dataesr/scientific-paragraphs-categorization huggingface dataset:
After an incubation for 24-48h, bacterial colonies were puri ed by subculture and identi ed using MALDI-TOF MS (Bruker Daltonics, Bremen, Germany) as previously described  (Lo et al. 2015a ). The unidenti ed spectra were imported into MALDI Biotyper 3. 0 software (Bruker Daltonics) and analyzed against two databases, that of Bruker and the constantly updated in lab URMS database (https://www. mediterranee-infection. com/acces-ressources/base-de-donnees/urms-data-base/).
16S rRNA gene sequencing In order to classify the isolated bacteria, the 16S rRNA gene sequencing was performed. The primer pair fD1 and rP2 (Eurogentec, Angers, France) was used to amplify the 16S rRNA gene prior to sequencing using the Big Dye® Terminator v1. 1 Cycle Sequencing Kit and a 3500xL sequencer (Thermo sher, Saint-Aubin, France) as previously described  (Drancourt et al. 2000). The 16S rRNA nucleotide sequences were assembled using CodonCode Aligner software (http://www. codoncode. com). The obtained sequence was matched against the GenBank database using  BLASTn (2015). A sequence similarity under 98. 7% and 95% with the phylogenetically closest species was used to de ne a new species and a new genus respectively  (Kim et al. 2014). A phylogenetic tree based on 16S rRNA gene was built with the MEGA 7 software  (Edgar 2004 ) with sequences aligned using the Muscle software  (Kumar et al.
Brie y, two samples were prepared with approximately 70 mg of bacterial biomass per tube harvested from several culture plates. FAMEs were prepared as described by Sasser  (Sasser). GC/MS analyses were performed as previously described  (Dione et al. 2016). FAMEs were separated using an Elite 5-MS column and monitored by mass spectrometry (Clarus 500 -SQ 8 S, Perkin Elmer, Courtaboeuf, France). A spectral database search was then performed using MS Search 2. 0 operated with the Standard Reference Database 1A (NIST, Gaithersburg, USA) and the FAMEs mass spectral database (Wiley, Chichester, UK). Antibiotic susceptibility pro le. The antibiotic susceptibility pro le of the strains was assessed using the disc diffusion method, speci cally E-test strips  (Citron et al. 1991; Balouiri et al. 2016)  to determine the minimal inhibitory concentration (MIC) of the following antibiotics: amoxicillin, erythromycin, clindamycin, rifampicin, oxacillin, penicillin, vancomycin, ceftriaxone, linezolid, gentamicin, fosfomycin and doxycycline.
Genome sequencing and analysis DNA extraction and sequencing. To study the genome properties of the studied strains, the genomic DNA (gDNA) was extracted using the EZ1 biorobot (Qiagen, Courtaboeuf, France) with the EZ1 DNA tissue kit prior to sequencing on the MiSeq technology (Illumina, San Diego, CA, USA) with the Nextera XT Paired end (Illumina), as previously described  (Lo et al. 2015b). Then, the quality control of raw data from DNA sequencing was performed using the FastQC software (https://www. bioinformatics. babraham. ac. uk/projects/fastqc/). Assembly and annotation. The assembly of the genomes of the strains was performed with multiple softwares (Trimmomatic software  (Bolger et al. 2014) , GapCloser  (Llorens et al. 2011)  and SPAdes  (Bankevich et al. 2012 )) as previously described  (Boxberger et al.
2019). Assembled genomes were annotated using Dfast (DDBJ Fast Annotation and Submission Tool) (https://dfast. nig. ac. jp/) and/or the PROKKA software  (Seemann 2014). Open Reading Frames (ORF) were predicted using Prodigal  (Hyatt et al. 2010 ) whereas protein-coding sequences were predicted by matching ORFs to the NR database using BLASTP with the following parameters: E-value of 1e -03 (1e -05 for a sequence shorter than 80 amino acids, coverage 0. 7 and identity percentage of 30%). The resulting protein sequences were matched against the Clutster of Orthologous Groups (COG) database  (Tatusov et al. 2000 (Tatusov et al. , 2015)). RNA sequences, speci cally ribosomal RNA (rRNA) and tranfer RNA (tRNA) were predicted using the RNAmmer  (Lagesen et al. 2007 ) and tRNAScanSE  (Lowe and Eddy 1997)  tools respectively.
Genomic comparison. RpoB gene sequences extracted from the genomes of the studied strains were used to further classify the aforementioned isolates within the Streptococcus genus though the construction of a phylogenetic tree based built with the Muscle  (Kumar et al. 2016 ) and MEGA 7 softwares  (Edgar 2004). To assess the level of genomic similarity of the described strains with closely related species, genomic data from the following species were used: Enterococcus hirae strain R17 (CP015516. 1), Streptococcus constellatus subsp. pharyngis C1050 (NC_022238. 1), Streptococcus cristatus ATCC 51100 (NZ_CP050133. 1) and Streptococcus gordonii strain FDAARGOS_257 (CP020450. 2). The Type Strain Genome Server web server available online (https://tygs. dsmz. de/) (Meier-Kolthoff and Göker 2019) was used for genomic comparison through in silico digital DNA-DNA hybridization (dDDH)  (Meier-Kolthoff et al.
Strain identi cation Strain isolation and growth conditions. Strain Marseille-P5794 T was isolated from the oral sample of a 39-year-old French female who spontaneously recovered from HIV while strain Marseille-P6264 T was isolated from the oral sample of a 28-year-old healthy French male. Similarly, strain Marseille-P7376 T was isolated from the oral sample of a 27-year-old healthy French male. Strains Marseille-P6264 T and Marseille-P7376 T were isolated after a 7-day pre-incubation in an aerobic blood culture bottle (bioMérieux) while strain Marseille-P5794 T was isolated after two days of pre-incubation in an anaerobic blood culture bottle. An identi cation attempt using MALDI-TOF MS allowed to the creation of the reference spectrum of each strain (Figure  1 ) which was subsequently incremented in our database that did not contain any matching spectrum.
Strain identi cation. The 16S rRNA gene of strains Marseille-P5794 T , Marseille-P6264 T and Marseille-P7376 T exhibited a 99. 47%, 99. 77% and 97. 9 % sequence identity respectively with Streptococcus cristatus strain ATCC 51100 (Genbank accession number EU156757), the phylogenetically closest species with standing in nomenclature (Figure  2 ). As the use of the 16S rRNA gene was not conclusive for the classi cation of species within the Streptococcus genus, the complete genome sequencing was performed and the rpoB gene sequences were extracted in silico as this gene was previously described as a useful marker to delineate species within this genus  (Drancourt et al. 2004 ). Using the rpoB gene sequence, strains Marseille-P5794 T and Marseille-P6264 T shared a 96. 1% and 95. 9% nucleotide sequence similarity respectively with Streptococcus cristatus ATCC 51100 (NZ_AFUE00000000.
9%) were the major fatty acids. The genome of S. resistens was 2. 07 Mbp long with 42. 3 % of G+C content. Strain Marseille-P5794 was isolated from an oral sample provided by a 39-year-old French female who spontaneously recovered from HIV. The 16S rRNA gene and genome sequences are available in GenBank under accession numbers LR597666 and CABPTQ010000000 respectively. This strain is deposited in the "Collection de Souches de l'Unité des Rickettsies" (CSUR) and "Spanish Type Culture Collection" (STCC) under number CSURP5794 and CECT 9902 respectively. Description of Streptococcus buccae sp. nov. Streptococcus buccae sp. nov. (buc. ca'e L. gen. fem. n. buccae, of the mouth, referring to the habitat where the strain was isolated). Streptococcus buccae consists of Gram-stain positive cocci which are facultative anaerobes.
The major fatty acids were C 16:0 (45. 1%), C 14:0 (25. 7%) and C 12:0 (14. 7%). Its genome was 2. 04 Mbp long with 42. 5 % of G+C content. The accession numbers of 16S rRNA and genome sequences are LR699782 and CABPTO010000000 respectively in the Genbank database. The type strain Marseille-P6264 was isolated from the oral sample of a 28-year-old healthy French male and is available in the CSUR and STCC collections under number CSURP6264 and CECT 9910 respectively. Description of Streptococcus mediterraneus sp. nov. Streptococcus mediterraneus sp. nov. (me. di. ter. ra'ne. us L. masc. adj. mediterraneus, from the Mediterranean Sea, which borders Marseille, where the strain was isolated). Cells are Gram-stain positive cocci which were facultatively anaerobic, non motile and non-spore-forming with a mean average diameter of 500 nm.
Catalase and oxidase activities are negative. S. mediterraneus grows optimally on COS agar after 24 hours in aerobic condition at 37°C at pH 7. 5. Using an API ZYM strip, a positive reaction is observed only for leucine arylamidase. Using an API 50 CH strip, positive reactions were obtained with N-acetylglucosamine, D-galactose, Dglucose, D-fructose, D-mannose, D-mannitol, D-sorbitol, arbutin, esculin, salicine, D-cellobiose, D-maltose, D-lactose, D-saccharose and D-trehalose. In addition, using API 20 Strep, S. mediterraneus can also ferment esculin iron citrate, 6-bromo-2-naphthyl-α D-galactopyranoside, L-arginine and D-ribose. The major fatty acids were C 16:0 (56 %), C 14:0 (19 %) and C 12:0 (7. 2%). Its genome was 2. 29 Mbp long with 41. 9 % of G+C content. The 16S rRNA gene and genome sequences are available in the Genbank database under number LR699798 and CABPTS010000000, respectively.
FundingThis study was supported by the Méditerranée Infection Foundation and the National Research Agency under the program « Investissements d'avenir », reference ANR-10-IAHU-03. This work was supported by the Région Provence-Alpes-Côte d'Azur and European funding FEDER PRIMI Summary table of the minimal inhibitory concentration in µg/ml for strain Marseille-P5794 T ,.
Background The research hypothesis is that commercially available mouthwash with ß-cyclodextrin and citrox (bio avonoids) could decrease the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) salivary viral load in adults with asymptomatic to mild COVID-19. Methods In this RCT, SARS-CoV-2 PCR-positive patients aged 18-85 years with asymptomatic to mild COVID-19 symptoms <8 days were recruited. A total of 154 eligible patients were randomly assigned (1:1) to antiviral ß-cyclodextrin and citrox mouthwash (CDCM) or placebo. Three rinses daily were performed for 7 days. Saliva sampling was performed on day 1 at 9 a. m. (T1), 1 p. m. (T2) and 6 p. m. (T3). On the following 6 days, one sample was taken at 3 p. m. Quantitative RT-PCR was used to detect SARS-CoV-2. The trial is registered at ClinicalTrials.
gov (NCT04349592). Findings CDCM was signi cantly more effective than placebo 4 hours after the rst intake (p<0•001), with a median percentage decrease T1-T2 of -14•25% [95% CI; -32•68% -0•06%]. In patients with an initial salivary load > 2•95 log 10 copies/mL, there was a signi cant difference in the reduction in viral load at T2. Over the course of one day, the rst mouthwash rinse signi cantly reduced the viral load, and the second dose maintained this low value, compared to placebo. At day 7, there was still a greater decrease in salivary viral load over time in the CDCM group. In individuals with an initial viral SARS-CoV-2 load higher than 4•12 log 10 copies/mL or 5•16 log 10 copies/mL, CDCM reduced the salivary viral load more quickly than placebo (MLM p-value = 0•03; 0•029). Interpretation This trial supports the relevance of using mouthwash with ß-cyclodextrin and citrox as an additional barrier measure on day 1 to reduce the dissemination of SARS-CoV-2.
RNA extraction was realized using the NucliSens easyMAG instrument (bioMérieux, Marcy-l'Etoile, France) following the manufacturer's instructions. RdRp-IP2 and RdRp-IP4 quantitative RT-PCR was used to detect SARS-CoV-2 with the Invitrogen SuperscriptTM III Platinum One-Step qRT-PCR system (Invitrogen, Illkirch, France). When a sample was positive for RdRp-IP4, the quanti cation of the number of RNA copies was performed according to a scale ranging from 10 2 to 10 6 copies per μL. The viral load in saliva was calculated as the number of RNA copies per mL of saliva. Primer and probe sequences (Euro ns, Genomics, Germany; Appendix Table  S1 ) correspond to the RdRp-IP2, the RdRp-IP4 assays designed at The Institut Pasteur to target a section of the RdRp gene based on the sequences of SARS-CoV-2 made available on the Global Initiative on Sharing All In uenza Data database on January 11, 2020.
e. , secondary endpoint) in both groups. Then the two groups were compared at each time thanks to a non-parametric Mann-Whitney U test. Finally, a mixed effect linear model (viral load repeated data along time from day 1 T1 to day 7) was performed with group (CDCM/placebo) as xed effect and individuals as random effect. All analyses were reperformed on the datasets with T1 values starting at the rst quartile (Q1), the second quartile (Q2) and the third quartile (Q3). No correction of p-values was made for multiple tests. Except for the Mann-Whitney test, the other tests were based on the unilateral hypothesis (H1: CDCM < placebo). The statistical methods are indicated in the table footnotes. All analyses other than sample-size calculations and graphic illustrations were performed using R (version 3.
Results Between June 9 and December 11, 2020, out of 1195 selected patients, 176 met the criteria for inclusion with COVID-19 symptom onset less than 8 days and were enrolled in this trial and then randomized (Figure  1 ). The baseline characteristics of the two study groups for which data were available (N=154) were similar (Appendix Table  S2 ). The mean age of the two groups was 43•89 ±15•55 years, ranging from 18 to 77 years; 45•75% of patients were male. A total of 95•21% were outpatients, and 78•32% of participants had no medical antecedents. Among the participants, 9•27% were asymptomatic (no clinical signs) and 90•73% had mild symptoms, with 3•68 ± 2•29 of the symptoms on the COVID-19 report forms. Adults with laboratory-con rmed COVID-19 were randomized within 4 days (95% CI; 3-5 days) of symptom onset to receive CDCM or placebo.
Seventy-ve percent of patients were between 30•2 and 55•0 years of age. Hospitalized patients (4•11%) had mild clinical cases. None of them had any health complications during the trial. The use of a daily antiviral mouthwash, as an additional barrier measure, could be important in the ght against the COVID-19 pandemic because the oral cavity is an important reservoir of SARS-CoV-2. Transmission from asymptomatic individuals was estimated to account for more than half of all transmissions, and 30% of individuals with infection never develop symptoms. 17 In addition, many individuals with symptomatic cases of COVID-19 did not seek medical advice despite recommendations. Collaborative surveillance data in France indicate that only 31% of people with COVID-19-like symptoms consulted a healthcare provider.
Radiological Acquisitions and Quantifications The samples were scanned with a SkyScan-1072 device (Bruker, Billerica, United States) under the following conditions: 70 kV, 142 µA, resolution = 18 µm, and single 360 • scan. Three-dimensional datasets were reconstructed with NRecon software (Micro Photonics Inc. , Allentown, United States). The bone volume (BV) and the tissue volume (TV) within the defects were quantified with the CTAn software. Treedimensional quantitative results were expressed as BV/TV (%) at 0, 3, and 7 weeks.
Statistical Analyses The statistical analyses were performed using GraphPad Prism 5. 0 software (GraphPad, San Diego, United States). Statistical significance was determined using one-way ANOVA followed by Bonferroni's post hoc test for multiple group comparisons. Statistical significance was set at p < 0. 05. The results are presented as means ± SD. The normality of the data distribution has been verified thanks to a Shapiro-Wilk test with a P < 0. 05.
Variables and data measurements The main outcome of this study was to analyze the taxonomic composition of the oral microbiota in both obese and normal weighted patients' groups. Sampling was performed during the inclusion consultation which was conducted as following: Medical and socio-demographic characteristics Medical and dental history were assessed (associated pathologies, drugs, level of stress scored on a 10points scale) as well as the hygiene-dietary behavior of the patients which was recorded from a questionnaire. This enabled us to focus on oral hygiene habits: frequency of visits to the dental surgeon, frequency and type of materials used (manual or electric toothbrush, mouthwash, interdental brushes, etc. ).
Statistical analyses Data were blinded to maintain participant con dentiality. The statistical analyses were corrected with the "false discovery rate" (FDR), a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons  29. The bacterial diversity analyses (Chao1 alpha diversity and Bray-Curtis beta diversity) were performed using the Phyloseq v1. 14. 0 R package. The differential taxa analyses were conducted using the linear discriminant analysis effect size tool LEfSe 30 using default parameters (alpha parameter signi cance threshold set to 0. 05 and the logarithmic LDA score cutoff set to 2. 0). Unpaired Mann-Whitney tests were performed using GraphPad Prism (GraphPad Software, San Diego, CA). A PERMANOVA test was performed with 999 permutations to assess the statistical signi cance of the difference between groups in beta diversity PCoA analyses (Figs.
Statistical analysis The SPSS software, version 25 (SPSS, Chicago, IL, USA) and GraphPad Prism 8. 0 (GraphPad Software, LA Jolla, CA, USA) were used to perform all the analyses with a signi cance level of 5% (α = 0. 05). The area under the receiver operating characteristic curve (AUC), sensitivity, and speci city were calculated. ANOVA two-way with post-hoc Tukey test was used to compare the AUC, sensitivity, and speci city values between the dose protocols and the different dispositions and compositions of the metallic materials in the exomass and/or endomass. Weighted Kappa test was used to measure the intra-and interobserver agreements and the results were interpreted according to Landis & Koch 27 (0. 00-0. 20, poor; 0. 21-0. 40, reasonable; 0. 41-0. 60, moderate; 0. 61-0. 80, good; 0. 81-1.
Near-complete 16S rRNA genes were amplified from genomic DNA extracted as described by Quéméneur et al. [28] , using the primers 27F and 1492R  [29] , then sequenced by GATC-Biotech (Konstanz, Germany). The 16S rRNA gene sequence was deposited and aligned with available sequences from NCBI database using the MUSCLE program  [30]  implemented in MEGA7 software  [31]. Evolutionary analyses were conducted from 16 nucleotide sequences using three different methods: maximum-likelihood (ML)  [32] , maximum-parsimony (MP)  [33] , and neighbor-joining (NJ)  [34]. Whole-genome analysis was performed from high molecular weight DNA of the isolate, extracted using a phenol-chloroform method, then sequenced at the GeT-PlaGe platform (INRAe Toulouse, France) by combining long reads (Oxford Nanopore) and short-reads (Illumina MiSeq) technologies, as described by Quéméneur et al.
[25]  with some modifications because it was sequenced by multiplex sequencing according to the manufacturer's instructions "1D Native barcoding genomic DNA" (EXP-NBD104 and SQK-LSK109)". Base-calling was carried out by MinKNOW-Live-Base-calling software version 3. 6. 0 (Oxford Nanopore Technologies, Oxford, UK). Read demultiplexing and adapter trimming were performed using qcat v1. 1. 0 (https://github. com/nanoporetech/qcat) and genome assembly with Unicycler v0. 4. 6  [35]. The genome sequence was deposited in the NCBI database and annotated using the MaGe (Microscope Genome Annotation)  [36]  and the Integrated Microbial Genomes (IMG) systems  [37]. The value of average nucleotide identity (ANI) was calculated using OrthoANI with usearch (http://www. ezbiocloud. net/tools/ani). Digital (or in silico) DNA-DNA hybridization (dDDH) was calculated using the Genome-to-Genome Distance Calculator (GGDC) 2.
1 (http://ggdc. dsmz. de/) [38]. A whole genome-based taxonomic analysis was performed using the bioinformatics platform Type (Strain) Genome Server (TYGS) (https://tygs. dsmz. de) [39]. In brief, the TYGS analysis included a determination of the closest type strain genomes by (i) comparison against all type strain genomes available in the TYGS database via the MASH algorithm  [40]  and (ii) the closely related type strains determined via the 16S rDNA gene sequences. For the phylogenomic inference, all pairwise comparisons among the genomes were conducted using Genome BLAST Distance Phylogeny (GBDP) and accurate intergenomic distances inferred under the algorithm 'trimming' and distance formula d5. The resulting intergenomic distances were used to infer a balanced minimum evolution tree with branch support via FASTME 2.
End products detected from pyruvate fermentation were acetate and formate. Both ferric citrate and thiosulfate were used as electron acceptors using pyruvate and reduced to ferrous iron and sulfide. Yeast extract was degraded into acetate, formate, H2, and propionate. Elemental sulfur, nitrate, nitrite, fumarate, sulfate, sulfite, and DMSO were not used as terminal electron acceptors. The predominant fatty acids were iso-C15:0 (15. 3%), C16:0 (10. 2%), C14:0 (8. 0%), cyclo-C17:0 (6. 9%), iso-C17:1 (8. 8%), and C18:0 (6. 1%). The GenBank accession number for the 16S rRNA gene sequence of strain LB2 T is KR349724, and that for the whole genome sequence is CP058559. The type strain LB2 T (= DSM 100588 T = JCM 30958 T ) was isolated from a sediment slurry of 'La Crouen' thermal spring near Canala, New Caledonia.
Funding Information This project was financially supported by the  French Research Institute for Development (IRD) , the  INTERVIE CNRS INSU program , the  H2NAT  project funded by the  Midi-Pyrénées Observatory  ( OMP, Toulouse ) and  ANR MICROPRONY  ( N°19-CE02-0020-02 ). We thank  Céline Roques  at the  GeT core facility, Toulouse, France  (http://get. genotoul. fr)for the genome sequencing of LB2 strain, supported by France génomique. The LABGeM ( CEA/Genoscope & CNRS UMR8030 ) is acknowledged for support within the MicroScope annotation platform.
Scaffolds characterization Scaffolds architecture was observed by micro-computed tomography (micro-CT, SkyScan 1272, Bruker, Belgium) at a source voltage of 90 kV and current of 111 μA, using an image pixel size of 15 μm. Subsequently 3D reconstruction was carried out using Nrecon software (Bruker). Surface morphology of both coated and uncoated scaffolds were analyzed by scanning electron microscopy (SEM, Zeiss Neon 40, Carl Zeiss, Germany), using a working distance of 12 mm and an acceleration voltage of 5 kV. Furthermore, the coating thickness was analyzed by studying cross-sectional SEM images of three samples that were previously immersed in liquid nitrogen and fractured. Energy-dispersive Xray spectroscopy (EDX) analyses of cryofractured samples were acquired with a FE-SEM JEOL JSM-7001F (Jeol, Tokyo, Japan) complemented fabrication parameters were discussed  [9].
Three measurements of the average surface roughness (R a ) were obtained at three different zones of the scaffold, using a 10× objective lens and a scanning area of 316 × 237 μm. Roughness data was analyzed with Wyko Vision 4. 10 software (Veeco Instruments). The response of the scaffolds to a compressive load, with and without coating, was also evaluated. Five scaffolds (n 5) of 18 × 13 mm were tested for each condition using a compression testing machine (Microtest machine EM1/20/FR, Microtest, Spain) at a speed of 2. 5 mm/ min, in accordance with ISO 13314:2011  [27]. The elastic modulus and ultimate strength were determined from the stress-strain curves as defined in the ISO standard.
Acknowledgments The authors thank the  Generalitat de Catalunya  financial support ( SGR 2017 SGR1165 ), the  Spanish Government  for financial support through project  RTI2018-098075-B-C21  ( MINECO/FEDER) , co-funded by the  EU  through  European Regional Development Fund ,  BIO-ACTISURF  project no. 14054394  of the  Région Midi-Pyrénées  and  COST Action Ipromedai   TD1305. EV acknowledges the  FI-DGR scholarship  and  MPG  the  ICREA Academia Prize , both by the  Generalitat de Catalunya.