dataesr/scientific-paragraphs-categorization huggingface dataset:
30 h with 0. 1 μg of LL-37. The percentage of surviving bacteria was reported. Data are the means ± SEMs of four replicates and are representative of six independent experiments. B HT-29 cells were stimulated for 3 h with LPS (10 μg/ ml) purified from E. coli mcr-1 + or E. coli mcr-1 -. The amounts of secreted IL-8 in the cell culture supernatant were quantified by ELISA. Data are the means ± SEMs of six replicates and are representative of two independent experiments. C HT-29 cells were infected for 3 h with E. coli mcr-1 + or with E. coli mcr-1 -. Adherent bacteria were counted, and the data are expressed as the number of colony-forming units (CFUs)/well. Data are the means ± SEMs of six replicates and are representative of two independent experiments antimicrobial peptides, increased bacterial adhesion, and decreased the pro-inflammatory properties of LPS.
B, D HT-29 cells were infected at an MOI of 100 for 3 h with E. coli WT mcr-1 + or with E. coli Inactivated mcr-1 -. C HT-29 cells were stimulated for 3 h with LPS (10 μg/ml) purified from E. coli WT mcr-1 + or E. coli Inactivated mcr-1 -. B, C The amounts of secreted IL-8 in the cell culture supernatant were quantified by ELISA. Data are the means ± SEMs of six replicates and are representative of two independent experiments. D Adherent bacteria were counted, and the data are expressed as the number of colony-forming units (CFUs)/well. Data are the means ± SEMs of six replicates and are representative of two independent experiments extensively investigated, few studies have focused on the determinants that enhance E. coli commensalism. Our results revealed a new facet of gut colonization by E.
Acknowledgements We thank  Dr. Marjiana Basic  and  Prof Andre Bleich  ( Hannover Medical School, Institute for Laboratory Animal Science, Hannover, Germany ) for providing gnotobiotic mouse breeding pairs. We thank the platforms  CLIC (Clermont-Ferrand Imagerie Confocale, Université Clermont Auvergne ) and  Dr. Caroline Vachias  for assistance with confocal microscopy. In addition, we thank  Dr. Denis Duché  ( Laboratoire d'Ingénièrie des Systèmes Macromoléculaires, Institut de Biologie Structural et Microbiologie, CNRS ) for providing colicinproducing strains. We are also grateful to  Anne-Sophie Marinelli  and  Sandra Lebeau  for their technical assistance.
Overview Thirty-five articles were identified from the targeted literature review, including primary randomized controlled trial (RCT) data and review articles (eAppendix Statement 2 reached consensus in round 1 of voting (100% of panel agreed). The efficacy of inebilizumab for the treatment of AQP4-IgG-seropositive NMOSD was demonstrated in an adult study population in the N-MOmentum trial during a study period of up to 197 days. 35  In the AQP4-IgG seropositive subgroup, the rate of attack, defined by prespecified attack criteria and adjudicated by committee, was 11% in the inebilizumab group and 42% in the placebo group (HR 0. 227; 95% CI 0. 121-0. 423; p < 0. 0001). 35  Statement 3 reached consensus in round 1 of voting (94. 4% of panel agreed). Efficacy for satralizumab was demonstrated in adults and adolescents (≥12 years) in the SAkuraSky and SAkuraStar trials, during double-blind study periods of up to 224 weeks and 216 weeks, respectively.
Safety Five consensus statements are related to the safety of eculizumab, inebilizumab, and satralizumab (Table  5 ). Statement 17 reached consensus in round 1 of voting (100% of panel agreed). The Delphi panel members suggested that infections were the main safety concern to be monitored over time, particularly opportunistic infections, meningococcal meningitis, herpes zoster, and progressive multifocal leukoencephalopathy. The risk of these infections is emphasized in the EMA and US Food and Drug Administration (FDA) labels of eculizumab, inebilizumab and satralizumab. Moreover, monitoring individual patients reporting significant infections such as these to the manufacturer and other postmarketing databases (e. g. , US FDA) would also be helpful in enabling wider monitoring of potential safety issues associated with these therapies.
Acknowledgment Oxford PharmaGenesis (Oxford, UK ), an independent HealthScience communications consultancy, conducted the targeted literature review and provided support to draft the consensus statements. Lisa Law, MSc , and  Rebecca Hornby, PhD  of  Oxford PharmaGenesis, Oxford, UK , are included as authors on this article for their contribution in drafting and editing the article and drafting responses to the reviewer comments. They are not members of the Delphi panel and did not vote in the consensus process. The authors also thank  Jessica Townson  of  Oxford PharmaGenesis, Oxford, UK , for providing administrative and logistical support for the Delphi process. Funding for the Delphi process and medical writing support was provided by  F. Hoffmann-La Roche Ltd. The funding organization did not contribute to the design, facilitation, or content of the Delphi consensus process.
participation in advisory boards from Sanofi, Merck, Roche, and Horizon Therapeutics and travel support for scientific meetings from Novartis, Roche, and ECTRIMS; is the editor for Europe of the MS Journal-Experimental, Translational and Clinical, and is a member of the International Women in MS (iWiMS) Network executive committee and of the European Biomarkers in MS (BioMS-eu) Consortium steering committee; S. Huda reports no disclosures relevant to the manuscript; M. I. Leite is funded by the NHS (Myasthenia and Related Disorders Service and National Specialised Commissioning Group for Neuromyelitis Optica, UK) and by the University of Oxford, UK. She has been awarded research grants from the UK association for patients with myasthenia-Myaware and the University of Oxford. She has received speaker honoraria or travel grants from Biogen Idec, Novartis, UCB, and the Guthy-Jackson Charitable Foundation and serves on scientific or educational advisory boards for UCB Pharma, Argenx, and Viela/Horizon; J.
Acquisition on the flow cytometer Timing: 1 h 30 min for sorting and setting samples (17 samples) This part details the acquisition of cellular fractions on the Cytoflex flow cytometer (Beckman Coulter) using CytExpert software. 73. For compensation setting, prepare unstained and single-stained controls for every fluorochrome-dye used in your panel. Note: For anti-CD45, anti-CD31, anti-Podoplanin, anti-CD26 and anti-EpCAM antibodies we recommend to used total tumor cell suspension. Due to the low expression of CD140a, CD140b and FAPA markers by the cells, we recommended to used compensation beads for them. Concerning the mortality dye used a mix of stained and unstained tumor suspension (Table  6 ). 74. Once controls are ready, go to your flow cytometer and create a new experiment. 75. Use unstained and single-stained cells or beads to set appropriate PMT voltage or APD gain and prepare compensation matrix.
ACKNOWLEDGMENTS L. K. , S. P. , L. G, S. L. F. G. , and E. L are supported by the  Ligue Nationale contre le Cancer (Equipes labellisees) , the  Ligue Nationale contre le Cancer Grand-Est , the  Institut National du Cancer (INCa) , the  Association pour la Recherche sur le Cancer (ARC) , the  Fondation AMGEN , the  LabEx LipSTIC , the  Region Bourgogne-Franche-Comte(BFC) , and the  I-Site-BFC Program. This study was also supported by the  Georges-Francois Leclerc Cancer Center.
Flow cytometry The following Abs were used: CD19-FITC (1D3), CD5-FITC (53-7. 3), IgD-FITC  (11-26c. 2a ), B220/CD45R-FITC (RA3-SB2), CD19-PE (1D3), IgM-PE (R6-60. 2), CD184(CXCR4)-PE (2B11), CD138-PE (281-2), CD23-PE (B3B4), CD95(Fas)-PE-Cy7 (Jo2), CD19-PerCP-Cy5. 5 (1D3), Streptavidin-PerCP-Cy5. 5, CD25-APC (PC61), B220/CD45R-APC (RA3-6B2), CD21-APC (7G6), IgG1-APC (A85-1), CD86-APC (GL1), IgM-PE-Cy7 (R6-60. 2), c-Kit(CD117)-PE-Cy7 (2B8), B220/ CD45R-APC-Cy7 (RA3-6B2), IgD-V450 (11-26c. 2a), biotin-IgG3 (R40-82) (all BD), CD27-AF647 (LG3A10) (BioLegend), Lectin from Arachis hypogaea-FITC (Sigma). Data were acquired on a FACSCanto or FACSAria cytometer and analyzed using FACSDiva 6. 0 (BD) software. Cells were stained in PBS for 10 min at room temperature (RT) with Abs to the appropriate markers, preceded by the blockade of Fc receptors with CD16/ CD32 Fc block (2.
The CPS/EDTA or Heat/EDTA Ag retrieval methods were used, according to the manufacturer's instructions. Abs: polyclonal BCL6 (Santa Cruz). AICDA transcript (ID: 11628) was detected using RNAscope 2•5 HD Detection Reagent-BROWN (Advanced Cell Diagnostic) in accordance with the manufacturer's protocol. Quantitative analyses of Aicda mRNA in situ hybridization signals were performed by calculating the average percentage of positive signals in five nonoverlapping fields at high-power magnification (X400) using the Positive Pixel Count v9 ImageScope software, Leica Biosystems.
Immunofluorescence Spleens were fixed with 4% paraformaldehyde for 3 hours, washed with PBS and left overnight in 20% sucrose to dehydrate. Eight mm thick-sections were blocked with 5% BSA in PBS, stained with surface Abs, washed and blocked with 5% BSA plus 0. 3% Triton X-100 in PBS, stained with intracellular Abs in 0. 3% Triton X-100 in PBS and mounted with a Fluoromount Aqueous Mounting Medium (Sigma) without DAPI. Abs used: FITC anti-CD169 (MOMA1; AbD Serotec), PE anti-IgM (R6-60. 2, BD), V450 anti-IgD (R6-60. 2; BD). Images were acquired with Zeiss LSM 700 confocal microscope and analyzed with ZEN software. Pictures were acquired using 10x/0. 3 dry and 20x/0. 8 dry objectives at RT and merged in three-color images with ImageJ.
Reads mapping and identification of differentially expressed genes Sequencing adapters were trimmed using cutadapt software  (27)  and reads shorter than 16bp were removed. Reads were aligned on the reference mouse genome (GTCm38/mm10 version) downloaded from Ensembl (http://www. ensembl. org/) using a two-step procedure. At first, reads were aligned using the STAR program  (28). All reads that did not align were realigned with bowtie (29) using a local alignment strategy. Gene expression was quantified using the Ensembl gene annotation, version 75, with htseq-count program (http://www-huber. embl. de/users/anders/HTSeq/doc/count. html). The row count matrix was normalized to consider the GC content biases and the different coverage depth. Normalization was performed using the full quantile normalization implemented EDASeq R package  (30) ; the differentially expression analysis with the EdgeR package  (31).
qRT-PCR RNA was extracted with the RNeasy mini kit (Qiagen) and reverse transcribed using the Reverse Transcription System (Promega). qRT-PCR was performed on the ABI PRISM 7000 Sequence Detection System (Applied Biosystems) using the FastStart Universal SYBR GREEN master (ROX) (Roche) or with QuantStudio 5 (Thermofisher) using Luna Universal qPCR Master Mix (New England BiLabs). Data were analyzed with the ABI PRISM 7000 software (Applied Biosystems) and with online tools on the Applied Biosystems platform (Thermo Fisher cloud); mRNA levels were normalized on the expression of Gapdh/Actin. Results are presented as ratio between normalized expression of the gene of interest in the target and in the calibrator samples. The complete list of primers is reported in Supplemental Table  1.
Analysis of Ca 2+ mobilization Splenic B cells pretreated or not with CX-4945 (Sellekchem) 5mM for 3 hours, were loaded with Fluo4-AM (4mg/ml; Molecular Probes) and FuraRed (16mg/ml; Molecular Probes), sulfinpyrazone (250mM; Sigma) and Pluronic F-127 (0,1% w/v, Life Technologies) in RPMI for 30 min at 37°C in the dark. Cells were washed with RPMI and resuspended in warm PBS at the density of 10 6 cells/ml. After recording for 30 sec to establish the baseline, cells were stimulated with 20 mg/ml F(ab') 2 rabbit antimouse IgM (Jackson ImmunoResearch Laboratories, Inc. ) for 6. 5 min. Then, ionomycin (2 mg/ml) was added to allow the complete emptying of Ca ++ stores. Measurements were monitored using a FACSCanto cytometer and analyzed using FlowJo software (Tree Star).
IP 3 uncaging B cells were seeded on poly-L-lysine (100 mg/ml, Sigma) coated coverslips (10 5 cells) and loaded with caged-IP 3 (1 mM; Enzo Life Science), Fluo-4-AM (0,5 mM; Molecular Probes), Pluronic F-127 (0,1% w/v; Life Technologies), sulfinpyrazone (250 mM; Sigma) in RPMI without FCS for 30 min at 37°C. Live calcium imaging was performed in HBSS using a Zeiss LSM700 laser scanning confocal microscope. Time-lapse images were acquired for 1 min (0,6 frame/sec), using a 40x water immersion objective (Zeiss W Plan-Apochromat 40x/1. 0 DIC M27). Fluo-4-AM was excited with a 488-nm laser (0,5% power). Regions of interest (ROIs) were drawn on four distinct cells per field; the UV laser (405 nm, 100% power, 10 ms pulse) was used to release active IP 3 within the ROIs. Images were analyzed using ImageJ software.
RNA sequencing analysis highlights a critical role for CK2b in peripheral B cell activation and the germinal center reaction To gain insights into the mechanisms underlying the Fo and MZ B cell unbalanced proportions in CK2b KO animals, we CK2b KO in B cells affects B cell number and Igs production. (A) CD19 + sorted marrow and splenic B cells analyzed for the expression of Csnk2b by qRT-PCR. The expression was corrected for Actin levels and normalized to CTRL B cells. Data are shown as mean ± SD (n=4 BM, n=5 spleen). Statistical significance was determined by Student's t test (**p < 0. 01; ***p < 0. 001). (B) CK2a and b levels in CK2b CTRL and CK2b kO marrow and splenic purified B cells were assessed by WB. GAPDH was used as loading control (whole cell lysates; one representative of 3 independent experiments).
Band quantitation was calculated using Quantity One 4. 6. 6 software; obtained values are reported on top of each band. (C) CK2 kinase activity in purified splenic B cells from CK2b CTRL and CK2b kO mice. Data are shown as mean ± SD (n=3 mice per genotype, 2 independent experiments). Statistical significance was determined by Student's t test (*p < 0. 05). In (A-C) the purity of sorted B cells was ≥94%. (D) p65/RELA and AKT phosphorylation in purified splenic B cells obtained by magnetic separation from CK2b CTRL and CK2b kO mice was assessed by WB. GAPDH was used as a loading control (whole cell lysates, one representative of 3 independent experiments). Band quantitation was calculated using Quantity One 4. performed RNA sequencing (RNAseq) on total splenic B cells purified from mice in basal condition.
We did not detect any increase in the mRNA levels of Notch1 nor in the amount of the active form of NOTCH1 protein amidst the genotypes (data not shown). To demonstrate that the observed skewing towards MZ B cell differentiation in CK2b KO mice is NOTCH2 dependent, we performed in vivo treatment with the NOTCH2 blocking antibody anti-negative regulatory region 2 (a-NRR2), which stabilizes NOTCH2 in its quiescent conformation  (44). The efficacy of NOTCH2 inhibition was confirmed by qRT-PCR, which evidenced a reduction in the expression of Hes1 and Dtx1 in a-NRR2 treated samples (data not shown). FACS analysis proved that the blockade of the NOTCH2 pathway caused a reduction in CK2b KO MZ B cells whereas treatment with non-specific IgG had no effect (Figure  4E ). Moreover, thinning of the MZ was detected by IF analysis of CK2b KO spleen sections stained for CD169, IgD and IgM after a-NRR2 or IgG treatment (Figure  4F ).
(A) CK2b expression and localization in the GCs of CK2b CTRL spleens after immunization with SRBC. Top, IF images of spleen sections showing PNA (green) and CK2b (red). Images were acquired with Zeiss LSM 700 confocal microscope and analyzed with ZEN software. Pictures were acquired using objectives 20X, zoom1, and merged in two-color images with ImageJ software. Bottom, IHC of CK2b (Abcam) counterstained with hematoxylin; the magnification highlights the GC region. (B) GCs by Flow Cytometry in CK2b CTRL and CK2b kO mice after immunization with SRBC or (C) with NP. In (B, C) at the bottom, representative scatter plots of the percentage of splenic GC B cells (B220 + CD95 hi PNA hi ) with each symbol representing a mouse. Data are shown as mean ± SD. Statistical significance was determined by Student's t test (***p < 0.
001). Top, a representative dot plot per genotype is depicted, numbers near gates indicate the percentage of B220 + CD95 hi PNA hi cells. (D) GCs in spleen sections from mice of the corresponding genotypes identified through BCL6 staining and counterstained with hematoxylin. Image acquisition was performed using the Leica DMD108 Digital Microimaging Device and Software (Leica Microsystems, Germany). One representative mouse out of 3 per group is shown. Upper panels: bar, 500mm, lower panels: bar, 200mm (3 independent experiments). (E) Histograms summarizing the number of GCs per unit area (n=4 mice per genotype) and the area of selected GCs (n=3 mice per genotype, 7 GCs per mouse) of spleen sections stained with H&E from CK2b CTRL and CK2b kO mice. Data are shown as mean ± SD. Statistical significance was determined by Student's t test (*p < 0.
Bar, 500mm upper panels; 100mm lower panels. Image acquisition was performed using the Leica DMD108 Digital Microimaging Device and Software (Leica Microsystems, Germany). Data show results from one representative mouse out of 3. Arrows indicate the MZ. (G) Ratio between MZ and lymphoid follicle areas in the spleen of CK2b CTRL and CK2b kO mice was calculated using the Leica DMD108 Digital Microimaging Device and Software (2 mice per genotype; 2 independent experiments; +/+= 32 follicles; fl/fl= 54 follicles). Data are shown as mean ± SD. Statistical significance was determined by Student's t test (*p < 0. 05). (H) CD169 (green), IgD (blue) and IgM (red) expression in spleen sections from CK2b CTRL and CK2b kO mice was analyzed by IF. One representative mouse out of 3 per genotype is shown; 3 independent experiments.
Acknowledgments The authors thank  S. Indraccolo  ( Istituto Oncologico Veneto, Padova, Italy ) for helpful discussion and critical reading of the manuscript;  A. Cabrelle  ( Venetian Institute of Molecular Medicine, Padova, Italy ) for FACS sorting;  M. Albiero  ( Venetian Institute of Molecular Medicine, Padova, Italy ) for murine retro-orbital blood uptake;  V. Guzzardo  ( Department of Medicine, Cytopathology and Surgical Pathology Unit, University of Padova, Padova, Italy ) for tissue inclusions and sections. The authors thank the reviewers for their valuable comments and suggestions to improve the original manuscript.
3  The latter was especially reported in the mouse. 4  All those data suggest that PMN link innate and adaptive immunities. In addition to non-classical functions, neutrophil heterogeneity has become apparent with the description of PMN sub-populations in blood and tissues. 5  Heterogeneity of human blood PMN was very recently confirmed by single-cell RNA-sequencing analysis. 6  Particularly interesting in the context of RA and SLE, pro-angiogenic PMN (recruited by vascular endothelial growth factor (VEGF)-A) have been reported in hypoxic tissues  7  whereas low-density granulocytes (LDG) are enriched in the circulation of patients with diverse inflammatory diseases (detailed below). Interestingly, particular functions or subsets have been identified in inflammatory autoimmune diseases. Thus, RA PMN differentiate into DC-like cells  8  and express RANKL  9  which plays a key role in osteoclastogenesis.
The research article by Li et al. investigated trends in clinical monitoring indices in HIV/AIDS patients after 9. 9 years of ART in Yunnan Province, China. Three machine learning models (support vector machine [SVM], random forest [RF], and multi-layer perceptron [MLP]) were constructed. They used clinical indicators such as routine blood examination, lymphocyte subset counts, and viral load as parameters to predict immune restoration. Baseline and follow-up results of routine blood and organ function tests were used to analyze and predict CD4 + T-cell data after treatment during long-term follow-up. The authors found that the predictive capability of the three models was better for patients with a CD4 T-cell count ≥ 200 cells/ml than for those with < 200 cells/ml. For both groups, the three models yielded the best predictive performance for the CD4/CD8 ratio, for which the results were highly consistent.
RABV Sequence and Metadata Acquisition and Composition All 25,787 available sequences for all ve genes of the RABV genome were downloaded from the NCBI Virus database  5. After quality control, the RABV data set was reduced to 14,752 sequences that spanned 121 countries and were extracted from 192 different host species from 1972 to 2020. The multiple sequence alignment (MSA) comprised a concatenation of the ve genes of the RABV genome (Fig. 1a , Supp. Table  2 ). The maximum likelihood (ML) tree from this MSA (Supp. Figure  2 ) revealed three major phylogenetic groups with bootstrap values greater than 0. 95 corresponding to bat-, skunk-/raccoon-, and canine-related RABV, consistent with previous global RABV analyses  26, 29. The tree topology is spatially structured with clades, while gene fragments had a very low impact on sequence clustering (Supp.
1b  and 1d ). Since the 1970s nearly all continents have experienced an exponential increase in RABV sequence submissions to the NCBI Virus database. This increase is most notable for the N gene and the G gene, while WGS have experienced a slower rate in submissions, especially for Europe and Asia (Fig. 1d ). WGS still only represents 13% of sequences and 62% of countries. This demonstrates the quantity of partial sequence diversity available and the potential loss of phylogenetic signal and resolution that occurs when only using WGS for phylogenetic studies. In addition, studies favor certain genes depending on which country/continent the study is located in. For example, proportionally, Europe sequences mostly the N gene, while Asia sequences many samples for the G, M, and P gene. As a result, only using the N gene or WGS introduces systematic sampling bias into any phylogeographic analysis by ignoring sequences that exist for other regions of the genome.
Years of Canine-Maintained RABV Spread To investigate the geographic transmission of canine RABV, we inferred the ancestral locations at the country level on the full and subsampled trees with PastML (https://github. com/amholtz/GlobalRabies/tree/main/data/ACR_Results). We created a consensus tree with 6,096 sequences by taking the union of all sequences in subsampled trees and reducing the full canine-tree through pruning. The clade ancestral estimates that were consistent between the aggregated subsamples and the full tree are shown in Fig. 3. For the rst time, we estimated the country origin of 34 out of the 44 identi ed canine-mediated clades in the consensus tree, with ancestral estimates as well for their internal nodes, revealing historical transmission between and across the clades (Supp.
We can see repetitive transmissions between Namibia, South Africa, and Zambia, representing Southern and Eastern Africa, supporting previous studies 56. From the same intermediary region in 1805 (1898-1911), canine rabies further spread to Western Asia in 1809 (1794-1823), and eventually to Europe leading to the emergence of European fox rabies in 1873 (1863-1881, green node "1873 Eastern europe" in Fig. 4 ). This is a major node of interest since it is a re ection point that led to non-imported European cases of Rabies. The CA1 subclade which contains sequences from Russia, Ukraine, Latvia, Tajikistan and even shows transmission to parts of China and Mongolia  57, 58  is estimated to have emerged in 1924 (1913-1935) via Russia (Fig. 3 ). 3 ). Additional patterns of rabies emergence can be seen on the PastML compressed visualization (https://github.