dataesr/scientific-paragraphs-categorization huggingface dataset:
ncbi. nlm. nih. gov). In the event of ambiguities relating to > 50% of the sequence, suggesting multiple amplifications, the PCR-amplified sequence was cloned using Plasmid pGEM ® -T Easy Vector according to the manufacturer's instructions (Promega, Charbonnières, France) and the cloning library was screened for appropriately sized inserts. Inserts were sequenced using amplicon-specific primers. Sequences were incorporated into a neighbor-joining phylogenetic tree using the maximum likelihood method with MEGA5. A 98% similarity in the 16S rRNA gene sequence was used as a cut-off to identify methanogens at the species level. The 16S rRNA sequences were deposited in GenBank under accession number LN610761-LN610766 and LN827537-LN827543, while the mcrA sequences were deposited under accession numbers LN624393-LN624397.
Image evaluation and study variables CBCT scans were analyzed using CS Dental Imaging Software 3D Module v3. 2. 9 (Carestream, Marne-la-Vallée, France). Two dental practitioners independently (B. Arcaute BA and E. Maury EM) evaluated the images twice at an interval of 2 weeks. A preview of the three planes was conducted and following by a visualization of all slices in the axial plan (coronal to apical and apical to coronal directions). The following variables were recorded: age, sex, type of tooth and number of teeth, jaw (maxillary/mandibular) or side (left/right). For each tooth, the number of roots and canals were noted. When reading the scans, third molars and root fragments were excluded. Have also not been considered teeth with orthodontic appliances, stirred images or presence of metallic artifacts preventing the adequate visualization of endodontic structures.
Statistical analysis Statistical analysis was performed using the STATA 13. 1 software (StataCorp, TX, USA). Inter and intra-examiner agreement was evaluated by the Kappa test. A random sample of 30 CBCT examinations was re-examined one week after the initial examination to test intra-examiner agreement with the Kappa test. The Kappa test was also used to assess inter-examiner agreement, again using a random sample of 30 CBCT examinations. The scans were read by 2 trained observers (BA and EM). The data were analyzed using descriptive statistics. A Stuart-Maxwell test was performed to compare left/right pairs of teeth (paired samples). When a 2x2 comparison was performed, this test acted as the McNemar test. The level of significance was set at 5% (p<0. 05). The effects of age, gender, jaw (maxillary/mandibular) or side (left/right) on the number of roots and canals were analyzed.
Conclusions The visualization of all canals is considered relevant in endodontic therapy. Can the presence of an additional canal on one tooth predict the chance to discover an additional canal on another tooth in the same patient? Although CBCT examinations are conducted in the first intention of making a diagnosis or prognostic evaluation, medium FOV acquisitions could be used as an initial database thus furnishing preliminary evaluations and information. Multiinstitutional studies may be undertaken to collect more CBCT images and perform additional statistical analyses.
Characterization of the proteins of interest After electrophoretic separation, the proteins of interest were excised from the gel and characterized by LC-MS/MS of the peptide mixture obtained after in-gel digestion. Protein sequence database searches identified the two proteins of interest as products of gene encoding a hypothetical 285-amino acid protein from the CAMP factor superfamily (Accession number gi| 488487765), covering 66% of the amino-acid sequence for the 27. 5-kDa protein and 61% of the sequence for the 24. 5-kDa protein (Table  1 ). The sequence of the 27. 5-kDa was 99%, 38%, 33%, 50% and 51% identical to the P. acnes CAMP factors 1, 2, 3, 4, and 5, respectively (Fig 5 ), and both proteins corresponded to the same P. acnes surface protein. The theoretical molecular mass of CAMP factor 1 is 30.
HaCaT cells were stimulated with the eluted proteins (20 μg) for 24 h at 37˚C and CXCL8 mRNA levels were evaluated by RT-qPCR (B), and CXCL8 protein levels were assessed by ELISA (C). Data are presented as the mean ± standard deviation of two independent experiments. We analyzed the recognition of CAMP factor 1 by TLR2 and found that most of the strains with strong TLR2 binding activity were of types IB and II (Table  2 ). We then measured CXCL8 production by keratinocytes stimulated with the 27 strains. We found that the P. acnes strains tested could be separated into two groups, one with low to moderate levels of CXCL8 production (93 to 400 pg/ml) and the other with high levels of CXCL8 production (>400 pg/ml) (Table  2 ). Most of the strains producing high level of CXCL8 were of types IB and II.
Peptide extracts were then dried and dissolved in the initial buffer for chromatographic elution, which consisted of 3% CH 3 CN and 0. 1% HCOOH in water. Peptides were enriched, separated and analyzed with a 6520 Accurate-Mass Q-TOF LC/MS machine equipped with an HPLC-chip cube interface (Agilent Technologies, Massy, France). The fragmentation data were interpreted with Mass Hunter software (version B. 03. 01, Agilent Technologies). For protein identification, MS/MS peak lists were extracted, converted into mzdata. xml format files and compared with the protein database, using the MASCOT Daemon (version 2. 1. 3; Matrix Science, London, UK) search engine. The searches were performed with no fixed modification, with variable modifications for methionine oxidation, and with a maximum of one missed cleavage.
Phylogenetic analysis Phylogenetic analyses were performed to assess the relationships between the P. acnes CAMP factor 1 sequences obtained in this study and other known CAMP sequences. These analyses were carried out with the maximum likelihood method. Multiple sequence alignments were obtained with Mafft version 7  [61]  and exported into Seaview software  [62] , for input into JModelTest  [63]  and ProtTest  [64]  to identify an appropriate substitution model for phylogenetic analysis with the Bayesian information criterion. The best model for nucleotides was HYK85 and the best model for proteins was WAG, both without a gamma distribution. The phylogenetic analysis was performed with PhyML3. 0  [65] , implemented in Seaview software  [16]. Sequences were randomized by 500 bootstrapping resamplings, and statistical analyses were performed on 100 datasets for each analysis.
Caspase activity fluorogenic assays To determine caspase-1, -3 and -9 activity, cells were sonicated and lysates were incubated with 200 μL of substrate solution (20 mM HEPES, pH 7. 4, 2 mM EDTA, 0. 1% CHAPS, 5 mM DTT and 0. 75 μM of caspase substrate) for 1 h at 37°C as previously described  [30]   [31]. The activities of caspase-1, -3 and -9 were calculated from the cleavage of the respective specific fluorogenic substrate (Ac-YVAD-AMC for caspase-1, AC-DEVD-AMC for caspase-3 and AC-LEHD-AMC for caspase-9) (Bachem, Bobendorf, Switzerland). Substrate cleavage was measured with a fluorescence spectrophotometer with excitation wavelength of 360 nm and emission at 460 nm. The data were calculated as fluorescence units/mg of total protein.
Outcomes The primary outcome is to compare overall (the mean of all extraction sites) mean bone ridge height loss (D365-D10) at 1 year after maxillary immediate complete denture placement with or without bone substitution. A quantitative evaluation method using CBCT was designed. The secondary outcomes are as follows: To compare mean bone ridge height loss, site by site (central incisor, lateral incisor, and canine), with the same technique after 3 months (D90-D10) and after 1 year (D365-D10) To compare mean bone ridge width, overall and site by site, with the same technique after 3 months (D90-D10) and after 1 year (D365-D10). CBCT data collection and ridge measurements are performed in an independent specialized radiology clinic. For the study purposes, a CBCT unit (NewTom VGi QR s. r. l.
©, Verona, Italy), with a 7. 5 × 12-cm field, was selected. CBCT data are collected at D10, D90, and D365. The volume CT dose index ranges from to 2 to 4 mGy per examination, according to the patient morphology. An original protocol was developed to perform reproducible measurements and to compare ridge resorption in the two treatment arms. Bone height and width are measured on CBCT reconstructions by using a radioopaque denture duplicate specifically designed for the study purposes.
Allocation concealment mechanism and implementation The patient has to be included/registered online with the RandoWeb® software (AP-HP, Paris, France) before complete denture delivery, so all data are recorded prospectively without inclusion being influenced by the allocation result. During the surgery, just after extraction of the last teeth, the allocation result can be obtained online by the surgeon if the patient has been included/registered online beforehand. The treatment arm is then attributed (control group: conventional surgery without osseous filling; experimental group: alternative surgery with socket filling). Operators have access only to the last inclusion result in the randomization table, to limit predictability. HFC conceived the minimization algorithm and Vincent Morice implemented it into the RandoWeb software.
Data collection Investigators will use a CRF to record all items required for the outcomes analysis. A clinical research assistant visits the investigation center every 6 months to monitor the collection of data (by checking that no CRF field is incomplete) and to assess the quality (by comparing the Fig. 5  Participant's timeline data in the medical record, the data entered through the online inclusion and randomization software RandoWeb (AP-HP, Paris; http://randoweb. aphp. fr), and the data in the CRF). Two independent calibrated operators, with blinding to the treatment arm, perform radiologic measurements. The data are transmitted to an adjudication committee to harmonize the collection standardization and data evaluation. This committee consists of a radiologist, a prosthodontist, and a surgeon.
Primary outcome analysis The main analysis will compare the final loss (D365-D10) of bone ridge height between the experimental and control group. This main analysis will be adjusted on the following prespecified variables: operator team, smoking habit, periodontal disease evolution, and age and sex of the patient. A linear mixed model (probably marginal) will be used to account the correlation between the different bone ridge height values in the same patient (level 1 will be the extraction site, and level 2 will be the patient; level 3 will be the investigator team, if necessary). The main analysis will take into account missing outcome data by multiple imputation, with the assumption that data are missing at random. We will report the unadjusted analysis as well; mean final loss of bone ridge height will be compared between the experimental and control group by Mann-Whitney test.
Data monitoring, harms and auditing The data will be monitored by an independent clinical research assistant who will compare the data entered in the CRF with those in the patient's clinical record. In case of disagreement, the patient's operator/investigator will be asked to clarify the data. No interim analysis is planned. Concerning harms monitoring, the CRF contains two adverse events forms: one concerning general health and one that is treatment-related. Trial management may be audited by the French Department of Health at any time; the audit would be independent of investigators and the sponsor. Investigators will not have access to the final trial data set; the latter will be accessed by clinical research assistants, data managers, and statisticians only.
Ethical considerations The trial received approval from the French Ethics Committee for the Protection of Persons (Comité de Protection de Personnes, trial number 13-019) in June 2013. The protocol is registered with the Agence Nationale pour la Sécurité du médicament et des Produits de Santé (ANSM, French National Agency for Medicines and Health Products Safety (2013-A00440-45 (IDRCB/ Eudract)) and ClinicalTrials. gov (no. NCT02120053, 18 April 2014). All amendments to the protocol will be justified, submitted to the scientific board, accepted by the CPP, and recorded by the ANSM. Changes and amendments will be also recorded at ClinicalTrials. gov. Informed consent will be obtained from trial participants after the trial is explained by an investigator or operator of the corresponding center.
Patients are informed that they have the right to withdraw from the study at any time without giving reasons. Regardless of withdrawal, patients will be provided any treatment in their best interest. Withdrawal will be documented. Data confidentiality was audited by the Comité National Informatique et Liberté (National Committee of Informatics and Freedom); last and first names of included patients are not recorded in the database. Moreover, the authors followed the SPIRIT 2013 checklist (Fig. 6 ).
Acknowledgments The authors thank  Geistlich Pharma AG® (Wolhusen, Swizerland)  for providing the xenograft material. This firm did not have any authority in the study design and will not have any role in the decision to submit the report for publication (except if they purchase the whole trial from  AP-HP ). The authors thank  Moufida Dabbech  (moufida. dabbech@aphp. fr) and  Karine Goude  (karine. goude@aphp. fr)from the DRCD for sponsoring/promoting the  PANORAMIX  project. The authors also thank the clinical research unit team from  Albert Chenevier Hospital  ( Samia Balloul ,  Fatiha Djennaoui , and  Amel Gouja ) for helping the authors.
Funding The PANORAMIX trial is funded by a  €120 , 000  grant from the  Ministry of Health of France  through the national programme for clinical research in hospitals ( Programme Hospitalier de Recherche Clinique ). The sponsor is AP-HP. The protocol was registered as number  P111116 -PANORAMIX by the promoter ( AP-HP and Département de la Recherche Clinique et du Développement ). This report is based on protocol version 1. 0. The PANORAMIX trial was authorized by the board for evaluating medical devices of the national agency for the security of drugs and health products in France ( Agence Nationale de Sécurité du Médicament et des Produits de Santé ) and is registered as 2013-A00440-45 (IDRCB/Eudract). The 1-year report will be submitted to the sponsor (in French) and then will be published (in English).
Micro-computed tomography The mandibles were scanned by micro-computed tomography (microCT; Skyscan 1076, Belgium). The x-ray source was operated at a voltage of 50 kV and a current of 200 µA. The detector was rotated to 180° in 0. 6° steps with an exposure time of 1. 7 s, giving a spatial resolution of 18 µm per voxel. The 3D reconstructions were made using CTVOX software.
The newly formed bone surface was expressed as a percentage of the ROI. The stained slices were scanned (NanoZoomer 2. 0RS, Hamamatsu Corp. Japan) and observed with the virtual microscope (NDP view software, Hamamatsu Corp). Tissues and cells in the different membranes were identified and scored by M F Heymann, a medical doctor specializing in anatomic pathology. Tissue necrosis, neovascularization, fibrosis and fat tissue infiltration were scored according to the 10993-6 standard  [26]. The number of granulocytes, lymphocytes, plasmocytes, macrophages and giant cells were numbered in the membranes at a magnification of ×400. A score of 0 was given in the absence of cells and score 4 corresponded to a high number of cells gathered in wideranging areas.
Quantification of mandibular alveolar bone resorption Hemi-mandibles were scanned using a high-resolution mCT (Viva CT40; Scanco Medical, Bassersdorf, Switzerland). 26 Data were acquired at 45 keV, with a 10 μm isotropic voxel size. Six linear measurements were obtained from each molar by using a stereomicroscope with an on-screen computer-aided measurement package. The alveolar bone loss (ABL) (mm) was measured from the cemento-enamel junction to the alveolar bone crest for each molar. 27 Three-dimensional reconstructions were generated from a set of 400 slices.
Cells subpopulations counting was done with the Panoramic Viewer software (3DHISTECH) and carried into the Lamina propria gingivae and periodontal ligament on average surface 0. 1 mm 2 on each tissue section. Five microscopic fields were counted on each slide by two independent naïve investigators. Surface staining and antibodies treatment of immune cells from cervical lymph nodes, spleen and blood Mononuclear cell suspensions were incubated for 15 min with anti-CD16/32 to block Fc receptors and then with antibodies, anti-CD4 APC (RMA4-5, eBioscience), CD8 V450 (53. 6. 7, BD Bioscience), anti-CD11b APC-eFluor780 (M1/70, eBioscience), CD45 V500 (30F11, BD Bioscience), anti-CD19 FITC (1D3, BD Bioscience) and anti-TCR PerCP-Cy5. 5 (H57, eBioscience) for 30 min on ice. LIVE/DEAD Fixable Cell Stain Kit (Life Technologies) was used to remove dead cells.
Statistical analysis Results are presented as mean±SEM. One-way analysis of variance (ANOVA) followed by Tukey's post-test was used to assess inter-groups differences, except for the IPGTT, where two-way ANOVA followed by Bonferroni's post-test was applied. *p<0. 05; **p<0. 01; ***p<0. 001 and ****p<0. 0001 when compared to HFD, § p<0. 05; § § p<0. 001 § § § § p<0. 0001 when compared to NC and $ p<0. 05 when compared to NC-Co defined statistical significance. Statistical analyses were performed using GraphPad Prism V. 5. 00 for Windows Vista (GraphPad Software, San Diego, California, USA). The dendrogram on figure 1L was drawn by PermutMatrix software;  30  figure 2I (principal coordinate analysis (PCoA)) was drawn by XLSTAT for Microsoft Windows Excel.
Acknowledgements The authors thank the  French Society of Arterial Hypertension (Société Française d'HyperTension Artérielle)  and the  French Diabetes Society  ( Société Francophone du Diabète ) for supporting  Dr Blasco-Baque. They also thank the zootechnie-Rangueil INSERM/UPS  US006  CREFRE; the  Phenotypage-ANEXPLO Platform  ( US006-CREFRE ) for biochemical assays; the microtomography facility in the medical faculty of the  University Jean Monnet (St. Etienne, France)  and especially  Dr Luc Malaval  ( INSERM U1059 ) for technical support;  Florence Capilla  and  Christine Salon  for technical assistance in histology for hemi-mandibles at the  Platform of Experimental Histopathology of the INSERM/UPS US006 CREFRE ,  Toulouse Purpan , France;  Catherine Le Iann  for technical assistance in P.
The pure culture of this halophilic archaea grew aerobically after 7-day incubation at 37°C. Strain Arc-Hr exhibits positive catalase and oxidase activities. The growing colonies on the halophilic medium were red, opaque and 0. 5 to 1 mm in diameter. Cells were Gram-negative cocci, nonmotile and non-spore forming with a diameter of 0. 9 μm. The 16S rRNA gene was sequenced using the primers as previously described  [4]  using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). Strain Arc-Hr exhibited 99. 3% sequence similarity with Haloferax volcanii JCM 8879 (GenBank accession no. NR113448)  [5] , the phylogenetically closest validated species with standing in nomenclature (Fig. 1 )  [6]. Because 16S rRNA gene sequence comparison has been proven to poorly discriminate Haloferax species, we sequenced the complete genome of strain Arc-Hr.
Setting and participants This study is being carried out in 13 academic hospitals and two private practices in France (study sites can be found at ClinicalTrials. gov; inclusion from February 2015 to July 2016). Eligible patients, and their parent(s), if necessary, receive the study information. Informed consent forms are given to the patient and to the parent(s) of minor patients (age 8-18 years), before inclusion. To be included in the trial, patients must 8-80 years old, able to receive dental care, covered under the national health coverage system, and have a mature permanent posterior tooth affected by a deep carious lesion. The tooth should have normal response to pulp sensitivity tests, without periapical pathology, and require direct restorative procedure. Exclusion criteria are not French-speaking, under guardianship or pregnant, have a pacemaker, or at risk of infectious endocarditis.
Data collection methods Trial data are collected in an eCRF. To promote data quality, investigators, and evaluators (examiners), who will assign scores, are trained in the FDI criteria by means of the e-calib web-based software (www. e-calib. info) and group training sessions. Two independent evaluators will perform the follow-up examinations. If disagreements occur during the evaluations, evaluators will have to reach consensus. Data collection forms can be found in the trial protocol as well as on the randomization website. To promote participant retention and complete follow-up, each patient will receive 90 € on completion of the trial as compensation for attending the follow-up appointments.
Statistical methods The statistical unit for analysis will be the tooth. Only one tooth per patient will be included and treated according to the protocol. The demographic and clinical characteristics of patients and treated teeth will be described for both treatment arms with mean and SD or median and interquartile ranges for quantitative variables and number of subjects, and percentages for qualitative variables. The analyses will be performed according to the intention-to-treat principle. To evaluate the primary objective, the probability of success in arms P and C at 1 year will be calculated and compared by Fisher's exact test. The probability of success for each arm (0 for treatment failure and 1 for success, at 1 year) will be assessed by a hierarchical logistic model. This model accounts for the correlation related to the hierarchical structure of the data (several patients treated by one practitioner) as well as any possible interpractitioner heterogeneity.
Data monitoring, harms and auditing The data will be monitored by an independent clinical research assistant, who will compare the data entered in the eCRF with those in the patient's paper clinical record. In case of disagreement, the patient's investigator will be asked to clarify the data. No interim analysis (other than that described above) is planned. If possible, the follow-up duration will be extended. Concerning harm monitoring, specific adverse events forms can be accessed in the eCRF. Trial management may be audited by the French Department of Health at any time; the audit would be independent of investigators and the sponsor. Investigators will not have access to the final trial data set; the latter will be accessed by clinical research assistants, data managers, and statisticians only.
Ethical consideration The Human Research Ethics Committee of the University Hospital of Lyon (Comité de protection des personnes or CPP Sud-Est IV) has approved the study protocol (2014-A00907-40). The protocol is registered with the Agence Nationale pour la Sécurité du Médicament et des Produits de Santé (ANSM, the French National Agency for Medicines and Health Products Safety; no. 2014-A00907-40) and ClinicalTrials. gov (no. NCT02286388). All amendments to the protocol will be justified, submitted to the scientific board, accepted by the CPP Sud-Est IV and recorded by the ANSM. Changes and amendments will be also recorded at ClinicalTrials. gov. Informed consent will be obtained from trial participants or authorized surrogates (parents of children aged 8-18) after trial explanation by an investigator or investigator of the corresponding center.