dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical Analysis. The experimental design included (i) two fixed crossed factors: irradiation [yes(I)/no(NI)] and adhesive system (XTR/FL) leading to 4 subgroups and (ii) a random factor (tooth) nested in each subgroup: 10 teeth per subgroup with one to four replicates per tooth. The conditions for the application of statistical treatment were carefully verified. The effect of the tooth factor on the explained variable (bond strength of sticks: TBS) was first assessed by a mixed linear model on the full dataset. In case of nonapplicability of this mixed model, we conducted a oneway nonparametric ANOVA per subgroup using Kruskal-Wallis test. Missing data were supposed to be missing at random and no data imputation was performed. In case of no tooth effect on TBS, normality of TBS data was checked graphically and using the normality Shapiro test for each of the 4 subgroups.
In case of nonrespect of normality in one subgroup, pairwise distributions comparisons were performed between subgroups. Four comparisons were a priori of interest: between the two control subgroups (NI:XTR versus NI:FL), between the two irradiated subgroups (I:XTR versus I:FL), and for each adhesive system: (NI:XTR versus I:XTR) and (NI:FL versus I:FL). Correction for multiple comparisons was performed to maintain the family-wise error rate at the significant level of 5%. For 4 pairwise comparisons, Bonferroni correction gave a significant level of 2-tailed single test equal to 0. 05/4, that is, 0. 0125. Data were reported as mean ± SD per subgroup. Statistics were performed using the R language, version 3. 1. 2 available on the https://cran. r-project. org/ website. Package nlme was used to perform mixed linear model.
The setting of this study is the Department of Paediatric Dentistry at 3 University dental hospitals in France. The primary outcome measure will be pain reported by the patient on a visual analogue scale concerning the insertion of the needle and the injection/infiltration. Secondary outcomes are latency, need for additional anaesthesia during the treatment and pain felt during the treatment. We will use a computer-generated permuted-block randomisation sequence for allocation to anaesthesia groups. The random sequences will be stratified by centre (and by dental arch for the parallel-arm RCT). Only participants will be blinded to group assignment. Data will be analysed by the intent-to-treat principle. In all, 160 patients will be included (30 in the split-mouth RCT, 130 in the parallel-arm RCT).
STATISTICAL METHODS The unit of analysis will be the tooth for the split-mouth RCT (two permanent first molars belonging to the same dental arch treated per patient) and the patient for the parallel-arm RCT (only one permanent first molar treated per patient). We will compare pain mean scores according to the VAS and mean latency between anaesthesia with conventional injection and intraosseous anaesthesia. We will report the mean differences between groups and the associated 95% CIs. For the split-mouth RCT, with each patient being his or her own control, our statistical analysis will take into account the paired nature of data and the results will be analysed by Student t test for paired samples. We will also compare intervention effect estimates between the split-mouth and parallel-arm RCTs.
The analyses will follow the intent-to-treat principle. 20 nitoring A Data Monitoring Committee is not needed because of the short duration of patient participation and known minimal risks. We did not plan any interim analysis or early stopping. Adverse events will be collected and reported according to the usual reported system of the sponsor. Audits may be mandated by the trial sponsor (Assistance Publique-Hôpitaux de Paris) and, if carried out, will be independent of the investigators.
Data Collection The PubMed database was searched in September 2014 for randomized controlled trials that evaluated the in vivo effect of RI on caries lesion progression. The search was undertaken with the following keywords: 'resin infiltration, dental caries', 'resin infiltration, carious lesions', 'resin infiltration, caries lesions', 'caries infiltration' and 'Icon DMG' with the 'clinical trial' filter activated. The articles were included for review on the basis of their compliance with the inclusion criteria, namely (1) the title or abstract was relevant to the topic and (2) they reported an in vivo trial. Each article that complied with the inclusion criteria was evaluated by two authors (R. D. and S. D. ) for study quality  [12]  , namely the generation of the randomization sequence (allocation), the study design, the blind outcome assessment, the control group and the completeness of follow-up (i.
The unit of analysis was the related lesion pair or a group of three lesions. The outcome variable was the proportion of lesions that progressed during the study period. In all 4 articles, outcomes were assessed by pairwise comparison of the depth of the lesions scored on bite-wing radiographs. Meyer-Lueckel et al. [16]  and Paris et al. [15]  , however, considered this direct scoring of lesion progression to be a secondary end point and used digital subtraction radiography of the scanned images as the primary end point. Martignon et al. [14]  also used digital subtraction radiography at the 1-year review but not thereafter. Ekstrand et al. [13]  based their assessment on radiographs and the collection data with a direct assessment using scoring according to the International Caries Detection and Assessment System (ICDAS).
The 4 articles differed in terms of study design, dentitions and observation periods, and there were some differences in evaluation methods. There was, however, homogeneity between the studies in terms of certain aspects of the protocol and outcome assessment (e. g. the proportion of caries lesions that progressed during the study period shown by pairwise comparison on digitized bite-wing radiographs) which allows for some comparisons to be made. Nevertheless, the compilation of the results was not deemed meaningful because 1 of the included studies was undertaken on primary teeth  [13]  whereas the others involved permanent teeth where RI was compared to different control/placebo groups  [14] [15] [16]. The major limitation of this paper is the small sample which was due to the restricted search of the articles published in only one medical database, PubMed.
The strain STAB10015 was grown in Todd-Hewitt medium supplemented with 0. 2% yeast extract (THY), and DNA for sequencing was extracted and purified using the phenol-chloroform technique. Genomic DNA was sequenced using HiSeq 2000 technology (Illumina, Inc. , San Diego, CA), and the paired-end library was built at the MGX facility of the CNRS in Montpellier, France. There is a total of 36,785,510 high-quality reads, giving an average of 1,933-fold coverage of the genome, which was assembled using the CLC Genomics Workbench version 6 software. The resulting assembly consisted of 56 contigs, which were oriented and connected with the module Microbial Genome Finishing Tools based on the MGAS6180 sequence. After reassembling, 11 gaps persisted, which were filled by PCR, followed by Sanger sequencing.
ACKNOWLEDGMENTS This work was supported by the  University of Rennes 1. Suzane de Andrade Barboza  was supported by the program Science without Frontiers (proc. no. 88888. 051167/2013-00 )and by the  CAPES Foundation, Ministry of Education of Brazil, Brasilia, Brazil. crossmark Genome Announcements July/August 2015 Volume 3 Issue 4 e00806-15 genomea. asm. org 1.
Results We discovered 21 novel pathogenic variants and identified the causative mutation in 39 unrelated patients in known genes (overall diagnostic rate: 39%). Among the largest subcohorts of patients with isolated AI (50 unrelated patients) and isolated STHAG (21 unrelated patients), we had a definitive diagnosis in 14 (27%) and 15 cases (71%), respectively. Surprisingly, COL17A1 mutations accounted for the majority of autosomal-dominant AI cases. Conclusions We have developed a novel targeted NGS assay for the efficient molecular diagnosis of a wide variety of orodental diseases. Furthermore, our panel will contribute to better understanding the contribution of these genes to orodental disease. Trial registration numbers NCT01746121 and NCT02397824.
Library preparation, sequencing and data analysis Targeted regions were captured using a Custom SureSelectXT2 in-solution target enrichment kit (Agilent) and libraries were prepared for sequencing (2×100 bp) on the HiSeq2500 (Illumina, USA) following the manufacturer's instructions. For v1. 0, 16 samples were multiplexed per lane for sequencing, whereas for v2. 0, 32 samples were multiplexed per flow-cell lane. Read alignment, and variant calling and annotation were performed using standard methods. Briefly, reads were aligned to the GRCh37 reference genome using Burrow-Wheeler aligner (v0. 7. 5a)  51  ensuring tagging of multi-mapped reads, and duplicates were marked with Picardv1. 102 (http://picard. sourceforge. net). 3] [54]  Variants were annotated using snpEffv. 3. 4. 55 Variant frequencies were compared with an internal exome database and prioritised using VARank.
56 Variants were prioritised by allele frequency (<1% in the Single Nucleotide Polymorphism database (dbSNP137), 1000 Genomes database,  57  Exome Variant Server (EVS) database  58  and our internal database, except for non-syndromic STHAG, for which we used a cut-off of <4%) and predicted functional effect (frameshift, invariant splice sites, nonsynonymous and splice affecting mutations). 3] [64] [65] [66] [67]  CNVs were detected as previously described. 44 45 ariant pathogenicity was interpreted according to the American College of Medical Genetics guidelines. 68 Evidence used to establish pathogenicity is provided in online supplementary figures S1-S45.
Mutation validation All mutations were validated by Sanger sequencing (GATC, Germany). Segregation analyses were performed whenever DNA was available for additional family members. Single-molecule PCR followed by Sanger sequencing was used to phase biallelic mutations when parental DNA was unavailable. 69 70 Deletions were validated by qPCR. The region of interest and an internal control region (RPPH1) were amplified from 2 ng of genomic DNA from the patient and a control using the iQ SYBR Green Supermix (170-8880, Biorad, USA) on a CFX96 Real-Time System (Biorad). Data were analysed using the Pfaffl method. 71.
The majority of these regions were in the discovery subpanel (28. 1 kb). Under-representation of high GC content and pseudogenic regions is a known issue with probe-based targeting strategies. However, these gaps can be filled in by Sanger sequencing for regions considered to be relevant on a case-by-case basis. On average, we detected ∼2648 variants/ sample, of which ∼87 variants/sample were rare (<1% in dbSNP137, 1000Genomes, EVS and an in-house database). Among these rare variants, we identified on average per sample ∼20 missense changes, 0. 38 nonsense mutations, 0. 25 splice-site changes and 0. 56 frameshift-inducing indels (see online supplementary table  S6 ).
Acknowledgements The authors would like to thank all patients and their families for participating in this study. They also thank  Ms Vanessa Stoehr  for administrative help,  Dr Mathilde Huckert  and  Jorel Salomon  for technical assistance,  Drs Elise Schaefer  and  Sophie Scheidecker  for help with obtaining clinical data, and  Dr Yaumara Perdomo-Trujillo  for the electroretinography examination. They would like to thank  Drs Alain Verloes ,  Jean-Yves Sire ,  Jean-Pierre Clavert ,  Béatrice Walter ,  Patrick Lutz ,  André Nirrengarten ,  Isabelle Rian ,  Thibault Sibert ,  Laurence Lustig-Grimm ,  Daniel Jasiak ,  James Lespinasse ,  Jacques Hassid ,  Smail Hadj-Rabia ,  Gabriel Dominici ,  Laurent Riguet ,  Dan Lipsker ,  Jean Luc Alessandri ,  Florence Rousselet ,  Philippe Schoenlaub ,  François Serres ,  Etienne Mornet ,  Thomas Edouard ,.
Materials and Methods Medline and Web of Science were searched for articles published before May 2014 without any limits for the publication date or language. We carried out a title/abstract search in the PubMed, abstract search in Medline and topic search in Web of Science, using the following terms: khat OR qat OR miraa OR Catha edulis. We did not limit the search to a particular health outcome to make sure not to miss any relevant papers. In addition, to the electronic database search, we reviewed the list of references of all eligible studies included in this systemic review. All search results were combined in a bibliographic management tool, EndNote ® , with duplicate record removed. Studies on potentially malignant oral disorders, based on the WHO definition,  39  or oral cancer were included in our review, if they met the following criteria: 1) published in English or Arabic, and 2) reported as case-series, case report, and cross-sectional, cohort and case-control studies.
Patients and Procedures The study design and inclusion/exclusion criteria for this open-label, phase II study were previously reported (ClinicalTrials. gov identifier NCT00680992). 23 Briefly, adults or skeletally mature adolescents (C12 years of age) weighing C45 kg with radiologic evidence of C1 mature long bone, histologically confirmed GCTB, radiographically measurable active disease within 1 year before study enrollment, and Karnofsky performance status C50 % were enrolled. Exclusion criteria included concurrent use of alternative treatments for GCTB; known or suspected diagnosis of sarcoma, non-GCTB, giant cell-rich tumors, brown cell bone tumor of hyperparathyroidism, or Paget disease; diagnosis of a second malignancy in the past 5 years; history or current evidence of osteonecrosis or osteomyelitis of the jaw, active dental or jaw problems necessitating oral surgery, or nonhealed dental or oral surgery; or pregnancy.
ACKNOWLEDGMENTS This work was funded by  Amgen Inc. Medical writing support was provided by  Rick Davis, MS ,  Meghan Johnson, PhD  (on behalf of  Amgen Inc. ), and  Albert Rhee, PhD  ( Amgen Inc. ). DISCLOSURE  Piotr Rutkowski  and  Leanne L. Seeger  have received honoraria from  Amgen Inc. ;  Stefano Ferrari  has served on advisory boards for  Amgen Inc. and  GlaxoSmithKline , has received research funding from  MolMed, Pharmar, Morphotek , and  Amgen Inc. , and has received honoraria from  Takeda ;  Robert J. Grimer  has served on advisory boards for  Amgen Inc. ;  Sander P. D. Dijkstra  has served on advisory boards for Implantcast GmbH; and  Amy Feng ,  Zachary J. Roberts , and  Bruce A. Bach  are employed by and own stock in  Amgen Inc. Paul D. Stalley ,  Andrzej Pienkowski ,  Gualter Vaz , and  Jay S.
Osteoarticular mycoses due to non-Aspergillus moulds are uncommon and challenging infections. A systematic literature review of non-Aspergillus osteoarticular mycoses was performed using PUBMED and EMBASE databases from 1970 to 2013. Among 145 patients were 111 adults (median age 48. 5 [16-92 y]) and 34 pediatric patients (median age 7. 5 [3-15 y]); 114 (79. 7%) were male and 88 (61. 9%) were immunocompromised. Osteomyelitis was due to direct inoculation in 54. 5%. Trauma and puncture wounds were more frequent in children (73. 5% vs 43. 5%; P ¼ 0. 001). Prior surgery was more frequent in adults (27. 7% vs 5. 9%; P ¼ 0. 025). Vertebral (23. 2%) and craniofacial osteomyelitis (13. 1%) with neurological deficits predominated in adults. Lower limb osteomyelitis (47. 7%) and knee arthritis (67.
Search Criteria To identify fungal osteomyelitis and arthritis caused by hyaline hyphomycetes, Mucorales, and dematiaceous fungi, we used the OvidSP search platform in the MEDLINE and EMBASE databases using the following keywords: fungi, Ascomycota, Pseudallescheria, Chaetomium, Schizophyllum, Mucorales, mitosporic fungi, Acremonium, Alternaria, Beauveria, Chrysosporium, Cladosporium, Exophiala, Fusarium, Helminthosporium, Madurella, Phialophora, Scedosporium, Scopulariopsis, Trichoderma, Ascomycetes, Basidiomycetes, blastocladiomycota, Deuteromycetes, zygomycetes, zygomycosis, systemic mycosis, entomophthoromycosis, mucormycosis, bone diseases, bone infection, osteitis, osteomyelitis, periostitis, spondylitis, discitis, osteochondritis, osteomyelitis, periostitis, infectious arthritis, bone and joint infections, and reactive arthritis.
Qatar Foundation proposal number NPRP 5-298-3-086 approved the study; the ethical approval was not necessary for the retrospective literature review nature of the research. We retrieved a total of 2421 references published from January 1970 to September 2013. Figure  1  shows the selection process applied to identify the osteoarticular infections. We included cases in the final analysis with data on osteomyelitis and or arthritis, site of infection, underlying disease, and medical and surgical therapy. Other parameters also considered in case analysis were radiological images, inflammatory markers, and disease manifestations. We excluded cases with bone extension from rhinosinusitis, outbreak of Exserohilum rostratum infections after injection of contaminated glucocorticosteroids in USA,  8  as well as cases with missing full texts, and cases of non-English literature.
Data Analysis and Statistical Methods Descriptive statistics were used to summarize all demographic and clinical characteristics of the patients. Quality of data (review of completeness, data verification, and validation and accuracy of data) was assessed by the lead investigators. Quantitative variables are presented as mean AE standard deviation (SD) or as medians (with range). Differences between continuous variables of at least 2 independent groups were analyzed using unpaired t test and 1-way analysis of variance (ANOVA). When an overall group difference was found to be statistically significant, pairwise comparisons were made using the appropriate post-hoc test. Differences between categorical variables were analysed using chi-square test and Fisher exact test, as appropriate. Relationships between 2 continuous variables were further examined using Pearson correlation coefficients.
Diagnostic Procedures and Cocultured Bacteria Median time to diagnosis from onset of symptoms was 90 (7-1825) days. Among 139 diagnostic procedures, diagnosis of fungal osteomyelitis was performed by open biopsy in 96 (69%), percutaneous biopsy in 31 (22. 3%), arthroscopy in 7 (5%), and other surgical procedures in 5 (3. 6%). From these specimens, fungi were detected by culture, direct microscopy, and histology. Bacteria were cocultured from the same specimen in 22 cases; documented bacteria included Staphylococcus aureus followed by Gram-negative organisms, including Escherichia coli and Pseudomonas aeruginosa (data not shown).
Supported by Grant  NPRP 5-298-3-086  from the  Qatar National Research Fund  (a member of  Qatar Foundation ) to  Saad J. Taj-Aldeen. Disclosures: Walsh receives support from the  Henry Schueler Foundation (Scholar in Mucormycosis) ,  Sharpe Family Foundation (Scholar in Pediatric Infectious Diseases) , and from the  Save Our Sick Kids Foundation. DPK is a consultant and board member and received payment for lectures from  Schering-Plough ,  Pfizer , and  Astellas Pharma US , and has received grant support from  Astellas Pharma US  and  Merck ; and has received honorarium from  Enzon Pharmaceuticals. Walsh has received research grants for experimental and clinical antimicrobial pharmacotherapeutics from  Astellas ,  Cubist ,  Novartis ,  Pfizer , and  Theravance. He  has served as consultant to Astellas, ContraFect, Cubist, Drais, iCo,  Novartis ,  Pfizer ,  Methylgene, SigmaTau , and Trius.
Dental caries is the most common chronic disease of childhood. Cariogram is a well-recognized algorithm-based software program based on different caries-related risk factors and intended to aid clinicians in performing more objective and consistent dental caries risk assessments. This type of approach precedes the diagnosis of caries and allows the dentist to identify at-risk patients and then take appropriate preventive measures before caries develop further. One of the etiological factors favoring the development of dental caries is the mutans streptococci. These acidogenic dental plaque inhabitants can be effectively antagonized by the activity of bacteriocins released by the probiotic Streptococcus salivarius M18 (salivarius M18). Moreover, salivarius M18 after colonizing the human oral mucosa produces the enzymes dextranase and urease that are able to counteract plaque formation and saliva acidity, respectively.
mutans counts in colonized primary-school-aged children,  29  and to reduce both moderate and severe gingivitis and periodontitis in adults. 30 n the basis of these biochemical, microbiological, and clinical findings, we determine whether the oral and daily use of the strain salivarius M18 affects or modifies the Cariogram outcome after 90 days of treatment in children at high risk of developing new dental caries. Cariogram is an algorithmbased software program developed in Sweden in 1997 by the University of Malmö, based on nine different caries-related risk factors, along with physician judgment, intended to aid clinicians in performing more objective and consistent dental caries risk assessments. 31 [34] [35] [36] [37] [38].
statistical analysis To study the null hypothesis of no effect of treatment on Carioblis ® for each clinical variable, and for a global summation, we applied the two-tailed Wilcoxon test for matched pairs with signed ranks. To study the effect of Carioblis ® therapy on Cariogram scores, using averaged clinical variables, we used the two-tailed Fisher's exact test. Statistical software JMP ® 10 for Mac OS X (SAS Institute Inc. , Cary, NC, USA) was used, and the threshold for statistical significance was 95%. To calculate the caries risk of a group of subjects (results are shown in Table  1  and Figure  2 ), we used the average value of  any single items of the Cariogram and considered equal to 0 if the decimal values stands between 0. 1 and 0. 4 and equal to 1 if the decimal values were between 0.
The Cariogram software was uniquely implemented to calculate the caries risk of individual subjects. Nevertheless, we have exploited the algorithm of the Cariogram software and used the average value of any single items of the Cariogram to calculate the caries risk of a group of subjects. This nonvalidated procedure allows construction of an image representative of the likely impact that a treatment can have on a group of patients. As shown in Table  1  and Figure  2 , treatment with the strain M18-based product significantly improves the "chances of avoiding new dental caries", from 20 to 70, reduces the parameter "bacteria", from 29 to 7, and reduces the "susceptibility", from 23 to 9. No relevant variations were evident in the untreated group. Finally, in Table  6 , the M18-based treatment demonstrated a very good safety profile with no treatment-related side effects and no subject dropout.
Discussion Caries risk assessment is an important tool assisting the dentist in obtaining a better understanding of the dental profile of a patient. The Cariogram software has been clinically proven to be effective in evaluating such a risk. 39 Cariogram is based on a set of nine pathological and protective factors, in addition to the professional judgment of the expert dentist. Among these factors, the likely most relevant variable in caries risk prediction is "caries experience" and, as a matter of fact, a strong relationship has been shown between caries experience and caries risk profile. 40, 41 Apparently, microbial tests, aimed at evaluating the presence of mutans streptococci, do not seem to be equally relevant. This could be because, in the presence of fluoride, along with an appropriate diet in terms of quality and quantity, a high number of mutans streptococci may be tolerated without causing significant harm to the teeth.