dataesr/scientific-paragraphs-categorization huggingface dataset:
Declaration of funding This study was funded by Basilea Pharmaceutica International Ltd. The funder was involved in the study design, data collection and data analysis. Author contributions: N. P. performed data analysis; all authors were involved in the design of the study, interpretation of the data, drafting the paper and revising it critically for intellectual content. All authors agree to be accountable for all aspects of the work. All authors had full access to all study data and had final responsibility for the decision to submit for publication. Declaration of financial/other relationships R. H. has disclosed that he has received honoraria from Astellas, Basilea, Gilead, MSD and Pfizer, and a research grant from Pfizer. D. K. and J. P. have disclosed that they are full-time employees of Basilea Pharmaceutica International Ltd, Basel, Switzerland and both hold stock options with Basilea.
There were dose constraints on the optic nerve, anterior part of brainstem, spinal cord and contralateral ear (maximum dose 56, 64, 55 and 55 GyRBE respectively). The ipsilateral ear did not have dose constraints. The gross tumour volume (GTV) was delineated on post-operative MRI or CT-scans. The clinical target volume (CTV) included the GTV and 5-to 20-mm 3D margins that were manually corrected depending on suspected microscopic spread, natural barriers and anatomy. The planning target volumes were calculated by adding a 2-to 3-mm safety margins around the CTVs. The patients' medical records were reviewed for clinical, imagery, treatment and follow-up data. The latest clinical examination, MRI imagery and audiometric tests were studied. All patients were contacted by phone or by e-mail using standardised questions to collect missing data and up-to-date symptoms.
Side-effects were graded according to the Common Terminology Criteria for Adverse Events, version 4. 0 (CTCAE)  [16]. The original data is available online (S1 Dataset). This is a retrospective study and has been approved by our Institution Review Board (IRB), the CEORL (Evaluation Commission of Observational Research of the French Society of Otorhinolaryngology) and all clinical investigation have been conducted according to the principles expressed in the Declaration of Helsinki. Informed consent, written and oral, has been obtained from the participants. Statistical analysis was made using XLstats (Addinsoft, New York, NY). Continuous data was summarised with means and range and compared using the nonparametric Mann-Whitney test. Categorical data was summarised with frequency counts and proportions and compared using the chi-square test.
A B S T R A C T Facial fractures are considered more common in young individuals. However, they are also increasing in the aging population. Investigation of the characteristics of such fractures is important so as to be able to devise preventive measures and specifications for their proper treatment. We carried out a descriptive retrospective epidemiological study. The information was taken from a database of medical files of patients over 65 years of age in the setting of the emergency ward. Patient information was included for 157 patients aged 65 to 100 years. Two-thirds of the individuals with facial trauma were women. Twenty-eight had a prior history of cognitive impairment. For half of the cases, the trauma occurred at their place of residence, while accidents and falls in public areas were not uncommon.
Patients and methods We carried out a descriptive retrospective epidemiological study. Patient information was obtained from a database derived from medical files of patients aged over 65 years who presented to the emergency ward of the Intercommunal Hospital Center of Villeneuve-Saint-Georges between January 1, 2014 and April 30, 2017, and who had at least one radiologically proven fracture of a facial bone. A total of 157 patients aged between 65 and 100 years fit the inclusion criteria and their information was included in this study. The studied variables were age; gender; prior medical history; lifestyle; the type of accident; time of the first medical consultation; types of fracture: nose, floor of the orbit, orbitozygomatic, lower jaw, maxillary sinus, upper jaw, etc. ; site of the accident; and associated lesions.
Data Analysis In order to investigate the relative variation of both indicators as a function of healing time, analyses of variance analyses (ANOVA) were performed for each implant to evaluate the effect of healing time on different indicators, such as UI, ISQ0, ISQ90, and ISQ. Statistical differences were defined at a 95% confidence level. ANOVA allows for determining whether healing time has a significant effect on the different parameters described above. The variation of each indicator (ISQ and UI) as a function of healing time was investigated by defining the following variables, which correspond to relative variation of the indicators between two healing time (here n and p weeks, p > n) for the same implant: ∆ (3) ∆ (4) In cases where ANOVA shows that the results obtained with the indicator X after n and p weeks of healing time are different, the sign of ∆ allows to determine whether the parameter X increases as a function of healing time (∆ 0) or whether it decreases (∆ 0).
Data Analysis In order to investigate the relative variation of both indicators as a function of healing time, analyses of variance analyses (ANOVA) were performed for each implant to evaluate the effect of healing time on different indicators, such as UI, ISQ0, ISQ90, and ISQ. Statistical differences were defined at a 95% confidence level. ANOVA allows for determining whether healing time has a significant effect on the different parameters described above. The variation of each indicator (ISQ and UI) as a function of healing time was investigated by defining the following variables, which correspond to relative variation of the indicators between two healing time (here n and p weeks, p > n) for the same implant: ∆ n-p ISQ = ISQ p m -ISQ n m (3) ∆ n-p U I = U I p m -U I n m (4) In cases where ANOVA shows that the results obtained with the indicator X after n and p weeks of healing time are different, the sign of ∆ n-p X allows to determine whether the parameter X increases as a function of healing time (∆ n-p X > 0) or whether it decreases (∆ n-p X < 0).
This study focused on the search for new biomarkers based on liquid chromatography-multiple reaction monitoring (LC-MRM) proteomics profiling of whole saliva from patients with periodontitis compared to healthy subjects. The LC-MRM profiling approach is a new and innovative method that has already been validated for the absolute and multiplexed quantification of biomarkers in several diseases. The dataset for this study was produced using LC-MRM to monitor protein levels in a multiplex assay, it provides clinical information on salivary biomarkers of periodontitis.
Subject area Biology More specific subject area Clinical chemistry, Salivary biomarkers, Oral disease, Periodontitis Type of data Tables, figures How data was acquired Liquid chromatography (LC) separation was carried out on a 1290 LC system (Agilent Technologies). Peptides were resolved on a reversephase column over 30 min at a flow-rate of 400 μL/min. Peptides were then analyzed on a triple quadrupole mass spectrometry (MS) system (6490, Agilent Technologies), equipped with an Agilent Jet Stream ESI interface. The MS was operated in dynamic MRM mode with a retention time window of 2. 5 min and a maximum cycle time set at 700 ms.
Data format Analyzed and processed data Experimental factors Whole saliva samples were collected without stimulating salivation. Samples, with a minimum volume of 3 mL of saliva, were collected over 5 min from each patient and healthy subject using cotton swabs (Sarstedt Salivette®), placed in the mouth between the upper jaw and the parotid duct close to the first molar. Samples from 33 patients were immediately centrifuged for 15 min at 2600×g, 4 °C to remove residual particles, such as bacteria and mucosal cells. After centrifugation, the supernatant was aliquoted in 1. 5 mL Eppendorf tubes and stored at -80 °C until analysis.
Data In this Data in Brief article, we present the salivary profiling of 28 plasma biomarkers from 33 patients (12 healthy individuals (control), 10 Chronic Periodontitis patients (CP) and 11 patients with Aggressive Periodontitis (AP)). Subjects were between 18 and 75 years of age. Saliva samples were processed in triplicate and analyzed in duplicate by LC-MRM. Quantitative results obtained for the 28 protein biomarkers studied were validated and are presented together in Table  1. Absolute quantification was obtained by spiking labeled proteotypic peptides containing heavy isotope equivalents of arginine ([13C6] or [13C6, 15N4]) or lysine ([13C6] or [13C6, 15N2]) residues. The analytical performance obtained for each biomarker is indicated in Table  1 , based on the following criteria: Linear concentration range (pg/mL), Linear response (R2), Limit of detection (LOD, pg/mL), Limit of quantification (LOQ, pg/mL), precision (CV %), clinical range in saliva samples (pg/mL).
Patient selection/population Patients (n ¼ 33) were recruited and screened at the Department of Periodontology, CHRU Montpellier (France): 10 were diagnosed with CP, 11 with AP and 12 were healthy controls. The control group was composed of patients presenting no evidence of periodontitis. Subjects' ages were between 18 and 75 years. Smoking status (current, former, never) was recorded for all individuals, with heavy smoking (4 15 cig/d) used as an exclusion criterion. Patients gave informed consent for participation in the study, and for conservation of their samples in a registered, ethically-approved biological collection (#DC-2008-417) that is stored at Montpellier University Teaching Hospital's certified NFS 96-900 biobank (Ref: BB-0033-00031 www. bio banques. eu). Authorization to handle personal data was granted by the French Data Protection Authority (CNIL) under number 1709743 v0.
Acknowledgements The authors thank  Bernard Senger  for his precious help in the statistical analysis. The authors thank  Damiano Pasqualini  ( DDS, Associate Professor ) for fruitful discussion. In addition, the authors wish to thank  Mrs Valentina Macaluso  and  Dr Figure  4 (A) Pre-operativee radiograph. (B) 48 months radiographic follow-up. (C) 48 months radiographic follow-up.
Patient Data Collection The civil data (age, gender, etc. ) and medical history were collected using a form. The retention index of Björby and Löe  [17]  was used to assess the oral hygiene level (Table  1 ). Once the causative tooth had been identified, a retro-alveolar radiography was performed. Then, a periodontal sounding measured the depth of the pockets. Patients were classified into 3 occupational categories: (i) low income category (farmers, students, pupils, and housewives), (ii) high income category (business people and private sector employees), and (iii) patients with a moderate income (public sector employees, informal sector workers, retirees). Legend: 0 = Score of zero, 1 = Score of one, 2 = Score of two, 3 = Score of three.
One well was fixed for subsequent visualization of primary bacterial adhesion. The medium (1 ml) supplemented with tested substances was then dispensed into the wells. The plates were incubated for 72 hr under static conditions at 37°C. The same technique was used for S. aureus except that the culture was realized in normal atmosphere and avec 24°C. For visualization, the biofilms were stained with SYTO9 Green and subsequently treated with ProLong ® Diamond Antifade Mountant (Molecular Probes ™ ). Images are representative of the biofilm structure observed in a mean of 20 different fields over a minimum of four independent studies. Biofilm density and thickness were calculated over the same number of observations using Zeiss Zen Image Analysis software for light microscopy (ImageJ software package).
In these conditions, bacteria are distributing between the water and solvent phases following their surface hydrophobic or hydrophilic character and Lewis acid/base balance (electronegative or electropositive character). The OD of the aqueous phase was measured at 400 nm. The percentage of cells in each solvent was calculated using the following equation: (1 -A/A 0 ) × 100. The experiments were carried out in at least five replicates. The data were analyzed using the Mann-Whitney nonparametric criterion. The differences between experimental and control variants were considered reliable at confidence coefficient >95% (p < 0. 05).
Finite element analysis of the starch-based tube-shaped material behavior Finite element computation was used to predict tube behavior until deterioration as a function of external pressure. Moreover, the evolution of material properties during an immersion that simulated body conditions was taken into account. A previous study showed the mechanical behavior of starch-based materials under physiological conditions (without enzymes). 16 All computations were performed using ANSYS structural analysis software (ANSYS, Canonsburg, PA, USA). The geometry was meshed using an irregular meshing scheme. Structural meshing was based on a tetrahedral structural solid element with a quadratic displacement behavior and ten nodes, where each node is capable of structural displacement in the three main directions.
Two slopes were determined for three immersion times on the basis of the stress/strain curves obtained. The first slope refers to the elastic modulus E Y. Beyond the yield stress value σ Y , the second slope is referred to as the tangent modulus E T. The full determination of starch behavior is based on the three mechanical quantities E Y , σ Y and E T indicated as a supplementary table (see online supplementary file 1). The optimization of these mechanical data using the Finite element computation is provided as supporting data as well (see online Supplementary Fig. S1 ). The geometry and the dimensions of the virtual tube for finite element study are adapted according to the experimental layout with a typical outer diameter of 1. 8 mm, an inner diameter of 0. 8 mm and a length of 10 mm. The mechanical data previously determined are injected into the model, giving the results shown in Fig.
Acknowledgments This work was funded by an  ANR   Emergence IRMAS grant  ( ANR-2010-EMMA-007 ),  France. Mr. Velasquez  would like to thank the  Pays de la Loire Region  for providing a partial Ph. D. scholarship. The authors are also grateful to  R. Desirest ,  A. Beilvert ,  M. De Carvalho ,  S. Langonnet  and  O Thibaudeau  for their precious support.
Histomorphometry Morphometry was performed at a constant magnification (260x) and analyzed with Image J software (NIH, Bethesda, MD, USA). The following parameters were measured in the zone immediately above the alveolar bone: 1/the total pocket area [pocket epithelium þ subepithelial infiltrated connective tissue (ICT) around the first molar; expressed in mm 2 ]; 2/the ICT area (in mm 2 ). This enabled us to calculate the pocket epithelium area (in mm 2 ); 3/the number of IL-1ß þ cells in the pocket tissues of the interdental septum between the first and second molars (N/mm 2 ). Bone reactions were evaluated along the alveolar wall of the third molar where the following parameters were quantified: 1/the length of the socket wall, 2/the resorption surface (Oc. S/BS), expressed as percentage of the socket wall; 3/the number of on-bone osteoclasts (cells in contact with the bone surface) per mm of bone surface (N.
DisCUssion The reported relative frequency in percentage of MBBCs in relation to all odontogenic cysts varies between 0. 9 and 4. 7%. 8 The cases reported in this study were in line with the data in the literature; the patients were 6-8 years old and two out of three were   The authors agree that the associated teeth show an altered eruption pattern, with a buccal tilting of the crown and a deep periodontal pocket on the buccal side. The vitality of the tooth always remains positive, and there can be some swelling, pain or tenderness, according to the degree of infection. No paresthesia is noticed in any known case, although the inferior alveolar nerve can be displaced lingually. Deep periodontal pockets can be measured on the buccal aspect of the tooth without gingival inflammation, and usually intraoral bony expansion, tender to palpation, is noticed.
Raman microscopy. Raman spectra are recorded using a Witec Confocal Raman Microscope System alpha 300 R (Witec Inc. , Ulm, Germany). Excitation in the confocal Raman microscopy is assured by a frequency doubled Nd: YAG laser (Newport, Evry, France) at a wavelength of 532 nm. The incident laser beam is focused onto the sample through a ×20 NIKON objective (Nikon, Tokyo, Japan). Then Raman backscattered radiation mixed with Rayleigh scattered are passed through an edge filter to block the Rayleigh's. Acquisition time of a single spectrum was set to 0. 05 s. Each spectrum corresponding to a spatial unit defined as a voxel (300 nm × 300 nm × 1 μm). All data acquisition and processing were performed using Image Plus software from Witec. Chemical mapping of dental enamel was carried out over cross sections of all specimens with naturally and artificially developed subsurface lesions.
Nanoindentation technique. A nanoindenter equipped with a Berkovich tip (CSM, Switzerland), was used to measure hardness (H) and Young's modulus (E) of enamel. Tests were made in lesion, intermediate and sound enamel areas respectively. Indentations with a maximum load of 10 mN were marked on the samples where nanoindentation test was performed. The distance between each 2 neighboring indentations was at least 10 μm. A load of 20 μN was set for all tests, and loading and unloading time was 270 s. At least; ten indentations were done on each zone of the examined enamel surface. H and E variables of samples were obtained from load-displacement loading/unloading curves, using Oliver and Pharr method  22  , which is the most successful model for nanoindentation data analysis. The hardness (H) is calculated at the maximum force according to the following relation: = H F A (1) P where F is the maximum force and A p is the projected surface contact area between the indenter and the sample.
Discussion Chemical composition and mechanical properties of WSLs and subsurface artificial lesions were described using Raman microscopy and nanoindentation techniques. Both techniques tested the same areas of each sample. To our knowledge, confocal Raman microscopy has been used for the first time in this study to detect WSLs and experimentally induced subsurface lesions. It can provide a high resolution chemical and morphological map of examined specimen, detecting even very small changes in its chemical composition. Data analysis of each acquired scan which is comprised of tenth thousands of single spectrums, is used to reconstruct different Raman detailed images. Transverse microradiography is a quantitative method depending on x-ray absorbance of an object and images reflect mineral concentration in mineralized tissue slices  24.
Whole-Genome Sequencing of Spontaneous Auto-aggregation Mutant Strains Streptococcus salivarius spontaneous mutants JIM9443 and JIM9447 were sequenced using the Illumina HiSeq 2000 system at I2BC 1 , with around 7 million paired-end 100 baselong reads. Strains JIM9442, JIM9445, JIM9446, and JIM9448 were sequenced using the SOliD technology 4 platform at MetaGenoPoliS 2 , with around 5 million single 50 base-long reads. SOLiD reads containing adapter and/or barcode fragments with a mean quality value <20 and low-quality reads (with 3 or more "N") were discarded. Clean reads were mapped to the reference JIM8777 strain using Bowtie  (Langmead et al. , 2009)  and variations were detected using the Tablet software  (Milne et al. , 2013). The Illumina and SOLiD sample sequences are available in the SRA database (project ID PRJEB23560).
Statistical Analysis Variables are expressed as the means and standard deviations of results obtained from three (auto-aggregation, coaggregation, and adhesion assays) or two (CLSM analysis) independent experiments. Comparisons between groups of variables were analyzed using the student's t-test. GraphPad Prism version 6 (GraphPad software Inc. , La Jolla, CA, United States) was used for statistical analyses. A P-value < 0. 05 was considered to be statistically significant.
ACKNOWLEDGMENTS This work has benefited from the facilities and expertise of the high-throughput sequencing core facility of the  I2BC (Centre de Recherche de Gif  -http://www. i2bc. paris-saclay. fr/) and MetaGenoPoliS (http://mgps. eu/). We thank the MIMA2 platform (http://www6. jouy. inra. fr/mima2) of the  INRA research center in Jouy-en-Josas (France)  for access to their confocal and electronic microscopy facilities. Julien Deschamps  ( Micalis Institute, France ) and  Sophie Chat  ( IGDR, Université de Rennes 1, France ) are warmly acknowledged for CLSM and TEM image analysis, respectively. We thank  Céline Gautier ,  Japhète Mbouyou-boungou ,  Fabienne Beguet-Crespel  and  Victor Bandaly  for technical assistance. We thank  Diana R. Martin  ( The Institute of Environmental Science and Research, New Zealand ) for providing S.
Results At the time of the dental examination, 21 patients had normal TSAT (≤45%) and 45 patients had high TSAT (>45%). Among the 45 patients with high TSAT, 19 had serum ferritin levels ≤50 μg/L and 26 had serum ferritin levels >50 μg/L. As shown in Table  1 , 33. 3% of the patients with normal TSAT presented severe periodontitis versus 68. 9% of those with high TSAT (χ 2 , =. p 0 006). A significant increase in all clinical attachment loss (CAL) measures was observed in the patients with high TSAT. Although not significant, we observed a trend towards increased pocket probing depth (PPD) measures in patients with high TSAT. Moreover, no significant differences in demographic data were found between the patients with normal and high TSAT (Supplementary Table  S1 ). In the high TSAT patients, no difference in the periodontitis severity was observed according to the serum ferritin levels: 68.
Microbiological analysis. Taxonomy at the genus level was assigned using the "Visualization and Analysis of Microbial Population Structures" (VAMPS) analysis pipeline web tool  63. Default parameters were used for assignment at the genus level with the "Ribosomal Database Project" (RDP release 11) classification  64. Through the VAMPS process, the best taxonomic hit was assigned for each read. Reads identified as Archaea, Eukarya, Organelle and unknown were excluded from the analysis. Alpha rarefaction and diversity were evaluated using the Observed Species metric (Sobs) and the Shannon-Weaver index  65. Beta diversity was calculated using Bray-Curtis  66  and UniFrac distances  67. Genera were removed if their relative abundances did not reach 1% in at least one sample or if their mean relative abundances did not reach 0.
5% in at least one group (normal or high TSAT) to avoid significant statistical changes with no biological relevance. Genera that had significant differences in presence/relative abundance between healthy and periodontitis subjects in previous studies  33, [68] [69] [70]  were marked as genera of interest for a species-level taxonomic assignment. This assignment was made using the "Quantitative Insights Into Microbial Ecology" (QIIME version 1. 9. 1) package software  71  with a curated database constructed with the "Human Oral Microbiome Database" (HOMD version 14. 51)  72  and full-length 16S rRNA gene sequences of all species belonging to the genera of interest present in the RDP. Statistics. The data were analysed using R (version 3. 3. 3)  73 with the RStudio software  74. Statistical tests were chosen following Shapiro-Wilk normality test results for the data distribution and were considered significant for <.