NOTE. -In the first column the SN name, followed by its reddening due to dust in our Galaxy (Schlafly & Finkbeiner 2011)  are listed. In column 3, we list host-galaxy heliocentric recession velocities. These are taken from the NASA Extragalactic Database (NED: http://ned. ipac. caltech. edu/). In column.
Radiometric data A detailed airbone radiometric survey was performed over the Armorican Massif by the BRGM (Bureau de Recherche Géologique et Minière). The detailed acquisition and treatment methods applied to the airborne radiometric data are provided in  Bonijoly et al. (1999). To get complementary radiometric data at a smaller scale, qualitative measurement of the U, Th and K contents were carried out on selected outcrops using a portable spectral gamma ray (RS-230 BGO Super-Spec -Radiation Solution, this study). The duration of analysis was 3 minutes and the results reported in Table  1  correspond to the average of three analyses performed on an outcrop surface of about 4 m². No analytical biases were noticed whether the measurements were done perpendicularly or parallel to the foliation planes.
Apatite fission tracks analysis Apatite fission track (AFT) analysis was performed on three samples from the Guérande leucogranite using the external detector method (see supplementary material for details on the method). The AFT measurements were made in Géosciences Rennes using a Zeiss Axioplan 2 microscope with a 1250x magnification under dry lenses. For each samples, a total of 20 inclusionfree apatite grains oriented parallel to the c-axis were measured using the TrackWorks software (on manual mode) developed by the Autoscan company (Australia). Age calculations were done using the TrackKey software  (Dunkl, 2002). A weighted mean zeta value of 335. 9 ± 6. 8 yr cm² (CB) obtained on both the Durango  (McDowell et al. , 2005)  and Mount Dromedary  (Green, 1985; Tagami, 1987)  apatite standards was used.
All ages reported in this study are central ages  (Galbraith and Laslett, 1993)  reported at ± 2σ. Measurements of the horizontal track lengths and their respective angle with c axis, as well as the mean D par value (e. g. Jolivet et al. , 2010; Sobel and Seward, 2010)  were obtained for each sample. The D par value corresponds to the etched trace of the intersection of a fission track with the surface of the analyzed apatite (parallel to the c axis). The mean D par value used for each A C C E P T E D M A N U S C R I P T sample was obtained by measuring more than 300 D par. Inverse time-temperature history modeling was performed using the QTQt software  (Gallagher et al. , 2009; Gallagher, 2012)  with the annealing model of  Ketcham et al. (2007)  that takes into account the D par parameter to constrain the annealing kinetic of fission tracks.
The rare earth element (La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu) concentrations in the uranium oxides were quantified using a LA-ICP-MS system composed of a GeoLas excimer laser (ArF, 193 nm, Microlas) coupled to an Agilent 7500c quadrupole ICP-MS. The detailed methodology is provided as supplementary material and followed the one proposed by  Lach et al. (2013). U-Pb isotope analyses were performed using a CAMECA IMS 1270 ion microprobe. The complete methodology is described in  Mercadier et al. (2010). Ages, calculated using the ISOPLOT software  (Ludwig, 2012) , are provided with their 2σ uncertainties. All the isotopic ratios are provided in supplementary Table  1.
12 ). The mean track lengths of the samples are similar, ranging from 13. 1 to 13. 3 µm. Yet, the GUE-5 sample displays a mean D par value of 1. 2 µm, slightly lower than the values obtained for the GUE-3 and GUE-4 samples (D par = 1. 5 µm). The lower D par value of the GUE-5 granite, which reflects a relatively faster rate of fission track annealing, could account for its younger apparent age. Data from the three leucogranite samples were used together to model the low-temperature thermal history of the Guérande leucogranite using the QTQt software (Fig. 12a )  (Gallagher, 2012). The muscovite 40 Ar/ 39 Ar dates available on the Guérande leucogranite range from ca. 307 to ca. 303 Ma  (Le Hébel, 2002). Consequently, based on the closure temperature for the muscovite 40 Ar/ 39 Ar geochronometer  (Harrison et al.
Acknowledgments This work was supported by the 2012-2013  NEED-CNRS (AREVA-CEA ) and 2014 -CESSUR-INSU (CNRS)  grants attributed to  Marc Poujol. We are grateful to AREVA (in particular to  D. Virlogeux  and  J-M. Vergeau ) for providing uranium oxides samples and for fruitful discussions. Many thanks to  S. Matthieu ,  L. Salsi ,  O. Rouer  from the  SCMEM (GeoRessources -Nancy) ,  M. C. Caumon.
Methods and analysis: This systematic review and meta-analysis will include cross-sectional, case-control and cohort studies of populations residing inside African countries, which have reported the prevalence of CHD, confirmed by an echocardiographic examination and/or describing different patterns of these abnormalities in Africa. Relevant abstracts published without language restriction from 1 January 1986 to 31 December 2016 will be searched in PubMed, Exerpta Medica Database and online African journals as well as references of included articles and relevant reviews. Two review authors will independently screen, select studies, extract data and assess the risk of bias in each study. The study-specific estimates will be pooled through a random-effects meta-analysis model to obtain an overall summary estimate of the prevalence of CHD across studies.
Search strategy for identifying relevant studies The search strategy will be implemented in two stages: Bibliographic database searches (A) Relevant abstracts published without language restriction on the prevalence, incidence, main aetiologies and clinical features of CHD in Africa will be identified via a search of PubMed, Exerpta Medica Database and online African journals. The search will be limited to studies published between 1 January 1986 and 31 December 2016. Both text words and medical subject heading terms will be used. Key search terms include: 'congenital heart defects' or 'congenital heart disease' as well as the name of every known pattern of these abnormalities. We will also use individual country names for the 54 African countries as additional key search terms for more abstracts on the subject.
Conference proceedings and studies from grey literature of the study period will also be identified through databases and checked. The main search strategy is shown in table  1. (B) The abstracts of all eligible papers will be reviewed and full articles will be accessed through PubMed, Exerpta Medica Database, Google Scholar, HINARI or journals' websites. Additionally, references of all relevant articles and reviews will be scrutinised for other potential data sources and their full texts will be accessed in a similar way. The authors whose full text papers will not be accessible by the numerous internet-based sources will be directly contacted to provide them. In case of no feedback from these authors, the corresponding studies will be excluded.
Data extraction and management A data extraction sheet will be used to collect information about the author, the country, the year of publication, the study design, the sample size population, the mean/median age of the population, the age range, the sex ratio, the prevalence of CHD as well as main patterns when available. Where prevalence or information for calculating them (eg, sample size, number of outcomes) is lacking, we will directly contact the corresponding author and request the information. In case of multinational studies, we will separate the results to show the prevalence and aetiologies within individual countries. Where it will not be possible to disaggregate the data by country, the study will be presented as one and the countries in which the study was carried out will be shown.