dataesr/scientific-paragraphs-categorization huggingface dataset:
| Periodontitis-diabetes direction Do people with periodontitis have a greater risk of developing type 2 diabetes? Overall, evidence from six studies representing populations from the United States, Japan and Taiwan, with a total sample of 77,716 participants, consistently demonstrated that patients with periodontitis exhibit a higher chance of developing pre-diabetes, referred to as non-diabetic hyperglycaemia (NDH) and diabetes (adjusted hazard ratio [HR] range: 1. 19-1. 33). Given the high prevalence of periodontitis in the population and the fact that periodontitis can be easily diagnosed and treated, even small adjusted HRs have potentially important public health implications  (Sanz et al. , 2018a). A recent large-scale study was carried out in Korea, using data from adult volunteers without diabetes who received health screening (National Health Insurance Service-National Health Screening cohort database, n = 111,611)  (Park, Kim, et al.
OSA and periodontitis Out of the 12 selected studies (7 cross-sectional, 5 case-control), a significant association between periodontal status and OSA was described in 10 investigations, while 2 studies did not identify any significant association between the two conditions  (Molina et al. , 2023). Data from six studies were included in meta-analyses, revealing a statistically significant association in both unadjusted (OR = 3. 66, 95% CI: 1. 05-12. 75, p =. 001; I 2 = 95. 3, p <. 001) and adjusted models (OR = 1. 65, 95% CI: 1. 21-2. 25, p =. 001; I 2 = 86. 5, p <. 001).
ACKNOWLEDGEMENTS We express our gratitude to the stakeholders who participated in the Workshop:  Andreas Stravropoulos  (as  European Federation of Periodontology (EFP) President) ,  Monique Danser  (as EFP Treasurer) and  Paola Della Bruna ,  Giulia Giovannardi ,  Matteo Basso  and  Alice Goddi  (as CURASEPT representatives). We thank  CURASEPT  for the support in the organization of this Workshop.
An 80 mm 2 lithium-doped silicon (Si(Li)) detector, commonly used in EDXS and low-energy gamma ray detection, equipped with a 12-µm-thick beryllium window and a 100-µm-thick aluminum "funny filter" (central hole diameter = 2 mm). Prior to the investigation of samples, soda-lime flat glass composed of ten oxides (NIST-620, USA) was used as a standard reference for calibration purposes. Conversion of X-ray peaks intensities to ion concentrations was carried out with Gupixwin software (Version 2. 2. 4, University of Guelph, Guelph, ON, Canada) to identify the local composition of desired ions.
Pair Distribution Function (PDF) Analysis Local atomic structure of Si/Ca 75/25, Si/Zn 75/25, and Si/Ca/Zn 75/15/10 sol-gelderived grounded BG powders have been measured with X-ray PDF analysis. All samples studied here were previously proved as amorphous according to their corresponding XRD patterns as perquisite prior to PDF analysis. The atomic PDF were obtained from X-ray total scattering data collected on a PANalytical Empyrean diffractometer equipped with a solid state GaliPIX3D detector, a focusing X-ray multilayer mirror, and an Ag anticathode (Kα1 = 0. 5594214 Å, Kα2 = 0. 5638120 Å). Powder samples were placed in glass capillaries of 0. 7 mm diameter. An empty capillary of the same type was measured in the same way for background subtraction. Data were recorded over the 1-145 • 2θ range, which corresponds to an accessible maximum value for the scattering vector Q max of 21.
4 Å -1. Data merging, background subtraction, and Kα2 stripping were conducted using HighScore 5. 1 Plus software provided by PANalytical Corporation (Malvern, UK). It was also used to generate a corrected and normalized total scattering structure functions S(Q) and consider the abovementioned bulk chemical compositions. Finally, the PDF or G(r) was calculated from the Fourier transforms of S(Q) truncated at 20 Å -1. Since the silicon content is the same in all samples, the number of the Si-O pairs (direct interatomic distance) is expected to be the same in all samples; the PDF curves were thus scaled to obtain a similar intensity for the Si-O PDF peak at 1. 62 Å. The simulated PDFs were calculated using PDFgui software version 1  [35].
Solid State 29 Si Magic Angle Spinning Nuclear Magnetic Resonance (MAS-NMR) Spectroscopy Q n silicon species distribution inside the binary and ternary BG compositions (75/25 Si/Zn and 75/15/10 Si/Ca/Zn) were determined using a Bruker Avance I spectrometer operating at a magnetic field of 9. 4 T (1H and 29 Si Larmor frequencies of 400. 2 and 79. 5 MHz) using a 4 mm double resonance MAS probe head. The Si quantitative MAS spectra were recorded at a rotor spinning frequency of 10 kHz after a RF pulse of 2. 4 µs (corresponding to a flip angle of 30 • ) and a recycle delay of 10 s. 29 Si chemical shifts were referenced relative to tetramethylsilane. The spectra were simulated using DMfit software dm2011 (CEMHTI, CNRS, Orléans, France). The following equation was used to calculate the Degree of Condensation (DC) of BG: DC = 100 × 2 × Q 2 + 3 × Q 3 + 4 × Q 4 4 (1).
X-ray Diffraction (XRD) Diffraction patterns were collected on a Philips X-Pert Pro equipped with a X'celerator 1D detector (2. 122 • active length) using CuKα1/Kα2 radiations (1. 5406/1. 5444 Å) in Bragg Brentano θ-θ geometry from 2 to 90 • (2θ) with a scan step of 0. 066 •. Data analysis was performed with HighScore Plus software provided by PANalytical Corporation and Crystallography Open Database (COD) to identify the crystalline peaks.
Statistical Evaluation Descriptive analyses were performed with GraphPad Prism 9. 4. 0 (673) (GraphPad Software, La Jolla, CA, USA). Statistical inferences regarding the indirect cell viability assay were based on random intercept models using the GLIMMIX procedure of the Statistical Analysis System SAS release 9. 04. 01M6P11072018 for Linux (SAS Institute, Cary, NC, USA). Fixed effects were material itself, time of incubation with the material, and interaction between material and length of incubation. Post-hoc tests were adjusted for multiple testing by multiplying the uncorrected p value by the number of tests (Bonferroni correction). Adjusted p values < 0. 05 were considered statistically significant.
In recent years, we produced several sets of RNA-seq data which were used to produce detailed coding gene annotation of the genomes of several pathogenic Cryptococcus species  (26) (27) (28). Our analysis also revealed that nearly all the genes contain several short introns, which are essential for gene expression  (29, 30). As expected, alternative splicing is prominent in Cryptococcus, although its impact on proteome structure is limited primarily to regulating gene expression  (27). More recently, we produced TSS-seq and 3UTR-seq data from C. neoformans and its sibling species Cryptococcus deneoformans grown under four conditions (i. e. exponential phase and stationary phase at 30 and 37°C)  (14). We used this dataset to re-annotate the transcript leader (TL) and 3'-UTR sequences in these species.
Trimmed reads were mapped to the Cryptococcus and S. cerevisiae genomes using Bowtie2  (37)  and Tophat2  (38)  as previously described  (14). RNA-seq reads counts were then normalized considering the ratios of DNA and RNA aligned to each genomes using the strategy previously described by Malabat and colleagues  (39). Differential gene expression analysis was performed using the DESeq2 package (40) using default settings but ommiting the associated read count normalization step. TSS-seq libraries preparations were performed as previously described  (14, 39)  replacing the TAP enzyme by the Cap-Clip TM Acid Pyrophosphatase (Cellscript). Sequencing was performed on Illumina HiSeq2500 to obtain fifty base single end reads. Data processing including reads trimming, clipping, and mapping were performed as previously described  (14).
TSS reads were first clustered using arbitrarily chosen maximum intra-cluster distance (d = 50 nt) between sites. We then looked for the optimal "d" value to define clusters, reasoning that an excessively small value would separate reads belonging to a single cluster into several ones, whereas an overestimated "d" would merge reads from different clusters into a single one. We thus tested increasing values of "d" (from d =1 to d =50) reasoning that the size of the clusters thus defined will also increase until their actual boundaries would be reached. We here considered only the genes with only one TSS cluster in their TL sequence using the exponential 30°C dataset and d =50 defined. We then plotted the "d" values with the percentage "P" of clusters reaching their maximum cluster size (Supplementary Figure  S1A.
TSS cluster subpopulation detection and cluster shape classification We considered only genes with only one TSS cluster in their TL and kept only clusters with both Size and SI between 2. 5% and 97. 5% quantiles, as evaluated using the data obtained in exponential phase 30°C (719 genes in exponential phase 30°C, 691 in stationary phase 30°C, 635 genes in exponential 37°C, 586 genes in stationary phase 37°C). To detect if there is more than one population of TSS clusters, the first principal component (PC1) of Size and SI was used as input for the function "emtest. norm" of R package "'MixtureInf"  (42)  with the default value of the finite mixture model under null hypothesis m0=1. The output of function "emtest. norm" includes the percentage of each sub-population together with the detected models with theirs mean and standard deviation.
Motif enrichment discovery in core promoter region To find motifs enriched in promoter regions, the genomic sequences from -100 to +30 of the major TSS peaks were extracted and used as input in MEME Suite software 5. 4. 1 (43) (de novo pattern discovery mode). Default settings were applied except these following parameters: number of motifs: 6, minimum width: 6, maximum width: 10, and search given strand only. The six motifs found were then scanned in each group of Sharp and Broad clusters in each condition with Fimo mode (threshold p-value ≤ 0. 0005) to examine their number and positions in each dataset.
One blank was run between each replicate to prevent sample carryover. Peptides eluting from the column were analyzed by data dependent MS/MS, using top-10 acquisition method. Peptides were fragmented using higher-energy collisional dissociation (HCD). Briefly, the instrument settings were as follows: resolution was set to 70,000 for MS scans and 17,500 for the data dependent MS/MS scans to increase speed. The MS AGC target was set to 3. 106 counts with maximum injection time set to 200 ms, while MS/MS AGC target was set to 1. 105 with maximum injection time set to 120 ms. The MS scan range was from 400 to 2,000 m/z. Dynamic exclusion was set to 30 seconds duration.
Data analysis The MS files were processed with the MaxQuant software version 1. 5. 8. 3 and searched with Andromeda search engine against the annotated C. neofomans database  (14)  but also against a database containing all alternative proteins potentially resulting for alternative TSS usage. To search parent mass and fragment ions, we set a mass deviation of 3 ppm and 20 ppm respectively. The minimum peptide length was set to 7 amino acids and strict specificity for trypsin cleavage was required, allowing up to two missed cleavage sites. NEM alkylation (Cys) was set as fixed modification, whereas oxidation (Met) and N-term acetylation, N-term Dimethylation (any N-term), Dimethylation (Lys) were set as variable modifications. The false discovery rates (FDRs) at the protein and peptide level were set to 1%.
TSS-cluster characterisation in Cryptococcus We previously used TSS-seq data obtained from cells grown under four conditions in triplicate to construct twelve GFF files defining the coordinates of several thousand TSS clusters associated with coding genes in two Cryptococcus species  (14). To evaluate alternative TSS usage, we aimed to construct a TSS cluster reference GFF file. We first thought to merge the twelve condition-specific GFF files originally constructed. However, this simplistic strategy resulted in a very poor result. Firstly, most of the resulting merged TSS were doubtful since they were only 1 bp-wide. Secondly, at several loci the TSS cluster size and number varied between conditions. This merging operation also resulted in the definition of very large TSS (more than 100 bp wide) with probably poor biological relevance (see Supplementary Figure  S2 ).
in the transcription of an mRNA which can code a protein truncated from its N-termini, thereby potentially lacking an N-terminal targeting motif (Figure  3 ). Accordingly, DeepLoc 2. 0 (59) analysis predicts that whereas for 169 of these genes the long isoform has a defined subcellular localization, for 87 of them the usage of an altTSS is predicted to result in the production of a shorter isoform with a different subcellular localization (Table  S5  and Figure  5 ). For instance, we identified an altTSS associated with the gene MAE102 (CNAG_06374) which encodes a putative mitochondrial malate dehydrogenase (Figure  6A ). Depending on the TSS used, the predicted translated protein contains a mitochondrial targeting signal (MTS) or not. Interestingly, the usage of this altTSS is regulated by the growth condition, the long isoform encoding the putative mitochondrial protein being transcribed in stationary phase at 30°C, whereas the exponential phase condition triggers mostly the transcription of the short isoform predicted to code a protein devoid of MTS.
Material and methods This study was a randomized, parallel-group, semi-double-blinded clinical trial evaluating the clinical safety, tolerability, and performance of Ivory Dentin Graft™ in comparison with a commercial bone-derived material in alveolar ridge preservation following tooth extraction (registered at ClinicalTrials. gov, May 12th, 2017, Identifier NCT03150472). Extraction sites were grafted with test or comparator material and a titanium implant placed at 4 months after taking a graft site biopsy. Primary endpoints were the extent of new bone growth and bone-graft integration at 4 months.
The study was sponsored by Ivory Graft Ltd. , Tel Aviv, Israel, and performed at a single clinical Written informed consents were obtained from all participants after provision of a detailed explanation of the protocol and the benefits or risks of participation. The study was registered at ClinicalTrials. gov on May 12th, 2017 (Identifier NCT03150472), prior to the enrolment of the first subject. This study was semi-double-blinded. Only the study staff member performing the grafting procedure, the study coordinator, and the study CRO were unblinded to the type of graft applied. The study assessors were located externally from the medical center, independent, and kept blinded to the subject allocations. Grafting procedures were conducted following mandibular pre-molar or molar tooth extraction.
Histological assessments were performed by L. E. M Laboratory Ltd. , Nes-Tziyona, Israel. Bone graft site quality was also assessed by the insertion torque during implant placement. Dental implant insertion torque has been shown to be correlated with bone density and is one of the most important factors for successful implant placement in a post-grafting site  [31, 32]. Bone density was evaluated using a volumetric CBCT imaging dental software (OnDemand3D™), which measured the radiodensity of the alveolar bone core using CBCT images obtained prior to dental implant placement. This method is objective, reliable, and offers the best radiographic method for the morphological and qualitative analysis of the residual bone  [31, [33] [34] [35] [36] [37]. A further efficacy endpoint was the success of the dental implant placement procedure.
Furthermore, as the dentin particles are resorbed slowly by sterile external replacement resorption, the stability is expected to be maintained throughout the resorption process. Consistent with the excellent data for Ivory Dentin Graft™ concerning the graft site, the implant placement success was 95% compared to 81. 25% for the comparator. This indicates that most implants did not require any additional intervention during implant placement or delaying of implant placement due to graft failure. Physician assessment of the usability of the products using a 10-point satisfaction scale indicated that the materials are similarly easy to use. Safety aspects were actively monitored throughout the study. There were no serious AEs, and also no severe adverse events, severe adverse reactions, or suspected unexpected serious adverse reactions for either product.
Clinical Study Design In this prospective study, we examined patients undergoing vocal folds surgery at the Besançon University Hospital between 2014 and 2016. "Fluorocord" trial received a favorable opinion from French ethical committee (CPP Est-II) on June 2014 (NCT03585075). Informed written consent was obtained from each patient. Biopsy sites for lesions were selected on a visual examination basis by the surgeon. Normal vocal fold biopsies were taken from total laryngectomy surgical specimens or from cordectomy specimens for non-tumoral indication. After AFS recording, biopsies were embedded in 10% neutral formalin and sent to histopathology for diagnosis confirmation.
Features Extraction The spectral features were estimated using a Principal Component Analysis (PCA) in order to reduce the high data dimensionality  22. The result of PCA is a set of new dimensions called Principal Components (PCs) which are uncorrelated and are computed by preserving as much variance as possible. In the present case, we selected a number of PCs allowing us to obtain at least 99. 9% of the amount of variance contained in the original data set. The fluorescent intensity (Ig) was also extracted from fluorescence spectra in order to be used as a reference during the classification step. This descriptor (Ig) was estimated by calculating the integral of the spectrum between 437 -750 nm.
Study design and setting This cross-sectional study is a part of the randomized controlled trial OP-PE protocol published by  Kanoute et al. (2021)  and registered at ClinicalTrials. gov (NCT04989075). The ethical committee of Dakar (Senegal) approved the protocol on 8 June 2021 (000086/MSAS/ CNERS/SP). The multicentre study occurred in 6 National Hospital Center of Dakar (Senegal) and carried out in conformance with the Declaration of Helsinki. Written informed consent was obtained from each participant before enrolment. This research was performed in accordance with the STROBE guidelines (Supplementary File 1).
Statistical analysis The statistical analysis consisted of three main steps: producing descriptive summaries of the data, modeling the data using a mixed (linear) model and assessing the correlations between bacterial abundances. SPSS Windows 20. 0 (IBM, Chicago, IL, United States) was used for the descriptive statistics median values and interquartile range (IQR) and mean values with SD for the quantitative variables and percentages for categorical variables. Microbiological variables will be presented as total periodontal bacteria counts, frequency of detection of target pathogens, counts of each pathogen studied, and proportions of each pathogen in the total microbiota. Total periodontal counts will be log-transformed to match a normal distribution. Descriptive bivariate analyses between participant characteristics and the outcome, gingivitis, were evaluated using t-tests and logistic regression for continuous and binary/categorical variables, respectively.
Kruskal-Wallis tests were performed to compare the mean counts for the different bacterial species relative to each clinical characteristic. The detailed statistical methods are indicated in the table footnotes. Shapiro-Wilk test was used to check the normality of the distribution. Results will be considered statistically significant at p < 0. 05. Principal component analysis (PCA) was performed to identify clusters of variables highly associated with each other and to visually assess whether groups with and without these outcomes of interest could be distinguished using the variables identified in both univariate and multivariate analyses. Briefly, the dataset was dimensionally reduced into linear variables termed principal components (PCs) with those possessing eigenvalues >1 included in further analyses.
Dimension reduction and clustering by PCA in the orange and red periodontopathogens subgroups Figure  4  presents the correlation plot from the principal component analysis (PCA) applied to demographic, behavioral, clinical parameters, and periodontopathogens from the orange and red complexes. A Bartlett sphericity test was performed and assessed the variables were dependent (value of p < 0. 0001). The Kaiser-Meyer-Olkin overall measure of sampling adequacy was 0. 51, which indicate a moderate level of sampling adequacy for PCA. The PCA revealed 4 principal components accounted for 55%, 88% of the overall variation of the data produced from the 19 active variables. The first 4 PCs, representing 17,09%, 14,86%, 14,00%, and 9,93% variance respectively, were included in PCA correlations with bleeding percentage; determined using Cattell's scree plot.
Degree of conversion measurements For each resin cement tested (n = 7), 6 cylindrical specimens (diameter 6 mm x height 3 mm) were made with Te on molds: 3 were performed in with light-activation for 60 s at 1200 mW/cm2 (Valo Grande lamp, Ultradent Products Inc, South Jordan, UT, USA) immediately after mixing, and 3 were performed only in self-curing mode (mixed in the dark). All samples were then stored in the dark in distilled water at 37°C for one week before the degree of conversion (DC) measurement. DC was determined using Fourier transformed infrared spectroscopy (FTIR) with a NicoletTM iS10 spectrometer (Thermo Fisher Scienti c, Waltham, MA, USA) in attenuated total re ectance (ATR) mode. These spectra were recorded with OMNIC software (Thermo Electron Corporation, Waltham, MA, USA).
Penetration/removal preclinical tests The development of an endodontic penetration/removal (P/R) protocol was carried out on a traction machine (Zwick/Roell -50N force cell, Ulm, Germany) controlled by the testXpert II software (Zwick/Roell) in the LEM3 laboratory (PolyTech, Nancy, France). 85  This protocol corresponds to a free P/R test involving 25 successive charge/discharge cycles, divided into 9 groups of cycles, allowing the descent and the work of the tested endodontic instrument in a resin block having a radius of curvature about 4. 5 mm (DENTSPLY MAILLEFER, Ballaigues, Switzerland). Complete instrumental removal is performed between each cycle allowing (i) a canal irrigation to remove debris and (ii) a veri cation of the maintenance of apical patency. This protocol was established in order to respect the clinical reality and to be reproducible.
Penetration/removal preclinical tests Numerical data were analyzed using non-parametric Kruskall-Wallis-type statistical tests. A Dunns correction with α = 0. 05 was performed for the two-by-two multiple comparisons. The results were considered statistically signi cant for a P value <0. 05. All statistical analyzes were performed using GraphPad Prism® 6 software (San Diego, California, US).
Sample preparation Five Wistar rats were included in the study: three males and two females, aged four months and weighing between 196 and 135 g. After euthanasia, rat tails were collected and fixed in 4% formalin for 24 h, washed three times in PBS, then cut to generate samples of approximately 1 cm long. These samples were first brought to analyze with µCT. After data acquisition, the samples were dehydrated through a 70%-100% alcohol series, then cleared through two changes of xylene. The specimens were progressively infiltrated with Technovit 9100 (T9100) and finally embedded in a polymerization solution of T9100 (Kulzer GmbH, Kulzer Technik, Wehrheim Germany) at -0. 5 • C in a freezer. Once the polymerization was complete, the blocks were brought to room temperature and removed from the molding containers.