dataesr/scientific-paragraphs-categorization huggingface dataset:
Proteolysis with alternative proteases allows access to larger boneproteomes A homogenized bone sample from each specimen was digested using six proteases separately. Each digest was injected in triplicate (technical replicates). Peptide and proteome identification was then performed twice on the resulting datasets, first via semi-specific protease settings and a second time using specific protease settings. Overall proteome deamidation indicates greater deamidation for asparagine (N) compared to glutamine (Q; Fig. S3, S4 ), and above that observed for our negative extraction controls (Fig. S5 ). Multiple t-testing for a difference in deamidation for each extraction control-sample pair supports this conclusion (Table  S4 ). Deamidation is therefore, given differences in protein and peptide numbers and proteome composition, relatively comparable across proteases for each bone specimen and suggests the recovery of endogenous, ancient bone proteomes from all four bone specimens.
d, Osteomodulin (OMD, F6ZRQ3). e, Alpha-2-HSglycoprotein (AHSG, F7C450). f, Chondroadherin (CHAD, F6WD70). Only data deriving from the three Equidae samples is included, with the three replicates kept separate. Note differences in y-axis scale between panels. Open symbols: specific search. Closed symbols: semi-specific search. Chymo = Chymotrypsin. Fig. 7. Sequence coverage obtained for six different proteins using six different proteases. a, Collagen type 1, alpha-1 (COL1A1, UniProt accession P02452). The mature region of COL1A1 is located between amino acid positions 162 and 1218. b, Collagen type 5, alpha-2 (COL5A2, P05997). c, Osteocalcin (BGLAP, P02818). d, Ficolin-1 (FCN1, O00602). e, Biglycan (BGN, P21810). f, Pigment epithelium-derived factor (SERPINF1, P36955). Data included from the Homo sp.
Moreover, we observed an activation of the interferon-γ response in OSCC from NSND, as previously reported in all HNSCC from NSND  (29). Our data highlighted the importance of the microenvironment, and also suggested a higher clinical benefit of indoleamine 2, 3-dioxygénase (IDO1) and programmed death-ligand 1 (PD-L1) inhibition in the subgroup of NSND patients with OSCC. Notably, we identified a set of ∼850 genes that were differentially expressed in NSND vs. SD (named NSND gene set), that were validated in four independent datasets: including one cohort of patients treated at our institution (Centre Léon Bérard, CLB, Lyon, France). CNA • ↓ 11q13 amplification • ↑IFN-γ • ↑ T-cell infiltrate • ↑ PD-L1 • ↑ IDO1 NS, non-smoker; S, smoker, NSND, non-smoker non-drinker; SD, smoker drinker; CNA, copy number alterations; LOH, loss of heterozygosity.
*Studies which concluded that NS (ND) were overall similar or different compared to S (D) are highlighted in blue and red respectively. Frontiers in Oncology | www. frontiersin. org FIGURE 1 | Enrichment scores for the non-smoker non-drinker (NSND) gene set in patients with OSCC from Sri Lankan and United Kingdom (UK). We previously identified a set of genes that were differentially expressed between NSND and smoker drinker patients  (14). Using the single sample Gene Set Enrichment Analysis, we computed a score of this gene set (NSND score) in a publically available gene expression dataset of OSCC from Sri Lankan and UK patients (GSE51010)  (30). Using the same methodology (single sample gene set enrichment analysis) and as shown in Figure  1 , we have computed the enrichment score of the NSND gene set in OSCC surgically resected in patients from United Kingdom or from Sri Lanka (GSE51010)  (30).
INCREASING INCIDENCE OF OROPHARYNGEAL SCC AND OSCC IN YOUNG NSND: A COMMON EPIDEMIOLOGICAL ORIGIN? From an epidemiological perspective, an intriguing observation over the past three decades has been the simultaneous increasing incidence of OPSCC in young men as well as OSCC in young women  (11, (38) (39) (40). In order to illustrate these observations, we mined the SEER database and compared the incidence of OT cancer in women and of OP cancer in men less than 50 years old  (41). As shown in Figure  3A , a parallel increase of the incidence of OT cancer in female and of OP cancer in males less that 50 was observed between 1980 and 2013. We contrasted this increase with the decrease in cigarette consumption during the same period of time based on data provided by Ng et al. (42). Consistently, Figure  3B  shows a Pearson correlation of 0.
57 (P = 0. 0006) between the incidence of OT cancer in women and of OP cancer in men <50 years old. This observation is consistent with a previous study showing that the increasing incidence FIGURE 2 | Janus kinase 2 (JAK2) alterations in human papillomavirus (HPV)-negative oral squamous cell carcinoma (OSCC) from non-smokers non-drinkers (NSND) and smokers drinkers (SD). (A) We extracted JAK2 gene expression data from four independent cohorts of HPV-negative OSCC, as previously defined (  14 ): The Cancer Genome Atlas (TCGA), GEO1 and GEO2 from GSE39366 and GSE65858 respectively, and Centre Léon Bérard (CLB, Lyon, France). Overexpression of JAK2 in NSND as compared with SD was observed in all four cohorts (Whitney test). In TCGA, we compared copy number linear value in OSCC from NSND and SD (Mann Whitney test) (B) and tested its correlation with gene expression in OSCC from NSND (Pearson correlation) (C).
FUNDING This work was supported by a  Priorité Cancers Tabac grant  ( TABAC-16-025 ) funded by  INCa ,  Fondation ARC  and  Ligue  nationale contre le cancer; the  LYriCAN Grant INCa-DGOS-4664 ;  INCa   PLBIO17-338  Projets  libres de Recherche Biologie et Sciences du Cancer ; JP-F was supported by a fellowship grant soutien pour la formation à la recherche translationnelle en cancérologie funded by l' ITMO cancer from  INCa  and  AVIESAN , and from the  Association Française pour le Développement de la Stomatologie (AFDS).
Surface roughness measurement and surface observation After surface treatments, the surface roughness (Ra) of all the posts was determined by a 3D non-contact profilometer (AEP Nanomap-1000WLI; AEP Technology, Santa Clara, CA, USA) with an optical resolution of 550 nm. Average of Ra values were calculated with SPIP software (Image Metrology A/S, Lyngby, Denmark) by using three single individual measurements, according to ISO 4287. 38 e structural surface topography of each group after surface treatment was observed under a scanning electron microscope (SEM) (Carl Zeiss EVO LS 10; Carl Zeiss NTS, Germany) at 250x magnification after sputter-coating with gold.
Statistical analysis Statistical analyses were made using standard statistical software (SPSS V23; IBM Armonk, NY, USA). All data were submitted to the Shapiro-Wilk test to verify the normality of data and one-way ANOVA was used to compare normally distributed data of Ra and TBS between groups. Multiple comparisons were carried out with Tukey's HSD and Pearson chi-square test was used to compare failure rates by groups. Analysis results were shown as means and standard deviation for quantitative data and as frequency (%) for categorical data. Significance level was considered for p<0. 05.
However, this study investigated only the bond strength of the PEEK posts and even though PEEK exhibits a high-fracture load, it is not possible to comment directly on the fracture resistance of these post system. 28, 30, 35 Therefore, the fracture resistance should be evaluated in further studies under an appropriate set-up to reveal whether this post system is clinically feasible or not. 71  adhesive procedures, SR is a significant factor, and it requires various surface treatment methods to increase the bonding area and microroughness of the dental material. 57 The quantitative Ra data measured corresponded to the qualitative investigation by SEM shown in Figure  2  that exhibit different surface appearances for the groups. Confirmed by SEM images, PEEK demonstrated pits and pores distributed with filler particles on the surface, as demonstrated by other previous investigations.
Isolation and growth conditions In 2015, we isolated from the dental plaque sample of a woman with periodontitis an unidentified bacterial strain. A screening was performed using MALDI-TOF MS on a Microflex LT spectrometer (Bruker Daltonics, Bremen, Germany) as previously described  [15]. The spectra obtained (Fig. 1 ) were imported into MALDI BIOTYPER 3. 0 software (Bruker Daltonics) and analysed against the main spectra of the bacteria included in two databases (Bruker and the constantly updated MEPHI databases). The study was validated by the ethics committee of the Institut Fédératif de Recherche IFR48 under number 2016-010. Strain Marseille-P4122 T was first isolated in aerobic conditions after incubation in a culture bottle (bioMe ́rieux, Marcy l'Etoile, France) supplemented with 5 mL sheep blood at 37°C.
Strain identification The 16S rRNA gene was sequenced to classify this bacterium. Amplification was carried out using the primer pair fD1 and rP2 (Eurogentec, Angers, France) and sequencing using the Big Dye® Terminator v1. 1 Cycle Sequencing Kit and 3500xL Genetic Analyzer capillary3500xL sequencer (Thermofisher, Saint-Aubin, France), as previously described  [16]. The 16S rRNA nucleotide     sequences were assembled and corrected using CODONCODE ALIGNER software (http://www. codoncode. com). Strain Marseille-P4122 T exhibited a 98. 19% sequence identity with Corynebacterium suicordis strain P81/02 (GenBank accession number NR042151. 1), the phylogenetically closest species with standing in nomenclature (Fig. 3a ). The rpoB gene that encodes the β subunit of bacterial RNA polymerase was targeted to discriminate the Corynebacterium species  [17].
Genome sequencing Genomic DNA was extracted using the EZ1 biorobot (Qiagen, Courtaboeuf, France) with the EZ1 DNA tissue kit and then sequenced on the MiSeq technology (Illumina, San Diego, CA, USA) with the Nextera Mate Pair sample prep kit and Nextera XT Paired end (Illumina), as previously described  [18]. The assembly was performed with a pipeline incorporating different softwares (VELVET  [19] , SPADES  [20]  and SOAP DENOVO  [21] ), and trimmed data (MISEQ and TRIMMOMATIC  [22]  softwares) or untrimmed data (only MISEQ software). GAPCLOSER was used to reduce assembly gaps. Scaffolds <800 bp and scaffolds with a depth value < 25% of the mean depth were removed. The best assembly was selected using different criteria (number of scaffolds, N50, number of N). The genome of Corynebacterium dentalis strain Marseille-P4122 T is 2 303 041 bp long with a 60.
μm. Strain Marseille-P4122 T produced esterase, lipase, acid phosphatase, naphthol-AS-BIphosphohydrolase, α-glucosidase, β-glucosidase, urease, D- fructose and D-trehalose. But no activity was observed with trypsin, β-galactosidase, α-glucosidase, glycerol, D-arabinose, D- ribose, D-xylose, D-glucose, D-fructose, D-mannose, L-rham- nose, D-lactose, D-saccharose, glycogen, D-fucose and D-arabitol. Strain Marseille-P4122 T is catalase-negative. It is susceptible to rifampicin, ciprofloxacin, amoxicillin, penicillin G, doxycycline and vancomycin, but resistant to erythromycin. The genome size of Corynebacterium dentalis strain Marseille-P4122 T is about 4. 04 Mb with 60. 1 mol% G + C content. The GenBank Accession number for the 16S rRNA gene sequence of strain.
5 5 μm. Strain Marseille-P4122 T produced esterase, lipase, acid phosphatase, naphthol-AS-BIphosphohydrolase, α-glucosidase, β-glucosidase, urease, D- fructose and D-trehalose. But no activity was observed with trypsin, β-galactosidase, α-glucosidase, glycerol, D-arabinose, D- ribose, D-xylose, D-glucose, D-fructose, D-mannose, L-rham- nose, D-lactose, D-saccharose, glycogen, D-fucose and D-arabitol. Strain Marseille-P4122 T is catalase-negative. It is susceptible to rifampicin, ciprofloxacin, amoxicillin, penicillin G, doxycycline and vancomycin, but resistant to erythromycin. The genome size of Corynebacterium dentalis strain Marseille-P4122 T is about 4. 04 Mb with 60. 1 mol% G + C content. The GenBank Accession number for the 16S rRNA gene sequence of strain.
All primers used in this study were designed with Primer3 plus software (Supplementary Table  S2 ) and were chemically synthesized and purified by Eurogentec (Liège, Belgium). The mRNAs expression levels were normalized on 16 S rRNA threshold cycle (Ct) values and calculated by comparing the Ct of targeted genes with those of control sample groups. The relative quantification data were determined with the 2 -∆∆Ct method using Microsoft Excel-based spreadsheet.
Confocal Laser Scanning Microscopy (CLSM) Prior to CLSM examination, bacteria were stained with 5 µM of SYTO9 Green 5 dye (Invitrogen, Carlsbad, CA, USA) for 15 min. Static biofilms were then washed twice with sterile physiological solution and dynamic biofilms were rinsed for an additional 10 min with a flow of medium. Biofilms were observed with a Zeiss LSM710 microscope (Carl Zeiss Microscopy, Oberkochen, Germany) using a 40× oil immersion objective. SYTO9 was excited at 488 nm and fluorescence emission was detected from 500 to 550 nm. Images were recorded every micrometer, visualized, and processed using the Zen 2. 1 SP1 software (Carl Zeiss Microscopy, Oberkochen, Germany). Quantitative analyses of 3D images (thicknesses and biovolumes) were performed using COMSTAT2 software (http://www.
The parameter settings were optimized by infusion experiments. Data were acquired in multiple reaction monitoring modes (MRM) using the Analyst software version 1. 6. 3 (Applied Biosystems, Toronto, ON, Canada). Identification and quantification of c-di-GMP were performed by using three specific mass transitions from molecule ion m/z 691 to the product ions 152, 135, and m/z 540. The external calibration was carried out at c-di-GMP concentrations ranging from 1 to 100 ng. mL -1 (ultrapure water), analyzed in duplicate.
5. 0. 0  [57]. The extracted phage sequence from P. aeruginosa PAO1 (Genbank accession number: GCA_000006765. 1) was mapped to the trimmed raw reads with BBmap v38. 69 from BBTools package  [58]. Mapped reads in SAM format were converted into fastq files using SamToFastq command in Picard (https://broadinstitute. github. io/picard/). The obtained reads covering the phage region were mapped to PAO1 and H103 reference genomes using Snippy v. 4. 3. 6 (https://github. com/tseemann/ snippy) to detect SNPs or deletions, and assembled into contigs as described above. Default parameters were used except where otherwise noted.
Statistical Analyses The data were statistically analyzed using two-samples unpaired (for dH103 and dH103Pf4 + analysis) and paired two-tailed t-test to calculate p values with GraphPad Prism (GraphPad Prism version 4. 0; GraphPad Software, San Diego, CA, USA). All values are reported and plotted as means with SEM of at least triplicate analyses for each experimental variable. NS (not significant); p > 0. 05; * p < 0. 05; ** p < 0. 01; *** p < 0. 001; **** p < 0. 0001.
Pf4 Phage Variant Infection Induces P. aeruginosa Membrane Fluidity Alteration SigX has also been reported to be involved in the modulation of membrane fluidity through the regulation of fatty acid biosynthesis, which results in changes in the cell membrane phospholipid composition in order to maintain envelope integrity  [37, 41, 42]. To evaluate P. aeruginosa's membrane fluidity post Pf4* infection, fluorescence anisotropy (FA) measurements using a 1,6-diphenyl-1,3,5hexatriene (DPH) fluorescent probe were performed. As shown in Figure  5B , FA values decreased when P. aeruginosa was infected with Pf4 phage variant, compared to H103, revealing increased membrane fluidity. Altogether, these data indicate that Pf4* infection increases membrane fluidity probably because of the strong activity of SigX.
Pf4 Phage Variant Infection Induces P. aeruginosa Membrane Fluidity Alteration SigX has also been reported to be involved in the modulation of membrane fluidity through the regulation of fatty acid biosynthesis, which results in changes in the cell membrane phospholipid composition in order to maintain envelope integrity  [37, 41, 42]. To evaluate P. aeruginosa's membrane fluidity post Pf4* infection, fluorescence anisotropy (FA) measurements using a 1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescent probe were performed. As shown in Figure  5B , FA values decreased when P. aeruginosa was infected with Pf4 phage variant, compared to H103, revealing increased membrane fluidity. Altogether, these data indicate that Pf4* infection increases membrane fluidity probably because of the strong activity of SigX.
Acknowledgments: The LMSM is supported by the  Région Normandie (France) ,  Evreux Portes de Normandie (France)  and  European FEDER  funds. D. T and A. D. are supported by doctoral fellowships from the  Région Normandie (France) , and M. C from the  French ministry (MENRT). A. T. , A. M. B. and S. R. are supported by post-doctoral fellowships from  European Union (FEDER)  and  Région Normandie (France). O. C. A. is a recipient of a postgraduate fellowship from  Campus France  and  FUNAI (Nigeria). M. N. and G. B. W. acknowledge support from the  Helmholtz program BioInterfaces in Technology and Medicine (BIFTM)  of  KIT. The funders had no role in study design, data collection and interpretation, or the decision to submit this work for publication. We thank  Professor Rob Lavigne  and  Jeroen Wagemans  ( KU Leuven, Belgium ) for the gift of the LUZ19 virulent phage.
La recherche a permis d'identifier un total de 3174 articles, soit 1834 articles après retrait des doublons, toutes bases de données confondues. Parmi ceux-ci, 23 articles publiés de 2001 à 2019 répondaient aux critères de sélection et ont été inclus. La majorité des articles ont été exclus parce qu'ils ne portaient pas sur l'association entre la carie précoce de l'enfant et un des domaines étudiés. Cinq articles supplémentaires ont été ajoutés sur la base des références des articles sélectionnés. Vingt-huit articles ont donc été inclus au total (« Flow-chart » en Figure. 4). Ce paragraphe présente dans un premier temps la conception, la population, et la méthodologie des études sélectionnées, puis dans un second temps l'analyse des principaux résultats de ces études (Tableau 2).
[77,78] études longitudinales[77,78]. Les études étaient toutes de nature quantitative. Les résultats de cette revue de portée ont permis de considérer en premier lieu des éléments de méthodologie. Cinq bases de données différentes ont été explorées, toutefois au vu du [30,57,58,[62][63][64]66,75,78] dans la revue de portée, il a été décidé de toutes les garder quel que soit leur niveau de preuve afin d'en discuter les résultats. Cette revue a retenu quatre études de grade A, deux études de grade B et vingt-deux études de grade C selon la classification de la Haute Autorité de santé. Il existe ainsi très peu d'études à haut niveau de preuve (quatre revues systématiques seulement dont deux ciblées sur un seul facteur : la littératie en santé orale) et prenant en compte l'ensemble des médiateurs et modérateurs impliqués dans la maladie carieuse au niveau individuel.
Human papillomavirus status was missing for 147 (27%) subjects (53 cases and 94 controls) who refused to provide a saliva sample, and for three controls for whom the quality of the specimen was considered inadequate for HPV detection. In addition, missing data were observed for smoking status (one case) smoking quantity (19 cases, 3 controls), smoking duration (6 cases, 1 control), alcohol quantity (4 controls), and alcohol duration (27 cases 56 controls). We used multiple imputations by chained equations to deal with missing data. 22 The imputation model contained all the basic characteristics of the study subjects (age, sex recruitment site and education level), variables related to alcohol and smoking (ever daily alcohol drinking, quantity of alcohol, smoking status, smoking duration, and smoking quantity), HPV status (low-risk, probable high-risk, high-risk, and other HPV types) and the case-control status.
In terms of oral HPV infections, no significant association with HNSCC was found for persons tested positive for HPV when compared to HPV-negative subjects. Non-high-risk HPV types as well did not show any significant difference in risk to HPV-negative subjects. On the other hand, subjects positive for Hr-HPV types were twice as likely to develop HNSCC compared to Hr-HPV-negative subjects. Among Hr-HPV types, we detected HPV16 in 4 cases and 2 controls. HPV18 was found only in 2 cases and 1 control. The other Hr-HPV types which were detected in greater proportion among cases than controls were HPV33 (3 cases 1 control), HPV51 (3 cases 0 controls), HPV52 (8 cases 12 controls), and HPV56 (5 cases 6 controls). We analyzed tobacco, alcohol, and oral HPV risk among oropharyngeal and non-oropharyngeal subsites separately; these results did not change in terms of direction of the association observed in the analyses with all HNSCC cases (data not shown).
ACKNOWLEDGMENTS The authors thank our clinical research associates  Lucina Lipau  and  Audrey Pomier  for their help in data collection. Aviane Auguste was supported by a grant from the  "Ligue contre le Cancer , comité d' Ille-et-Vilaine " for this work. This study was funded by the  French National Cancer Institute (Institut National du Cancer)  and the  Cancéropôle Ile-de-France.
A 52-year-old female patient was diagnosed with chronic periapical periodontitis associated with severely calcified lower central incisors. Radiographic examination revealed no visible root canal in the coronal-third of the root. After choosing the guided endodontic treatment, an intraoral scan (Trios, 3shape, Copenhagen, Denmark), in conjunction with a cone beam computed tomography (CBCT) scan, was taken in order to design and fabricate a printed guide. Virtual implant software was used to visualize the surgical access into the sclerosed root canals. After locating the canals, the guide was removed, and the teeth were treated under a rubber dam. The guided approach allows predictable, efficient endodontic treatment of teeth presenting calcified canals, with minimal removal of sound dentine and less risk of root perforations.
Guided endodontic treatment was offered to the patient. The purpose of this report was to evaluate the benefits and limitations of the micro-guided technique. The patient gave her informed consent before the treatment. This treatment was conducted in accordance with good clinical practice (GCP) established in the declaration of Helsinki, and the council for international organization of medical sciences guidelines (CIOMS). The protocol was approved by the Ethics Committee of "Hotel Dieu de France (HDF)" (Tfemd/2020/28) on March 26, 2020. After the patient's consent, a 3D intraoral scan was taken of the lower arch (Trios, 3shape, Copenhagen, Denmark) in order to have a 3D virtual model. The intraoral impression was then converted to a 3D stereolithography file (STL file) and imported to Implant studio (3shape, Copenhagen, Denmark), a virtual implant planning software.
A virtual sleeve was also designed in order to maintain the axis during the trepanation of dentin. In contrast with previous guide designs  [14] , no pins were used to enhance the guide's stabilization (Figure  4A ). The patient gave her informed consent before the treatment. This treatment was conducted in accordance with good clinical practice (GCP) established in the declaration of Helsinki, and the council for international organization of medical sciences guidelines (CIOMS). The protocol was approved by the Ethics Committee of "Hotel Dieu de France (HDF)" (Tfemd/2020/28) on March 26, 2020. After the patient's consent, a 3D intraoral scan was taken of the lower arch (Trios, 3shape, Copenhagen, Denmark) in order to have a 3D virtual model. The intraoral impression was then converted to a 3D stereolithography file (STL file) and imported to Implant studio (3shape, Copenhagen, Denmark), a virtual implant planning software.