dataesr/scientific-paragraphs-categorization huggingface dataset:
Taken together, these data demonstrate the ability of PCL-CH hybrid scaffolds to form bone like minerals in vitro. Finally, the cytotoxicity of the samples was evaluated. Primary osteoblasts were cultured in the presence of preconditioned PCL-CH, preconditioned PCL-CE, or without material for the control condition and the cell viability was determined after 6 days. Figure  7  demonstrates that the dissolution products of the hybrids are noncytotoxic, given that no statistical difference is observed with the control conditions.
MATERIAL AND METHODS The protocol for this systematic review (CRD42017076069) was registered in the international prospective register of systematic reviews (https://www. crd. york. ac. uk/PROSPERO/). This systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. 29 An electronic search was performed, using 3 electronic databases (PubMed/MEDLINE, Scopus, and Web of Science) for studies published between January 1, 2007 and September 20, 2017. A search strategy was prepared for each database using 4 levels: level 1 considering the adaptation quality, level 2 considering the type of material, level 3 considering CAD-CAM technology, and level 4 considering the type of restoration. The search strategy included the following medical subject headings (MeSH): 'Ceramic', 'Inlay*', and the following text words: 'fit', 'gap', 'marginal', 'internal', 'adaptation', 'discrepancy', 'resin', 'composite', 'CAD', 'computer-aided', and 'onlay'.
Then, the 20 most intense ions were selected for MS 2 experiments, from which the singly charged species were excluded. Dynamic exclusion of already fragmented precursor ions was applied for 30 s, with a repeat count of 1, a repeat duration of 30 s, and an exclusion mass width of ±10 ppm. Fragmentation occurred in the linear ion trap analyzer with a collision energy of 35 eV. All measurements in the Orbitrap analyzer were performed with on-the-fly internal recalibration (lock mass) at m/z 445. 12002 (polydimethylcyclosiloxane). Raw data were then imported to Progenesis LC-MS software (Nonlinear Dynamics). For comparison, one sample was set as a reference, and the retention times of all other samples within the experiment were aligned. After alignment and normalization, statistical analysis was performed for one-way analysis of variance (ANOVA) calculations.
Only peptide features with a p-value < 0. 05, q-value < 0. 05, and power > 0. 8 were retained for quantification. MS/MS spectra from selected peptides were exported for peptide identification with Mascot (Matrix Science) used against the database restricted to C. acnes. Database searches were performed with the following parameters: one missed trypsin cleavage site allowed; variable modifications: carbamidomethylation of cysteine and oxidation of methionine. For each growth condition, the total cumulative abundance of the protein was calculated by summing the abundances of the peptides. Proteins with a p-value < 0. 05, q-value < 0. 05, and power > 0. 8 were retained. Moreover, only proteins for which the average normalized abundances between growth conditions differed by more than twofold were retained.
Nuclear Magnetic Resonance (NMR) Spectroscopy of Sugars Samples were deuterium exchanged by freeze drying twice from 99. 9% D 2 O and then examined as solutions in 99. 95% D 2 O. 1 H and 13 C NMR spectra were recorded on a Bruker Avance II 600 MHz spectrometer (Germany) at 45 • C using internal sodium 3-trimethylsilylpropanoate-2,2,3,3-d4 (δ H 0. 0, δ C -1. 6) as a reference. Bruker TopSpin 2. 1 software was used to acquire and process the NMR data. A spin lock time of 60 ms and a mixing time of 200 ms were used for the total correlation spectroscopy (TOCSY) and rotating-frame Overhauser spectroscoPY (ROESY) experiments, respectively. A 1 H, 13 C heteronuclear multiple bond correlation (HMBC) experiment was performed with a 60-ms delay to study the evolution of long-range couplings. The 13 C NMR chemical shifts were analyzed and compared to published values by GODDESS  (Kapaev and Toukach, 2016)  and GRASS NMR  (Kapaev and Toukach, 2018)  simulation, and structure elucidation web services were implemented at the platform of the Carbohydrate Structure Database  (Toukach and Egorova, 2016).
, 2009)  at a concentration of 100 µg/mL of the extract (data not shown). We performed wet combustion and calculated the proportion of all major polymers in the C. acnes RT5 matrix. Approximately 23. 8% of the organic carbon found in the TSM was not from peptides, sugars, or DNA, accounting for 23. 3% of the total organic carbon in the SUP and 26. 5% in the SLP (Table  3 ). Given the metabolism of C. acnes, it is likely that these compounds represent various metabolites, including essentially porphyrins and their precursors. Indeed, a qualitative reaction showed a high amount of α-aminolevulinic acid (data not shown).
C. acnes normally contains five Christie, Atkins, Munch-Peterson (CAMP) factors  (Valanne et al. , 2005). We did not find any CAMP factors in the matrix, but rather proteins that are very similar to them. For example, hypothetical protein HMPREF9571_02536 shares more than 99% similarity with the CAMP-1 factor of other strains of C. acnes (according to the Uniprot 2  and NCBI 3  databases). It consists of a 285-amino-acid molecule with a molecular weight of 30. 394 kDa. Sugar residue H-1 H-2 H-3 H-4 H-5 H-6 C-1 C-2 C-3 C-4 C-5 C-6 →6)-duD-Galp-(1→ (.
, 2002; Kairyte et al. , 2012). These peaks are characteristic of microbial cells and were absent from the spectra of the separated matrix. We plotted the spectrum of each sample on a graph with a displacement along the ordinate axis to avoid superposition of the spectra. Differences between the spectra of the isolated matrix and biofilm biomass suggest successful extraction of the matrix and not a suspension of cell debris after the extraction procedures. We show that SERS can be used to rapidly verify the successful extraction of the matrix. In addition, we obtained the total biomass spectra of the biofilm and the matrix, which will be added to the database of microorganism spectra and used to identify C. acnes in complex biological materials and samples with the help of SERS. SERS has the advantages of very simple sample preparation and rapid obtention of the results.
It is, thus, a promising tool for bacterial detection. SERS spectroscopy by itself is also a potentially powerful tool for the detection of compounds that are generally normally present in bacterial biofilm matrices. However, a more complete picture, of course, needs to be built using a combination of SERS with other methods. To date, the weak point of SERS is the absence of a large spectra database of organic polymers, which greatly complicates the analysis. The essential value of the present data is as a contribution to the formation of this first SERS data base of bacterial spectra.
, 2015; Toukach and Egorova, 2015) , defined the positions of substitution of the monosaccharides in the polysaccharide. These data revealed the structure of the polysaccharide (Figure  6 ). According to a systematic search in the Carbohydrate Structure Database  (Toukach and Egorova, 2016) , this structure (CSDB ID 29100) was reported earlier for P. acnes (equivalent of C. acnes) strain C7  (Nagaoka et al. , 1985). In the matrix, it has a molecular weight of at least 12 kDa (because of pore size). Analysis of the matrix polysaccharides showed that the dominant polysaccharide in the matrix is exactly the same as that of the C. acnes cell wall. Moreover, we found no signal of PNAG. Instead, we found N-acetylgalactosamine and N-acetylmannosamine. We did not find residues of 2-acetamido-2-deoxy-galactose in the polysaccharide, which is characteristic of PNAG.
acnes strains. The authors performed dot-blot analysis using wheat germ agglutinin conjugated to horseradish peroxidase. They found PNAG in all the strains tested, whereas we did not find any PNAG residues in the present study. The different methodologies and strains used could explain the difference between these results. For example, the difference may be based on strain and environmental specificity. Different strains of C. acnes can produce different sugars in different amounts. There are currently no published data about any other polysaccharides in the biofilm matrix of C. acnes, but this possibility is reasonable. In addition, this hypothesis is consistent with the data of  Holmberg et al. (2009) , who showed differences in the ability to form biofilms between C. acnes strains from infected implants and those from skin.
, 2019). Here, we conducted the first SERS analysis of a C. acnes biofilm matrix. Analysis of the SERS peaks also confirmed the isolation of the biofilm matrix, as more than 40 peaks in the matrix and biomass of the cells were different. The most intense peaks of both phases of the matrix were found at 370-386 cm -1. However, the spectra of SERS alone do not carry information about the nature of most of the matrix substances, because there is currently no SERS database of organic compounds, in particular organic polymers. Therefore, SERS is used in combination with other techniques, such as MS and NMR. The identification of spectra peaks requires the obtention of spectra for each compound of the matrix. Also, SERS is a relatively poor tool for the identification of molecules at low concentration.
Nevertheless, we have successfully performed the first typing of biofilms and C. acnes matrix using the SERS method. This approach could help to determine the presence of C. acnes in complex biological samples in the future. It could also be used in the construction of a microorganism SERS spectra database. This database could allow the rapid and simple identification of microbes without the need of molecular biology approaches, such as polymerase chain reaction or fluorescence in situ hybridization. responsible for directing the work and development of the general strategy.
FUNDING The computer-assisted NMR studies were funded by the  Russian Science Foundation  (project no. 18-14-00098 ). The surface-enhanced Raman spectroscopy of the biofilm matrix was supported by the  Russian Science Foundation  (project no. 17-79-10489 ). In France, this work was supported by the  Région Normandy and FEDER (UE). AG was the recipient of a Campus France doctoral grant. The work of AG, VP, MZ, and EB was partially supported by the  Ministry of Science and Higher Education of the Russian Federation.
Singly charged species were excluded for MS2 analysis. Dynamic exclusion of already fragmented precursor ions was applied for 30 s, with a repeat count of 1, a repeat duration of 30 s, and an exclusion mass width of ±10 ppm. Fragmentation occurred in the linear ion trap analyzer with collision energy of 35. All measurements in the Orbitrap analyzer were performed with on-the-fly internal recalibration (lock mass) at m/z 445. 12002 (polydimethylcyclosiloxane). Raw data files were processed using Proteome Discoverer 1. 3 software (Thermo Scientific, Villebonsur-Yvette, France). Peak lists were searched using the MASCOT search engine (Matrix Science, Boston, Massachusetts) against the database Swiss Prot database. Searches were performed with the following parameters: 1 missed trypsin cleavage site allowed; variable modifications: carbamidomethylation of cystein, and oxidation of methionine; mass tolerance on parent and daughter ions: 10 ppm and 0.
| Cytotoxicity, inflammatory, and β-defensin 2 inducing potential of acneic and non acneic strains of C. acnes are poorly affected by growth conditions The cytotoxicity of the two strains was studied on HaCaT keratinocytes by assay of LDH released using bacteria at an MOI = 50. Even in these conditions of high infection level, the two C. acnes strains showed limited cytotoxicity (Figure  4a ). Bacteria were tested at higher concentrations (MOI = 100 and 200) but no increase in cytotoxicity was observed (Data not shown). Moreover, in all tested conditions, no difference of cytotoxicity was observed between acneic and non acneic bacteria. When bacteria were grown in BHI their cytotoxicity was close to the basal values of HaCaT spontaneous cell death. Bacteria grown in RCM showed a higher cytotoxicity, nevertheless, this level remained low, with a mean cell death between 19% and 23%.
Morphology, viability and proliferation of DP-MSCs cultured within hydrogels Encapsulated DP-MSCs were analyzed within either type of hydrogels, immediately after gelation or after 7 days of culture. At Day 0, living (green) DP-MSCs displayed a rounded morphology in fibrin-chitosan hydrogels (Fig. 4A ), whereas, at Day 7, living cells were mostly elongated and fibroblast-like (Fig. 4B ). Results were similar in fibrin-alone hydrogels (data not shown). The percentage of viable DP-MSCs (relative to the total number of DP-MSCs) was similar in fibrin-alone and fibrin-chitosan hydrogels, both at the beginning (Day 0) and at the end (Day 7) of culture (Fig. 4C ). Cell proliferation was assessed by the expression of the nuclear marker MKI67 both at gene and protein level with RT-qPCR and immunohistochemistry, respectively.
Acknowledgements This work was supported by the  Gueules Cassées foundation , the  French National Centre for Scientific Research (CNRS)  and the  French Ministry of Higher Education and Research. The authors acknowledge the contribution of the  Centre Technologique des Microstructures (Université Lyon 1, Villeurbanne, France ) for help with electron microscopy and  Novotec (Bron, France)  for help with immunohistochemistry.
Data were analysed using the Kruskal-Wallis test (p < 0. 05) followed by the Dunn test. Results: For the hardness and roughness of nanocomposite resin, the QWB sequence was significantly more effective than QB (p < 0. 05). The Filtek Z500 showed significantly harder surfaces regardless of the finishing-polishing sequence (p < 0. 05). Conclusions: QWB yielded the best values of surface roughness and hardness. The hardness and roughness of the 5 nanocomposites presented less significant differences when QWB was used.
Surface roughness test The roughness of the 5 resin composites polished with the 2 finishing-polishing sequences was measured and compared to the values of the strip-finished control-group specimens. A total of 60 specimens were analysed using an optical profilometer (Micromesure 2, STIL, Aix-en-Provence, France). This optical profilometer is based on the chromatic confocal imaging technology recommended by the ISO 25178 standard. Once the analysis is completed, the Gwyddion 2. 26 software (STIL) was used to visualize the 3-dimensional surfaces of the different specimens and to calculate their roughness values. This optical profilometer was able to measure the surface roughness Ra (arithmetic mean of the absolute departures of the roughness profile from the mean line). This measure was used to define roughness.
ACKNOWLEDGEMENTS The authors would like to thank  Professor B. Monasse  ( CEMEF, Mines ParisTech ) for his help regarding roughness analyses; as well as  F. Bartel  and  M. Bianchi  for labwork; Komet,  Ivoclar, Dentsply  and  3M  for supplying materials for this study. The authors do not have any financial interest in the companies whose materials are included in this article.
Micro-CT Analysis Three-dimensional images were reconstructed using Quantum FX micro-CT ® software (March 2013, PerkinElmer Health Sciences, Hopkinton, MA, USA). An automatic rigid registration was achieved using the MATLAB ® software (MATLAB 9. 3, MathWorks, Natick, MA, USA) to align the three stages of acquisition for comparison. A global thresholding technique, which is based on Otsu's method  [18] , was applied to segment the hard tissue of the teeth, the background, and the filling material remnants. Volumes were then binarized to retain only the remnants, and the preoperative and postoperative filling material volumes were quantified and expressed in mm 3  [19]. The localization of the residual filling material was performed according to the canal thirds. The percentage of remaining filling material after retreatment was calculated, as follows: A/B × 100 = Volume (%) of the remaining filling material, where A represents the postoperative volume of the filling material and B represents the preoperative volume of the filling material.
Statistical Analysis The data was analyzed using the SPSS software for Windows (version 24. 0, Chicago, IL, USA). The level of significance was set at 0. 05 (p < 0. 05). The normality distribution of the continuous variables was assessed with the Kolmogorov-Smirnov test. Since the variables were not normally distributed, non-parametric tests were performed. The Wilcoxon test was used to compare the volume of the filling material before and after retreatment and the volume of the residual material before and after PUI usage. The Mann-Whitney test was used to compare the percentage of the residual material after retreatment between the two systems. The Kruskal-Wallis tests was used to compare the percentage of residual product remaining, after activation, between the four groups.
Material and methods: After having provided written consent, 60 second-year students were divided into two groups. One group used a 1-mm rounded bur to perform depth grooves, whereas the second group used the innovative guided bur, consisting in a 2-mm-depth marker with a stopping surface. Once the grooves were obtained, they were then connected using the same wheel bur in both groups. The aim was to obtain a final 2-mm reduction of the incisal edge. Quality of the learning experience (stress level, motivation to restart, self-evaluation of the preparation, and difficulty) was quantified using a visual analog scale. Duration of the procedure was also measured in both groups. 3D measurements for each tooth were performed using an STL comparison software. Results: There were no significant differences between groups in terms of stress and self-evaluation of the preparation.
An unprepared reference tooth was scanned using a laboratory scanner (LabScan HD®, Bego France, Villeurbanne, France). All the prepared teeth were scanned by intraoral scanner (Trios 3®; 3Shape, Copenhagen, Denmark) in STL format. These files were blinded before analysis. STL files for each prepared tooth were then superimposed to the reference STL of the unprepared tooth, using automatic matching algorithm of the software (Geomagic®, Design X, 3D Systems). Fifteen 3D measurements for each tooth were performed using an STL comparison software (Geomagic®, Design X, 3D Systems; Figure  1e ).
| Data collection and statistical analysis Questionnaires were collected, and visual analog scales were converted to a numerical value on a scale of 10. The 3D STL measurements were then compiled and blinding lifted. All quantitative data were verified for normal distribution using the Shapiro-Wilk test (α =. 05). All data are expressed as median, interquartile range  [IQR]  in grades/10, seconds, or millimeters where appropriate. Data are presented as box plots (GraphPad Prism 7, GraphPad, La Jolla, CA, USA). Data were not normally distributed, and a Wilcoxon test was applied. Differences between groups were considered statistically significant for p ˂. 05.
Samples A power analysis was conducted using G*Power Software, version 3. 1. 9. 2 (Heinrich-Heine-Universität, Düsseldorf, Germany). Considering the repeated measures design of the trial, and accounting for an effect size of 0. 2 (small effect size), a 5% level of significance and an 80% power, the required sample size was around 60 teeth. the presence of caries using the International Caries Detection and Assessment System II (ICDAS II)  [23]. ICDAS II is a universal 7-point ordinal scale that detects early lesions, as well as changes in the longitudinal follow-up. Teeth having ICDAS score from 0 to score 3 were included, as follows: • Score 0 -no evidence of visible caries; • Score 1 -first visual change in enamel; • Score 2 -distinct visual change in enamel; • Score 3 -localized enamel breakdown with no visible dentin or underlying shadow.
Statistical analysis The normality of the data was checked using Kolmogorov-Smirnov test. In each group, the values for these outcome variables were compared using Wilcoxon Signed Ranks test. Change in mineral content between the 4 groups of comparison was assessed using Kruskal Wallis Test, and that between two groups using Mann Whitney U test. P < 0. 05 was considered significant with a Bonferroni correction where multiple comparisons were conducted. The Statistical Package for Social Sciences (IBM SPSS), version 21 was used for statistical analysis. Parametric data were expressed as mean and standard deviation (M [SD]).
Study population. This study included 25 Caucasian adults aged 20 to 35 years old. Subjects were recruited from a pool of first-time volunteers who were referred to the Department of Public Health of the Faculty of Oral Medicine at the University of Lyon, France. All participants signed an informed consent form in accordance with the Declaration of Helsinki. The study protocol was reviewed and approved by the Local Ethics Committee "University Hospital Center of Lyon" (Rech_FRCH_2015-0181) and by the National Commission of Informatics and Liberties, France (1845681v0). This study was retrospectively registered with ClinicalTrials. gov (identification number: NCT03714295). Subjects were included if they were aged between 20 and 35 years, in good general health, not pregnant or breastfeeding, and periodontally healthy and if they had no health conditions that required antibiotic prophylaxis before interproximal probing, no experience with interdental cleaning (interdental brushing or dental flossing), and no intake of systemic antimicrobials during the previous 6 months.
Statistics. The statistical analysis consisted of three main steps, namely, producing descriptive summaries of the data, modeling the data using a mixed (linear) model and assessing the correlations between the bacterial abundances. Descriptive statistics (percentages, means and standard deviations) were calculated with SPSS 12. 0 (SPSS Inc. , Chicago, IL). The statistical tests (p-values) were calculated with SUDAAN 7. 0 (Research Triangle Institute, Research Triangle Park, NC) to account for clustering (multiple sites within the mouth) and repeated measures (measurements along the follow-up period). Statistical methods are clearly indicated in table footnotes. All data were considered statistically significant at p < 0. 05.
ethics approval and consent to participate. The study protocol was reviewed and approved by the Local Ethics Committee "University Hospital Center of Lyon" (Rech_FRCH_2015-0181) and by the National Commission of Informatics and Liberties, France (1845681 v 0). All participants signed a consent form in accordance with the Declaration of Helsinki. This study was registered with ClinicalTrials. gov (identification number: NCT03714295).
BONE SARCOMAS (BS) AFFECTING THE MAXILLOFACIAL REGION Definition and Epidemiological Impact of Bone Sarcomas Bone Sarcomas (BS) are rare primary mesenchymal bone tumors (<0. 2% of malignant tumors of EUROCARE database), including osteosarcoma (OS), Ewing sarcoma (ES) and chondrosarcoma (CS)  (162). BS affects more frequently the appendicular skeleton (lower limbs) than the craniomaxillofacial skeleton. In this area, maxilla and mandible are more affected bones over cranial bones  (163). Thus, maxillofacial (MF) OS (MFOS), ES (MFES), and CS (MFCS) are considered malignant tumors of the maxillofacial region according to the 4th edition of the World Health Organization Classification of head and neck tumors  (164). Here, we will focus specifically on MFOS, MFES, and MFCS, highlighting the role of immune response on their pathophysiology and, also, revising experimental approaches for therapy.