dataesr/scientific-paragraphs-categorization huggingface dataset:
The slides were thoroughly washed with PBS between each incubation step. Immunocomplexes were finally visualized by exposure to the diaminobenzidine chromogen (DAB; BioGenex, Fremont, CA, USA) in the presence of H 2 O 2. After rinsing, the sections were counterstained with luxol fast blue and mounted with a synthetic medium. To exclude antigen-independent staining, the incubation step with primary antibodies was omitted from the protocol as negative controls. In all cases, these controls were negative (data not shown). The specificity of gal-1 and gal-3 antibodies was validated by western blotting in different thyroid cancer cell lines (B-CPAP, FTC133C and 8505C cell lines derived from papillary, follicular and anaplastic thyroid carcinoma respectively) reporting immunoreactive band for gal-1 at 14 kDa and for gal-3 at 26 kDa (data not shown).
Statistical analysis. Groups of data were compared using the non-parametric Mann-Whitney test. The diagnostic performances of single or combined immunomarkers and the identification of the optimal cut-off points for the diagnosis of malignancy were evaluated using the receiver operating characteristic (ROC) curves and the assessment of the area under the ROC curve (AUC). The specificity, sensitivity, positive predictive value (PPV) and negative predictive value (NPV) of markers, alone or combined, were evaluated from crosstabs based on cut-off points and significance were calculated using the Fisher's exact test. P-value <0. 05 was considered as significant. Statistical analyses were performed with IBM SPSS Statistics 23 (IBM, Ehningen, Germany).
001, Fisher's exact test). HBME-1 and TPO exhibited good sensitivities (88 and 83%, respectively) and good specificities (79 and 80%, respectively) (Table  I ). Statistical analysis for all possible permutations using the five markers to discriminate between FA and PC was shown in Table  II. Of note, as TPO is a negative diagnostic marker for cancer, we used its inverse score (6-score) to combine it to others, and mean scores (0-6) were calculated for all combinations. The diagnostic performance of the combination of markers was evaluated by comparing areas under the ROC curves. The data revealed that the combination of gal-3/CK19/HBME-1 exhibits the highest performance to assess the diagnosis of malignancy (AUC=0. 994, cut-off >2. 5) (Table  II  and Fig. 3B ). The sensitivity, specificity, PPV and NPV were also calculated for the panel of combined markers.
Acknowledgements The study received financial support from the  University of Mons  (Mons, Belgium). We thank  Dr Köhrle  ( Institute of Experimental Endocrinology of the Charité, Humboldt University, Berlin, Germany ) and  Professor C. Maenhout  ( IRIBHM ULB, Brussels, Belgium ) for providing the FTC133C and 8505C cell lines (derived from follicular and anaplastic thyroid carcinoma respectively).
ncbi. nlm. nih. gov/Blast. cgi?PAGE_TYPE= BlastSearch). Alignments between cDNA and amino acid sequences of all clones and C. elongatus pgp-9 (A. N. KJ701410. 1) were created using Clustal Omega, and percentage identity calculated. A maximum likelihood tree with 500 bootstraps using a kimura 2-parameter model, was constructed comparing DW1 A1-5 and B1-5, C. elongatus pgp-9 (A. N. KJ701410. 1), H. contortus pgp-9 (A. N. JX430937. 1), T. circumcincta pgp-9 (A. N. FR691848. 1), C. elegans pgp-9 (C47A10. 1 wormbase i. d. ) and Caenorhabditis briggsae pgp-9 (XM_002638567. 1) created using MEGA version 6. 06 software.
N. M21017); Strongyloides stercoralis, (A. N. M84229); and Enoplus brevis, (A. N. U88336). Primers were as follows; 18SRTf 5′ GATTGATTCT GTCAGCGCTATA 3′ and 18SRTr 5′ TAATGAGCCGTTCGCAGT 3'. A standard consensus synthetic 99 bp 18S template corresponding to the cyathostomin species above, was manufactured by Sigma-Aldrich, UK. For pgp-9, primers were designed using Primer 3 version 4. 0. 0 (http:// primer3. ut. ee/) based on the sequence data from DSW A1. The primers with the best thermokinetic parameters were chosen and aligned with all 10 sequenced pgp-9 sequences and C. elongatus pgp-9 (A. N. KJ701410. 1), degenerate primers were designed to maximise amplification of pgp-9 from multiple cyathostomin species. The degenerate primers for pgp-9 were PGP9RTF 5′ AYATTGGGCTYGGTCTTGCT 3′ and PGP9RTR 5′ ACCGTTCCYCCTTTCATCGT 3'.
Duplicates were run for each standard concentration and a non-template control (dH 2 O) was included. The plate was run on a DNA Engine Opticon 2 Continuous Fluorescence detector (BioRad), with the reaction conditions: 95°C for 10 min, followed by 35 cycles of 95 °C for 15 s, 53 °C for 30 s and 72 °C for 15 s. The standard curve was repeated with the addition of serial dilutions of cDNA from DSW. Analysis of cDNA concentration, showed that pgp-9 detection was best at a concentration of 4 ng/μl. The optimised real time PCR was also run on cDNA from Cylicocyclus nassatus, Cyathostomum pateratum and Cyathostomum catinatum parasites to ensure that the assay could detect pgp-9 from a range of cyathostomin species (data not presented). 2. 3. Evaluation of pgp-9 transcript levels after ivermectin exposure of third stage larvae from mixed species cyathostomin populations of differing ivermectin sensitivity A total of ∼800,000 and ∼1.
Analysis of real time PCR data Raw data from the real-time PCR was evaluated using Opticon Monitor 3 version 3. 1. 32. 0 software. Standard graph correlations were examined and melting curves observed for each sample; those that did not have a single peak at the expected temperature were excluded from further analysis. Raw data from the qPCR reactions were entered into a Microsoft Excel spreadsheet. The percentage genomic contamination in each sample was calculated from the reverse transcriptase negative control for the raw 18S data; this was used to correct the raw data for 18S and pgp-9 so that genomic DNA was not counted. The average copy number between each technical repeat was taken for each sample for 18S and pgp-9, and the relative transcript level of pgp-9 gene compared to the 18S gene, calculated for each biological repeat.
1 ) indicated with a 100% bootstrap probability that the sequences from DSW are more closely related to C. elongatus than to sequences from other nematode species. For the 10 sequences from DSW, there was an 80% bootstrap probability that these constitute a single cluster forming a sister group to C. elongatus pgp-9. Within this cluster, there were few differences between sequences and it was unlikely that these represented phylogenetically distinct sequences from different species, as reflected by the lower bootstrap values. The alignment of deduced amino acid coding sequences for the 10 DSW sequences and the corresponding gene region of C. elongatus, is shown in Supplementary Fig. 1. The sequence revealed the typical domain arrangement of one half of the P-gp gene with an ABC transporter transmembrane domain containing transmembrane helices followed by the first part of the first nucleotide binding domain containing the highly-conserved Walker A/ P loop (CDD accession number cd03249).
Discussion This study demonstrated that pgp-9 mRNA is upregulated in cyathostomins with phenotypic ML resistance, and that P-gp inhibitors increase the effect of IVM against these ML-resistant cyathostomins in a LMIT. Taken together, this suggests a role for P-gps in IVM resistance in these nematodes, and raises the possibility that P-gp inhibitors could be used in equids, in combination with IVM, to increase efficacy against IVM-resistant cyathostomin populations, as has been done in sheep and cattle  (Lifschitz et al. , 2010a (Lifschitz et al. , , 2010b)). In this study, to design a real-time PCR assay to measure pgp-9 transcript in cyathostomins, pgp-9 cDNA was amplified from a mixed species cyathostomin population. Preliminary analysis of the data in a maximum likelihood phylogenetic model predicted with 100% certainty that there was a true difference between the sequences defined in this population and the previously characterised C.
Acknowledgements The authors would like to acknowledge  Claire McArthur ,  Marie Mitchell  and  Valerie Relf  at the  Moredun Research Institute  for their assistance with optimisation of in vitro bioassays;  Nikki Stradling  and  Liz Hazell-Smith  at the  Donkey Sanctuary UK  for their assistance with sample collection; Carol Laidlaw at the  National Trust  for facilitating sample collection from Konik horses; and  Catherine Hartley  at the  University of Liverpool  for her assistance in the laboratory.
Florescu et al's meta-analysis included data on 1756 solid-organ transplant patients that were evaluated for hypogammaglobulinemia and subsequent posttransplant infections. Within the first year posttransplantation, the rate of hypogammaglobulinemia (IgG <7 g/L) was 45% (95% CI: 0. 34-0. 55), the rate of mild hypogammaglobulinemia (IgG = 4-7 g/L) was 39% (95% CI: 0. 22-0. 56), and severe hypogammaglobulinemia (IgG <4 g/L) developed in 15% (95% CI: 0. 08--0. 22). Hypogammaglobulinemia occurred in 40% of kidneytransplant recipients  (14). In addition, the odds ratio of a respiratory infection (OR = 4. 83; 95% CI: 1. 66--14. 05; P = 0. 004), cytomegalovirus (OR = 2. 40; 95% CI: 1. 16--4. 96; P = 0. 02), Aspergillus (OR = 8. 19; 95% CI: 2. 38--28. 21; P = 0. 0009) or other fungal infections (OR = 3.
Granularity of HMGB1-GFP and streptavidin-AF568 was quantified after the cells were exposed to biotin (C). (D) HMGB1 releasing agent mitoxantrone (MTX, 2 µM) induced the exodus of HMGB1 only in the presence of biotin. Cytoplasmic HMGB1 was quantified after the cells were exposed to MTX either in the absence or presence of biotin (E). Data are reported as means ± SEM at 24 h post treatment (n = 4; *P < 0. 05, **P < 0. 01, and ***P < 0. 001, two-tailed Student's t test, compared to control cells). Scale bar = 10 µm. cause an increase in histone acetylation, while none of the other agents did so (Fig. 8 ). One physiological cellular state in which HMGB1 is released from the nucleus is mitosis where HMGB1-SBP-GFP can be found in a cytoplasmic location, provided that biotin has been added to the cells to unlink reporter and hook (Fig.
Stable plasmid transduction. Lentiviral particles were produced using the ViraPower ™ Lentiviral Packaging Mix (Thermo Fisher Scientific, Waltham, MA) according to the manufacturers' protocol. U2OS cells were infected with the RUSH hook streptavidin-NLS3-bearing lentiviral particles and following the transduced cells were selected for 2 weeks under the continuous presence of G418 (0. 5 mg/mL). U2OS-NLS3 hook clones were generated by single cell-sorting on a FACS ARIA III cytofluorometer (Becton Dickinson, San José, CA, USA), and the most potent U2OS-NLS3 hook clone was selected by immunofluorescence staining. For the expression of HMGB1 reporter, U2OS NLS3 hook cells were further transfected with RUSH reporter-HMGB1-SBP-GFP-bearing (HMGB1 accession number: NM_002128. 4) lentiviral particles by means of ViraPower ™ lentiviral expression system.
edge 5. 5 camera (PCO, Kelheim, Germany) and a 20 X PlanAPO objective (Nikon, Tokyo, Japan) was used to acquire at least 4 view fields of each well. Following images were processed with the MetaXpress image analysis software (Molecular Devices). Images were segmented using the built-in custom module editor to identify nuclei (based on Hoechst 33342 signal), and cytoplasmic regions (based on CellTracker ™ Orange CMTMR fluorescence), allowing the quantification of nuclear/cytoplasmic HMGB1-GFP intensity. Data were mined and statistically evaluated using the freely available software R (https://www. r-project. org). Data were intra-plate normalized by evaluating the ratio to plate means and inter-plate normalized by calculating Z-scores. Flow cytometric analysis of cell cycle. U2OS cells were synchronized in G1 phase by double thymidine blockade and washed twice before treatment with SAHA, Azacitidine, Decitabine, Oxaliplatin, Fenbendazole and Oxibendazole for additional 24 h.
The concentration of extracellular HMGB1 in cell culture supernatant and murine blood plasma was quantified, by mean of the HMGB1 ELISA KIT (Tecan, Switzerland) following the manufactures' instructions. Statistical analyses. Unless otherwise specified, data are reported as mean ± SEM. Statistical significance was analyzed using the Student's-test. Differences in treated and control cells were considered to be significant if * p < 0. 05, ** p < 0. 01 *** p < 0. 001.
Cytoplasmic HMGB1 was quantified after the cells were exposed to MTX either in the absence or presence of biotin (E). Data are reported as means ± SEM at 24 h post treatment (n = 4; *P < 0. 05, **P < 0. 01, and ***P < 0. 001, two-tailed Student's t test, compared to control cells). Scale bar = 10 µm.
Acknowledgements PL is supported by the Chinese scholarship council, LZ obtained a fellowship from  la Ligue contre le Cancer, FP  and GB are supported by The  Institut Curie ,  CNRS  and as well as  CelTisPhyBio Labex  ( ANR-10-LBX-0038 ) part of the  IDEX PSL  ( ANR-10-IDEX-0001-02 PSL ), GK and LZi are supported by the  Ligue contre le Cancer  (équipe labelisée);  Agence National de la Recherche (ANR) -Projets blancs ;  ANR  under the frame of E-Rare-2, the  ERA-Net for Research on Rare Diseases; Association pour la recherche sur le cancer (ARC) ;  Cancéropôle Ile-de-France ;  Institut National du Cancer (INCa) ;  Institut Universitaire de France ;  Fondation pour la Recherche Médicale ; the  European Commission (ArtForce) ; the  European Research Council (ERC) ; the  LeDucq Foundation ; the  LabEx Immuno-Oncology ; the  RHU Torino Lumière , the  SIRIC Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE) ; the  SIRIC Cancer Research and Personalized Medicine (CARPEM) ; and the  Paris Alliance of Cancer Research Institutes (PACRI).
NAB2 increases type I IFN responses in vivo To examine whether the differential response induced by NAB2 and poly(I:C) was detectable in vivo, we injected mice with the two PRR agonists, and 4 h later we measured the cytokine levels in the serum. Again, while we did not detect a statistical significant difference in IL-6 production (data not shown), NAB2 induced a markedly increased IFN-α serum expression, compared to poly(I:C) (Figure  4 ). Of note, we did not observe any signs of toxicity following NAB2 injections. Thus, NAB2 is more efficient than poly(I:C) in promoting a type I IFN response, in vitro as well as in vivo.
Data were analyzed using FlowJo vX. 0. 7 software (Tree Stat, Inc. , Ashland, USA). For the flow cytometry analysis of human monocytes, cells were incubated for 20 min with human FcR Blocking Reagent (Miltenyi Biotec) and APClabeled anti-CD86 (clone FM95, Miltenyi Biotec). Dead cells were labeled by automatic propidium iodide staining before cell acquisition recorded using MACSQuant cytometer (Miltenyi). Data were analyzed using Kaluza software (Beckman Coulter). Cytokine levels in the supernatant of stimulated cells and serum of treated mice were quantified by sandwich ELISA, following the kit protocols (BD Biosciences and BioLegend, San Diego, CA). For human monocytes, the supernatant of stimulated cells was taken and IFN-alpha levels were measured (Human IFN-alpha Simplex, ProcartaPlex, eBiosciences) on a MAGPIX device (Luminex XMAP Technologies).
VaxigripTetra Ò (Sanofi Pasteur, Lyon, France) is a quadrivalent split-virion inactivated influenza vaccine (IIV4) containing two B-lineage strains approved in the European Union and Taiwan in 2016 for individuals 3 years of age. Here, we describe an observer-blind, randomized, controlled, multicenter trial study evaluating the immunogenicity and safety of the Northern Hemisphere 2015-2016 formulations of IIV4 and the licensed split-virion trivalent inactivated influenza vaccine (IIV3) in the Republic of Korea (ClinicalTrials. gov no. NCT02550197). The study included 300 Korean adults 18-60 years of age randomized 2:1 to receive a single injection of IIV4 or IIV3. For each of the four vaccine strains in IIV4, 21 days after vaccination, geometric mean post-/pre-vaccination ratios of hemagglutination inhibition titers were 3.
Study design This was an observer-blind, randomized, controlled trial (Clini-calTrials. gov no. NCT02550197) conducted at five centers in the Republic of Korea. The objectives of this study were to evaluate the immunogenicity and safety of the IIV4 and IIV3 Northern Hemisphere 2015-2016 formulations and the compliance of IIV4 with the requirements of the CHMP former Note for Guidance CPMP/BWP/214/96  13  as requested by the Republic of Korea Ministry of Food and Drug Safety.
Safety and reactogenicity Unsolicited AEs and SAEs were collected according to the International Committee for Harmonization E2A Guideline for Clinical Safety Data Management: Definitions and Standards for Expedited Reporting. 17 Investigators recorded unsolicited AEs, SAEs and AESIs occurring within 21 days. AESIs included anaphylaxis, Guillain-Barr e syndrome, encephalitis/myelitis, neuritis,.
Acknowledgments This work has been presented in part at the  CROI 2016 in Boston (Abstract 351 ) We particularly thank the OPTIPRIM study participants and investigators for their valuable contribution. We also thank  Laurent Tran ,  Georges Nembot ,  Ingrid Be  ´nard, Celine Chaillot,  Theodora Harambure  for data monitoring,  Sandrine Couffin-Cadiergues  and  Juliette Saillard  from the  Clinical Research Department at ANRS , and  David Young  for editing the manuscript. We thanks the members of the  OPTIPRIM ANRS-147 Study Group , lead author,  Antoine Che  ´ret, antoinecheret@aphp. fr. CHRU Saint-Jacques (Besancon ),  Service de Medecine Interne: B. Hoen, C. Bourdeaux. Hopital de Bicêtre (Paris) ,  Service de Medecine Interne et Maladies Infectieuses :  J. F. Delfraissy ,  C. Goujard ,  I.
Microscopy Images were taken with a Nikon Eclipse E800, digital camera DXM1200, at 203 or 403 magnification and at a resolution of 1,280 3 1,024, and analyzed with the ACT-1 (v. 2) software. NK Cell Isolation and Culture NK cells were isolated from peripheral blood mononuclear cells derived from buffy coats obtained from 14 healthy volunteer donors with donor consent and approval from the Ethics Committee of the Canton de Vaud (project authorization no. P-108). NK cells were cultured in RPMI1640 (Gibco) supplemented with 10% heat-inactivated human serum (Sigma and Life Technologies), 1% PS, and IL-2 (10 ng/mL; R&D Systems; NK medium; see Supplemental Experimental Procedures).
ACKNOWLEDGMENTS We thank  Jean-Christophe Stehle  at the  Mouse Pathology Facility  for assistance with immunohistochemical staining and  Prof. Christophe Galland  for helpful suggestions. This work was supported by the  Swiss National Science Foundation  grants  310030_150024  and  310030_169563  (I. S. ) and an  MD-PhD Fellowship   323630_151474/1  (S. G. ).
Common features to all results are that a helix is predicted downstream of the PDZ domain (residues 605-614) and that the linker after residue 615 does not adopt any regular secondary structure. We have previously reported the resonance assignments of the linker (residue 605 to 637) for the PDZ-linker and the bidomain constructs (Fig. 1 ). Using the TALOS-N approach  17  based on the resonance frequencies, the stretch of residues 605-614 is predicted as a β-strand with a low probability (<0. 6) below the significant threshold (Fig. 2b ). Thus, the linker is predominantly disordered in solution. In addition, we used IUPred program from IUPred web server (http://iupred. enzim. hu)  18 to determine the ordered or disordered characteristics of the linker in the PTPN4 PDZ-PTP. Interestingly, IUpred predicts a disorder tendency in the linker (residues 621 to 633) (Fig.
3b  is representative of pattern also obtained with the other limited proteolysis conditions. The bands corresponding to the major proteolysis products were identified by mass spectrometry. Surprisingly, chymotrypsin, trypsin and subtilisin cleave only in the PDZ or PTP domains, while the linker is only cleaved by the non-specific papain in its C-terminal part. The observation that the linker is rather resistant to the proteolysis, suggests that the accessibility of this region is sufficiently low to protect it from the hydrolysis of peptide bonds. The linker-PTP construct is also rather resistant to the proteolysis (data not shown). We previously collected dynamical parameters in solution of the bidomain PDZ-PTP C/S (inactive enzyme by mutation of the catalytic cysteine) and of the PDZ-linker constructs both in the absence of PBM (unliganded) and with a PBM bound (liganded) to the PDZ domain.
Kinetics experiments of PTPN4 bidomain constructs were first performed in the absence of PBM corresponding to the inhibited state of the phosphatase to determine catalytic parameters of the PTPN4 mutants. We showed that    1. Kinetic parameters of the hydrolysis of pNPP by PTPN4 constructs. The experimental errors are derived from a bootstrap analysis except those with an asterisk that come from three independent experiments as described previously  13. PDZ-PTP mutants dephosphorylate the pNPP substrate following Michaelis-Menten kinetics as previously reported for the PDZ-PTP WT and linker-PTP (Fig. 5a ). In all cases, we observed a clear substrate inhibition effect and, therefore, we employed a corrected Michaelis-Menten equation taking into account this effect. The Michaelis constant (K M ) and the turnover number (k cat ) values obtained by fitting the experimental data are listed in Table  1.
The bands corresponding of the major proteolysis products were then identified by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Sequence alignment. Sequence of PTPN4 (accession number NP_002821. 1) was used as query on the InterEvolAlign server  19  to retrieve one single homolog per species assessed as probable ortholog through a reciprocal blast search procedure against the non-redundant database. Retrieved full-length sequences were re-aligned using MAFFT  23  and displayed using Jalview  24.
Acknowledgements We thank  Pascal Lenormand  ( Structural Mass Spectrometry and Proteomics Unit ) for its technical expertise. PM was supported by grants from the  Ministère de l'Enseignement Supérieur et de la Recherche  and the  Fondation pour la Recherche Médicale  [FDT20130927999]. KS was a recipient of  Erasmus + grant. Work was partly supported by grants from the  Italian Ministero dell'Istruzione dell'Università e della Ricerca  ( Progetto di Interesse 'Invecchiamento ' to S. G. ) and  Sapienza University of Rome  ( C26A155S48  and  B52F16003410005  to S. G) and the  international division of Institut Pasteur.
Study inclusion criteria Included cases met either the MRC ('pathologically defined', 'clinically defined' or 'possible'), Griggs et al ('definite' or 'possible') or ENMC ('clinicopathologically defined', 'clinically defined' or 'probable') diagnostic criteria for IBM and had sera available for anti-cN-1A antibody testing. 9 11 ta collection methodology Swedish, French and Dutch ('non-UK') patients were identified from clinical databases. Researchers blinded to anti-cN-1A antibody status (AR, MTJP, KRG, KM) reviewed the medical records and retrospectively completed a standardised data collection pro forma. UK patients were identified from six centres contributing to the UKMYONET research study, coordinated by The University of Manchester. As part of this study, data are captured using a standardised pro forma at the time of study recruitment (ie, before serological test results are available).