dataesr/scientific-paragraphs-categorization huggingface dataset:
Purpose. e aim of this systematic review is to assess whether the anatomy of mental foramen is precisely evaluable with cone beam computed tomography (CBCT) before implantation in humans. Methods. A systematic review was carried out to evaluate the anatomy of mental foramen (size, position, symmetry, anterior loop, and accessory mental foramen or multiple mental foramina). According to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, an electronic search of three databases (Medline, Web of Science, and Cochrane Library) was undertaken until June 2020 and was supplemented by manual searching. Two reviewers will independently perform the processes of study inclusion, data extraction, and quality assessment. Systematic reviews, studies about children, and case reports were excluded.
Introduction: Interbody Fusion (IF), performed anteriorly (Ant-IF) or posteriorly (Post-IF), is frequently used in Adult Spinal Deformity (ASD) surgery to promote fusion and restore sagittal alignment. Posterior-only approaches were predominant for years. Recent technological advances and deficiencies of posterior-only approaches have boosted the use of anterior-posterior surgeries. There is no definitive evidence describing the benefits of Ant-IF vs Post-IF in ASD. The objective of this study was to critically assess surgical outcomes in comparable ASD patients treated with Ant-IF vs Post-IF. Methods: We identified all patients included in an international prospective ASD database, operated before December 2018, receiving IF and having 2YFU data. A Propensity Score (PS) analysis was performed to adjust Ant-IF and Post-IF attributes making the populations comparable.
The PS was built using 21 confounding variables defined by a multicentre team of experienced surgeons through 2 rounds of consensus. To guarantee a high overlap of treatment distributions, patients included in the PS area 0-0. 5 were selected. We compared 6w and 2y radiographic outcomes, 2y gain in HRQL gain and incidence of postoperative adverse events. Differences among groups were assessed with average treatment effects (ATEs) based on PS. Statistical significance was set for ATE>2 SE (Standard error). Results: 431 patients were treated with IF before December 2018. 369 (93. 3%) had 2yFU data and were included in the study (79. 4% females, mean age 62. 9, coronal cobb 33. 7, SVA 60. 8). 47 (12. 7%) received Ant-IF and 322 (87. 3%) Post-IF. Before PS-adjustment, Ant-IF population was younger (58.
Ceramic scaffold characterization The apparent density and porosity of the samples were determined by measuring sample mass under different conditions (dry, humid and under water) based on Archimedes' principle using deionized water as the liquid medium. The pore size was measured by image analysis of the Scanning Electron Microscopy (SEM) micrographs (JEOL JSM 5900 LV, Japan), the average values was determined using 5 micrographs and more than 50 pores in total were investigated for each structure specimen condition using MESURIM software (ACCES, France). Three types of HA ceramic scaffolds have been tested under compression to determine the ultimate compressive strength as a function of the macrostructure. The specimens were surface grinded in order to obtain a cylinder with consistent and even surfaces for testing.
0 Fluorometer together with the Qubit® RNA BR assay kit, following manufacturer's instructions. Total RNA (500 ng) was reverse transcribed to cDNA using the High-Capacity cDNA Reverse Transcription Kit, according to manufacturer's instructions. Quantification of gene expression, using Taqman assays (Applied Biosystems), for Alkaline phosphatase (ALP, HS01029144_m1), Osteonectin (SPARC, HS00234160_m1), Osteocalcin (BGLAP, HS01587814_g1), Osteopontin (SPP1, HS00959010_m1), Collagen 15 (COL15A1, HS00266332 m1) and glyceraldehyde 3-phosphate dehydrogenase, used as housekeeping gene, (GAPDH, Hs99999905_m1) was performed by use of the StepOne™ Real-Time PCR System (Applied Biosystems). N. 2 scaffolds for each sample were analysed, using three technical replicates for each experiment. Data were collected using the OneStep Software (v.
The collected data were entered on the Statistical Package for Social Sciences (SPSS) version 11. 5. The results indicate a statistically significant difference between the two groups, with a mean bone loss after treatment of 2. 3 mm for OHLLT with a surgical approach and 3. 8 mm for OHLLT with a non-surgical approach; according to the Kolmogorov-Smirnov test, the overall data followed a normal distribution (value of the Kolmogorov-Smirnov test statistic = 0. 0891; p = 0. 35794). Thus, a surgical approach in the case of peri-implantitis seems to be more effective, probably due to the possibility of a deeper sanitization of implant surfaces, hardly reachable with only non-surgical approach.
In the group of OHLLT with a non-surgical approach (OHLLT non-s. a. ; test group) 67 implants were performed in the upper arch, 72 in the mandible; for the group of OHLLT with surgical approach (OHLLT s. a. , control group) 54 implants were performed in the upper arch, 34 in the mandible (Table  3 ). We investigated bone loss post-operative for both groups. We stated five years as the minimum follow-up period for T 1. The collected data were entered on the Statistical Package for Social Sciences (SPSS) version 11. 5. The results were thus expressed as proportions using appropriate tables. The OHLLT non-surgical procedure consisted of (Figures  2 3 4 ): local anesthesia, ultrasonic instrumentation for supra and subgingival scaling combined with water-betadine irrigation (5:1 ratio), an air flow device with sodium bicarbonate powder (high-abrasive powder), mechanical instrumentation and the removal of necrotic tissues with Gracey curettes.
By western blot analysis, we could not detect the 9-kDa and 6-kDa SPARC fragments, whereas we identified all five SPARC main fragments (34-, 27-, 16-, 9-and 6-kDa) in the TAILS analysis of the secretomes of MDA-MB-231 / HMF co-cultures. Moreover, in breast cancers of transgenic mice, in TNBC PDXs, and in two clinical TNBC samples that express high or low cath-D levels, we found that cath-D expression was inversely correlated with SPARC levels, and detected the SPARC fragments of 34-kDa and 27-kDa only in samples that strongly expressed cath-D. Altogether, our data strongly suggest that cath-D cleaves SPARC in its extracellular Ca 2+ binding domain in vitro, in the secretome of TNBC cell lines, and in vivo in TNBC. Importantly, SPARC peptides corresponding to the 27-kDa (207 -218), , 9-kDa (236 -256), and 6-kDa (258 -268) fragments have been found in BC samples by using an on line proteomic database (https://cptac-data-portal.
A previous work showed that FL SPARC inhibits endothelial cell spreading and induces endothelial cell rounding by affecting the early stages of the counter-adhesive process through the loss of vinculin-containing focal adhesion plaques and the concomitant reorganization of actin-containing stress fibers  [47]. This might correspond to an intermediate adhesive state that was previously observed in endothelial cells incubated with FL SPARC  [64] , and in some cancer types, such as gliomas  [65] , and that promotes cell motility and invasion  [51]. The 9-kDa C-terminal fragment is located in the extracellular Ca 2+ binding domain of SPARC. The crystal structure of this SPARC domain (Protein Data Bank DOI: 10. 2210/pdb2V53/pdb) shows a canonical pair of EF-hand calcium binding sites that are essential for stabilizing Ca 2+ binding  [66].
After two washes with cold methanol, the pellet was resuspended in 100 mM HEPES at pH 8 at a final protein concentration of 2 mg/mL and digested with trypsin (trypsin/total protein (1:100); Trypsin V511A, Promega) overnight. N-terminal peptide enrichment was performed on the digested sample by removing the internal tryptic peptides with a 1:5 mass excess of dialyzed HPG-ALD polymer (Flintbox, University of British Columbia). Enriched N-terminal peptides were then desalted with a C18 spin column (Thermo Fisher Scientific) and the eluate fraction was freeze-dried, resuspended in 0. 1% formic acid and analyzed by LC-MS/MS on a Q-Exactive HF mass spectrometer (three replicates), as described for ATOMS experiments. Data files were analyzed with Proteome Discover 2. 4 using the SEQUEST HT algorithm against the human protein database (SwissProt release 2019-12, 43835 entries).
After iTRAQ labeling in DMSO, the two samples with/without pepstatin A were mixed and precipitated with eight volumes of freezer-cold acetone and one volume of freezer-cold methanol. The pellet was washed extensively with cold methanol, dried and resuspended in 5 µl of 50 mM NaOH. The pH was adjusted to 8 with 1. 8 M HEPES pH 8. 0, and the sample was digested at 37 °C with sequencinggrade trypsin (Promega; 1 : 50 protease:protein w/w ratio) or at 25 °C with Glu-C (Promega; 1:20 protease:protein w/w ratio) overnight. After desalting on a C18 column (Pierce), the sample was analyzed by LC-MS/MS on a Q-Exactive HF mass spectrometer operated with the Xcalibur software (version 4. 0) and equipped with a RSLC Ultimate 3000 nanoLC system (Thermo Scientific), as previously described  [75]. Data files were analyzed with Proteome Discover 1.
4 using the MASCOT (2. 2 version) algorithm against the human protein database (SwissProt release 2017-01, 40500 entries including reverse decoy database). Precursor mass tolerance was set at 10 ppm and fragment mass tolerance was set at 0. 02 Da, and up to 2 missed cleavages were allowed. Oxidation (M), deamidation (NQ), acetylation (Protein N-terminus), and iTRAQ 8Plex (N-term, K) were set as variable modifications, and carbamidomethylation (C) as fixed modification. Peptides and proteins were filtered using Percolator and a false discovery rate (FDR) of 1%. Peptides with N-terminal iTRAQ labeling were manually validated. Quantification was performed with the Reporter Ions Quantifier node. The peak integration was set to the Most Confidence Centroid with 20 ppm Integration Mass Tolerance on the reporter ions.
Expression and purification of recombinant proteins The cDNA encoding human SPARC (303 amino acids according to the GenBank reference NP_003109) and its truncated fragments were PCR-amplified using the pcDNA3. 1-SPARC plasmid as template  [77] , cloned into pGEM®-T Easy Vector (Promega), and then into the pSec-Tag2/hygroA vector (Thermo Fisher Scientific) by Not I digestion. Orientation and sequence were verified (Table  S2 ). Human embryonic kidney 293 (HEK-293 T) cells were stably transfected with the plasmids using Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions, and were selected with 400 µg/mL hygromycin B Gold TM (Invivogen). Recombinant His-tagged proteins were purified from cell lysates on a nickel-chelating column (Ni-nitrilotriacetic acid agarose; His-select high flow nickel affinity gel; Sigma-Aldrich), as described previously  [53].
The isolated recombinant proteins were analyzed by western blotting using anti-mouse Myc (clone 9B11) and anti-SPARC (clone AON-5031) antibodies and quantified using the Image J densitometric software (National Institutes of Health). To immunodeplete purified SPARC or its fragments, protein supernatants were incubated with an anti-Myc antibody (clone 9B11) overnight and protein G-Sepharose at 4 °C for 4 h, and supernatants were analyzed by immunoblotting to validate SPARC depletion. SPARC-immunodepleted supernatants were used as internal controls in the biological assays.
14 (18) VTLYERDEDNNLLTE (176-190) 16-kDa Glu-C 14. 3 (12) YERDEDNNLLTE (179-190] Glu-C 13. 1 (43) FGQLDQHPIDGYLSHTE (235-251) 9-kDa Glu-C 9. 2 (3) GQLDQHPIDGYLSHTE (236-251) Glu-C 10. 4 (12) DQHPIDGYLSHTE (239-251) Glu-C 4. 7 (6) High-confidence peptides with N-terminal iTRAQ labelling matching the FL SPARC protein (Uniprot accession number P09486) identified by TAILS in the conditioned medium of co-cultured MDA-MB-231/HMFs, or by iTRAQ-ATOMS after in vitro cleavage of recombinant SPARC by recombinant cath-D. Peptides defining cleavage sites with iTRAQ ratios >2 and <0. 5 for TAILS and ATOMS, respectively, are shown. CM, conditioned medium; pepst, pepstatin A; *, according to the silver staining. Ratio; <0. 5 or >2 for trypsin; Ratio; <0. 5 or >2 in bold for Glu-C; CM, conditioned medium; pepst.
The force value was then set to zero. The tap displacement was set at a rate of 0. 5 mm/min until rupture occurred. Force values were recorded during tests using the Bluehill ® universal software. The SBS was measured in megapascals (MPa), which was obtained by dividing the maximum load force (N) at the time of debonding by the bonded area (mm 2 ). After the SBS test, an optical numeric microscope (Keyence, Osaka, Japan) was used to investigate the failure mode in each specimen. VHX-5000 software was used to calculate the percentage of each area at 50× magnification to define the type of fracture. The failures were categorized into cohesive, adhesive, and mixed failure modes.
Statistical Analysis The Shapiro-Wilk test was used to verify the normality of the data within all groups. One-way analysis of variance (ANOVA) was assessed using SigmaPlot software (release 11. 2, Systat Software, Inc. , San Jose, CA, USA) to determine whether significant differences existed in the SBS values (24 h and 6 months), adhesive layer thickness, and antibacterial activity after 24 h. In all tests, a statistical significance level of α = 0. 05 was adopted.
Variables and Data Measurements The main outcome of this study was to analyze the oral microbiota's taxonomic composition in both obese and normal weighted patients' groups. Sampling was performed during the inclusion consultation which was conducted as following: 2. 4. 1. Medical and Socio-Demographic Characteristics Medical and dental history were assessed (associated pathologies, drugs, level of stress scored on a 10-points scale) as well as lifestyle and nutritional behavior of the patients, which were recorded from a questionnaire. This enabled us to focus on oral hygiene habits: frequency of visits to the dental surgeon and frequency and type of materials used (i. e. , manual or electric toothbrush, mouthwash, interdental brushes).
Statistical Analyses Data were blinded to maintain participant confidentiality. The statistical analyses were corrected with the false discovery rate (FDR), a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons  [32]. The bacterial diversity analyses (Chao1 alpha diversity and Bray-Curtis beta diversity) were performed using the Phyloseq v1. 14. 0 R package. The differential taxa analyses were conducted with the linear discriminant analysis effect size tool LEfSe  [33]  using default parameters (alpha parameter significance threshold set to 0. 05 and the logarithmic LDA score cutoff set to 2. 0). Unpaired Mann-Whitney tests were performed using GraphPad Prism (GraphPad Software, San Diego, CA, USA). A PERMANOVA test was performed with 999 permutations to assess the statistical significance of the difference between groups in beta diversity PCoA analyses (Figures  1D, 2E,  and 4E ).
The survey The World Health Survey (WHS) was a cross-sectional survey conducted in 70 countries between 2002 and 2004. Singlestage and multistage random cluster samplings were undertaken in 10 and 60 countries, respectively. More details on the WHS are accessible at https://appswhoint/healthinfo/ systems/surveydata/indexphp/catalog/whs/about. To summarize, the eligible sample included all people aged ≥18 years who had a valid home address at the time of the survey. One individual per household was selected using Kish tables, and the probability to be selected was equal between all members of the same household. To ensure comparability between countries, questionnaires were translated using standard procedures. Data were collected by trained staff during face-to-face and telephone interviews.
The overall response rate in the WHS was 98. 5%. Based on the United Nations Statistical Division's population distribution, sampling weights were created to adjust for non-response. Informed consent was obtained from each participant. Data were publicly available for 69 countries. Among these 69 countries, there was a lack of sampling information for 10 countries, and these countries were therefore excluded. Furthermore, given that this study focused on LMICs, 10 high-income countries were further excluded from the analysis. Eight LMICs with more than 25% of missing data on edentulism or diabetes were also excluded. Finally, there were no data on diabetes in Turkey, and this country was also omitted from the study. Thus, the final sample consisted of 40 LMICs including 175 814 individuals.
Fourth, this study only included people with a valid home address, and as poor oral health may be higher in homeless or institutionalized individuals,  48  the prevalence of edentulism may have been underestimated in this study. Fifth, the data were collected in 2002-2004, and thus it is possible that the results do not reflect the current situation as the profiles of diabetes and edentulism could have changed. Sixth, this was a cross-sectional study, and it was not possible to determine the causality or the temporality of the association between diabetes and edentulism. Thus, these results should be considered preliminary, and future prospective studies are warranted on this topic.
Search strategy, selection of studies and inclusion criteria We conducted this systematic review of the literature using the Preferred Reporting Items for Systematics Review and Meta-Analyzes (PRISMA) method. An electronic search was carried out via the PubMed, Cochrane Library and Science Direct databases in May 2019, specific biomarkers for oral cancer (OSCC) found by salivary samples. Our keywords "Medical Subject Heading" (MeSH) have been determined beforehand; we used the terms "Diagnosis AND Biomarker AND Saliva". Two observers first determined the potential for inclusion of each article, by reading the titles and abstracts. Subsequently, the articles were fully read by an examiner, to include or not include the first selection, as well as their data. The exclusion criteria are: literature reviews, editorials, articles not in French or English and dating back more than 5 years, articles dealing exclusively with exosomes, the Human Papilloma Virus (HPV), produced in vitro condition, concerning a target population or not including clear salivary measures and/or measures in patients with cancer of the oral cavity and finally articles extended to cancers of the head and neck.
The articles included relate to various types of studies, including a population with oral cancer and a control/control population, or even one or more additional populations with various lesions (pre-cancerous or others such as apthous lesions). Salivary concentrations of biomarkers are provided, whether or not accompanied by blood or tissue concentrations. These included articles bring together prospective studies of different types: case-control, cross-sectional or cohort study. The included studies could also present the blood or tissue concentrations of the selected biomarkers. We have reported this data in our study table; they were compared to saliva concentrations in an identical manner, in order to identify possible links between saliva, blood and tumor.
Risk of bias assessment The PEDro score (the Physiotherapy Evidence Database) was calculated for each article included, to assess its level of relevance, compared to its methodological quality  [40]. All of these results give an indication of the reliability and level of scientific evidence of our study. This scale, taken from an evidence-based physiotherapy database, groups 11 items to analyze: -Item 1: external validity (relating to its "applicability"). -Items 2-9: internal validity (randomization, blind procedure, quality of monitoring and analysis of all patients). -Items 10 and 11: the amount of statistical information provided. One point is awarded for an affirmative answer to each of the 11 internal validity criteria, except for item 1 (not counted). The overall score varies between 0 and 10.
Risk of bias assessment and data interpretation Concerning the quality of the included studies, several limits have to be taken into account. The number of patients included is generally limited and varies from one study to another. Larger samples of the population are needed to homogenize the results. The characteristics of the population samples studied are not systematically similar from one group to the other (case/ control groups) due to the prevalence of cancer: age, sex, etc. Sometimes it is difficult to include patients with the same characteristics on reduced patient samples. In addition, men, aged 50-60, are more affected by oral cancers. The results are therefore not always applicable to the greatest number. We assessed the methodological quality (see Tab. III), and therefore the credibility, of the studies collected using the PEDro scale: the Physiotherapy Evidence Database.
Here, the inclusion or exclusion criteria as well as the conditions for carrying out the study vary from one article to another and are more or less described. Most studies are not randomized or double blind for the full procedure. For example, only 6 studies have evaluated certain parameters "blind" such as the diagnosis of lesions by two independent assessors. The PEDro (Physiotherapy Evidence Database) scores are affected (Tab. III). After analyzing the articles, we count: -2 articles with a score of 3/10 (poor). -11 articles with a score of 4/10 (fair). -19 articles with a score of 5/10 (fair). -4 articles with a score of 6/10 (good). The average of the scores being 4. 69/10, we conclude that the level of evidence in our study is considered to be fair. We therefore chose not to limit the values included in our study to those considered significant with p < 0.
Conclusion After studying these 36 articles and 46 molecules, we were unable to identify any biomarker applicable to date for the diagnosis of oral cancer by salivary samples. Studies with better methodologies, sampling and quantification protocols and population samples (number and characteristics) are necessary. In addition, other parameters influencing the concentration of biomarkers such as systemic diseases, tobacco, age and sex of patients, etc. must be taken into account during analyzes. Saliva remains a major asset in the diagnosis and early management of oral cancer: it is a non-invasive method, reliable, easy to use, economical and fast. It will be a good tool in addition to the biopsy. PEDro score of 36 included studies, allowing their methodological evaluation. Q1 (in italic, because will not be counted) = Eligibility criteriahave been clarified; Q2 = Subjects were randomly assigned to groups; Q3 = the allocation respected a secret assignment; Q4 = the groups were similar at the start of the study with regard to the most important prognostic indicators; Q5 = all subjects were «blind»; Q6 = all therapists who administered treatment were «blind»; Q7 = all reviewers were «blind» for at least one of the essential judgment criteria; Q8 = the measures, for at least one of the essential judgment criteria, were obtained for more than 85% of the subjects initially divided into the groups; Q9 = all subjects for whom results were available received treatment or followed the control intervention according to their distribution or; when this was not the case, the data of at least one of the essential endpoints were "intention to treat" analyzed; Q10 = the results of the intergroup statistical comparisons are indicated for at least one of the essential criteria; Q11 = for at least one of the essential judgment criteria, the study indicates both of the effects and the estimation of their variability.