dataesr/scientific-paragraphs-categorization huggingface dataset:
These PCR primers were manufactured by Metabion International AG (Planegg, Germany). The assays were performed on the Rotor-Gene R Q thermal cycling system (Qiagen, Hilden, Germany) with the following program: 95 • C for 30 s, followed by 40 cycles of 10 s at 95 • C, 10 s at the appropriate annealing temperature (Table  1 ), and 35 s at 72 • C. For the total bacterial load and that of all species, a final melting curve analysis (70-95 • C in 1 • C steps at 5 s increments) was performed. Fluorescence signals were measured every cycle at the end of the extension step and continuously during the melting curve analysis. The resulting data were analyzed using Rotor-Gene Q Series software (Qiagen, Hilden, Germany). Serial dilutions of a bacterial standard DNA provided by Institut Clinident SAS (Aix en Provence, France) were used in each reaction as external standards for the absolute quantification of the targeted bacterial pathogens.
This new sample collection method is based on two basic principles: (i) the calibrated interdental brush must penetrate the space in an unconstrained manner and (ii) it must completely fill the interdental space with necessary mechanical contact with dental hard surfaces and in the gingival sulcus, as described (Supplementary Figure  S2 ). Our results showed that the interdental space is an area in which biofilm accumulates. In periodontally healthy young adults aged from 20 to 35 years, it contains approximately 10 10 bacteria, whereas in other studies, such as the study by  Field et al. (2012) , the interdental space has a total count of 10 7. 56 bacteria for supragingival biofilm in periodontally healthy adults aged from 35 to 56 years. To collect the best data on the composition of interdental biofilm, real-time PCR was used to study the periodontal pathogens expressed in the interdental biofilm of periodontally healthy sites.
Sharing tools with colleagues Orthodontists may share patient monitoring files in read-only mode with the corresponding dental surgeons, periodontists, maxillofacial surgeons, or other professional correspondents. from the dashboard, they simply has to type in the practitioners' email, possibly with an associated message. Orthodontic monitoring paves the way to a connected orthodontics, in line with the progress of modern orthodontic practices which include the following: Orthodontic monitoring controls treatments so as to optimize their treatment progress. This is done by empowering patients and by tracking the effects and undesirable incidents. It is a remarkable efficiency factor. The accumulation of treatment data at a high frequency creates, for the first time, a huge database of dental movements that "threatens" to challenge our daily practices.
A large family from a small village in Madagascar, Antanetilava, is known to present with colored teeth. Through previous collaboration and 4 successive visits in 1994,  2004, 2005, and 2012, we provided dental care to the inhabitants and diagnosed dentinogenesis imperfecta. Recently, using whole exome sequencing we confirmed the clinical diagnosis by identifying a novel single nucleotide deletion in exon 5 of DSPP. This paper underlines the necessity of long run research, the importance of international and interpersonal collaborations as well as the major contribution of next generation sequencing tools in the genetic diagnosis of rare oro-dental anomalies. This study is registered in ClinicalTrials (https://clinicaltrials. gov) under the number NCT02397824.
Progressive pulp chamber obliterations as well as absent root canals were noticed, confirming the diagnosis. A first pedigree was drawn and demonstrated that the genetic disease affected 5 generations and 46. 7% of the family members. After a 2004 preparatory mission, JM returned to Mahajanga and visited Antanetilava in 2005 after a difficult journey consisting of 6 h of bus, 8 h of bush taxi, 1 dugout canoe river crossing and a further hour of walking. Twenty seven participants (25 affected) and 2 nonaffected family members were examined during this 2005 visit. Affected and unaffected family members gave written informed consent and, the study was approved by the village council. The orodental phenotypes were documented using the D[4]/phenodent registry: a Diagnosing Dental Defects Database (see www.
phenodent. org, to access assessment form). This registry allows the standardization of data collection and assists in orodental phenotyping. It also facilitates providing clinical care to patients, a basis for genotype/orodental phenotype correlations, and sharing of data and clinical material between clinicians. D[4]/phenodent registry is approved by CNIL (French National commission for informatics and liberty) under the following number 908416. This clinical study has been registered in Clinical trials (https://clinicaltrials. gov) under the number NCT02397824 and is registered by the French Ministère de l'enseignement supérieur et de la recherche, DGRI/Cellule de bioéthique (bioethics committee) under DC-2012-1677. It was acknowledged by the CPP (person protection committee) Est IV on the 11/12/2012.
The genomic DNA was then sequenced on a sequencer as paired-end 2X75 base pair reads (Illumina HISEQ2000, Illumina, San Diego, USA) resulting in an average coverage of 200X. Image analysis and base calling was performed using Real Time Analysis (RTA) Pipeline version 1. 9 with default parameters (Illumina). The bioinfomatic analysis of sequencing raw data was based on the pipeline provided by the company (CASAVA 1. 8, Illumina and finally detects from 80965 to 82263 variants (SNPs and Indels) per proband (Table  1 ). Annotation, ranking, and filtering of genetic variants were performed with the VaRank program  (Geoffroy et al. , 2015). Very stringent criteria were used for excluding non-pathogenic variants, in particular: (1) variants represented with an allele frequency of more than 1% in dbSNP 138, the EXAC database or the NHLBI Exome Sequencing Project Exome Variant Server (EVS), (2) variants found at the homozygous state or more than once at the heterozygous state in 48 control exomes, (3) variants in the 5 ′ or 3 ′ UTR, (4) variants with intronic locations and no prediction of local splice effect, and (5) synonymous variants without prediction of local splice effect.
FUNDING This work was financed by grants from: the  University of Strasbourg , the  Hôpitaux Universitaires de Strasbourg (API , 2009(API, -2012, "Development of the oral cavity: from gene to clinical phenotype in Human"), 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 , a contribution from  EAPD  and the  INTERREG V RARENET program. This study was also supported by 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. ABZ is a fellow of  University of Strasbourg Institute for Advanced Study (USIAS)  and received USIAS Fellowship.
Study population Included in the study were patients over 20 years old, covered by the French National Health Insurance General Regime, with a diagnosis of epithelial infiltrating HNC reported between 1 January 2010 and 31 December 2010 (N = 342, Table  1 ). Head and neck cancer cases were comprised of the anatomic sites oral cavity, oropharynx, hypopharynx and larynx (International Classification of Diseases for Oncology, 3rd edition -ICD-O 3 codes : C01-C06, C09-C10,C12-C14 and C32). The patients were taken from the cancer registries of the Calvados, Manche and Somme départements and the area around Lille (ZPL). These registries meet highquality criteria : the completeness and data quality are regularly assessed by the Comité National des Registres. Patients with a prior invasive or in situ cancer (excepting basal-cell and squamous-cell skin tumours) were excluded from the study.
Medical data As part of a high resolution study, data were extracted from the medical files and included the patient's date of birth, gender, address, comorbidities, date of diagnosis, the topography and morphology of the cancer according to the ICD-O 3, the clinical stage of the tumour at diagnosis (TNM stage from the International Union Against Cancer's TNM Classification of malignant tumors, 7th edition) and the existence of a synchronous HNC (within a 6-month period). Comorbidities were classified using the Charlson comorbidity index  [25]. Patients were divided into 3 groups for comorbidity: 0 (no comorbidity), 1-2 (moderate comorbidity), 3 and over (severe comorbidity).
Data regarding uptake of healthcare For patients included in the study, data concerning healthcare uptake were supplied by the general regime of the national health insurance (ERASME database -Extraction, Research, Analysis and Medico-Economic monitoring) which covers 88 % of the French population  [26]. Data extracted included dates of consultation and the speciality of the medical practitioner consulted. They also concerned the date of declaration of the referring doctor. Since 2004, each patient has to declare a referring doctor for the reimbursement of care in France. The referring doctor, usually a general practitioner, is the first medical practitioner contacted by the patient. He regulates access to specialist. Patients who had declared a referring doctor in the 2 months preceding diagnosis or after diagnosis were considered to have no referring doctor before diagnosis.
Socio-economic data As there is no individual socio-economic data in the medical records, the socio-economic status of patients was evaluated by measuring that of their place of residence using a social deprivation index. The index used was the EDI  [27]. This is based on both individual data from the European Union Statistics on Income and Living Conditions (EU-SILC) survey and aggregated data (at the IRIS level -Ilots Regroupés pour l'Information Statistique-, which is the smallest geographical unit for which figures are available) from the 2007 French national census carried out by INSEE, the national institute for statistics and economic studies. The IRIS for each patient was determined by the home address at the time the HNC diagnosis was made. In our statistical analyses, we used the national quintile of this index.
Finally, the association between a localised stage at diagnosis and consultation with an ENT specialist does not reflect the practice of early diagnosis of these cancers in the general population. It may be interpreted as the follow-up of various pathologies such as leucoplakia, erythroplakia or dysplastic lesions of the oral cavity and vocal cords, which can subsequently degenerate  [32, 33]. The main strength of this study resides in the crossanalysis of data taken from cancer registries situated in high incidence areas and that from the national health insurance system. The study design was based on the method of 'high-resolution population-based study': data was collected in a precise and rigorous manner from the medical files in order to know all the characteristics of the cancer cases included.
The inclusion of patients from the cancer registries allowed us to overcome the recruitment bias of hospital studies and give information on the totality of cancer cases in a given geographic area. Data taken from the national health insurance enabled us to identify all the health professionals consulted. This cross-analysis of nominative databases between the registries and the national health insurance is unusual because they do not operate on the same time frame. The cross-analysis of databases was carried out in January 2011 with the health insurance data which covered the period from 01. 01. 2009 to 31. 12. 2010 (data regarding utilization of healthcare are conserved for only two years). Thus, it was possible to have one full year of healthcare utilization data prior to diagnosis only for patients diagnosed in 2010.
Nevertheless, habits of medical care uptake concern the same at-risk population. The small number of patients limits the scope of our study. However, the study provides information on how patients recruited from four different cancer registries in a high-incidence area take up medical care. Lastly, data regarding uptake of healthcare are only available on patients registered under the general regime of the national insurance service but this covers 88 % of the French population  [26]. Moreover, the patients unregistered (12 %) are affiliated to other public regimes. They have the same access to medical services and receive the same reimbursement rate than patients recorded to the general regime of the national insurance service. However, we don't know the socio-economic status of this population.
Classification and features Information about the fecal sample collection and conservation are described previously  [1]. Strain G3 T (Table  1 ) was isolated in January 2012 as part of a culturomics study  [1]  by cultivation on Columbia agar supplemented with sheep blood (BioMérieux, Craponne, France). When compared to sequences available in GenBank, the 16S rRNA gene sequence of M. gorillae strain G3 T (GenBank accession number JX650056) exhibited an identity of 98. 2 % with Microbacterium thalassium, the closest validly published Microbacterium species. This value was equal to the percentage of 16S rRNA gene sequence threshold recommended by Meier-Kolthoff et al. for class Actinobacteria to delineate a new species without carrying out DNA-DNA hybridization with maximum error probability of 0.
Extended feature descriptions Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) MS protein analysis was carried out as previously described  [17]  using a Microflex spectrometer (Bruker Daltonics, Leipzig, Germany). Twelve distinct deposits were done for strain G3 T from 12 isolated colonies. Two microliters of matrix solution (saturated solution of alpha-cyano-4-hydroxycinnamic acid) in 50 % acetronitrile and 2. 5 % trifluoroacetic-acid were distributed on each smear and submitted at air drying for five minutes. Then, the spectra from the 12 different colonies were imported into the MALDI BioTyper software (version 2. 0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against 5,626 bacterial spectra including 43 spectra from 33 Microbacterium species, used as reference data, in the BioTyper database.
Briefly, a score ≥ 2 with a species with a validly published name provided allows the identification at the species level, a score ≥ 1. 7 but < 2 allows the identification at the genus level; and a score < 1. 7 does not allow any identification. For strain G3 T , no good score was obtained, suggesting that our isolate was not a member of any known species. We incremented our database with the spectrum from strain G3 T (Additional file 2: Figure  S1 ). The gel view highlighted spectrum differences with other Microbacterium species (Additional file 3: Figure  S2 ). Fig. 1  Phylogenetic tree highlighting the position of Microbacterium gorillae strain G3 T relative to other type strains within the Microbacterium genus using 16S rRNA gene. GenBank accession numbers are indicated in parentheses.
Genome project history According to phenotypic characteristics of this strain and MALDI-TOF result and because of the low16S rRNA similarity to other members of the genus Microbacterium, it is likely that the strain represents a new species and thus it was chosen for genome sequencing. It was the 20 th genome of a Microbacterium species (Genomes Online Database) and the first genome of Microbacterium gorillae sp. nov. A summary of the project information is shown in Table  2. The GenBank accession number is CDAR00000000 and consists of 14 contigs. Table  2  shows the project information and its association with MIGS version 2. 0 compliance  [18].
Normalized libraries were pooled for sequencing on the MiSeq. The pooled single strand library was loaded onto the reagent cartridge and then onto the instrument along with the flow cell. Automated cluster generation and  paired end sequencing with dual index reads were performed in a single 39-h run in 2x250-bp. Total information of 7. 6 Gb was obtained from a 931 K/ mm 2 cluster density with a cluster passing quality control filters of 82. 8 % (17,658,000 clusters). Within this run, the index representation for M. gorillae was determined to 5. 11 %. The 732,922 paired end reads were trimmed and filtered by Trimmomatic tool using the recommended parameters for Illumina sequence data  [19]. Two mate pair libraries were prepared with 1 and 1. 5 μg of genomic DNA using the Nextera mate pair Illumina guide.
65 and 0. 59 nmol/l respectively. The libraries were normalized at 2nM and pooled. After a denaturation step and dilution at 15 pM, the pool of libraries was loaded onto the reagent cartridge and then onto the instrument along with the flow cell. Automated cluster generation and sequencing run were performed in a single 39-h run in a 2x251-bp. The first libray was loaded three times on a flowcell and the second once. Within these runs, the index representation for M. gorillae was determined as an average at 3. 51 %. The 1,881,286 paired reads were filtered according to the read qualities. The global paired end and mate pair libraries lead to 2,614,208 paired reads which were trimmed by Trimmomatic  [19]  then assembled by Spades software using the recommended options "-careful" and "-k 127" to fix the kmer size to 127  [20].
Genome annotation Open Reading Frames (ORFs) were predicted using Prodigal  [21]  with default parameters but the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank database  [22]  and the Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAScanSE tool  [23]  was used to find tRNA genes, whereas ribosomal RNAs were found using RNAmmer  [24]  and BLASTn against the GenBank database. Lipoprotein signal peptides and the number of transmembrane helices were predicted using SignalP  [25]  and TMHMM  [26]  respectively. ORFans were identified if their BLASTP E-value was lower than 1e-03 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we used an E-value of 1e-05.
Such parameter thresholds have already been used in previous works to define ORFans. Artemis  [27]  was used for data management and DNA Plotter  [28]  for visualization of genomic features. The Mauve alignment tool (version 2. 3. 1) was used for multiple genomic sequence alignment  [29]. To estimate the mean level of nucleotide sequence similarity at the genome level between M. gorillae sp. nov. strain G3T and other members of the genus Microbacterium, we used the MAGI home-made software to calculate the average genomic identity of gene sequences (AGIOS) among compared genomes  [30]. Briefly, this software combines the Proteinortho software  [31]  for detecting orthologous proteins in pairwise genomic comparisons, then retrieves the corresponding genes and determines the mean percentage of nucleotide sequence identity among orthologous ORFs using the Needleman-Wunsch global alignment algorithm.
M. gorillae is susceptible to amoxicillin, erythromycin, doxycyclin, rifampicin, vancomycin, amoxicillin-clavulanic acid, trimethoprim-sulfamethoxazole and imipenem but resistant to ciprofloxacin and gentamycin. The G+C content of the genome is 69. 3 %. The 16S rRNA and genome sequences are deposited in GenBank under accession numbers JX650056 and CDAR00000000, respectively. The type strain G3 T (= CSUR P207 = DSM 26203) was isolated from the fecal sample of a western lowland gorilla from Cameroon.
Two authors (DB, JL) searched the following electronic databases: Embase via OVID (from 2000 to 20 December 2014), MEDLINE via OVID (1972 to 20 December 2014) and the Cochrane Library, but no studies were identified. Thus, this challenge is necessary to clarify the needs of healthy adults for efficient oral prophylaxis and for the control of dental plaque, periodontal diseases and dental caries. Thus, there is a need for a more comprehensive and rigorous assessment to ensure that the adult population is able to perform optimal biofilm disruption. The purpose of this study was to provide estimates on the prevalence and extent of the diameter access of interdental spaces in the 18-to 25-year-old adult population free of periodontal disease. A second objective was to describe the environmental factors, which favor or limit the interdental diameter and thus the performance of daily IDB activities.
Young's modulus and compressive strength The Young"s modulus and compressive strength were determined for monoliths and scaffolds for both 1HCP and 1HCPS systems. These preliminary studies were carried out to determine the materials" utility as potential implants in bone tissue engineering. The collected data were compared with results obtained for cortical  [23] [24] [25] [26]  and cancellous bone  [27] [28] [29] [30]  in the case of monoliths and scaffolds, respectively. The mechanical tests were performed with ElectroForce 5100 BioDynamic Test Instrument from BOSE company and using a TA-XT texture analyzer (TA Plus, Lloyd Instruments) equipped with mechanical grips. Test instruments provide accurate characterization of biomaterials and biological specimens. They can be used for the evaluation of a variety of specimens, including biomaterials, cellular and cell-seeded scaffolds, native tissue samples and tissue-engineered constructs.
Properties of the organic-inorganic hybrid system These studies are preliminary in nature, to collect data concerning the properties of the resulting materials. Depending on the properties to be determined, samples were examined in the form of thin films, monoliths, or scaffolds. Only pure samples were used in these studies. No samples after biomineralization or coating with synthetic hydroxyapatite were analyzed. Compressive strength and Young"s modulus were studied for both 1HCPP and 1HCPSP. Studies were performed for two different structures, monoliths and threedimensional scaffolds. To obtain monoliths, composites were collected into polypropylene molds directly after synthesis and cured at 65 °C for 12 h. Scaffolds were obtained as described in Experimental Section. The results are shown in Table  2  and Fig.
The 16S rRNA gene sequence was determined directly from the dental calculus specimen in 37 specimens (N17A, 385, 153, D314, GenBank LN610761; N17G, 529, 502, 497, 339, 145, 140, D353, D264, D208, GenBank LN610762; N57, N58C, N79, GenBank LN610763; N58T, GenBank LN610764; N70, GenBank LN610765; N71, P2, P4, P14, P26, F6, D222, GenBank LN610766; F27, GenBank LN827537; P27, GenBank LN827540; 138, GenBank LN827541; 142, GenBank LN827542; 486, GenBank LN827543; N102, D238, D362, GenBank LK054637; 105, 123, 356, 363, D230, GenBank LK054634). As for three other dental calculus specimens, direct sequencing indicated mixed sequences and the 16S rRNA gene sequences were determined after sequencing 10 clones for each specimen (N89-12, GenBank LN827538 and N89-2, GenBank LN827539; P16, P22, GenBank LN827539).
The mcrA gene was determined directly from the dental calculus in 28 specimens (N10, P4, GenBank LN624393; N17, GenBank LN624394; N57, N58, N87, 529, 123, 140, 502, 497, 363, 385, 339, 356, 145, 153, D314, D353, D264, D208, GenBank LN624395; N70, GenBank LN624396; N71, GenBank LN624397; P14, P26, GenBank LK054628; F6, D222, D238, GenBank DQ251045). In a third step, sequence analyses identified Candidatus Methanobrevibacter sp. N13 in 23 (41. 1%) specimens, M. oralis in 11 (19. 6%) specimens and Methanoculleus bourgensis in one specimen (1. 8%) (Table  1 , Fig. 1 ), respectively. Further 16S rRNA gene cloning revealed a sequence exhibiting 86% similarity with M. luminyensis (ref|NR_118098. 1|) further referred to herein as M. luminyensis-like, in calculus specimen P22; a mixed M. luminyensis-like and Candidatus Methanobrevibacter sp.