dataesr/scientific-paragraphs-categorization huggingface dataset:
Data retrieval Data that were used for our retrospective analysis correspond to 885 messages sent between March 2006 and February 2020, by AFGS members on discussion forum entitled "Mouth-Nose", available on association's website. Anonymous data have been extracted by AFGS in an Excel ® file. The "participatory framework" of "Mouth-Nose" forum includes all AFGS members who have at any time consulted or participated in the forum. Note that all participants of this forum are AFGS members, up to date in their membership fees. includes the initial request (first post) as well as all responses to that request. Number of messages of each thread has been counted. 188 threads were identified, two of which were excluded because they corresponded to two posts from the same person and on the same day, without giving rise to an exchange, and without any mention of Sjögren' syndrome or Sicca.
Data collection and study procedures Participants will undergo HPV sampling by means of an oral rinse and gargle (ORG) before any procedure (including any COVID-19 preventive intervention) and complete a self-administered questionnaire. For those who report receiving an HPV vaccine or are unsure whether they had been vaccinated, the dental staff will follow up with participants by phone 1 or 2 weeks after visit 1 to confirm their vaccination status. For US participants, 6-month follow-up visits will include ORG sampling and completion of a self-administered questionnaire to assess changes since the previous visit. Dentists and study support staff at the dental office will be trained on the study protocol, study procedures, and data collection protocols. As shown in Tables  2  and 3 , the following data will be collected during the study: (1) clinical data reported by the dentist (at visit 1 and follow-up visits in the US) and HPV vaccination status (at visit 1 only), (2) participant self-reported study questionnaire (at visit 1 and followup visits in the US), and (3) laboratory test data obtained from the ORG sample collected at visit 1 (European countries and US) and followup visits (US only).
Clinical data reported by the dentist During visit 1, dentists will record study participant data, oral health status, and HPV vaccination details. During follow-up visits (US only), the dentist will repeat the oral examination and record any updates to all variables assessed at visit 1. Table  2  shows a detailed list of the variables reported by the dentist at each study time point. Those participants who provided no HPV vaccination data at visit 1 will be contacted by dental office staff to clarify vaccination status.
Participant self-reported study questionnaire data The study questionnaire for visit 1 assesses sociodemographic and general clinical factors, general risk behaviors, medical history, and sexual risk behavior characteristics. During follow-up visits (US only), participants will report on smoking and alcohol consumption behaviors, medical history, as well as sexual behavior since their last visit. The participant self-reported study questionnaire variables are listed in. Table  3. The study questionnaire will be completed either electronically or in paper form. Any paper questionnaires will be sealed by the study participants immediately upon completion to ensure confidentiality and transported by courier to the clinical research organization to be entered into an electronic database. Dentists will not have access to individual participant-related information collected during the study.
Laboratory test data 2. 7. 1. ORG sampling procedure Dentists will collect ORG samples during visit 1 and follow-up visits. Study participants will be asked to remove any external material from the mouth (chewing gum or dentures) before the procedure. They will then be asked to rinse with alcohol-based mouthwash (Long Spin®; manufactured by Okina Co. , Ltd. ; in a 14 mL single-use pod) for 15 s, gargle for an additional 15 s, spit the gargled liquid into a 50 mL Falcon tube, and return the tube to the dentist. The tube will then be capped and kept in a -18 • C freezer at the dental offices for approximately 4 to 8 weeks, after which a courier service will collect and transport the specimens to a central laboratory for testing.
Data management and analysis All data generated throughout the study will be stored electronically. Statistical analyses will be conducted with SAS® and R statistical software packages. Descriptive statistics will be used to report continuous and categorical variables, overall and stratified by sex and age category. All analyses will be performed at the country and global level if results are comparable between countries. The overall oral HPV prevalence will be calculated by dividing the number of study participants with prevalent HPV (as defined above) by the total number of study participants. Prevalence will also be calculated by HPV genotype. The overall incidence of oral HPV will be calculated by dividing the number of study participants with incidentally detected oral HPV (as defined above) by the total person-time at risk.
Incidence will also be calculated by HPV genotype among study participants who had a negative HPV test result for the corresponding genotype at prior visits. Oral HPV clearance will be reported at 12, 18, and 24 months using the prospective data collected, and clearance of incident and prevalent cases will be presented separately. At each time point, clearance (overall and by genotype) will be calculated by dividing the number of study participants with two consecutive study visits with a negative HPV test by the total number of study participants with positive HPV in the previous visit. In addition, incidence, persistence, and clearance will be described using Kaplan-Meier curves, and clearance will also be assessed by all HPV genotypes. Factors associated with oral HPV, including demographic and sexual behavior factors, will be compared according to the presence of oral HPV at visit 1.
[20]  involved such patient populations. The PROGRESS study will use a systematic consecutive targeted sampling protocol to recruit study participants who present for their regular check-ups at dental offices. This methodology is expected to provide information more representative of the general population, as the study sites were carefully selected to cover diverse (urban and rural) areas of varying socioeconomic profiles  [36]. The multi-country setting, standardized study protocol, and central analysis of collected samples will permit the comparative analysis of data across different geographical locations. Furthermore, dental practices are increasingly important in the diagnosis and prevention of oral diseases and have been proven to be an ideal setting to study oral HPV, given the high number of potential target participants for whom they provide care  [37] [38] [39].
In addition, a randomized, placebo-controlled trial (NCT04199689) has been initiated to directly evaluate efficacy of the nonavalent HPV (9vHPV) vaccine against oral persistent infection in adult men  [47]. Together, data from these three studies will shed light on the potential impact of HPV vaccination on both sexes. The increasing incidence of HPV-related OPC underlines the importance of effective screening and prevention efforts, which rely on robust and extensive epidemiological data. The PROGRESS study is a large, multi-country observational study, which will provide additional information on the prevalence and natural history of oral HPV infection in the general population, as well as the factors associated with infection, aiding the planning and monitoring of future HPV vaccination programs  [48].
Study Population. e Ethical Committee of Strasbourg University Hospital has independently reviewed and approved this cross-sectional study (AMK/BG/2016-95 -ClinicalTrials. gov-https://ClinicalTrials. gov ID: NCT03841656). e subjects gave their written consent to participate after being informed of the study objectives. e study was conducted according to the principles stated in the Declaration of Helsinki  [27]. To be included in this study, participants had to fulfill the following criteria: (a) patients had one or more implants for at least 1 year of function that was placed at the Department of Periodontology of the Dental Faculty, University of Strasbourg, (b) patients had the initial periodontal diagnosis and the active and supporting periodontal therapy performed at the same Department of Periodontology before the implant placement, (c) patients had available and reliable updated demographic, medical, periodontal, and implant data, (d) patients were ≥20 years at implant placement, and (e) patients had at least 12 residual teeth at the implant placement.
Patients in need of antibiotic prophylaxis for clinical periodontal examination and treatments were excluded. Dentate adults who had undergone periodontal and implant treatment from 1999 to 2017 at the Department of Periodontology of the Dental Faculty of Strasbourg were identified from the clinic's database as previously described  [28]. Initial periodontal diagnosis, i. e. , gingivitis/mild periodontitis, moderate periodontitis, and severe periodontitis based on criteria defined by the 1999 International Workshop for a Classification of Periodontal Diseases and Conditions  [29] , was established from patient file data. After active periodontal therapy (APT) was completed, the supporting periodontal therapy (SPT), scaling and root planing were performed in residual and recurrent sites with PPD 2 International Journal of Dentistry ≥4 mm.
Examination. Periodontal and implant examinations were performed at the final re-evaluation. Demographic data, medical history, and smoking status data were recorded. Regarding smoking, patients were divided into 3 groups: the nonsmokers (who had never smoked), former smokers (who quit > 5 years ago), and current smokers (who had at least one cigarette/day). At the re-evaluation, the periodontal status of patients was classified according to the 2017 World Workshop on the Classification of Periodontal and Peri-implant Diseases and Conditions  [14]. Clinical examination was performed by two calibrated examiners (IP and PV). e full-mouth plaque score (FMPS), PPD, CAL, gingival recession (REC), and BOP around teeth were recorded. e PiPD, clinical attachment level (CALi), mucosa recession (RECi), implant plaque score (IPS), BOPi, and suppuration around implants were recorded.
Radiographic Analysis. A radiographic examination was performed with digital orthopantomography and periapical radiographs (Planmeca, Roselle, IL, USA) obtained using the long-cone parallel technique and Rinn system (XCP Instruments, Rinn Corporation, Elgin, IL, USA). Measurements were performed with Centricity Enterprise web-specific software (GE Medical Systems IT, Wauwatosa, WI, USA). Bone level around the implant was measured on periapical radiographs as the distance from the junction between smooth and rough implant surfaces for the tissue-level implants and from implant shoulder for bone-level implants to the first bone-to-implant contact on mesial and distal aspects of the implants by the same two calibrated examiners (I. P. and P. V. ). e most elevated measurement (mesial or distal) was selected to represent BLi  [33].
Materials and Methods No human or animal subjects were used in this study; therefore, ethics committee approval was not required  [15]. Based on the results of similar previous studies  [2, 4] , sample size estimation was calculated a priori with G*Power 3. 1. 9. 2 software (Heinrich-Heine-University at Dusseldorf, Dusseldorf, Germany) to have 80% power and alpha error probability of 0. 05. The 2Shape TS2 mini 1. 0-mm and TS2 1. 2-mm files, differently heat-treated (i. e. , T-wire and prototypes CM-wire), were used. All files were 25 mm long, with 10 instruments in each group used in cyclic fatigue and torsional resistance tests. Prior to testing, all files were inspected using a stereomicroscope (SZR-10; Optika, Bergamo, Italy) to verify any deformation  [2]. None were discarded.
Design of the study A retrospective multicentric observational comparative study was designed. All the departments of oral surgery and/or maxillofacial surgery currently involved in the medical care of head and neck cellulitis in French public hospitals have been invited to participate to the study. Invitations to participate to the survey were sent by e-mails addressed to the heads of each department: one invitation e-mail followed by at least 4 reminder e-mails. The first e-mails have been sent at the end of the lockdown period, on the 15th of May 2020. The data collection period was planned to last at least four months and/or the necessary time to get data from at least 15 OMF departments.
Materials Bidirectional fiber reinforced composite "bFRC" and bidirectional spiral winding fiber reinforced composite "bswFRC" (Bio Composants Médicaux, Auvergne-Rhône-Alpes, France) were used in the present study. All specimens were prepared using CAD/CAM equipment "INDEX 35I Pro" (imes-icore GmbH, Eiterfeld, Germany) with WORKNC software (Hexagon, Charnay-les-Mâcon, France) in order to obtain 20 cylinders (4 mm in diameter and 4. 5 mm in height) for each group.
X-ray Tomography The internal structure of the specimens created with bFRC and bswFRC was inspected in 3D by means of micro-computed X-ray tomography (µCT) (EasyTom 160 from RX Solutions, Chavanod, France). Imaging was conducted at a voltage of 45 kV and a current of 160 mA, using a micro-focused tube equipped with a tungsten filament. The sourceto-detector distance (SDD) and the source-to-object distance (SOD) were adjusted in such a way to obtain a voxel size of around 2. 3 µm. The volume reconstruction was executed through the software Xact64 (RX Solutions) after applying treatments such as geometrical corrections and ring artefact attenuation. The image treatment was performed with Avizo software (ThermoFisher, Waltham, MA, USA) that enabled us to (i) de-noise the images with a median filter, (ii) segmentate the image intensity to reveal the objects of interest (here the pores), (iii) remove insignificant small objects (below a size of 10 pixels) from the segmented 3D data, and (iv) determine the 3D geometrical aspects of the objects of interest (volume and equivalent diameter)  [26].
Therefore, it would be required to explicitly disclose the names of the active chemicals, the quantity of these compounds, and whether or not they pose a potential toxicity concern. Given the scientific proof of "natural" toothpaste's efficacy in oral prophylaxis, they demonstrate that there should be a growing interest in it. The evaluation contains both strengths and weaknesses. Its adherence to the methodological criteria for conducting a review, in particular the participation of two independent investigators for article selection and data retrieval, is one of its strengths. However, several databases (Elsevier through Scopus) were inaccessible; considering the huge number of the databases investigated, the chance of selection bias is minimal.
The scale-sensitive fractal analysis (SSFA) of dental microwear textures is traditionally performed using the software Toothfrax. SSFA has been recently integrated to the software MountainsMap® as an optional module. Meanwhile, Toothfrax support has ended. Before switching to the new module, the outputs between the two software packages must be compared for consistency. We have performed such a test using Bayesian modelling on three datasets including dental surfaces of sheep  (Merceron, Ramdarshan, et al. , 2016)  and guinea pigs  (Winkler, Schulz-Kornas, Kaiser, Cuyper, et al. , 2019)  from controlled feeding experiments, as well as surfaces of quartzite and flint flakes used in an actualistic archeological experiment on cleaning procedures (Pedergnana, Calandra, Bob, et al. , 2020). We found that the two software packages calculate significantly different values for the SSFA parameters epLsar, Asfc, HAsfc9 and R 2 , even when the same settings are used.
, 2019). Originally, the SSFA for DMTA has been performed with a custom-made software called Toothfrax, in combination with Sfrax, developed by SurFract Corp (Worcester, MA) (see details in  Scott et al. , 2006). It computes five parameters: area-scale fractal complexity (Asfc, referred to as "complexity"), scale of maximum complexity (Smc), length-scale anisotropy of relief (epLsar, "anisotropy"), heterogeneity of areascale fractal complexity (HAsfc, "heterogeneity"), and textural fill volume (Tfv). Only Tfv is calculated in the software Sfrax; the other four parameters are computed with the software Toothfrax. Some recent studies have focused only on complexity and anisotropy because these parameters seem to be the most discriminant ones to reconstruct diets (e. g. Kubo et al. , 2017; Schmidt et al.
, 2019; Arman et al. , 2019; Winkler, Schulz-Kornas, Kaiser, & Tütken, 2019; Ackermans et al. , 2020; Ungar et al. , 2020). However, analyses of incisor microtextures have found that Tfv is an important parameter related to anterior tooth loading and tooth use  (Krueger & Ungar, 2010; Krueger, 2015; Delezene et al. , 2016; Krueger et al. , 2017 Krueger et al. , , 2019 ; see also  Caporale & Ungar, 2016 on rodents). Many manufacturers of 3D profilometers and confocal microscopes use the MountainsMap® software solution by Digital Surf (Besançon, France) as a software platform for their instruments. They also adjust the modularized MountainsMap® software for their requirements, resulting for example in ConfoMap by Carl Zeiss Microscopy (Jena, Germany), LeicaMap by Leica Microsystems (Wetzlar, Germany), SensoMAP by Sensofar (Barcelona, Spain) and µsoft analysis by Nanofocus  (Oberhausen, Germany).
Second, the Tfv parameter is not available in the SSFA module, even in the latest release of MountainsMap® (v. 9. 2. 10170), although it will probably be released with a future update. Third, starting with MountainsMap® version 8, a new anisotropy parameter called NewEpLsar is available, alongside the original one. This new parameter is meant to correct a mistake in the code of Toothfrax (see section 4. 3 below). The majority of the published data were calculated with the software packages Sfrax and Toothfrax, and this remains true for many recent studies (e. g. Berlioz et al. , 2017 Berlioz et al. , , 2018;; Percher et al. , 2018; Ungar & Berger, 2018; Smith & DeSantis, 2018 , 2020; Merceron et al. , 2018 Merceron et al. , , 2021;; Hofman-Kamińska et al. , 2018; Tanis et al. , 2018; Schmidt et al.
, 2019; Sewell et al. , 2019; Arman et al. , 2019; DeSantis et al. , 2019 DeSantis et al. , , 2020;; Stynder et al. , 2019; Catz et al. , 2020; Ungar et al. , 2020; Robinet et al. , 2020). Others have already moved to MountainsMap's SSFA module (e. g. Böhm et al. , 2019; Winkler, Schulz-Kornas, Kaiser, & Tütken, 2019; Ackermans et al. , 2020; Prassack et al. , 2020; Schulz-Kornas, Winkler, et al. , 2020; Winkler, Tütken, et al. , 2020; Winkler, Schulz-Kornas, et al. , 2020; Ungar et al. , 2021). Sfrax and Toothfrax are not supported anymore; hence, the move to the new SSFA module is inevitable. This raises the question of whether the new module produces results that are identical to the ones from the original software, given identical contexts and configurations. In other words, can the output from the new SSFA module be directly compared to the published output of the Toothfrax software? Should this not be the case, are the results at least close enough, so that the functional interpretations (e.
g. animal diet or tool use) remain? And how does the new anisotropy parameter (NewEpLsar) perform and compare to the original one? Four years after the first release of MountainsMap's SSFA module, we believe it is now time to take a step back and address these questions. In this paper, we compare the outputs from the two software packages on three published datasets of experimental sheep teeth  (Merceron, Ramdarshan, et al. , 2016) , guinea pig teeth  (Winkler, Schulz-Kornas, Kaiser, Cuyper, et al. , 2019)  and lithic flakes  (Pedergnana, Calandra, Bob, et al. , 2020). These datasets cover a range of biological and archeological applications on different materials (enamel, flint and quartzite) and at different sizes (guinea pig and sheep teeth, and lithic flakes). Additionally, the data were acquired using three types of confocal microscopes (programmable array scanning, disc-scanning, and laser-scanning confocal microscopes;  Artigas, 2011) , with objectives having different magnifications and numerical apertures (100×/NA=0.
Sheep dataset This dataset has been collected and analyzed by  Merceron, Ramdarshan, et al. (2016). It contains data on a feeding experiment on 40 ewes (Ovis aries) fed four different diets for about 11 weeks: clover, grass, clover + dust, and grass + dust (10 ewes per diet). The disto-labial enamel band of the protoconid of one of the lower second molars was molded using a polyvinylsiloxane elastomer. The molds were then scanned with a Leica DCM8 confocal profilometer (Leica Microsystems; see Table  1  for details on acquisition settings). Among other pre-processing steps (Table  1 ), abnormal peaks were automatically erased with a batch algorithm computed on IMAGEJ software based on mathematical morphological tools (this procedure can now be applied in MountainsMap® 8 and its derivatives directly).
Guinea pig dataset This dataset has been collected and analyzed by  Winkler, Schulz-Kornas, Kaiser, Cuyper, et al. (2019). It contains data on a feeding experiment on 18 guinea pigs (Cavia porcellus) fed three different diets for three weeks: dry grass, dry lucerne and dry bamboo (6 individuals per diet). The original dataset includes three extra fresh diets that were not included in the present analysis. The mesial enamel band on the right upper fourth premolars was molded. The molds were scanned using a μsurf Custom confocal disc-scanning microscope (NanoFocus AG; see Table  1  for details on acquisition settings). For each specimen, four non-overlapping scans were taken. For individuals 2CC5G1 and 2CC5G2 (dry grass group), only three scans could be acquired, as the enamel bands were too thin or showed damage.
Lithic dataset This dataset has been collected and analyzed by  Pedergnana, Calandra, Bob, et al. (2020). It contains data on an actualistic brushing experiment on eight flakes. Flakes were knapped from two raw materials, flint or quartzite (four flakes each), and were subjected to four treatments: application of sediment and cleaning through rubbing with fingers (RubDirt), application of sediment and cleaning through brushing (BrushDirt), only brushing (BrushNoDirt), and control (no sediment and no brushing/rubbing), with one flake of each raw material per treatment. The samples were scanned at two spots before and after treatment using a coordinate system to relocate the spots  (Calandra, Schunk, Rodriguez, et al. , 2019) , resulting in 32 scans. An LSM800 MAT laserscanning confocal microscope (Carl Zeiss Microscopy GmbH) was used for the scanning (see Table  1  for details on acquisition settings).
One spot of one sample ("Area 1" of sample FLT3-8) was not correctly acquired before the experiment but this was noticed only after the experiment had been performed; this area was therefore excluded from the subsequent analyses (see section 6. 3. 2 Exclude FLT3-8_Area1 ("before" wrongly acquired) in the R script "R_analysis/scripts/SSFA_1_Import" on Zenodo https://doi. org/10. 5281/zenodo. 7219855). Note that this did not exclude the sample, as the second spot was included. In sum, 32 scans were processed (Table  1 ) but only 30 scans were included in the statistical analysis (see section 2. 2. 3). Unlike  Pedergnana, Calandra, Bob, et al. (2020) , we restricted the analysis to a smaller, manually chosen area of the surface (Table  1 ) to limit the number of non-measured points to be filled later (see section 2.