dataesr/scientific-paragraphs-categorization huggingface dataset:
Nursing homes are also free to promote the appropriate use of medication through various local programs led by pharmacists or physicians, who often participate in continuing medical education. The aim of our study was to observe specific trends in drug prescriptions in nursing homes, and to assess the impact of the implementation of a designated educational booklet on the prescription of medications. Our study included a high number of facilities and measured drug prescriptions with an automated data collection process. Our observation of a general decrease in drug consumption over the study period is in agreement with the data in the literature  [40, 41] , although our analysis precludes any conclusion that the booklet was the driving force behind this reduction. There is a growing body of evidence in the literature in favor of the efficacy of educational approaches in reducing polypharmacy  [42].
A study by  Blochet et al. [34]  using a similar electronic pill dispensing system observed an overall decrease in the number of tablets taken per resident per day from 2011 to 2013 in a sample of 338 nursing homes in France. A recent study of prescriptions in 1890 residents in nursing homes in France using national health insurance data reported that 42. 9% had polypharmacy (defined as 5 to 9 drugs per day) and 46. 7% of the study sample received at least one potentially inappropriate medication  [43]. In a study using the same pill-dispenser database as in our analysis, these same authors also reported a significantly lower risk of excessive polypharmacy in private for-profit nursing homes, with an OR (reference group: public nursing homes) of 0. 81 (95% CI, 0. 68 to 0. 98, p = 0. 026)  [9].
(30). Pre-PCR products were diluted 4,000× for CD4, 400× for sj, and 100× for Dβ quantification both for thymus and spleen samples, and relative CD4 and TREC number of copies were determined by qPCR by adding 4 µl of diluted pre-PCR products to 7 µl of Takyon TM No Rox SYBR MasterMix Blue dTTP (Eurogentec), 0. 2 µl of CD4 and TREC inner (In) primers (purchased from Eurogentec; Table  1 ) each at 100 mM, and completed with nuclease-free water to reach a total volume of 14 µl. The amplification program was composed of 5 min at 95 • C for initial denaturation; 40 cycles of amplification each consisting of 10 s at 95 • C, 15 s at 60 • C and 10 s at 72 • C, and cooling at 4 • C. All reactions were run on a LightCycler 480 thermocycler (Roche Diagnostics) and analyzed using the LightCycler 480 Software by the second derivative max method.
Data were log-transformed before analysis. loads were recorded in samples at days 1 and 5 from offspring born to dams inoculated at day 10G, ranging between 4 × 10 4 and 9 × 10 4 copies per 100 ng of total RNA (Figure  5A ). Thymuses sampled from fetuses presented a lower level of CV-B4 RNA, ranging from 2,073 to 8,215 copies, comparable to those from offspring born to dams inoculated at day 17G and sampled at day 1 or 5. Similarly to the thymus, ∼78% of spleens sampled from offspring born to dams inoculated at day 10G were positive against only 33% when inoculation was performed at day 17G. The viral load in the spleen was lower and almost the same following CV-B4 inoculation either at day 10G or 17G, ranging from 1,440 to 8,440 copies, with only a slight increase at day 5 when it reached 14,707 copies per 100 ng of total RNA (Figure  5B ).
Let us remember that Ptk7 gene expression declines progressively with maturation until its repression in SP T cells in the thymus and shortly after exportation in RTE SP4 T cells  (8) (9) (10). Phenotypic characterization of T lymphocytes in the periphery, precisely in the spleen, was assessed by flow cytometry by using previously established phenotypic characteristics of naive and memory T cells, identified as CD62L + CD44 -or CD62L -CD44 + , respectively, for both SP4 and SP8. However, as shown by TREC quantification, the number of T cells in the periphery was very low, which prevented us from phenotyping and quantifying both different cell categories (data not shown). In utero infection of the spleen by CV-B4 was explored for the first time. The less important effect recorded within the spleen may be explained by lower viral loads.
MCMV Affects Survival of Both Mouse and Human Cancer Cells We next assessed cell survival of MCMV-infected cancer cells. As measured by dye compound 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromidefo (MTT) assay, all cells tested were sensitive to MCMV-mediated growth inhibition (Figure  4A ). The viral dose inhibiting 50% of growth (IC 50 ) 3 days post-infection related to 1 < MOI < 10 for B16F10 and 3T3, 10 < MOI < 100 for HT29, and MOI > 100 for MC38 (Figure  4A ). The concomitant assessment of apoptosis by flow cytometry revealed that at MOI = 1, 30% of 3T3, 20% of B16F10, 5% of MC38, and 8% of HT29 cells were annexin V+ after 3 days of infection. MOI = 100 was 100% lethal for B16F10 and 3T3 cells, while 20% of MC38 and 30% of HT29 were annexin V+ (Figure  4B ). These data confirm that B16F10 cells are more sensitive to MCMV infection than MC38 cells.
After centrifugation for 5 min at 400 g, cells were washed once using PBS, 1% BSA. Cells were then stained with 0. 5 mg/mL 4 0 ,6-diamidino-2-phenylindole (DAPI) (Sigma Aldrich, St. Louis, MO, USA) for 30 min. Acquisition was made using BD LSRFortessa and analysis with BD-DIVA software.
Annexin V Detection Murine NIH 3T3, MC38, B16F10, and the human HT29 and SW480 colon cancer cells were seeded at a density of 3,000 cells per well in a 96-well plate in 100 mL of complete medium. After 24 h of adhesion, the cells were infected at different MOI and incubated for 72 h at 37 C, 5% CO 2. After PBS washing, cell apoptosis was determined with the BD PharMingen FITC Annexin V Apoptosis Detection Kit I (BD, Allschwil, Switzerland). Staining of annexin V was carried out according to the manufacturer's instructions. Acquisition was made on BD LSRFortessa and analysis was done with the FlowJo (Tree Star) software.
Wound Healing Assay For wound-healing assays, HT29 (1 Â 106) were cultured in 6-well plates for 24 h to obtain a confluent monolayer. Vertical artificial scratches were made in the wells by scraping the cell monolayer along the diameter of each well using a 10 mL pipette tip. Cells that separated from the monolayer were removed. Then, medium with or without MCMV at MOI = 20 was added. After 48 h in culture, the microscopic images of the scratched area before and after treatment were obtained. The percentage of wound healing was analyzed using ImageJ software.
ACKNOWLEDGMENTS This work was supported in part by grants from the  Centre National de la Recherche Scientifique (CNRS, France) ; the  Fondation pour la Recherche Médicale  ( DEQ20110421287 ) and the Victor and Ermina Mescle price 2017; the  Agence National de la Recherche  ( ANR-12-BSV3-0024-02 ); and the  Ligue Contre le Cancer  ( 15454 ) and SIRIC BRIO. C. K. 's doctoral funding was from the  Conseil Régional d'Aquitaine  and the  Fondation pour la Recherche Médicale  ( FDT20140931227 ). L. M. 's doctoral funding was from the  Centre National de la Recherche Scientifique (CNRS, France). We thank  Anaëlle Stum  for technical assistance at the flow cytometry facility.
Statistical analysis. Marker levels measured out of range of the calibration curve (sCD23 = 6. 3%, sCD30 = 0. 8%, sCD27 = 0. 5%, CXCL13 = 19. 1%) and missing values of smoking status (2%), education (7%), alcohol intake (0. 4%), physical activity (2. 7%) covariates (Supplementary Table  10 ) were imputed based on a maximum likelihood estimation method which was informed by the observed correlation structure within the data  45. Blood levels of soluble markers were log transformed to normalize their distributions. Differences between cases and controls in baseline continuous covariates were assessed using the paired t test, and by χ 2test, for categorical variables. Spearman rank correlation was used to measure the degree of correlation between markers. Odds ratios (OR) and 95% confidence intervals (95% CI) for the subtypes of BCL in relation to immune markers (as continuous variables) were calculated by conditional logistic regression (CLR).
Acknowledgements The authors thank  Dr. Marco W. J. Schreurs  and the laboratory technicians  Cindy Kneppers ,  Pamela Vasic , and Anneloes van Krimpen who performed the immune marker assays ( Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands ), Moreover, the authors thank the  National Institute for Public Health  and the  Environment (RIVM) ,  Bilthoven , the  Netherlands , for their contribution and ongoing support to the  EPIC Study. European Commission (DG-SANCO) ,  International Agency for Research on Cancer ,  Danish Cancer Society (Denmark) ,  Ligue Contre le Cancer ,  Institut Gustave Roussy, Mutuelle Generale de l'Education Nationale ,  Institut National de la Sante et de la Recherche Medicale (INSERM) (France) ,  German.
1 , right panel), showing no leakage of the UAS construct. Microscopy analyses confirmed the RT-PCR results. While we observed endogenous Cherry fluorescence in hemocytes collected from hml > mCD8::Cherry females 24h PBM (Fig. 2 ), no Cherry fluorescence was detected in hemocytes perfused from the control progeny of the crosses between the hml-Gal4 line or the UAS-mCD8::Cherry line to the E docking line 24h PBM (data not shown). Perfused granulocytes can rapidly bind to the glass surface, start to enlarge and develop filopodia. Therefore, perfused hemocytes from BF females were fixed either 10 or 45 min after perfusion to analyze Cherry fluorescence at different hemocyte activation stages, e. g. small and round granulocytes as well as large granulocytes. The hemolymph fixed 10 min after perfusion contained a large proportion of small hemocytes (cell diameter of 5-6 μm) with a high nuclear to cytoplasm ratio and starting to produce filopodia (Fig.
Acknowledgments We thank  Frank Schnorrer  for supply of pUAS-mCD8::Cherry plasmid,  Amy Lind  and  Gareth Lycett  for pSL[UAS-eYFPnls-g] and pSL [UAS-eYFPnls-g] and useful discussions,  Ernst Wimmer  for pBac[3xP3] and pslfa1180,  Michele Calos  pour pattB,  Francois-Xavier Camval  for pFPV 25. 1 and  Anthony James  for phiC31 integrase optimized mutant plasmid template. We are also grateful to  Jacques Montagne  for confocal access.
Funding Support to E. P. was from an  ANR-07-MIME-O25-01  award from the  French Agence Nationale de la Recherche  to C. B. , from  Fondation Roux  ( Institut Pasteur) fellowship  and by the  UK Medical Research Council  to E. P. ( MC_UU_12014/8 ), to C. B. from  ANR-07-MIME-O25-01  award from the  French Agence Nationale de la Recherche  to C. B. and  ANR-10-LABX-62-IBEID. R. M. W. was supported by  Swiss National Science Foundation  grant  PP00P3_170664.
Expression of IFNγR1 and Phosphorylation of STAT1 on Monocytes by Flow Cytometry Assay IFNγR1 cell-surface expression was assessed on monocytes (CD14+ cells) by using a standard flow cytometry protocol that requested a staining of 100 µl of fresh whole blood with PEconjugated anti-human IFNγR1 mAb (BD Biosciencies). Blood samples were acquired using a FACSCalibur flow cytometer (Becton Dickinson, San Diego, Calif) and analyzed by the FlowJo software version 7. 5 Software (TreeStar, Ashland, Ore). Cells were fixed and permeabilized, following the manufacturer's instructions (BD Biosciences). Similarly, analysis of STAT1 phosphorylation was performed on 100 µl of fresh whole blood that was left unstimulated or stimulated with IFN-γ (1,000 U/ml for 30 min). Blood cells were fixed and permeabilized, following the manufacturer's instructions (Becton Dickinson) and intracellular staining was performed using a PE-conjugated anti-human pSTAT1-Tyr-701 mAb (BD Pharmigen).
Immunophenotype Analysis by Flow Cytometry Whole blood (100 or 200 ml) was stained for immunophenotypic analysis using a combination of monoclonal antibodies (mAb) (Becton Dickinson, San Diego, Calif), according to standard multiparametric flow cytometry protocols, in order to identify different lymphocytes and DCs subsets. Blood samples were acquired using a FACSCantoII flow cytometer (Becton Dickinson) and analyses were performed with the FlowJo software version 8. 8. 7 (TreeStar, Ashland, Ore). Immunological data were compared to the reference values of the "A. Nocivelli" Institute for Molecular Medicine of Brescia that performed the analysis, based on a database obtained from a pool of age-matched healthy subjects. The values out of range are marked in bold numbers.
Statistical Analysis Statistical significance of immunological studies was analyzed by non-parametric two-side Mann-Whitney U-test with 95% confidence bounds. For all analyses p < 0. 05 was considered statistically significant. Statistical analyses were performed using GraphPad Prism Version 5. 0 (GraphPad Software, San Diego, CA). Pakistani non-consanguineous parents; her past medical history was uneventful, and the family history was unremarkable. She had not received BCG vaccine, nor had never been to Pakistan. At admission, her blood tests revealed microcytic anemia (Hb 6. 5 g/dl, MCV 60. 9 fl, RDW 19. 4%), raised C-reactive protein (CRP 125 mg/L, range <5 mg/L) and procalcitonin (9. 2 ng/ml, range <0. 1 ). IFNGR1 gene sequencing revealed a heterozygous small deletion in the exon 6, the c.
Clones from the positive pools were screened individually against the hybridoma bait. The inserts of positive clones were   GFP reporter by representative hybridoma activated by titrated aCD3 mAb. Nur77 GFP (C) and IL-2 (D) expression by hybridoma from CD4 + TCR + Foxp3 + T regs. GFP and IL-2 expression were measured by FACS/RT-qPCR or by HT-2 assay/RT-qPCR, respectively, from five randomly selected hybridomas. (E) Nur77 GFP expression in hybridomas declines gradually following antigen withdrawal. Hybridomas were stimulated with plate-bound aCD3 for 16 hours and then moved to uncoated wells. GFP expression was measured by FACS (left) or RT-qPCR (right) at indicated time points. Means ± SD are shown, and each symbol represents an individual hybridoma. RT-qPCR data were normalized to -actin.
Paired t test; *P < 0. 05, **P < 0. 01, ***P < 0. 001. For statistical analysis, data points in (C) were compared to unstimulated (aCD3 = 0 ng/ml) samples, and for (D), to samples of t = 0 hours. sequenced, and their sequences were blasted against the specific bacteria genome, then aligned to annotated open reading frames, and the peptide-binding motifs to A b were predicted using public data tools [NetMHCII, IEDEB (Immune Epitope Database), and Rankpep]. Only DNA fragments encoding membrane or extracellular but not secretory proteins were considered for further screening. The minimal fragments anticipated to confer antigenicity were further verified by stimulating hybridomas with synthetic peptides (GenScript and ABI Scientific). Overall, using this approach, we identified six recombinant peptides derived from three ASF bacterial components that stimulated a total of 21 hybridomas representing colonic CD4 + Foxp3 + cells and another 35 hybridomas established from CD4 + Foxp3 -cells (Fig.
These epitopes were synthesized and used to rescreen hybridomas previously identified as A. muciniphila specific, and to immunize TCR mini Foxp3 GFP mice. Overall, four A. muciniphila-derived epitopes that activated at least one of eight hybridomas were found (Fig. 4A ). The A. muciniphilaspecific hybridomas expressed six different TCRs, which, in our database of TCRs sequenced from TCR mini mice, were found on CD4 + Foxp3 -, CD4 + Foxp3 + cells, and tT regs from TCR mini CNS1 k/o mice (Fig. 4A ). This result suggested that in the TCR mini model, these epitopes may support both pT regs formation and tT regs expansion. Consequently, we choose the synthetic peptide 2C. 1 that was capable of activating three different hybridomas ex vivo (Fig. 4 , A to C) for immunization of SPF TCR mini Foxp3 GFP mice.
A recent study that used live or pasteurized A. muciniphila to treat patients with obesity, untreated type 2 diabetes mellitus, or inflammatory bowel disease (IBD) concluded that daily administration of dead bacteria provides health benefits including improved insulin sensitivity, reduced levels of insulin, and enhanced gut barrier as compared with controls receiving a placebo  (39). Although the involvement of intestinal T regs in the therapeutic effect of A. muciniphila in humans still has to be determined, the fact that live or dead bacteria had similar therapeutic effects suggests that recognition of specific epitopes may regulate mucosal adaptive immune cells. Because A. muciniphila can degrade the mucus layer, which negatively affects gut wall integrity, the use of pasteurized bacteria is clinically more compelling than its use as live probiotic  (40) , as also illustrated by ongoing clinical trial NCT01314690 that uses pasteurized A.
Fecal DNA was isolated from 100. 0 mg of freshly obtained mouse feces with QIAamp PowerFecal DNA Kit (Qiagen) according to the manual. One microliter of each DNA was run in triplicate on QuantStudio 3 real-time polymerase chain reaction (RT-PCR) instrument using SsoAdvanced Universal IT SYBR Green kit (Bio-Rad). The melting curve was run for each reaction. The comparative CT (CT) method was used for analysis with data normalized to UniF340/UniR514 universal bacteria primers and then to appropriate control as indicated. For green fluorescent protein (GFP) and IL-2 expression studies, hybridomas were treated as indicated and total DNA-free RNA was isolated with RNeasy kit (Qiagen). One microgram of each RNA was reverse transcribed using SuperScript III kit (Invitrogen) using random hexamers.
Fecal bacteria 16S rDNA sequencing Sequencing was done at the Genomics Facility at Cornel University, and data analysis was done as reported  (47). Briefly, sequences were demultiplexed, quality filtered using QIIME2 software package 39, and forward and reverse Illumina reads were joined using the fastqjoin method. QIIME default parameters for quality filtering were used before assigning sequences to operational taxonomic units (OTUs) using UCLUST algorithm with a 97% threshold of pairwise identity and classified taxonomically using the Greengenes reference database. A single representative sequence for each OTU was aligned, and a phylogenetic tree was built using FastTree and used for computing the unweighted UniFrac distances between samples. Data were analyzed with QIIME [reads were classified to taxonomic groups (class), and relative abundance was calculated].
Fluorescence-activated cell sorting (FACS) data were analyzed with FlowJo v. 10 (FlowJo, LLC). IL-6 expression was assessed in culture supernatant by a commercial kit (eBioscience) per included instructions. Cells were seeded at 1 × 10 6 on aCD3 (1 g/ml)and aCD28 (0. 1 g/ml)-coated wells and restimulated overnight.
Acknowledgments: We thank  J. Pihkala  ( Augusta University ) for help with cell sorting and  H. Ignatowicz  ( GSU ) with maintenance of mouse colony. We thank  T. Schoeb  ( UAB ) for rederivation of our mice to GF status and  C. Jin  ( GSU ) for rederivation of our mice to ultraclean status. We also thank  T. Denning  for critically reading the manuscript. Funding: This work was supported by  NIH   R01DK099264  and  1R01AI121151  research grants and  GSU  funding to L. I. The work was supported by the  German Research Foundation (DFG)   Priority Programme   SPP1656  ( DFG STE1971/4-2 ), the  German Center for Infection Research (DZIF) , and the  Center for Gastrointestinal Microbiome Research (CEGIMIR)  to B. S. J. G. F. is supported by  NIH  grants  P30ES002109 ,  P01CA028842 , and  R35 CA210088.
falciparum-or P. vivax-IRBC, IGFBP7 did not induce rosetting. Heparinases also affected the size of rosettes (numbers of URBC in a rosette) (Figure  6C , green arrows). Notably, addition of IGFBP7 induced autoagglutination-like clustering of IRBC (which were not enzyme- Source data 1. Raw data (rosetting rates, %) for the data set presented in the bar graph (Figure  1D ). treated) (Figure  6C , red arrow). IRBC-autoagglutination was absent in the control groups (untreated and enzyme-treated groups without addition of IGFBP7) (data not shown). Complement receptor 1 (CR1) expressed on URBC is a receptor for PfEMP1 in P. falciparum rosetting  (Rowe et al. , 1997). However, it did not play a significant role in IGFBP7-mediated rosetting for both parasite species. Anti-CR1 mAb reduced P. falciparum rosetting rates in the absence of  IGFBP7, confirming that this molecule is involved in the direct interaction between IRBC and URBC (Figure  6D ).
The online version of this article includes the following source data and figure supplement(s) for figure  8 : Source data 1. Raw data (rosetting rates, %) for the data set presented in bar graph (8F). Source data 2. Raw data (phagocytosis rates, %) for the data set presented in bar graph (8G). of uncomplicated and severe malaria patients from the same area to understand better the role of IGFBP7 in malaria pathogenesis. The importance of monocytes/macrophages in eliminating Plasmodium during its course of infection has been reported  (Groux and Gysin, 1990; Theander, 1992). Peripheral monocytes  (Turrini et al. , 1992; Muniz-Junqueira and Tosta, 2009) , as well as the tissue-resident macrophages  (Tosta et al. , 1983; Sponaas et al. , 2009) , have been shown to engulf IRBC readily. To survive, parasites must counter or avoid this host's immune responses.
5/Solvent B: 10 mM ammonium formate pH10. 5/90% acetonitrile) was performed on an A ¨KTA Micro system using Gemini 5 u/C-18/110A, 150 mm Â 1 mm column. Collected fractions were combined into 14 fractions, evaporated and used for mass spectrometry analysis. Mass spectrometry analysis was performed on an Orbitrap Fusion mass spectrometer coupled to nano-ultra-high-performance liquid chromatography (UHPLC) Easy nano liquid chromatography (nLC 1000 system). Fractions were injected and separated on in-house prepared (C-18 ReproSil Pur Basic beads 2. 5 um) fused silica emitter column 20 cm Â 75 mm in 75 min gradient (solvent A: 0. 1% formic acid; solvent B: 0. 1% formic acid/99. 9% acetonitrile) in data dependent mode using Orbitrap (OT) and Ion trap (IT) detectors simultaneously (speed mode À3 s cycle) with ion targets and resolution (OT-MS 2xE5, resolution 60K, OT-MS/MS 3.
5E4, resolution 15 k; IT-MS/MS 2E4, Normal scan). Peak lists were generated with Proteome Discoverer 1. 4 software and searches were done with Mascot 2. 5 against forward and decoy Human-HHV4 Uniprot database (88,559 entries) with the following parameters: precursor mass tolerance [mass spectrum (MS)] 30 ppm, OT-MS/MS 0. 06 Da, IT-MS/MS 0. 6 Da; two miss cleavages; static modifications: carbamidomethyl (C), variable modifications: oxidation (M), deamidated (NQ), acetyl N-terminal protein. Forward/decoy searches were used for false discovery rate (FDR) estimation (FDR 1%). Peak lists were generated. Following data review, coupled with critical information (i. e. the protein's subcellular location and cellular functions) from UNIPROT (UniProt Consortium, 2015), candidates were shortlisted for further validation.
Statistical analyses GraphPad Prism 7. 0 was used for data analysis. For normally distributed data (Shapiro-Wilk normality tested), a paired t-test was conducted for pairwise comparison. Matched measurement comparison for non-normally distributed datasets was done using Friedman test with Dunn's multiple comparison test. To compare two sets of non-normally distributed data, a Mann-Whitney test was used. One-way ANOVA tests were conducted for grouped data set comparison. For a normally distributed dataset, Tukey's test was applied for multiple group comparisons. Dunnett's test was used to compare groups against a control. Two-way ANOVA was used to study the effect of multiple experiment conditions on rosetting in different parasite lines, each with different culture batches. Any p values < 0.