conversation_id int64 1 7.5k | category stringclasses 3
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1 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nDown-regulation of interferon regulatory factor 4 gene expression in leukemic cells due to hypermethylation of CpG motifs in the promoter region \nAlthough the bcr-abl translocation has been shown to be the causative genetic aberration in chronic myeloid leukemia (CML), there is m... |
2 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation events from the text:\nINTRODUCTION\nChronic myeloid leukemia (CML) is a clonal myeloproliferative disorder with a typical three phased course (chr... |
3 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nCell lines\nK-562, Jurkat and U-937 were obtained from the ATCC (American Type Culture Collection, Rockville, USA) and EM-2, LAMA-84, CML-T1, BV-173, SD-1 and RPMI-8226 from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany). All cell lin... |
4 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Cell culture and stimulation\nAll cell lines were maintained at 5% CO2 in RPMI 1640 medium with 1% glutamine (Gibco/BRL Eggenstein, Germany) supplemented with 10% fetal calf serum (Gibco/BRL), 1% penicillin/streptomycin (Biochrom, Berlin, Germany). When indicated, cells were treated wi... |
5 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nSequencing of the IRF-4 promoter\nFor analysis of the IRF-4 promoter region for permanent aberrations such as insertions/deletions or mutation, we PCR-amplified two fragments from genomic DNA, which was extracted from depicted cell lines with a commercial kit (Qiagen, Hilde, Germa... |
6 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract events from the following text: \"Expression analysis\nTo analyze the IRF-4 transcriptional level, RNA was extracted from cells using the commercial RNAzol-kit (Paesel, Frankfurt, Germany). An aliquot of 1 mug total RNA was used for cDNA synthesis as described previously (27). RNA expression... |
7 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Methylation-specific restriction-PCR-assay\nDNA was extracted with a commercial kit (Qiagen) as recommended. Since the restriction ability of several endonucleases is inhibited by methylation of their target sequence, we used methylation-sensitive enzymes HpaII and HaeII-isochizomer Bs... |
8 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nBisulfite treatment\nDNA was extracted as described above. Bisulfite treatment of DNA, leading to conversion of unmethylated cytosine to uracil residues and no change of methylated cytosine residues, was performed as described as follows. Briefly, 1 microg of DNA and 2 microg of p... |
9 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nIn vitro methylation and reporter gene assays\nThe IRF-4 promoter-reporter gene construct was generously provided by J.Hiscott (31). Constructs were methylated in vitro with CpG Methylase (M.Sss I) as recommended by the manufacturer (NE Biolabs) and complete methylation was checke... |
10 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation events from the text:\nAbsence of IRF-4 expression in leukemia cells is not due to promoter alterations\nWe have previously demonstrated a lack of ... |
11 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nIncrease of IRF-4 expression in hematopoietic cells after demethylating treatment\nWe next analyzed whether promoter methylation could be responsible for down-regulation of IRF-4 expression. A region including exon1 in the IRF-4 promoter exhibited a large number of CpG-rich sequen... |
12 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nMethylation-sensitive enzymes do not cut specific sites in the IRF-4 promoter in hematopoietic cells\nTo further investigate promoter methylation as a regulatory mechanism of IRF-4 gene expression, restriction-PCR-assays were performed (20,24), where only methylated DNA would not ... |
13 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Specific CpG sites in the IRF-4 promoter are methylated in hematopoietic cells\nIn order to exactly map the methylation sites within the IRF-4 promoter, we treated DNA of Jurkat, CML-T1, U-937, K-562 and EM-2 cells as well as of SD-1, RPMI-8226 and BV-173 control cells with bisulfite, ... |
14 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"In vitro methylation of an IRF-4 promoter-reporter construct decreases its activity\nTo provide evidence for a direct effect of methylational status on IRF-4 promoter activity we performed reporter gene assays with IRF-4 promoter constructs before and after their in vitro methylation. ... |
15 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract events from the following text: \"mRNA expression of DNA methyltransferases and methyl-CpG-binding proteins may not be associated with IRF-4 promoter methylation\nSince abundance of DNMT and MBP contribute to promoter regulation via methylation (25,26,28), we studied their mRNA expression to... |
16 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation events from the text:\nDISCUSSION\nMany genetic lesions are known to influence gene expression of tumor suppressor genes. Whereas mutations and del... |
17 | EE | bionlp_st_2011_ge | en | [
{
"human": "Foxp3 Represses Retroviral Transcription by Targeting Both NF-kappaB and CREB Pathways \nForkhead box (Fox)/winged-helix transcription factors regulate multiple aspects of immune responsiveness and Foxp3 is recognized as an essential functional marker of regulatory T cells. Herein we describe downst... |
18 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nSynopsis\nOver the past several years, mounting evidence has shown that immune tolerance in healthy individuals can be maintained by a population of T lymphocytes known as regulatory T cells (Tregs). As a component of this system, a protein known as Foxp3 has been shown to be abso... |
19 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract events from the following text: \"Introduction\nImmunological tolerance to self-antigens is the result of the deletion of self-reactive T lymphocytes in the thymus (central tolerance) and suppression of the activation of potentially self-reactive T lymphocytes in the periphery (peripheral to... |
20 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract events from the following text: \"Foxp3 Suppresses NF-kappaB Dependent Transcriptional Activation\nTo ascertain the molecular mechanisms by which Foxp3 functions to promote the regulatory function of CD4+CD25hi T cells, we first confirmed the function of Foxp3 as a repressor of activation of... |
21 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nThe Carboxyl-Terminal FKH Domain Is Not Required for Suppression of NF-kappaB Activation in T Cells\nTo define the requirements of Foxp3 with respect to inhibition of NF-kappaB-dependent transcription, we utilized a mutant of Foxp3 lacking the FKH domain (Figure 2A) [16], similar ... |
22 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nFoxp3 Suppresses HIV-1 Gene Expression in Part through Blocking Activation of NF-kappaB\nIf Foxp3 functions as a repressor of NF-kappaB-dependent gene expression, then we hypothesized that Foxp3 overexpression could selectively down-regulate transcription from promoters previously... |
23 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nThe Transactivation Functions of HTLV-I Tax Are Suppressed by Foxp3\nPrevious studies by Bettelli and colleagues have demonstrated that Foxp3 can repress both the basal levels of NF-kappaB activation as well as tumor necrosis factor-alpha-stimulated NF-kappaB activation [15]. Our ... |
24 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Increased Foxp3 Protein Expression Is Associated with Low HTLV-I Proviral Load\nSince Foxp3 is expressed almost exclusively within CD4+CD25+ T cells, a major viral reservoir for HTLV-I [33], it was important to determine whether there was an association between Foxp3 and HTLV-I replica... |
25 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation events from the text:\nCREB Is a Target for Transcriptional Repression by Foxp3\nAlthough Foxp3 could down-regulate Tax-dependent transactivation o... |
26 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract events from the following text: \"Foxp3 Antagonizes CREB Transcriptional Activation by Disrupting Coactivator Recruitment\nStimulation of CREB-dependent transcription by reagents that activate adenylate cyclase and increase cAMP levels (e.g., forskolin) increase the transactivation potential... |
27 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract events from the following text: \"Discussion\nIn the present study, we show that Foxp3 functions as a potent repressor of NF-kappaB- and CREB-dependent transcriptional activation. Furthermore, the carboxyl-terminal FKH domain appears to be dispensable for mediating these effects, at least in... |
28 | EE | bionlp_st_2011_ge | en | [
{
"human": "Cell culture.\nHEK 293T cells were cultured in Dulbecco's modified Eagle medium (Invitrogen, Carlsbad, California, United States). Jurkat T cells and primary human CD4+ T cells were cultured in RPMI-1640 medium (Invitrogen). Media were supplemented with 2 mM L-glutamine, 100 U/ml penicillin, 100 mug... |
29 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nPatients and cell preparation.\nPBMCs were prepared by centrifugation over Ficoll-Hypaque gradients (BioWhittaker, Walkersville, Maryland, United States) from eight HAM/TSP patients and eight ACs, and the cells were viably cryopreserved in liquid nitrogen until tested. HAM/TSP was... |
30 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract events from the following text: \"Plasmids.\nExpression vectors encoding human Foxp3 (pCMV-Foxp3-IRES-EGFP) and human Foxp3 lacking the forkhead (FKH) domain (pCMV-DeltaFKH-IRES-EGFP) were generous gifts from S. Ziegler (Benaroya Research Institute). pEGFP-C2 was provided by I. Lipinski (NID... |
31 | EE | bionlp_st_2011_ge | en | [
{
"human": "Isolation of primary human CD4+ T cells.\nCD4+ T cells were isolated from cryopreserved healthy donor PBMCs by negative selection with the CD4+ T Cell Isolation Kit II (Miltenyi Biotech, Bergisch Gladbach, Germany) according to manufacturer's guidelines. Purity of negatively selected CD4+ T cells wa... |
32 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Transient expression and luciferase assays.\nHEK 293T cells were plated at a density of 5 x 105 cells/well in six-well culture plates (BD Biosciences, San Diego, California, United States) 1 d prior to transfection with the appropriate plasmid DNA (~2 mug total) using FuGene 6 transfec... |
33 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Foxp3 and HTLV-I Tax expression analysis by real-time RT-PCR.\nReal-time RT-PCR analysis of Foxp3 and HTLV-I Tax expression was performed as previously described [8,47]. Briefly, total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, California, United States) according t... |
34 | EE | bionlp_st_2011_ge | en | [
{
"human": "Real-time PCR.\nReal-time PCR analysis of HTLV-I (Tax) proviral load was performed as previously described [47,50]. DNA was extracted from 1 x 106 cells using Puregene DNA Isolation Kit (Gentra, Minneapolis, Minnesota, United States), and 100 ng of the sample DNA solution was analyzed by this system... |
35 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nWestern blot analysis.\nHEK 293T cells were plated at a density of 5 x 105 cells/well in six-well culture plates (BD Biosciences) 1 d prior to transfection with the appropriate plasmid DNA (2 mug total) using FuGene 6 transfection reagent (Roche). Cells were harvested 24 h posttra... |
36 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract events from the following text: \"Transcription factor DNA-binding analysis (TF-ELISA).\nCREB-1 and ATF-2 DNA-binding activity was analyzed with the TransFactor Profiling (Inflammation 1) Kit (BD Biosciences) according to the manufacturer's protocol. Nuclear extracts were prepared from HEK 2... |
37 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nFlow cytometric analysis of Foxp3 protein expression.\nCryopreserved PBMCs from HAM/TSP patients or HTLV-I-infected ACs were thawed and washed with FACS buffer (1x PBS, 0.1% NaN3, 5% FBS). Cells (1.5 x 106) were fixed by sequential formaldehyde/methanol fixation as follows. Cells ... |
38 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nStatistical analyses.\nThe Mann-Whitney U test was used to compare the data between patients with HAM/TSP and AC.\nEven Type: Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation\nRole Type... |
39 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract events from the following text: \"EBV Latent Membrane Protein 1 Activates Akt, NFkappaB, and Stat3 in B Cell Lymphomas \nLatent membrane protein 1 (LMP1) is the major oncoprotein of Epstein-Barr virus (EBV). In transgenic mice, LMP1 promotes increased lymphoma development by 12 mo of age. Th... |
40 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation events from the text:\nIntroduction\nEpstein-Barr virus (EBV) is a ubiquitous gamma-herpesvirus that infects humans predominantly at an early age w... |
41 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"High Levels of LMP1 Expression Correlates with the Development of Lymphoma\nLMP1 expression in IgLMP1 mice was directed to B cells under the control of the Ig heavy chain promoter and enhancer. It has previously been shown that in these transgenic mice, LMP1 expression was restricted t... |
42 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nLMP1 Promotes B-1a Lymphomas That Can Escape Allelic Exclusion\nTo determine if LMP1 signaling affects B cell differentiation and to immunophenotype the lymphomas that arise from LMP1 expression, surface Ig expression of heavy chains (IgM, IgG, IgD) and light chains (kappa, lambda... |
43 | EE | bionlp_st_2011_ge | en | [
{
"human": "LMP1 Promotes B Cell Survival and Proliferation In Vitro\nPrimary B cell cultures can be maintained through CD40 ligation and supplementation with IL4 [32]. To investigate whether LMP1 affects primary B cell survival and proliferation, splenocytes were cultured in the presence or absence of IL4 and ... |
44 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Wild-Type and LMP1 Transgenic Lymphoma Cells Do Not Require IL4 and Stat6 Signaling\nTo investigate whether IL4 independence was due to endogenous IL4 expression, IL4 transcription was assessed by an Rnase protection assay (RPA). IL4 transcription was detectable with control RNA and fa... |
45 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nLMP1 Upregulates IL10 and Constitutively Activates Stat3\nTo identify cytokines that may contribute to the increased survival and growth of lymphomas, the expression levels of a panel of cytokines were screened on CD19+ MACS-purified B cells, using an RPA probe set for IL4, IL5, I... |
46 | EE | bionlp_st_2011_ge | en | [
{
"human": "LMP1 Activates Akt Signaling and Deregulates the Rb Cell Cycle Pathway\nLMP1 transformation of rodent fibroblasts requires activation of PI3K and Akt [5]. Additionally, activated pAkt is frequently detected in NPC and the neoplastic Reed-Sternberg cells of classical HD [39,40]. To determine if Akt s... |
47 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation events from the text:\nLMP1 Promotes Tumor Growth and Survival through Activation of Akt, NFkappaB, and Stat3 Pathways\nTo explore which pathways w... |
48 | EE | bionlp_st_2011_ge | en | [
{
"human": "Discussion\nThis study defines the oncogenic properties of LMP1 in promoting B cell lymphomagenesis. LMP1 transgenic mice have a higher incidence of lymphoma [26] and the progression to lymphoma correlates with higher expression levels of LMP1 (Figure 1A and 1B), suggesting that LMP1 is directly inv... |
49 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nTransgenic mice.\nGeneration of LMP1 mice under the Ig heavy chain promoter and enhancer have been described previously and were maintained as heterozygotes on a Balbc background [26]. LMP1 mice were genotyped by Southern blot and PCR analysis of tail DNA as described previously [... |
50 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nIsolation and growth of B cells.\nSplenocytes were prepared by homogenizing spleen tissue with two frosted slides and debris was filtered through a 100-mum cell strainer. Erythrocytes were lysed using 0.8% ammonium chloride solution (StemCell Technologies) for 10 min on ice and wa... |
51 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nMTS assay.\nThe 3-(4, 5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium inner salt (MTS) cell cytotoxicity/proliferation assays were performed using the CellTiter 96 aqueous one-solution cell proliferation assay (Promega), according to manufacture... |
52 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Immunohistochemistry.\nParaffin-embedded spleen sections were deparaffinized in Histoclear (National Diagnostics) and rehydrated in graded ethanol. Sections were antigen retrieved by microwaving in citrate buffer (pH 6.0) for 15 min (LMP1 staining) and 10 min (pStat3 staining). For LMP... |
53 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation events from the text:\nFlow cytometry.\nOne million splenocytes were stained with the appropriate primary antibody unconjugated or conjugated to FI... |
54 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation events from the text:\nRnase protection assay.\nTotal RNA was isolated from CD19+ MACS-purified B cells using the Rneasy midi purification kit with... |
55 | EE | bionlp_st_2011_ge | en | [
{
"human": "PCR analysis of kappa chain rearrangement.\nDNA was isolated from splenocytes using the Dneasy Tissue Kit (Qiagen), with Rnase treatment. PCR reactions contained 100 ng of genomic DNA, 0.2 muM each primer, 0.2 mM dNTPs, and 2.5 U Taq DNA polymerase (NEB) performed in 1X ThermoPol buffer (NEB). Prime... |
56 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nImmunoblot analysis.\nWhole cell lysates were prepared in radioimmunoprecipitation assay (RIPA) buffer (20 mM Tris-HCl [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with 2 mM phenylmethylsulfonyl fluoride, 1 mM Na3VO4, and 1:100 prote... |
57 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nAntibodies.\nFITC-conjugated goat anti-mouse IgM, rat IgG2akappa anti-mouse IgD (clone 11-26), rat IgG1kappa anti-mouse kappa (clone 187.1), rat IgG2bkappa anti-mouse lambda (clone JC5-1); PE-conjugated goat anti-mouse IgG; un-conjugated goat anti-mouse kappa and anti-mouse lambda... |
58 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Accession Numbers\nThe GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) accession number for the EBV genome sequence is AJ507799. The gene identifier for LMP1 is BNLF1.\"\nEven Types: Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative r... |
59 | EE | bionlp_st_2011_ge | en | [
{
"human": "High LMP1 Expression Correlates with the Development of Lymphoma\nLMP1 expression is shown by (A) immunoblotting of purified B cells (CD19+) and (B) immunohistochemistry staining of spleen tissue from wild-type (WT) and LMP1 transgenic mice. \n(A) Lymphomas are identified with a number (1-7). Arrows... |
60 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nLMP1 Promotes B-1a Lymphomas That Can Escape Allelic Exclusion\n(A) Flow cytometry analysis of splenocytes from a WT or LMP1 transgenic lymphoma for the pan-B cell (CD19), B-1a cell (CD5), and Ig heavy chain (IgM and IgD) and light chain (kappa and lambda) markers. Shown are the r... |
61 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nLMP1 Promotes B Cell Survival and Proliferation In Vitro\n(A) MTS assay of splenocytes from WT and LMP1 transgenic mice. Splenocytes were cultured in the presence (grey bars) or absence (black bars) of IL4 for 3 d. The results are the mean +/- SEM of triplicate samples averaged fr... |
62 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Summary of Analysis Performed on Wild-Type and LMP1 Transgenic Lymphomas\"\nEven Types: Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation\nRole Types: Cause, Theme, ToLoc, Site, AtLoc, CSite\... |
63 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Wild-Type and LMP1 Transgenic Lymphoma Cells Survive Independently of IL4/Stat6 Signaling in Culture\n(A) Rnase protection assay for IL4 mRNA from purified B cells (CD19+) from WT and LMP1 transgenic splenocytes. The L32 and GAPDH housekeeping genes were used as a loading control. Arro... |
64 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nLMP1 Upregulates IL10 Expression and Constitutively Activates Stat3\n(A) Relative expression of IL10, IL15, and IFNgamma mRNA in WT and LMP1 transgenic B cells (CD19+), as detected with an Rnase protection assay. Mouse lymphoma cell lines 967 and K46mu were used as controls. Expre... |
65 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nLMP1 Activates Akt Signaling and Deregulates the Rb Cell Cycle Pathway\n(A and B) Immunoblot analysis of purified B cells (CD19+) from the spleens of WT and LMP1 transgenic mice for Akt signaling, probing for (A) activated pAkt and downstream targets, including inactivated pGSK3al... |
66 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Akt, NFkappaB, and Stat3 Signaling Are Required for the Growth and Survival of Lymphoma Cells\nMTS assay of splenocytes from (A and B) WT or (C and D) LMP1 transgenic lymphomas and (E and F) LMP1 transgenic lymphoctyes. Splenocytes were cultured with or without inhibitors of NFkappaB (... |
67 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nAnalysis of Akt, NFkappaB, and Stat3 Pathways in Contribution to the Growth and Survival of Lymphoma Cells\n(A-D) Immunoblot analysis of wild-type and LMP1 transgenic lymphomas for Akt, NFkappaB, and Stat3 signaling after treatment with (A) an Akt inhibitor, triciribine, (B) an NF... |
68 | EE | bionlp_st_2011_ge | en | [
{
"human": "Lymphomas Are Clonal by kappa Light Chain Rearrangement\nPCR analysis of total spleen genomic DNA for the mouse kappa locus. Primers were designed to amplify all V-J rearrangements, including VJ1, VJ2, VJ4, and VJ5. Specific PCR products for the four rearrangements corresponding to the calculated si... |
69 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Click here for additional data file.\"\nEven Types: Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation\nRole Types: Cause, Theme, ToLoc, Site, AtLoc, CSite\nPlease extract events from the inpu... |
70 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nRunx3 and T-box proteins cooperate to establish the transcriptional program of effector CTLs \nActivation of naive CD8+ T cells with antigen induces their differentiation into effector cytolytic T lymphocytes (CTLs). CTLs lyse infected or aberrant target cells by exocytosis of lyt... |
71 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nINTRODUCTION\nNaive CD8+ T cells differentiate into effector CTLs with the ability to lyse antigen-bearing target cells by exocytosis of lytic granules containing perforin and granzymes, and to produce inflammatory cytokines such as IFN-gamma and TNF upon restimulation through the... |
72 | EE | bionlp_st_2011_ge | en | [
{
"human": "A cell culture system to monitor effector CTL differentiation\nWe used a simple cell culture system to examine the kinetics of effector gene expression during CD8+ T cell differentiation. Naive CD8+ T cells from P14 TCR transgenic mice were activated for 2 d with anti-CD3 and anti-CD28 or with splen... |
73 | EE | bionlp_st_2011_ge | en | [
{
"human": "Distinct expression kinetics of perforin and granzyme B during CTL development in culture\nOur experiments revealed clear differences in the kinetics of perforin, granzyme B, and cytokine expression during CD8+ T cell activation (Fig. 1). Naive T cells showed detectable expression of perforin mRNA a... |
74 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nDistinct kinetics of T-bet and Eomes expression during CTL differentiation\nThe T-box transcription factors T-bet and Eomes have been linked to the regulation of genes encoding effector cytokines (e.g., Ifng) and genes important for cytolytic function (e.g., Prf1 and GzmB) (20). W... |
75 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Perforin and granzyme B expression are not appreciably regulated by T-bet\nTo test the model outlined in the previous paragraph directly, we compared the expression of IFN-gamma, perforin, and granzyme B in CD8+ T cells from WT and Tbx21 (T-bet)-deficient mice. As expected (17, 21), na... |
76 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Runx3 controls multiple aspects of the CTL differentiation program, in part through induction of Eomes\nBecause Runx3 is highly expressed in peripheral CD8+ T cells, and because of the T-bet-Runx3 cooperation we observed earlier in CD4+ T cells (15), we examined the role of Runx3 in ef... |
77 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nRunx3 and T-box factors control a complex program of transcriptional regulation during CTL differentiation\nCollectively, these data provide evidence that Runx3, together with T-box factors, orchestrates a complex program of transcriptional regulation in differentiating CTL (Fig. ... |
78 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nAntibodies and reagents.\nThe following antibodies used for intracellular or surface stains were obtained from eBioscience: anti-IL-2, anti-IFN-gamma, anti-TNF, anti-granzyme B, anti-CD8, anti-CD25, and anti-CD44. Anti-CD69 was purchased from BD. For ChIP experiments, the anti-Eom... |
79 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Isolation and culture of primary CD8+ T cells.\nCD8+ T cells from 4-8-wk-old Tcra-/- x P14 TCR transgenic (Taconic), C57BL/6J WT, or Tbx21-/- (The Jackson Laboratory) mice were purified (>95% purity) by negative selection (Invitrogen) from pooled spleen and lymph node cells. CD8+ T cel... |
80 | EE | bionlp_st_2011_ge | en | [
{
"human": "Isolation of CD8+ T cells from Runx3-/- mice.\nRunx3-deficient T cells fail to silence CD4 expression normally (Fig. S1) (12, 13). We therefore further fractionated the positively selected CD8+ T cells from Runx3 KO mice into CD8+CD4- SP or CD8+CD4+ DP cells by separation using anti-CD4 magnetic bea... |
81 | EE | bionlp_st_2011_ge | en | [
{
"human": "FACS-based cytotoxicity assay.\nTo measure cytotoxicity, EL4 thymoma target cells were loaded with 0 or 1 muM Gp33 peptide for 2 h before a 2-h coincubation with P14 CD8+ T cells at the effector-to-target ratios indicated in the figures in 96-well round-bottom plates. After the coincubation period, ... |
82 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nCytokine and surface marker staining.\nTo assess cytokine production, cells were restimulated with 10 nM PMA + 1 muM ionomycin for 6 h (unless indicated otherwise in the figures), and intracellular cytokine stains were performed as previously described (28). To detect expression o... |
83 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nRetroviral transduction of primary CD8+ T cells.\nFor transduction experiments, viral supernatants were generated by calcium phosphate transfection of Phoenix cells and concentration by overnight centrifugation at 6,000 g. At approximately42 h after the initial TCR activation of 1... |
84 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nChIP and real-time PCR analysis.\n20 x 106 CD8+ T cells per immunoprecipitation were fixed by adding a 1/10th volume of fixation solution (11.1% formaldehyde, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 50 mM Hepes) to 1 volume of culture media and were incubated for 10 or 30 min at RT. ... |
85 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Northern and Western blot analyses.\nRNA isolation and Northern blot analysis was performed as previously described (29). In brief, 10 mug of total RNA was loaded per lane and transferred to positively charged nylon membranes (Hybond-N+; GE Healthcare), which was confirmed by ethidium ... |
86 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nOnline supplemental material.\nFig. S1 shows the characterization of peripheral CD8+ T cells from Runx3-/- mice. Fig. S2 shows effector protein expression by Runx3 WT and KO cells at day 4 of in vitro culture. Primer sequences used for ChIP experiments are shown in Table S1. Onlin... |
87 | EE | bionlp_st_2011_ge | en | [
{
"human": "Supplementary Material\n[Supplemental Material Index]\nEven Types: Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation\nRole Types: Cause, Theme, ToLoc, Site, AtLoc, CSite\nExtract events from the text.",
... |
88 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Kinetics of gene expression during CD8+ T cell differentiation. (A) Kinetics of Prf1, Gzmb, Tbx21 (T-bet), and Eomes mRNA expression in differentiating P14 CD8+ T cells analyzed by Northern blotting. RNA from day 7 Th1 cells was used as a control. Sizes of mRNA transcripts are indicate... |
89 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation events from the text:\nRegulation of perforin, granzyme B, and IFN-gamma expression by T-bet and Eomes in differentiating CTLs. (A) IFN-gamma expre... |
90 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation events from the text:\nKey role for Runx3 in effector CTL differentiation. (A) Western analysis of Runx3, Eomes, T-bet, and perforin expression in ... |
91 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Runx3 controls Eomes, perforin, granzyme B, and IFN-gamma expression in effector CTLs. Runx3+/+ or Runx3-/- CD8+ T cells were activated and transduced with retroviruses bearing an empty IRES-GFP cassette (GFP) or also encoding Eomes-VP16 (Eo-VP16) or Myc-Runx3 (Runx3). The frequency of... |
92 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"[Supplemental Material Index]\"\nEven Types: Gene expression, Regulation, Binding, Protein catabolism, Transcription, Positive regulation, Negative regulation, Localization, Phosphorylation\nRole Types: Cause, Theme, ToLoc, Site, AtLoc, CSite\nPlease extract events from the input text.... |
93 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"Interleukin-10 Production by Th1 Cells Requires Interleukin-12-Induced STAT4 Transcription Factor and ERK MAP Kinase Activation by High Antigen Dose \nSummary\nCD4+ Tcells producing interleukin-10 (IL-10) and interferon-gamma (IFN-gamma) are reported in chronic infections. However, the... |
94 | EE | bionlp_st_2011_ge | en | [
{
"human": "Introduction\nInterleukin-10 (IL-10) is a cytokine with broad anti-inflammatory properties that inhibits macrophage and dendritic cell (DC) function (Moore etal., 2001). IL-10 limits the immune and inflammatory responses to pathogens and gut flora and prevents damage to the host (Moore etal., 2001; ... |
95 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"IL-12 and High Doses of Antigen Induce the Development of Th1 Cells Producing IL-10\nTo study the differentiation of Th1 cells coproducing IFN-gamma and IL-10, we cultured purified TCR-transgenic DO11.10 naive CD4+ Tcells with purified DCs as APCs and increasing doses of ovalbumin pept... |
96 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nIL-10 Production by Th1 Cells Is Dependent on STAT4 but Not on STAT6, IFN-gamma, or IL-4 Signaling\nTo further elucidate the mechanisms required for the development of Th1 cells producing IL-10, we investigated the role of STAT4, one of the signaling pathways activated by IL-12 (M... |
97 | EE | bionlp_st_2011_ge | en | [
{
"human": "Extract events from the following text: \"High Antigen Doses and STAT4 Are Required for the In Vivo Generation of IL-10-Producing Th1 Cells\nTo address the mechanisms regulating IL-10 production by Th1 cells invivo, we transferred DO11.10 cells into BALB/c recipient mice and immunized the recipients... |
98 | EE | bionlp_st_2011_ge | en | [
{
"human": "Input text: \"IL-10 Production Is Maintained by High TCR Signal Strength and IL-12\nWe next investigated whether repeated strong TCR activation is a compensatory signal for IL-12-induced STAT4 signaling in the induction of IL-10 in Th1 cells. For this, CD4+ Tcells were differentiated for 2 consecuti... |
99 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nIL-10 Production by Th1 Cells Requires ERK1 and ERK2 Activation\nOur data showed that the maintenance of IL-10 induction in Th1 cells required stimulation with high antigen dose, which to some extent could be compensated for by the addition of IL-12. Signaling through the TCR with... |
100 | EE | bionlp_st_2011_ge | en | [
{
"human": "Event extraction:\nIL-10 Production by Th2 and Th17 Cells Also Requires ERK1 and ERK2 Activation\nTo address whether IL-10 production by Th2 and Th17 cells was also dependent on ERK1 and ERK2 activation, we differentiated these cells with anti-CD3 and anti-CD28 in the absence of APCs (Shoemaker etal... |
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