dataesr/scientific-paragraphs-categorization huggingface dataset:
Methods We retrospectively reviewed all QFE cases diagnosed at our center during 2009-2018. The Prince Sultan Cardiac Centre in Riyadh is one of the main cardiac centers in the Kingdom of Saudi Arabia and has 186 beds. Both adults and children and medical and surgical patients are admitted. A registry of all patients admitted with endocarditis was reviewed using an infectious disease consult database and echocardiogram records. Patients with identified microorganisms were excluded, excepting those with Q fever dual infection. Also excluded were patients with blood culture-negative endocarditis (BCNE) who were not tested for Q fever. Ultimately, our study comprised patients with established Q fever. The ethical committee of our hospital approved the study. Data collected included the following: patient demographics, risk factors for Q fever, past history of cardiac surgery, symptoms and findings at presentation, underlying cardiac abnormalities, investigations performed, surgical intervention, anticoagulant or antiplatelet treatment, anti-microbial therapy type and duration, and patient outcomes.
Results Establishing culture conditions for CLL cells proliferation ex vivo. To establish culture conditions for CLL cells proliferation after ex vivo activation, we first evaluated CFSE labeling in a small series of patient samples (n = 8). This approach allows calculating the percentage of dividing cells and the number of cell generations (Fig. S1 ). We first confirmed data from previous studies showing that ex vivo BCR activation by means of anti-IgM ligation does not induce CLL cells proliferation when these cells are cultured in soluble medium (Figs 1A and S2A). Similarly, stimulation with IL-4, IL-21 or CD40L, used separately, in soluble medium, did not induce CLL cells proliferation either (Fig. 1A ). We also confirmed that different combinations of cytokines, [CD40L + IL-4], [CD40L + IL-21] and [CD40L + IL-4 + IL-21] induced a weak (less than 40%) proliferation of CLL cells (Fig.
CFSE-based proliferation assays. Freshly isolated B cells were labeled with 0. 5 μM CellTrace TM CFSE (ThermoFisher, Waltham, MA, USA) and incubated for 10 min at 37 °C in the dark. Washed CFSE-labeled cells were stimulated and cultured at 37 °C/5% CO 2. Four or six days later, B cell proliferation was evidenced by a cell division-dependent decrease in CFSE staining intensity as evaluated by flow cytometry (Fig. S1 ). Fluorescence data were analyzed with CXP (Beckman Coulter, Fullerton, CA) and FlowJo v. 8. 7 (TreeStar, Ashland, USA) softwares.
Statistical analyses. Statistical analyses were performed using R 3. 2. 4 (R Core Team, 2016, R Foundation for Statistical Computing, Vienna, Austria). Graphics were created using Graphpad Prism 7. 0 (Graphpad Software; Inc, La Jolla, CA, USA). We used permutational ANOVA for repeated measurements (lmPerm R package, https://github. com/mtorchiano/lmPerm) to compare more than two groups. Posthoc tests were done using nonparametric multiple comparisons tests carried out with the nparcomp R package  51. Differences between two groups were assessed using either nonparametric Wilcoxon matched-pairs signed rank test of nonparametric Mann-Whitney test (unpaired, when applicable). A p value of <0. 05 was considered statistically significant. *p < 0. 05; **p < 0. 01; ***p < 0. 001.
Acknowledgements We would like to thank  Drs Fanny Baran-Marszak ,  Frédéric Davi ,  Jean-Noël Freund ,  Delphine Rolland ,  Paolo Ghia  and  Robert Zeiser  for critical reading of this manuscript. We are grateful to  Drs Anne-Cécile Galoisy  and  Carine Gervais  ( Laboratoire d'Hématologie, Hôpitaux Universitaires de Strasbourg, France ) for cytology analysis,  Beatrice Uring-Lambert  ( Laboratoire d'Immunologie, Hôpitaux Universitaires de Strasbourg, France ) for help with flow cytometry,  Laurent Mailly  ( INSERM UMR_S 1110, Strasbourg, France ) for access to the cell irradiaiton platform,  Shanti Amé  and  Blandine Guffroy  ( Service d'Hématologie Adulte, Hôpitaux Universitaires de Strasbourg, France ) for providing CLL samples,  Manuela Tavian  ( INSERM UMR_S 949 ,  Etablissement Français du Sang Grand Est, Strasbourg, France ),  Anne-Sophie Korganow  ( CNRS UPR9021 , Strasbourg, France),  Cendrine Seguin  ( CNRS UMR 7199, Illkirch, France ) and  Jozo Delic  ( Commissariat à l'Energie Atomique, Fontenay-aux-roses, France ) for helpful suggestions and  Ms Nathalie Perrusson  ( Laboratoire d'Hématologie, Hôpitaux Universitaires de Strasbourg, France ) for technical help.
This work was supported by grants from the  Institut Thématique Multi-Organism  (ITMO) cancer initiative within the framework plan cancer  2009-2013  " GenPred project " , Initiative d'Excellence-CNRS , the  Association pour la Recherche contre le Cancer (ARC) ,  Alsace Cancer association , the  Genomax , the  Strasbourg School of Medicine Next Generation Sequencing center , the  Institut Universitaire de France (IUF) , the  Ligue contre le Cancer  and the  LABEX Transplantex  [ ANR-11-LABX-0070_Transplantex ] ( French National Research Agency; ANR) ,  INSERM UMR_S1109  and  UMR_S1113.
Conclusions • Unmanipulated DLI from a haploidentical donor appears to be relatively safe and reasonably effective in patients who relapse after a T-cell replete haplo-HCT. Patients given haplo-DLI should be enrolled in a clinical trial whenever possible, as data regarding optimal cell dose, timing and role of concurrent systemic therapies with haplo-DLI are limited. Information about the application of unmanipulated DLI after T-cell depleted transplantation is limited, which is why dosing should be managed with caution. • The risk of GvHD after unmanipulated DLI in the haplo-HCT/PTCy setting is comparable to an unmanipulated DLI from an HLA-matched donor. • Cytoreductive therapy prior to DLI from a haploidentical donor should be considered in patients with a hematologic relapse after haplo-HCT.
Acknowledgments Additional contributions: PHRC T21 study group:  Emmanuel Andres, MD, PhD ,  Xavier Argemi, MD, PhD ,  Frédéric Blanc, MD, PhD ,  Isabelle Brun, MD ,  Salima El Chehadeh, MD ,  Jean-Luc Davideau, MD ,  Jean-Louis Dietemann, MD, PhD ,  Hélène Dollfus, MD, PhD ,  Elise Gazzano, MD ,  Bernard Goichot, MD, PhD ,  Julie Helms, MD ,  Jean-Michel Hiebel, MD ,  Georges Kaltenbach, MD, PhD ,  Anne Koenig, MD, PhD ,  Marie-Cécile Manière, PhD ,  Yaumara Perdomo, MD ,  Hélène Petit-Eisenmann, MD, PhD ,  Alain Pradignac, MD, PhD ,  Anne-Elisabeth Quoix, MD, PhD ,  Philippe Sauder MD PhD ,  Elise Schaefer, MD ,  Francis Schneider, MD, PhD ,  Dana Timbolschi, MD ,  Jean-Christophe Weber, MD  ( Strasbourg University Hospital ) contributed clinical and administrative collaborative efforts.
S1 ). Considering only biallelic SNPs with a minor allele frequency (MAF) ≥ 0. 01, haplotypes within these blocks were extracted with the Pegas package in R  (20, 21). Within the smaller 2795 bp region, we identified 19 haplotypes among 16 SNPs, and within the larger 22 945 bp region, we identified 378 haplotypes among 83 SNPs (Supplementary Material, Table  S1 ). Relationships among haplotypes occurring at ≥0. 5% were inferred using network analysis (Fig. 2 ). Of the eight haplotypes with frequency ≥0. 5% in the region of high LD, the majority of individuals in all populations carry the same haplotype with the derived G allele (n = 3848); two less frequent haplotypes carrying the derived allele are found in various geographic regions. The ancestral A allele is found in the remaining five haplotypes, which vary in their distributions across regions.
Materials and Methods Datasets 1000 genomes project. Individual level phased sequencing data from the 1000 Genomes Project Phase 3 dataset were downloaded from ftp://ftp. 1000genomes. ebi. ac. uk/vol1/ftp/ release/20130502/  (19). Neandertal and Denisovan. Genotypes for the Vindija, Altai and Denisovan genomes generated using snpAD, an ancient DNA damage-aware genotyper, were downloaded from http://cdna. eva. mpg. de/neandertal/Vindija/VCF/ (52). Great apes. Genotypes of primate sequences were obtained from https://eichlerlab. gs. washington. edu/greatape/data/ and converted to the corresponding human regions with the LiftOver software  (30).
Haplotype networks Indels and multiallelic sites were filtered out with bcftools  (53). Variants having a Hardy-Weinberg equilibrium exact test P-value below 1 × 10 -5 as calculated using the -hwe midp function in PLINK1. 9 (54)  in any of the 26 populations were removed from all populations. The core haplotype surrounding rs6967330 was identified using biallelic markers within ±50 kb of rs6967330 in Haploview (55) from all 26 populations in the 1000 Genomes Phase 3 release (Supplementary Material, Fig. S1 ). A large haplotype block was defined on chromosome 7 from 105 657 078 to 105 680 022, and a smaller haplotype of chromosome 7 from 105 657 078 to 105 659 873. Haplotypes within the defined haplotype blocks were extracted from biallelic markers with a minor allele frequency (MAF) > 0. 01 with the Pegas package  (20, 21).
Multipopulation (MP) combined statistic For each SNP and each population, we determined the empirical P-value of iHS and nS L , i. e. the rank of each statistic in the genome-wide distribution divided by the number of SNPs. We then used the combine_pvalues function implementation of Fisher's method (56) of the SciPy python package to compute MP-iHS and MP-nS L for every SNP (passing the criteria above to compute iHS and nS L ) found in at least two populations. β test for long-term balancing selection β scores for each population in the 1000 Genomes Project were obtained from https://github. com/ksiewert/BetaScan.
ABC estimation of the age of the rs6967330 mutation In ABC, estimations are performed by comparing summary statistics of data simulated according to specified prior distributions to those of empirical data  (62). To minimize unwanted noise due to limited sample sizes, we merged samples from multiple populations into super populations according to their continent of origin (AFR, EUR, EAS), and excluded populations with significant levels of admixture. For the simulated datasets, the age of the derived mutations were drawn from a flat prior distribution ranging from present until 200 000 years ago. The selection coefficients, s, for the derived mutation were drawn from a flat prior distribution ranging from very low selection coefficients (0. 001) to very high selection coefficients (0. 1). As summary statistics, we used four haplotype-based statistics as previously described: iHS, nS L , iHH and DIND  (45).
In addition, we also used the current derived frequency of the selected mutation and the number of segregating sites (θ S ) computed 100 kb around the site, in order to ensure that our estimates were generated from simulations that closely match the genetic diversity observed in the studied populations. We used three different ABC methods implemented in the abc R package  (21, 63)  setting the tolerance parameter ('tol') equal to 0. 005. The three posterior distributions obtained were combined into a single posterior distribution as previously described  (45). As punctual estimates of the age of the mutation, we cite the posterior mean and the 95% CIs obtained from posterior distributions. We tested the accuracy of each ABC method used, including the combined one, by treating simulated data as empirical data for which parameter values were known (Supplementary Material, Fig.
S7 ). To this end, we compared the estimated and simulated parameter values, denoted here by θi and θ i , respectively, using classic accuracy indices: the averaged relative error rError (i. e. averaged difference between estimated and true values, expressed as a proportion of the true value, rError = 1 J J i ( θi -θ i )/θ i , with J simulated datasets), the root of the relative mean square error and the proportion of true values falling between bounds of the 95% CIs computed from posteriors, 95%CIcov = 1 J J 1 1(q 1 < θ i < q 2 ) where 1(C) is the indicative function (equal to 1 when C is true, 0 otherwise) and q 1 and q 2, the corresponding percentiles of the posterior distributions.
On the one hand, the duration of TL positivity after successful cure  [23, 27]  may be regarded as a limitation, as the percentage of TL positivity may take time to decline (e. g. , in Bonon), even though transmission has been severely impacted, but on the other hand, absence of TL positivity in the population (e. g. , in Boblénou or Gaoua) appears to be a strong indication that transmission was indeed interrupted some years ago. In addition to being a sensitive and specific test for individual HAT diagnosis, TL thus also appears to be a promising biomarker to monitor the elimination of gambiense-HAT at the population level, especially in areas where the interruption of transmission needs to be validated. This study was based on the analysis of five unique datasets for which TL results were available for the whole population screened with CATT during active case detection.
Acknowledgements. Activities within the scope of this work were conducted in the context of the HAT elimination project supported by the  WHO  and  UMR Intertryp IRD-CIRAD. The teams involved were supported by the  JEAI  programme of the IRD. We acknowledge all the technicians from the HAT teams of  Institut Pierre Richet (Bouaké, Côte d'Ivoire), University Jean Lorougnon Guédé (Daloa Côte d'Ivoire) ,  Centre International de Recherche-Développement sur l'Élevage en zones Subhumide (Bobo-Dioulasso ,  Burkina Faso ) and  Programme National de Lutte contre la Trypanosomose Humaine Africaine (Conakry, Guinea). We acknowledge the  WHO  for kindly providing the data on the number of HAT cases reported in the study areas between 2010 and 2014. The authors declare that they have no competing interests.
Materials and Methods This retrospective epidemiological study was conducted at the pediatric emergency department of Armand-Trousseau Hospital in Paris (France). We analyzed medical records from children who presented with acute vesicular stomatitis over a period of 5 years, from August 2008 (when electronic medical records were first implemented) to June 2013 (when use of codeine in children was restricted). Eligible files were selected from the database of URQUAL software and included all of the medical files whose International Classification of Diseases 10 (ICD-10) diagnosis codes were K12 K120 K121 (gingivostomatitis, stomatitis, aphthosis, vesicular oral lesions), B001 B002 (herpes viral infection), B084 B085 (vesicular pharyngitis, vesicular oral lesions), B370 B379 (candida stomatitis), and R13 (dysphagia).
After the electronic selection of relevant medical records, cases were checked manually by a physician to ensure inclusion of any observations evoking clinical features of herpetic gingivostomatitis (HGS), Coxsackie virus stomatitis (herpangina; H), or hand, foot, and mouth disease (HFMD). Any other diagnosis was excluded. Using a structured questionnaire specifically designed for this study, we were able to obtain anonymous data on patient demographic characteristics, primary reasons for consultation, pain assessment on arrival in the emergency department, clinical features, impact on appetite, emergency care management, and patient outcomes. Three scales were available to evaluate pain in the emergency department: the EVENDOL Pain Scale with scores ranging from 0 to 15; the Visual Analog Scale (VAS); and the Faces Pain Scale (FPS-R) with scores ranging from 0 to 10.
It should be stated that the EVENDOL Pain Scale was already in use in the department before it was published. The EVENDOL scale was to be used in children under 8 years of age but health-care providers were free to judge which scale they thought most relevant for each situation. Some of them also used the VAS and the Faces Scale to obtain proxy ratings. We collected data on treatment and analgesics: administered prior to emergency consultation; during emergency care; prescribed at discharge; and where appropriate during hospitalization based on inpatient records. Questionnaire data capture was conducted using EXCEL ® (Microsoft, Redmond, Washington, USA) software and data were analyzed using SPSS17 (SPSS Inc. , Chicago, Illinois, USA) software. Qualitative variables were defined in terms of number of participants and percentages.
Comparisons were made using the chi-square test or Fisher's exact test where appropriate. Quantitative variables were expressed as mean values with standard deviation or median values and interquartile ranges. Mean values of various groups were compared by analysis of variance (ANOVA). All of the data were anonymized via standardized file format. Statistical analysis was performed after the data had been anonymized. The investigators have no conflicts of interest to declare in connection with this study. This study was submitted for approval by the Ile-de-France (Paris) Ethics Committee/Institutional Review Board in February 2015 and it was concluded that no further authorization was required. Data collection by the URQUAL Emergency Database is copyprotected and registered with the French National Commission for Data Protection and Liberties.
ACKNOWLEDGEMENTS This work was supported by grants from  Fondation ARC  ( PJA 20161204724 ),  INCa  ( PLBIO15-256 ),  ANR  ( 2017-CE15-0024-01 ),  Ligue Contre le Cancer  ( CD87 ,  CD19 ,  CD23 ), and  Fondation Française pour la Recherche contre le Myélome et les Gammapathies monoclonales (FFRMG). JML was funded by  French government and Ligue Contre le Cancer  fellowships. NS was funded by  Région Limousin  and  Fondation ARC  fellowships.
Study area, study design and follow-up Our study took place in Allada, a town located 56 km North Cotonou, the economic capital of Benin. The study participants were residents of 21 villages surrounding two primary health facilities: Sékou and Attogon. This study is part of a larger one encompassing 1,183 human immunodeficiency virus (HIV)-negative pregnant women participating in the randomized Malaria in Pregnancy Preventive Alternative Drugs (http://clinicaltrials. gov/ct2/show/ NCT00811421) trial, designed to compare intermittent preventive malarial treatment  (IPTp)  with either sulfadoxine-pyrimethamine or mefloquine. The study protocol has been described in detail elsewhere  (Accrombessi et al. , 2015; Ouedraogo et al. , 2012). The first 400 children of these women were followed-up to investigate the impact of sociodemographic, economic, environmental and biologic factors such as the parasitological status (geohelminth and P.
falciparum carriers) during pregnancy on infant health during the two years of life in southern Benin  (Accrombessi et al. , 2015; d'Almeida et al. , 2017). The 400 mothers included in the present study are the mothers of these 400 children. Women were included before a gestational age (GA) of 28 weeks, and two doses of IPTp were administered at antenatal visits (ANV). The second dose was given at least 1 month after the first one. During the first ANV, a total dose of 600 mg of mebendazole was given to the women to be taken at home (100 mg two times per day for 3 days) according to the guidelines of the Beninese Ministry of Health. Between antenatal visits, women were encouraged to attend the health facility for any health complaint. At inclusion, a questionnaire was applied by the midwife to obtain data regarding socio-demographic characteristics, gynecological and obstetrical history.
Clinical and biological data during asthma exacerbation Demographic data such as age, sex, body mass index, smoking status quantified in packs per year (P/A), inhaled treatment prescribed before exacerbation, as well as the use and duration of oral steroids during the exacerbation were collected. The total serum IgE concentration (immunoassay technique, ImmunoCAP IgE total, Thermo Fisher Scientific, Phadia AB, Uppsala, Sweden), blood eosinophilia (Beckman Coulter LH 780 Controlled Analyzer), and C-reactive protein (Beckman Coulter LH 780 Controlled Analyzer, Holliston, Mass) were also collected. The severity of exacerbations was characterized by the length of the hospital stay including the time spent in the emergency room and if the patient needed to be treated in the intensive care unit.
Statistical analyses Quantitative data with a normal distribution were expressed as mean and SD, and quantitative data with no normal distribution were expressed as median deviation (interquartile range). Qualitative data were expressed as frequencies (%). A Student t test (parametric) was used to compare continuous variables with normal distribution. The Mann-Whitney test was used for quantitative data and had no normal distribution. Statistical significance was defined as a P value of less than. 05. Receiver operator characteristic curves were used to assess serum IgG concentrations as a potential marker of a positive virus specimen. The best IgG cutoff was determined using the Youden index. Sensitivity and specificity of IgG cutoff for a positive virus sample were also defined. A Spearman test was used to assess the correlation between serum IgG concentrations and other continuous variables.
Immunofluorescence staining and confocal microscopy Cells monolayers grown on glass coverslip were fixed for 20 min with 4% PFA (paraformaldehyde) and permeabilized for 15 min with 0. 1% Triton X-100 in PBS (phosphate-buffered saline). Cells were incubated with the indicated primary antibodies for 1 h at RT, washed and incubated for 1h with Alexa fluor conjugated secondary antibodies. Following washing, cells were mounted with Immu-Mount (Shandon) containing DAPI (4,6 diamidino-2-phenylindole) to stain nuclei. Images were captured in sequential recording mode using a Leica SP8 confocal microscope (63X oil-immersion objective). For 2D reconstruction, confocal stacks were treated with ImageJ Software.
DAPI was used to stain the nuclei. Images were captured in sequential recording mode using a Leica SP8 confocal microscope (63X oil-immersion objective). For each field (about 40 cells/field), 35 planes were acquired by confocal microscopy and a max intensity Z-projection was done using ImageJ. Quantifications of Gcontaining spots were performed using the image toolbox of MatLab software. Each spot was considered as a single virion and the total number of spots in the image was divided by the number of nuclei in the field.
Acknowledgement We thank  Ahmet Civas  for helpful discussions. The present work has benefited from the light microscopy facility of  Imagerie-Gif , (http://www. i2bc. paris-saclay. fr),member of IBiSA (http://www. ibisa. net),supported by " France-BioImaging " ( ANR-10-INBS-04-01 ), and the  Labex  " Saclay Plant Sciences " ( ANR-10-LABX-0040-SPS ).
Result submission, evaluation and EQA scoring We provided the Laboratories with a link to an online form to submit their EQA results. Laboratories could indicate for which of the four target viruses they had tested the EQA panel and background information of the diagnostic tests that the laboratory assessed with the EQA. Data were collected and analysed in Microsoft Excel 2011. Fisher's exact test (www. socscistatistics. com/tests/fisher/Default2. aspx) was used to compare the rate of false-negative results obtained with virusspecific real-time assays and with other assays for TOSV, USUV, TBEV and WNV. Fisher's exact test was used because the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with the chi-squared test.