dataesr/scientific-paragraphs-categorization huggingface dataset:
Parameters of acquisition and reconstruction Acquisitions were performed with rotation time of 0. 5s/rot and tube current modulation was disabled. Tube voltage was 120kV and tube current (mAs) was adjusted to obtain a volume computed tomography dose index (CTDIvol) determined for a 32 cm-diameter reference phantom of 3. 0 and 7. 0mGy, corresponding to the delivered dose in our institution for thoracic and abdominal-pelvic acquisitions, respectively. Acquisitions were performed on helical mode with a pitch factor close to 1, which corresponds to the intermediary pitch factor between thoracic and abdominal-pelvic acquisitions. Raw data were reconstructed using "soft tissue" kernel, with FBP and intermediate iterative level of IR algorithm available on each system and used in clinical practice (Asir-V ® for GE Healthcare, iDose 4® for Philips Medical Systems, ADMIRE ® for Siemens Healthineers and AIDR 3D ® for Canon Medical Systems).
CT-number and image-noise Image-quality evaluations were performed using in-house MATLAB ® routines. Two square regions-of-interest (ROI) were centered in the titanium rod core insert (Figure  1c ): a ROI of 11x11 pixels surrounds the insert (ROI Insert ) and a ROI of 45x45 pixels includes the Plastic Water ® and the titanium insert (ROI Tot ). A third ROI (ROI Tot-Insert ) was defined by using all pixels contained in ROI Tot except the pixels inside the ROI Insert. This ROI Tot-Insert was composed only with Plastic Water® (N CT ≈ 10HU). Average and standard deviation of the pixel values were computed in ROI Tot-Insert. The former corresponds to the mean of CTnumber (N CT ) and the latter to the image-noise (standard deviation of N CT value). values within ROI Tot-Insert.
24 An array is created using the raw sequence files and the program loops through examining one sequence at a time, looking for a "string" that fully matches one of the probes. The total number of matches, or unique in silicohybridization events, are then counted with each match representing the conceptual identification of 1 bacterial cell. ProbeSeq is an iterative process, and sequences not detected by a species-level probe are then processed against genuslevel probes. The final HOMINGS data output for each individual are expressed as the relative abundance of each target taxa (by dividing the respective HOMINGS hits for that taxa by the sum of all taxa hits within the individual, ie, percent proportions of each target taxa). Overall, each sample had an average of 22% (SD=12%) unmapped reads that matched to neither species nor genus probe.
Each food group has a range of 0 to 10 points, which are then summed to create the overall score. The AHEI 2010 score ranges from 0 to 110, with higher AHEI scores associated with a lower risk of coronary heart disease and diabetes mellitus. 33 Leisure-time physical activity was assessed and converted to metabolic equivalents, and participants were categorized into 4 leisure-time physical activity categories as previously described. 32 Measures of periodontitis were obtained from the clinical periodontal examinations as previously published,  4  and periodontal status was measured by the percentage of periodontal sites with attachment loss ≥3 mm. (see Data S1 for additional information on risk factor operationalization. ).
Acknowledgments We thank the following individuals for their invaluable contributions to this research:  Consuelo Mclaughin ,  Bennett Batista , and  Victor Rivera  for their assistance with recruitment;  Romanita Celenti  for her efforts in performing phlebotomy and processing and analyzing plaque samples;  Aleksandra Zuk  and  Garazi Zulaika  for their leadership and excellent program coordination; and  Drs Nidhi Arora ,  Ashwata Pokherel ,  Publio Silfa , and  Thomas Spinell  for their skilled examinations and essential participant engagement. We are also profoundly grateful to the ORIGINS participants, for their participation in this research.
Introduction: Periodontitis is an inflammatory dysbiotic disease. Among putative dysbiosis causes, transmission of Porphyromonas gingivalis between individuals of the same family remains unclear. The aim of this systematic review and meta-analysis is to assess the likelihood of shared detection of Porphyromonas gingivalis among cohabiting family members. Methods: A literature search was conducted on different databases up to September 2018. Articles assessing the presence of P. gingivalis between members of the same family were screened. Only English literature was retrieved, whereas no limits were applied for bacterial sampling and detection methods. Results: Overall, 26 articles published between 1993 and 2017 met the inclusion criteria. Of these, 18 articles were used for meta-analyses.
Data extraction and analysis Data from the selected studies were processed for quality synthesis. Relevant findings and outcomes were extracted from the original studies and summarized in tables. Extracted data included first author, year of publication, patient numbers, study design, periodontal status of the probands, bacteria sampling, detection methods, transmission rate. Whenever the transmission rate was not provided or not estimable from the article data, corresponding authors were contacted by email to obtain data on the proportion of family members sharing P. gingivalis. Consequently, whenever possible, studies were grouped by detection method and type of familial relationship, and a proportion meta-analysis was run. The meta-analysis and forest plots were derived by using MedCalc software (version 17.
Conservation of the three-dimensional aspect of bitemarks is important to optimize their correct analysis. Bitemarks could be recorded with a surface scanner. In clinical dentistry, optical cameras are used as an alternative to conventional dental impressions. They scan the dental relief for prosthetic design. We propose a three-dimensional bitemark analysis protocol using an intraoral scanner. Eight volunteers bit on different materials: dental wax and hard cheese. Then, bitemarks and dentitions were scanned with the intraoral scanner. The scans obtained were exported into the mesh comparison software, CloudCompare ® , which can automatically generate overlays. For this purpose, dentition were aligned and compared with indentations. The meshing and non-meshing areas were easily visualized using a colorimetric scale.
Three-dimensional scan: Dentitions and bitemarks were scanned using the intraoral digital scanner PlanMeca Emerald, and Romexis ® , which is the software for digital acquisition and prosthetic 3D design (www. planmeca. com, Version 5. 1. 0. R). The shot is a video flux, not requiring powder coating of the surface to be recorded. It produces a monochrome image as well as a colored image by the transposition of tissue color. The process of digital impression involves triangulation. Laser light is projected onto the surface and the angle of reflected light is analyzed by the receiver. The live acquisition was visible thanks to the software, which allowed the missing zones to be easily visualized and scans to be corrected. The same operator scanned all bitemarks and dentitions. Scans were exported in ply format and forwarded to the software CloudCompare ® (www.
Preliminary treatments: To facilitate comparative analysis, preparation steps were necessary for 3D images. On dentitions scans, only incisors, canines and first pre-molar teeth were kept. The surrounding tissues (palate and gingival mucosa) were also removed. Thanks to the 3D modelling software MeshMixer ® (www. meshmixer. com, Version 3. 4. 35), a planned cut was created to only conserve the occlusal edges. Bitemark scans from materials 1 and 2 were also modified. On the same bitemark, maxillary indentations were separated from mandibular indentations. Indeed, maxillary indentations were compared separately from mandibular indentations. Bitemark scans from material 3 were not modified.
However, if important artefacts were observed on the 3D image, it was better to repeat the scan. With the Romexis ® software, the 3D modelling was very fast; a few seconds was enough for the 3D object to be ready to be exported. With our protocol, the full analysis took approximately 20 minutes. Therefore, the wrong dentition can be rapidly excluded. The conservation of the 3D aspect allowed the easy analysis of bitemarks and interactively meshing dentition. With this 3D technique, it is easy to match teeth with indentations, even for avulsive bitemarks. Photography does not allow this dynamic analysis. Therefore, an intra-oral camera could be easily used for bitemark analysis on food or inanimate materials. Handling of the intraoral scanner is intuitive and requires little practice to perform correctly.
Statistical analyses The analyses in the current manuscript present the comparison between the two treatment groups, ART/HVGIC and CRT/resin composite restorations, for the variables 'all restorations', 'all single-and all multiple restorations' and 'restorations in permanent teeth'. Restorations with no defects, or defects of less than 0. 5mm at the restoration margin, were considered to have survived. All other assessment codes were considered failures. Data were entered into a database and analysed using SAS 9. 2 software. The Proportional Hazard Rate Regression Model  16  with frailty correction  17  was used to estimate cumulative survival percentages of ART and CRT restorations. The Jackknife method  18  was applied to calculate standard errors for comparison of the 5-year results. Statistical significance was set at α = 0.
Clinical Samples This study has been approved by the Ethics Committee of the IHU Méditerranée Infection (N • 2016-011). Accordingly, all the participants gave and signed an informed consent. A total of 90 saliva specimens were prospectively collected in individuals presenting at the Faculty of Odontology and the IHU Méditerranée Infection, located in Marseille, France. Salivary samples were collected using sterile swabs (Deltalab, Carcassonne, France) that were soaked in saliva after being rubbed into the oral cavity in the space between the buccal wall of the upper molar and also under the tongue. They were then deposited in a liquid transport (SAB-medium)  (4). The data regarding age, sex and smoking frequency estimated as cigarette packages per year were collected anonymously from every volunteer participant.
ACKNOWLEDGMENTS This study was supported by  IHU Méditerranée Infection, Marseille, France  and by the  French Government  under the  Investissements d'avenir (Investments for the Future) program  managed by the  Agence Nationale de la Recherche  ( ANR , fr:  National Agency for Research) , (reference: Méditerranée Infection  10-IAHU-03 ). This work was supported by  Région Provence Alpes Côte d'Azur and European funding FEDER IHUBIOTK.
The lateral cephalographs were taken in the CSERD radiography department at 4metre distance using the same equipment and trained technicians. They were carried out before any treatment. Measurements were made using Cephalometrics® Software for the calculations of angular and millimetric values. The entire sample was classified by malocclusion type: class I (no horizontal overjet, normal overbite: 2mm); class II division 1 (maxillary incisor proversion Ans-Pns / I > 110°, horizontal overjet > 4mm); class II division 2 (maxillary and/or mandibular incisor overbite, deep bite: Ans-Pns / Ols > 15°; MP / Oli < 15°, maxillary incisor retroclination: Ans-Pns / I < 105°); class III (edge-to-edge occlusion, horizontal overjet ≤ 1mm). The sagittal and vertical severity of the different malocclusions was apprehended in a binary way: severe (1) or non-severe (0).
The hypodivergence was judged severe with an angle Ans-Pns / MP < 22 °; the sagittal severity was judged severe with an AOBO distance > 2 or < 0 mm. We quantified Noffel's warning signs on lateral cephalographs by length (mm) and area (mm²) measurements with the ImageJ ® software according to the following protocol. The axes required for the various measurements were previously plotted in white on the lateral cephalographs and then the scales were calibrated (pixel equivalence in mm) using the cephalostat (40 mm). The measurements were taken by the same operator twice. The ramal height (warning sign 1) was evaluated by measuring the distance between the Gonion point (Go) and the Articulare point (Ar), which is the posterior facial height defined by Merrifield (Fig. 4 ). The "Smiling chin" (warning sign 2) was defined by measuring the "Total Chin" of the Tweed analysis: orthogonal distance between the cutaneous Pogonion and the Na-B line (Fig.
Statistical analysis Analysis of variance (ANOVA) and X² tests were performed to initially compare the means and percentages of variables in the various groups. For the analysis of the main objective, a logistic regression was used to assess the pathognomonicity of Noffel's criteria in the assessment of class II division 2. A decision tree was used to complement the logistic regression: it showed to what extent Noffel signs were indicative of class II division 2. For the analysis of the secondary objectives, a multifactorial ANOVA with Bonferroni correction was used. The various statistical tests were conducted with the Mystat / Systat® software and RapidMiner® (decision tree).
00164, p=0. 0000173, p=0. 00365 respectively). This was also the case for the "Total Chin" parameter, which was significantly correlated with vertical severity, age and gender (p=0. 000366, p=0. 04, p=0. 05 respectively). However, the results did not show a correlation of Noffel signs with sagittal severity, nor with the three factors combined "Vertical severity, Sagittal severity, Sex". A decision tree with a depth of 4 was calculated with RapidMiner® software to predict whether the patient had a class II division 2 malocclusion or not by considering "Noffel's criteria". It was a mathematical predictive model that produced a class II division 2 prognostic guide. Two Noffel signs ("Total Chin" and "B-line space") were retained in the tree: an increased "Total Chin" (> 17,890) predicted a class II division 2.
Amplification of the archaeal 16S rRNA gene (primers used: SDArch0333aS15, 5′-TCCAGGCCCTACGGG-3′ and SDArch0958aA19, 5′-YCCGGCGTTGAMTCCAATT-3′) and the methylcoenzyme M reducer (mcrA) gene (primers used: mcrA-For, 5'GCTCTACGACCAGATMTGGCTTGG-3′ and mcrARev, 5′ CCGTAGTACGTGAAGTCATCCAGCA -3′) genes was performed as previously described  [22]. Sequencing reactions (Sangers' method) were carried-out using the Big-Dye Terminator, version 1. 1, cycle sequencing kit DNA according to the manufacturer's instructions (Applied Biosystems, Foster City, USA). Nucleotide sequences were assembled using Chromas Pro software, version 1. 7 (Technelysium Pty Ltd. , Tewantin, Australia) and compared to the GenBank database by similarity search using the BLASTN program (http://www. ncbi. nlm. nih. gov/blast/).
Unfortunately, SSCs are frequently refused by parents for esthetic reasons  [5]. Recently, some manufacturers-Hass Corporation (Gangwon-do, Korea), Kinder Krowns (St Louis Park, MN, USA), NuSmile (Houston, TX, USA), and Sprig Oral Health Technologies (Loomis, CA, USA)-have proposed esthetic PPCs called zirconia crowns (ZCs). Another systematic review  [6]  published in 2016 having the primary objective of comparing the effectiveness of PPCs by including at least one group of esthetic crowns did not identify any randomized clinical trial (RCT) that compared ZCs with one of the other categories of PPCs on the PMs. Since 2016, only two RCTs were identified on https:// clinicaltrials. gov and http://apps. who. int/trialsearch/Default. aspx; one published  [7]  and the other not yet completed. The published RCT (NCT03067337, first submitted 22 January 2017) assessed the effectiveness of ZCs (NuSmile) compared with SCCs.
This RCT reported that the effectiveness of ZCs was similar to that of SCCs in terms of cracks, chips, and fractures. However, gingival and plaque indices were lower among ZCs than SCCs. Even if this RCT suggests that ZCs are better than SCCs, caution is necessary in interpreting the results. First, the power of the analysis comparing cracks, chips, and fractures between ZCs with SCCs may be lower since the author justified the sample size based only on the gingival index. Second, it was also unclear how many teeth per participant were included since the authors reported that a sample of 120 contralateral molars in 26 patients had been treated  [7]. The incomplete RCT (NCT01919515) comparing ZCs (NuSmile ZR) with SSCs in PMs is noted to be without recruitment since 2014. ZCs manufactured by NuSmile differ from other ZCs by having no grooves on their inner surface.
Both the ITT and secondary analyses will be performed within a 2-year period at 6, 12, 18, and 24 months. Repeated measures analysis (mixed model approaches) will be performed, and the principal independent variables will be treatment and time. The alpha level will be equal to 5%. All analyses will be performed with SAS (version 9. 4; Cary, NC, USA). The intra-and inter-investigator agreements for primary and secondary outcomes will be assessed using weighted Cohen's Kappa. After calibration, the evaluators (one per center) will be tested by repeated exercises on the Socrative website (https://socrative. com/) with clinical cases suggested in a random way on the e-calib model (http:// zep01793. dent. med. uni-muenchen. de/moodle/). Different clinical pictures were assessed twice, 15 days later.
Data monitoring, harm, and auditing The various centers will send their data to the coordinating center and data will be entered by the coordinating center. The data will be monitored by an independent clinical research assistant (MM-B; Clinical Research Direction, CHUN). No interim analysis is planned. Serious and nonserious adverse events will be assessed during the study by the evaluators. Trial management may be audited by the French Department of Health at any time; the audit would be independent of the investigators and sponsor. Investigators will not have access to the final trial dataset, which will be assessed by the blinded epidemiologist AMV following the recommendations of the statistician.
Ethical consideration The Clermont-Ferrand Committee of Protection of the People (CPP; Sud-Est VI) has approved the study protocol in February 2018 (2017-A01952-51). The protocol is registered with the IDRCB (2017-A01952-51) at the French National Agency for Medicines and Health product Safety (ANSM) and in Clinicaltrials. gov (NCT03296709). All amendments to the protocol will be justified and submitted to the scientific board, accepted by the CPP, and recorded Note: Rate of the outcome for the study groups, power = 90%, alpha = 5%, equivalence margin = 10% by the ANSM. Changes and amendments will be also recorded at ClinicalTrials. gov. Informed consent will be obtained from each eligible child and their legal guardians after an explanation of the trial by an investigator of the corresponding center.
Patients and legal guardians are informed that they have the right to withdraw from the study at any time and without giving reasons. Regardless of withdrawal, patients will be provided with any necessary treatment in their best interest. Withdrawal will be documented. Data confidentiality was audited by the National Committee of Informatics and Freedom (CNIL; reference methodology 001). First and last names of included patients are not recorded in the database. Neither additional visits nor complementary examinations are needed compared with the conventional caries management for children at high risk of caries (our target population). However, the consultation may take a little longer because of the indicators used and the data collection. These methods of monitoring due to the research requirements involve only negligible constraints.
Dissemination of the results The Consolidated Standards of Reporting Trials (CONSORT) guidelines will be used in the preparation of the manuscripts reporting the results of this RCT, and the results will be published in international peer-reviewed journals  [17]. Authors of the publications will be people involved in the elaboration of the protocol, the implementation and conduct of the trial, and the writing of the manuscript and 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. Access to the full protocol can be granted to anyone upon request.
Acknowledgements Institut Français pour la Recherche en Odontologie (IFRO)  funded this study. This work was sponsored by the  Centre Hospitalier Universitaire de Nice (CHUN)  for regulatory and ethics submission. Sprig Oral Health Technologies,  3M , and GC kindly provided ZCs, SSCs, and both high-viscosity GIC (Equia Forte GC) and glass ionomer cement ( CVI Fuji Plus, GC).
However, the imbalance of the ecosystem, which can be caused by a weak immune system, leads to a challenge for oral and systemic health. The ecological conditions of these habitats are constantly changing, so ecosystems are subject to frequent variations. The oral microbiome is a key factor in health or disease  [10]. Its modification contributes to oral and systematic diseases  [11]. Moreover, dysbiosis of the oral ecosystem is associated with systemic diseases, such as cardiovascular diseases, cancers, and diabetes  [12]. A systematic literature search was conducted, fulfilling PRISMA criteria (Preferred Reporting Items for Systematic reviews and Meta-analyses). Electronic research was organized in Pubmed, Embase, and Cochrane databases. No language filters were implemented. The research was performed from 2000 to April 2019.
clinical assessment. Modified International Caries Detection and Assessment System (ICDAS II) criteria were used for caries assessment. ICDAS II was developed for clinical use in caries management and epidemiology, as the measure correlates the clinical appearance of a lesion with its histological depth or severity. ICDAS II is validated for use with children, comparable to standard criteria in epidemiological surveys  18  , and has acceptable validity and reproducibility for all codes when used with primary molar teeth  19. The need to collect data in the field rather than a dental clinic setting precluded the use of compressed air, therefore Code 1 lesions could not be recorded unless they were located in pits or fissures. The caries assessment was conducted by three dental practitioners who had been trained, calibrated and were familiar with the screening methodology before clinical data collection  17.
Purified barcoded amplicon libraries were quantified using a LabChip GX Touch 24 nucleic acids separation system using the DNA high sensitivity kits (Perkin Elmer). Emulsion PCR of pooled amplicon libraries was performed using an Ion OneTouch ™ 2 System with 400 bp protocols and multiplex sequencing was performed on an Ion Torrent Personal Genome Machine, utilising Hi-Q chemistry with 525 reagent flows per run (Thermo Fisher Scientific). Bioinformatics and statistical analyses. Torrent Suite Software was used to demultiplex samples and trim sequencing adapters and barcodes. The Galaxy/GVL 4. 1. 0 workbench and FROGS  21  was used for filtering and clustering of sequences, essentially as described previously  20. Primer sequences were trimmed and sequences were removed that did not contain both forward and reverse primers, were less than 220 bp in length or greater than 350 bp, contained ambiguities, contained homopolymers with size >7 nt, or contained two poor qualities scores (<10) that were <= 10 nt apart.