dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements The authors thank head nurse Linda Ljones, radiographer  Marianne Lothe , prosthodontist  Christine Jonsgar  ( University of Bergen, Norway ), and research coordinator  Marianne Lehmann  ( Haukeland University Hospital, Bergen, Norway ) for their expertise and help. They would also like to acknowledge the important contribution of the patients, without whom this study could not have been undertaken. The authors acknowledge the contribution of  Endre Hellem  and  Daniele de Santis  for valuable discussions. They also thank  Prof. Kristina Arvidson Fyrberg  and  Prof. Michele Cottler-Fox  for input to the protocol and helpful comments on the manuscript and  Prof. Stein A. Lie  ( Biostatistician ) for statistical analysis. The authors also acknowledge  Jerome Amiaud  for performing decalcified histology on biopsies ( Inserm/University of Nantes, France ).
Funding The financial support of the  European Union 's  Seventh Framework Programme  under grant agreement number  241879 -REBORNE is acknowledged. The authors also acknowledge the significant contribution by  Institut Straumann AG (Basel, Switzerland)  for providing the dental implants,  Osteogenics Biomedical (Lubbock, TX, USA  for the Cytoplast polytetrafluoroethylene membranes, and  Ostell (Gothenburg, Sweden)  for the Ostell device.
Search methods, search strategy, and study selection The period of search was limited till 1 July 2018. A detailed search was conducted in MEDLINE via the electronic database PubMed. Electronic search of the publications was carried out by using controlled index terms and relevant specific free text words without any language restrictions. Furthermore, manual screening of all references to earlier systematic reviews and selected full-text articles was accomplished for finding potentially useful articles. Specific strategies were applied for each subject. The search strategy encompassed appropriate variations in the keywords, following the syntax rules of the database (Supplementary Appendix I). The PICO approach was applied to obtain data from the included articles independently by two review authors.
Study selection The result of this systematic review was based on the PRISMA statement (10). We found a total of 2806 publications from the PubMed database. After first assessment and removal of duplicates, a total of 186 publications were selected. Sixty-seven articles were rejected based on exclusion criteria. Following QUADAS assessment, a total of 37 articles were included in the protocol (Figure  1 ). The period of search was limited from 1997 until 1 July 2018, since CBCT in dentistry was introduced in 1998 (2). Currently, there is ample literature on the use of CBCT imaging for diagnosis and treatment planning of dentomaxillofacial deformities in paediatric patients, yet most of them are described in the form of case reports or case series due to the rarity of appearance. We did not want to withhold these reports and summarized them in Supplementary Table  1.
Subjects For the ex vivo reproducibility HR-pQCT images, scanning was performed on a total of 15 fresh frozen cadaveric forearms (left forearm, male/female: 21-81/45-95 years old, respectively). All forearms were disarticulated at the elbow, thawed and scanned three times within 48 hours. The time lag between each scan was within the same day and scanning was performed by a single operator. None of the donors were from a vulnerable population and all donors or next of kin provided written informed consent that was freely given. The study was approved by an independent Ethics Committee (Comitede Protection des Personnes Sud-Est II). For the in vivo reproducibility HR-pQCT images, image data from a previous study  [13]  were used. Scanning was performed on a total of 15 healthy individuals (21-47 years old).
Image registration Several image registration algorithms have been reported for the processing of time-lapse in vivo micro-CT images  [5, 17]. Here, we use 3D rigid image registration and an algorithm that maximises image correlation in three different image resolution steps as implemented in the scanner software (Image Processing Language IPL, V5. 16/FE-v01. 16, Scanco Medical AG, Bru ¨ttisellen, Switzerland). The image registration method was applied to the grey-level images (2 bytes per voxel, 110 slices) where the follow-up images were registered individually to the baseline images. This procedure provides a transformation matrix that contains rigid body rotations and translations needed to transform the follow-up image and the associated mask (periosteal contours) to the baseline image.
A significantly higher percentage of CD27 + memory B cells was observed in patients with SP. Among these CD27 + B cells, the proportion of the switched memory subset was significantly higher. At the same time, human B1 cells, which were previously associated with a regulatory function (CD20 + CD69 -CD43 + CD27 + CD11b + ), decreased in SP patients. The RANKL expression increased in every B cell subset from the SP patients and was significantly greater in activated B cells than in the subjects without periodontitis. These preliminary results demonstrate the altered distribution of B cells in the context of severe periodontitis. Further investigations with a larger cohort of patients can elucidate if the analysis of the B cell compartment distribution can reflect the periodontal disease activity and be a reliable marker for its prognosis (clinical trial registration number: NCT02833285, B cell functions in periodontitis).
Subject recruitment This publication is conformed to the STROBE guidelines (Fig  1   ). This study was conducted in a dental clinic at Brest Hospital in France. The protocol was registered on clinicaltrials. gov (NCT02833285) (S1 and S2 Figs) and approved by the ethical committee of the Brest hospital (April 9th, 2015) (S3 Fig). Between May 2015 and December 2016, 28 subjects were recruited and included in two different groups, namely, 15 subjects with SP and 13 subjects without periodontitis [non-periodontitis (NoP) control group], according to the definition proposed by the CDC periodontal disease surveillance work group and supported by the American Academy of Periodontology to define periodontitis severity  [18]. SP was defined as the presence of two or more interproximal sites with ! 6 mm clinical attachment loss (CAL, not on the same tooth) and one or more interproximal site(s) with ! 5 mm pocket depth (PD).
Objective. The aim of this study was to perform an analysis of angular measurements (from both the full face and profile), according to shapes of the human face. Method. It was a descriptive and cross-sectional study of 108 black Ivorian subjects. For each subject selected, two standardized photographs (full face and profile) were taken, followed by anthropometric measurements. The data collected were analyzed using the SPSS 20. 0 statistics software for Windows. Results. In the present work, the faces were considered according to three particular qualifiers: broad face, medium face, and narrow face. Thus, 45. 37% of the faces in this study were large, 31. 48% on average, and 23. 15% narrow. The interlabial angles of average face and long face were wider than that of large face with  < 0. 01.
It is literally presented as follows: facial index (FI) = (height of the face/facial width) × 100 (Figure  2 ). Faces arranged according to the different forms were subject to some 20 angular measurements (among which, there were 8 full faces and 12 profiles). The data collected were analyzed using the statistical software IBM SPSS 20. 0 for Windows. The quantitative variables had a normal distribution as shown by their means and a Levene test. An univariate ANOVA was carried out to compare the photogrammetric variables according to appraisal category and gender (Table  4 ). The significance threshold was set at  < 0. 05. The attempt to reduce alpha error accumulation was made with a Bonferroni test. When the null hypothesis was rejected, a Bonferroni test was used to correct errors and determine the level of differentiation between these subjects.
Strain identification by MALDI-TOF MS and 16S rRNA gene sequencing No significant MALDI-TOF MS score was obtained for strain EL1 T against the Bruker Daltonics (Leipzig, Germany) database, suggesting that our strain was not a member of any known species. The reference mass spectrum of strain EL1 T was added to our database (Supplementary Fig. S1 ). A gel view comparing the spectrum of strain EL1 T with those of other Peptoniphilus species is shown in Supplementary Fig. S2. To identify strain EL1, the 16S rRNA gene was sequenced, and the obtained sequence (GenBank accession no. LN867000) showed a 96. 76% similarity with P. tyrrelliae strain RMA 19911 T (accession number GU938835), the phylogenetically closest bacterial species with a validly published name (Fig. 1 ). The general characteristics of strain EL1 T are presented in Supplementary Table  S1.
Genome properties The final assembly was made of three contigs. The genome is 1 863 688 bp long (one chromosome, but no plasmid) with a 29. 9% G+C content (Fig. 3 , Supplementary Table  S3 ). Of the 1793 predicted genes, 1750 were protein-coding genes and 43 were RNAs (two genes are 5S rRNA, one gene is 16S rRNA, one gene is 23S rRNA and 39 genes are tRNA genes). A total of 1321 genes (75. 49%) were assigned a putative function. Twenty genes were identified as ORFans (1. 14%). The remaining genes were annotated as hypothetical proteins (429 genes, 24. 51%) (Supplementary Table  S3 ). Table  2  shows the distribution of genes into Clusters of Orthologous Groups (COGs) functional categories. The genome sequence has been deposited in GenBank under accession numbers FNWF01000001 to FNWF01000003.
COGs, Clusters of Orthologous Groups database. P. lacydonensis sp. nov. to other species, AGIOS values were in the same range, from 62. 54% with P. coxii to 80. 54% with P. timonensis (Table  4 ). Among Peptoniphilus species with standing in nomenclature, digital DNA-DNA hybridization (dDDH) values ranged from 20. 10% between P. indolicus and P. harei to 45. 1% between P. indolicus and P. coxii. When comparing P. lacydonensis sp. nov. to other species, dDDH values were also in the same range, from 20. 2% with P. indolicus to 39. 5% with P. duerdenii (Supplementary Table  S4 ). Among species with standing in nomenclature, average nucleotide identity (ANI) values ranged from 64. 4% between P. timonensis and P. coxii to 82. 8% between P. timonensis and P. harei. When comparing P. lacydonensis to other species, the ANI value ranged from 66.
Catalase and oxidase production reactions are negative. The major fatty acid is the saturated hexadecanoic acid. Using API 20A and API ZYM strips, positive reactions are observed for indole formation and naphthol-AS-BIphosphohydrolase, respectively. Negative reactions are observed for alkaline phosphatase, esterase, esterase-lipase, lipase, leucine arylamidase, valine arylamidase, cystine arylamidase, trypsin, α-chymotrypsin, phosphatase acid, α-galactosidase, β-galactosidase, β-glucuronidase, α-glucosidase, β-glucosidase, α-mannosidase, α-fucosidase and N-acetylβ-glucosaminidase using API ZYM strips. In addition, no acid The genome is 1 863 688 bp long with a 29. 9% G+C content and is accessible under GenBank accession numbers FNWF01000001 to FNWF01000003. The 16S rRNA gene sequence is also accessible in GenBank under number LN867000.
Sample information and EL1 T strain isolation In February 2015, a sinus sample from an 85-year-old man with chronic refractory sinusitis complicating an ethmoidal adenocarcinoma was collected in Marseille, France. The patient provided written informed consent, and the study was validated by the Sud Mediterannée 1 ethics committee under number 15-12. The study was also registered at ClinicalTrials. gov as NCT02407275. After 10 days' culture in an anaerobic blood culture vial that contained 5% sheep's blood-enriched and sterile-filtered sheep rumen, we grew a bacterial strain that we named EL1 T (= CSUR P2013 = DSM 100661). The strain was subsequently subcultured on 5% sheep's blood-enriched Columbia agar (bioMérieux) in anaerobic atmosphere at 37°C.
Strain identification by MALDI-TOF MS To identify the strain, MALDI-TOF MS protein analysis was performed as previously described using a Bruker Microflex spectrometer  [12]. Twelve spectra obtained from 12 individual colonies were imported into MALDI BioTyper 2. 0 software (Bruker) and analysed by standard pattern matching (with default parameter settings) against the main spectra of 8500 bacteria, including those of 15 Peptoniphilus species. Spectra were recorded in the positive linear mode for the mass range from 2000 to 20 000 Da (parameter settings: ion source 1 (ISI), 20 kV; IS2, 18. 5 kV; lens, 7 kV). A spectrum was obtained after 675 shots with variable laser power. The time of acquisition was between 30 seconds and 1 minute per spot. From the resulting scores, the tested species may or may not be identified when compared to the instrument's database; a score 2 with a validly published species enables identification at the species level; a score 1.
Strain identification by 16S rRNA gene sequencing The 16S rRNA gene nucleotide sequence was obtained by amplification and sequencing using the fD1 and rP2 primers as previously described  [13]. Kim et al. [11]  determined a 98. 65% similarity level threshold to define a new species without performing DNA-DNA hybridization (DDH). A BLASTN was then systematically performed (http://blast. ncbi. nlm. nih. gov. gate1. inist. fr/Blast. cgi). Sequences were aligned and phylogenetic inferences obtained using MUSCLE  [14]  and MEGA (maximumlikelihood method)  [15]  software, respectively.
Genome annotation and comparison Open reading frames (ORFs) were predicted using Prodigal  [18]  with default parameters. However, the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against the GenBank  [19]  and COGs databases using BLASTP. The tRNAs and rRNAs were predicted using the tRNAScan-SE  [20]  and RNAmmer  [21]  tools, respectively. Signal peptides and numbers of transmembrane helices were predicted using SignalP  [22]  and TMHMM  [23] , respectively. Mobile genetic elements were predicted using PHAST  [24]  and RAST  [25]. The CRISPRFinder algorithm was used to identify putative CRISPR (clustered regularly interspaced short palindromic repeat) loci  [26]. ORFans were identified if their BLASTP E value was lower than 1e-03 for an alignment length >80 amino acids.
If alignment lengths were <80 aa, we used an E value of 1e-05. Such parameter thresholds have been used in previous work to define ORFans. Artemis  [27]  and DNAPlotter  [28]  were used for data management and visualization of genomic features, respectively. A phylogenomic tree was constructed using an FastTree  [29]  based on Mauve programme genome alignment  [30]. To evaluate the degree of genomic similarity at the nucleotide level among studied strains, we determined two parameters: dDDH and AGIOS. The former exhibits a high correlation with DDH, using Genome-to-Genome Distance Calculator (GGDC), formula 2, software  [31]. The latter was designed to be independent from DDH. It combines Proteinortho  [32]  to detect orthologous proteins between genomes compared two by two, then retrieves the corresponding genes, and then determines the mean percentage of nucleotide sequence identity among orthologous ORFs using the Needleman-Wunsch global alignment algorithm  [10].
ANI at the genome level between P. lacydonensis and the other species P. lacrimalis (ARKX01000001. 1), P. indolicus (AGBB01000001), P. duerdenii (AEEH01000001), P. harei (AENP01000001. 1), P. coxii (LSDG00000000) and P. timonensis (CAHE00000000) was estimated using the OrthoANI software  [33].
34 Amino acid transport and metabolism F 52 2. 97 Nucleotide transport and metabolism H 52 2. 97 Coenzyme transport and metabolism I 41 2. 34 Lipid transport and metabolism P 75 4. 29 Inorganic ion transport and metabolism Q 9 0. 51 Secondary metabolites biosynthesis, transport and catabolism R 158 9. 03 General function prediction only S 111 6. 34 Function unknown - 417 23. 83 Not in COGs COGs, Clusters of Orthologous Groups database. a Total is based on total number of protein-coding genes in annotated genome.
We hypothesized that in the rat tail vertebrae, osseointegration of titanium implants could be quantitatively monitored by a combination of biomechanical resonance frequency analysis and pull-out test, and by structural micro-CT and histomorphometry methods. We found that all of these test systems were applicable for the evaluation of the implant osseointegration process. However, the simultaneous application of these measurement methods and a combined evaluation based on the obtained data were much more advantageous to provide highly reliable and reproducible outcome using a limited number of small experimental animals.
Animals A total of 63 male Wistar rats (Crl(Wi)Br, Charles River; 450-550 g) from the breeding colony of Semmelweis University were used. They were kept in light-controlled, air-conditioned rooms before and after the surgery in individual stainless steel cages. The surgical procedure was carried out in a specialized operating room. Since we did not have preceding data with the presently developed methodology, for sample size calculation, we used the pull-out evaluation data at the 4th and 8th week endpoints. At these endpoints, we had 14 animals per group. Then, we used the G*Power free software (University of Dusseldorf, http://www. gpower. hhu. de/en. html). The α-error probe was 0. 05, the power was 0. 8, the allocation ratio N2/N1 was 1, and the effect size was counted as 2. 87. Based on this calculation, we applied sample size n = 7 in consecutive experiments.
Structural analyses Twenty-one specimens (n = 7 animals per group) were used f o r s t r u c t u r a l a n a l y s i s s u c h a s m i c r o -C T a n d histomorphometrical analysis. Micro-CT analysis Before histological testing, we performed a 3D radiographic data acquisition to detect the structural basis of implant stability in the reconstructed 3D images (SkyScan 1172, Kontich, Belgium). The device has an X-ray source from a sealed micro focus X-ray tube with a spot size of 8 μm. In the present work an Al+Cu filter (Al 1 mm and Cu 0. 05 mm) was used. Recovered implant samples with bone were scanned at 360°r otation at 0. 3°rotation step at 80 kV, 124 mA, 4598 ms exposure time with an isometric voxel size of 12 μm. For the reconstruction of raw images, a cone-beam volumetric algorithm was used with the NRecon V1.
6. 10. 1 version software (SkyScan, Kontich, Belgium). Measurements were performed within a certain region of interest (ROI) in the reconstructed images using the software CTAn, version 1. 14. 4. 1+ (SkyScan, Kontich, Belgium)  [33]. The described protocol for scanning and reconstruction was designed and optimized to our experimental conditions in order to overcome the x-ray scattering on the metal surface. The scanned samples were evaluated in 2D and 3D perspectives with task lists developed for this purpose in the CTAn software. The calculated intersection surface/tissue surface ratio (i. S/TS) was used in 2D analysis for characterizing the bone to implant contact. Based on the manufacturer's instruction (SkyScan 1172, Kontich, Belgium) and our calibration process, we chose the 12-pixel wide dilation length around the implant for determining the intersection surface value expressed in percentage.
Acknowledgements The adaptation of RFA for the newly developed mini-implants was fully controlled and approved by chief Operating Officer Anders Peterson of Osstell Ltd. The described protocol for scanning and reconstruction was overviewed and adapted to our experimental conditions with the valuable help of  Phil Salmon , applicant scientists of  Burker micro-CT (Bruker micro-CT, Belgium). We also thank  László Pató  ( FullTech Ltd. ) for developing and providing the mini-implants.
Acknowledgments This research was supported by the  UBS Optimus  and the  Medicor Foundations , as well as the SOFI funds from the  EWI Ministry  and  ERC starting Grant   311725 INTERRUPTB  to  Bouke C. de Jong. The authors are grateful to the families of the patients, who agreed on the publication of this case report. They are also grateful to  Paulin Déguénon  and  Michel Assogbaga  from the  Nutritional health center "Gbemontin" of Zagnanado  and to  Thierry Kinkpé  for their support.
Acknowledgements This research was partially supported by the  EU Consortium HUMAN  ( EU-FP7-HEALTH-602757 ) and by the  ANR  grants  TARGETBONE  ( ANR-17-CE14-0024 ) and  METACOGNITION  ( ANR-17-CE37-0007 ) to GL, and an  ATM grant  (FORMs) to YG, CdL is supported by a grant of the  French Ministry of Research. This work was supported in part by  grants-in-aid for scientific research  from the  Ministry of Education, Culture, Sports, Science and Technology, Japan  ( 15H02536 ) and  Core Research for Evolutional Science and Technology (CREST)  of the  Japan Science and Technology Agency (JST), Japan  ( JPMJCR13W2 ). A particular thank goes to the team in charge of mouse animal care and in particular  M Stéphane Sosinsky  and  M Fabien Uridat  and to  Pr. Amaury de Luze  in charge of animal well-being.
Sample size calculation Sample size calculation is based on the following assumptions: (1) Multivariable analysis of Covariance (MANCOVA) model (Cf. Statistical analysis); (2) an effect size f = 0. 5, based on the effect size found at 3 weeks after RME by Melgaço et al. ,  [9]  and since T2 assessment in the current study will be performed at 6 months, the effect size estimation is conservative; (3) α error probability = 5%; (4) power (1 -β error probability) = 90%; (5) two groups' design (RME and control); (  6 ) two repeated measures (T1 and T2); (7)  correlation among repeated measures assumed to be equal to 0. 7. Sample size calculation was performed using the Gpower® 3. 1. 9. 2 software (Universität Düsseldorf),  [16]  yielding 38 patients.
Sample Size. In total, 7 PWS participated in the two FG meetings. Generally, FGs are composed of groups of 4 to 12 people. In this case, the sample size of the FG meetings was su cient  [14]. Guest et al. [15]  suggested that a sample size of two to three FGs will likely capture at least 80% of the themes. us, 7 individuals were su cient to assess the feasibility of the TEPOH and to o er complimentary data for some adjustments if necessary  [16].
Acknowledgments e authors would like to thank  Philip Bastable  for his help with English language correction and are grateful to the  French Ministry of Health (Direction Générale de l'Offre de Soins)  and the  University Hospital of Dijon  for the support given to the study. e authors would like to especially thank the schizophrenic persons for their contribution to the study. is trial was funded by the  French Ministry of Health (Direction Générale de l'Offre de Soins).
As of now, platinum-based chemotherapy is the standard management for patients with CUPs. More recently, an alternative strategy offers treatment targeting the assumed primary tumour according to its molecular signature  [11]. With this in mind, the randomized phase III trial GEFCAPI04 comparing standard chemotherapy to a chemotherapy regimen tailored to the primary site defined by the gene expression profile is currently recruiting patients in France (clinicalTrials. gov NCT01540058)  [1]. Overall, the final diagnosis of CUPs is performed on small-sized samples that are essential to ensure that complementary IHC tests and molecular analyses can be performed without prejudice to the management of the patient. In addition, the myriad of IHC markers required to guide the diagnosis may question their availability and the budgetary impact for each pathology laboratory as well as the potential implementation at a national level of 'IHC expert centres' to provide second opinion IHC services.