dataesr/scientific-paragraphs-categorization huggingface dataset:
We investigated the effect of ABX464 on the HIV transcription profile and total and intact HIV DNA in CD4+ T cells from ART-suppressed participants enrolled in the ABIVAX-005 clinical trial (NCT02990325). Methods: Eleven participants on suppressive ART were treated daily with 150mg of ABX464 for 4 weeks. Peripheral CD4+ T cells from nine study participants were available for HIV transcription profile and reservoir size analysis. Total HIV DNA, intact HIV DNA (IPDA), and Read-through, total/initiated, 5'elongated, unspliced, polyadenylated and multiply-spliced Tat-Rev HIV transcripts were quantified at weeks 0, 4 and 8 using ddPCR.
In France, the National Reference Laboratory for Campylobacter has access to a large and representative collection of isolates, representative of the diversity of poultry isolates. This collection is a valuable reference to this first investigation conducted in Lebanon in order to map the isolates collected according to their genotypes. Therefore, the aims of this study were to estimate the prevalence of Campylobacter spp. in the ceca and on carcasses of farmed broiler chickens collected in Lebanese slaughterhouses, to identify the main species isolated from positive samples and analyze the genetic diversity of C. jejuni isolates. The genetic profiles obtained herein were compared to those of the French poultry database. On another hand, because of the lack of surveillance program for campylobacteriosis in the Lebanese population, the genetic profiles of Lebanese poultry isolates were compared to those of French human clinical isolates  (Thépault et al.
Ethics Statement The study was approved by the research ethics committee "Comité Interne d'Ethique de la Recherche Médicale (CIER) du Groupement des Hôpitaux de l'Institut Catholique de Lille (GHICL)" (France) with reference number 2016-04-02. Oral and written informed consents were obtained from all subjects included in this study after a clear explanation of the research objectives prior to enrolment. The subject data was collected anonymously (with encryption of the identity of individuals). This study was conducted in accordance with the Code of Ethics of the World Medical Association (Declaration of Helsinki). All chicken samples were collected after slaughter under the supervision of slaughterhouses staff. No approval from the Institutional Animal Care and Use Committee or ethics committee was necessary, as no experiments involving live chickens were performed.
The reference C. jejuni strain NCTC11168 was used as positive control in all assays, since it exhibits the 40 targeted markers in its genome. The PCR results were converted to binary values, with 0 representing the absence of the marker gene and 1 indicating its presence in the bacterial genome, resulting in a 40-digit binary profile for each isolate. The isolate profiles were stored in BioNumerics software (v7. 6, Applied Maths, Sint Martens-Latem, Belgium). A dendrogram was thus built using the simple matching distance and unweighted-pair group method using average linkages (UPGMA) of clustering in BioNumerics, with 90% fingerprinting similarity to analyze the population structure of isolates  (Taboada et al. , 2012). CGF40-90% clusters including at least 4% of the isolates of the broiler chickens population were defined as predominant in the population.
ACKNOWLEDGMENTS This work was supported by grants from the  Programme Orientations Stratégiques  from the  University of Lille 2 , the  Partenariat Hubert Curien (PHC)  France Lebanon CEDRE 2015 Project no. 32684NM  from the  Ministère des Affaires Etrangères et du Développement International and the Ministère de l' Éducation Nationale, de l'Enseignement Supérieur et de la Recherche , the  Centre National de la Recherche Scientifique , the  Institut Pasteur of Lille , the  Lebanese University , and the  Catholic University of Lille. SG was supported by a Ph. D. fellowship from the  Azm & Saade Association of Lebanon. The authors would like to thank all those who participated in the study from the  HQPAP Unit of Anses, Hamidi Medical Centre of Tripoli  and the 3 poultry slaughterhouses for their assistance in sample collection and processing.
Acknowledgements The authors wish to thank  PATH  for their invitation to host this workshop at the VASE conference. The authors would also like to thank  Dr. Richard Walker  for critical reading and comments on this manuscript. Research outlined in this manuscript were supported in part by the following grants -grants  R01-AI036525 ,  U19-AI082655  ( Cooperative Center for Human Immunology [CCHI] ) and  U19-AI109776  ( Center of Excellence for Translational Research [CETR]  from the  National Institute of Allergy and Infectious Diseases (NIAID)  at the  National Institutes of Health (NIH) ; grant  GR01263  through  PATH Enteric Vaccine Inititative (EVI) , with additional support from the  Bill and Melinda Gates Foundation  and the  Swedish Research Council ; and grant  261472  ''STOPENTERICS" from the  European Union Seventh Framework Programme.
The Human CCR7 Fluorescein-conjugated Antibody (clone 150503) was purchased from R&D Systems, and phycoerythrin (PE)-conjugated anti CD1c (clone AD5-8E7) was purchased from Miltenyi Biotech. Samples were acquired on a BD-LSR Fortessa (Becton Dickinson), and all data were analyzed using FlowJo software (Tree Star, Ashland, OR, USA). iDCs were identified by expression of CD1a and CD1c and loss of CD14 expression, and DC maturation was monitored by expression of CD40, CD80, CD83, and CD86 in the HLA-DR+ cells.
Cell staining was performed using fluorescent conjugated murine monoclonal antibodies. V500conjugated anti CD4 (clone L200), PerCP-Cy5. 5-conjugated anti CD25 (clone MA251), V450-conjugated anti Foxp3 (clone 259D/C7), PE-conjugated anti CD127 (clone HIL7RM21), PE-Cy7-conjugated anti IFN-g (clone B27), and PerCP-Cy5. 5conjugated anti IL-17a antibodies were obtained from BD Biosciences. PB-conjugated anti CD4 (clone 13B8. 2) and APCconjugated anti CD8 (clone B9. 11) were purchased from Beckman Coulter. Stained samples were analyzed on a Gallios flow cytometer (Beckman Coulter) using Kaluza software. The experiment was performed in triplicate, and the results are expressed as mean ± SEM.
5% FBS. Cells were then washed and suspended in 200-250 µL of the same media. Stained samples were analyzed on a Gallios flow cytometer (Beckman Coulter) using Kaluza software. Viable lymphocytes were gated using FSC/SSC and 7AAD staining. B cells (CD19 + ), T cells (CD3 + CD56 -), and NK cells (CD56 + CD3 -) were distinguished using CD19, CD3, and CD56 antibodies, respectively.
NK Degranulation Assay This was done as previously described  (15). Briefly, 50 × 10 3 target cells per well were placed in RPMI, 10% FBS, IL-2 100 U/mL with monensin (BD Biosciences) in a 96-well V-bottom plate. NK and target cells were incubated overnight at 37 • C in 5% CO 2 , and living cells were counted using a Muse cytometer (Millipore) with a count and viability kit (Millipore). As a control, NK cells were incubated without target cells. CD107a + NK cells were analyzed on a Gallios flow cytometer (Beckman Coulter) using 7AAD, CD45RO-FITC, CD19-PE, CD56-PECy7, CD3-APC, CD45RA-APCAlexaFluor750, CD16-KromeOrange, and CD107a-HV500 (BD Biosciences). The results were analyzed using Kaluza software.
Statistical Analysis Experimental values were processed and statistical analysis was performed using GraphPad Prism (v6. 0) software. All statistical data are provided as * p < 0. 05; * * p < 0. 01; * * * p < 0. 001, and * * * * p < 0. 0001. Mean values are expressed as mean plus or minus the standard error of the mean (SEM). Results were obtained from three individual donors of the "Etablissement français du sang" (EFS). We prepared three biological samples from each buffy coat for each of the following experiments: PO concentration and cell type.
As NK cells provide anticancer defense  (18, 19) , we analyzed the effects of PO on NK-cell activation and expansion. CD3 + -depleted PBMC cells were incubated at different PO concentrations, and the cell number was analyzed at day 7, 14, and 21. We observed decreased counts only at 500 µg/ml concentrations, but the effect was not statistically different at any concentration (Supplementary Figure  7 ). In fact, the raw data were very heterogeneous due to differences in the initial NK cell numbers in the blood bags and the response to the activation/expansion protocol. This was expected, given the variable percentages of NK cells in healthy humans (roughly 5-20%) and the NK cell responses to different stimuli  (14). To counteract this issue, we calculated the average cell counts for each donor and produced a normalized value.
Finally, over the past two decades, several studies in Western countries have reported on high acceptability of home sampling with equivalent or superior number of screening diagnosis completed for chlamydia and gonorrhea as compared to conventional sampling and detection methods  [5, [7] [8] [9] [10] [11] [12] [13] [14]. Limited data currently exist on the performance of genital self-sampling for STIs detection by NAATs in general female population living in resource-constrained countries  [15, 16]. The main objective of the present study, so-called GYNAUTO-STI operational research project, was to assess the performance of a novel genital veil (V-Veil-Up Gyn Collection Device, V-Veil-Up Pharma Ltd. , Nicosia, Cyprus) as a genital self-sampling device to collect genital secretions to diagnose STIs by multiplex real-time PCR as compared to reference clinician-collected genital specimens, in adult women living in N'Djamena, the capital city of Chad.
The multiplex PCR reaction was carried out on the CFX966 real-time PCR instrument (Bio-Rad, Marnes-la-Coquette, France) using 5 L of extracted DNA and 15 L of PCR mix. The test was applied to all samples according to manufacturer's recommendations, using the Seegene viewer software (Seegene, South Korea) per the manufacturer's guidelines. The microbiology laboratory was accredited by the Comité Francais d'Accréditation according to the ISO 15189 norma for molecular biology.
Statistical Analyses. Data were entered into an Excel database and analyzed using IBM5 SPSS5 Statistics 20 software (IBM, SPSS Inc, Armonk, New York, USA). Means and standard deviations (SD) were calculated for quantitative variables and proportions for categorical variables. The results were presented along with their 95% confidence interval (CI) using the Wilson score bounds for categorical variables. The overall prevalences of bacteria DNA detection between the two collection methods were compared using the MacNemar's test for paired data. The mean numbers of detected genital bacteria by the two collection methods were compared using the Wilcoxon signed-rank test. The agreement between the two collection methods was estimated by Cohen's  coefficient, and the degree of agreement was determined as ranked by Landlis and Koch  [32].
Discussion The present study reports on the prevalences of common curable STIs (N. gonorrhoeae, C. trachomatis, M. genitalium, and T. vaginalis) as well as genital mycoplasmas (M. hominis, U. urealyticum, and U. parvum) colonization among community-recruited asymptomatic adult women living in N'Djamena, Chad. The results showed low incidence of common STIs, as only seven women (2. 8%) were infected. The prevalences of genital mycoplasmas (apart from M. genitalium) were much higher in more than half women with a predominance of U. parvum. Furthermore, the genital microorganisms DNA diagnostic accuracy of a novel genital veil (V-Veil-Up Gyn Collection Device) was assessed as female genital self-sampling device to collect cervicovaginal secretions. All specimens collected by the veil were found positive for the -globin gene, demonstrating the lack of PCR Epidemiological data on the prevalences of common bacterial STIs in Chad have been until now poorly reported.
In the GYNAUTO-STI study, we have had the opportunity to evaluate the genital microorganisms DNA diagnostic accuracy of a novel genital veil (V-Veil-Up Gyn Collection Device) as female genital self-sampling device to collect cervicovaginal secretions. The percent of agreements between clinician-based collection and veil-based self-collection to detect any vaginal microorganisms was above 90%, and all Cohen's  coefficients were between 0. 81 to 0. 99 demonstrating "almost perfect" agreement between collection methods  [32]. Although no data exists on the performance of self-collected specimens by veil for female genital bacteria DNA testing for which to compare our results, several previous reports evaluating the use of self-collection by vaginal swab for C. trachomatis and N. gonorrhoeae testing may be useful to contextualize our observations  [14].
Furthermore, 9 (3. 5%), 19 (7. 5%), and 8 (3. 2%) study participants were HIV-, HBsAg-, and HCV-specific antibody positive, respectively, in accordance with the high endemicity of these three major chronic viral infections in Chad  [48, 49]. However, our study has limitations. First, although 251 women were enrolled to the study, the insufficient size of the study population may have introduced bias. The fact that women participated on a voluntary basis and were recruited from community-churches and mosques and associative networks may also have led to recruitment bias. Secondly, we had to rely on a face-to-face questionnaire to collect sociodemographic data and information on sexual behaviors, a method that may be prone to reporting bias for sensitive and intimate questions  [50]. Thirdly, we did not evaluate the acceptability of the veil in this study, especially in the African cultural context.
Acknowledgments Zita Aleyo Nodjikouambaye  is a Ph. D. student of the  Ecole Doctorale en Infectiologie Tropicale, Franceville ,  Gabon. Ralph-Sydney Mboumba Bouassa  is a Ph. D. student of the  Ecole Doctorale en Infectiologie Tropicale, Franceville, Gabon , benefiting of a scholarship from the  Gabonese Government  and is holder of merit from the  Agence Universitaire de la Francophonie. The authors are grateful to  Bernard Chaffringeon ,  V-Veil-Up Pharma, Ltd. , Nicosia, Cyprus , for providing the  V-Veil-Up Gyn Collection Devices  and the multiplex PCR kits for the study. They are greatly appreciative to all women who participated in the study.
Data overview We analyzed the RNA-sequencing (RNA-seq) data, which consisted of samples collected from five cattle pregnancies terminated at gestation day 18 (Gene Expression Omnibus database GSE74152  [27] ). The conceptus was dissected, and transcriptome data were generated for extraembryonic tissue, whereas the endometrium was dissected into caruncular (gland-free) and intercaruncular (containing endometrial glands) areas, and transcriptome data were generated from both regions of the endometrium (Fig  1A ). Therefore, the data set analyzed was comprised of three sample types collected from each pregnancy: extraembryonic, caruncular, and intercaruncular tissues  (Fig 1B). Alignment of the sequences to the B. taurus genome (University of Maryland [UMD] assembly 3. 1) resulted into an average of 22, 31.
Visualization of coexpressed networks in extraembryonic tissue and endometrium Our analysis was not an exhaustive evaluation of all potential coexpression networks that exist between extraembryonic tissue and the endometrium. Thus, we developed a web interface for dynamic and interactive data visualization based on the coexpression analysis conducted in the present study  [37, 38]  (https://biaselab. shinyapps. io/eet_endo/). The public access to this web application allows a user to produce networks for genes of their choosing. Furthermore, each network is accompanied by supporting data such as scatter plots and heatmaps of the geneexpression values. The raw data and codes for reproduction of this interface can be downloaded from a GitHub repository (https://github. com/BiaseLab/eet_endo_gene_interaction).
Discussion In mammals and particularly in cattle, a large body of gene-expression data was produced at various steps of early pregnancy derived from in vitro-or in vivo-produced embryos  [6, 27, 28, 40] , varied physiological status of the dam  [41] , and fertility-classified heifers  [30]. Altogether, results based on group analyses (extraembryonic tissue or endometrium) have demonstrated different degrees of interactions between the extraembryonic tissue and endometrium at the initial phases of implantation. In the present study, our objective was to shed light on the subtle interactions between the extraembryonic tissue of a conceptus and the endometrial tissue of the uterus hosting this conceptus in normal pregnancy using paired coexpression analyses of gene transcript abundances. Our analyses were carried out using biological material collected from the single conceptus and the endometrium from the same pregnancy, a critical aspect to determine the crosstalk during implantation at the level of one individual pregnant female.
It must be noted that our study has some limitations that may reduce the extent of the insights into individual pregnancies. First, we worked with samples collected at one developmental stage (gestation day 18). Gestation is a highly dynamic process; thus, we can anticipate that the gene interactions will also be dynamic. Second, the endometrium is a tissue diverse in cell types (e. g. , epithelial lumen, stromal tissue, immune cells, glandular epithelia) that were not dissected at collection. Therefore, we did not dissect the cellular origin of the signals. This work provides a snapshot of the rich and unique interactions between extraembryonic and endometrial tissues at the tissue level that will deserve to be refined at the cell-type level. Our analyses of transcriptome data from extraembryonic tissue and endometrium pairs identified key signatures of gene expression that are likely to be linked to the success of pregnancy recognition and implantation.
Data analyzed and estimation of gene-expression levels All analytical procedures were carried out in R software  [37]. The files and codes for full reproducibility of the results are listed in the file S1 Code. The appropriate approval from institutional committees of ethical oversight for animal use in research was obtained as reported previously  [27]. All five cattle (B. taurus, Holstein breed) gestations were initiated by artificial insemination using semen from a single bull and later terminated on gestation day 18 for sample collection. We analyzed RNA-seq data (100-base long reads, GSE74152  [27] ) generated from samples obtained from cattle gestations interrupted at day 18 (n = 5). The samples were extraembryonic tissue (n = 5), caruncle (n = 5), and intercaruncle (n = 5) regions from the endometrium.
Testing for enrichment of gene ontology terms or KEGG pathways We tested for enrichment of gene ontology  [67]  categories and KEGG pathways  [68]  using the "goseq" package  [69]. Subsets of genes were defined according to appropriate thresholds and defined as "test genes"; the genes expressed in the corresponding tissue were then used as background for the calculation of significance values  [70]. Significance values were then adjusted for FDR according to the Benjamini and Hochberg method  [71]. We further tested the likelihood of significant categories of gene ontology or KEGG pathways to have been identified by chance by a bootstrapping approach. We selected tested genes randomly (2,000 rounds of randomized subsetting) from the genes expressed and carried out the procedure for detection of enrichment described above.
[GEMIN6]; pre-mRNA processing factor 4B [PRPF4B]; RNA-binding motif protein 39 [RBM39]; survival motor neuron domain containing 1 [SMNDC1]; SPT4 homolog, DSIF elongation factor subunit [SUPT4H1]; splicing factor U2AF 26-kDa subunit [U2AF1L4]; FDR = 0. 13, Fig 2E), "chromatin organization" (codanin 1 [CDAN1], nucleoporin 133 [NUP133], SUPT4H1, FDR = 0. 13, Fig 2E), and "protein autoubiquitination" (CCR4-NOT transcription complex subunit 4 [CNOT4], membrane-associated ring-CH-type finger 5 [MARCH5], ubiquitin-like with PHD and ring finger domains 1 [UHRF1]). We also interrogated the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways database and identified an enrichment for the "RNA transport" pathway (eukaryotic translation initiation factor 4E binding protein 1 [EIF4E], GEMIN6, karyopherin subunit beta 1 [KPNB1], protein mago nashi homolog 2 [MAGOHB], NUP133, NUP54, PYM homolog 1, exon-junction-complex-associated factor [PYM1], SUMO1/sentrin/SMT3-specific peptidase 2 [SENP2], small ubiquitin-like modifier 1 [SUMO1], THO complex 1 [THOC1], FDR = 0.
Acknowledgments The authors would like to thank the staff of  INRA experimental units (Leudeville, France ;  Saint-Genes-Champanelle, France ;  Nouzilly, France)  for animal management as well as past and present members of UMR BDR, including  Dr. H. Jammes ,  M. Guillomot ,  A. Chaulot Talmon , and  Corinne Giraud-Delville  for help in sample collection and preparation.
Statistical analysis The effects of nutritional stimulus (HP, LP and HPR diets) at the first feeding on the different parameters were tested using one way ANOVA test (statistical R software/R Commander package). For statistical analyses, differences were considered significant at p < 0. 05. Normality of distributions was assessed using the Shapiro-Wilk test whereas the homeostatiscity of variance was evaluated using the Brown-Forsyth test. The results are presented as mean ± SD (standard deviation).
Acknowledgements Y. S. gratefully acknowledges a doctoral fellowship from the  China Scholarship Council (CSC). We thank  E. Plagnes-Juan ,  V. Véron ,  A. Surget ,  M. Sérusier  and  E. Gazzola  for technical assistance in the laboratory. We also acknowledge the technical staff of the  INRA  experimental facilities ( F. Terrier ,  F Sandres ,  A Lanuque ) at  Donzacq, Landes, France  for fish rearing and feed producing.
82 Å (Fig. 1A  and Table  1 , PDB code 6FGA). The complex crystal structure includes four homodimeric TRIM21 R and seven UBE2E1 C entities in the unit cell, which together form four TRIM21 R :UBE2E1 C assemblies: two well-defined 2:2 complexes (chains IFDL and MBCO), one 2:2 complex with poor density in one of the E2 entities (chains NEAK), and one 2:1 complex (chains JHG) (Fig. 1A ). TRIM21 R is predominantly a dimer both in crystal and in solution as estimated by small-angle X-ray scattering (SAXS) and analytical gel filtration (Figs. 1B  and S3  and Tables  S2  and S3 ). SAXS measurements of TRIM21 R reveal an overall similar shape in solution as in the corresponding crystal structure dimer (Fig. 1B ). The quaternary arrangement of E2 and E3-RING dimer modules is highly similar to that in previously determined E2-RING-Ub assemblies  (24, 26 -31)  (Figs.
1C and S2B and Table  S1 ). Finally, to compare free and bound E2 states in this study, we obtained a crystal structure (1. 4 Å) of similarly prepared free UBE2E1 C (Table  1 , PDB code 5LBN), which is similar to matching residues within full-length UBE2E1 (PDB code 3BZH, r. m. s. d. 0. 47 Å (  38 )) (Fig. S2C ). The interface connecting UBE2E1 C -H1, -L4, and -L7 with TRIM21 R -L1, -H1, and -L2 (where H represents helix and L represents loop) is well-defined in the TRIM21 R -UBE2E1 C crystal structure (Fig. 1 , D and E, and Table  S1 ). Significant amide chemical shift perturbations (CSPs) were observed by NMR in the direct interface (Fig. 1F ), and a K d of 24 Ϯ 11 M was estimated for the TRIM21 R -UBE2E1 C interaction, based on CSPs in five titration points for nonbroadened residues (Fig.