dataesr/scientific-paragraphs-categorization huggingface dataset:
0 and 4. 75 with steps of 0. 25 dex. We can also mention the PHOENIX  (Husser et al. , 2013)  models database for stars having T eff <12 000 K and 6 pollux. oreme. org the AMBRE (de Laverny et al. , 2012) project that contains high-resolution FGKM stellar synthetic spectra. As an output of the new Gaia Data Release 2,  Cropper et al. (2018)  describe the Gaia RVS specification as well as the predicted performance at the end of the mission. Gaia RVS will provide us with a large number of spectra in the calcium triplet regime (845-872 nm). This triplet is very sensitive to T eff and log g. The medium resolution (11 500) of the RVS and the small range in wavelength would require LDB smaller than the ones used in our work, leading to a fast application of the RSIR. As we did for the inversion of the S 4 N data in Sec.
1 and 10 pulses per second. The UV output was determined by calculating the output voltage energy in combination with the sample distance from the xenon lamp, the area of the vessel, the PPS and the HRT. It is important to note that the adjustable factors listed as well as the type of sample medium influences the penetration of the PUV light thus the energy delivered by the lamp is different to the energy received by the sample. For example, at 900V, 2PPS and 100s HRT, the UV output was calculated to be 2052 mJ/cm 2 (20. 5 mW/cm 2 ; 112 mW/cm 2 broadband output). All PUV outputs are presented to include only the wavelengths below 300 nm. The total broadband dose received by the sample was analysed using a thermopile power detector (Model: XLP12-3S-H2-IN, Gentec-EO, Quebec, Canada) in conjunction with Integra software.
Statistical Analysis As some of the data sets were not normally distributed and small in sample size it was decided to apply nonparametric analysis. The Kruskal-Wallis test (one-way non-parametric ANOVA) was used to determine significant differences between sample populations. If the null hypothesis for the Kruskal-Wallis test was rejected, this was then followed by a post-hoc Dunn Test for pairwise multiple comparisons to determine significant differences between sample populations. Analysis was carried out using IBM SPSS Statistics 23.
Analytical method and data processing FTIR microscopic analysis to analyze structural hydroxyl in NAMs was performed in the Research Centre for Natural Sciences of the Hungarian Academy of Sciences in Budapest using a Varian FTS 7000 FTIR spectrometer coupled to a Varian UMA-600 IR microscope, and at the Geochemical Analysis Unit at Macquarie University in Sydney, applying a ThermoFisher iN10 FTIR microscope attached to a Varian FTS-60A spectrometer. The analyses were performed using unpolarized infrared light. Infrared spectra of olivine and pyroxenes were obtained between 4000 and 400 cm -1 , using a maximum of 100 × 100 μm aperture size. The samples were measured with a 'Globar' light source, KBr beam-splitter and an MCT detector. At least 128 scans were accumulated from each spot with a 4 cm -1 resolution.
15, a criterion that was always met in this study. The total polarized absorbance (A tot ) is estimated as three times the average unpolarized integrated absorbance. The A tot for each NAM in each sample was obtained using the OPUS® software, applying the following steps: (1) background correction using the concave rubber-band correction routine with 2 iterations and 64 baseline points; (2) averaging the spectra; (3) integration of spectral ranges of structurally bound hydroxyl with B-type integration applying uniform intervals for each mineral (3583-3505 and 3290-3170 cm -1 for olivines; 3740-3020 cm -1 for orthopyroxenes and 3765-3000 cm -1 for clinopyroxenes). Integrated total absorbance values are normalized to 1 cm thickness. The thickness of the sections was measured with a Mitutoyo analogue micrometer, which is accurate to 2-3 μm within the thickness range considered.
2b ). Usually, the former is more intense (NFL1324, NMM1115, NMM1126, NMM0318, NME1122), but in two xenoliths (NMS1310, NTB1124) the latter shows higher absorption intensity. Besides these main absorption bands, there are less frequent bands occurring at ~3695-3675 cm -1 (Supplementary Fig. 1a ) and ~3270-3200 cm -1 (Table  1 ; see spectra on PULI spectral database at puli. mfgi. hu). Bands in the former range are normally well-defined narrow bands (their half width ~10-20 cm -1 ). In contrast, bands at lower wavenumbers are broader and weaker and only minimally contribute to the hydroxyl signal of the orthopyroxenes. The structural hydroxyl contents in orthopyroxenes are extremely variable, ranging between 1 and 147 ppm (with an average of 31 ppm) (Table  1 ). In all three types, most orthopyroxenes have structural hydroxyl contents lower than 30 ppm (54, 62 and 100% of type 1, 2a and 2b, respectively) (Fig.
In addition to the two main bands, several further bands appear in some of the clinopyroxene spectra (see spectra on PULI spectral database at puli. mfgi. hu). In several samples, spectra have shoulders at high wavenumbers (3695-3670 cm -1 ) as in the orthopyroxenes (Supplementary Fig. 1b ; Table  1 ). However, there are only a few lherzolite xenoliths (NTB0307, NFR0307, NFL1305, NBN0311) where these shoulders appear simultaneously in both pyroxenes. Further weak bands are sometimes present at ~3455-3445 and ~3250-3230 cm -1 (Table  1 ; see spectra on PULI spectral database at puli. mfgi. hu). Xenoliths with type 1 clinopyroxenes have higher maximum and average contents of structural hydroxyl (0. 5-894 ppm with an average of 217 ppm) than xenoliths with type 2a and type 2b clinopyroxenes (53-360 and 19-294 ppm with an average of 134 and 98 ppm, respectively) (Fig.
Acknowledgements The authors are grateful to  Csaba Németh  for his help with FTIR measurements in the  Research Centre for Natural Sciences of the Hungarian Academy of Sciences in Budapest. The authors also owe thanks to  Norman J. Pearson  and  David Adams  for their assistance in FTIR analyses at  Macquarie University. The analytical data were obtained using instrumentation funded by  DEST Systemic Infrastructure Grants ,  ARC LIEF ,  NCRIS/AuScope , industry partners and  Macquarie University. The authors are grateful to the  Lithosphere Fluid Research Lab (LRG) of the Eötvös Loránd University  to provide appropriate circumstances for doing research. Sonja Aulbach  is thanked for her constructive comments and thorough structural shaping of the paper. This project has been implemented with the support provided to I.
J. K. from the  National Research, Development and Innovation Fund of Hungary , financed under the  K128122 funding scheme and the Bolyai Postodoctoral Fellowship program  of the  Hungarian Academy of Sciences. The study was also supported by a  Lendület Research Grant  to the  MTA CSFK Lendület Pannon LitH 2 Oscope Research group. The work was further supported by the  Marie Curie International Reintegration Grant  ( NAMS-230937 ) of I. J. K. The FTIR spectra are available on the PULI (Pannonian Uniform Lithospheric Infrared spectral database) website (http://puli. mfgi. hu/). This is the 88th publication of the  Lithosphere Fluid Research Lab (LRG). This is contribution 1239 from the  ARC Centre of Excellence for Core to Crust Fluid Systems  (http:// www. ccfs. mq. edu. au) and 1278 in the  GEMOC Key Centre  (http:// www.
Study cohort and design We conducted a retrospective analysis of prospectively collected data from the EPIPAGE 2 study. EPIPAGE 2 is a population-based prospective study that recruited subjects between March and December 2011 in all the maternity hospitals (levels 1, 2 and 3) in 25 French regions. This study's detailed design was previously described  [15, 16]. Briefly this cohort included all infants live born or stillborn and all terminations of pregnancy between 22 and 31 completed weeks of gestation (WG) and a sample of moderate preterm births between 32 and 34 WG. The number of infants required according to the initial sample size calculations was provided by an 8-month recruitment period for births at 22 through 26 WG, a 6-month period for 27 through 31 WG, and a 5-weeks period for 32 through 34 WG  [16].
Data collection and definitions A premedication was defined as the use of a sedative and/or an analgesic before any tracheal intubation. The use of atropine alone was excluded. At birth and during the neonatal period, data were collected from medical records and completed by questionnaires filled by obstetrical and neonatal teams. The following neonatal data available from the EPIPAGE 2 study were used: gender, gestational age at birth, birth weight, intra-uterine growth restriction based on Olsen's curves  [17] , mode of delivery, Apgar score and management in the delivery room, including tracheal intubation, age at tracheal intubation, chest compression, epinephrine use and drugs used in the DR. Some data were unavailable to guarantee anonymisation of included subjects: precise date of birth and consequently week-days, weekends, ferial days or bank holidays.
The parents of the participants provided their oral consent to participate in this study. Since this study was observational, according to the French legislation, oral consent to anonymously collect data was obtained from the parents. In case the parents expressed their opposition to data collection, the neonates were excluded from the study (around 7% of eligible patients in the main study  [15] ). The oral agreement to participate in the study was written in the medical records of the mothers and the newborns included. If the consent was not obtained or if the patients refused, it was also tracked in the medical charts and the data were not recorded. The ethics committees approved this consent procedure.
This study was supported by the  French Institute of Public Health Research /Institute of Public Health  and its partners the  French Health Ministry , the  National Institute of Health and Medical Research , the  National Institute of Cancer , and the  National Solidarity Fund for Autonomy ; grant  ANR-11-EQPX-0038  from the  National Research Agency  through the  French Equipex Program of Investments  in the Future; and the  PremUp Foundation. The funders/sponsors had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; or decision to submit the manuscript for publication.
The EBSD signals were acquired using the AzTec analysis software (Oxford instruments). We used a sample holder pre-tilted at 70°with respect to the electron beam, an accelerating voltage of 20 kV and a working distance of 20-25 mm. The step size for automatic mapping was in the range of 1-2 µm, dependent of the required resolution, grain size and size of the area measured. Pole figures were calculated using HKL Channel 5 software (Oxford instruments) and the MTEX software  (Bachmann et al. , 2010)  from the raw EBSD output. The latter software was used to colour EBSD maps and for misorientation analysis. For grain reconstruction a thresholding value of 10°was used. The internal misorientation within grains is dependent on the density of geometrically necessary dislocations and thus a measure of the crystal-plastic strain (e.
Acknowledgements. This study was funded by the Deutsche Forschungsgemeinschaft (DFG grant TR534-4-1). Bernhard Stöckhert is gratefully acknowledged for discussions. Namvar Jahanmehr and Michael Herrmann are acknowledged for preparation of thin sections, as are Patrick Eschenbacher and Dominique Mackensen for helping with field work. 13 Solid Earth Discuss. , https://doi. org/10. 5194/se-2018-81 Manuscript under review for journal Solid Earth Discussion started: 21 August 2018 c Author(s) 2018. CC BY 4. 0 License.
Data collection Sixty patients presenting with a unilateral ZMC fracture at the Oral and Maxillofacial Surgery Department of Nantes University Hospital (Center 1) or at the Maxillofacial and Facial Plastic Surgery Department of Tours University Hospital (Center 2) between 2010 and 2017 were included in the study and analyzed retrospectively. All of the patients exhibited a surgically unstable tetrapodal fracture, defined as a type B fracture according to the classification of Zingg et al. [17]. Patients with a fracture of the contralateral ZMC, an isolated zygomatic arch fracture, a ZMC comminutive fracture, or any combined mid-face fracture were excluded from the study. Patients who did not have preoperative or postoperative CT images were also excluded. The medical charts were reviewed and data documenting their date of birth, the side involved, the mechanism of the fracture, clinical findings, the type of surgery, and the duration of the surgery were compiled.
Tomographic evaluation Preoperative and postoperative CT scans or CBCT were comparatively analyzed. Landmarks were placed manually by the same operator (other than the surgeons), either on sagittal, coronal, or axial sequences using Simplant O&O software (Materialise Dental N. V. , Leuven, Belgium). Five landmarks were drawn on 3D images to assess the ZMC projection. The four classical landmarks Zygomaxillare (Mp), Orbitale (Or), Zygotemporale inferior (Zt), and Zygomaticofrontale (FZS) were chosen to represent each pillar of the zygomatic tetrapod (Fig  2 ). These anatomical points of the skull base were considered to be stable in light of their use in craniometry analysis, forensic sciences, and anthropology  [18]. The fifth landmark, chosen as it is reproducible, was the foramen of the zygomaticofacial nerve (Fzf), which represents the projection of the zygomatic body  [19].
Statistical analysis In 20 randomly selected patients, the cephalometric landmarks were positioned by a different operator in order to determine concordance. The methodical error of cephalometric measurements was assessed by Dahlberg's formula (mean square error (S. E 2 ) = d 2 /2N, where d is the difference between the first and the second measurements and N is the number of double measurements)  [22]. The statistical analysis was performed using GraphPad Prism 6. 0 software (GraphPad Software, La Jolla, CA, U. S. A. ). The parametric function of our series was tested with a Shapiro- Wilk test. Comparative analysis of non-inferiority was carried out with a confidence interval of [-2. 5; 2. 5], considering that an asymmetry of 2. 5 mm was the limit for an acceptable result  [23]. The data were secondarily adjusted for age and gender.
Epidemiological data Thirty patients presenting with a surgical ZMC fracture were reviewed and included in each center. Of the included patients, 48 (80%) were men and 12 (20%) were women. The average age at the time of the surgical procedure was 35. 5 ± 16. 4 years at Center 1 and 40. 1 ± 18. 9 years at Center 2 (Table  2 ). We noted a significant predominance of the affected side being on the left malar bone (60% versus 40% for the right side). According to the etiologies of the fractures, physical assaults represented 40% of the cases, followed by traffic accidents (22%), falls (20%), and sports-related injuries (18%). In regard to the clinical findings, 57 patients (95%) had a lack of zygomatic protrusion that was clinically objectivized. The three other patients had a substantial edema or no clinical issues.
Cells were washed, and the cell nuclei were counterstained using DAPI. Fluorescence micrographs were collected by confocal microscopy. Fluorescent foci were quantified using the Blobfinder program (http://www. cb. uu. se/amin/BlobFinder/). As negative control uninfected samples were stained and processed at the same time. Blobfinder analysis was performed using a 7 by 7 blob size and at least 50 cells per sample were analyzed. The average number of blobs counted in the uninfected cells was subtracted from the infected samples. Experiments were performed in triplicate and error bars denote standard error.
QUANTIFICATION AND STATISTICAL ANALYSIS Information about the data quantification and statistical analysis is described in the figure legends. A Student's t test was used to calculate the p value of each experiment using Microsoft Excel. Blobfinder program (http://www. cb. uu. se/~amin/BlobFinder/) was used to determine the number of fluorescent foci per cell in the proximity ligation assay quantification shown in Figure  1. Fiji was used to determine the Mander's coefficient showed in Figure  S3  using the plug in Coloc 2.
33 were assumed. The mobility μ of the migrating particles was converted into the ζ-potential using the Smoluchowski relation (eq 1) (Zetasizer Software 6. 34). ζ μ η ε = • (1) The presented ζ potential titration curve contains three individual measurements on different days. Small-and Wide-Angle X-ray Scattering. The SAXS/WAXS data were recorded at the High Brilliance Beamline ID02 (ESRF, France) with an energy of the incident X-ray beam equal 12. 5 keV (λ = 0. 995 Å). The beam size was about 100 × 100 μm 2 and the sample-todetector distance was 1. 2 m. The small-angle diffraction patterns were collected by a 4 FT-CCD detector (Rayonix MX-170HS). For SAXS, a q range from 0. 006 to 0. 65 Å -1 with a detector resolution of 3 × 10 -4 Å -1 (full width at half-maximum) was used. WAXS data were obtained in a q range from 0.
72 to 5. 1 Å -1. To avoid sample damage by radiation, each sample was measured with 10 frames with an exposure time of 0. 05 s per frame. For data analysis, the average of all 10 frames was used. The collected 2D powder diffraction spectra were reduced and background subtracted using SAXSutilities and analyzed in Origin. The SAXS/WAXS data were corrected for the empty sample holder with pure buffer solution at the corresponding temperature. The angular calibration of the SAXS detectors was performed using silver behenate powder as reference. For WAXS, para bromobenzoic acid was used. The temperature was adjusted with a Huber Unistat with an accuracy of ±0. 1 °C. Experiments have been performed at 20, 25, and 37 °C. The sealed glass capillaries containing the lipid dispersions were well-positioned in a Peltier controlled automatic sample changer.
This bacterium was tested for identification with a Microflex spectrometer (Brüker Daltonics, Leipzig, Germany) as previously described  [9, 10]  and the 12 spectra generated were compared to the 7,567 different bacteria found in our database by standard pattern matching (for which default parameter settings were applied), using MALDI BioTyper database software (version 2. 0, Brüker). A resulting score of <1. 7 didn't enable identification, and a 16S rRNA gene sequencing was performed as previously described  [11]. Codon Code Aligner software (http://www. codoncode. com) was used to assemble and correct sequences, and BLASTn searches were performed in the National Center for Biotechnology Information (NCBI; http://blast. ncbi. nlm. nih. gov. gate1. inist. fr/Blast. cgi). Concerning similarity levels, for thresholds of 98.
Phylogenetic analyses We used a custom python script to automatically retrieve all species belonging to the family of the new species and then downloaded 16S sequences from the NCBI by parsing NCBI eUtils results and NCBI taxonomy page. Only sequences from type strains were kept. In case of multiple sequences for one type strain, the sequence with the best identity rate from the BLASTn alignment with our sequence was selected. The 16S sequences are then separated into two groups: one containing the sequences of strains from the same genus (group a) and one containing the others (group b). The 15 closest strains from group a and the closest one from group b are finally kept. If the script is unable to get 15 sequences from group a, it selects more sequences from group b to get at least nine strains from both groups.
We conducted GC/MS as previously described  [15]. Briefly, we separated FAMEs using an Elite 5-MS column monitored by mass spectrometry (Clarus 500 -SQ 8 S, Perkin Elmer, Courtaboeuf, France). We performed a spectral database search using MS Search 2. 0 operated with the Standard Reference Database 1A (NIST, Gaithersburg, USA) and the FAMEs mass spectral database (Wiley, Chichester, UK). DNA extraction and genome sequencing DNA of strain Marseille-P2817 T was extracted on the EZ1 biorobot (Qiagen) with EZ1 DNA tissues kit following a pretreatment by a lysozyme incubation at 37°C for 2 h. The elution volume was 50 μL. Genomic DNA (gDNA) was quantified by a Qubit assay with the high-sensitivity kit (Life technologies, Carlsbad, CA, USA) to 46. 6 ng/μL. Then gDNA was sequenced by the MiSeq Technology (Illumina Inc, San Diego, CA, USA) with the mate pair strategy.
Genome assembly, annotation and comparison The assembly of the genome was carried out using a pipeline combining different softwares (Velvet  [16] , Spades  [17]  and Soap Denovo  [18] ) on trimmed (MiSeq and Trimmomatic  [19]  softwares) or untrimmed data (MiSeq software only). For each of the six assemblies performed, GapCloser  [20]  was used to reduce gaps. We identified contamination with Phage Phix (BLASTn against Phage Phix174 DNA sequence) which was then eliminated. The scaffolds (<800 bp) were then removed, and scaffolds with a depth value < 25% of the mean depth were removed as they were identified as possible contaminants. The best assembly was selected by using different criteria (number of scaffolds, N50, number of N). For the strain Marseille-P2817 T , Spades gave the best assembly, with depth coverage of 239x.
We predicted open reading frames (ORFs) using Prodigal  [20]  with default parameters, but the predicted ORFs were excluded if they spanned a sequencing gap region (contains N). We searched for the predicted bacterial protein sequences against the clusters of orthologous groups (COGs) database using BLASTP (E-value 1e -03 , coverage of 0. 7 and identity percentage of 30%). If no hit was found, we searched against the NR database using BLASTP with E-value of 1e -03 , coverage of 0. 7 and identity percentage of 30%. If sequence lengths were <80 amino acids, an E value of 1e -05 was used. The tRNA genes and rRNAs were found using tRNAScanSE tool  [21]  and RNAmmer  [22] , respectively, while we predicted lipoprotein signal peptides and the number of transmembrane helices using Phobius  [22]. ORFans were identified if all the performed BLASTP did not give positive results (E-value <1e -03 for ORFs with sequence size >80 aa or E-value <1e -05 for ORFs with sequence length <80 amino acids).
The HMMscan of the HMMER3 suite  [23]  were used to search PFAM conserved domains (PFAM-A and PFAM-B domains) on each protein. We searched PKS and NRPS against the ClusterMine360  [24]  and analysed the resistome by using ARG-ANNOT database  [25]. Toxin and antitoxin were found using a database composed of TADB database  [26]  and homemade toxin and antitoxin of NMNI Mbogning Fonkou et al. New microbes in humans Rickettsia and Wolbachia (which were provided by Cristina Socolovschi). The mobilome was analysed using Phantome  [27] , ICEs (ICEberg)  [28] , ACLAME  [29] , GYSPSYDB  [30]  and CRISPR  [31]. For the latter we used spacer and repeat database to reconstruct CRISPR module. A homemade database  [32]  was used to find bacteriocin. Virulence factors were analysed by using both VFDB  [33]  and MvirDB  [34].
Results Strain identification and phylogenetic analysis Strain Marseille-P2817 T (Table  1 ) was first isolated in March 2016 by a 10-day preincubation in a blood culture bottle supplemented with 4 mL rumen fluid. This bacterium was isolated and cultivated on 5% sheep-blood-enriched Columbia agar in an aerobic atmosphere at 30°C. Strain Marseille-P2817 T was not identified by MALDI-TOF MS because its spectrum did not match any of the spectra present in our database. The 16S rRNA nucleotide sequence (accession number LT576388) exhibited 95. 99% sequence identity with Enterococcus hirae strain ATCC9790 (Genbank accession number NR_075022), the closest validated species. Thus, we can classify strain Marseille-P2817 T as a new species in the Enterococcus genus (Fig. 1 ). A representative reference spectrum was therefore added to our IHU Méditerranée Infection database (http://www.