dataesr/scientific-paragraphs-categorization huggingface dataset:
Clustering was performed using the Swarm method  22  , chimeric DNA sequences were detected and removed as were any clusters containing only a single sequence. After trimming and filtering a total of 31,714,787 amplicon sequences remained with an average read length of 255 nt. Statistical analyses were carried out using R CRAN version 3. 4. 3 and specific R packages  23. The Phyloseq package  24  was used to compare community structure, and DESeq. 2 was used for differential abundance analysis. The HOMD database was used to assign cluster taxonomy  25. The multivariate longitudinal analyses were conducted as follows: OTU count table were transformed as relative proportions using Total Sum Scaling, followed by Centered Log Ratio transformation  26. Principal Component Analysis was conducted using the mixOmics R package  27.
Acknowledgements The authors would like to acknowledge all the families who have given up time to be involved in the cohort, the Maternal and  Child Health Nurses  and administration staff who assisted with recruitment. We also acknowledge  Dr. Andrea de Silva  as well as the project staff who have been involved in the cohort. This research was supported by: The  National Health and Medical Research Council (Primary Health Care  Project Grant  425829 , Career Development Fellowship 1087415 to KALC);  Dental Health Services Victoria ;  Financial Markets Foundation for Children ;  Jack Brockhoff Foundation ;  La Trobe University , the  Victorian Government Department for Education and Training  and the  Australian Government Department of Industry, Innovation and Science  Grant  ID 20080108  through the  Oral Health Cooperative Research Centre.
For each patient, volume of parotid and submandibular glands was obtained by multiplication of the diameters in every plane divided by two. Volume was statistically smaller for women amongst asymptomatic controls; it was not linked to any anthropometric data otherwise. In this study, submandibular glands volume was reduced for SS patients (by 33% for female patients with pSS) compared to asymptomatic controls, whilst parotid volume was not. The authors suggest it may be related to histological differences, the mucous component of submandibular glands being more developed and more affected by SS. Clinical description of salivary glands was not detailed in the article. Volumetric approach of parotid glands by US is limited by its morphologic features; it is composed of two parts, the deepest one being inaccessible to palpation or US assessment  [34].
Isolation and growth conditions In February 2018, we isolated two bacterial strains from the oral cavity of a healthy 32-year-old man that could not be identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The screening was performed on a Microflex LT spectrometer (Bruker, Daltonics, Bremen, Germany) as previously reported  [6]. Spectra obtained of strain Marseille-P6182 T (Fig. 1 ) and of strain Marseille-P6184 T (Fig. 2 ) were imported and analysed using the BIOTYPER 3. 0 software against the Bruker database, which was continually incremented with the MEPHI database  [6]. The strain was isolated on 5% sheep blood-enriched Columbia agar (bioMérieux, Marcy l'Etoile, France) at 37°C in an anaerobic atmosphere (anaeroGEN; Oxoid, Dardilly, France) after a 2-day preincubation in an anaerobic bottle supplemented with 5% sheep blood and 5% rumen fluid, previously sterilized through a 0.
Strain identification In order to classify these bacteria, the 16S rRNA gene was amplified using the primer pair fD1 and rP2 (Eurogentec, Angers, France) and sequenced using the Big Dye® Terminator v1. 1 Cycle Sequencing Kit and 3500xLGenetic Analyzer capillary sequencer (Thermofisher, Saint-Aubin, France) as previously described  [7]. The 16S rRNA nucleotide sequence was    Strain Marseille-P6182 T exhibited a 92. 49% 16S rRNA similarity with Actinotignum urinale strain R9242 (GenBank accession number NR_028978. 1), the phylogenetically closest species with standing in nomenclature (Fig. 5 ). We consequently proposed to classify strain Marseille-P6182 T as a new genus within the family Actinomycetaceae in the phylum Actinobacteria. Strain Marseille-P6184 T exhibited a 98. 36% 16S rRNA similarity with Pseudopropionibacterium propionicum strain NCTC11666 (GenBank accession number LR134535.
Genome sequencing Genomic DNA was extracted using the EZ1 biorobot with the EZ1 DNA tissue kit (Qiagen, Hilden, Germany) and then sequenced on a MiSeq sequencer (Illumina Inc. , San Diego, CA, USA) with the Nextera Mate Pair sample prep kit and Nextera XT Paired End (Illumina), as previously described  [8]. The assembly was performed using a pipeline containing several softwares (VELVET  [9] , SPADES  [10]  and SOAP DENOVO  [11] ) on trimmed data (MISEQ and TRIMMO-MATIC  [12]  softwares) or untrimmed data (only MISEQ software). GAPCLOSER was used to reduce assembly gaps. Scaffolds <800 bp and scaffolds with a depth value <25% of the mean depth were removed. The best assembly was selected using different criteria (number of scaffolds, N50, number of N). The genome of strain Marseille-P6182 T was 1 867 681 bp long with a 62.
88 mol% G + C content. The degree of genomic similarity of strain Marseille-P6182 T with closely related species was estimated using the ORTHOANI software  [13]. ORTHOANI values among closely related species (Fig. 7 ) ranged from 66. 12% between Actinotignum schaalii and Arcanobacterium phocae, to 93. 84% between Trueperella bernardiae and Trueperella pyogenes. When Neoactinobaculum massilliense was compared with these closely related species, values    ranged from 66. 08% with Arcanobacterium phocae, to 86. 50% with Actinobaculum suis. The genome of strain Marseille-P6184 T was 4 393 662 bp long with a 543 mol% G + C content. The degree of genomic similarity of strain Marseille-P6184 T with closely related species was estimated using the ORTHOANI software  [13]. ORTHOANI values among closely related species (Fig.
Nucleotide sequence accession number The 16S rRNA gene and genome sequences of Neoactinobaculum massilliense gen. nov. , were deposited in GenBank under accession number LS999995 and UWPE00000000, respectively. The 16S rRNA gene and genome sequences of Pseudopropionibacterium massiliense sp. nov. , were deposited in GenBank under accession number LS488977 and UWTZ00000000, respectively.
Acknowledgements A large portion of the work was performed in the framework of the  SISCERA  project funded by the  European Union 's  Horizon 2020 Research and Innovation Framework Programme -Fast Track to Innovation Pilot  ( FTIPilot2016-1 ) -under Grant Agreement No. 737954. F. Zhang  thanks the support of the  Research Foundation Flanders (FWO Vlaanderen ), who awarded her a post-doctoral fellowship ( 12S8418N ) during the time the manuscript was written. We thank  Ivoclar Vivadent  for providing the IPS e. max CAD samples (HT,  A2/B40 L ), PhD student  Evita Willems  and  Prof. Jef Vleugels  (both from  KU Leuven ) for preparing some zirconia samples, and  Prof. Marleen Peumans  ( KU Leuven ) for the translucency measurements.
This study confirms GWAS and pan-GWAS trait associations can be performed for biofilm phenotype and produce data in agreement with each other. This panel of 280 study isolates, matched to genomic data has potential for the investigation of other phenotypes in P. aeruginosa perhaps as part of a growing database / collection. A representative, curated, genome sequenced collection should increase in usefulness as it grows offering increasing statistical power. Importance P. aeruginosa is a major cause of multiply antibiotic infections worldwide but it is also found in many hospital and natural environments, especially aquatic ones. In this study we examined genetic polymorphism associated with biofilm production at room temperature and at body temperature, the biofilm associated gene repertoire of two major MDR clones and also genetic polymorphisms associated with biofilm production on stainless steel.
Bacterial isolates and genome sequences This study analyzed two different sets of P. aeruginosa isolates. The first set, here-on-in described as 'temperature-dependent biofilm analysis' contained 280 isolates (Supp Table  1 ), for which genomic data and antibiotic susceptibility phenotype has previously been described  7, 8. The second set, here-on-in described as 'stainless steel biofilm analysis' contained 260 P. aeruginosa genomes (Supp Table  2 ), 153 of which belong to the ST111 clone and 107 to the ST235 clone. Of these, 25 ST111 and 23 ST235 isolates were used to study biofilm phenotypes. All genomic data were downloaded from Genbank as fasta nucleotide sequences. Bacterial strains used for biofilm phenotyping were provided by bioMérieux (France) and Synthetic Genomics (USA) and were analysed in two previously published studies  6, 7.
Construction of phylogenies Core Single Nucleotide Polymorphisms (SNPs) were identified using the KSNP3 pipeline  24. Kmer lengths of 21 were used for temperature-dependent biofilm analysis, whilst for stainless steel biofilm analysis, kmer lengths for ST111 and ST235 were 21 and 23 nucleotides respectively. Kmer lengths were selected using the KCHOOSER module within the KSNP3 suite. Bayesian phylogenetic analysis was performed using BEAST 2  25. The following conditions were set: gamma site heterogeneity model, Hasegawa-Kishino-Yano (HKY) substitution model, relaxed-clock log-normal, chain length 5,000,000. BEAST 2 output was summarized using TreeAnnotator with a 5% burn in.
Pan-genome-wide association analysis Scoary is a software tool able to provide pan-genome associations (pan-GWAS) based on user-defined traits using an input (gene presence / absence) file generated by Roary  31. Analysis was performed independently for temperature-dependent biofilm traits as for both ST111 and ST235 genomes in the stainless steel biofilm analysis. Statistical significance of the associations was tested by Scoary with a Fisher's exact test, and a pairwise comparisons algorithm to control spurious associations from stratified populations. P values were corrected for multiple comparisons using the Bonferroni adjustment. Where Scoary analysis provided genes significantly (p<0. 05) associated with the biofilm phenotype that had not previously been annotated in PROKKA, and therefore considered hypothetical / putative, the amino acid sequence was searched in BLASTP, and if no hit was found, assessed using the sensitive protein homology detection, function and structure prediction tool HHPred (MPI Bioinformatics Tool Kit)  32.
SNP genome-wide association study We used PLINK v1. 90b5. 3  33 to explore SNP-based associations with user-defined traits. Analysis was performed in PLINK to test case / control associations with Fisher's exact test, and return Bonferroni adjustments for statistical significance. Analysis was performed independently for temperature-dependent analysis as before for both ST111 and ST235 genomes in the stainless steel dataset using core SNP data produced by the KSNP3 pipeline. SNPs significantly associated with phenotype (p<0. 05) where located in the genome using Artemis genome browser  34. Genes containing SNPs of interest were interrogated using BLASTP and HHpred, with the top three predictions with a probability match of over 80% considered for assumed protein function.
Background EMONO is an equimolar mixture of oxygen and nitrous oxide available in France for dental care. It has an analgesic effect with a reduction of the perception threshold of different painful stimuli and an anxiolytic effect. It causes modifications in consciousness: patients are relaxed, sedated and less aware of their surroundings. Pulmonary absorption and elimination of nitrous oxide occur very quickly because of its low solubility in blood and tissues, explaining the rapidity of the analgesic effect and quick return to the initial status after discontinuation of inhalation  [1] [2] [3] [4] [5]. Based on the product characteristics summary available in the French government's public drug database [base-donnees-publique. medicaments. gouv. fr/], EMONO indications in dentistry are dental care for infants, children and adolescents, as well as for anxious and patients with disabilities.
Study design This observational, descriptive, transversal study aims to evaluate the effects sought and felt by children when EMONO is used in paediatric dentistry. Subjects needing dental care under EMONO were recruited by 12 French dental service university hospitals. Thereafter, the data are collected by practitioner observation, direct interview after dental care under EMONO and using the subject's medical record. This project received the financial support from the French National Agency for Medicines and Health Products Safety (ANSM) as part of the 2017 'national call for tender' and also received funding from the local Scientific Committee of the Faculty of Dental Surgery in Nantes as part of the 2017 call for tender.
Objectives to describe and compare the clinical and biological characteristics of subjects with primary Sjögren's syndrome (pSS) with and without anti-rnP antibodies. Methods Patients fulfilling the american college of rheumatology (acr)/eUlar 2016 criteria for pSS and having anti-rnP antibodies, without other connective tissue disease diagnosed and no anti-dsDna antibodies were retrieved from the database from our French national reference center. these patients were compared with all other patients with pSS with negative anti-Sm, anti-rnP and anti-dsDna antibodies. Results Overall, 21 patients with pSS positive for anti-rnP antibodies and 446 negative for anti-rnP antibodies were retrieved. anti-rnP-positive patients had a lower median age at onset of pSS symptoms (41. 0 vs 50. 0 years, p=0.
Patient selection Patients fulfilling the American College of Rheumatology (ACR)/EULAR 2016 criteria for pSS without other CTD diagnosis and having anti-RNP antibodies, without anti-DNA antibodies were searched in the database from the French National Reference Center for pSS in Paris-Sud University. 2  Patients fulfilling Systemic Lupus International Collaborating Clinics (SLICC) criteria for SLE (positive if ≥4) were excluded. 8 We compared these patients with all patients with pSS from the Paris-Sud cohort with negative anti-Sm, anti-RNP and anti-DNA antibodies. Paris-Sud cohort is a prospectively collected database of all patients participating in multidisciplinary sessions to assess a suspicion of pSS since 2000 in the Rheumatology Department of Paris-Sud University Hospital. All patients gave their informed consent to their data collection.
G ( ) J ( ) I with β the dilatancy parameter. The material parameters were identified via an inverse method. This method consisted in simulating the indentation test and adapting the materials parameters in order to minimize the difference between the numerical simulation and the corresponding experimental results. This minimization was made in the least squares sense. The resolution of this optimization problem was implemented in MIC2M software using a Levenberg-Marquardt algorithm (see details in the method in  [25] ,  [47] ,  [48] ).
Acknowledgements: Emmanuel Artiges  for the compression tests,  Marc Bohner  ( RMS foundation, Switzerland ) for the supply of the β-TCP samples,  Jérôme Adrien  ( MATEIS ) for X-ray tomography,  Laurent Gremillard  ( MATEIS ) for Rietveld refinements of X-ray diffractograms. This work was supported by the  European Commission  funding of the  7th Framework Program (Marie Curie Initial Training Networks ; grant number:  289958 ,  Bioceramics  for bone repair) and by the  French Ministry for Education and Research , through a  "Thématiques prioritaires" grant.
| Defining dental anomalies Existing terminology of dental anomalies was analyzed by obtaining data from several databases, nomenclatures, and ontologies (Supplementary Data Table  S1 ): HPO (Human Phenotype Ontology  (Groza et al. , 2015) , Orphanet  (Rath et al. , 2012 ), NEN9313:2015, D[4] phenodent  (Bloch-Zupan, 2004 ), ICD10-ICD11, and the standard terminology of Elements of Morphology for the lips, mouth, and oral region  (Carey et al. , 2009). When worded differently, the present definitions supersede the ones from  Carey et al. , 2009. Data collected  were formatted according to Elements of Morphology series  (Allanson et al. , 2009). T A B L E 1 Nosology of rare dental disorders listing 408 different conditions  (Issa et al. , 2016) ,  (Kantaputra et al. , 2015) ,  (Peled et al. , 2016) ,  (Laugel-Haushalter et al.
Maxillary molars have three roots, two vestibular, and one palatal. Mandibular molars have two roots, one mesial, and one distal. Their shape and size may vary according to sex, ethnicity, and geography. F I G U R E 1 The oral cavity and its mean structures (modified from Carey et al. , 2009) [Color figure can be viewed at wileyonlinelibrary. com] F I G U R E 2 The normal oral mucosa around teeth (G gingiva, LM lining mucosa, MGJ mucogingival junction) [Color figure can be viewed at wileyonlinelibrary. com] F I G U R E 4 (a) Teeth in the dental arches, th odontogram is from D[4]/phenodent database. (b) This table represents the normal mesiodistal and standard deviation (M=Male; F= Female) [Color figure can be viewed at wileyonlinelibrary. com] F I G U R E 3 Major anatomical landmarks of the teeth (see text) [Color figure can be viewed at wileyonlinelibrary.
We hope that these clinical descriptions are useful in patient's care, especially in case of multi-disciplinary discussions. Dental anomalies are relevant clinical signs and may provide key clues for F I G U R E 5 9 Overjet increased evident in the increase of horizontal distance between maxillary and mandibular teeth [Color figure can be viewed at wileyonlinelibrary. com] F I G U R E 6 0 Gingival overgrowth [Color figure can be viewed at wileyonlinelibrary. com] la Recherche under the frame programme Investissements d'Avenir labelled ANR-10-IDEX-0002-02. This work was also funded by INSERM.
ACKNOWLEDGMENTS This initiative participates to the actions of the project No. 1. 7 "RARENET: a trinational network for education, research and management of complex and rare disorders in the Upper Rhine" co-financed by the  European Regional Development Fund (ERDF)  of the  European Union  in the framework of the  INTERREG V Upper Rhine program  as well as to the  ERN (European reference network) CRANIO initiative. BF is the holder of an INTERFACE contract,  INSERM/APHP , which supported this study. We are grateful to la  Fondation des "Gueules Cassées " who supported this research field and several authors research. ABZ is a USIAS 2015 Fellow of the  Institute of Advanced Studies (Institut d'Etudes Avancées) de l'Université de Strasbourg, France. International Collaboration Capes-Cofecub Grant, Brazil and France  (MDLD, ACA, AB).
We thank  Karen Niederreither  for careful and critical reading of the manuscript. We are grateful to patients and their families for continuous support. We would like to acknowledge and pay tribute to  Robert James Gorlin ,  Crispian Scully ,  Heddie Sedano , and  Robin Winter  for their invaluable contributions to the field. We assure no conflict of interest. The grant  ANR-10-LABX-0030-INRT , a  French State  fund managed by the  Agence Nationale de.
Materials and methods: We modeled and reconstructed the paranasal sinuses of two patients, before and after trauma, using two different softwares (3DSlicer and Blender). Both patients had different numbers and locations of fractures. The 3DSlicer® software was used to create a 3D model from CT data. We then imported the 3D data into the Blender® software, to reconstruct and compare the dimensions of the paranasal sinuses before and after trauma.
However, as a limitation, a number of victims who could benefit from this technique have severe and distorting craniofacial trauma that could hamper this comparative analysis. For instance, in case of mass disaster such as an earthquake or an aircraft crash, the visual comparison of pre and post-mortem CT data could not be achieved due to the victims' shattered facial bones. To address this limitation, we hypothesized that advances in the analysis and post-processing of CT data could allow a virtual reconstruction of facial bone anatomy when it is modified by a trauma. The purpose of this study was to report the feasibility of computed modelization and reconstitution of the paranasal sinuses, before and after trauma, from CT data.
Patients We retrieved the CT data of two patients' skulls from the digital archiving network of our institution, choosing cases where pre-and post-trauma acquisitions were available, with different numbers and locations of fractures. We anonymized and labelled them "patient A" and "patient B" (Fig. 1 ). Patient A was a 45-year-old man with 3 fragments, involving a piece of the lateral wall of the right maxillary sinus and two parts of the right zygomatic arch. Patient B was a 59-year-old man with 7 fragments, involving both maxillary sinuses, the nasal septum and the right frontal sinus.
Modelization steps For each of the four CT acquisitions, we successively performed the following steps of analysis. We imported DICOM CT data from the skull (in a "soft" filter) on an open source software, 3DSlicer®, developed by the Laboratory of Mathematics in Imaging of the Harvard Medical School. We then used the "Crop Volume" module of this software to focus the volume of interest on the paranasal sinuses and the mastoids, in the transverse, sagittal and coronal planes, after having modeled the cranial volume in three dimensions (3D), using the volume rendering application. We used the "threshold effect" function of the "Editor" module to semi-automatically generate a highlighting of bone walls Then to refine the modeling manually, we used the "Paint Effect" function of the same module (Fig.
Reconstitution steps The reconstruction part required the Blender® software, developed by the Blender Foundation. We started by importing 3D volumes from "pre-trauma" acquisitions into the Blender® workspace. The next step was to make the outlines of the volumes transparent. To do so, we clicked on the "Material" tab located in the right column and then on "+ New". We checked the "Transparency" box that appears in the drop-down menu below, then set the "Alpha" value of the "Z Transparency" submenu to 0. 300. The last step was to click on the bottom menu tab that changes the way the 3D object is seen ("Viewport shading" menu), and to select "Material". This visualization mode makes it possible to measure distances inside the paranasal sinuses. To carry out these measurements, it was necessary to use the left column, to select the "Grease Pencil" tab, then to click on "Ruler / Protractor".
Results Patient A had facial bones fractures consecutive to a brawl. Patient B had Parkinson's disease and fell from his height. For both patients we were able to modelize CT data and reconstruct the traumatized facial anatomy in the same configuration as pre-traumatic CT. The various intra-sinus measurements of the two patients, including width, height and depth of each paranasal sinus are reported in Table  1. The dimensions of the different paranasal sinuses were similar between pre and post-fracture volumes, with a maximum error of 0. 06 mm. The inner angle of the pre-fractured right zygomatic arch of the patient A was 146°, vs. 143° on the reconstructed post-fractured volume. The angle was measured in the middle of the arch (Fig. 4 ).