dataesr/scientific-paragraphs-categorization huggingface dataset:
All dental materials were supposed homogeneous and linearly elastic except the periodontal ligament, which was supposed hyper-elastic. The three root-end filling cements were considered: BD, BR, and WR, and the attributed material properties were referenced from the literature [15] (Table  1 ). There was a perfect bonding between each component and a vertical load of 150 n was applied on the top of the root following published protocols  [14, 16]. The nodes of the lateral faces of the cortical bone were constrained to prevent displacement. The FEA was conducted on the software Abaqus (Version: Abaqus 6. 7 2021, Dassault Systèmes, Vélizy-Villacoublay, France) to calculate the von Mises stresses of the root-end filling.
Introduction Oral cavity squamous cell carcinoma (OCSCC) is the most common malignancy in the oral cavity. Two types of mandibular resections have been described: the segmental mandibulectomy and the marginal mandibulectomy. Both may have a different impact over the quality of life, oncological prognosis, and functional or aesthetic result. Objectives The aim of this study was to systematically explore the literature to determine the survival outcomes and disease control rates in patients who underwent segmental or marginal mandibulectomy for OCSCC with histological evidence of cortical and medullary bone invasion. Data Synthesis This review involved a systematic search of the electronic databases MEDLINE/PUBMED, Google Scholar, Ovid Medline, Embase, and Scopus including articles from 1985 to 2019.
Statistical Analysis A meta-analysis of selected studies with an odds ratio (OR) comparing patients who underwent MM (experimental group) and patients who underwent SM (control group) was performed with the Cochrane Review Manager 5. 4 (Nordic Cochrane Centre, Cochrane Collaboration, 2020, Copenhagen, Denmark). A fixed-effects model was used in this study. The heterogeneity assumption was checked using the Q-test and the I2 test. The Cochrane Review Manager uses the Mantel-Haenszel method for calculating the weighted summary OR under the fixed-effects model, and the heterogeneity statistic is incorporated to calculate the summary OR under the randomeffects model. The pooled OR with 95% confidence interval (CI) is given for both fixed-effects model and random-effects model. Regarding the meta-analysis, dichotomous data and timeto-event data were considered.
The dichotomous data were measured by relative risk (RR) with 95% of confidence interval and by hazard ratio (HR) for time-to-event data. The statistical significance for the hypothesis test was set at p < 0. 05. The subgroup analysis was based on different types of mandibular invasion and different types of data. Besides, a chi-squared test with Yates correction for continuity was applied with a 2-tailed p-value for the comparison according to sex, histology, and type of procedure from independent samples. A p-value < 0. 05 was considered statistically significant. A number-needed-to-treat (NNT) analysis was adopted as a method of sensitivity analysis, when possible. A total of 201 manuscripts were revised, 107 were excluded due to duplication and 97 studies met our inclusion criteria. From those, 51 were excluded due to the absence of randomization, 37 due to inclusion of oropharyngeal tumors, 3 due to the inclusion of parapharyngeal tumors, and 3 because they reported less than 5 years of follow-up.
(►Fig. 1) Five-year LC, DFS, and OS data were included in ►Supplementary Table  S1  and tumor, node, metastasis (TNM) stage and radiological data were included in ►Supplementary Table  S2. Fifteen articles were included for qualitative analysis, 15-29 and 11 articles were considered for meta-analysis calculations. 2, 6, [16] [17] [18] [19] [20] [21] 23, 28, 29  All of them correspond to retrospective cohort studies comparing the effectiveness of horizontal marginal and segmental mandibulectomy. Twothousand and twenty-three patients were included; 857 patients in the MM group, and 1,166 patients in the SM group. Variables like age, sex, histology, type of surgery, and maximum time to follow-up were compared between both groups (►Table 1). The demographic data between the MM and SM groups were similar.
Study Design and Participants PROGRESS is a cross-sectional study assessing oral HPV infection in the US. A detailed description of the study design and methodology, including data collection, HPV testing procedures, and sample size calculations, has been published previously. 11  Eligible participants were men and women aged 18 to 60 years accessing routine dental care who could provide written informed consent. All participants diagnosed with or who were suspected to have HNC were excluded. The PROGRESS study protocol was approved by the Western Institutional Review Board in 2020 and by the corresponding institutional review board/ethics committee at dental sites when required. The study followed the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) reporting guideline.
Site Recruitment and Site Initiation Study sites (n = 43) were dental clinics across 21 US states and included urban (population ≥50 000; n = 24), urban cluster (population between 2500 and 49 000; n = 13), and rural sites (population <2500; n = 6). The 2020 IQVIA OneKey database, a national database of health care providers updated on a continuous basis through government and nongovernment industry sources, was used to identify and recruit dental sites. Participating dental clinics used targeted sampling to recruit equal distributions of men and women and across age groups. 11.
Data Collection and Study Procedures Data were collected between March 2021 and April 2022. Participants underwent HPV sampling via oral rinse and gargle and completed self-administered questionnaires to collect sociodemographics, including self-reported sex; age; race and ethnicity; medical history, including immunosuppression (if a participant reported having a blood disease/cancer, autoimmune disease, HIV, or if they are currently receive corticosteroids, chemotherapy, biologic therapy, or other immunosuppressants) and previous diagnosis of a sexually transmitted infection (STI, including HIV, syphilis, gonorrhea, genital herpes, chlamydia, or anogenital warts); and other risk factors shown or hypothesized to be associated with HPV, like tobacco use and sexual behaviors. 9  Dentists counted the number of missing teeth and identified presence of gingivitis and/or periodontitis.
Key Points Question What is the burden of oral human papillomavirus (HPV) in a general US population? Findings In this cross-sectional study of 3196 participants, oral HPV prevalence was 6. 6% for any detected genotype, and 2. 0%, 0. 7%, and 1. 5% for high-risk (oncogenic), HPV-16, and 9-valent-HPV vaccine types, respectively. Among HPV-positive participants, HPV-16 was the most prevalent genotype (12. 4% among men and 8. 6% among women); HPV prevalence was higher in men than women and highest among men aged 51 to 60 years (16. 8%, 6. 8%, and 2. 1% for any HPV, high-risk HPV, and HPV-16, respectively). Meaning Oral HPV burden was highest among older men who may be more at risk of developing oropharyngeal cancer. process and participant-and dentist-collected data are described elsewhere. 11.
Statistical Analysis Statistical analyses were performed with SAS, version 2. 0 (SAS Institute). A sample was considered positive for any HPV genotype if it tested polymerase chain reaction (PCR) positive. This includes specimens testing positive for 1 or more of the 25 HPV types included in the assay and those that tested positive by PCR but without positive genotyping for any of 25 types, which we labeled untypable HPV and grouped with LR HPV types. 14  A sample was considered HR HPV if any of 12 types were detected, regardless of the presence of LR HPV: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, and 59. A sample was considered LR if 1 or more LR-only types were detected: 6, 11, 34, 40, 42, 43, 44, 53, 54, 66, 68, 70, or 74, or were PCR positive but did not hybridize to 1 of 25 probes (ie, untypable).
Our study uniquely identified associations between oral HPV infection and oral health indicators and found that LR infection was more prevalent among those with periodontitis, but the CI width prevents making definitive conclusions regarding the strength of the association. A key strength of our analysis was the use of oral health data obtained by dental examination. While the link between oral health and oral HPV has not been fully elucidated, possible explanations include that poor oral hygiene induces viral replication of HPV in the oral cavity  22  and that inflammatory periodontal tissue may increase the probability for exposed basal cells to become infected with HPV. 23  Associations between oral health and oral HPV infection are mixed in the literature, necessitating further research.
Limitations Findings must be interpreted considering limitations. While prevalence data were stratified by sex in bivariate analyses, it was not possible to create separate multivariable models by sex due to relatively small numbers of HR and LR infection detected (65 HR and 145 LR). Dentists collected selfreported HPV vaccination data, which were not verified by medical records. Given limitations of self-reported vaccination data, data must be interpreted with caution. The study's dental settings might introduce bias toward participants with higher socioeconomic levels because of their potential for better access to dental care. 28  Despite limitations, this study has several strengths. Our study collected data from a large sample of the US general population within 21 states spanning urban, urban cluster, and rural areas, increasing generalizability of the study.
An osteotome used clinically (32-6002-10, Zepf, Tuttlingen, Germany) having a 10 mm-long cutting edge was used to cut each sample along its entire length. To do so, the osteotome was impacted with a 260 g surgical mallet (32-6906-26, Zepf, Tuttlingen, Germany) equipped with a dynamic piezo-electric force sensor (208C04, PCB Piezotronics, Depew, NY, USA). This sensor, which has a measurement range up to 4. 45 kN in compression, was screwed in the center of the impacting face of the hammer. The time variation of the force was recorded by a data acquisition module (NI 9234, National Instruments, Austin, TX, USA) with a sampling frequency of 51. 2 kHz and a resolution of 24 bits and transferred to a computer using a LabVIEW interface (National Instruments, Austin, TX, USA) for a duration of 2 ms.
45 kN in compression, was screwed in the center of the impacting face of the hammer. The time variation of the force was recorded by a data acquisition module (NI 9234, National Instruments, Austin, TX, USA) with a sampling frequency of 51. 2 kHz and a resolution of 24 bits and transferred to a computer using a LabVIEW interface (National Instruments, Austin, TX, USA) for a duration of 2 ms. For each impact, the time dependence of the force applied to the osteotome was measured, leading to a radio frequency signal denoted s(t). An example of typical signals obtained for each sample is shown in Figures  2  and 3      During all experiments, the position of the osteotome tip was assessed using a video camera (L-920M3, Spedal, Taiwan) positioned perpendicularly to the plane of the sample. This camera has a resolution of 1920 × 1080 pixels: the image has 1920 pixels in the xdirection and 1080 pixels in y-direction.
This project has received funding from the project  OrthAncil  ( ANR-21-CE19-0035-03 ) and from the project  OrthoMat  ( ANR-21-CE17-0004 ). This project has received funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (Grant Agreement No  101062467 , project  ERC  Proof of concept 2022 Impactor). Institutional Review Board Statement: All the animal bones are supplied by a local butcher. This statement is therefore not applicable.
It is thus tempting to speculate that BlpT activity may be particularly important in the anaerobic environment that SGG encounters in the colon. The structural models of gallocin A peptides differ from those of other twopeptide bacteriocins. Structural modeling of GllA1 and GllA2 pre-and mature forms was performed using ColabFold  (10)  and showed that the putative N-terminal leader sequences adopt disordered and extended conformations (Fig. 5A  and B ). The structural models of mature GllA1 and GllA2 are composed of two antiparallel alpha-helices, FIG  2  Gallocin A is active against most streptococci, lactococci, and enterococci. Phylogenetic tree based on the 16S RNA sequence (from the Silva online database) of different bacterial species that are resistant (green) or susceptible (red) to gallocin A, as determined by agar diffusion assay (Fig.
6  (29) , leading to a main chromosome of 2,210,410 bp and a plasmid of 12,729 bp (PRJNA940176). The annotation was subsequently made with Prokka (30) before variant calling was performed using the Sequana (31) variant-calling pipeline. Of note, variants were called with a minimum frequency of 10% and a minimum strand balance of 0. 2. Many mutations, probably due to the different method used to sequence the reference sequence, were present in the control SGM WT strain and the RSM mutants. Therefore, only RSM-specific mutations occurring at a frequency of. 0. 5 compared to the control SGM WT were considered for this analysis and are shown in Table  S1.
ACKNOWLEDGMENTS We especially thank  Tarek Msadek  for careful and critical reading of the manuscript. This study has been funded by the  Institut National Contre le Cancer (INCA)   PLBIO 16-025 , attributed to S. D. , and by the  French Government 's  Investissement d'Avenir program ,  Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases  (grant no. ANR-10-LABX-62-IBEID )". This study was also funded by the  National Science Foundation  ( NSF , no. CHE-1808370  to Y. T. -G. ).
Multivariate analysis of variance (ANOVA) and principal component analysis (PCA) Statistical analyses were carried out using R. Multivariate analysis of variance (ANOVA) and multiple-pairwise comparison t-tests (with Benjamini and Hochberg p-value adjustment) were conducted using the aov and pairwise. t. test functions as part of the stats package  (Team, 2013). Principal component analysis (PCA) was performed using the prcomp function as part of the stats package, by singular value decomposition of the centered and scaled data matrix  (Team, 2013). Results of this analysis were visualized using the factoextra package (version 1. 0. 5) and ggplot2  (Wickham, 2016). Exploratory analysis graphs and additional plots were constructed using the various functions available in the ggplot2 and ggraph packages.
Objectives: The aim of this systematic review is to help the reader in their selection of analytical techniques for a complete and accurate assessment of artificial caries remineralization. Data, sources and study selection: Four databases were scanned independently following PRISMA guidelines and, after setting of inclusion and exclusion criteria, 255 potentially-relevant articles were scrutinized for selection. Based on our hypothesis that at least three characteristics of the newly-formed mineral, i. e. spatial extension, chemical composition and morphology, are requested for assessment, focus was made on 24 articles where at least three methods were used. Conclusion: Twenty different analytical methods were used and 11 studies used at least one technique relevant to each of the three characteristics.
Information sources and search strategy Detailed individual search strategies were developed, in English, for each bibliographic electronic database: PubMed (including Medline), Embase, Scopus and Web of science. All database searches were conducted from the starting coverage date through June 31th 2022. More information on the search strategies is provided in Appendix 1 (Supplementary Material). All references were managed and the duplicated hits were removed by a reference manager software (EndNote X7® Basic-Thomson Reuters, New York, USA).
Selection process and data collection process This part followed a two-phase process. In phase one, two authors (T. C. and J. B. ) independently evaluated the titles and abstracts of all identified electronic database citations. In phase-two, the same authors evaluated full-text data. They independently screened papers on phase one and two, applied the eligibility criteria, collected key information from the selected studies, and crosschecked the information. The references of these papers were also checked to include any interesting papers that were missed during the search. The final selection was based solely on full-text assessment of the studies. When disagreement appeared, a third author (A. L. P. ) was involved to make a final decision about the inclusion or exclusion of studies. The section phasis were managed by Rayyan on line software (www.
Study risk of bias assessment The methodology of the selected studies was assessed using the Critical appraisal tool for in vitro studies, adapted from CRIS Guidelines. Two reviewers (J. B and T. C) had independently scored each item as "yes", "no" or "unclear", and classified independently the quality of each included study as "high", "low" or "moderate" risk of bias. The same two reviewers worked out on any differences regarding data analysis. A third author (A. L. P) was involved to steer decision in case of uncertainty. Figures of the quality assessment of all included studies were generated with Review Manager 5. 3 (RevMan 5. 3, The Nordic Cochrane centre, Copenhagen, Denmark).
Risk of bias across studies and reporting bias assessment The risk of bias across studies was assessed as an overall risk the study results may present, on which could influence meta-analysis data. Methodological and statistical heterogeneity were evaluated by comparing the variability in study design and the risk of bias. When the required data were not complete, the reviewer (J. B) attempted to contact the study authors to retrieve any unpublished information. Three attempts were made in a 30 days' period, by email for the first, second and last author.
Study selection Our initial database searches identified 588 studies. After eliminating duplicated hits, 459 studies remained of which 234 were excluded after title and abstract review, resulting in 225 articles. No additional study was selected following hand-searching of the reference lists of the included studies. During phase-2, 201 studies were excluded, leaving 24 studies for qualitative and quantitative synthesis. A flowchart of the process of identification, inclusion and exclusion of studies, and reasons for exclusion is shown in Fig. 1.
Surface morphology Besides remineralization extent and chemical nature, one half of the considered studies investigated the surface morphology of the tissue after treatment. All of them used SEM imaging for this purpose. Additional quantitative data about surface topology were obtained using CSLM or AFM (Atomic Force Microscopy). In the first case, CSLM imaging is performed without staining so that only the autofluorescence of the sample is monitored  [23]. As this fluorescence is very weak, only its surface is imaged. After 3D reconstruction, it is possible to determine surface roughness average, i. e. the average height difference between peaks or pits and the mean surface. AFM is a very powerful tool for surface analysis as it allows very high-resolution imaging. It consists in scanning a rigid probe with diameters 100 nm or below attached to a flexible cantilever very close to the surface of interest.
SOLUTION A hybrid assessment solution was tested combining visual feedback and a rubric system on 69 ivorine first left molars (ANA 4; Frasaco, GmbH) prepared by the students. A support was edited and 3D printed that was created to hold 24 teeth with flat areas allowing retention by a tabletop scanner fixture (Figure  1 ). For collaborative purposes, the 3D support files (Standard Tesselation Language) are available. Instead of scanning the prepared teeth individually, we scanned 24 teeth for each acquisition to save time (InEos ×5; Dentsply Sirona, Inc) (Figure  2 ). The surfaces were segmented, registered, and compared with a non-prepared tooth using free 3D computer graphics software (MeshLab, Deformetrica). The procedure was partially automated by a code edited in Python (Python 3. 7. 9.
ACKNOWLEDGEMENTS Supported by the  National Natural Science Foundation of China  (Nos. 82001042 ,  82170964 , and  81873716 ), the  Taishan Scholars Program of Shandong Province  (Nos. ts20190975 and tsqn201909180), the  Major Innovation Projects in Shandong Province  (Nos. 2018YFJH0503 ,  2021SFGC0502 , and  2021ZDSYS18 ),  Qilu Young Scholar Foundation of Shandong University, Rongxiang Regenerative Medicine Foundation of Shandong University  (Nos. 2019SDRX-15  and  2019SDRX-14 ), the  Fundamental Research Funds of Shandong University  (No. 2018JC005 ),  Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of Shandong, and Open Foundation of Shandong Provincial Key Laboratory of Oral Tissue Regeneration  (Nos. SDKQ201901  and  SDKQ201904 ), the  Interdisciplinary Thematic Institute SysChem via the IdEx Unistra  ( ANR-10-IDEX-0002 ) within the program " Investissement d'Avenir ".
Data Extraction The results of the selected studies were extracted using Microsoft Office Excel 2019 (Microsoft Corporation, Redmond, WA, USA). These data comprised the year of publication, the type of adhesive system, strategy evaluated for bonding to dentin, outcomes evaluated, the type of bond strength test evaluated, and storage conditions. Additionally, the mean, SD, and number of specimens from the bond strength test were collected, and these data were then subjected to meta-analysis.
Statistical Analysis Meta-analysis was performed using Review Manager Software version 5. 3. 5 (The Nordic Cochrane Centre, The Cochrane Collaboration, Copenhagen, Denmark). The analysis was carried out using the random-effects model, and pooled-effect estimates were obtained by comparing the standardized mean difference between bond strength values obtained from the control and experimental groups. The control group was considered when the adhesive system was applied according to the manufacturers' instructions, while the experimental group was considered when the adhesive system was applied using a different approach. In studies where several experimental groups were compared with the same control group, data from the experimental groups (mean, SD, and sample size) were combined for the meta-analysis  [27].
Results The electronic research through three different databases generated a total of 8318 references, which were reduced to 6441 after duplicate removal. After the examination of titles and abstracts, 6335 studies were excluded because of their study design incompatibility with this review. A total of 106 potentially relevant studies accessed the full-text evaluation phase. From these, 19 were excluded because there was no access to the full-text manuscript  [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] , resulting in a final number of 87 publications included for further qualitative assessment (Figure  1 ). After a full-text review, 9 articles were excluded because the bond strength was not tested  [46] [47] [48] [49] [50] [51] [52] [53] [54] , leaving 78 publications for qualitative analysis.
Of these, 10 studies were excluded from the quantitative analysis: 1 study did not present the data in the form of mean and SD  [55] , 3 studies did not have other studies for making comparisons  [43, 56, 57] , 3 studies did not contain a clearly defined control group  [58] [59] [60] , and in 3 articles, complete data could not be extracted  [32, 61, 62]. Thus, 68 studies were included in the meta-analysis.