dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2017; Theunissen, et al. , 2017). Bulk-lysis is especially recommended in childhood MDS, in which about 50% of patients have refractory cytopenia of childhood (RCC), frequently with hypocellular BM  (Aalbers et al. , 2013; Aalbers et al. , 2015). For lysis of the nonnucleated RBCs, ammonium chloride (either homemade or commercially available) can be used. Other (commercial) lysing solutions may be used after parallel testing and comparison. Within the EuroFlow protocol, erythrocyte lysis is performed after the antibody incubation phase. This results in the lowest cell loss, and the presence of a fixative prevents the decrease in MFI during the period between staining and data acquisition  (Kalina, et al. , 2012). Alternatively, it is possible to adopt a Lysis-no-Wash method. With such procedures, aliquots of 50 to 100 μl of whole BM or PB are incubated with the antibody cocktail of each tube.
The Study We used PubMed and ISI Web of Knowledge search engines with no restriction on language and the phrase "Toscana AND virus AND (case report OR case-report OR travel* OR import*). " We conducted a systematic search on ProMed and Google Scholar, as well as cross-reference checking. The inclusion criteria were laboratory-documented acute TOSV infection, indication of a travel-related infection in a TOSVendemic area, and number of days between travel return and symptom onset. Two reviewers screened titles, abstracts, and full-text articles independently. We extracted clinic and biologic elements from neuroinvasive TOSV case reports. For each patient, data related to the duration of travel and the time of symptom onset, gender, age, country in which case was reported, and country of infection were reported.
Incubation Period for Neuroinvasive Toscana Virus Infections Lison Laroche, 1 Frédéric Jourdain, 1  Toscana virus (TOSV) is an emerging pathogen in the Mediterranean area and is neuroinvasive in its most severe form. Basic knowledge on TOSV biology is limited. We conducted a systematic review on travel-related infections to estimate the TOSV incubation period. We estimated the incubation period at 12. 1 days. package (R Foundation for Statistical Computing, https://www. r-project. org). We defined the data distribution with 4 parametric models (log-normal, loglogistic, Gamma, and Weibull). To determine the best model for our distribution, we calculated the Akaike information criterion. We used the nonparametric log-rank test from the interval package to assess the effect of age and gender as covariates.
To check the result stability, we performed an additional Bayesian approach, fitting with the Weibull distribution. Regarding imported case reports, 142 documents were identified on PubMed and 133 on Web of Knowledge. We removed 79 duplicates and excluded 118 records after screening titles and abstracts. A total of 42 articles were eligible after full-text reading. We then selected 22 documents for data extraction. A total of 24 cases were selected (Appendix Table  2,   Figure). All travel-associated cases fulfilling the inclusion criteria were neuroinvasive; these cases were diagnosed in a non-TOSV-endemic area after a stay in a proven TOSV-endemic area (Figure  1 ). We selected Weibull distribution because it presented the lower Akaike information criterion (Figure  2 ; Appendix Table  3 ).
Conclusions In the literature, the IP values of TOSV are often heterogeneous, unsourced, or without evidence and therefore do not constitute a valid estimate for clinical or infection control decisions. Our literature review identified 24 neurologic cases of TOSV infection. Some travel durations were reported approximately in case reports and were not included in the analysis. All the data used were based on severe neurologic forms of the disease, which required hospitalization soon after the exposure period. We estimated the median IP of TOSV at 12 (95% CI 10. 2-14. 4) days. Considering the delay from infection to symptom onset, this value is greater than that for most other arboviruses  (11). Our estimate of the IP is evidence-based and relies on data from well-characterized cases. However, cases that cause mildersymptoms, as opposed to neuroinvasive forms of the disease, might have a shorter IP (similar to We also cannot exclude infections by other sandfly fever Naples phleboviruses because of crossreaction risk in serologic analyses due to their close genetic relationships  (12).
Acknowledgments We thank  Julian Wei-Tze Tang ,  James Farrugia ,  Jonas Schmidt-Chanasit ,  Josef Georg Heckmann , and  David Breen  for answering our questions by email to clarify information regarding the TOSV case reports. We also thank  Eric Elguero  for his support in statistical analysis,  Heïdi Lançon  for the English revision of the manuscript, and  Jérôme Depaquit  for reviewing the manuscript. This research was funded by the  IRD (Institut de Recherche pour le Développement) ,  CNRS  ( Centre National de la Recherche Scientifique ),  UM (Université de Montpellier ) and by the by the  European Virus Archive Global  ( EVA-GLOBAL)  project that has received funding from the  European Union 's  Horizon 2020-INFRAIA-2019 research and innovation program  under grant agreement No  871029.
Overview of the phenotype, cytokine, and inflammatory profiles of patients with COVID-19 Patient characteristics from the French COVID cohort enrolled in this analysis are shown in Table  1. All patients from this cohort were stratified as severe as per criteria of the French COVID cohort (clinicaltrials. gov NCT04262921)  (Yazdanpanah, 2020) , with 53 (87%) being hospitalized in an ICU (either initially or after clinical worsening or death) and eight were not. The median age was 60 years (interquartile range, 50-69) and 80% were men. Sampling for immunological analyses was performed within three days of entry and after a median of 11 days  [7] [8] [9] [10] [11] [12] [13] [14]  after the onset of symptoms. We first assessed leukocyte profiles by flow cytometry using frozen peripheral blood mononuclear cells (PBMCs) from 50 patients with COVID-19 (with available PBMC samples) and 18 healthy donors (HDs) (14 or 15 HDs were used as controls per immune cell subset).
The data were acquired using a Bio-Plex 200 system. Extrapolated concentrations were used and the out-of-range values were entered at the highest or lowest extrapolated concentration. Values were standardized for each cytokine across all displayed samples (centered around the observed mean, with variance equal to 1). CD177 quantification was performed on non-inactivated serum samples (diluted 1:2 or 1:10) using a Human CD177 ELISA Kit (ThermoFisher Scientific), according to the manufacturer's instructions.
Cell phenotyping Immune-cell phenotyping was performed using an LSR Fortessa 4-laser (488, 640, 561, and 405 nm) flow cytometer (BD Biosciences) and Diva software, version 6. 2. FlowJo software, version 9. 9. 6 (Tree Star Inc. ), was used for data analysis. CD4+ and CD8+ T cells were analyzed for CD45RA and CCR7 expression to identify the naive, memory, and effector cell subsets for coexpression of activation (HLA-DR and CD38) and exhaustion/senescence (CD57and PD1) markers. CD19+ B cell subsets were analyzed for the markers CD21 and CD27. ASC (plasmablasts) were identified as CD19+ cells expressing CD38 and CD27. We used CD16, CD56, and CD57 to identify NK cell subsets. gd T cells were identified using an anti-TCR gd antibody. HLA-DR, CD33, CD45RA, CD123, CD141, and CD1c were used to identify dendritic cell subsets, as previously described  (See et al.
RNA sequencing Total RNA was purified from whole blood using the Tempusä Spin RNA Isolation Kit (ThermoFisher Scientific). RNA was quantified using the Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher Scientific) and quality control performed on a Bioanalyzer (Agilent). Globin mRNA was depleted using GLOBINclear Kit (Invitrogen) before mRNA library preparation with the TruSeqâ Stranded mRNA Kit, as per the Illumina protocol. Libraries were sequenced on an Illumina HiSeq 2500 V4 system. Sequencing quality control was performed using Sequence Analysis Viewer. FastQ files were generated on the Illumina BaseSpace Sequence Hub. Transcript reads were aligned to the hg18 human reference genome using Salmon v0. 8. 2  (Patro et al. , 2017)  and quantified relative to annotation model "hsapiens_gene_ensembl" recovered from the R package biomaRt v2.
ACKNOWLEDGMENTS We thank the patients who donated their blood. We thank  F. Mentre ,  S. Tubiana , the  French COVID cohort, and REACTing (REsearch & ACtion emergING infectious diseases)  for cohort management. We thank the scientific advisory board of the French COVID-19 cohort composed of  Dominique Costagliola ,  Astrid Vabret , HerveRaoul, and  Laurence Weiss. We thank  Romain Le  ´vy for fruitful discussions. This work was supported by  INSERM  and the  Investissements d'Avenir program ,  Vaccine Research Institute (VRI) , managed by the  ANR  under reference  ANR-10-LABX-77-01  and the  CARE  project funded from the  Innovative Medicines Initiative 2 Joint Undertaking (JU)  under grant agreement No  101005077. The JU receives support from the  European Union 's  Horizon 2020 research and innovation programme and EFPIA  and  Bill & Melinda Gates Foundation ,  Global Health Drug Discovery Institute, University of Dundee.
Cats  nderwent a standardized diagnostic evaluation including history, physical examination, CBC, serum biochemistry profile (including serum cobalamin concentration), urinalysis, fecal analysis, and abdominal ultrasound examination (days 1-7). Abdominal ultrasound examination was performed within 48 hours of biopsy. Cats were excluded from the study if another tumor was suspected before surgery or if other comorbidities were present that could lead to complications (data presented in companion article). 25.
| Biopsy sampling Surgical biopsies were performed in all cases to assess all layers of the intestinal wall, taking into consideration the risks of complications. 5  In cases where the surgical procedure was declined, endoscopic biopsies were performed. Biopsy sites were selected according to: (a) the literature data, with the most reported sites involving the jejunum and ileum,  1, 3, 4  (b) abdominal ultrasonographic data (data are presented in companion article),  25  and (c) macroscopic changes observed during surgery (eg, intestinal wall thickness of each digestive segment, lymph node enlargement). Surgical biopsy samples were immediately mounted on a moisturized synthetic foam sponge, placed in a fenestrated plastic cassette and immersed in 10% formalin.
Data from recent literature have shown that LPE cases usually display a polyclonal pattern whereas >90% of LGITL cases exhibit clonal or oligoclonal TCRγ gene rearrangement. 4, 20 In our study, clonality testing was performed in all LGITL and LPE cases. Fourteen percent of LGITL cases showed TCR polyclonal rearrangement, with 1 case having a strong apical-to-basal gradient, and a high percentage of LPE cases showed monoclonality or monoclonality in a polyclonal background. This finding possibly can be explained by the coexistence of neoplastic and inflammatory cells in the same area of the sample, where inflammatory cells react to clonal T-lymphocytes. Mild neoplastic populations characterized by nests and plaques also could emerge in an inflammatory background. 8] [39]  In humans, inflammatory bowel disease can be associated with a clonal lymphoid population that is not correlated or predictive of an associated lymphoid neoplasia.
Forms of elastase expressed in IEC To determine the identity of the elastase form(s) expressed in IEC, RT-PCR was performed with mRNA from Caco-2 cells, a human IEC line, using primer pairs targeting the five known human elastase genes (neutrophil elastase: ELANE, members of the chymotrypsinlike elastase family: CELA1, 1, CELA2, and CELA3, and matrix metalloproteinase-12: MMP12). RT-PCR analysis revealed the presence of only one enzyme transcript in IEC (Fig. 2a  and Supplementary Fig. 1a-f ). Sequencing of the PCR product revealed 100% identity with the full-length cDNA from CELA2A gene (NCBI accession number NM_033440; Swiss-Prot accession number P08217, ELA2A as protein name). ELA2A protein expression was then confirmed in IEC line Caco-2 and in human colonic tissues (Fig. 2a-e ). Analysis of ELA2A localization showed that in IEC monolayers, ELA2A signal was concentrated at the membrane level.
Control and regulation of ELA2A in intestinal epithelium As previously described in the skin,  18  ELA2A activity can be tightly controlled by ELAFIN, an elastase inhibitor (Supplementary Fig. 2a ). To assess possible interactions between ELA2A and ELAFIN in colonic tissues, double-labelling immunofluorescence experiments were performed. ELAFIN staining appeared as dots in cytoplasm and also concentrated at the plasma membrane (Supplementary Fig. 2b ). ELA2A and ELAFIN immunoreactivity overlapped in plasma membrane, cytoplasm, as well as in the lumen. These data thus support possible interactions between the ELA2 protease and its inhibitor ELAFIN in the colonic mucosa. Proteolytic activity is also regulated by the pro-peptide cleavage of inactive zymogen forms of proteases. A previous study has demonstrated that ELA2A exists as a pro-form, and that pro-ELA2A could be converted into an active form, by trypsin cleavage.
13 Cela2a upregulation (twofold increase, p < 0. 05) was observed in different models of colitis such as acute DSS-induced colitis (analysis of GEO data base number GSE5864  26  ) or chronic colitis induced by TNBS administration (analysis of GEO data base number GSE35609  27  ). These results are in accordance with the increased elastolytic activity we observed in epithelium from mouse model of colitis. 13 IEC also express ELAFIN, which is a potent ELA2A inhibitor. 18 Co-immunolocalisation of ELA2A and ELAFIN shows that both proteins are secreted together in the colonic lumen. Consistently with our previous observation,  13  we showed in the present study that concomitantly with CELA2A upregulation, ELAFIN expression is abolished in epithelial cells. Therefore, the absence of endogenous inhibitor would allow ELA2A to participate to the elevated elastolytic activity released by IBD biopsies.
28 TLR5 stimulation could be involved in CELA2 upregulation observed in epithelial cells from IBD patients. However, Cela2 expression was unchanged after antibiotics treatment for 17 days in mice (analysis of GEO data base number GSE22648  29  ), suggesting that microbiota changes are not sufficient to modify Cela2a expression. We showed that ELA2A hyperactivity released at the apical side of epithelium triggers a decreased amount of membrane occludin and E-cadherin. This mechanism may lead to increased paracellular permeability to macromolecules and highlights the critical role of epithelium-derived proteases in the loss of barrier function. 30 The observed reduction of occludin and E-cadherin presence in ELA2A transgenic mouse colonic tissues was not the consequence of displacement of protein into the cytoplasm (see immunohistochemistry data, Fig.
Patients Human colonic tissues were obtained from individuals treated at the Centre Hospitalier de Toulouse (France). Biopsies were collected during colonoscopy procedures aimed at clinically evaluating the disease of established and well-characterized CD and UC patients or they were realized in individuals undergoing colon cancer screening who were otherwise healthy (here, healthy controls). The written and verbal informed consent was obtained before enrolment in the study, and the Ethics Committee approved the human research protocol (ClinicalTrials. gov identifier: NCT01990716 or DC-2015-2443). Fresh biopsies were proceeded as previously described  13  and used for in situ zymography (n = 15 for healthy controls, n = 7 for CD patients, and n = 11 for UC patients) and immunostaining (n = 7 for healthy controls, n = 9 for CD, and n = 8 for UC).
5 mM) by the EnzChek Elastase Assay Kit (Invitrogen) according to a previously published protocol. 18 As control of elastase activity, slices were pre-treated with 100 nM ELAFIN for 15 min. All sections were analyzed with Zen 2009 software (Carl Zeiss), by observers unaware of the origin and treatments. Fluorescent intensity in epithelium was quantified in at least five crypts per slide using Image J software. For each experiment, mean of fluorescent intensity from healthy controls was used as a reference to normalize data throughout the different acquisitions.
To validate the absence of non-specific binding of anti-ELA2 antibodies, two different sources of anti-ELA2 (from rabbit, from goat) were used and, isotype controls were used, incubated at the same concentration and under the same experimental conditions. Images representative of each group were selected. Epcam staining was used to estimate the epithelium surface on each cryosections of biopsy. For each patient, eight random images were obtained, intensity of ELA2A staining and epithelium surface were quantified using image J software. Cell culture Human colonic epithelial (Caco-2) cells (American Type Culture Collection, Manassas, VA) were grown in GlutaMAX DMEM (Invitrogen, Cergy-Pontoise, France) as previously described. 13 lls were grown on culture-treated plates (Becton Dickinson, Sparks, MD) under standard conditions and then transferred on transwell filter units with semipermeable filter membranes (0.
Signal density was calculated using Image Lab software (Bio-Rad). Actin was used as a loading control for total and soluble fraction and Vinculin as control for insoluble fraction. In vitro permeability measurements To assess epithelial permeability, FITC-dextran (4 kDa, 100 μM) was added to the apical compartment of the transwells for 4 h. Basolateral samplings were harvested at each sample timepoint. The apical-to-basolateral flux of FITC-dextran was measured on a fluorescence plate reader (NOVOstar, BMG Labtech) with an excitation wavelength of 496 nm, emission at 524 nm, and a cut off of 515 nm. Paracellular permeability to dextran-fluorescein isothiocyanate was expressed in relative permeability or µmole × cm 2 of dextran-fluorescein isothiocyanate. The synthetic molecules F16357,  44  GB88, and HC047067 corresponding to PAR1, PAR2, or TRPV4 antagonist, respectively, were pre-incubated for 45 min at 5 μM or 10 μM for HC047067.
Statistical analysis Statistical analysis was performed with GraphPad Prism version 5. 0. According to dataset structure, multiple comparisons were performed using either Student's t test, Bonferroni post-hoc test, or Mann-Whitney post-hoc test following ANOVA analysis, as indicated in figures legends. p values < 0. 05 were considered to be statistically significant (*p < 0. 05, **p < 0. 01, and ***p < 0. 001). Figures using human biological samples are represented with scatter plot with the median. Statistical analysis was processed only when number of patients was superior to five. Unless otherwise stated, all other graphics are expressed as mean ± SEM or scatter plot with mean. Independent biological replicates as well as the total n number values are indicated in figures legends.
ACKNOWLEDGEMENTS The authors would like to thank  ANEXPLO platforms  ( UMS 006 ) animal care facility and histopathology core facility ( F. Capilla ,  C. Salon , and  A. Alloy ),  S. Allart ,  A. Canivet , and  S. Lachambre  from the cellular imaging core facility for the development of image quantification ( U1043 ) and  F. L'Faqihi-Olive  for cell sorting ( U1043 ). The authors would like to thank  Sylvie Robine  and  Fatima El Marjou  from  UMR 144 CNRS-Institut Curie  who generously provided the transgenic pVillin::Cre-ER T2 mice. The authors would like to thank  Pr Morley Hollenberg  for helpful discussion and critical readings. The authors would like to thank  V. Payssan  for the management of human biopsies collected ( Pole Digestif ,  CHU Toulouse ). This work was supported by grants from the  French Ministry of Research and Technology , the  National Agency for Research  ( ANR JCJC-11JSV1 001 01  to C.
D. , and  ANR-12-BSV1-0030-01  to N. V. ), the  European IOF Marie Curie Action Project  ( FP7-627487 ) to C. D. , and  European Research Council  ( ERC-PIPE-310973 ) and by a grant from the delegation régionale à la recherche clinique des hôpitaux de Toulouse, through the  AOL-MICILIP  project, to N. V. Author E. F. V. holds a Canada Research Chair and is funded by a  CCFC  grant. This work was also supported by the " Programme des Investissements d'Avenir "  ANINFIMIP  ( ANR-11EQPX-0003 ). A patent was filed ( PCT/EP2017/064786 , application WO2017216352A1) using data from the present study.
Vaccination remains the best strategy to reduce invasive meningococcal disease. This study evaluated an investigational tetanus toxoid-conjugate quadrivalent meningococcal vaccine (MenACYW-TT) vs. a licensed tetanus toxoid-conjugate quadrivalent meningococcal vaccine (MCV4-TT) (NCT02955797). Healthy toddlers aged 12-23 months were included if they were either meningococcal vaccine-naïve or MenC conjugate (MCC) vaccine-primed (≥1 dose of MCC prior to 12 months of age). Vaccine-naïve participants were randomised 1:1 to either MenACYW-TT (n = 306) or MCV4-TT (n = 306). MCC-primed participants were randomised 2:1 to MenACYW-TT (n = 203) or MCV4-TT (n = 103). Antibody titres against each of the four meningococcal serogroups were measured by serum bactericidal antibody assay using the human complement.
Study design and participants This was a Phase III, modified double-blind, randomised, parallel-group, an active-controlled study conducted from 24 February 2017 to 26 October 2017 (study period) at 34 sites over four countries; Germany, Finland, Hungary and Spain (NCT02955797). Healthy toddlers aged 12-23 months were recruited if they were either meningococcal vaccine-naïve or if they had received at least one dose of MCC vaccine prior to 12 months of age (MCC-primed). Participating countries were selected according to their national immunisation programmes/ recommendations, in order to include both meningococcal vaccine-naïve and MCC-primed participants: in Germany, MCC vaccine is recommended from only 12 months of age and Finland does not include a meningococcal vaccine in their national immunisation programme; while in Hungary and Spain, MCC vaccines are recommended from infancy.
All immunogenicity analyses were performed on the perprotocol analysis set (PPAS), which comprised participants who met all eligibility criteria, received the study vaccine according to randomisation, had a valid post-vaccination serology result and had no protocol deviations that affected the participant's immune response. Safety assessments were carried out on the safety analysis set (SafAS), which included all participants who had received at least one dose of study vaccine and had safety data available. Categorical variables were summarised and presented as frequency counts with 95% confidence intervals (CIs) calculated using the normal approximation for quantitative data and the exact binomial distribution (Clopper-Pearson method) for percentages. For both co-primary objectives, the non-inferiority of the hSBA seroprotection for each of the serogroups, A, C, W and Y, was tested separately.