dataesr/scientific-paragraphs-categorization huggingface dataset:
Background: Root caries among adults is a concern and requires special attention. This systematic review aimed to assess the ndings on the effectiveness of different agents to treat root caries in middle age and older adults. Methods: PubMed, Scopus, and Web of Science databases were searched systematically, following PRISMA guidelines. Clinical trials that evaluate the effectiveness of preventive and/or arresting agents for root caries in patients over 50 years old, published from 2011 to 2019 (June). This review has been registered at PROSPERO database (CRD42018104399). Results: Twelve of 277 studies fully encountered the inclusion criteria and were selected for this review. Eight agents were identi ed in the studies and their e cacy were assessed by different methods. The agents that presented valuable results on arresting or preventing root caries were 38% SDF, arginine-containing toothpaste and high-uoride toothpastes.
Search strategy PRISMA guidelines for systematic review and meta-analysis have been used for this review manuscript  [19]. PubMed, Scopus, and Web of Science databases were searched to identify the most recent scienti c articles on the subject (from 2011 to present date). The research took place on 1th June, 2019, and no language restriction was used. The keywords used were: "root caries"; "dental caries"; "humans"; and "aged". The search strategy for each database are described on Table  1. This review has been registered at PROSPERO database, from the Centre for Reviews and Dissemination of the University of York, UK (CRD42018104399).
Database Strategy PubMed ((("root caries") AND "dental caries") AND humans) AND aged Scopus (ALL ("root caries") AND ALL ("dental caries") AND ALL (humans) AND ALL (aged)) AND PUBYEAR > 2010 AND (LIMIT-TO (DOCTYPE, "ar") OR LIMIT-TO (DOCTYPE, "cp") OR LIMIT-TO (DOCTYPE, "ip")) AND (LIMIT-TO (SUBJAREA, "DENT")) AND (LIMIT-TO (SRCTYPE, "j")) Web of Science TOPIC: ("root caries") AND TOPIC: ("dental caries") AND TOPIC: (humans) AND TOPIC: (aged).
Cancer registries of CUP may not truthfully reflect the true incidence of CUP as they are also affected by the inadequate and low utilization of diagnostic services as well as poor documentation and notification of diagnostic results. Moreover, the CUP incidences are affected by inadequate cancer registry practices  [16]. An audit of the New South Wales Central Cancer Registry reclassified 30. 0% of the CUP cases into known primary tumors thus decreased the incidence rates of CUP  [17]. This issue may be speculated in the Swedish database especially that 2% of the patients with CUP were diagnosed with a new cancer within 5 years which may be suggestive of a potential primary culprit  [13]. The differences in the CUP incidence-rates across the different age groups show that the main variations occur among older patients  [5, 13].
Acknowledgements The authors would like to acknowledge the  National Natural Science Foundation of China  for grant No. 81503594 , No. 51302320  and No. 81800740. China Postdoctoral Science Foundation  for grant No. 2018M630761  and  Weihai Postdoctoral Foundation ,  Development Program  of  Traditional Chinese Medicine of Shandong Province  for grant no. 2013ZDZK-069 ,  Key Research and Development Program of Shandong Province  for grant No. 2017GGX20123 , and  Fundamental Research Funds for the Central Universities  for grant No. 19CX05001A ,  16CX05011A  and  17CX02063.
Construction of mutants. The genome sequence assembly of E. faecalis OG1RF (GCF_000172575. 2) was obtained from the NCBI Reference Sequence Database  (O'Leary et al. , 2016). Primers used in this study are listed in Table  S3. The malR null mutant was obtained by introducing two stop codons at the beginning of the open reading frame (stop corresponding to the parental amino acids 57 and 60) in order to produce a small truncated and presumably nonfunctional protein. The ccpA mutant was constructed by deleting nucleotides 49 to 899 of the parental gene, presenting approximately 85% of the entire sequence. PCR products were obtained with the Phusion polymerase (ThermoFisher Scientific) and appropriate primers using the genomic DNA of E. faecalis OG1RF as template. The desired amplicons were then cloned into the pMAD vector  (Arnaud et al.
5X buffer under constant voltage (140 V) in a dark-chilled room. Fluorescence was read with a ProXpress apparatus (PerkinElmer) with the following settings (top Synthesis of phosphorylated carbohydrates. M6'P and maltotriose-6''-P were obtained as previously described  (Thompson et al. , 2001). G6P and FBP were purchased at Sigma-Aldrich. illumination Thermal Shift Assay (TSA). Sypro™ Orange (Sigma-Aldrich) was used as dye, fluorescence (Ex: 515-535 nm, Em: 560-580 nm HEX™ filter) was monitored in a temperature gradient of +0. 5°C per minute from 25°C to 80°C in a CFX96™ Real-Time PCR Detection System (Bio-Rad). Temperatures of hydrophobic exposure (Th) were determined with Boltzmann regression on the sigmoid part of each curve using GraphPad Prism 7 software. The variation of Th (ΔTh) was calculated by subtracting Ths from Th determined without a ligand.
Proteins were used at a final concentration of 2 µM and interaction assays were carried out in a solution containing 10 mM NaH 2 PO 4 /Na 2 HPO 4 pH 7. 6, 125 mM NaCl, 1 mM DTT, 0. 1 mM EDTA, 7. 5% (v/v) glycerol with a final concentration of Sypro™ Orange dye of 11X. Apparent dissociation constants (K D ) were calculated using Differential Scanning Fluorimetry assuming a single binding event with the GraphPad Prism 7 software for windows, GraphPad Software, La Jolla California USA, www. graphpad. com with the following formula  =  + (( -) * (1as previously described, (refer to  Vivoli et al. , 2014  for more ( 𝑃 -𝐾 𝐷 -𝑋 + (𝑃 + 𝑋 + 𝐾 𝐷 ) 2 -4𝑃 * 𝑋 𝑃 ) ) details).
Accepted Article Multiple alignments. Phyre2  (Kelley et al. , 2015)  was used to generate a model of the MalR tridimensional structure. The PDB entry 1ZVV, corresponding to the CcpA-Crh-DNA complex from Bacillus subtilis was listed with the highest scoring template. The resulting alignment was used as template to perform a multiple alignment with the primary sequence of CcpAs and the RbsR protein using Clustal Omega  (Sievers et al. , 2011).
Acknowledgements We thank  Reinhold Brückner  for the generous gift of plasmid pRB473,  John Thompson  for the supply of the phosphorylated sugars and  Isabelle Rince  for technical assistance. The supports of  Olivier Lesouhaitier  and  Pierre Soule  for MST experiments were particularly precious. This work was funded by a chair of excellence for  Dr. Magni  co-financed by the  European Union  and the  Normandy County Council  in the framework of the ERDF-ESF operational programme 2014-2020 and by the  French Ministry of Education, Research and Innovation.
In any case, the immune system is unable to eliminate the virus completely and in a minute fraction of B cells, the virus acquires a latent state with minimal immune exposure and persists for life  [30]. Evidently, both the virus and the host have evolved multiple elaborate strategies to prevent the possible fatal consequences of EBV infection. However, if the delicate balance between the host immune system and the virus is not maintained, it may lead to EBV-associated diseases. This review discusses novel viral aspects of the etiopathogenesis of non-tumorigenic diseases in the oral cavity, in particular, the contribution of EBV in oral inflammatory diseases, the tropism of EBV infection and the major players involved in the etiopathogenic mechanisms. For the literature search, we identified the most relevant articles reporting the above-mentioned topics using web-based search engines including Google, Google Scholar and PubMed database.
Chappuis et al. , in 2017, showed that the recipient site would not have a significant influence on the post-transplant bone resorption rate  [11]. This is in agreement with our study. The data generated by our study are interesting but must be interpreted with caution. Indeed, our study had several limitations: The lack of reliability with a small sample of patients but also significant variations around the mean values was a limitation. In fact, volume analysis showed resorption rate differences both for the ramus and parietal groups. Therefore, larger number of patients should be recruited. In addition, this study was based on the clinical experience of a  single surgical team; hence, the study results cannot be generalized. To overcome this bias, it would be appropriate to perform such a study at multiple centers.
Materials and methods: A total of 730 maxillary right central brackets manufactured by seven companies (Dentsply Gac, American Orthodontics, Rocky Mountain Orthodontics, GC Orthodontics, 3M Unitek, and Dentaurum) were studied. The sample included 0. 018 × 0. 025 and 0. 022 × 0. 028 in. , metal and ceramic, conventional and self-ligating brackets. Images were obtained with an Olympus BX51 optical microscope. Slot dimensions were measured at the base and at the face on both mesial and distal sides using ImageJ software. Data were analyzed using Wilcoxon, sign tests, two-and three-way ANOVA, and Tukey's tests. Intraclass correlation coefficient was employed to assess the intraobserver and interobserver variability. The threshold for statistical significance was p ≤. 05. Results: Statistical analysis showed that the slot dimensions of 90% to 97% of studied brackets were significantly different from nominal values.
| MATERIALS AND METHODS A total of 730 maxillary right central brackets were provided by seven companies (Dentsply GAC, Bohemia, NY; American Orthodontics, Sheboygan, WI; Ormco, Glendora, CA; Rocky Mountain Orthodontics, Denver, CO; GC Orthodontics, Breckerfeld, Germany; 3M Unitek, Monrovia, CA; and Dentaurum, Ispringen, Germany). All brackets were preinformed, 0. 018 × 0. 025 or 0. 022 × 0. 028 in. , metal or ceramic, conventional or self-ligating. Self-ligating bracket clips were either passive or active. In accordance with these criteria, 73 different series (with the same batch) of brackets were put together, and a sample of 10 brackets of each series was randomly selected. Bracket slot images were obtained using a calibrated Olympus BX51 optical microscope. Each bracket slot was measured at base and at face, using ImageJ software (National Institute of Health).
Data analysis Local sample deformation was calculated using DIC with the image data collected by the cameras. This was carried out using the DIC software named Vic3D (version 7, Correlated Solutions Inc. , South Carolina, USA). The pattern and step size were 15 and 5 pixels, respectively; the image pixel size was calculated to be 0. 1 mm. An in-house script written in ScilabV R v 6. 0. 2 was used to process the data from the testing machine and from the Vic3D software for all the loading cycles. The images corresponding to maximum screw displacement were identified and extracted. A grid of nodal points was applied to the correlated image and the nodes with the maximum positive and negative deformation values were identified. The mean strain was calculated and the zone in which this value ±1 SD could be observed, were recorded as range and angle in a polar coordinate system (Figure  2 ).
Molecular identification and typing of isolates Primer design. Based on the analysis of Malik et al. [33] , we designed specific primers in the 3,048 bp sequence of the RNA polymerase II rpb1 gene available on the NCBI website (accession number: HM016234. 1 for T. tenax strain NIH4). Primers were designed using Primer-BLAST (https://www. ncbi. nlm. nih. gov/tools/primer-blast/) with standard parameters (Fig  1F). Genome sequencing of Trichomonas tenax. Briefly, 15 vented Corning 75cm 2 (NY, USA) flasks containing LYI medium of T. tenax NIH4 reference strain (ATCC number 30207) were pelleted at 2000 g for 15 minutes, rinsed twice with the same centrifugation parameters in Page's amoeba Saline before final re-suspension in 1 mL of phosphate buffered saline. Concentrated cells were placed at -80˚C before DNA extraction and sequencing.
Total information of 10. 5 Gb was obtained from a cluster density of 1,288,000 per mm 2 with 86. 3% (20,305,000 clusters) of the clusters passing quality control filters. Within this pooled run, the index representation of T. tenax was determined to 39. 43%. The 8,005,980 paired end reads were filtered according to the read qualities. Multilocus sequence typing. The reads obtained were assembled using the CLC Genomics Workbench. Protein sequences were predicted using the Prodigal platform  [34]  and analysis. A local Blastp on the predicted proteins was performed on NCBI Blast (Basic Local Alignment Search Tool) against non-redundant protein sequences (nr) database using the standard parameters. The T. tenax NIH4 genome sequence was deposited on the EMBL-EBI website (Bioproject: PRJEB22701 and whole contigs under accession numbers OCT-D01000001-OCTD01004161).
Seven single-family household genes were selected ranging in length from 450 to 500 bp (Table  1 ) based on MLST designed for Trichomonas vaginalis  [35]. Single standard PCRs were performed to allow DNA amplification of each selected gene. Primer hybridization was conducted at 59˚C and amplified products were sequenced as described previously  [36]. Sequences were corrected and assembled using the ChromasPro software version 1. 71 (Technelysium, Australia). Obtained sequences were aligned using MUSCLE tool in the Molecular Evolutionary Genetics Analysis software (MEGA) version 7. 0. 18 (Pennsylvania State University, United-States) and, finally, phylogenetic trees were generated using the maximum-likelihood (ML) method within FastTree version 2. 0  [37]. MLST nucleotide sequences data are available in the EMBL-EBI database under accession numbers LT934459 to LT934497.
Statistical analysis The statistical analysis was performed using "R" software (Version 3. 5. 1) using a ordinal logistic regression with a four-modalities qualitative variable to investigate the correlation between health status and detection methods (culture or PCR) with the existence of T. tenax. χ 2 tests for sex and smoking status descriptive statistics and Fisher test for the phylogenetic tree analysis using Statistical Package for the Social Sciences (SPSS Inc, IBM Company).
Isolation of Trichomonas sp. Fifty-three strains of Trichomonas sp. were obtained from periodontal samples, 37/106 from patients with periodontitis and 16/85 from control patients (p = 0. 018) (Table  2 , Table  3 ). Six isolates were lost before conservation. Protists were likely to be T. tenax based on their morphology as observed by microscopy. For a definitive identification, we first performed alignment of available rpb1 gene using online Clustal Omega  [39]  with standard parameters for 11 sequences of Trichomonas spp. and we visualized it using MView online software (http://www. ebi. ac. uk/Tools/msa/mview/). Following the 100% consensus sequence available (S1 Scheme), we designed degenerated primers on conserved regions between the 11 different Trichomonadidae strains. In order to evaluate the intra-species diversity of the rpb1 gene, we amplified and sequenced the rpb1 gene from 15 randomly chosen strains isolated from our control and diseased patients.
for which a draft genome is available. In the T. vaginalis G3 genome, about 250 genes were annotated as ribosomal proteins  [40]. In T. tenax, we obtained in the draft 52 ORFs annotated as the 40S ribosome and 68 annotated as the 60S ribosome. We isolated the complete sequence of the rpb1 gene measuring 4,962 nucleotides and, congruently, the alignment with the same strain in the database showed 61% of coverage with 100% identity. The alignment starts at position 229 and finishes at position 3,276 of the complete sequence and makes the 3'end of this gene available.
This work was supported by a grant from the  French State  managed by the  National Research Agency  under " Investissements d'avenir (Investments for the Future)" program  with the reference  ANR-10-IAHU-03  ( Mediterranee-Infection ) and by  Region Provence-Alpes-Cote d'Azur and European funding FEDER PRIMI. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.
S1 ). Critical exposure ages for development of dental fluorosis are from 1 to 7 years of age during permanent dentition development when excessive fluoride exposure disrupts enamel mineralization, with dental fluorosis externally evident, visually, upon eruption of these permanent teeth. We also asked about water source, as ESCC risk has been linked to consumption of non-piped water,  22, 23  and in Kenya surface waters have some of the highest fluoride levels worldwide. 24 or the present investigation, socioeconomic factors (job, education and amenities), age, ethnicity, alcohol (by type), tobacco (smoking and smokeless), hot beverages, household air pollution, and family history of ESCC represent potential confounders or effect modifiers. Place of birth and of current residence were obtained, and, with the aid of databases of all Kenyan places (www.
Acknowledgements We express our thanks to the participants in this case-control study for their support and time. This work was supported by the  International Agency for Research on Cancer (IARC) ,  NIH/NCI  grant  R21CA191965 , an  IARC-UICC   Development Fellowship  to SKM and an  IARC post-doctoral fellowship  to DM partially supported by the  European Commission FP7 Marie Curie Actions -People -Co -funding of regional, national and international programs (COFUND).
The authors declare no completing interests. Grant sponsor:  European Commission   FP7 Marie Curie Actions; Grant sponsor: IARC post-doctoral fellowship ; Grant sponsor:  IARC-UICC Development Fellowship ; Grant sponsor:  NIH/NCI ; Grant number:  R21CA191965 ; Grant sponsor:  International Agency for Research on Cancer (IARC) DOI :  10. 1002/ijc. 32086.
Responses such as, "God/my religion does not approve" and "the Bible says …" were classified as "religious reasons". The statistical analysis was done with SPSS/PC+ v. 20. 0 software (SPSS, Chicago, IL, USA). Descriptive statistics were calculated for the different variables using absolute frequencies and percentages. The relationships between the categorical variables were estimated with Pearson's chi-squared test (a value of P,0. 05 was selected as the threshold for statistical significance) and post hoc testing. Ordinal logistic regression was calculated to predict the degree of acceptance to each bone graft based on sex, age, educational level, religious affiliation and country of origin.
Construction of the questionnaire and validation A steering committee composed of a public health odontologist, an anaesthesiologist and an oral surgeon developed a set of questions to carry out data collection with the least bias possible. A series of closed multiple-choice questions was formulated, as well as open-ended questions allowing respondents to freely express themselves. Prior to the completion of the survey, a feasibility study was conducted to ascertain whether some questions were difficult to understand and if additional questions needed to be added. This stage of the study was also intended to test the practicality of the Google Docs © software.
Data collection We obtained the e-mail addresses of 250 oral surgeons and stomatologists practicing in the public or private sectors from databases of the French Society of Oral Surgery. This request was made during the French Society of Oral Surgery congress 2017 at Rouen. For reasons of time and cost, we limited our survey to this available database. Our questionnaire was submitted anonymously by e-mail to all these practitioners. It was sent out over a 3-week period of time.
Strategy of the documentary research A bibliographic search was conducted on the MEDLINE database (PubMed) covering the period of January 2000 to September 2017 with no language restrictions. The following MESH words were queried: LA, GA, nerve block. With these words, 825 references were obtained. We searched for the terms "oral surgery, otorhinolaryngological surgery, dental surgery or maxillofacial surgery" in titles and abstracts. A second bibliographic search on Medline with the same method found two additional articles from the journal Oral Medicine and Oral Surgery, and one more from Science Direct. The identified studies were first sorted by title and abstract, we only included studies that explore the effects of LA under GA in oral sphere operations. Nine articles were selected. Two independent reviewers read the abstracts and included articles in the final selection based on their content.
Construction of the questionnaire On the basis of the clinical experience of the members of the steering committee, a first questionnaire consisting of an open question and nine closed questions was developed. This questionnaire, together with an acceptability questionnaire, was sent electronically (google docs © software), to 11 oral surgeons and to an anaesthesiologist who frequently works in stomatology. All the questions were perfectly understood except one concerning "the knowledge of the role of the anaesthesiologist". Two suggestions were made to add a question about the use of vasoconstrictors and to add prilocaine to the choice of LAs. An additional indication for LA was suggested by two people "the detachment of the mucosal foreground facilitated by infiltration". The final questionnaire resulting from the feasibility study is presented in the Appendix.
Introduction: Spaceborne remote sensing datasets, providing information with a good spatial coverage over areas that are difficult to access, have proven to be powerful tools to study lava flows. Radar images have the advantage that they are insensitive to cloud cover and solar lighting. They can be used to detect and map new lava flows with either coherence or amplitude based methods  (Schaber et al. , 1980; Zebker et al. , 1987 Zebker et al. , , 1996;; Gaddis, 1992; Rowland et al. , 2003; Dietterich et al. , 2012). They are also commonly used to estimate their thickness and volume, and thus determine volcano extrusion rates  (Stevens et al. , 1999; Rowland et al. , 2003; Terunuma, et al. , 2005; Poland, 2014; Bato et al. , 2016; Arnold et al. , 2017) , which is key information in terms of hazard assessment.
An estimation of the magma bulk viscosity is also derived based on the downward lava displacement. Along-track incidence angles of the two images are -9. 3° and -13. 1°, while the across-track angle varies between -14. 5° and -9. 6°. The DEM was computed using the NASA open source software Ames Stereo Pipeline  (Broxton and Edwards, 2008). Disparities between the two images are searched for; this provides a point cloud of the surface topography which is then converted onto a grid regularly spaced every 3 m. In this way we obtain a Digital Surface Model, but as no vegetation is present on the region of interest, where lava flows are emplaced, it corresponds to a DEM.
Data and processing Surface displacements induced by the lava flows were quantified based on 36 SAR images acquired from November 23, 2014 to February 10, 2016, on both ascending and descending tracks, by the European satellite Sentinel-1A with a Vertical-Vertical polarization ( close to or even greater than the incidence angle, inducing low resolution and a possible layover effect on the flanks facing the satellite. This is particularly true for the descending track where the incidence angle is very close to the volcano slope on the eastern flanks around the summit area (~35°). Ground area affected by low resolution was estimated and consequently masked based on acquisition geometries. Interferograms as well as coherence images were computed on ascending and descending tracks from SLC images using the NSBAS processing chain as described in Doin et al (  2012 ) and modified to allow for TOPSAR data ingestion  (Grandin, 2015).