dataesr/scientific-paragraphs-categorization huggingface dataset:
Operational taxonomic unit clustering and taxonomic assignment. From the filter-passed reads, 2,500 high-quality reads/sample were randomly chosen. The total reads were then sorted according to the average quality value  47  , and grouped into operational taxonomic units (OTUs) using UCLUST (http://www. drive5. com/) with a sequence identity threshold of 96%. The representative sequences of the generated OTUs were subjected to homology search against the databases mentioned above using the GLSEARCH program for taxonomic assignments. For assignment at the phylum, genus and species levels, sequence similarity thresholds of 70%, 94% and 96% were applied, respectively. The ratio of the OTUs accurately assigned to particular taxa in the databases was 100% at the phylum level, 61. 3% at the genus level, and 46.
Statistical analysis. Statistical significance was determined using one-way Anova for multiple comparisons, the Mann-Whitney t-test, the Friedman test, and the Chi-Square test, as appropriate; differences P < 0. 05 were noted as significant. All analysis was performed using Graph Pad Prism software. Permutational Multivariate Analysis of Variance (PERMANOVA)  48  was applied to verify differences based on subject, age (younger vs older) and body site (cheek vs forehead vs scalp vs forearm) using the function "adonis" Vegan package (v 2. 2-1) in R software program. PERMANOVA global R 2 value ranges from 1 to -1 (R ~ 0 indicates the same level of variation within and between groups). Permutation test for homogeneity of multivariate dispersion were performed using the function "betadisper" Vegan package.
Acknowledgements T. Hanaya ,  S. Yamamoto ,  D. Velleman , and  F. Flament  conducted instrumental analyses of subjects' skins. This work was in part supported by a grant from  L'Oréal  to N. S. , C. C. , P. B. and  L. B. (L'Oréal Research and Innovation) , the global  COE project of 'Genome Information Big Bang'  from the  Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan  to M. H. , and a grant from the  University of Tokyo.
[25]. The texture of Zn:HAp coatings deposited on pure Si and Ti substrate was obtained by performing a 3D surface plot of their SEM images using Image J software. The surface morphologies of the Zn:HAp coatings deposited on a pure Si and Ti substrate were compared by SEM analysis. A difference in the morphology of the Zn:HAp_Si and Zn:HAp_Ti coatings can be noted, although a dense layer with a homogeneous structure was obtained in both cases. Zn:HAp layer covering the pure Si substrate is uniform while the Zn:HAp layer covering the Ti substrate shows a rougher surface. Bright regions corresponding to the surface of Si or Ti were not observed. It is well known as the distribution widespread of infectious diseases, due to the emergence and development continue of antifungal treatments resistant yeasts, represents a big challenge for human health worldwide.
This behavior might suggest that HAp_Ti and HAp_Si layers had a temporary and reversible effect against the proliferation of C. albicans cells. The number of surviving cells on Ti and Si substrate and on the Zn:HAp_Ti and Zn:HAp_Si layers decreased when the samples were exposed to daylight (Figure  6G-L ) and UV light (Figure  6M-S ). In comparison, fewer surviving cells of C. albicans were found on Zn:HAp_Ti (Figure  6I, O ) and Zn:HAp_Si (Figure  6L ,S) samples. On the other hand, for Zn:HAp_Ti and Zn:HAp_Si samples, it can be seen that the number of surviving cells decreased when the samples were exposed to UV light (Figure  6O, S ). The 3D composite images analyzed using Image J software  [33]  presented in Figure  7  displays the structure and spatial distribution of C. albicans surviving cells on different surfaces (HAp_Ti, Zn:HAp_Ti, HAp_Si, Zn:HAp_Si, Ti and Si) kept in the dark and after exposure to day light and UV light.
The images exhibited in Figure  7  reveal the spatial distribution of C. albicans surviving cells (red color) along horizontal (coverage) and the vertical (thickness) distributions on Ti, PDMS, HAp-PDMS, Zn:HAp-PDMS and Ag:HAp-PDMS surfaces. The CLSM images presented in Figure  7  demonstrated that the survival of C. albicans cells have been significantly reduced in the presence of Zn:HAp_Ti layers (Figure  7I ,O) depending on the light. A decrease of C. albicans surviving cells depending on the light exposure was also observed in the presence of Zn:HAp_Si layers (Figure  7L, S ). The 3D composite images analyzed using Image J software  [33]  presented in Figure  7  displays the structure and spatial distribution of C. albicans surviving cells on different surfaces (HAp_Ti, Zn:HAp_Ti, HAp_Si, Zn:HAp_Si, Ti and Si) kept in the dark and after exposure to day light and UV light.
Acknowledgments: This work was supported by projects  PN II 259/2014 ,  PN II 131/2014  and  PN16480103. Author Contributions: D. P. conceived and designed the experiments; N. B. performed the zeta potential and DLS experiments; A. M. P. performed the in vitro experiments; D. P. , N. B. , S. L. I. and A. M. P. analyzed the data; D. P. wrote the paper; all authors have read the final version of the manuscript.
(f) This procedure does not require purification and destabilization of the methacrylates used for infiltration and polymerisation  (17) (18) (19). The morphometric study of the bone was carried out by means of a Zeis Axioscop II microscope (Axioscop 40, Goettingen, Germany) using 4×, 10×, and 20× lenses. Pictures were taken with a digital signal processor (DSP) 3CCD camera (Sony, Tokyo, Japan), and Intelicam 8. 0 software (Smart Matrox Imaging, Montreal, Canada). To quantify the newly regenerated tissue and to compare it with the original bone tissue, an assessment from distal (external) to proximal (internal) was made using ROI (region of interest) colour analysis with specific software (Fiji Is Just ImageJ, Tokyo, Japan). The following parameters were assessed by a different, blinded operator: percentage of new bone formation, length of mineralised bone formed daily in the grown defects (mm/day), concentration of osteoclasts (number of osteoclasts/mm 2 ), and intensity of bone ostheosynthetic activity.
The first worldwide application of E-Oral Health technology was in fact designed to extend dental diagnosis and treatment in rural areas. The project was conducted in 1994 by the US military  [16, 18]. Today, the use of E-Oral Health technology has been reported in dental education, preventive dentistry and oral medicine, among many other areas  [19, 20]. The most common forms of telecommunication involve real-time consultations, store-and-forward consultations or a combination of both  [15, 18, 20]. Our scoping searches of the most relevant databases showed that the original research on this topic is observational in nature and lacks the use of robust qualitative research methodology or mixed-methods studies. Furthermore, no systematic reviews have been carried out on the effect of E-Oral Health technology on patient satisfaction in rural and remote settings  [18, [21] [22] [23] [24] [25].
Information sources An electronic literature search will be conducted in the following databases: Cochrane Central Register of Controlled Trials (The Cochrane Library, current issue), MEDLINE (OVID interface, 1946 onwards), EMBASE (OVID interface, 1974 onwards) and Global Health (OVID interface, 1973 onwards). The electronic literature search will be complemented by hand searching the list of references in the identified publications or relevant reviews. NICE Evidence and TRIP database will be searched for gray literature using subject keywords. Members of the E-Oral Health Network of the International Association of Dental Research will be contacted by email to identify any unpublished studies. Ongoing studies will not be considered in the review.
Search strategy A draft version of literature search strategies to be used in this work has been developed with the help of an expert librarian at Université de Montréal (PD) and a researcher with experience in the conduct of systematic reviews (EE) using medical subject headings (MeSH), EMTREEs and text words related to the field of the study. A draft of the MEDLINE search strategy can be found in Additional file 2. Once the MEDLINE search strategy is finalized, it will be adapted to the other databases using the proper syntax, subject headings and controlled vocabulary considering maximized sensitivity of the search. There will be no language restrictions in the search strategy to maximize the sensitivity and to identify the number of publications in other languages and to verify the existing risk of bias.
Data management, selection and date collection process The identified articles from search results will be transferred to EndNote software. A screening tool will be developed according to inclusion and exclusion areas. The process of data selection and collection will be pilot tested in 10% of randomly selected included articles. Cohen's kappa test will be used to assess the reviewers' agreement on study eligibility  [31]. Two independent reviewers will screen all retrieved titles and abstracts using the inclusion criteria. In case of incomplete information provided by the title and abstract, the full text will be used to determine a study's eligibility to be included for the full analysis. In order to avoid overlapping data, publications related to the same study will be verified, and the most relevant report (according to study outcomes) will be selected for full review.
Data items Two reviewers will independently extract the data from the full text of the included studies by adapting the review form from Effective Practice and Organization of Care (EPOC) Resources for review authors  [32] , as a data extraction method (Additional file 3). A meeting will be held for the data extraction and a pilot test will be conducted to get feedback from the reviewers and to ensure consistency across them. The extraction form will be modified if necessary to confirm its completeness. The extracted information will include general information about publication such as sources of funding and possible conflicts of interest, authors, country, year of study publication, aim of the study, study design, sample size, participant characteristics (age, gender), target population, intervention description, type of E-Oral Health technology, conventional comparator, the outcome of interest, other outcomes, measurement instruments, the length of follow-up and the main results.
Data synthesis The descriptive synthesis will be conducted in line with the guidance from the Centre for Reviews and Dissemination  [36]. Text and tables will summarize and explain the characteristics of the findings in the included studies. Where possible, the mean differences with 95% confidence interval (CI) will be calculated for continuous outcomes (patient satisfaction). Patients' satisfaction change scores will be computed. Effect sizes (ES) will be calculated to compare the results across studies. Effects will be expressed as standard mean differences (SMD). For dichotomous outcomes (the presence of diagnostic errors, access to care), odds ratio with 95% CI will be reported. Since access to care is a composite outcome, the defined items will be combined before dichotomization. The summary likelihood ratios will be calculated.
The Cochrane Q test and I 2 statistic will be used to test heterogeneity  [40, 41]. Subgroup analyses (patient characteristics, type of e-tool, degree of rurality) will be conducted to identify the sources of heterogeneity across the studies. If the selected publications include qualitative data, a thematic analysis approach  [23, 42]  will be included in the data synthesis. Furthermore, if the studies provided insufficient quantitative data (missing data, unpublished outcome), we will contact authors for additional information. If the missing data could not be rectified by author contact via email, we will use narrative approaches to describe the major findings.
Amelogenesis imperfecta (AI) designates a group of genetic diseases characterized by a large range of enamel disorders causing important social and health problems. These defects can result from mutations in enamel matrix proteins or protease encoding genes. A range of mutations in the enamel cleavage enzyme matrix metalloproteinase-20 gene (MMP20) produce enamel defects of varying severity. To address how various alterations produce a range of AI phenotypes, we performed a targeted analysis to find MMP20 mutations in French patients diagnosed with non-syndromic AI. Genomic DNA was isolated from saliva and MMP20 exons and exon-intron boundaries sequenced. We identified several homozygous or heterozygous mutations, putatively involved in the AI phenotypes. To validate missense mutations and predict sensitive positions in the MMP20 sequence, we evolutionarily compared 75 sequences extracted from the public databases using the Datamonkey webserver.
Data Set Mammalian MMP20 sequences were extracted from public databases, NCBI [http://www. ncbi. nlm. nih. gov] and Ensembl [http://www. ensembl. org]. A total of 75 sequences representative of the main mammalian lineages (55 families distributed within 19 orders) were retained for our analyses (Supplementary Table  1 ). Identical sequences (such as species from the same genus) were not included in our dataset. MMP20 being enamel specific the sequences of species lacking either teeth or enamel (i. e. , Xenarthra, Pholidota, Mysticeta, and Tubulidentata) were not included in our study because they display various mutations. Among the selected MMP20 sequences only five were published in GenBank. Of the 70 other sequences, 65 were computer-predicted from sequenced genomes and six were obtained using Basic Local Alignment Search Tool (BLAST) of the whole genome shotgun (WGS) repository sequences in NCBI (Supplementary Table  1 ).
The coding sequences were traduced into amino acid sequences and unpublished sequences were validated through alignment to published ones using Se-Al v. 2. 0a11 software [http://tree. bio. ed. ac. uk/software/seal]. The intron-exon boundaries were also carefully checked. The dataset of the 75 MMP20 sequences is available in Supplementary Data 1. Our final alignment consisted of 483 positions, and no insertions were needed (Supplementary Figure  1 ). A few residues were missing in some, uncompletely sequenced genomic DNA (i. e. , 726 nucleotides, nt, representing <0. 7% of the data), and the corresponding positions were treated as "unknown data". In addition, we aligned 21 nucleotides of the intronic region located on both sides of the exons from 12 MMP20 sequences representative of the main mammalian lineages, known to be important for correct intron splicing (Supplementary Table  2 ).
Patients The patients and their families were selected from the pool of patients participating in the French Ministry of Health National Program for Clinical Research, PHRC 2008 HUS (Strasbourg University Hospital) N • 4266, Amelogenesis Imperfecta, AI (for further details see  Gasse et al. , 2013)  and in the INTERREG IV Offensive Sciences A27 "Orodental manifestation of rare diseases" EU funded (ERDF) project. These patients came to The Reference Centre for Orodental Manifestations of Rare Diseases (CRMR Strasbourg, France) or other affiliated Competence Centres (CCMR) for clinical diagnosis and management. Dentists specializing in rare diseases diagnosed amelogenesis imperfecta. The oral phenotypes were documented using the D[4]/phenodent registry, a Diagnosing Dental Defects Database [see www.
phenodent. org, to access assessment form], which is approved by CNIL (French National commission for informatics and liberty, number 908416). This clinical study is registered at https://clinicaltrials. gov: NCT01746121 and NCT02397824, and with the MESR (French Ministry of Higher Education and Research) Bioethics Commission as a biological collection "Orodental Manifestations of Rare Diseases" DC-2012-1677 within DC-2012-1002 and was acknowledged by the CPP (person protection committee) Est IV on the 11 Dec 2012. Affected and unaffected family members gave informed written consents both for the D4/phenodent registry and for genetic analyses performed on the salivary samples included in the biological collection. In this study, we selected patients from unrelated families suffering from non-syndromic AI, some of them displaying clinical diagnoses matching possible MMP20 mutations.
Analyses Patients spit into an Oragene kit (Oragene DNA R , DNA Genotek, Canada) and genomic DNA was then isolated from saliva according to the manufacturer's protocol. We used previously defined primers (see  Gasse et al. , 2013). Mutational analysis was performed for the 10 exons of MMP20 including exon-intron boundaries. PCR products were sent to GATC Biotech for purification and sequencing in both directions in order to minimize sequencing artifacts. The sequences were aligned manually with the reference human MMP20 sequence NG_012151. 1 using Se-Al v2. 0a11 software. When necessary the sequences were analyzed for splicing site prediction using the NetGene2 server (http://www. cbs. dtu. dk/services/NetGene2/) and MaxEntScan (http://genes. mit. edu/ burgelab/maxent/Xmaxentscan_scoreseq.
ACKNOWLEDGMENTS We would like to thank the family members for their invaluable contribution and generous help throughout the investigations. We are grateful to colleagues and general dental practitioners ( Drs J. M. Schweitzer ,  A. Froehly ,  F. Charton ,  P. Basson ) for their collaboration with the Strasbourg Reference Centre for orodental manifestations of rare diseases. This work was supported by grants from the  French Ministry of Health (National Program for Clinical Research ,  PHRC 2008 N • 4266 Amelogenesis imperfecta ), the  EU-funded project (ERDF)   A27  " Oro-dental manifestations of rare diseases , " supported by the  RMT-TMO Offensive Sciences initiative, INTERREG IV Upper Rhine program  and the  INTERREG V RARENET program , the grant  ANR-10-LABX-0030-INRT , a  French State  fund managed by the  Agence Nationale de la Recherche  under the frame programme  Investissements d'Avenir labeled   ANR-10-IDEX-0002-02.
Micro-CT imaging The heads of five adult male Ltbp3-/-mutant mice and of five corresponding age/sex-matched wild-type (WT) littermates were examined at 3. 5 months of age. To investigate malformations at slightly later stages, two male 5. 5month-old Ltbp3-/-mutants and two WT matching controls were also examined. All samples were scanned using the Quantum FX micro-CT pre-clinical in vivo imaging system (Caliper Life Sciences, Hopkinton, MA, USA), which operates at an energy of 80 kV and current intensity of 160 lA. We found no obvious skull morphological changes with aging. Micro-CT data acquisitions (with resolution at 80, 40, 20, and 10 lm pixel sizes for skulls, mandibles, incisors, and molars, respectively) were reconstructed using Analyze11. 0 (Biomedical Imaging Resource, Mayo Clinic, Rochester, MN, USA).
Acknowledgements -We would like to thank  Brigitte Schuhbaur  and  Val erie Fraulob  for their help in histological procedures,  Isabelle Goncalves Da Cruz  for her help in micro-CT training, and  Arnaud Duchon  for his expertise in applying 3D landmark coordinates analysis. This work was supported by a training grant from the  Centre Europ een de Recherche en Biologie  et en M edecine (CERBM GIE), institutional funds from the  CNRS, Inserm , and  University of Strasbourg , grants from the  French Ministry of Health (National Program for Clinical Research , PHRC 2005 # 4266  'Amelogenesis imperfecta',  HUS ,  API 2009-2012  'Development of the oral cavity: from gene to clinical phenotype in Human'), and  IFRO (Institut Franc ßais pour la Recherche Odontologique)  to  Agn es Bloch-Zupan , grant  CA034282  from the  National Institutes of Health  to  Daniel B.
Contact angle measurement Distilled water and diiodo-methane were used as test fluids for contact angle measurements on the surface of titanium discs and 3-dimensional screw dental implants using a drop shape analyzer (Krűss, DSA25). The measurement was performed on surfaces that had been produced 3 months before the experiment and were stored in non-sealing containers under ambient atmosphere. The surfaces were not subjected to UV irradiation or any other manipulation before contact angle measurement in order to allow the investigation the real performance of the surfaces as they were on off-the-shelf products. The measurement started after 3 sec of dropping, the drop volume was 0. 3 ± 0. 05μl. Conic section method was used to determine the contact angles of the drops, while surface free energy, polar part and disperse part were calculated (ADVANCED Software, Krűss).
X-ray photoelectron spectroscopy Surface chemical analysis of the surface types was performed on discs by X-ray photoelectron spectroscopy (XPS) with an Amicus spectrometer (Kratos Analytical, UK) using non-monochromatic Al-Ka X-ray source operated at 240 W with 8 kV. High-resolution spectra were acquired at 75 eV pass energy at an electron take-off angle of 0° between surface normal and the electron-optical axis of the analyzer. Peak positions on the binding energy scale were corrected with respect to the Ti 2p3/2 peak for TiO2 (458. 8 eV). The spectra were fitted with the CasaXPS software (version 2. 2. 67). Quantitative elemental compositions were calculated from peak areas using experimentally determined sensitivity factors tabulated in CasaXPS and the spectrometer transmission function.
present work was funded by the REA in the 7 th Framework Program within the funding scheme of SME Instrument under the scope of the NANOTI Project (FP7-SME-2013-606624) and Hungarian National Research, Development and Innovation Fund VKSZ_14-1-2015-0151. 7. DISCLOSURE Miklós Weszl and Krisztián Tóth László are the shareholders of NANOTI Limited. Nihal Engin Vrana is a full time employee of Protip Medical and holds stock options of Protip Medical. There are pending patent applications that cover the subject matter of the anodic surface treatment of titanium implants (PCT/IB2016/050464) and (P1600046).
A total of 4,394,492 reads were assembled into 21 contigs with an average coverage of 205ϫ. Contig reordering and annotation were performed with Mauve 2. 3. 1 and the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP), respectively  (15, 16). Sequence alignment and comparison were performed with CLC Sequence Viewer 7. 0 and BLAST. Average nucleotide identity (ANI) to the P. acnes reference strain KPA171202 was calculated using Oat 0. 91  (17). The draft genome of strain HB (GenBank accession no. MDGS00000000) contains 2,328 genes, 2,275 coding sequences (CDSs), 45 tRNAs, four rRNAs, and four noncoding RNAs. The GϩC content was 60. 0%, and the ANI value was 99. 1%. Although Propionibacterium species on healthy human skin could be highly diverse  (18, 19) , an increased frequency of IA1/A1 phylotype/SLST has been observed, especially in case of severe acne  (5).
Despite a conserved core genome of 83% for P. acnes  (20) , with more than 100 genome sequences of P. acnes from different clonal complexes or sequence types at that time, genome analysis compared with clinical data can help to better understand how the inflammatory potential of P. acnes sequenced strains may influence the severity of skin lesions (4). P. acnes HB belongs to ST18, phylotype IA1, and SLST A1. Sequence analysis revealed that the 23S rRNA gene is mutated at position 2059 (according to the Escherichia coli numbering), thus leading to a high-level resistance to erythromycin. This draft genome will be also used for studying the impact of different virulence factors, especially lipase or hyaluronate lyase on skin innate immunity  (21). Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number MDGS00000000.