dataesr/scientific-paragraphs-categorization huggingface dataset:
0. 13. SNP calls were made using the Torrent Variant Caller v. 5. 0. 3, and variants were annotated with HPV gene/region using snpEff v. 3. 6c  87. Pipeline settings and parameters can be found at https://github. com/cgrlab/cgrHPV16. HPV16 variant lineage classification. HPV16 variant lineage assignment was based on the maximum likelihood (ML) tree topology constructed using RAxML MPI v7. 2. 8. 27  88  that included 16 HPV16 European and non-European variant lineage reference sequences. We excluded samples with overall poor coverage, per individual nucleotide site per sample with low reads (<5), as previously described  24. Statistical analyses. To identify the mutational processes generating the HPV variants, we carried out a de novo mutational signature analysis. There are a total of 12 possible single-nucleotide variants (SNV).
A total of 15 µL of the release samples collected at the different time points were compared with the same volume of native ipilimumab antibodies. Capillary zone electrophoresis-mass spectrometry (CZE-MS) experiments were performed using a 7100 Agilent capillary electrophoresis, ESI-QTOF 6540 mass spectrometer (Agilent Technologies, Santa Clara, California, USA) and Mass Hunter B. 07. 00 software. Analysis of ipilimumab were performed on the triple-layer coated capillary of Polybrene-dextran sulfate-Polybrene. 28 leased anti-CtlA4 antibody functional evaluation To assess the functionality of the released anti-CTLA4 antibodies, we performed an ex vivo competitive binding assay on a cell line, and then an in vivo mouse experiment.
Materials and methods Patient recruitment and monocyte isolation. CD patients were recruited at the Gastroenterology and Endoscopy Unit of the University Hospital of Parma, Italy, between September 2018 and June 2019 in occasion of their access to the hospital for treatment administration. Adult patients with a histologically confirmed diagnosis of CD of at least 6 months and under therapy with IFX were included in the study. Exclusion criteria included refusal to sign the informed consent form; diagnosis of UC or indetermined colitis; ongoing therapy with corticosteroids; presence of abscess; and contraindications for or reactions to IFX therapy. Demographic and clinical data were extracted from patient records and included body mass index (BMI), comorbidities, and ongoing medical therapies.
Materials. Fetal bovine serum and RPMI-1640 medium were purchased from EuroClone (Milano, Italy). Sigma-Aldrich (Milano, Italy) was the source of all other chemicals. Statistics. GraphPad Prism 5. 0 (GraphPad Software, USA) and SPSS (IBM, Statistics, USA) software were used for the statistical analyses. Clinical data are expressed as frequencies (n, %) or means (standard deviation). Group comparisons were carried out by using the chi-squared test and Mann-Whitney U test for categorical and continuous variables, respectively. Gene expression and cytokine production were analyzed with a two-tailed Student's t-test for unpaired data. Differences were considered statistically significant when p < 0. 05.
| Ex vivo Epstein-Barr transformation of B cells To prolong the viability of primary human B cells (n = 4 anti-MAG neuropathy patients) ex vivo, the cells were transformed with Epstein-Barr virus (EBV)  (Hollyoake, Stühler, Stühler, Farrell, Gordon, & Sinclair, 1995). Marmoset B95. 8 Epstein-Barr virus-producing cells (RRID:CVCL_1953; Vircell) were maintained in complete RPMI 1640 medium containing 10% FBS, 1% AA, and 1% l-Gln. The supernatant containing the EBV was collected after 20 days by centrifuging cells (1400g, 15 min) and filtering the supernatant with a 0. 45 μm and a 0. 2 μm Filtropur S filter (83. 1826; Sarstedt). Freshly isolated human PBMC (1x10 6 cells) were resuspended in 3 ml EBV supernatant and incubated for 24 hr before adding 7 ml complete RPMI 1640 medium supplemented with 20 ng/ml cyclosporin A (30024; Sigma-Aldrich).
Whole blood (40 µl) was stained with 1 µl of anti-mouse CD19-PECy7 (RRID:AB_657664; eBioscience) for 45 min at 4°C (protected from light). The samples were then diluted with PBS to a final volume of 200 µl and stained with 1 µl of DAPI (4',6-diamidino-2-phenylindol, D3571; Invitrogen) prior to the analysis of the cells by flow cytometry with the LSR Fortessa (Becton Dickinson). At least 10'000 events were recorded and data were further gated and analyzed with FlowJo v 10. 2 (FlowJo LLC).
Follow-up forms were also designed to be filled at different time points: the start of letermovir administration, then once a month, and finally at end of prophylaxis, for whatever the reason for treatment discontinuation. Remote monitoring was performed on a subset of data to confirm patient eligibility to the compassionate program. The letermovir dose was 480 mg once daily and adjusted to 240 mg once daily when coadministered with cyclosporine. The duration of prophylaxis was determined by the local physician. The drug request had to be renewed from month to month.
RESULTS Between January 8, 2018, and January 20, 2019, early access to letermovir was requested for 217 patients and delivered by the French Drug Agency to 214 patients from 21 transplant centers (Figure  1 ). Among these 214 patients, 182 received at least 1 dose of letermovir: 96 (53%) for PP, 6 (3%) for late PP, and 80 (44%) in 15 centers for SP. Data collection was censored on January 20, 2019, including for patients who went on letermovir prophylaxis after this date, and except for the pharmacovigilance follow-up data, which were censored on February 18, 2019, that is, 4 weeks after the end of the compassionate program. Due to the paucity of data on SP in the literature, this report focuses on the 80 SP patients. The treatment initiation forms were received for 62 patients, and at least 1 follow-up form was obtained for 67 patients.
Abnormal liver tests 1 Values are presented as number or number (%) unless otherwise indicated. * The duration of treatment was calculated both for patients who discontinued the treatment before or on January 20, 2019, date of data censor, and for patients still under letermovir at this date, together. y This patient died of grade 4, uncontrolled, acute GVHD. Although the availability of letermovir for PP of CMVseropositive allogeneic HCT recipients should considerably reduce the need for SP, there are several situations where letermovir SP might be useful. First, some patients who received letermovir PP may experience CMV infection or disease more than 3 months after transplant. A prospective study comparing letermovir to placebo for 3 additional months after day 100 in patients who have received PP letermovir until day 100 without CMV breakthrough infections will address this question (ClinicalTrials.
ACKNOWLEDGMENTS The authors thank the pharmacists of the participating centers for their help in the compassionate program and drug delivery. Collaborators include  Ana Berceanu ,  Etienne Daguindeau ,  Eric Deconink ,  Fabrice Larosa ,  CHU Besançon; In es Boussen, V eronique Morel, St ephanie Nguyen-Quoc, Françoise Norol, Laetitia Souchet, Hopital Piti e Salp etri ere, Paris ;  Claude-Eric Bulabois ,  Martin Carre ,  Anne Thiebaut ,  CHU Grenoble ;  Arnaud Campidelli ,  Maud D'Aveni ,  Marie Detrait ,  Marie-Th er ese Rubio ,  CHRU Nancy Brabois ;  Patrice Ceballos ,  Sylvain Lamure ,  Laure Vincent ,  CHU Saint Eloi, Montpellier ;  J er emie Cohen ,  Romain Gu  ery,  Hopital Necker , Paris;  Catherine Cordonnier ,  C ecile Pautas ,  Christine Robin ,  Mathieu Leclerc ,  Rabah Redjoul ,  CHU Henri Mondor, Cr eteil ;  C ecile Borel ,  Karen Delavigne ,  Institut UCT, Oncopole, Toulouse ;  Deborah Desmier ,  Natacha Maillard ,  CHU Poitiers La Mil etrie ;  Sophie Ducastelle-Lepretre ,  Marie Larcher , hospices civils de Lyon;  Sabine Furst ,  Angela Granata ,  Rafael Hernani-Morales ,  Institut Paoli Calmettes ,  Marseille ;  Charles Herbaux ,  CHU Lille ;  Magalie Joris ,  CHU Amiens ;  Amandine Le bourgeois ,  Rapha€ el Lecomte ,  Pierre Peterlin ,  CHU Nantes ;  David Michonneau ,  Simona Pagliuca ,  Flore Sicre de Fontbrune, Aur elien Sutra Del Galy, Hopital Saint-Louis, Paris.
Statistical analysis Data were reviewed, extracted, coded and entered into Epi data v3. 1, then exported to SPSS v20 for cleaning and analysis. Descriptive analyses were performed for summary statistics. Figures and tables were constructed with SPSS or Excel (Microsoft). The progress of districts towards trachoma elimination was analyzed by comparing prevalence survey data in relation to the WHO classification criteria of "eliminated", "low", "moderate" and "high"  [5]. In addition, the implementation of SAFE strategy for the year 2017 was evaluated and compared with the trachoma endemicity status of districts.
Lack of complete reported data on the SAFE strategy and the difficulty in finding reliable sources of information and indicators for the facial cleanliness and the environmental sanitation components of the program were the major limitations of this study. This data incompleteness made it impossible to compare the high and low performing districts with regard to SAFE strategy implementation. The major implications of this study are that districts with a high and moderate prevalence of trachoma should get the required attention to receive the expected rounds of Zithromax® and to be timely surveyed. Moreover, all districts should fully implement and report all components of the SAFE strategy to properly evaluate and improve the strategy. Furthermore, facial cleanliness and environmental improvement should be assessed at individual and household level by means of operational research.
Acknowledgements This research was conducted through the  Structured Operational Research and Training Initiative (SORT IT ), a global partnership coordinated by  TDR , The Special  Programme for Research and Training in Tropical Diseases  hosted at the  World Health Organization. The training model is based on a course developed jointly by the  International Union Against Tuberculosis and Lung Disease  and  Médecins Sans Frontières-Luxembourg (LuxOR). The specific SORT IT program that led to these publications included a joint implementing partnership between TDR the  Institute of Tropical Medicine Antwerp, Belgium , the  University of Gondar, Ethiopia , The WHO country office in Ethiopia,  Médecins Sans Frontières, Luxembourg (LuxOR)  and The  International Union Against Tuberculosis and Lung Disease, Paris France.
B3,BD Biosciences), GzmB (GB11, BD Biosciences), TNF-A (MAB11, BD Biosciences), NKP44 (REA1163, Miltenyi Biotec), and CD14 (TÜK4, Miltenyi Biotec). Reference listing the cross-reactivity of each antibody is listed in Supplementary Table  S1. The anti-NKG2A antibody used recognizes both NKG2A and NKG2C on simian cells. Due to the lack of information on the KIR polymorphism in African NHP and the rare anti-KIR antibodies specific for NHP, the KIR expression has not been analyzed. Flow cytometry acquisitions were performed on an LSRII (BD Biosciences). The data were further analyzed using FlowJo 10. 4. 2 software (FlowJo, LLC, Ashland, OR, United States). Intracellular staining was performed using BD Cytofix/Cytoperm TM. Uniform manifold approximation and projection was performed with Flojow, using 1,000 iterations and perplexity of 0.
Statistics The GraphPad Prism 7 (GraphPad Software, San Diego, CA) was used to analyze data and to perform statistical analyses. Statistical significance of differences was assessed using non-parametric Mann-Whitney U tests (Figures  1A, 3B, C ) or Wilcoxon matched-pairs signed-rank test for paired samples (Figures  1E, F, H ). All group comparisons were carried out using a one-way analysis of variance and followed by a Tukey's multiple-comparison test. The latter is a post hoc test based on the studentized range distribution (Figures  2E, F, 4E, F, 5A, B, E, F ). Values of p < 0. 05 were considered significant. NK cell populations were analyzed by the uniform manifold approximation and projection method provided by the FlowJo plugin version 3. 1. Heatmap of the Log2(FC) of the marker expression was compared with the median across all samples.
e. , mucosa as a site of viral entry and replication and SLT for the education of B and T cell responses. We compared here the NK cells present in such anatomic sites with body compartments where NK cells are more frequent and more often described (blood and liver). We performed these analyses in representative species from Asia and Africa. We, thus, studied four NHP species and only two of them extensively: one Asian (CM) and one African (AGM) species. Of note, these two species are among the most used NHP models in biomedical research. Also, the data observed here for CM might be similar in related species, such as RMs. Here, we performed a multiparameter flow cytometry. Even if we did not use next-generation sequencing technology, such analysis allowed us to focus on specific markers and to analyze a wide range of tissues (blood, liver, spleen, lymph nodes, ileum, jejunum, colon, and rectum) concomitantly.
We would like to acknowledge grant support from  French National Agency for Research on AIDS , the  National Institutes of Health  ( R01AI143457 ), the  Vaccine Research Institute , the Fondation  J. Beytout , and the  Fondation Les Ailes  to MM-T. We gratefully acknowledge the support to IDMIT from the  French government: Investments for the Future program for infrastructures (PIA)  through the  ANR-11-INBS-0008  grant as well as from the  PIA  grant  ANR-10-EQPX-02-01  to the  FlowCyTech facility at IDMIT.
ACKNOWLEDGMENTS We are grateful for the excellent help from the veterinarians and staff at the  IDMIT Center (Benoit Delache ,  Jean-Marie Helies ,  Raphaël Ho Tsong Fang , and  Julie Morin ). We thank  M. Mietsch  and  M. Daskalaki  for comprehensive veterinary support and  S. Heine ,  J. Hampe , and  N. Leuchte  for excellent technical assistance.
PROM2 gene, also called prominin-2, with some of the highest d-scores at 4. 6 and fold change of 3. 3 (Table  S2 ), and because PROM2, a membrane glycoprotein and a second member of the prominin family, induces membrane protrusions  5  and could thus be implicated in invasive processes. Using reverse transcription-polymerase chain reaction (RT-qPCR), the median expression of PROM2 mRNA was significantly higher in metastatic lymph nodes from patients who subsequently developed brain metastases (Δ cycle threshold [Ct] = 4. 9, interquartile range [IQR] = 6. 3 vs ΔCt = 2. 1, IQR = 3. 9; P =. 005; Figure  1A ). We then analyzed transcriptomic data downloaded from three public databanks (the Cancer Genome Atlas SKCM and GSE22155 and GSE65904 cohorts  [6] [7] [8]  ), and found that a high PROM2 expression in melanoma metastatic lymph nodes was associated with poor survival (Figure  S3 ).
5 µM of each primer, 0. 2 units of KOD XL DNA Polymerase (EMD Millipore Corporation, https://www. emdmillipore. com), and 2 µL of DNA template (Appendix Tables  1  and 2 ). We purified and sequenced PCR products using Eurofins Genomics (https://www. eurofinsgenomics. com) and then edited and assembled contigs using CodonCode Aligner 8. 0. 1 (https:// www. codoncode. com/index. htm). We aligned the noncoding ITS and 12S regions using MAFFT v7  (32)  with automated selection of parameters and aligned the protein-coding mtDNA genes (i. e. , cox1, cox3, nad4, and nad3) with respect to their amino acid translations using MACSE  (33)  as implemented in Codon-Code Aligner 8. 0. 1. Molecular sequences from the S. mansoni samples are deposited in GenBank (accession nos. MN593375-434).
Phylogenetic Approach We concatenated the 12S rRNA gene and the 4 protein-coding mtDNA genes of each S. mansoni specimen (i. e. , adult worms and miracidia from rodents, miracidia from humans, and cercariae from snails), as well as those from S. mansoni specimens previously collected from Hubert's multimammate mice (Mastomys huberti) and Nile grass rats (Arvicanthis niloticus) in Senegal  (21). In addition, we also obtained and concatenated the respective sequences from publicly available genomes of S. mansoni previously isolated from school-aged children in Uganda  (34)  and Schistosoma rodhaini from an undetermined intermediate host in Burundi  (6). In brief, we downloaded an S. mansoni reference genome (GenBank accession no. SAMEA2272516) from WormBase ParaSite  (35)  and aligned the 5 specified mitochondrial genes with those of S.
2%) had S. mansoni infections, which were identified by using molecular tools. On a local scale, 1. 8%-7. 1% of B. pfeifferi snails were infected with S. mansoni (Table  1 ). The dataset including ITS, 12S rRNA, and the protein-coding mtDNA sequences (i. e. , cox1, cox3, nad4, and nad3) of S. mansoni from school-aged children, rodents, and B. pfeifferi snails (Table  2 ) showed no intraspecific variability within the ITS alignment (914 bp), whereas variability was present within the 12S (760 bp, polymorphism <0. 52%) and concatenated mtDNA (2,874 bp, polymorphism <0. 77%) gene alignments. Intraspecific single-nucleotide polymorphisms within protein-coding mtDNA genes represented nonsynonymous amino acid substitutions in 4. 4% (35/796) of codons, and saturation at model-corrected genetic distances was not detected (Appendix Figure  3 ).
Acknowledgments We are extremely grateful for the contribution made by all the personnel who supported this study, in particular  Alassane Ndiaye ,  Lucy Yasenev ,  Mapaté Gaye , and the  Schistosomiasis Collection  staff at the  Natural History Museum (Aidan Emery ,  Fiona Allan , and  Muriel Rabone ). We thank  Chiara Crestani  and  Kathryn Berger  for their helpful advice during data analysis. Special thanks to  Boubacar Bâ ,  Cheikh Thiam , and their families for enormously facilitating fieldwork and logistics. We are grateful to the communities involved in the study for their friendly participation and hospitality. This work was funded by the  Biotechnology and Biological Sciences Research Council , the  Department for International Development , the  Economic and Social Research Council , the  Medical Research Council , the  Natural Environment Research Council , and the  Defense Science and Technology Laboratory  under the  Zoonoses and Emerging Livestock Systems program  ( BB/L018985/ 1  and  BB/N503563/1 ).
Introduction: Infliximab (IFX) was the first anti-tumor necrosis factor (TNFa) antibody to be used in the treatment of severe chronic inflammatory diseases, such as Crohn's disease and rheumatoid arthritis. A number of serious adverse drug reactions are known to be associated with IFX use; they include infections, malignancies, and injection site reactions. Although a few case reports have described potential psychiatric adverse events (including suicide attempts and manic episodes), the latter are barely mentioned in IFX's summary of product characteristics. The objective of the present retrospective study was to detect potential psychiatric adverse events associated with IFX treatment by analyzing a national discharge abstract database.
Materials and Methods: We performed an historical cohort study by analyzing data from the French national hospital discharge abstract database (PMSI) between 2008 and 2014. All patients admitted with one of the five diseases treated with IFX were included. Results: Of the 325,319 patients included in the study, 7,600 had been treated with IFX. The proportion of hospital admissions for one or more psychiatric events was higher among IFX-exposed patients (750 out of 7,600; 9. 87%) than among non-exposed patients  (17,456 out of 317,719; 5. 49%). After taking account of potential confounders in the cohort as a whole, a semi-parametric Cox regression analysis gave an overall hazard ratio (HR) [95% confidence interval] (CI) of 4. 5 [3. 95; 5. 13]  for a hospital admission with a psychiatric adverse event during treatment with IFX.
According to the SPC for IFX, depression and insomnia are frequent, amnesia, agitation, confusion, drowsiness, and nervousness are uncommon, and apathy is rare [Agence Nationale de sécurité du médicament et des produits de santé (ANSM), 2020]. In contrast, some studies have suggested that IFX treatment is associated with better quality of life in patients suffering from treatment-resistant mood disorders  (Soczynska et al. , 2009). The characterization of these psychiatric adverse events is therefore essential for adequately assessing the riskbenefit ratio and improving the management of these events when they occur. Over the last few decades, the systematic collection of inpatient data (notably as part of health payment systems) has enabled the implementation of large-scale, retrospective, observational analyses of administrative medical databases.
These databases contain "big data"  (Baro et al. , 2015) , and their analysis raises a number of new methodological issues  (Chazard et al. , 2018). In France, IFX is obligatorily administered during an inpatient stay, and so is recorded in hospital databases. Moreover, most serious psychiatric events also lead to hospital admission, and so are tracked in the same databases. Hence, the objective of the present retrospective analysis of the French national hospital discharge database was to detect potential psychiatric effects of IFX therapy (including manic episodes, depressive disorders, suicide attempts, and psychotic disorders) leading to hospital admission, while taking account of potential confounders (such as the underlying disease).
Data Source We performed a historic cohort study by reusing data contained in the French national hospital discharge database (Programme de Me ́dicalisation des Systèmes d'Information, PMSI). The PMSI database contains standardized discharge reports for all inpatient admissions to nonprofit or for-profit general acute care and psychiatric hospitals in France. Around 29 million inpatient stays are recorded each year. Each discharge report contains the following information: the primary and associated diagnoses coded according to the International Classification of Diseases, 10 th revision (ICD-10) (WHO, 2020), the therapeutic and diagnostic procedures coded according to the French Classification commune des Actes Me ́dicaux (CCAM) terminology [L'Assurance Maladie (Ameli), 2020], and the dispensation of certain expensive drugs coded according to the French Unite ́Commune de Dispensation (UCD) classification (Unite ́s communes de dispensation prises en charge en sus Publication ATIH).
Study Population We first identified all patients aged from 18 to 99 admitted with a primary or associated diagnosis corresponding to an indication for IFX (namely rheumatoid arthritis, Crohn's disease, ankylosing spondylitis, psoriatic arthritis, ulcerative colitis, and plaque psoriasis) between January 1, 2009, and December 31, 2014. The ICD-10 codes for these diagnoses are listed in Table  1. Next, we extracted all the patients' inpatient stays between January 1, 2008, and December 31, 2014, in order to obtain at least one year of historical data before the study inclusion date. Hence, we excluded patients with a history of psychiatric disease at some point between January 1, 2008, and the study inclusion date. To that end, we searched for hospital admissions with the same ICD-10 codes as those used to definition the study outcomes (i.
The following covariates were tested: IFX exposure as the time-dependent variable with multiple changes, the patients' characteristics (age and sex), the disease of interest, and comorbidities. Cox models were built for each stratum: rheumatoid arthritis, Crohn's disease, ankylosing spondylitis, psoriatic arthritis, ulcerative colitis, plaque psoriasis, and two or more indications in the same patient. The results were calculated as the hazard ratio (HR) (95CI%). Several sensitivity analyses were performed. Firstly, we tested the Cox model with a negative control for the CCAM code "AHPA009", corresponding to carpal tunnel surgery. Secondly, we varied the exposure period from 4 to 28 weeks, according to the SPC [Agence Nationale de sécurité du médicament et des produits de santé (ANSM), 2020].