dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGMENTS The authors thank all the clinical trial participants, the investigators, the nurses, clinicians, laboratory personnel and other staff members for conducting this study, and in particular  Dr. Reiner Bonnet ,  Dr. Elisabeth Quoix ,  Dr. Yves Pachecot , and  Dr. Alberto Sobrero. Matthew Morgan  ( MG Science Communications, Rixensart, Belgium ) provided scientific writing services and  Véronique Duquenne  ( XPE, Pharma and Science, Wavre, Belgium ) coordinated the manuscript's development.
This case report illustrates the possibility of discriminating strains with VNTR analysis by increasing the number of PCR cycles in such situations. This should encourage the development of a database of MLVA profiles for L. interrogans serovars. A disadvantage of VNTR analysis is that this method has been developed mainly on L. interrogans species and only a few studies have performed VNTR analysis on other Leptospira species such as Leptospira santarosai. 5 Thus, VNTR analysis still needs improvement by performing the technique on L. interrogans strains, but also on other Leptospira species. Moreover, it is also possible that in certain cases this approach will lack sensitivity, for example when the DNA load is very low or when there is a delay in sampling following the onset of disease.
Microarray Analyses Day 5 iDCs (0. 5 × 10 6 cells for each condition) were exposed to lipopolysaccharide (LPS) (100 ng/mL; Sigma-Aldrich), HIV, or HIV-C (300 ng p24/mL each) or left untreated (iDC control) for 24 hours. All experimental parameters, protocols, and raw and transformed data were submitted to a public repository (ArrayExpress; E-MEXP-3706), and the procedure is described in the Supplementary Data. Whole Human Genome Microarray Kits 4 × 44 K (Agilent Technologies) were used to determine up-or down-modulated genes in treated versus untreated cells.
Th1/Th17-Inducing Cytokine Profile in Human DCs by Complement Opsonization of HIV To determine the effect of HIV-1 complement opsonization, we performed microarray analyses according to the scheme in Supplementary Figure  1A. For these, the opsonization patterns of HIV preparations incubated with human complement serum (HIV-C) or C3-deficient serum as a control for nonopsonized  HIV (HIV) were analyzed by a virus capture assay, as described in "Methods" section and depicted in Figure  1A. In independent experiments, iDCs from 5 donors were loaded with HIV, HIV-C, or LPS or left untreated. LPS treatment served as positive control for DC maturation. Within each donor, all treated samples were normalized to untreated iDCs to exclude donor-specific variations. Pathway analyses for up-and down-regulated genes of DCs exposed to LPS, HIV, or HIV-C were obtained using MetaCore analyses software (GeneGo), and the major immune response stimulated in iDCs, due to HIV-C treatment, was dedicated to the Th1/Th17-inducing pathway (Figure  1B ).
As a member of the gut flora of Ngousso mosquitoes, strain Ag1 may be involved in the susceptibility to Plasmodium and O'nyongnyong virus  (9). Recently, several genomes of mosquito associated bacteria have been sequenced, including Elizabethkingia anophelis  (10, 11) , Asaia spp. (12) , Enterobacter spp. (13) , Pseudomonas spp. (  14 ), and Spiroplasma diminutum and S. taiwanense  (15, 16). The available genomes will facilitate to characterize the structure and function of the mosquito microbiome. Nucleotide sequence accession numbers. The genome sequences have been deposited at GenBank under the accession numbers JQEI00000000 (Serratia sp. Ag1) and JQEJ00000000 (Serratia sp. Ag2).
Study population The ANRS PRIMO cohort consists of 1450 HIV-infected patients enrolled during PHI between June 1996 and December 2013 in 94 French hospitals. Primary infection is confirmed by an incomplete Western blot, or detectable p24 antigenemia, or detectable plasma viral load with a negative or weakly reactive enzyme-linked immunosorbent assay (ELISA), or an interval of less than 6 months (3 months since 2002) between a negative and positive ELISA. Clinical and biological data are collected at months 1, 3 and 6 and every 6 months thereafter, as previously described  [17]. The HIV envelope gene was sequenced from frozen plasma samples collected at enrolment in the cohort and HIV tropism was determined using Geno2Pheno algorithm (FPR 10%). All patients are antiretroviral-naïve at enrollment and give their written informed consent.
Percentage CD4 cell counts were also modeled. The best model (Akaike's criterion) for CD4% increase was obtained with one slope change at M3. The multivariate model comprised the same variables as in the CD4 cell count model. The mean CD4 count and percentage evolution were depicted by plotting the mixed model predictions. P values <0. 05 were considered to denote statistically significant differences. Analyses were performed with STATA software (release 13; Stata Corp. , College Station, Texas, USA).
Flow cytometry Cells were labeled as described in  [12]  using 2 or 4% paraformaldehyde fixation. For intracellular staining, cells were incubated for 4 hours at 37°C with monensin (GolgiStop, BD Pharmingen, San Diego, CA). After Fc receptor blocking using anti-CD16/CD32 (BD Pharmingen) and staining with anti-CD4, anti-CD8 and anti-NK1. 1 Abs, intracellular IFN-γ and granzyme B production was determined using FoxP3/Transcription Factor Staining Buffer Set (Ebioscience, San Diego, CA). Fluorescence was quantified using a Gallios flow cytometer (Beckman Coulter, Roissy CDG, France). Data were analyzed using FlowJo software (Tree Star, San Carlos, CA). The results are expressed as percentages of fluorescent cells stainted by specific Ab minus percentages of fluorescent cells stained by isotype Ab.
Cytokine detection in DC-culture supernatants Culture supernatants were collected for cytokine detection by ELISA (for IL-12, Ozyme; for IL-15, Raybiotech, Inc. Norcross, GA) and by RayBio® Mouse Cytokine Antibody Array I (RayBiotech), before being revealed using Gbox system (GeneSnap software, Syngene, Ozyme).
Statistical analysis The statistical analysis was performed using the two-way analysis of variance (ANOVA) test followed by a Bonferroni test, and the Mann-Whitney, the Kruskall-Wallis and the Fisher's exact tests. Values are reported as means ± SEM. Values of P < 0. 05 were considered significant; P < 0. 1, borderline significant. The survival curves were determined using the Kaplan-Meier method. The log-rank test was used to compare curves between study and control groups. Principal component analysis (PCA) on variances of MRI parameters was performed with JMP 9 software.
ACKNOWLEDGMENTS We are deeply indebted to  Pr Olle Hernell (Paediatrics ,  Univ of Umea, Sweden)  and  Martine Armand, PhD  ( Centre de Résonance Magnétique Biologique et Médicale, CRMBM-UMR CNRS 7739, Campus Santé-Timone, Marseille, France ) for the generous gift of BSSLs and to  Pr Olivera J. Finn  and  Dr John R. McKolanis  ( Immunology, Univ of Pittsburgh School of Medicine, Pittsburgh, PA ) for the generous gift of TnMUC1. We thank  Pr David A. Tuveson , ( Cambridge Research Institute ,  Univ of Cambridge, Cambridge, UK)  and  R. Tomasini, PhD  ( Cancer Research Center of Marseille, Parc scientifique de Luminy, Marseille, France ) for the gift of respectively PDX-Cre/Kras  G12D /Ink4a /Arf lox/ lox and Pdx-1-Cre ; LSL-Kras GD12 ; LSL-Trp53 R172H mouse pancreatic tumor slices. We are grateful to  Pr Nadine Girard  ( Service de Neuroradiologie, AP-HM, Hôpital de la Timone, Marseille, France ) for helpful discussion on tumor imaging,  Dr Jean Del Grande  ( Laboratoire d'Anatomie Pathologique et Neuropathologie APHM, Hôpital de la Timone, Marseille, France ) for helpful discussion on tumor pathology, and to  Dr Anderson D.
Funding The HIV-2 cohort of the WADA Collaboration is partly funded by the  National Cancer Institute (NCI) , the  Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD) , and the  National Institute of Allergy and Infectious Diseases (NIAID ) of the  US National Institutes of Health (NIH) , as part of the  International Epidemiologic Databases to Evaluate AIDS (IeDEA)  under Award #  U01AI069919. The  ANRS (France REcherche Nord & sud Sidahiv He  ´patites: FRENSH) supported part of the laboratory work performed within this study.
Cloning, expression and purification of DENV3 NS5 for crystallization To facilitate protein crystallization, we removed five flexible amino acids each from the N-and C-terminal ends of NS5, based on inspection of missing electron density in the structures of the individual MTase and RdRp domains from DENV3 (PDB codes 3P97 and 2J7U). The fragment corresponding to amino acid residues 6 to 895 of DENV3 NS5 (GenBank accession number AY662691. 1) was amplified and cloned into pNIC28-Bsa4 plasmid using ligation independent cloning methods  [34]. The expressed construct comprises the hexa-histidine tag and a Tobacco Etch Virus (TEV) protease cleavage site fused at the N terminus of DENV3 NS5. Transformed E. coli BL21-CodonPlus (Stratagene) was grown in LB medium containing 50 μg/ml kanamycin and 34 ug/ml chloramphenicol to an A 600nm of 0.
Structure solution and refinement The crystals have an estimated solvent content of 50. 2% based on a Matthews coefficient (Vm) value of 2. 47  [36]. The structure was solved by molecular replacement with the program PHA-SER  [37]  using the DENV3 MTase (Protein Data Bank [PDB] accession code 3P97)  [38]  and DENV3 RdRp (PDB accession code 2J7U)  [13]  as search probes. Refinement cycles carried out using REFMAC5  [39]  and PHENIX  [40]  were interspersed with manual model rebuilding sessions using Coot  [41]. TLS refinement was introduced in the last refinement steps. The quality of the structure was analyzed using Molprobity  [42]. A summary of structure refinement statistics is given in Table  1. Solvent-accessible surfaces areas were calculated using CCP4 program AREAIMOL with a 1. 4-Å radius sphere as a probe.
Superimpositions of structures were carried out using the program LSQKAB from the CCP4 suite. Figures were prepared using the program Pymol  [43]. In the crystal structure of NS5 with GTP bound to the MTase domain (Table  1 ), the overall conformation of NS5 is very similar to the NS5: SAH structure: The root mean square deviation (r. m. s. d. ) is 0. 17 Å for a total of 719 Cα atoms superimposed. Buried surface areas were calculated with the PISA server (www. ebi. ac. uk/pisa) using the following domains definition: MTase residues 6-262 in DENV3 and 6-265 in JEV; RdRp residues 273-883 in DENV3 and 276-896 in JEV (S2 Table)  [44]. The relative reorientation between domains was assessed using the program DynDom  [45]. The refined coordinates were deposited in the PDB under accession codes 4V0Q (NS5: SAH) and 4V0R (NS5: SAH: GTP).
3% (v/v) formic acid), followed by washing with 90% buffer B for 3 min and equilibration with 1% buffer B for 5 min) at a flow rate of 15 μl min -1 driven by LC NC pumps. MS raw data were acquired in the range of m/z 300-2000 for 30 min in positive mode on a LTQ-Orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with an ESI source (capillary temperature 275°C and spray voltage of 5 kV). All the HDX separations were performed at 0°C except for on-line pepsin digestion that was carried out at 16°C. Blank injections were made between runs to remove carry-over peptides. At least three independent deuterium exchange experiments were carried out for each time point. All HDX data were normalized to 100% D 2 O content, corrected for an estimated average deuterium recovery of 70%, and analyzed by the software HD Desktop  [46].
Generation of DENV4 NS5 mutant replicons The K95A, Y119A, R263A (R262 in DENV3), E268A (E267 in DENV3), E270A (E269 in DENV3), and R353A (R352 in DENV3) mutants in the DENV4 NS5 sequence (GenBank accession number AF326825) were engineered into the subclone, pACYC-DENV4-F shuttle, using the QuikChange II XL site-directed mutagenesis kit according to the manufacturer's protocol (Stratagene). This plasmid harbours nucleotides 7564-10653 (from NS3-3'UTR) from the DENV4, MY01-22713 strain, linked at the 3' end to the Hepatitis D virus ribozyme (HDENVr) sequence  [47]. Following sequence verification, the plasmids were digested with NotI and KpnI and inserted with a PCR product comprising the sequence spanning nucleotides 1-7563 under the control of the upstream T7 promoter in which the region from nucleotides 217-2291 in this cDNA had been replaced by renilla luciferase and foot-and-mouth disease virus 2A protease cDNAs  [38].
Construction of mutant DENV2 full-length infectious clone Mutations of K95A, Y119A, E268A (E267 in DENV3) and R353A (R352 in DENV3) were constructed into full-length DENV2 cDNA clone (GenBank accession EU081177. 1) using the subclone pWSK29 D2 fragment 3 as described  [17]. Briefly, mutations were generated using the QuikChange II XL site-directed mutagenesis kit (Stratagene) according to the manufacturer's protocol. Primers used for mutagenesis are listed in S1D.
In vitro transcription and replication profiling of mutants The genome-length wild-type DENV2 infectious clone plasmid pWSK29 (GenBank accession EU081177. 1) and the mutants were linearized with SacI and purified with phenol-chloroform. A quantity of ~2 μg linearized DNA was used for in vitro transcription with T7 mMESSAGE mMACHINE kit (Ambion). BHK-21 cells were trypsinized, washed twice with cold PBS and resuspended in Opti-MEM (Gibco) at a cell density of 1 × 10 7 cells/ml. 10 μg of in vitro transcribed RNA (wild-type DENV2 and mutants) were mixed with 800 μl cell suspension in a pre-chilled 0. 4 cm cuvette, and electroporated at settings of 850 V and 25μ F, 2 pulses at 3 seconds intervals. Electroporated cells were allowed to recover at room temperature for 10 minutes prior to resuspending in complete RPMI 1640 media.
Absolute copies of the viral RNA genome was normalized to actin expression with β-actin primers (forward, 5'-TCACCACACACTGTGCCCATCTACGA-3' and reverse, 5'-CAGGGGAACCGCT-CATTGCCAATGG-3'); and reported as viral RNA genome copy per μg RNA. IFA against dsRNA with anti-dsRNA mAb J2 (Scicons) and NS5 protein with anti-NS5 hAb 5R3 were performed as described  [52]. Images were captured on an inverted fluorescence microscope (Olympus IX71, Center Valley, USA) at 20× magnification and image analysis was done with ImageJ software.
GTP is stabilized by base stacking with the aromatic ring of F25 and electrostatic interactions with residues L17, N18, and L20 of the MTase domain (S1 Fig in  S1  Text)  [5, 54]. Likewise, superimposition with the DENV3 NS5-RdRp (PDB codes 2J7U and 4A11) yields RMSD values of 0. 47 Å and 0. 43Å for 492 and 495 Cα atoms respectively  [13, 32]. Like in the isolated RdRp domain structure reported earlier  [13] , however, two segments of the polypeptide chain are disordered in the present NS5 structure: residues 406-417 that harbor motif G, which regulate access of the ssRNA substrate to the template tunnel  [13]  and residues 455-468 which contain motif F. The latter were proposed to bind Stem Loop A, the viral promoter, prior to viral RNA replication  [55]. Two Zinc ions bound to the RdRp domain are also observed as reported earlier  [12, 13].
Y119A mutation did not yield any viable virus or increased intracellular RNA quantified by qRT-PCR. This is likely due to the defective MTase activity (Fig. 5 ; Table  2 ). The K95A mutant virus replicated much slower than WT with a 10-fold lower intracellular and extracellular RNA level at 72 hr post electroporation. No RNA replication or virus recovery was detected for mutant R353A (R352 in DENV3). Immuno-fluorescence analyses at 72 hr using anti-dsRNA and anti-NS5 antibodies confirmed the intracellular levels for WT and mutant viruses (Fig. 5E ). Taken together, these data demonstrated: (i) most interestingly, conserved residues that form the major inter-domain polar contacts, K95 and R353 (R352 in DENV3), play critical but non-enzymatic roles in virus RNA replication and infectivity; (ii) alanine mutation of E268 (E267 in DENV3) have no impact on the enzymatic activities of NS5 nor on virus RNA replication and infectivity (iii) Within the MTase domain, Y119, is important for the MTase enzymatic activity of NS5 and is therefore essential for the virus replication.
), the MTase and RdRp domains of NS5 display only minimal differences at surface exposed regions compared to the individual enzymatic domains (S3 Fig in S1 Text). Superimposition with the NS5-MTase domain structures (PDB codes 3P97 and 1L9K) returns RMSD values of 0. 42 Å and 0. 40 Å for 221 Cα and 219.
(A) DENV3 NS5 is in purple, DENV3 NS5-MTase (PDB code: 3P97) is in yellow, DENV2 NS5-MTase (PDB code: 1L9K) in orange, DENV3 NS5-RdRp (PDB code: 4C11) in Cyan, DENV3 NS5-RdRp (2J7U) in gray. N' and C' stands for N-terminal and C-terminal of NS5 protein; G: motif G, residues 406-417; F: motif F, residues 455-468; Zn1 and Zn2 are two zinc cations in their binding sites. (B) Zoom-in view of the linker region. Key residues are displayed as sticks and the Cα atoms are shown as spheres. S4 Fig. Structure alignments of JEV full length NS5 with JEV RdRp domains. (A) JEV NS5 (PDB Code: 4K6M) is in red and JEV RdRp (PDB Code: 4HDG) is in blue. The structures are aligned and displayed as ribbon. Motifs F and G are shown as connected spheres and each sphere represents one residue. (B) Enlarged view at the domain linker region.
This work was supported by the  National Medical Research Council , Singapore (http://www. nmrc. gov. sg),under grant  NMRC/1315/2011  to the  SGV Lab , a  Competitive Research Program Grant   CRP2008  from the  National Research Foundation  to the JL lab, and a start-up grant to the DL lab from  Lee Kong Chian School of Medicine, Nanyang Technological University. YZ is supported by an  NGS  scholarship from  National University of Singapore. We acknowledge support provided by a  CBRG (Collaborative Basic Research Grant ) grant  May14  from the  Singapore National Medical Research Council. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Costs associated with HIV routine care (determined by CD4+ cell count), OI management and death were derived from a French study by Sloan et al. (2012) (Table  3 ). [4]  Resource use associated with HIV routine care include inpatient hospitalizations, outpatient visits, clinical procedure, prophylactic treatments of opportunistic infections as well as treatment for HBV, HCV, hyperlipidemia and diabetes, and laboratory tests (excluding CD4+ cell count, HIV viral load and genotyping tests). [4]  The costs of ART, laboratory tests and treatment switches (nurse and physician visits as well as additional costs of tests) were obtained from the French Healthcare Insurance Database consulted in October 2014 (Table  3 ). [25] [26] [27] [28] [29]  Utilities. Utilities stratified by CD4+ cell count were pooled from EQ-5D scores from DTG phase III studies in treatment-naïve patients: SPRING-2, SINGLE and FLAMINGO.
The sensitivity analyses showed that the results were robusts, and few parameters had an impact on the ICER. Only the cost of subsequent therapy, with a maximum cost for OBTs was found to modify the conclusions of the analysis. The average life expectancy of patients entering the model was estimated to be around 18 years. The reported life expectancy published in comparable models of ART varied greatly, between 8. 9 and 29 years. [12, 36, 37]  In the model, the QALYs accrued over a lifetime was estimated between 10. 41 and 10. 75. These numbers were consistent with recently published costeffectiveness analyses for RAL, etravirine, or maraviroc, varying between 5. 7 and 14. 6 QALYs. [12, 36, 37]  Several reasons could explain these differences, including varying stages of disease progression in considered populations, different sources of data for utilties, or the country of analysis.
However, this last hypothesis is not thought to be very probable as it is based on the assumption that all patients receive T-20 (Enfuvirtide). Although DTG has been used in the context of a NPP in France, in patients who have reached a therapeutic "dead end", it was not considered as a possible option in the comparator's treatment algorithm (RAL). It was assumed that the RAL strategy corresponded to a world without DTG, so as to ease the interpretation of results, and evaluate the impact of the introduction of DTG. Efficacy data for DTG after one year were taken from clinical trials evaluating other treatments (RAL). This is thought to be a conservative assumption as DTG was shown to be superior to RAL at 48 weeks. However, the long-term treatment efficacy may have been overestimated in the model compared to a real-life setting, as observed in another adaptation of the DTG ARAMIS model to Canada using real-life data.
2 ng/l. Library preparation was performed using the Nextera XT DNA sample preparation kit (Illumina, San Diego, CA). Sequencing was performed on an Illumina MiSeq 2000 sequencer with V3 chemistry using 2 ϫ 75-bp paired-end reads. Illumina sequencing resulted in 4,367,802 reads of an average length of 74. 31 nucleotides, giving a total 324,574,495 nucleotides. These generated reads were assembled using Velvet (8) and computed using CLC Workbench version 8. 5. Two hundred forty con-tigs, giving a genome of 4,929,307 bp with a GϩC% of 59. 3%, were obtained from these raw data and then annotated using the RAST server (http://rast. nmpdr. org/). The RAST system predicted 4,522 coding sequences involved in essential functions, such as cell wall synthesis or RNA/DNA metabolism. One hundred ninety-eight coding sequences (CDSs) were predicted in cell wall and capsule synthesis, with 106 involved in virulence, disease, and defense; 38 involved in cell division and cell cycle; 153 involved in fatty acid and lipid metabolism; 134 involved in the stress response; and 216 and 231 involved in protein and RNA metabolism, respectively.
High content analysis (HCA) was performed in a Scan ∧ R automated microscope station (Olympus, Hamburg, Germany), and nuclear (DAPI) and cytoplasmic (Texas-Red) staining areas were quantified for GR intensity (AlexaFluor488) by Scan ∧ R software, with at least 2500 cells per slide analyzed in each compartment  [2, 3, 44, 45]. To measure the area and circularity in individual cells, the Scan ∧ R phase contrast images were processed using NIH ImageJ 2. 0 software (Bethesda, MD). Briefly, circularity was measured using the formula 4 * area/perimeter 2. A value of 1. 0 indicates a perfect circle. As the value approaches 0. 0, it indicates an increasingly elongated shape  [2, 3, 46].
The nuclear and cytoplasmic compartments were then fractionated and their lysates studied by Western blot with anti-GR antibody. Anti--tubulin (-tub) and -p53 antibodies are controls for the correct cytoplasmic (a) and nuclear (b) compartment fractionation, respectively, in the representative blots ( = 3). Quantitation of cytoplasmic (c) and nuclear (d) GR protein by densitometry. Data are represented as mean ± SEM. #  < 0. 05, differences in cytoplasmic GR protein content between cells treated with 16 h veh/16 h 5 ng/mL IL-1 (c2), 16 h veh/16 h 25 ng/mL IL-1 (c3), 32 h 5 ng/mL IL-1 (c4), 32 h 25 ng/mL IL-1 (c5), or 30 h veh/2 h DEX (c6), compared with 32 h vehicle-treated cells (c1). ¶  < 0. 05, difference in cytoplasmic GR protein levels between cells treated with 5 ng/mL (c2) and 25 ng/mL (c3) IL-1 for the last 16 h.