dataesr/scientific-paragraphs-categorization huggingface dataset:
Patients are informed that they have the right to withdraw from the study at any time without giving reasons. Regardless of withdrawal, patients will be provided any treatment in their best interest. Withdrawal will be documented. Data confidentiality was audited by the Comité National Informatique et Liberté (CNIL, National Committee of Informatics and Freedom); last and first names of included patients are not recorded in the database. No Data Monitoring Committee is needed for a DEep CAries Treatment (DECAT) study as no or very few serious events are expected from this study limited to common dental care. No interim analyses are planned.
Dissemination of results The Consolidated Standards of Reporting Trials (CON-SORT) guidelines will be used to report the results of this study and the results will be published in international peer-reviewed journals  [50]. Authors of the publications will be people involved in the elaboration of protocol, the implementation and conduct of the trial, and the writing of the manuscript and report. The results related to the main objective will be authored by the coordinator, the methodologists, the investigators who have included at least 15 cases and other people who will have significantly contributed to the planning of the trial, its implementation, or the writing of the report. A summary of the study results will be posted at ClinicalTrials. gov to allow general access to the findings. Data sharing will be at the participant level.
Representative genomic 16S rRNA sequences of the strains were compared with those of other type strains belonging to Actinobacteria present in the Ribosomal Database Project. (Figure  2 ) shows the phylogenetic tree. CIRM-BIA129 (ITG P20) was found to be able to utilize glycerol, erythritol, L-arabinose, adonitol, galactose, D-glucose, D-fructose, D-mannose, inositol, arbutine, esculine, lactose, lactate and gluconate as carbon sources according to the gallery-API results. CIRM-BIA129 (ITG P20) was shown to grow with up to 1 M NaCl in a chemically defined medium in presence of osmoprotectant (G. Jan, personal communication).
2  The evolutionary history of the strain was inferred using the Neighbor-Joining method  [12]. The optimal tree with a sum of branch lengths = 0. 80 is shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method  [13]  and are in the units of the number of base substitutions per site. The analysis involved 18 nucleotide sequences. All positions containing gaps and missing data were eliminated. There were a total of 1376 positions in the final dataset. Evolutionary analyses were performed under MEGA5  [14]  two hours at 55 °C. DNA integrity was checked on an 0. 8 % agarose gel. The OD 260/280nm was 1. 9.
Genome annotation Automatic and manual annotations were carried out with the AGMIAL platform  [4] , using P. freudenreichii CIRM-BIA 1 T as the reference  [5]. Sub-cellular localization was predicted using SurfG+  [6] , a software specific to sub-cellular prediction in Gram-positive bacteria. A comparison of the predicted proteome of CIRM-BIA129 with that of the sequenced type strain CIRM-BIA1 was performed with Koriblast software (Korilog, France) with its default parameters. Genes present in CIRM-BIA129 and not in the type strain CIRM-BIA1 were searched by tblastn of the CIRM-BIA129 predicted proteome against the complete genome of CIRM-BIA1. No hit proteins were specific to CIRM-BIA129. In order to search for genomic islands specific to CIRM-BIA129, a blastp of the CIRM-BIA129 proteome against the CIRM-BIA1 proteome was performed.
Characterization of ASC From GFP+ Mice The ASC phenotype (passage 1) was confirmed by flow cytometry  [23]  using fluorescent-labeled anti-SCA-1 antibodies as a positive marker and anti-CD45 and anti-CD31 antibodies as negative markers (supplemental online Table 1) (BD Biosciences, East Rutherford, NJ, https://www. bdbiosciences. com). Exclusion of 49,6-diamidino-2-phenylindole was used for cell viability assessment. Fluorescence-activated cell sorting (FACS Fortessa and FACS Diva software; BD Biosciences) revealed that 97% of ASC were positive for GFP (supplemental online Fig. 1A, 1B ). Additionally, ASC/GFP+ were submitted to adipogenic or osteogenic media for 7 and 14 days. Multilineage differentiation was confirmed using quantitative polymerase chain reaction by Osterix, alkaline phosphatase 2, runt-related transcription factor 1, adipocyte fatty acid-binding protein, lipoprotein lipase, adiponectin, and peroxisome proliferator-activated receptor-g expression, respectively (details on primers are found in supplemental online Table  1 ).
Hough Transform Analyses to Quantify Entropy of PDL Fibers A measure of the PDL fiber architecture was achieved using the Hough transform (HT). Images were first oriented vertically using a line tangent to the root. The red component of the color image was kept to better visualize the fibers. We submitted the oblique and horizontal fibers of PDL to HT using Matlab 2012 software (Mathworks, Meudon, France, http://www. mathworks. com). Supplemental online Figure  3  summarizes the processing steps. Using HT, we drew lines corresponding to the main directions of detected fibers. The probability for each angular direction was derived from the Hough transform matrix and plotted as a histogram distribution. The entropy of this distribution was computed, which provided a statistical measure of randomness.
ACKNOWLEDGMENTS This study was supported by funding from the  Midi-Pyrenees region, Paul Sabatier University, Toulouse University Hospital , and the  research platform of Toulouse Dental Faculty. The authors thank  Susan Becker  for proofreading the manuscript,  Florence Capilla  and  Talal Al Saati  (histopathological research platform, CPTP, Toulouse Purpan),  Marion Taurand (STROMALab) , and the research platform of  Toulouse Dental Faculty  for their technical help, and  Prof. Gérard Brunel  for his help in the study design and for his constant inspiration.
Raman spectroscopy Raman spectra were collected using a Witec Confocal Raman Microscope System alpha 300R (Witec Inc. , Ulm, Germany). Excitation in the confocal Raman microscopy is assured by a double frequency Nd:YAG laser 532 nm (Newport, Evry, France). The incident laser beam is focused onto the sample through a 20Â NIKON objective (Nikon, Tokyo, Japan). Data acquisition is performed using Image Plus software from Witec. Spectra were acquainted on five different areas of the sample of each group. The acquisition time was 90 s. Fresh samples of set cement without PBS immersion were used as control. The apatite intensity was calculated as apatite/belite assigned peak height ratio using a spectral software analysis (WITec Project version 2. 06, Witec, Germany). The data were analyzed by one-way ANOVA (analysis of variance) following Tukey's HSD post hoc pairwise comparisons at the significance level of 0.
Clinical, Radiographic, and Microbiological Parameters. The initial treatment consisted of a medical history, photographic documentation, periodontal examination, and periapical radiographs (Figure  1 ). Data were collected at baseline and 6 months after surgery. For each patient periodontal charting was performed, assessing probing depth, Plaque Index, and bleeding on probing. Microbiological analysis was performed with PCR Real Time, using paper tips to withdraw gingival fluid in periimplant pockets before and after treatment.
Fortunately, the numbers required to answer these questions seem to be achievable within reasonable timeframes, based on the successes of the initial and subsequent trials of Denosumab in GCT of bone  [25, 26, 54]. Safety for long term use is unknown and should be reported as soon as possible with the full dataset of the large phase II study. Due to the challenges of treating this disease and the unanswered questions regarding optimal use of Denosumab, referral and follow-up of complicated cases of GCT requiring Denosumab should be within expert centres with a multidisciplinary team. Further clinical trials are mandated to identify the optimum indications for using Denosumab in GCT.
Data analysis Raman imaging. Raman spectra were processed using the Labspec software (HORIBA, Jobin-Yvon, France). A Savitzky-Golay smoothing filter (filter width: 2; and polynomial order: 2) was applied. The intensity is integrated over defined Raman shift regions in the spectrum using a sum filter  [37, 38]. The filter calculates the intensities within the chosen borders and the background is subtracted by taking the baseline from the first to the second border  [37, 38]. This procedure was applied on the Raman peaks 960 cm -1 (peak-ROI 900-990 cm -1 ), 1070 cm -1 (peak-ROI 1052-1092 cm -1 ) and 1669 cm -1 (peak-ROI 1610-1700 cm -1 ). The intensity, the PCPs and their spatial distributions were calculated using the PLS toolbox (v8. 2, Eigenvector Research, Inc. , Wenatchee, WA, USA) and a custom-developed script in Matlab R2013a (Mathworks Inc, Natick, MA, USA).
1. Intensity maxima with polynomial baseline (Int. Max + Poly. Bsl. ): polynomial baseline correction (degree 4) is done on the entire spectrum and the peak maxima is extracted. A special care was taken that polynomial baseline correction do not distort the Raman bands. [35]  2. Integrated intensity with straight baseline (Integrated Int. + Str. Bsl): the sum of the whole area beneath the peaks with a straight baseline between the chosen spectral peak-ROI  [37, 38]. The peaks 1244 and 1270 cm -1 were deconvoluted with a Gaussian function with Labspec software. 3. Intensity maxima with straight baseline (Int. Max + Str. Bsl): the maxima peak intensity with straight baseline between the spectral peak-ROI. This method is combination of the both above. This comparison helped to determine the optimal method to evaluate peak intensities and use them in the Eq  (1).
bizertensis (Gen-Bank accession no. HQ534365), the phylogenetically closest bacterial species with a validly published name (Figure  1 ). Its 16S rRNA sequence was deposited in GenBank under accession number HG315673. This value was lower than the 98. 7% 16S rRNA gene sequence threshold recommended by Stackebrandt and Ebers  [46]  to delineate a new species without carrying out DNA-DNA hybridization. Different growth temperatures (30, 37, 45, 55°C) were tested. Growth occurred between 37 and 45°C, but optimal growth was observed at 37°C after 48 hours of incubation in anaerobic conditions. The colonies were 1. 3 mm in diameter and moderately opaque on 5% sheep's blood-enriched agar (bioMérieux). Growth of the strain was tested under anaerobic and microaerophilic conditions using GENbag anaer and GENbag microaer systems respectively (bioMérieux) and under aerobic conditions with and without 5% CO 2.
Twelve individual colonies were deposited on a MTP 384 MALDI-TOF target plate (Bruker). The 12 ND1 T spectra were imported into MALDI BioTyper 2. 0 software (Bruker) and analysed by standard pattern matching (with default parameter settings) against the main spectra of 4706 bacteria, including one spectrum from Anaerosalibacter bizertensis, used as reference data in the BioTyper database. A score enabled the presumptive identification and discrimination of the tested species from those in the database; a score of >2 The pH range is 7-7. 5, with optimal pH at 7. MIGS, minimum information about a genome sequence. a Evidence codes are as follows: IDA, inferred from direct assay; and TAS, traceable author statement (i. e. a direct report exists in the literature). These evidence codes are from the Gene Ontology project (http://www.
Genome Sequencing Information Genome project history The organism was selected for sequencing on the basis of its phylogenetic position and 16S rRNA similarity to A. bizertensis and other members of the family Clostridiaceae. It is part of a culturomics study of human digestive flora that aims to isolate all bacterial species within human faeces  [2]. It was the first genome of Anaerosalibacter species and the first genome of A. massiliensis sp. nov. A summary of the project information is shown in Table  4. The GenBank accession number is CCEZ01000001 and consists of 82 contigs. Table  4  shows the project information and its association with minimum information about a genome sequence (MIGS) version 2. 0 compliance  [21]. Growth conditions and DNA isolation A. massiliensis sp. nov. , strain ND1 T (= CSUR P762 = DSM 27308), was grown on 5% sheep's blood-enriched Columbia agar (bioMérieux) at 37°C in anaerobic atmosphere.
Genome annotation Open reading frames (ORFs) were predicted using Prodigal  [49]  with default parameters, but the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank database  [50]  and the Clusters of Orthologous Groups (COGs) databases using BLASTP. The tRNAScanSE  a Mean peak area percentage calculated from analysis of FAMEs in three sample preparations ± standard deviation (n = 3).
NMNI tool  [51]  was used to find tRNA genes, whereas ribosomal RNAs were found by using RNAmmer  [52]  and BLASTn against the GenBank database. Lipoprotein signal peptides and the number of transmembrane helices were predicted using SignalP  [53]  and TMHMM  [54]  respectively. ORFans were identified if their BLASTP E value was lower than 1e-03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E value of 1e-05. Such parameter thresholds have already been used in previous works to define ORFans. Because no genome was available for A. bizertensis  [3] , the only Anaerosalibacter species with standing in nomenclature, we compared the genome from A. massiliensis strain ND1 T to those of other members of the family Clostridiaceae, including Clostridium ultunense strain Esp (CARA00000000)  [29] , C.
acidurici strain 9a (CP003326)  [23, 33]  C. dakarense strain FF1 (GenBank accession no. CBTZ00000000)  [36]  and C. senegalense strain JC122 (CAEV00000000)  [7]. The last two species have as yet no standing in nomenclature but were proposed as new species  [7, 36]  and are phylogenetically close to A. massiliensis. Ortholog sets composed of one gene from each of these five genomes were identified using Proteinortho 1. 4 software  [55]  using threshold values of 30% protein identity and a 1e-05 E value. The average percentages of nucleotide sequence identity between corresponding orthologous sets were determined using the Needleman-Wunsch algorithm global alignment technique. Artemis  [56]  was used for data management, and DNAPlotter  [57]  was used for visualization of genomic features. The Mauve alignment tool was used for multiple genomic sequence alignment and visualization  [58].
Genomic comparison with other members of the family Clostridiaceae We compared the genome of A. massiliensis strain ND1 T those of C. acidurici strain 9a (GenBank accession no. CP003326)  [23, 33] , C. dakarense strain FF1 T (CBTZ00000000)  [36] , C. senegalense strain JC122 T (CAEV00000000)  [7]  and C. ultunense strain Esp (CARA00000000)  [29].
Two microlitres of FAME extracts were volatized at 250°C (split 20 mL/min) in a Focus liner with wool and separated on an Elite-5MS column (30 m, 0. 25 mm i. d. , 0. 25 mm film thickness) using a linear temperature gradient (70 to 290°C at 6°C/min), enabling the detection of C4 to C24 fatty acid methyl esters. Helium flowing at 1. 2 mL/min was used as carrier gas. The MS inlet line was set 250°C and EI source at 200°C. Full scan monitoring was performed from 45 to 500 m/ z. All data were collected and processed using Turbomass 6. 1 (Perkin Elmer). Fatty acid methyl esters were identified by spectral database search using MS Search 2. 0 operated with the Standard Reference Database 1A (National Institute of Standards and Technology [NIST], Gaithersburg, MD, USA) and the FAMEs mass spectral database (Wiley, Chichester, UK).
29 Nucleotide transport and metabolism H 94 2. 87 Coenzyme transport and metabolism I 64 1. 96 Lipid transport and metabolism P 115 3. 52 Inorganic ion transport and metabolism Q 69 2. 11 Secondary metabolites biosynthesis, transport and catabolism R 324 9. 91 General function prediction only S 203 6. 21 Function unknown - 1169 35. 73 Not in COGs COGs, Clusters of Orthologous Groups database. a Total is based on total number of protein-coding genes in annotated genome.
International data confirm that oral health is poor in PWS. Dental caries and periodontal measurement indexes are often twice the level found in the general population  [8, 14, 20, 21]. Generally speaking, less than 10 % of the population of industrialized countries suffer from severe forms of periodontitis  [24, 25]. Periodontal health is assessed using different indexes. The periodontal index, called the CPI (community periodontal index), is the World Health Organization's (WHO) reference index  [26]. It is estimated that 40 % of schizophrenics exhibit a CPI ≥ 3 according to the literature  [27, 28]. A CPI ≥ 3 indicates advanced periodontal disease, with a loss of alveolar bone depending on severity. The most consistent predictors of periodontal disease are age, education, income, smoking status, dental visits, the number of remaining teeth, the number of decayed coronal surfaces, the number of decayed root surfaces and diabetes.
e. , the existence of the intervention and control groups and the comparison of outcomes between them). Upon debriefing at the end of the study, the PWS who were in the no-TEPOH group could benefit from TEPOH. Participants may withdraw from the trial either at their own request or at the discretion of the Investigator (acute psychiatric disorders). Participants will be made aware that withdrawal will not affect their future care. All participants (PWS and caregivers) will be made aware (via the information sheet and consent forms) that should they withdraw, the data collected to date cannot be erased and may still be used in the final analysis.
The trial team will determine the seriousness and causality in conjunction with treating medical practitioners. Serious adverse events are divided into two categories, those that seem likely to be independent of TEPOH and those connected with TEPOH. All adverse events will be recorded and closely monitored until resolution, stabilization, or until it has been shown by the data monitoring committee that involvement in the trial is not the cause. All treatment-related serious adverse events will be recorded and reported to the Research Ethics Committee (REC) as part of the annual reports. Unexpected serious adverse events will be reported to the REC by the chief investigator, who will take appropriate medical action, which may include halting the trial and informing the sponsor of such action.
Finally, a panoramic radiograph will be done if the patient does not have radiographs dating back less than 3 months. The dental panoramic film (orthopantomogram) is to detect periodontal disease, fractures, tumours and bone disorders from teeth and conditions that may affect the jaw and sinuses. A qualitative analysis of data collected during the TEPOH will make it possible to determine the evolution of representations, knowledge, attitudes and the practices of patients and professionals, and the ability of patients and professionals to assimilate an educational process.
Sample/randomization and data-management The literature highlights that up to 40 % of PWS disorders have a mean CPI ≥ 3  [27, 28] , compared with less than 10 % in general population  [24, 25]. Anticipating that the TEPOH will lead to a mean 20 % reduction in the CPI index of patients, taking into account cluster variability (CV = 0. 37) and the intra-class correlation coefficient (CCI = 0. 01), we will have to recruit a total of 202 patients to highlight a statistically significant difference between the two groups with a type-I error of 5 % and type-II error of 20 %. Randomization will be done using SAS version 9. 3 (SAS Institute Inc) by the team of statisticians of the Methodological Support Unit, Direction of Clinical Research, UHD, France. All participating hospitals will be randomly allocated to TEPOH or not using a random stratified sampling method depending on their location (urban/mixed/extra-urban) and their level of activity (number of patients per year).
Statistical analysis The interview data will be transcribed and coded using NVivo software to facilitate analysis of the factors identified by participants as affecting their attitudes and behaviours relating to changes in perception in OHRQoL. This process will yield a comprehensive account of the relevant barriers, motivators, and facilitators of OHRQoL. Among the intervention group participants, changes in attitudes will be documented. Results for qualitative covariates will be expressed as proportions. Quantitative variables will be expressed as means ± standard deviations (SD) when normally distributed, or as medians and ranges in other cases. Comparison of persons' characteristics between a group of interest and the general population of PWS will be performed using Student's t test, analysis of variance, Kruskal-Wallis non-parametric tests and Pearson's Chi square or Fisher's exact test when appropriate.
Operators and evaluators standardization Operators carry out prosthetic treatment. Evaluators assign scores according to FDI criteria. Both operators and evaluators are experienced dentists in the field of fixed prosthodontics. They are trained in the FDI criteria by means of the e-calib web based software (http://zep01793. dent. med. uni-muenchen. de/moodle/ website) and group training sessions. Operators cannot evaluate their own treatments. Trained researchers and technicians perform ex vivo analyses.
Provisional restoration Before the manufacture of zirconia restorations, CAD-CAM composite provisional crowns (Lava Ultimate, 3M ESPE, Seefeld, Germany) or PMMA provisional bridges are made. After die scanning, the restoration design is carried out with CAD/CAM software, either Exocad (Darmstadt, Germany) or Dental Wings (Montreal, Canada) (DPI Lava milling center, Anderlecht, Belgium). Specific buccal and palatal grips are added to the crown design to facilitate cemented crown removal. The file is then transferred to the milling machine for manufacturing (Lava CNC 500, Serial Number: 07019 (2009), 3M ESPE). The provisional restorations are adapted inmouth and used as a template for the design of the zirconia restoration. Particular attention is paid to occlusal contact points adjustment, in order to obtain at least one flat contact surface of approximately 1 mm 2 per cusp, by either grinding or by adding composite (Fig.
Sample size The determination of the sample size (N) was based on the following considerations. The statistical unit was the tooth characterized by its maximum LTD value recorded at each time point (baseline, 6 months, 1, 2, 3, 4 and 5 years). An LTD value above 50% was considered as treatment failure for the tooth. The overall proportion (p) of such treatment failures was defined as the primary outcome measure of the study. The study rationale was to reject the proposed treatment if p > 0. 20, i. e. more than 20% treatment failures over time. Assuming a significance level a of 1% (Bonferroni correction for multiple time testing), a power 1-b of 90%, a proportion p of at most 0. 08 (margin 0. 12) and a one-sided Z test for a Binomial proportion of 0. 20, a sample of 91 teeth would be needed to detect a percentage > 20% of treatment failures at each data point collection.