dataesr/scientific-paragraphs-categorization huggingface dataset:
A 45 questions questionnaire, divided into six sections, was administered to three dentists who worked in private practices in Guadeloupe. After the questionnaire was revised on the basis of the responses of the dentists, it was posted on the Google Form platform, and was disseminated via email from November 2016. A reminder email was sent after 2 weeks. Data collection was completed in January 2017. The statistical processing was done on www. openepi. com and with the Epi info software. We calculated the means and medians of the quantitative variables as well as the frequencies and percentages of the qualitative variables. The chi-square and Fisher's exact tests were used to compare the distributions of the qualitative variables according to the territories, and the Kruskal-Wallis test was used to measure quantitative variables.
Collection and analysis of African healer's terminology From 2002 to 2011, we collected 30 commercial information sheets from African traditional healers in various countries (Benin, Burkina Faso, Gabon, Gambia, and Mali). These paper documents provided a range of information about the healers and their services such as: the therapies available, the illness or problems treated, and the medical products used. From these information sheets, we extracted frequently-used terms using natural language processing procedures. A corpus of 10,800 words was established, unidentifiable words were checked for spelling mistakes, and the text was pre-processed using a corpus processing system (Unitex 2. 1). Terms were extracted manually according to token frequency, the identification of collocations, the use of patterns for locating information, and statements about the definition of pain.
25, 31 A knowledge representation language (the Ontology Web Language, OWL) was selected to operationalize the ontology. Protégé, a free open-source ontology editor and knowledge-based framework was used to analyze it. 32 4] [35] [36] [37]  First we selected descriptors (terms). Then we identified most frequent ontological relationships of each term (associative, hierarchical). Experts in the field of alternative medicine provided an opinion on the definition and meaning of certain concepts. Although these experts had an intellectual and academic profile they had also acquired traditional knowledge. Finally, a thesaurus was constructed semiautomatically using software (Thesaurus Builder professional version 6. 5. 5. 1) which is compliant with ISO 5964. 38.
1). In a second step, we studied 48 specimens which were in sufficient volume to be investigated by applying fluorescence in situ hybridization (FISH) and direct microscopic examination. While sterile PBS negative controls remained negative, FISH detected methanogens in a total of 19/48 (40%) of investigated specimens including 16 (84. 2%) specimens collected from tobacco-smokers (Fig. 1 ) (Appendix). More precisely, FISH yielded methanogens presenting a bacillary morphology suggesting M. oralis in 10 cases including eight tobacco smokers and a diplococus morphology suggesting M. smithii in nine cases including eight tobacco smokers; for a total of nine cases of co-infection with both methanogens (Fig. 1 ). These results confirmed that PCR-based data did not merely result from the contamination of the specimens.
e. FISH, PCR-sequencing and culture was performed. The PCR-sequencing detection of methanogens was not surprising on the basis of previous observations of methanogens in the oral cavity  11, 12. Indeed, this molecular detection may have merely resulted from bypassing   DNA contamination of the oral fluid from neighbour dental plaque. However, isolation and culture of M. oralis and M. smithii indicated that in some individuals, some methanogen organisms were living in the oral fluid; and the positivity of FISH reinforced this interpretation by excluding a mere contamination of the specimens by a few methanogens. The data suggest that oral fluid is one component of the oral cavity where methanogens live and that in some individuals, M. oralis and M. smithii are oral fluid-borne methanogens. Further studies will have to confirm the data here reported; and to determine more precisely the oral fluid component where oxygen-susceptible and hydrogen-requiring methanogens are residing as the oxygen-rich and hydrogen-free extracellular component of oral fluid may not support living methanogens for minutes.
One crystal Three spots from one crystal were used. Values in parentheses are for highest-resolution shell a Rfactor square b R-meas is a redundancy-independent R-factor defined in 76 c CC1/2 is percentage of correlation between intensities from random half-datasets  77 d  Number of reflections corresponds to the working set e Rwork corresponds to working set amyloid stability, consistent with the previous suggestion that this mating configuration could be associated to the transient nature of amyloid oligomers  26, 29. The contrasting levels of stability of PSMα3-LFKFFK and PSMα4-IIKIIK fibrils, inferred from structural analyses, were verified experimentally. Specifically, PSMα3-LFKFFK fibrils dissolve upon heating to 50 °C, and reform upon cooling, whereas PSMα4-IIKIIK fibrils remain stable (Fig.
Methods Peptides and reagents. PSM native peptides and shorter derivatives (custom synthesis) at >98% purity (see Table  2 ) were purchased from GL Biochem (Shanghai) Ltd. , as well as from GenScript. The short (6-7 residues) PSMα segments were synthesized with capped termini (acetylated in the N-terminus and amidated in the C-terminus) or with unmodified termini for crystallography. PSMα full-length peptides were synthesized with unmodified termini. Hexafluoroisopropanol (HFIP) and Thioflavin T (ThT) were purchased from Sigma-Aldrich. Ultra-pure water was purchased from Biological Industries. Dimethylsulfoxide (DMSO) was purchased from Merck. PSMαs wild type (WT) and mutant peptide sequences (Uniprot accession codes are in parenthesis); segments of short derivatives used here are marked in bold; introduced proline substitutions are underlined.
X-ray diffraction data from fibrils of IIKVIK and IIKIIK was collected at the micro-focus beamline MASSIF-3 (ID30A-3) of ESRF, Grenoble, France. Thioflavin T fluorescence fibrillation kinetics assay. Thioflavin T (ThT) is a widely used "gold standard" stain for identifying and exploring formation kinetics of amyloid fibrils, both in vivo and in vitro  63. Fibrillation curves in presence of ThT commonly show a lag time for the nucleation step, followed by rapid aggregation. Pre-treated PSMα1, PSMα1 I7P/K9P, PSMα4, and PSMα4 I8P/I10P peptide aliquots were dissolved in DMSO to 10 mM and immediately diluted to 50 μM in Tris buffer pH 7. 5 for PSMα1 and PSMα1 I7P/K9P, or in ultra-pure water for PSMα4 and PSMα4 I8P/I10P, containing filtered ThT diluted from stock made in ultrapure water. Final concentrations for each reaction were 50 µM peptide (PSMα1, PSMα4, or their mutants) and 200 µM ThT.
The drop was a mixture of 10 mM peptide and reservoir solution as follows: IIKVIK: 0. 5 M Lithium sulfate; 15% polyethylene glycol 8000. IIKIIK: 0. 2 M Ammonium sulfate; 20% polyethylene glycol 3350. LFKFFK polymorph I: 0. 2 M Potassium thiocyanate, 20% polyethylene glycol 3350. LFKFFK polymorph II: 0. 1 M Sodium acetate pH 5. 1; 45% polyethylene glycol 400; 0. 09 M Lithium sulfate. Micro-crystals grew after a few days and were mounted on glass needles glued to brass pins  64. Crystals were kept at room temperature prior to data collection. Structure determination and refinement. X-ray diffraction data was collected at 100 K. The X-ray diffraction data for IIKVIK, IIKIIK, and LFKFFK polymorph I was collected at the micro-focus beamline ID23-EH2 of the European Synchrotron Radiation Facility (ESRF) in Grenoble, France; wavelength of data collection was 0.
8729 Å. The X-ray diffraction data for LFKFFK polymorph II was collected at the micro-focus beamline P14 operated by EMBL at the PETRAIII storage ring (DESY, Hamburg, Germany); wavelength of data collection was 0. 9763 Å. Data indexation, integration and scaling were performed using XDS/XSCALE  65  or with DENZO/ SCALEPACK  66. Molecular replacement solutions for all segments were obtained using the program Phaser 67 within the CCP4 suite  67, 68. The search models consisted of available structures of geometrically idealized β-strands. Crystallographic refinements were performed with the program Refmac5  69. Model building was performed with Coot 70 and illustrated with Chimera 71. There were no residues that fell in the disallowed region of the Ramachandran plot. Crystallographic statistics are listed in Table  1.
Calculations of structural properties. The Lawrence and Colman's shape complementarity index  72  was used to calculate the shape complementarity between pairs of sheets forming the dry interface. Area buried was calculated using AREAIMOL  73, 74  with a probe radius of 1. 4 Å. Calculations were performed using the CCP4 package  68. The summation of the differences between the accessible surface areas of one molecule alone and in contact with the other strands on the same sheet or opposite sheets, as indicated in Supplementary Table  1 , constitutes the reported area buried. Bacterial strains and culture media. Micrococcus luteus (an environmental isolate) was a kind gift from Prof. Charles Greenblatt from the Hebrew university in Jerusalem, Israel. An inoculum was grown in Luria-Bertani (LB) medium at 30 °C with 220 rpm shaking overnight.
Acknowledgements We are grateful to  M. Sawaya ,  N. Ben-Tal ,  M. Chapman ,  N. Jain ,  M. Evans ,  A. Syed ,  Z. Hayouka ,  H. Bochnik-Tamir ,  O. Tabachnikov ,  T. Gera ,  E. Tamar ,  I. Yelin ,  O. Snitser , and  R. Edrei  for help with experiments and fruitful discussions. We acknowledge  Y. Pazy-Benhar  and  D. Hiya  at the  Technion Center for Structural Biology (TCSB) , and the  Electron Microscopy Center  located at the  Technion's Department of Materials Science & Engineering , and the  Russell Berrie Electron Microscopy Center of Soft Matter. This research was supported by the  I-CORE Program of the Planning and Budgeting Committee  and  The Israel Science Foundation ,  Center of Excellence in Integrated Structural Cell Biology  (grant no. 1775/12 ),  DFG: Deutsch-IsraelischeProjektkooperation (DIP)  (Grant No.
LA 3655/1-1 ),  Israel Science Foundation  (grant no. 560/16 ),  University of Michigan-Israel Collaborative Research Grant , and  BioStruct-X , funded by  FP7. J. -P. C. acknowledges financial support by  CEA ,  CNRS ,  Université Grenoble Alpes , and the  Agence Nationale de la Recherche  (Grant No. ANR-15-CE18-0005-02 ). The synchrotron MX data collection experiments were performed at beamlines  ID23-EH2  and  MASSIF-3 (ID30A-3 ) at the  European Synchrotron Radiation Facility (ESRF), Grenoble, France , and at beamline P14, operated by  EMBL  Hamburg at the  PETRA III storage ring  ( DESY, Hamburg, Germany ). We are grateful to the teams at  ESRF  and  EMBL Hamburg.
Data availability The data that support the findings of this study are available on request from the corresponding author. Coordinates and structure factors for the X-ray crystal structures have been deposited in the protein data bank (PDB) with accession codes 6FG4 (IIKVIK), 6FGR (IIKIIK), 6FHC (LFKFFK polymorph I) and 6FHD (LFKFFK polymorph II).
Based on our limited survey of 116 oral condylomas published in 1988, HPV detection rate was 75%. 11 In the genital tract, the terminology was revised in 1970 genital papilloma being replaced by genital condyloma. 3] [24] [25] [26]  Even today, the number of analyzed samples is limited, and the data hampered by the lack of unanimous histological criteria, creating controversy on their etiological association with HPV. Among the 31 samples of Dona et al. ,  12  of the 22 HPV DNA positive cases, 68% represented mucosal and 32% cutaneous HPV types. The present study identified 83 randomly selected oral samples in the archives, diagnosed as papilloma, condyloma, verruca vulgaris, or papillary hyperplasia, first assessed for the pathognomonic signs of HPV infection, ie, koilocytosis. In the next step, all samples were analyzed for the presence of α-, β-, and γ papillomaviruses.
Statistics Statistical analyses were carried out using JMP Pro, Version 12 and SAS system for Windows, Version 9. 4 (SAS Institute Inc, Cary, NC, USA). Continuous variables were characterized using means and standard deviations (SD) and in case of categorical variables frequencies and percentages were used. The association of histological diagnosis and HPV DNA detection was tested using Pearson's chi-squared test. The association of Ki-67 and p16-staining to α-HPV or combined HPV positivity was analyzed using logistic regression models, where Ki-67 and p16 were included in the same model. Also the interactions of Ki-67 and p16 were tested but if not significant, it was omitted from the model. The numbers for β-HPV and γ-HPV were too low for separate analyzes. The results were quantified using odds ratios (OR) with 95% confidence intervals (95% CI).
NutriNet-Santé e-Cohort This study is part of the multidisciplinary ALIMASSENS Project launched in France in 2014  [17]. The epidemiological component of the project is based on data from the ongoing NutriNet-Santé e-cohort launched in France in 2009 (www. etude-nutrinet-sante. fr) [18]. Volunteers aged ≥18 years with Internet access are recruited by means of traditional strategies (e. g. , flyers) and multimedia campaigns. The NutriNet-Santé study was approved by the ethics committee of the French Institute for Health and Medical Research (No. 0000388FWA00005831) and by the National Commission on Informatics and Liberty (No. 908450 and No. 909216). Eligible participants provide informed consent and an electronic signature, and afterwards complete five baseline questionnaires: sociodemographics and lifestyle, health status, physical activity, anthropometrics, and diet.
Diet Quality Assessment The nutritional quality of diet was assessed in terms of adherence to French dietary guidelines established by the National Program on Nutrition and Health (PNNS) in 2001, with the most current update published in 2011  [22]. Individual dietary intake data were obtained from ≥3 24-h dietary records provided within 2. 5 ears around the oral health questionnaire administration. Twice a year participants were asked to provide three 24-h records from non-consecutive days spread over a 2-week period. The user-friendly dietary record tool featured a food/beverage browser, a search engine, a user's guide, and a built-in control system with cues and prompts designed to help minimize the chance of forgetting consumed items. For each food/beverage consumed over a period of 24 h, participants were asked to provide information about quantity/portion size, recipe/seasoning, and corresponding settings (time and place).
The PNNS-GS is calculated on the basis of 13 components one of which pertains to physical activity and the remaining 12 to diet. The modified score (mPNNS-GS) is calculated on the basis of the 12 diet components only. Among those, 8 pertain to recommended intake quantities [fruit and vegetables (0-2 points); starchy foods (0-1 point); whole-grain foods (0-1 point); dairy (0-1 point); meat/poultry/eggs (0-1 point); seafood (0-1 point); vegetable fat (0-1 point); non-alcoholic beverages/water (0-1 point)]; four components pertain to recommended moderation in intake [added fat (0-1 point), salt (-0. 5-1. 5 points), sweets/desserts (-0. 5-1 point), and alcohol (0-1 point)]. Details about categorization of the quantitative dietary data into the 12 mPNNS-GS components have been published  [27]. Points are deducted if the reported energy intake >105% of estimated energy needs.
Covariates We collected self-report sociodemographic (sex, age, marital status, education, occupation, income), lifestyle (physical activity, smoking), and health data (weight, height, diabetes, cancer, hypertension, cardiovascular diseases). Leisure-time physical activity was assessed with the International Physical Activity Questionnaire-Short Form, and scoring followed established protocol  [29]. Missing data (education, n = 24; physical activity, n = 2; occupation, n = 260) were imputed using the mode of the respective variable. BMI was calculated as the weight (in kg) divided by the squared height (in m). Regarding health status, data on prevalent and incident events were collected. As enrollees were asked to provide this information on an annual basis for record updating purposes, we used information provided closest to the oral health questionnaire administration.
Model 2 was additionally adjusted for BMI (continuous variable) and incident or prevalent cancer (any site), diabetes (self-report and/or anti-diabetic drug use), hypertension (self-report and/or antihypertensive drug use), and major cardiovascular disease (myocardial infarction, stroke, or acute coronary syndrome). Because both oral health and dietary intake (including diet quality) likely vary by age  [27, 30] , we performed tests for interaction between GOHAI score and age. All tests were two-sided and p < 0. 05 was considered statistically significant. All analyses were conducted with SAS (version 9. 4, SAS Institute, Inc. , Cary, NC, USA).
Mean age in the sample was 56. 5 ± 13. 8 years and mean overall GOHAI score was 54. 5 ± 4. 3. Mean mPNNS-GS score was 7. 7 ± 1. 6 and it was normally distributed in the full sample. Descriptive characteristics by the three-level GOHAI score are presented in Table  1. Values refer to number (%) except when noted otherwise; GOHAI, General Oral Health Assessment Index. 1 p-values obtained from chi-squared tests and ANOVA, as appropriate. 2 Assessed with the International Physical Activity Questionnaire-Short Form; scoring followed established protocol. 3 Prevalent or incident diabetes type 1 or type 2 based on self-report and/or report of anti-diabetic drug use. 4 Prevalent or incident cancer (any site) based on data validated by a medical expert committee. 5 Prevalent or incident hypertension based on self-report and/or report of antihypertensive drug use.
Acknowledgments: This work is part of the  ALIMASSENS  Project supported by the  French National Research Agency  (grant #  ANR-14-CE20-0003-01 ). The epidemiological research work within ALIMASSENS is based on data from the  NutriNet-Santé  study which is supported by the  French Ministry of Solidarity and Health , the  National Agency for Public Health  ( Santé Publique France ), the  National Institute for Health and Medical Research (INSERM) , the  National Institute for Agricultural Research (INRA) , the  National Conservatory of Arts and Crafts (CNAM) , the  Sorbonne-Paris-Cité Center for Epidemiological Research and Statistics , the  NutriNet-SU. VI. MAX Association , and the  University of Paris 13. The authors thank  Anouar Nechba  for the statistical analysis.
, 2016 (Jans et al. , , 2013a (Jans et al. , , 2012b)). The dairy adaptations of Sii lineages seem to parallel the evolution of Streptococcus thermophilus as starter culture in Western fermented dairy products and suggest an important technological role during tFDP manufacturing  (Jans et al. , 2013a). In this context, African variants of Sii have been suggested for evaluation as indigenous starter culture for African tFDP  (Jans et al. , 2016 (Jans et al. , , 2013a)). Therefore, a thorough safety assessment of Sii for any future product development and estimation of its public health risk is necessary. However, basic appropriate epidemiological data on Sii in Africa and even worldwide is currently lacking. To provide the first epidemiologic data on CRC, tFDP and Sii, we implemented a hospital-based study and enrolled patients at the endoscopy unit of Kenyatta National Hospital (KNH) in Nairobi, Kenya, a country with well-characterized Sii-containing tFDP.
Statistical data analysis The database was created in Microsoft Access (Microsoft Corporation, Redmond, WA, USA) and statistical data analysis conducted using Stata version 14 (Stata Corporation, College Station, TX,  USA, 1984 USA, -2000)). Dietary intake variables assessed by a semi-quantitative food frequency questionnaire were analysed by using logistic regression adjusted for age group (< 40, 41-60 and > 60yrs), gender and rural residency. Odds ratios (OR) with their corresponding 95% confidence intervals (CI) were used to measure strength of associations with P-values of less than 0. 05 considered statistically significant. All DNA sequence analyses were performed in CLC Genomics Workbench (version 7. 5, Qiagen Aarhus A/S, Denmark). Raw sequence chromatograms were trimmed for quality using a minimum stringency setting of 0.
Available patient data from KNH do not allow separating the study population into non-neoplastic and neoplastic polyp types. Therefore, a mixed health status concerning non-neoplastic (benign) and neoplastic (adenoma) polyp types was obtained for all participants classified as polyp carriers in this study. Alternative case definitions were defined to perform corresponding sensitivity analyses. The usual intake of various foods including FDP was assessed by food frequency questionnaires. Thereby, data on quantification of portion sizes or daily intakes was limiting. However, such questionnaires were successfully employed by others suggesting their applicability to the settings in this study  (Haftenberger et al. , 2010; Tantamango et al. , 2011).
Acknowledgements We acknowledge the support we received from KNH Endoscopy Unit nurses and Doctors, as well as support from the  University of Nairobi, Laboratory of Medical Microbiology specifically from Mr. Jonathan Oloo. Funding: Part of this project was funded by  DAAD ,  UoN Deans Committee Research Grant. The main funding source for this project was provided by the  UBS Optimus Foundation Switzerland, ERAfrica "New Ideas " and the  consortium Afrique One-ASPIRE  funded by the  Wellcome Trust  ( WT087535MA ) and DELTAS AFRICA ( 107753/A/15/ Z ). The funding agencies had no involvement in study design, analysis, interpretation and writing of the manuscript.
Conclusion It is widely accepted that the use of implant techniques in cancer patients is sometimes essential to ensure functional prosthetic rehabilitation. This retrospective study, which was conducted on patients who had specifically received oral radiotherapy, confirmed that it was a reliable therapeutic treatment for radiation doses of 45-50 Gy. However, the small number of patients in this study prevents the extrapolation of results to larger populations, considering the significant morbidity and lower success rate than patients who were not irradiated. Thus, the inherent risk of a past history of radiotherapy must be taken into account. The use of software like Dentalmaps®  [24]  allows a better evaluation of the doses received at potential implantation sites. This software is based on the automatic segmentation and delineation of the dental zones, making it possible to estimate the dose received at different points of the dental arch to the nearest 2-Gy fraction.
_ 2 ) T D $ F I G ] Standard settings of the Autodesk Inventor ® 3D software were applied in order to obtain a generic FE approach that enables estimation of the microgap formation. According to the software description, all of the mesh elements are solid tetra 10 type (4 physical points and 10 nodes for the interpolation). These are volumetric elements with the mesh size at the implant shoulder set to 0. 1 mm. At less critical positions the meshes were reduced up to 0. 3 mm element size. The FE analysis was calculated with approximately 151 000 [ 1 0 _ T D $ D I F F ] nodes and 96 000 elements. The contact condition of the different implant components were defined to be separated  [24, 25]  (in detail: brass cylinder and implant: bonded, abutment and steel ball: bonded (cf. sample description in Section 2.