dataesr/scientific-paragraphs-categorization huggingface dataset:
Screening and selection criteria The results of this systematic review were reported following the PRISMA guidelines  (Moher, Liberati, Tetzlaff, Altman, & PRISMA Group, 2009). Studies were identified independently by two blinded researchers from the following databases: MEDLINE and Web of Science up to December 2019. An additional hand search was also performed in references list of included articles and reviews. The following strategy was used in the search using Boolean operators and an asterisk symbol (*) as truncation to identify papers using MesH, keywords and other free terms: ((PTH) OR (parathyroid hormone) AND (periodontitis OR alveolar bone OR periodontal treatment OR periodontal healing OR periodontal destruction)) AND (mouse OR rat). Only articles published in English language have been considered.
Studies selection The flow diagram of the literature search is presented in Fig. 2. Overall, 247 articles were identified by querying selected databases (Medline/Pubmed and Web of Sciences). After removal of duplicates, 183 articles were screened. 158 articles were excluded based on title and abstract. Amongst the 25 remaining articles, 10 were selected for fulltext review. Three studies were excluded as they evaluated socket healing after teeth extraction, 8 because PTH was used in combination with other therapeutic modality or hormone and 4 were excluded because they were not focused on periodontal healing. Regarding the 10 included studies, 5 used a model of periodontitis induced by ligatures, 4 analyzed bone healing after a periodontal defect created by dental bur or orthodontic forces and one used streptozotocin-induced diabetic periodontitis.
Technical note A computed tomography (CT) scan was performed systematically to confirm the diagnosis of mandibular septic pseudarthrosis (Fig. 1 ). The surgical approach was intended to be as limited as possible and therefore, a customized 3D-printed mandibular EF together with a positioning and drilling guide were designed and manufactured according to the following procedure. The DICOM files from the patient's mandibular CT scan were converted to STL files using InVesalius 3. 01 software (CTI, Campinas, Sa ˜o Paulo, Brazil). Surgical planning was conducted using Meshmixer1 software (Autodesk, Mill Valley, CA, USA) (Fig. 2 ). It consisted of the insertion of three standard 3mm pins (Stryker, Kalamazoo, MI, USA) on each side of the pseudarthrosis site whilst preserving the inferior alveolar nerve and the teeth apices.
90 g. L -1 ), PIPES (7. 5 g. L -1 ), MOPS (5. 23 g. L -1 ), HEPES (5. 96 g. L -1 ), tricine (4. 48 g. L -1 ), bicine (4. 08 g. L -1 ) over a pH range from 5. 5 to 9, with 0. 5 increments. The NaCl tolerance for growth was determined at 25°C from 0 to 100 g. L -1 NaCl, with 10 g. L -1 increments, in reconstituted MB (according to the composition indicated by Difco, except for NaCl). Growth was estimated by measuring the turbidity at 600 nm. Growth ranges and optima data missing for the other strains were also determined under the same conditions. Cellobiose, D-arabinose, D-fructose, D-glucose, D-mannose, D-raffinose, D-sorbitol, D-sucrose, Dtrehalose, L-rhamnose, L-xylose, melezitose, myo-inositol, xylitol, glycogen (5 g. L -1 ), starch (1 g. L -1 ), acetate, gluconate, malate, pyruvate, succinate, ethanol, glycerol, L-proline, peptone, tryptone, ethyl palmitate, lecithin, tricaprylin, cholesterol, triolein, octanol, 1-phenyldecane, pristane, heptamethylnonane, methyl laurate, hexadecane, octane and decane were tested as sole carbon sources in minimal MB (MBmin) with a concentration of 20 mM (unless otherwise specified).
The targeted gene sequences were selected in Rhodobacteraceae genomes in which these genes were correctly annotated, based on an examination of both INTERPRO and IMG databases  [24, 36]. For fatty acids, polar lipids and quinones determination, all strains were cultured in MB. They were harvested during their exponential phase and lyophilized. Analyses were performed by the Identification Service of the DSMZ. FAMEs were prepared from 40 mg cells, as described by Miller  [38]  and Kuykendall et al. [28] , and identified using the Sherlock Microbial Identification System (MIDI, Microbial ID, Newark, DE 19 711 USA). Polar lipids were extracted using the method of Bligh and Dyer  [4] , separated by two dimensional silica gel TLC, and analyzed according to the procedures described by Tindall et al.
Public genome dataset. Representative genomes of Rhodobacteraceae were downloaded from GenBank and Roseobase (http://www. roseobase. org/), as available in June 2018. In order to root phylogenetic trees, we also downloaded two outgroups from GenBank (Thiothrix nivea DSM 5205 T and Methylococcus capsulatus ATCC 19069 T ). Genomes that seemed incomplete (≤ 3 Mb and L90 value above 115 (defined as the smallest number of contigs whose length sum accounts for 90 % of the genome)) were removed. The accession numbers of the 66 genomes are given in Table  S1. The main features of MOLA 401 T genome was described by Doberva et al. [17]  Orthologous genes. The 16S rRNA sequences were obtained using the original annotation of genomes. Genomic annotation of strain MOLA 401 T was used to identify sequences of housekeeping genes (gyrB, recA, rpoC and rpoD).
Annotation of these genes was checked using BLASTP  [2]  and the non-redundant protein database of NCBI. The proteome of strain MOLA 401 T was then used as a pivot to identify the whole orthologous genes with the 65 genomes (bi-directional best hits, BLASTP (identity ≥ 40 %, coverage ≥ 50 %, E-value ≤ 10 -5 )). The core genome was defined as the intersection of the lists of orthologs between the pivot and each genome.
Measures of similarity between genomes. For each pair of genomes, we computed three measures of similarity, one based on gene repertoires (POCP) and two others based on the sequence similarity between two genomes (AAI and ANI). The percentage of conserved proteins (POCP) between two genomes was calculated as previously described  [45] : [(C1+C2)/(T1+T2)] x 100 %, where C1/C2 and T1/T2 represent the number of orthologous proteins and the total number of proteins in the two genomes being compared, respectively. In particular, the orthologous proteins between a pair of genomes were determined as described above using BLASTP and bi-directional best hits. Pairwise average amino acid identities (AAI) were assessed using BLASTP identity values obtained to estimate POCP. Pairwise average nucleotide identities (ANI) were calculated using the pyani Python3 module (https://github.
3. 8. The best parameters were identified based on the Bayesian information criterion (BIC). Lastly, maximum likelihood trees were computed with IQ-TREE v1. 3. 8 using the appropriate model, and validated via an ultrafast bootstrap procedure of 1000 replicates  [39]. Statistical analyses. Statistical analyses were done using R version 3. 3. 1  [46]. The correlation between measures of similarity between genomes and phylogenetic trees was assessed using patristic distances (R package {stats}, cophenetic) and Mantel test (R package {vegan}, mantel)  [34]. Biofilm growth and quantification. Biofilm formation was performed on 24 well polystyrene plates (Evergreen Scientific). Biofilm cultures were initiated with 1 mL per well of cells in exponential phase suspended in MBmin at an OD600 of 0. 1.
Acknowledgements We acknowledge the  BIOPIC platform (CNRS-Sorbonne Université ,  Observatoire Océanologique de Banyuls-sur-Mer ). We wish to thank  Marie-Line Escande  and  Nicole Batailler , from the  Observatoire Océanologique of Banyuls sur Mer , for technical support and TEM preparation and images. We thank  Elodie Courtade  for the realization of physiological and biochemical tests. This work was supported by the  Conseil Général des Pyrénées-Atlantiques  ( CG64 ).
Exhaustive data will be obtained as HPV whole-genome sequencing/HPV molecular status (integrated or episomal)/HPV integration site, both in virus and human genomes/HPV genotype variant sequences. "HPV capture" technology has already been performed on HPV cervical and anal cancers  (135, 139)  to determine a potential prognosis value of the HPV molecular signatures described. Investigations based on this new technology are actually in process in HPV oropharyngeal cancer. The deep information obtained with such technology such as viral molecular status, genotype variants, integration of viral genes deletion, and sites of integration could be extremely informative regarding the viral oncogenic process and could allow the possibility to ultrastratify HPV-driven OPSCC based on virological information.
X-ray diffraction X-ray diffraction was performed (D8 Advance; Bruker) with Cu Kα radiation at 40 mA and 45 kV over 15 ~45˚2θ, stepping 0. 02˚per 0. 6 s. Phase identification for crystalline reaction products was by search-match software (PDXL v. 2. 2. 1, Integrated X-ray powder diffraction software; Rigaku, Ettlingen, Germany) against included Powder Diffraction File (PDF) data (International Centre for Diffraction Data, Newtown Square, PA, USA), verified by inspection. Patterns were obtained at each sampling time.
Acknowledgments Ing James Camilleri  of the  Department of Metallurgy and Materials Engineering, Faculty of Engineering  and  Mr Jonathan Spiteri  of the  Department of Chemistry, Faculty of Science  for their technical support. Prof Kristian Zarb Adami  of the  Institute of Space Sciences, University of Malta ,  Dr Edward Sammut  of the  Department of Oral Rehabilitation and Community Dental Care, Faculty of Dental Surgery, University of Malta  and  Mr Lawrence Spiteri  of  Diagnostic Science laboratories, Heritage Malta  for access to equipment.
These steps were to be repeated every 6 hours 3 times per 24h, during 7 days. Pain severity was assessed as the mean pain felt during the last day on a 11 point numeric rating scale [NRS] (0 was defined as the absence of pain and 10 the maximal pain imaginable). Pain score was assessed as baseline (D0) before MB application and at three time points (D3, D5 D7) after MB application, and after 3 and 6 months. Patients were also asked to report any unpleasant sensation or adverse effect relating to MB use. Self-evaluated general Quality of Life and Stess/anxiety was noted as Good or Bad and Yes or No. Statistical analyses were performed using GraphPad software. Pain intensity ratings before (D0) and after MB mouthrinse at D7, 3M and 6M use were compared using ANOVA followed by Dunns post-tests.
(5. ) For quality control, the molecular data is obtained using agarose gel migration, melting curve comparison, and sequencing. slightly modify the methodology, for example by customizing primers and/or PCR conditions. Targeting specific 16s rRNA gene sequences for periodontal pathogens can be implemented with primers previously used in the literature or designed by dedicated software like Primer-BLAST. This tool is easy to use and it helps select custom primers that meet the specific requirements of the selected PCR protocol. However, these newly generated primers will not have been tested, unlike those published in the literature. Without a consensus on optimal primers, scientists must first systematically test the selected primers on known bacterial culture samples and on clinical subgingival bacterial samples.
Once primers have been positively confirmed on standard samples, they can then be used for sequencing and comparison with a 16s rRNA gene database, like the one from the Ribosomal Database Project (RDP)  [44]. To improve bacterial detection, some studies increase the number of PCR cyles (>40) to increase the DNA copy number  [4, 21, 29, 30]. This approach is not recommended because it increases the risk of false positives, which decreases specificity. Some authors pooled duplicate or triplicate samples to increase the likelihood of detection  [34]. However, comparing results from duplicate or even triplicate samples instead of pooling, improves the sensitivity of bacterial identification. Based on our experience, we recommend using 3 dilutions of DNA extracts because human atherothrombotic plaque samples contain variable concentrations of bacterial DNA.
Sampling (Fig. 1) We sampled eight fully-dentate entire mandibles (specimens I to VIII) and split them in two. The left side was used for the traction-to-fracture test within an unfinished SSRO and the right side was used for the hardness tests. First "testing specimens" (specimens IX and X, data not shown) were used to develop our protocol and ensure the reproducibility of our tests and were excluded. Each right side was sampled in five parts underlying the process of the osteotomy: lingual cortical bone sample; vestibular diagonal ramus cortical bone sample; vestibular horizontal corpus cortical bone sample; full ramus piercing sandwich, with vestibular cortical, medullary and lingual cortical bone sample, tested on the lingual face; and full body piercing sandwich, with vestibular cortical, medullary, and lingual cortical bone sample, tested on the vestibular face.
Acknowledgements We thank  L'École   de Chirurgie du Fer à Moulin, de l'AP-HP , its scientific director and headmaster  Pr Pascal Frileux , his associate  Djamel Taleb  and all the staff, as they kindly supported all anatomical experiments inside the school. We also thank la  Fondation des Gueules Cassées  and la Fondation pour l'étude et la recherche du corps médical, as they supported this original study financially. All authors agree with the submission. This work has not been published or submitted for publication elsewhere, either completely or in part, or in another form or language. This study has been performed thanks to a  Fondation des Gueules Cassées  Grant, N •  16-2018  and a  Fonds Pour l'Etude et La Recherche du Corps médical Grant , Appel à projets 2018-2019.
Documentary research The first step to carry out this study was to identify and collect the documentation. Thus, Pubmed, Medline, Pascal and Cochrane databases were consulted primarily. The choice of these databases was based on their contents' credibility. The "snowball" documentary research method which consisted of finding some strategic articles and searching for others through their references was used. Publications between 2000 and 2018 were used. Forty-Five articles out of the 152 consulted were selected. Keywords used were people living with HIV + oral health promotion + quality of life. These words were combined with the Boolean operators "AND", "OR", "EXCEPT". Thus, abstracts of relevant articles were identified, including international conferences on HIV and oral health, their management and quality of life.
Study design In this phase III, double-blind, placebo-controlled trial ( Clini-calTrials. gov: NCT02915159), eligible patients with active pSS were randomised 1:1 to receive either weekly SC abatacept 125 mg or SC matching placebo for 169 days. A subsequent 197-day (365-day in Japan) open-label extension followed the initial double-blind period, when all eligible patients received SC abatacept 125 mg/week (those receiving placebo switched to abatacept). Post-treatment safety follow-up lasted an additional 168 days. Patients were recruited from December 2016 to January 2018 from 60 centres in 13 countries. Random assignment of study treatment was performed by a central system. Randomisation schedules were generated by the Randomisation Group within Drug Supply Management of Bristol Myers Squibb Company.
Downloaded from Sjögren's syndrome microglobulin. Serum biomarker chemokine ligand 13 (CXCL13) analyte was measured using the SIMOA assay from Myriad RBM. Immune cell phenotyping of whole blood samples was assessed in a subpopulation of patients from sites that participated in the flow cytometry analysis with data analysed using BD FACSDiva software. Adverse events (AEs) were monitored throughout the study.
All efficacy analyses used the modified intent-to-treat (mITT) population, which comprised all randomised patients who received ≥1 dose of study medication. Missing data for responders were imputed as non-responders. Estimates of adjusted mean change were derived from a repeated measures mixed model; model analysis details are included in the online supplemental appendix. Safety was summarised descriptively throughout the trial up to 56 days after last study drug dose.
The safety profile of abatacept in patients with pSS was similar to that in other diseases treated with abatacept. 40 otably, abatacept therapy did have a clear impact on selected disease-relevant markers of biological activity likely related to central mechanisms of pSS pathogenesis. In a recent randomised, placebo-controlled, investigatorinitiated, single-centre study of SC abatacept in patients with early active pSS in the Netherlands (ASAP III NCT02067910; n=80), results for the primary endpoint (ESSDAI at 24 weeks) were similar to the present study. 41 In contrast to the current study, the secondary ESSPRI endpoint (ESSPRI responders at weeks 12 and 24) was significantly different, in favour of abatacept versus placebo. Differences in results between ASAP III and the current study may be due to variations between study populations and designs, including the single-centre versus multiplecentre nature of the two studies.
Design and manufacture of porous Ti6Al4V ELI scaffolds Detailed information of the SLM Ti6Al4V ELI porous scaffolds used in this work is provided in Fig. 1. Octahedron crystal lattice with horizontal struts was adapted as the basic unit of the porous structure as shown in Fig. 1a. The overhanging cuboid strut has an inclined angle of 45°. The octahedron lattice can improve the isotropic properties of the structure under multidirectional compressive force and hence confers high safety as the bone substitute. The structure of the scaffolds was designed using CAD software UG NX 10 (Siemens PLM Software, Germany). Fig. 1b  and 1c  show the CAD-designed porous Ti6Al4V ELI scaffolds in flat shape (10 mm × 10 mm × 2 mm, layer thickness of 2 mm) for in vitro experiments and in cylindrical shape (3 mm in diameter and 4 mm in length) for in vitro experiments, respectively.
Micro-CT assay In order to evaluate the effectiveness of new bone ingrowth formation, the rats with porous scaffold implantation were scanned using X-ray micro computed tomography (μ-CT, X5000, North Star Imaging, USA). The scanning resolution was approximately 4 μm/voxel. Three-dimensional (3D) volume of the scaffolds and bones were reconstructed by Amira-Avizo software. VGStudio MAX (Volume Graphics, Germany) was used for data analysis. The scaffolds and the bone tissues growing into the inner space of the scaffolds were defined as the volume of interest for detailed data analysis. Bone volume (BV) and total pore volume (TV) were measured using the μ-CT. The ratio of BV to TV (BV/TV) was then calculated to quantitatively evaluate the bone ingrowth performance. A higher value of BV/TV indicates better bone growth into the pore space.
Acknowledgements The authors would like to acknowledge financial supports provided by the founds of Guangdong Academy of Science Projects  2019GDASYL-0502006 ,  Science and Technology Planning Project of Guangdong province  ( 2016B090916003 ),  Science and Technology Planning Project of Guangzhou  ( 201704030111 ), 201807010030,  2017A070701027 ,  2016A030312015 ,  2017G1FC0008 ,  2018GDASCX-0402. Sanming Project of Medicine in Shenzhen  ( SZSM201612023 ).
ROLES OF OF IN TRANSMISSION DYNAMICS OF SARS-CoV-2 Transmission Routes of SARS-CoV-2 Human Expression of ACE2 and Furin for SARS-CoV-2 Cell Entry The expression and distribution of the ACE2 in human body is essential to understand the potential infection routes of SARS-CoV-2 infection. ACE2 expression profile can be analyzed at single-cell resolution using the single-cell RNA sequencing (scRNA-Seq) technique and the single-cell transcriptome database. High ACE2 expression was identified in various cells from different organ systems such as respiratory tract (type II alveolar cells of lung), salivary glands, mucosa of oral cavity, esophagus upper and stratified epithelial cells, cholangiocytes, and absorptive enterocytes from ileum and colon, urinary tract, and also myocardial cells  (30) (31) (32) (33) (34).
Background: Adenoid cystic carcinoma (ACC), or cylindroma, is a rare malignancy believed to arise from epithelial cells of salivary glands. It is a slow-growing but aggressive tumor with a propensity for perineural invasion. Metastases are common to the lung, but rare to the spine. The natural history of ACC spine metastases is unknown and progression is unpredictable. Methods: 1) A case report was described for a patient diagnosed with spine ACC metastasis of the T6/T7 vertebrae. 2) A literature search was conducted on Medline via PubMed and the Cochrane databases according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to identify articles from 1973 to March 2019 using following keywords: adenoid cystic carcinoma, cylindroma, metastasis, salivary glands.
MATERIALS AND METHODS Here we report the case of a 71-year-old woman with a spine metastasis emanating from late (35 years) relapse of the disease. A literature search was conducted on Medline via PubMed and the Cochrane databases according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to identify articles from 1973 to March 2019, using following keywords: adenoid cystic carcinoma, cylindroma, metastasis, salivary glands. Twenty articles were retrieved. With inclusion criteria comprising adult patient, male or female, histologic proof of ACC spine metastasis, and year of diagnosis >1973, 8 articles were included, for a total of 16 patients (Figure  1 , flowchart).
However, identifying genetic or functional determinants of sitespecificity requires the investigation of microbial pangenomes. The human oral cavity is one of the most well characterized microbial habitats of the human body. The Human Oral Microbiome Database (HOMD) (http://www. homd. org) (Chen et al. , 2010; Escapa et al. , 2018)  describes more than 750 oral taxa based on fulllength 16S rRNA gene sequences, 70% of which have cultured representatives, enabling genome-resolved analyses that cover a considerable fraction of oral metagenomes  (Nayfach et al. , 2016 ). Yet, one-third of the known oral taxa are missing or poorly represented in culture collections and genomic databases, and include some that are common in the oral cavity  (Vartoukian et al. , 2016) , including members of the Candidate Phyla Radiation (CPR)  (Brown et al.
, 2013; Espinoza et al. , 2018) , and recently the first targeted isolation of oral SR1 strains has been reported, but genomes were not produced  (Cross et al. , 2019). Despite the promise of these studies, our understanding of the ecology and evolution of these fastidious oral clades is incomplete. Here we investigated phylogenetic and functional markers of niche partitioning of enigmatic members of the oral cavity, with a focus on members of the candidate phylum TM7. We used a metagenomic assembly and binning approach to recover metagenomeassembled genomes (MAGs) from the supragingival plaque and tongue dorsum of healthy individuals, and used long-read sequencing to associate TM7 MAGs with previously identified phylotypes through 16S rRNA sequence comparison. Our genomes represent prevalent and abundant lineages that lack genomic representation in the HOMD and National Center for Biotechnology Information (NCBI) genomic databases, including members of the CPR.