dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We would like to thank  Prof. Jain  for providing Surflex, and  Chemaxon  for providing the Marvin suite. H. G. and H. M. are recipients of CIFRE fellowships from  Association Nationale de la Recherche et de la Technologie (ANRT). J. P. and N. B. N are recipients of fellowships from the  French Ministère de l'Enseignement Supérieur et de la Recherche (MESR). We would like to thank  O. De Oliveira  for her technical support during the in vivo experiments;  Prestwick Chemical and CMGPCE, CNAM  for their support in analytical chemistry and the HistIM platform for technical support with the immunochemistry and histology experiments. This work was funded in part by grants from  Conservatoire National des Arts et Métiers  and from  Peptinov SAS.
The pacific orange Live/dead Ò fixable aqua dead cell stain kit (Invitrogen, molecular probes Ò , France) was used to stain dead cells, according to the manufacturer's protocol before fixing them for intracellular staining. PE-conjugated anti-CTLA-4 (clone UC10-4F10-11) and anti-T-Bet (clone 4B10) and isotype antibodies were purchased from BD Pharmingen and eBioscience and used for intracellular staining. Foxp3 C cells were detected by intracellular staining with FITC-conjugated anti-Foxp3 mAb (clone FJK-16), according to the manufacturer's protocol (eBioscience). Streptavidin-PE-conjugated H-2D b /E7 49-57 tetramers were purchased from MBL International Corporation. The cells were acquired on a CyAn Coultronics (Beckman Coulter) flow cytometer and analyzed with FlowJo software (Tree Star).
Background Epidemiological and experimental data indicate that diets rich in saturated fatty acids (SFA) and simple sugars favour the development of metabolic and physiological dysregulations that characterize the metabolic syndrome and increase the risk of cardiovascular disease and type-2 diabetes  [1]. These dysregulations includes oxidative stress, low-grade inflammation and endothelial dysfunction, which are well known as being pivotal to the initiation and progression of the metabolic syndrome. Importantly, in the last decade, a large body of evidence has accumulated demonstrating that a single high-lipid/high-sucrose meal transiently elicits a cluster of low-grade postprandial inflammatory responses (PPIR)  [2] [3] [4] [5]. PPIR can be measured in plasma as an increased concentration in a number of inflammatory and vascular markers.
Analyses Real-time quantitative PCR (RT-qPCR). Total RNA was extracted using Trizol reagent from adipose tissue, liver and aorta samples. Five hundred nanograms of total RNA were converted into cDNA using the High Capacity cDNA Reverse-Transcription Kit (Applied Biosystems, Villebon-sur-Yvette, France) on a PTC-200 thermocycler (MJ Research/Biorad). Real-time PCR amplifications were performed with a Prism7300 sequence detection system using SYBR Green MasterMix (Applied Biosystems). Il-6, Il-1β, Il-10 (Interleukin-10), Tnf-α (Tumor necrosis factor-α), Pai-1, Mcp-1, Tlr2, Tlr4, Fas (Fatty acid synthase), Lpl (Lipoprotein lipase), Icam-1 and Vcam-1 (Vascular cell adhesion molecule-1) mRNA levels were expressed as a ratio of Hprt1 mRNA levels. Primer sequences (Table  1 ) were designed using Primer Express™ (Applied Biosystems) software and were from Eurogentec (Seraing, Belgium).
Statistical analyses Data are reported as means ± SEs. Statistical analyses were performed with SAS (version 9. 3; SAS Institute). Significance was set at P < 0. 05. Kinetics data (from study #1) were analysed using mixed models (PROC MIXED) for repeated measurements with covariance structure modelling. Outcomes were explained by the following fixed factors: time after meal (pre/postprandial, i. e. 0 h, 1 h, 2 h, 3 h, 4 h, 5 h and 6 h), treatment (INH or VEH), period of treatment (first or second), treatment by time, and treatment by period interactions (to test for the possible existence of a carry-over). Treatment and time were considered as repeated factors on subject. Subject was analysed as a random effect. Multiple comparisons between treatment and time points were adjusted by Tukey-Kramer test.
Acknowledgements We are most grateful to all of the patients who participated in the present study. We acknowledge use of the confocal imaging platform (ICCF, https://www. gred-clermont. fr/directory/platform/)at the  GReD laboratory, Faculty of Medicine, University of Auvergne. We thank  Caroline Vachias, Ph. D. ( GReD laboratory, Faculty of Medicine, University of Auvergne ) for excellent technical assistance in confocal microscopy. This study was supported in part by  Karl Storz Endoscopy & GmbH (Tuttlingen, Germany ).
Additionally, hA3H hapII showed resistance to SIVcpzPttMB897 Vif, but this resistance was partially lost when the K97Q mutation was introduced (Fig  6A ). In contrast to SIVcpzPttMB897 Vif, both wild-type hA3H hapII and its K97Q mutant showed resistance to SIVcpzPtsTAN1 Vif (Fig  6C ). Furthermore, we analyzed the protein expression level of these A3H mutants in the presence of SIVcpz Vifs. hA3H E121K was included as a control mutant that could not be degraded by HIV-1 Vif  [48, 49]. SIVcpzPttMB897 Vif slightly reduced the protein level of cpzA3H Q97K compared to the no-Vif control, which is consistent with the infectivity data (Fig 6A  and 6B ). SIVcpzPts-TAN1 Vif did not affect the expression of cpzA3H Q97K (Fig  6D ). hA3H hapII K97Q was depleted by co-expression of SIVcpzPttMB897 Vif, while the presence of SIVcpzPtsTAN1 Vif did not affect hA3H protein levels (Fig 6B  and 6D ).
2%, 19. 6%, and 34. 4%, respectively. The detailed SNP and zygosity information is described in Table  1. These four SNPs including the reference cpzA3H were named from haplotype I (hapI) to haplotype V (hapV) (Fig  7A ). In addition, we performed a phylogenetic   The protein stability differs in human A3H haplotypes and it is one of the determinants of its antiviral activity  [29] [30] [31]. Thus, the expression of five cpzA3H haplotypes in 293T cells was tested by immunoblotting. All cpzA3H haplotypes produce stable proteins and had similar expression levels (Fig  7C ). Moreover, these five cpzA3H haplotypes displayed similar anti-SIVcpz activities and were all sensitive to Vifs from SIVcpz lineages (Fig 7D  and 7E ). These data indicate that the polymorphism of cpzA3H does not affect its protein stability or antiviral activity.
Flow cytometry To analyze CD4 and CCR5 expression level of SupT11 cell lines, 5×10 5 cells were stained by α-hCD4 PE mouse IgG1 k (Dako, Hamburg, Germany) and α-hCCR5 FITC (BD Bioscience, Heidelberg, Germany) separately according to the manufacturer's instruction. The mouse IgG1/ RPE isopeptidase was used as negative antibody control for CD4 staining. The measurement was carried out by BD FACSanto (BD Bioscience). Data analysis was done with the Software FlowJo version 7. 6 (FlowJo, Ashland, USA).
Acknowledgments We thank  Wioletta Ho  ¨rschken for excellent technical assistance. We thank  Viviana Simon ,  Michael Emerman ,  Frank Kirchhof ,  Nathanial R. Landau ,  Marcel Ooms ,  Daniel Sauter  and  Jonathan Stoye  for reagents. We thank  Daniel Sauter  for discussing the propagation of SIVcpz molecular clones.
Cloning of LmlRAB and plasmid constructions The full-length Lmlrab gene (1,833 bp; GenBank: AY962589) and LmlrabC, corresponding to the divergent carboxy-terminal part (1,286 bp) were amplified by PCR from genomic DNA of L. major (MHOM/ TN/94/GLC94) using specific primers (Table  2 ). The purified PCR products were digested with specific restriction enzymes and cloned in pET-22b (+) expression vector (Novagen, EMD Millipore). The transformed BL21 E. coli were screened for the presence of recombinant plasmid with the Lmlrab or LmlrabC insert by gene-specific PCR. Isolated positive clones were subsequently sequenced. Production of purified recombinant rLmlRAB and its divergent carboxy-terminal part rLmlRABC BL21 E. coli strain cells harboring the recombinant plasmid pET-LmlRAB and pET-LmlRABC were grown in LB medium, induced with 1 mM isopropyl-1-thio-β-dgalactopyranoside (IPTG) for 4 h and lysed.
Analysis and comparison of DNA and amino acid sequences Nucleotide and deduced amino acid sequences of LmlRAB were downloaded from the GenBank database using the ID: AY962589. 1 and used as a query to run the NCBI-Blast program hosted on the online Kinetoplatid Genomics Ressources (tritrypdb. org). The similarity analysis of LmlRAB sequences was performed over the whole genome sequences of the following Leishmania strains (L. major strain Friedlin; L. major strain SD 75. 1; L. major strain LV39c5; L. infantum strain JPCM5; L. donovani strain BPK282A1; L. tropica strain L590; L. mexicana strain U1103; L. amazonensis strain M2269; L. aethiopica strain L147; L. braziliensis strain M2904 and L. braziliensis strain M2903). The corresponding genomic sequences were downloaded from the TriTrypDB plateform and translated into amino acid sequences using Geneious Pro version (3.
Cytometric Bead Array assay (CBA) Granzyme B and tumor necrosis factor-alpha (TNF-α) were detected and quantified from culture supernatants (50 μl) of PBMC exposed for 120 h to PHA (10 μg/ml), SLA (10 μg/ml), rLmlRAB or rLmlRABC (10 μg/ml), using the BD CBA Human Soluble Protein Flex Set system, according to the instructions of the manufacturer (BD Biosciences). Granzyme B was analysed only in CCLm, HHRLm and HLR groups. In order to quantitate samples, the BD™ CBA Human Soluble Protein Flex Standard was performed for each cytokine and in each experiment. Data were acquired by flow cytometry (FACS Canto II, BD Bioscience) using 2color detection. Flow Cytometric Analysis Program Array (FCAP Array™; BD Biosciences) software was used for samples analysis.
Acknowledgements The authors thank  W. Markikou-Ouni ,  E. Petitdidier ,  R. Bras-Gonçalves ,  Z. Ben Lasfer ,  A. N. Ben Khalaf  and  J. L. Lemesre  for their professional assistance in laboratory work. Authors are also grateful to the staff of the  Regional Directorate of Public Health of Kairouan, Tunisia.
Construction of an in silico structural model of IL-26 Amino acid sequence analysis, using ClustalW software, showed better identity between IL-26 and IL-10 (26%) compared with IL-19 (20%) and IL-22 (21%). Structural hypothesis of IL-26 was thus built by comparative modeling using the IL-10 x-ray crystal structure as a template for a-parallel bundles. Secondary structure assignments from the amino acid sequence analysis of IL-10 were used to model helices. Virtual 3D construction of the IL-26 model was performed using Modeler software and was validated by Procheck. Electrostatic surface charges were calculated using Adaptive Poisson-Boltzmann Solver (APBS). MetaDBsite was used to determine potential DNA-binding residues. Amphipathic helices were identified using AmphipaSeek.
Statistical analysis Data were expressed as mean 6 SEM. Statistical analyses were performed using GraphPad Prism 5 (version 5. 02; GraphPad Software, La Jolla, CA). Differences between two groups were assessed using the nonparametric Mann-Whitney U test. When analysis included more than two groups, the nonparametric Kruskal-Wallis test or the two-way ANOVA was applied with the Bonferroni-Dunn's posttest comparison. Spearman correlation coefficient was used in univariate analysis. Significant differences are illustrated as *p , 0. 05, **p , 0. 01, ***p , 0. 001.
This model, generated using the ClustalW software and validated using the Procheck software, showed that. 90% of residues are located in allowed regions of the Ramachandran plot. Interestingly, analysis with APBS software  (38)  and with MetaDBsite (39) defined two regions rich in positively charged residues and with predicted DNA-binding properties, composed by helix E and by helix B plus the N terminus of helix C (Fig. 2D, 2E ). As observed with the IL-22-based IL-26 model (  26 ), the electrostatic potential on the molecular surface of IL-26 was globally positive. These results show that IL-26 binds to DNA to form complexes, a property supported by its unconventional cytokine structure.
We first analyzed by immunochemistry the expression of IL-26 in kidney biopsies of active AAV patients. Kidney is one of the main target organs in AAV, with glomerulonephritis characterized by crescentic necrotizing lesions  (53). Biopsies of active patients revealed an intense staining with an anti-IL-26 mAb of vascular SMCs from arteries (Fig. 5A ) and from afferent glomerular arterioles (data not shown), whereas endothelial cells and fibroblasts were not stained (Fig. 5A ). No staining of vascular SMCs was observed with a control mAb. Kidney arteries and afferent glomerular arterioles from healthy subjects were not stained by the anti-IL-26 mAb (Fig. 5A ). Confirming that SMCs may represent a novel source of IL-26, we observed that cultured human primary SMCs constitutively expressed IL-26 mRNA (Fig.
g. , case series of Streptococcus suis, HIV or viral meningitis) and brain abscesses. Two authors independently assessed studies for inclusion and extracted data on the speciality of all authors and a third author resolved disagreement. Searches were reported according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The speciality of each author was derived from his or her departmental affiliation stated in the publication. Specialities were recorded as microbiology, virology, infectious diseases, neurology, paediatrics, research/public health and other. Bacteriology was not described as an affiliation in any paper and we assumed that microbiology did not include virology as a subspeciality. The data were summarized for each study as one point for a speciality if one or more authors reported an affiliation for that speciality.
In June 2016, after her 5th injection, she reported an unintended pregnancy. The last dose of ustekinumab had been administered at week 4 of gestation. Ultrasound (US) examination confirmed this inadvertent pregnancy and ustekinumab therapy was subsequently discontinued due to the lack of clinical data supporting this medication's use during pregnancy. A systematic folic acid supplementation (1 mg/day) was started immediately according to French recommendations. In July 2016, while the patient was still in remission, a second US exam was performed and reported in utero fetal death (dating from week 4, close to the last ustekinumab injection) and ultimately leading to a miscarriage at 8 weeks of gestation.
Gels were stained using regular silver staining, and comparative analysis of digitized proteome maps was performed using the PDQuest 7. 4. 0 image analysis software (Bio-Rad). Only spots whose abundance was significantly different between exposed and control conditions at a significance level of p< 0. 05 based on one-way ANOVA analysis (assuming equal variance) and a ratio above 1. 5 were considered. Selected spots were manually excised from MS-compatible silver stained gels using a Onetouch Plus Spot Picker Disposable (Harvard Apparatus) equipped with specific 1. 5 mm methanol-washed tips. Gel plugs were first destained following a potassium ferricyanide/sodium thiosulfate procedure and then, proteins were trypsin-digested overnight at 30˚C. Peptides were recovered after three washes a solution of formic acid (1%) and acetonitrile (50%).
Peptides were lyophilized and sent to the PISSARO proteomic platform (University of Rouen, France) for identification with a nano-LC1200 system coupled to a Q-TOF 6550 mass spectrometer equipped with a nanospray source and an HPLC-chip cube interface (Agilent Technologies). For protein identification, peak lists were extracted (merge MSn scans with the same precursor at +/-30 s retention time window and +/-50 ppm mass tolerance) and compared with S. mansoni genome as reference database by using the PEAKS studio 7. 5 proteomics workbench (Bioinformatics Solutions Inc. , build 20150615). Only significant hits with a false discovery rate (FDR 1) for peptide and protein cut off (-logP ! 20 and unique peptides ! 2) were considered.
Pathways analysis To improve our understanding of the changes caused by latex exposure in both sexes, a pathway analysis combining transcripts and proteins differentially abundant for each sex and each exposure group was conducted. First of all, the biological functions of the transcripts/proteins differentially expressed in female and in male between control and exposed groups were annotated by Gene Ontology Annotation and AmiGO2. We focused our analysis on biological processes only and the number of GO terms in each category was analyzed for each parasite sex. To obtain a more synthetic overview, we used the highest hierarchical level as categories. Additionally, to gain insight into predicted protein-protein interactions and affected pathways on female and male, enrichment analysis using String Database were performed by focusing on pathways containing genes and/or proteins that were under-expressed or over-expressed  [29].
Only the highest confidence interactions (i. e. , interactions with a score larger than 0. 9) were considered, including direct (physical) and indirect (functional) associations derived from four different sources: "genomic context" (associations based on physical location of genes on genome that indicates that encoded proteins participates in the same metabolic pathway), "high throughput" (associations based on the function of proteins), "co-expression" (associations based on simultaneous expressions of different genes in the same organism) and "previous knowledge" (associations from previous annotations in other databases).
Thirty-nine genes show differences in RNA level in adults when cercariae had been exposed to latex In total, the transcriptome sequencing of the two experimental groups yielded 1,080,386,261 Illumina single reads and 981,363,482 of them (90. 8%) were mapped to the S. mansoni  reference genome (v5. 2). These mapped reads in female samples were reconstructed into 6,654 genes (XLOC) ans 9,598 unique transcripts (TCONs) (S1 Table ). In male samples, they were 16,192 unique genes and 33,396 transcripts, respectively (S1 Table ). Quantification of read abundance and DEseq2 analysis of differential gene expression between sexes and experimental groups (adjusted P-value < 0. 05) identified 24 genes that were under-expressed in female adults from the exposed group as compared to those from control group (S2 Table ).
Our integrated transcriptomics, proteomics and ultrastructural analysis converge towards a scenario in which a short latex contact at larval stage has a lasting schistosomastatic action affecting the development into adult worms. Several studies reported that congruency between omics data and phenotypic features are difficult when analyzed independently  [32, 33]. Transcriptome analysis gives insights into the dynamic expression of genes while proteomic takes into account all post-transcriptional and post-translational events to quantify proteins abundance, which is influenced by proteins half-life. This is why it is often difficult to predict the abundance of proteins based only on the patterns of gene expression, and vice-versa. Functional annotations are indicated for integrative approaches using heterogeneous datasets to improve the understanding of a determined biological event.
This study received funding from  Wellcome Trust (Flatworm Functional Genomics Initiative (FUGI)   -107475/Z/15/Z ),  Coordenacão de Aperfeicoamento de Pessoal de Nı ´vel Superior  ( CAPES Parasitologia Basica/2011 ), Fundacão of the treatment campaign. This type of treatment could also provide a rational for the control of other pests. Carlos  Chagas Filho de Amparo à Pesquisa no Rio de Janeiro  ( FAPERJ-BIOTA 2012 ),  Conselho Nacional de Pesquisa (CNPq) -Edital Universal   2014  and  PAEF/Fiocruz  ( PAEF no. IOC-008-FIO-04 ),  CNPq fellowships  ( 205872/2014-0 -SWE ) and  MATER-IMMUNITY   Project  ( ANR-14-CE02-0009 ) of the  French National Research Agency (ANR). The funders did not participate in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Ectopic Expression and Confocal Microscopy GFP-LC3, YFP-Gal8, YFP-Gal3, YFP-Gal9, YFP-Gal10, YFP-Gal4, YFP-Gal, YFP-Gal8 (R275H), YFP-Gal8 (R69H), and GFP-Gal3 (R186S) or RFP-NDP52 transfected CHO cells were analyzed by confocal microscopy using an Olympus FluoViewTM FV1000 confocal microscope (Olympus, Argentina), with the FV10-ASW (version 01. 07. 00. 16) software. Images were processed using Adobe CS3 (Adobe Systems). Confocal images (0. 39-µm sections) were collected.
Video-Microscopy Some in vivo experiments were recorded using an inverted AxioObserver Z1 microscope fitted with a Zeiss Axiocam R MRm camera (Carl Zeiss, Oberkochen, Germany) and operated by Axiovision R software. Images were acquired with a Plan-Apo 100×/1. 46 oil immersion objective (Carl Zeiss, Oberkochen, Germany). For video microscopy, the fluorophore excitation system was composed of a Colibri system (Zeiss, Carl Zeiss, Oberkochen, Germany) with 365, 470, 555, and 590 nm LEDs. For pH measurements, images were adquired in a LEICA fluorescence microscope spinning disk (AF6000-X; Campus CNRS CCHB, Bio Imaging Center Lille-Campus Lille 1, Université de Lille).
ACKNOWLEDGMENTS We are grateful to  Dr. Robert Heinzen  ( Rocky Mountain Laboratories, NIAID/NIH, Hamilton, Montana, USA ) for generously providing mCherry Coxiella burnetii. We also thank  Matteo Bonazzi  for providing GFP-C. burnetii and the corresponding DotA mutant. We thank  Dr. Felix Randow  ( MRC Laboratory of Molecular Biology, Hills Road, Cambridge ,  CB2 0QH ,  U. K. )  for the plasmids encoding  YFP-Gal4 ,  YFP-Gal9 ,  YFP-Gal3 ,  YFP-Gal10 ,  YFP-Gal1 ,  YFP-Gal8 , and  RFP-NDP52. We are also grateful to  Dr. Gabriel Rabinovich  ( Instituto de Biología y Medicina Experimental INYME-CONICET, Buenos Aires ) and to  Giannina Pasquini  ( UBA ) for the generous gift of rabbit and mouse polyclonal antibodies anti-Gal3,  -Gal1 ,  -Gal8 , and plasmid encoding Gal3. We are indebted to  Dr.
HIV-1 sequences in the epidemic suggest an alternative pathway for the generation of the Long Terminal Repeats Pierre Cappy 1,2,3 , Alice Moisan 2,3 , Fabienne De Oliveira 2 , Jean-Christophe Plantier 2,3 & Matteo Negroni  1  To generate the long-terminal repeats (LTR) that border the integrated viral genome, two-strand transfer steps must occur during reverse transcription. Analysis of the genetic polymorphisms that are present in the LTR of HIV-1 heterozygous virions in single infection cycle studies has revealed which of the two copies of genomic RNAs is used for each transfer event. Thus, the first event of strand transfer has been described to be either intra-or intermolecular, while the second event is generally intramolecular. Here, we repeated these analyses using sequences from HIV databases and extended the study to the regions surrounding the LTR.
For the human immunodeficiency virus (HIV), studies of a single infection cycle in cell culture have concluded that the first strand transfer can be intra-or intermolecular with comparable frequencies. In the first case, minus-strand strong-stop DNA (-sssDNA) is transferred to the 3′ end of the same gRNA used as the template for its synthesis, while in the second event, -sssDNA is transferred onto the 3′ end of the second copy of gRNA present in the virion. By contrast, the second strand transfer is generally intramolecular (see panels F and G in Fig. 1 ), indicating that the 5′ ends of the annealing (-) strand DNA and (+) strand DNA PBS sequences originate from the same gRNA strand rather than from an inter-strand interaction. To address the question of the relative use of the two gRNAs for the generation of the LTR using sequences issued from natural infections, one must rely on the sequences of recombinant viruses available in databases.