dataesr/scientific-paragraphs-categorization huggingface dataset:
Because V. parvula is a non-sporulating Firmicute, the role of this SpoIVB domain remains to be determined. The other domain, DUF1090, is an uncharacterized domain found in all three domains of life, and predominantly present in Bacteria. For example, the E. coli YqjC protein only contains this domain. Only one study has been performed on the corresponding gene and it was found to be down regulated when the sigma factor rpoS gene was mutated  (Zhang et al. , 2012). In the Stepdb database that details the localization of all E. coli proteins  (Orfanoudaki and Economou, 2014) , YqjC is annotated as periplasmic. In some bacteria, this domain constitutes the C-terminal hydrophobic substrate-binding domain of the chaperone DnaK and it may have a similar function in Vpar_0521. These indications, and the conservation of Vpar_0521 in diderm Firmicutes, make this protein an important target of future study.
D. fellowship from the Institute Pasteur PPU program. CB is supported by the Institut Pasteur, the French Government Investissement d'Avenir Program Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases" (grant no. ANR-10-LABX-62-IBEID), Fondation pour la Recherche Médicale grant "Equipe FRM DEQ20140329508. " SG acknowledges support by Investissement d'Avenir Grant "Ancestrome" (ANR-10-BINF-01-01).
The last decade has seen an increasing number of optical IOS, and these are based on different technologies; the choice of which may impact on clinical use  [6]. To allow the practitioner to make an informed choice before purchasing or renewing an IOS, this article is divided in three distinct parts. The first presents the different technologies employed by the current IOS for the capture of image and the generation of a digital file by the software, the second is dedicated to the clinical pitfalls associated with these technologies during IOS use, and the last part reports on the accuracy of these current technologies.
IOS Technologies IOS is a medical device composed of a handheld camera (hardware), a computer, and a software. The goal of IOS is to record with precision the three-dimensional geometry of an object. The most widely used digital format is the open STL (Standard Tessellation Language) or locked STL-like (Figure  1(a) ). This format is already used in many industrial fields and describes a succession of triangulated surfaces where each triangle is defined by three points and a normal surface (Figure  1(b) ). However, other file formats have been developed to record color, transparency, or texture of dental tissues (such as Polygon File Format, PLY files). Irrespective of the type of imaging technology employed by IOS, all cameras require the projection of light that is then recorded as individual images or video and compiled by the software after recognition of the POI (points of interest).
However, among the IOS that employ the same technology, clinical differences are reported; it is reported that participants preferred the use of Trios over iTero although these are both based on confocal technology  [17]. This is related to the time for operators to familiarize themselves with the ergonomics and software of each IOS, and the learning curve can be initially slow. Indeed, a study compared experience curves between initial scan and after repeated scans using two IOS with confocal technology. It was found that, although scanning time decreased with training for both scanner, the average scanning time for Trios was always shorter than that for iTero  [22]. In addition, the software, the technology employed, and the scanning path all seem to affect handling time during digital impression that has been reported to be between 4 and 15 minutes with no clear determining factor  [12].
3. 2. Powdering. Dental tissues present many reflective surfaces, such as enamel crystals or polished surfaces, that could disrupt the matching of POI by the software due to overexposure. To prevent this, practitioners could change the orientation of the camera to increase diffuse light (Figure  4(a) ). Another strategy to overcome this difficulty employed by some systems is to use cameras with a polarizing filter  [23]. For other scanners, a 20-40 μm powder coating is required during the digitizing process to reduce reflectivity (Figure  4(a) ). Theoretically, the powder thickness could vary between operators and reduce file accuracy, but the software of the IOS is capable of taking an average thickness into account  [24]. Powder-based digital impression has been previously shown to be very accurate for partial impressions  [25, 26].
This rematching of POI is directly influenced by a complex geometry of the object such as high curvatures or many hidden faces that reduce the number of POI and complicates the process for the software  [31, 32]  (Figure  4(d) ). 3. 5. Mesh Quality. The IOS software can generate files of varying mesh densities (Figures  5(a ), 5(b), and 5(c)). However, a high mesh density for the whole tooth is not relevant due to high computing time involved. Some files incorporate a routine mesh on flat zones (vestibular face of incisive) and a more dense mesh for high curvatures (incisal edge or gingival sulcus, for example; Figures  5(d ) and 5(e)). Indeed, a large number of triangles are sufficient to follow precisely the emergence profile whereas a low number could lead to smoothing of margins (Figures  5(f ) and 5(g)).
and C. albicans. Enterococci may cause a variety of oral infections. Surprisingly, there is little data concerning their oral incidence and prevalence  [60]. In our cohort, 99% of caries-free young adults carried Enterococcus spp that is higher than previously described by Sedgley and colleagues (20%)  [61]. Komiyama and colleagues  [62]  detected Enterococci in the saliva of 14% of young adults whose periodontal and cariogenic status were not determined. Two main reasons could explain this difference. First, our study analyzed the interdental biofilm, while all other studies focused on the saliva, the lingual biofilm, or the supragingival biofilm. Second, we quantified bacterial amounts by real-time PCR and not by bacterial culture. The quantity of Enterococcus spp. is lower in 30 to 35-year-old subjects than in 20 to 30-year-old subjects.
High sugar consumption has long been linked to dental caries  [30]. A quarter of USA Midwestern university students reported eating sugary foods (including foods and drinks, such as candies, soft drinks, juices, doughnuts, jellies, etc. ) more than once daily. Among the 89% of students who reported drinking pop, 69% selected regular pop as their favorite as opposed to diet pop  [27]. Smoking habits may also be associated with a higher risk of dental caries  [31]. Self-reported use of tobacco among adolescents was significantly associated with an increased incidence of dental caries over a 3-year period  [32]. This association was also apparent with alcohol  [33] [34] [35]  and drug abuse  [36] [37] [38]. No data are available in France concerning the specific caries risk factors among university students.
Collected data A closed room was equipped with a dentist chair to provide privacy for study participants. Appropriate dental lighting was a part of the unit. Disposable periodontal examination kits with a probe, mirror and cotton rolls were used, as were masks and disposable gloves. Data entry was anonymous, and no information in the electronic file could be used to identify the source person. The students were interviewed using standardized modalities and a questionnaire with closed questions about sociodemographic data that included the following: areas of study (Health and Sport, Science and Technology, Law and Economics, Management and Business, or Letters and Arts and Humanities), age, gender, social security coverage (French social security system, health mutual or supplementary universal health-care coverage, or other systems), father's and mother's professions (management profession, employees, or without employment), accommodation status (living with their parents or away from the parental home for at least part of the time), part-time jobs, dietrelated behaviors (number of main daily meals; number of snacks between meals; daily consumption of sugary drinks, candies, sugar-free chewing gums; the drink consumed when thirsty, i.
Image treatment and analysis Image treatment and analysis were performed with ImageJ software (Rasband, W. S. , ImageJ, U. S. National Institutes of Health, http://imagej. nih. gov/ij/). 2. 5. 1. 3D visualization and morphological analysis 2. 5. 1. 1. 3D vizualization. The stack of images obtained by CLSM were used to visualize the microstructure of the porous media. 3D representations were obtained using ImageJ (Volume Viewer by Barthel K. U. and 3D viewer by Schmid et al. [29] ) after binarization. 2. 5. 1. 2. Tubule shape characterization. The image treatment and analysis protocol used in this study is described in Fig. 1. The selected tubule is isolated using the ''crop" and ''erosion dilation" tools of Image J and the ''Particle Analyser" of the Bone J plugin  [30]. The shapes of the tubules in the area chosen were analyzed using Image J and the ''Particle Analyser" of the Bone J plugin which allows particle counting and characterization.
The principal direction of inertia of the selected tubule was deduced and a projection along this axis was performed using the ''Z-project" tool. 2. 5. 1. 3. Y-shaped branches. Five Y-shaped branches were isolated and analyzed to derive the skeleton. The treatment consisted in thresholding, filtering and removing numerical artefacts manually. The skeleton was obtained using the Matlab (MathWorks) ''Skeleton3D" and ''Skel2Graph3D" functions proposed by Kerschnitzki et al. [31]  and then analyzed using the ImageJ function ''Analyse Skeleton (2D/3D)". 2. 5. 2. Pore size distribution and porosity 2. 5. 2. 1. SEM images analysis. The protocol used to analyze the SEM images is described in Fig. 2. The original SEM images were filtered using a median filter to reduce noise and binarized by thresholding (preserving the tubule's shape as close as possible as the observed one).
Acknowledgments This work benefited from the financial support of the  LabeX LaSIPS  ( ANR-10-LABX-0040-LaSIPS ) managed by the  French National Research Agency  under the '' Investissements d'avenir" program  ( n°ANR-11-IDEX-0003-02 ) and the  ANR-11-LABX-0030 (LabEx Tec 21 ).
reliability of us-sG core items on static us images Twelve experts performed a web-based standardised form (table  1 ) to evaluate 60 static images (30 parotid glands (PGs) and 30 submandibular glands (SMGs)) (Philips iU22, 12. 5 MHz linear array transducer; Philips Healthcare, Amsterdam, The Netherlands). The set of B-mode images (with the same setting) of the major SGs, from Brest centre data bank, of patients with pSS and normal individuals was chosen in order to have both images of normal (healthy individuals) and abnormal SG parenchymal echostructure (pSS patients) and were sent to other centres. Each expert evaluated the items selected.
Acknowledgements We thank the  French Society of Rheumatology (SFR)  for funding this study. We also thank the  French Sjögren 's patients who participated in the study. We are grateful to  Florence Morvan ,  Céline Dolou  and  Floriane Masson  (DRCI). We also thank the staff for their time and commitment to this work. Contributors All authors have equally contributed to all steps of this study.
4 AE 0. 1 mm to 4. 2 AE 0. 3 mm), and the grain size (1. 2 AE 0. 3 mm to 3. 4 AE 0. 3 mm; Fig. 1 ; Supplementary Data 1), whereas the macroporosity was kept in a narrow range of 75 to 84%. These two in vivo studies provide an excellent basis to investigate the effect of micropore size and microporosity on the bone healing process, and in particular to determine the amount and location of MTs found within the micropores. For that purpose, histological sections/blocks of the two studies were analyzed by light microscopy, white light interferometry, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), Fourier-transform infrared spectroscopy (FTIR), instrumented indentation, and nano-computed tomography (nCT). Histomorphometrical results were assessed using an 'effective implantation time' (EIT), which allowed combining the results of the two studies.
The same procedure was adopted with scanning electron microscopy (SE and BSE mode; EVO MA 25, Carl-Zeiss SMT AG, Oberkochen, Germany) after coating the histological sections with a carbon layer (SCD 050, BAL-TEC, Balzers, FL). Selected sections were polished with a 0. 5 mm diamond paste to remove the carbon coating and the TB stain. These sections were then imaged by differential interference contrast light microscopy (Leica DMI5000 M, Leica Instruments GmbH, Germany). Some sections were analyzed by FTIR in ATR mode (LUMOS FTIR, Bruker Optics Inc. , Ettlingen, Germany; Supplementary Data 2), stained with methylene blue/basic fuchsin instead of TB to better visualize cells in the MT, and/or coated with carbon to take new SEM images. Ca, P, and C elemental maps were collected with EDX (Oxford EDX X-Max, Oxford, UK).
Selected histological blocks were polished with a 0. 5 mm diamond paste, coated with a thin carbon layer, and observed by SEM-SE and SEM-BSE. The topography of two selected samples was investigated using white light interferometry (S neox from Sensofar, Spain, SensoSCAN software, Version 6. 1. 3, Sensofar, Spain) using the 20Â and 50Â objectives. Stitching was performed to enlarge the field of view. Data processing was performed with the software SensoMAP Premium (Version 7. 3. 7690, Digital Surf, France). A MT-rich Ø 0. 5 mm Â L 2 mm cylinder was milled from size D block (6 weeks implantation) and evaluated with phasecontrast nano computed tomography (nanoCT) on beamline ID16B (ESRF, Grenoble, France)  [22]  following the protocol described elsewhere (Supplementary Data 3)  [23]. The energy of the beam was set to 29.
6 keV to allow for both sufficient transmission and good contrast. A LSO:Tb 17 mm thick scintillator was used to convert the X-rays into visible light which was then recorded using a PCO camera (PCO. edge 5. 5, Kelheim, Germany). The sample was first scanned at a voxel size of 240 nm to obtain an overview image of the sample, using only 1251 projections of 0. 25 s each to keep the imaging dose low  [24]. This image was used to select a region of interest in the sample, which was then scanned with a higher resolution. The field of view corresponding to the chosen settings was approximately 100 mm in diameter and height. The histological block used for the nanoCT measurement was mechanically tested by instrumented indentation in ambient temperature using a G200 apparatus (Agilent, USA; Supplementary Data 4) to determine Young's modulus and hardness.
Characterization of TB+ tissues in the ceramic micropores The TB+ tissues found in Ø 2. 6-2. 9 mm micropores of scaffolds A-D (Fig. 1 ; Supplementary Data 1) were characterized by various means with the general aim to detect the main components of bone including calcium-phosphate (CaP) minerals, collagen, and interconnected cells. CaP minerals were identified by a combination of SEM-BSE images and EDX measurements. SEM-BSE images of the histological sections revealed that the radio-density of the TB+ stained trabecula-like structures within the ceramic micropores was higher than that of adjacent unstained ceramic micropore regions (Fig. 3b ), due to the presence of a radiodense tissue formed within the ceramic micropores (Fig. 3g ). The EDX analysis demonstrated that this radiodense tissue consisted of phosphorus (P, Fig.
MT role in the bone healing process A crucial question, for practical purposes, is the MT role of in the bone healing process. To address it, all histological sections stained with TB were analyzed for the thickness and volume fraction of bone, MT, and ceramic on concentric circles of 1-7 mm in diameter. No significant difference in bone and ceramic content was measured between groups A to D at 6 and 12 weeks of implantation (Supplementary Data 12), which agrees with past analysis  [17]. Interestingly, after pooling the results of groups A to D at 6-week implantation, the TB+ volume fraction was found to decrease linearly (r 2 = 0. 99, Supplementary Data 12) while moving into the scaffold, with the intercept with the diameter axis at 0. 56 mm. In fact, the healing process appeared to be summarized chronologically when moving from the inner part of the defect outwards: more intact ceramic, thinner trabeculae, and more woven bone in the inner parts; more ceramic resorption, thicker trabeculae, and more lamellar bone in the outer parts of the defect.
Postulating that MT presence should have important temporal biomechanical effects, instrumented indentation tests were performed on a histological section (size D, 6 weeks of implantation). The results showed that MT zones (Young's modulus E = 31 AE 9 GPa) were much stiffer than MT-free PMMA-filled ceramic zones (E = 16 AE 5 GPa; p < 0. 001; Supplementary Data 4, 5). In comparison, the Young's moduli for both old bone and new bone were measured to be E = 11 AE 1 and E = 6 AE 2 GPa, respectively. Evaluation of surface irregularities using differential interference contrast light microscopy (Fig. 3d ) suggested that MT zones were more abrasion-resistant than ceramic or PMMA. This result was indeed confirmed by white light interferometry (Supplementary  Data 11). In the current study, b-TCP cell-mediated resorption (Supplementary Data 8) occurred faster than that of DCP.
Acknowledgements The authors would like to thank the following:  N. Biedert  and  C. Delfini  for light microscopy images;  C. May  for statistics;  S. Tadier  for SEM images;  A. Lau ,  O. Loeffel , and  F. Bigolin  for their technical support for light microscopy, electron microscopy, polishing, and EDX measurements;  J. Villanova  and  J. -P. Suuronen  for their support during acquisition of the nanoCT data; O. Guiraud for 3D visualization;  D. Bosshardt ,  J. Davies ,  R. Egli ,  M. -P. Ginebra ,  P. Habibovic ,  W. Hofstetter , and  A. Wagoner Johnson  for fruitful discussions and  Mathys Ltd  ( Bettlach, Switzerland ) for their financial support.
X-ray microtomography (µCT) analysis Femurs were scanned using a SkyScan 1174 tomograph (SkyScan, Belgium) with the following parameter setup: source energy at 50 keV, intensity of 800 µA and isotropic voxel resolution of 15 µm with a 0. 5 mm depth aluminum filter. After 3D reconstructions with Nrecon V1. 4 software (SkyScan, Belgium), bone structure was analyzed using CTan software (SkyScan, Belgium). The newly mineralized bone volume fraction in the defect cavity was defined as the BV/TV parameter (Bone Volume/Tissue Volume ratio). For C35 ceramics, global segmentation was determined in order to separate newly mineralized elements from C35 ceramics background using the CTan software histogram tool to threshold gray level values.
To analyze ALP and TRAP activities and blood vessel density, 5 consecutive sections were randomly chosen. From each section, neovascularization and ALP positive osteoblasts or TRAP positive osteoclasts were estimated in the randomly chosen field of 500 µm 2 on a semiquantitative scale: (0) None; (1) Low; (2) High by 2 blinded pathologists. For some samples at day 30, number of vessels was manually counted in the defect area. Detection of Quantum Dot ® -labeled MSCs and MAR measurements on bone sections were achieved using a fluorescence microscope (Olympus IX71, Melville, NY) connected to a spot Sony SE digital camera. For MAR measurements (µm/day), the distance between the two fluorescent calcein lines (corresponding to the position of the mineralization front by the time of the calcein injections) was measured using a semi-automatic image analyzer software (Histolab, Microvision, France).
Acknowledgements The authors wish to thank  Catherine André ,  Xavier Butigieg  and  Sylvie Renault  for their valuable technical assistance in our laboratory. The authors are also grateful to Dr. Charles Chapus  for his statistical expertise. This work was supported by a grant from  DGA  ( Délégation Générale pour l'Armement ; Grant  PDH-1-SMO-0206 ) of the  French Ministry of Defense.
In this study, we focused on the skin microbiome of only women to exclude considerable differences in the ecosystem of skin microbiomes between both genders  23. Skin bacterial diversity and composition were characterized and compared between two different age groups: younger (23-37 y) and older (60-67 y) Japanese women. Samples from four skin sites, representative of dry (volar forearm) and sebaceous (scalp, forehead, cheek) skin areas were analyzed. The bacterial communities were evaluated based on the 16S rRNA gene sequence data obtained by high-throughput pyrosequencing.
Differences in taxonomic profiles of skin microbiomes between the age groups. The changes in taxonomic profiles in the age-related diversification of the four skin microbiomes were next investigated. The OTUs were assigned to taxonomies according to the phylotypes in the microbial 16S rRNA gene databases. The phylum-level assignment showed that four major phyla, Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria dominated the four skin microbiomes. Among them, Actinobacteria was most predominant, accounting for the average abundance of 61. 8%, 40. 3%, 67. 6%, and 83. 3% in the cheek, forearm, forehead, and scalp microbiomes of the all subjects, respectively (Supplementary Fig. S4a ). Comparing the abundance of the four phyla between the two age groups revealed that Actinobacteria showed a significantly lower abundance in the cheek, forearm and forehead microbiomes in the older than the younger group with a concurrent increase in the other three phyla (Supplementary Figs  S4a  and b ).
Regarding the skin sites, 19, 18, 22, and 13 species were significantly changed in the cheek, forearm, forehead, and scalp microbiomes, respectively. Of them, 15 species showed a skin site-specific change; three in the cheek, five in the forearm, four in the forehead, and three in the scalp microbiome. The other 23 species were altered in more than two different skin sites and only Klebsiella and Prevotella were enriched in all of the skin sites of the older group (Fig. 4 ). To determine the skin specificity of these 38 species, the similarity search was performed against the CORE database compiling the species detected in the oral cavity  26. The results indicated that 16S sequences of 30 species had high similarities of ≥97% with those of the species in the CORE database. Of them, we considered 16 species to be normal oral bacteria, which hit to sequences of ≥3 different CORE IDs (Supplementary Table  S4 ).
Hypervariable regions (V1-V2) of 16S rRNA gene were PCR-amplified, and multiplexed amplicon pyrosequencing was carried out using 454 GS FLX Titanium or 454 GS JUNIOR (Roche Applied Science) as previously described  46. The reads obtained were assigned to samples on the basis of their barcode sequence. Reads with an average quality value <25 and inexact matches to both universal primer were filtered off. For chimera checking and taxonomy assignment of the 16S reads, we used three publically available databases: Ribosomal Database Project (RDP) v. 10. 27, CORE (http://microbiome. osu. edu/), and a reference genome sequence database obtained from the NCBI FTP site (ftp://ftp. ncbi. nih. gov/genbank/, December 2011). Reads having BLAST match lengths <90% with the representative sequence in the three databases were considered as chimeras and removed.