dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments: We thank  Xavier Vanden Eynde  ( CRM group ) for his advice after reading our manuscript. This research project has been initiated under the iPROMEDAI COST action  TD1305. A. J. and M. S. would like to acknowledge funding from the  European Union 's  Horizon 2020 research and innovation program  under grant agreement No. 952033. V. M. -S. thanks the  University Union-Nikola Tesla, Belgrade, Serbia , for the support.
Materials and methods This clinical case was conducted in compliance with the CARE guidelines. Inclusion criteria were people over 6 years old with PFE. Exclusion criteria were: children under 6 years old, endocrine pathology that may interfere with dental eruption, rickets, chemotherapy/radiotherapy, bisphosphonate treatment. The patients were examined at the Centre de Référence des Maladies Rares orales et dentaires (O-Rares), Hôpitaux Universitaires de Strasbourg, France. The oral phenotype was documented using the D [4]/ phenodent registry protocol, a Diagnosing Dental Defects Database [see www. phenodent. org, for assessment form], which is approved by CNIL (French National commission for informatics and liberty, number 908416). Parents gave written informed consent for the transfer of clinical data in D [4]/phenodent database, genetic testing (Geno-DENT  19, 20  ), DNA biobanking, and the current publication.
This clinical study is registered at https://clinicaltrials. gov: NCT02397824, and with the MESR (French Ministry of Higher Education and Research) Bioethics Commission as a biological collection "Orodental Manifestations of Rare Diseases" DC-2012-1677 within DC-2012-1002 and was acknowledged by the CPP (person protection committee) Est IV December 11th , 2012. Clinical and radiological examination is planned as part of the study "Primary Failure of Eruption (PFE): Highlighting of Clinical, Radiological and Genetic Diagnostic Criteria: Consequences on the Therapeutic Management", registered at https://clinicaltrials. gov: NCT03580785. The proband and the affected and non-affected family members gave written informed consents in accordance with the Declaration of Helsinki, for the D [4]/phenodent registry, clinical and radiological examinations and for genetic analyses performed on the salivary samples included in the biological collection.
Genetic testing Each patient received a detailed explanation of the nature of the study and informed consent was obtained. Saliva of participants was sampled using Oragene-DNA® (Genotek) and DNA was extracted. GenoDENT 4. 0, a designed NGS panel targeted towards orodental rare diseases  19  was used to explore the genotype of I. 1. This genetic diagnostic solution highlighted a heterozygous substitution in PTH1R (NM_000316. 3): c. 899T > C. This substitution variant is predicted to change a well-conserved amino acid though evolution. The in silico predictive algorithms SIFT (v6. 2. 0),  21  MutationTaster (v2013)  22  and PolyPhen-2 (v2. 2. 2r398)  23  predict a deleterious variant. This variant localizes into one of the transmembrane protein domains. It is not present in the gnomAD database  24, 25  and to the best of our knowledge never reported in the literature.
Additional funding were provided by the University Hospital of Strasbourg (HUS, API, 2009-2012, 'Development of the oral cavity: from gene to clinical phenotype in Human', the EU-funded projects (ERDF): A27 'Oro-dental manifestations of rare diseases, supported by the RMT-TMO Offensive Sciences initiative, INTERREG IV Upper Rhine program (www. genosmile. eu), by the INTERREG V N • 1. 7 "RARENET" project and by Fonds d'Intervention Régionale (FIR) de l'Agence Régionale de Santé Grand Est Innovation en santé (2019-2022) e-Gen-oDENT project; NCT02397824.
Introduction: Burning Mouth Syndrome (BMS) is defined by a burning sensation or intraoral dysesthesia without obvious causal lesion. Despite the development of research, diagnostic aids for this syndrome are nonexistent and treatments are partially ineffective. Some studies have shown changes in salivary composition, viscosity or flow in patients with BMS. The evaluation of the salivary biochemical characteristics of patients with BMS could then help to better understand the pathogenesis of this disease. The objective of this meta-analysis is to perform a qualitative and quantitative synthesis of the literature concerning the salivary biomarkers present in patients with BMS in comparison to healthy subjects. Materials and methods: The PubMed, Web of Science and Cochrane databases were searched to identify articles corresponding to the defined inclusion criteria.
Review Manager 5. 4. 1 software was used to perform the quantitative analysis. Results: The quantitative analysis included 15 articles and found a significant increase in salivary concentrations of cortisol and immunoglobulin A (IgA) with a standardized mean difference SMD = 0. 53 and a 95% confidence interval CI [0. 33 to 0. 74] and SMD = 0. 32 to 95% CI [0. 10 to 0. 55] respectively. For calcium and copper, the analysis found no significant difference in patients with BMS with SMD = 0. 06 at 95% CI [-0. 19 to 0. 32] and SMD = -0. 19 at 95% CI [-0. 44 to 0. 06]. Finally, for magnesium, the analysis found a probable decrease with SMD = -0. 29 at 95% CI [-0. 52 to -0. 06]. Four other biomarkers (potassium, alpha amylase, zinc and total protein) showed too high levels of heterogeneity (I² > 44%) to be able to interpret the results with confidence.
Search strategy We conducted a systematic review and a meta-analysis according to the Preferred Reporting items for Systematic Reviews and Meta-Analyses Protocols (PRISMA) statement. The proposed systematic review was registered in PROSPERO under registration number CRD42023403447. A bibliographic research was conducted in the following databases: PubMed, Web of Science and The Cochrane Library. The following keywords were used for the search strategy: biomarker, saliva, burning mouth syndrome. All reference lists of previously selected studies were manually reviewed to identify articles on salivary biomarker concentration in patients with burning mouth syndrome compared to a cohort of healthy subjects. Two examiners carried out the bibliographic search in parallel and compared the selected articles.
Quantitative analysis Quantitative data on salivary biomarker assays from BMS and control patients were extracted to calculate, for each study, the standardized mean difference (SMD) and the 95% confidence interval (95% CI). All data were reported in summary tables. Statistical measurements were performed with Review Manager 5. 4. 1 software. Standardized mean difference (SMD) is used as a statistical tool in meta-analysis when all selected studies assess the same outcome but measure it in different ways. In these circumstances, it is necessary to standardize the results of the studies on a uniform scale before they can be grouped. The standardized mean difference expresses the size of the intervention effect in each study compared to the variability observed in that study.
Materials and Methods: A literature search was performed without any time limit on different databases up to August 2022. Interventional and observational studies with at least 6 months of follow-up were considered. The occurrence of peri-implant mucositis and/or peri-implantitis was the primary outcome. Pooled data analyses were performed using random effect models according to the type of risk factor and outcome. Results: Overall, 48 studies were selected. None assessed the efficacy of primordial preventive interventions for PIDs. Indirect evidence on the primary prevention of PID indicated that diabetic patients with dental implants and good glycaemic control have a significantly lower risk of peri-implantitis (odds ratio [OR] = 0. 16; 95% confidence interval [CI]: 0. 03-0. 96; I 2 : 0%), and lower marginal bone level (MBL) changes (OR = -0.
| Literature sources and search The literature search and selection were carried out by two independent reviewers (NBS, AC). The following electronic databases were searched during April 2022 and updated during August 2022: MED-LINE (through PubMed), EMBASE, Cochrane Central Library, Base-Search, Open Access Thesis and Dissertation (openthesis. org), and ClinicalTrials. gov. A specific research equation was formulated in each database, using appropriate keywords and MeSH terms for exposure and outcomes, as detailed in Table  S1. In addition, reference lists from eligible studies and previously published review articles were crosschecked to identify additional pertinent studies. Only articles in English were considered but no publication date limit was applied.
| Study selection and data extraction Records from the literature searches were merged into a single list imported into an EndNote library (EndNote software, Clarivate, Cleverbridge GmbH, Gereonstr. , Cologne, Germany), in which duplicates were automatically removed. Two independent reviewers (NBS, AC) undertook the study screening process by using Rayyan software  (Intelligent Systematic Review, 2022)  to support the reviewers at all different stages of the systematic review. Records were first screened at the title and abstract level. Each record had to be screened and voted upon (to be included or excluded) by the two reviewers, and blinded to the other reviewer's assessment. Any disagreement was resolved by a third author (MCC or PhB) acting as a moderator. Subsequently, reviewers performed a full-text evaluation of the pre-selected articles.
Similarly, this evaluation was performed independently, and disagreements were resolved by the moderator to reach the final selection of the articles. Agreement between the reviewers was assessed by calculating Cohen's Kappa. A dedicated Microsoft EXCEL spreadsheet was created to facilitate the data extraction process, which was conducted by three reviewers (MCC, NBS, AC). Study characteristics and principal findings were collated, analysed, and then summarized into tables to be processed for qualitative and quantitative analyses.
| Data synthesis and analysis Whenever information essential for inclusion (e. g. , duration of followup, outcome measures) or potentially relevant data were missing in the published documents, the corresponding authors were contacted by email. When no answer was forthcoming, the record was excluded. The feasibility and appropriateness of meta-analyses was checked once data extraction was completed, and the selected studies were re-grouped by the type of exposure and outcome(s). Outcome measures were extracted as frequency or rate (in percentage), mean (standard deviation, SD), or median (interquartile range, IQR). For the pooled data analysis, the odds ratio (OR) and 95% confidence intervals (95% CIs) between the compared groups were estimated using the Mantel-Haenszel method for binary outcomes.
For continuous data, the mean difference (MD) or the standardized mean difference (SMD) with 95% CI between the groups were estimated using inverse variance weighting. Heterogeneity was assessed by the I 2 statistic, with values <40% considered as negligible, 40%-75% as moderate, and >75% as substantial heterogeneity (https://training. cochrane. org/handbook/current). Random effect models were used as a more conservative approach, as a significant inter-study heterogeneity was expected. The pooled effect was considered significant if p <. 05. The meta-analysis was performed by using RevMan software (Version 5. 3; Cochrane Collaboration) and OpenMetaAnalyst.
| Study selection and characteristics By merging the searches of the two independent reviewers on the different databases, 7565 records were initially identified. Figure  2  shows the flow-chart of the study selection. The list of excluded articles after full-text evaluation is provided in Table  S2. Finally, 48 articles were selected and distributed according to the type of risk factor. The kappa value was 0. 612 (99. 2% of agreement) for the selection upon title and abstract, and 0. 466 (89. 9% of agreement) for the selection after full-text evaluation.
[13]  2016 Undesired tooth movement Egli et al. [14]  2017 Unexpected posttreatment changes Jacobs et al. [15]  2017 Single tooth torque problems Beitlitum et al. [16]  2020 Unwanted effects such as inadvertent tooth movement and torque changes Kim et al. [17]  2020 Unexpected tooth movements Klaus et al. [18]  2020 Unwanted tooth movements Knaup et al. [19]  2021 Side effects of twistflex retainers Singh et al. [20]  2021 Extreme complication of a fixed mandibular lingual retainer The first systematic review on wire syndrome (WS) was published by Charavet et al. [21]  in 2022, defining its prevalence and associated characteristics. This review involved an electronic search strategy on four databases supplemented by a manual search. All prospective and retrospective clinical studies, including case reports and case series written in English or French, with a clear description, detection, or management of WS, were included.
Materials and Methods Registration: This study has been approved/registered by the Data Protection Officer of the Digital Innovation and Information Systems Department on the Nice University Hospital's data processing register (reference 2023-EI 548). Patient selection: Three clinical cases of wire syndrome of increasing severity in patients who were admitted to the orthodontic department of the University Hospital of Nice were retrospectively included. They presented early wire syndrome, intermediate wire syndrome, and severe wire syndrome. Data collection: A full set of photographs were taken from the following perspectives: frontal view, different lateral views, and different occlusal views. Data analysis: The description and analysis of the pictures mainly focused on the detection of a wire syndrome; other elements were not considered.
Data Collection The peri-implant marginal radiographic bone loss (MBL) was determined at TB (baseline) and at latest follow-up examination TF (final) by taking linear measurements (DB-SWIN, DÜRR DENTAL ® ) from the most mesial and distal point of each implant platform to the crestal bone on each intraoral periapical radiograph positioned on a Rinn angulator using a long-cone parallel technique. Characterization of the peri-implantitis defect morphology was classified on radiographs as follows: Class I: infra-osseous defect, Class II: supra-crestal /horizontal defect, and Class III: combined defect  [25]. Our collected radiographic data were analysed as a percentage rate at implant and patient levels. Our study was conducted in accordance with the Helsinki declaration of studies on humans. Before participation, each patient was given a detailed description of the procedure and was required to sign an informed consent form.
Demographic Data Fifty-seven patients (mean age = 66. 2, SD = 10. 5) and ninety-one implants were assessed with a mean ratio of 1. 6 implant/patient. Mean follow up was 24 months (range = 12 to 42 months). A total of 14% of peri-implantitis defects were class I treated by REC, 55% of periimplantitis defects were class II treated by ARP, and 31% were class III treated by COM (Table  1 ). Two failures occurred in class II and one in class III but none in class I. The three implants were dropped out.
Materials and methods Analyzed articles were selected from Pubmed/Medline database following Problem, Intervention, Comparison, Outcome, Study (PICOS) criteria  [18] , where: P-regenerative endodontics, I-vital pulp capping for vital teeth, or regenerative endodontic procedure for necrotic teeth, Ccomparison between study design using different cell lines, growth factors or scaffolds, O-dental origin cell behavior, pulp-like tissue formation, and S-in vitro, ex vivo, in vivo studies. Exclusion criteria: randomized clinical trials, nonrandomized clinical trials, prospective cohort studies, clinical cases, and articles whose methodology was inadequately explained.
Methods Literature review was conducted following the PRISMA-ScR protocol. PubMed, Web of Science and Cochrane library databases were searched for peer-reviewed articles by two blinded reviewers. Studies based on the evaluation of mandibular bone density and/or bone volume with imaging examination in adult patients were examined. The selected articles were summarized in PICOS tables and assessed for methodological quality. Results Nine articles were included, according to the inclusion criteria. They showed that bruxer patients had more bony exostoses of the mandibular angle, smaller condyles, and morphological changes for cancellous and cortical mandibular bone compared to non-bruxer patients.
Data collection The search of scientific articles was conducted in three online databases, PubMed, Web of Science Cochrane library, up to February 05, 2023 by two blinded operators. Studies were excluded on the basis of titles and abstracts, and upon reading the full article. All phases were independently assessed by two evaluators (EC and BS), and in case of doubt or disagreement, a consensus between the two evaluators was sought. The search procedure used the keywords "bruxism" and "bruxer" together with keywords related to medical imaging examinations and others related to changes in the characteristics of the mandibular bone. Search equation for PubMed: ("bruxism"[TIAB] OR "bruxer*"[TIAB]). AND ("radio*" OR "panoramic*" OR "scanner*" OR "CBCT" OR "cone-beam" OR "cone beam" OR "Radiography"[Mesh] OR "Radiography, Dental"[Mesh] OR "Radiography, Panoramic"[Mesh] OR "Cone-Beam Computed Tomography"[Mesh] OR "Tomography, X-Ray Computed"[Mesh]).
Data extraction and analysis [21-29] The study search strategy is shown in a flow chart (Fig. 1 ). Nine articles that met the inclusion criteria were selected. The characteristics for each data category were extracted into Table  2  (PICOS analysis, bruxism diagnosis and principal results). Methodological quality assessment of these nine studies is proposed in Table  3. The papers included in the final step of the review covered a wide geographical area, including the Middle East (Turkey, n = 5 studies), South America (Brazil, n = 1), Asia (India, n = 1), and Europe (France, n = 1, Switzerland, n = 1). All studies were approved by the ethics committee of their respective institutions or hospitals. The strategies adopted to study bone characteristics were different, with different types of radiological examinations, so a direct comparison of bone density and bone volume could not be performed.
Five of them  [21, 23, 25, 26, 29]  used the same imaging analysis software: ImageJ ®. Three studies  [22, 24, 27]  did not use analysis software. However, the parameters studied differed greatly between studies: 1 out of 9 studies evaluated the surface area of certain areas of the mandible  [21, 22] , 3 studies evaluated presence of exostoses in the mandibular angle  [22, 27, 29] , 3 studies evaluated measurements associated to bone morphological characteristics (e. g. bone thickness or width of mandible, condylar volume)  [23, 24, 28] , 3 studies evaluated the different grey values in the selected regions of interest, using various analytical methods (fractal dimensions, grey value averages, grey value ratios)  [25, 26, 29]. The 9 selected studies found a significant difference between bruxers and non-bruxers for at least one parameter studied.
Limitations A scoping review was chosen by the authors to identify the types of evidence available in the field of research on the impact of bruxism on the mandibular bone and to analyse the knowledge gaps. The main limitation of this review lies in the search strategy. Indeed, it may have prevented the identification of all studies of interest because of limitations in database coverage and to the particularities of article indexing. Moreover, the articles from the grey literature were not taken into account: perhaps other studies could have been found by this means. The possibility of comparing the results of these different studies is therefore limited because of their great methodological disparity and the small number of articles available. For this reason, it was not possible to carry out a meta-analysis on the basis of this review.
| Data collection The following data were collected: ̶ Untreated dental caries. ̶ The Silness and Loë's (1967) plaque index (0: no plaque, 1: plaque not visible to the naked eye but removable with the probe; 2: plaque visible to the naked eye; 3: abundant plaque visible to the naked eye in the sulcus and on the marginal gingiva)  (Abreu et al. , 2008). Tongue thrust swallowing data was obtained at the time of the clinical examination. To examine the presence of tongue thrusting, the patients were asked to swallow their saliva three times during the same visit. There should be no facial contraction or lingual interposition, and the arches should remain in occlusion. When in doubt, another swallow was requested until the orthodontist was satisfied with their judgment. Tongue thrust was defined as a protrusion of the tongue between the upper and lower incisors or the cuspids during swallowing.
The attributed material properties were referenced from the literature  [40]. There was a perfect bonding between each component, and an oblique load of 300 N was applied on the vestibular cupid of the premolar to simulate masticatory forces. The nodes of the lateral faces of the mesial and distal cortical bone were constrained to prevent displacement following previous protocols  [41, 42]. Finite element analysis (FEA) was conducted on the software Abaqus (Dassault Systèmes, Vélizy-Villacoublay, France) to calculate the strain and von Mises stresses of the premolar. The Weibull analysis (WA) was combined with FEA to assess the risk of fracture of dentin. Failure was assumed to occur from the maximum principal stress on stress concentration areas. The survival probability P s for a load F can be expressed as: P s (σ) = exp - σ σ 0 m where σ represents the maximum principal stress, σ 0 represents the characteristic strength and m represents the Weibull modulus of the dentin.
Statistical Analysis The Shapiro-Wilk test was used to verify the normality of data within all groups. One-Way Analysis of Variance on ranks (ANOVA) including Pairwise Multiple Comparison Procedures (Tukey test) was applied to determine whether significant differences existed in the fracture resistance values of the different groups. Data analyses were performed with Sigma Plot (11. 2, Systat Software, Inc. , San Jose, CA, USA). A Chi-square test was used to determine whether there were significant differences between the failure mode in the different groups. A significance level of p < 0. 05 was adopted.
gingivalis  11, 13, 14  and others have since been found in other species of Bacteroidetes, including T. forsythia. 11, 15 The proteomic analysis of the T. forsythia outer membrane revealed at least 26 proteins with a potential C-terminal domain. 16 ecently, comparative genomics has revealed that the T. forsythia genome features two exclusive loci encoding six peptidases from ve disparate families according to the MER-OPS database  17  (Fig. 1 ). One locus encodes forsilysin, a thermolysin-type M4-family metallopeptidase (MP), and miropsin-1, a trypsin-like S1D-family serine peptidase. The other encodes two metzincin-clan MPs,  18  specically mirolysin from family M43 (pappalysins;  19, 20  ) and karilysin from family M10A (matrix metalloproteinases (MMPs);  21, 22  ), as well as miropsin-2 (a trypsin-like S1D-family serine peptidase) and mirolase (a subtilisin-type S8A-family serine peptidase).