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PMC:3320587 / 8020-9155 JSONTXT

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2_test

Id Subject Object Predicate Lexical cue
22496647-11909956-98010786 603-605 11909956 denotes 34

pmc-enju-pas

Id Subject Object Predicate Lexical cue
T3793 1108-1109 -LRB- denotes (
T3792 1099-1107 NN denotes protocol
T3791 1096-1098 POS denotes 's
T3790 1084-1096 NN denotes manufacturer
T3789 1080-1083 DT denotes the
T3788 1077-1079 TO denotes to
T3787 1067-1076 VB denotes according
T3786 1061-1066 NN denotes assay
T3785 1052-1060 NN denotes reporter
T3784 1036-1051 NN denotes dual-luciferase
T3783 1033-1035 IN denotes by
T3782 1021-1032 VB denotes quantitated
T3781 1017-1020 VB denotes was
T3780 1006-1016 NN denotes expression
T3779 1001-1005 NN denotes gene
T3778 992-1000 NN denotes Reporter
T3777 985-990 NN denotes hours
T3776 983-984 CD denotes 8
T3775 979-982 IN denotes for
T3774 966-978 JJ denotes unstimulated
T3773 961-965 VB denotes left
T3772 958-960 CC denotes or
T3771 951-957 NN denotes lysate
T3770 943-950 NN denotes CDC1551
T3769 939-942 NN denotes MTb
T3768 933-938 NN denotes µg/ml
T3767 930-932 CD denotes 10
T3766 925-929 IN denotes with
T3765 914-924 VB denotes stimulated
T3764 909-913 VB denotes were
T3763 904-908 PRP denotes they
T3762 898-903 WDT denotes which
T3761 892-897 IN denotes after
T3760 886-891 NN denotes hours
T3759 883-885 CD denotes 16
T3758 879-882 IN denotes for
T3757 874-878 NN denotes 37°C
T3756 871-873 IN denotes at
T3755 861-870 VB denotes incubated
T3754 856-860 VB denotes were
T3753 850-855 NN denotes Cells
T3752 847-848 -RRB- denotes )
T3751 833-847 NN denotes www.qiagen.com
T3750 831-832 -COLON- denotes ;
T3749 825-831 NN denotes Qiagen
T3748 824-825 -LRB- denotes (
T3747 816-823 NN denotes reagent
T3746 803-815 NN denotes transfection
T3745 793-802 NN denotes Effectene
T3744 787-792 VB denotes using
T3743 780-786 NN denotes vector
T3742 772-779 NN denotes control
T3741 770-771 -RRB- denotes )
T3740 764-770 NN denotes pRL-TK
T3739 763-764 -LRB- denotes (
T3738 752-762 NN denotes luciferase
T3737 744-751 NNP denotes Renilla
T3736 738-743 NN denotes µg/ml
T3735 733-737 CD denotes 0.03
T3734 728-732 IN denotes with
T3733 716-727 NN denotes combination
T3732 713-715 IN denotes in
T3731 704-712 NN denotes plasmids
T3730 695-703 NN denotes reporter
T3729 687-694 VB denotes mutated
T3728 684-686 CC denotes or
T3727 682-683 -RRB- denotes )
T3726 680-682 NN denotes WT
T3725 679-680 -LRB- denotes (
T3724 669-678 JJ denotes wild-type
T3723 665-668 NN denotes LTR
T3722 659-664 NN denotes µg/ml
T3721 655-658 CD denotes 0.3
T3720 650-654 IN denotes with
T3719 638-649 VB denotes transfected
T3718 633-637 VB denotes were
T3717 631-632 -RRB- denotes )
T3716 621-631 NN denotes 0.8×106/ml
T3715 620-621 -LRB- denotes (
T3714 614-619 NN denotes cells
T3713 608-613 NN denotes THP-1
T3712 605-606 -RRB- denotes ]
T3711 603-605 CD denotes 34
T3710 602-603 -LRB- denotes [
T3709 594-601 NN denotes methods
T3708 582-593 NN denotes mutagenesis
T3707 572-581 JJ denotes PCR-based
T3706 563-571 JJ denotes standard
T3705 560-562 IN denotes by
T3704 552-559 VB denotes created
T3703 548-551 VB denotes was
T3702 540-547 NN denotes plasmid
T3701 531-539 NN denotes reporter
T3700 529-530 -RRB- denotes )
T3699 523-529 NN denotes N5-Mut
T3698 522-523 -LRB- denotes (
T3697 510-521 JJ denotes site-mutant
T3696 502-509 NN denotes binding
T3695 496-501 NN denotes NFAT5
T3694 487-495 NN denotes HIV-1Lai
T3693 483-486 DT denotes The
T3692 480-481 -RRB- denotes )
T3691 457-480 NN denotes www.ebi.ac.uk/clustalw/
T3690 456-457 -LRB- denotes (
T3689 454-455 NNP denotes W
T3688 446-453 NN denotes CLUSTAL
T3687 441-445 IN denotes with
T3686 432-440 VB denotes analyzed
T3685 428-431 CC denotes and
T3684 420-427 VB denotes aligned
T3683 415-419 VB denotes were
T3682 405-414 NN denotes Sequences
T3681 398-403 NN denotes sites
T3680 391-397 NN denotes enzyme
T3679 379-390 NN denotes restriction
T3678 375-378 CD denotes III
T3677 370-374 NN denotes Hind
T3676 366-369 CC denotes and
T3675 364-365 CD denotes I
T3674 360-363 NN denotes Xho
T3673 354-359 VB denotes using
T3672 352-353 -RRB- denotes )
T3671 337-352 NN denotes www.promega.com
T3670 335-336 -COMMA- denotes ,
T3669 324-335 NNP denotes BioSciences
T3668 316-323 NNP denotes Promega
T3667 315-316 -LRB- denotes (
T3666 310-314 NN denotes pGL3
T3665 303-309 NN denotes vector
T3664 294-302 NN denotes reporter
T3663 290-293 DT denotes the
T3662 285-289 IN denotes into
T3661 283-284 -RRB- denotes )
T3660 276-283 NN denotes subtype
T3659 274-275 NN denotes E
T3658 273-274 -LRB- denotes (
T3657 263-272 NN denotes HIV-1KR25
T3656 259-262 CC denotes and
T3655 257-258 -COMMA- denotes ,
T3654 246-257 NN denotes HIV-192TH51
T3653 244-245 -COMMA- denotes ,
T3652 233-244 NN denotes HIV-192TH53
T3651 231-232 -COMMA- denotes ,
T3650 220-231 NN denotes HIV-193TH64
T3649 218-219 -COMMA- denotes ,
T3648 217-218 -RRB- denotes )
T3647 210-217 NN denotes subtype
T3646 208-209 NN denotes C
T3645 207-208 -LRB- denotes (
T3644 198-206 NN denotes HIV-1CM9
T3643 196-197 -COMMA- denotes ,
T3642 185-196 NN denotes HIV-198CH01
T3641 183-184 -COMMA- denotes ,
T3640 172-183 NN denotes HIV-198IN22
T3639 170-171 -COMMA- denotes ,
T3638 159-170 NN denotes HIV-198IN17
T3637 157-158 -COMMA- denotes ,
T3636 156-157 -RRB- denotes )
T3635 149-156 NN denotes subtype
T3634 147-148 NN denotes B
T3633 146-147 -LRB- denotes (
T3632 137-145 JJ denotes HIV-1Bal
T3631 135-136 -COMMA- denotes ,
T3630 127-135 NN denotes HIV-1Lai
T3629 124-126 IN denotes of
T3628 119-123 NN denotes site
T3627 108-118 NN denotes initiation
T3626 92-107 JJ denotes transcriptional
T3625 88-91 DT denotes the
T3624 85-87 TO denotes to
T3623 76-84 JJ denotes relative
T3622 72-75 CD denotes +64
T3621 69-71 TO denotes to
T3620 64-68 CD denotes −208
T3619 52-63 NN denotes nucleotides
T3618 42-51 VB denotes inserting
T3617 39-41 IN denotes by
T3616 27-38 VB denotes constructed
T3615 22-26 VB denotes were
T3614 13-21 NN denotes plasmids
T3613 4-12 NN denotes reporter
T3612 0-3 NN denotes LTR
T3797 1133-1134 -RRB- denotes )
T3796 1118-1133 NN denotes www.promega.com
T3795 1116-1117 -COLON- denotes ;
T3794 1109-1116 NNP denotes Promega
R2831 T3614 T3612 arg1Of plasmids,LTR
R2832 T3614 T3613 arg1Of plasmids,reporter
R2833 T3614 T3615 arg1Of plasmids,were
R2834 T3614 T3616 arg2Of plasmids,constructed
R2835 T3616 T3615 arg2Of constructed,were
R2836 T3616 T3617 arg1Of constructed,by
R2837 T3618 T3617 arg2Of inserting,by
R2838 T3618 T3673 modOf inserting,using
R2839 T3619 T3620 arg1Of nucleotides,−208
R2840 T3619 T3637 arg1Of nucleotides,","
R2841 T3620 T3621 arg1Of −208,to
R2842 T3622 T3621 arg2Of +64,to
R2843 T3622 T3623 arg1Of +64,relative
R2844 T3623 T3624 arg1Of relative,to
R2845 T3628 T3624 arg2Of site,to
R2846 T3628 T3625 arg1Of site,the
R2847 T3628 T3626 arg1Of site,transcriptional
R2848 T3628 T3627 arg1Of site,initiation
R2849 T3628 T3629 arg1Of site,of
R2850 T3628 T3631 arg1Of site,","
R2851 T3630 T3629 arg2Of HIV-1Lai,of
R2852 T3632 T3631 arg2Of HIV-1Bal,","
R2853 T3632 T3633 arg1Of HIV-1Bal,(
R2854 T3635 T3633 arg2Of subtype,(
R2855 T3635 T3634 arg1Of subtype,B
R2856 T3636 T3633 arg3Of ),(
R2857 T3637 T3618 arg2Of ",",inserting
R2858 T3637 T3662 arg1Of ",",into
R2859 T3637 T3667 arg1Of ",",(
R2860 T3638 T3639 arg1Of HIV-198IN17,","
R2861 T3639 T3641 arg1Of ",",","
R2862 T3640 T3639 arg2Of HIV-198IN22,","
R2863 T3641 T3643 arg1Of ",",","
R2864 T3642 T3641 arg2Of HIV-198CH01,","
R2865 T3643 T3649 arg1Of ",",","
R2866 T3644 T3643 arg2Of HIV-1CM9,","
R2867 T3644 T3645 arg1Of HIV-1CM9,(
R2868 T3647 T3645 arg2Of subtype,(
R2869 T3647 T3646 arg1Of subtype,C
R2870 T3648 T3645 arg3Of ),(
R2871 T3649 T3637 arg2Of ",",","
R2872 T3650 T3651 arg1Of HIV-193TH64,","
R2873 T3651 T3653 arg1Of ",",","
R2874 T3652 T3651 arg2Of HIV-192TH53,","
R2875 T3653 T3656 arg1Of ",",and
R2876 T3654 T3653 arg2Of HIV-192TH51,","
R2877 T3656 T3649 arg2Of and,","
R2878 T3656 T3655 arg1Of and,","
R2879 T3657 T3656 arg2Of HIV-1KR25,and
R2880 T3657 T3658 arg1Of HIV-1KR25,(
R2881 T3660 T3658 arg2Of subtype,(
R2882 T3660 T3659 arg1Of subtype,E
R2883 T3661 T3658 arg3Of ),(
R2884 T3666 T3662 arg2Of pGL3,into
R2885 T3666 T3663 arg1Of pGL3,the
R2886 T3666 T3664 arg1Of pGL3,reporter
R2887 T3666 T3665 arg1Of pGL3,vector
R2888 T3669 T3667 arg2Of BioSciences,(
R2889 T3669 T3668 arg1Of BioSciences,Promega
R2890 T3669 T3670 arg1Of BioSciences,","
R2891 T3671 T3670 arg2Of www.promega.com,","
R2892 T3672 T3667 arg3Of ),(
R2893 T3674 T3675 arg1Of Xho,I
R2894 T3674 T3676 arg1Of Xho,and
R2895 T3676 T3673 arg2Of and,using
R2896 T3681 T3676 arg2Of sites,and
R2897 T3681 T3677 arg1Of sites,Hind
R2898 T3681 T3678 arg1Of sites,III
R2899 T3681 T3679 arg1Of sites,restriction
R2900 T3681 T3680 arg1Of sites,enzyme
R2901 T3682 T3683 arg1Of Sequences,were
R2902 T3682 T3684 arg2Of Sequences,aligned
R2903 T3682 T3686 arg2Of Sequences,analyzed
R2904 T3684 T3685 arg1Of aligned,and
R2905 T3685 T3683 arg2Of and,were
R2906 T3686 T3685 arg2Of analyzed,and
R2907 T3686 T3687 arg1Of analyzed,with
R2908 T3689 T3687 arg2Of W,with
R2909 T3689 T3688 arg1Of W,CLUSTAL
R2910 T3689 T3690 arg1Of W,(
R2911 T3691 T3690 arg2Of www.ebi.ac.uk/clustalw/,(
R2912 T3692 T3690 arg3Of ),(
R2913 T3699 T3698 arg2Of N5-Mut,(
R2914 T3700 T3698 arg3Of ),(
R2915 T3702 T3693 arg1Of plasmid,The
R2916 T3702 T3694 arg1Of plasmid,HIV-1Lai
R2917 T3702 T3695 arg1Of plasmid,NFAT5
R2918 T3702 T3696 arg1Of plasmid,binding
R2919 T3702 T3697 arg1Of plasmid,site-mutant
R2920 T3702 T3698 arg1Of plasmid,(
R2921 T3702 T3701 arg1Of plasmid,reporter
R2922 T3702 T3703 arg1Of plasmid,was
R2923 T3702 T3704 arg2Of plasmid,created
R2924 T3704 T3703 arg2Of created,was
R2925 T3709 T3704 arg1Of methods,created
R2926 T3709 T3705 arg2Of methods,by
R2927 T3709 T3706 arg1Of methods,standard
R2928 T3709 T3707 arg1Of methods,PCR-based
R2929 T3709 T3708 arg1Of methods,mutagenesis
R2930 T3709 T3710 arg1Of methods,[
R2931 T3711 T3710 arg2Of 34,[
R2932 T3712 T3710 arg3Of ],[
R2933 T3714 T3713 arg1Of cells,THP-1
R2934 T3714 T3715 arg1Of cells,(
R2935 T3714 T3718 arg1Of cells,were
R2936 T3714 T3719 arg2Of cells,transfected
R2937 T3714 T3744 arg1Of cells,using
R2938 T3716 T3715 arg2Of 0.8×106/ml,(
R2939 T3717 T3715 arg3Of ),(
R2940 T3719 T3718 arg2Of transfected,were
R2941 T3719 T3720 arg1Of transfected,with
R2942 T3719 T3744 modOf transfected,using
R2943 T3721 T3722 arg1Of 0.3,µg/ml
R2944 T3723 T3721 arg1Of LTR,0.3
R2945 T3723 T3724 arg1Of LTR,wild-type
R2946 T3723 T3725 arg1Of LTR,(
R2947 T3723 T3728 arg1Of LTR,or
R2948 T3726 T3725 arg2Of WT,(
R2949 T3727 T3725 arg3Of ),(
R2950 T3728 T3720 arg2Of or,with
R2951 T3728 T3732 arg1Of or,in
R2952 T3731 T3728 arg2Of plasmids,or
R2953 T3731 T3729 arg2Of plasmids,mutated
R2954 T3731 T3730 arg1Of plasmids,reporter
R2955 T3733 T3732 arg2Of combination,in
R2956 T3733 T3734 arg1Of combination,with
R2957 T3738 T3735 arg1Of luciferase,0.03
R2958 T3738 T3736 arg1Of luciferase,µg/ml
R2959 T3738 T3737 arg1Of luciferase,Renilla
R2960 T3738 T3739 arg1Of luciferase,(
R2961 T3740 T3739 arg2Of pRL-TK,(
R2962 T3741 T3739 arg3Of ),(
R2963 T3743 T3734 arg2Of vector,with
R2964 T3743 T3738 arg1Of vector,luciferase
R2965 T3743 T3742 arg1Of vector,control
R2966 T3747 T3744 arg2Of reagent,using
R2967 T3747 T3745 arg1Of reagent,Effectene
R2968 T3747 T3746 arg1Of reagent,transfection
R2969 T3747 T3748 arg1Of reagent,(
R2970 T3749 T3748 arg2Of Qiagen,(
R2971 T3749 T3750 arg1Of Qiagen,;
R2972 T3751 T3750 arg2Of www.qiagen.com,;
R2973 T3752 T3748 arg3Of ),(
R2974 T3753 T3754 arg1Of Cells,were
R2975 T3753 T3755 arg2Of Cells,incubated
R2976 T3755 T3754 arg2Of incubated,were
R2977 T3755 T3756 arg1Of incubated,at
R2978 T3755 T3758 arg1Of incubated,for
R2979 T3757 T3756 arg2Of 37°C,at
R2980 T3760 T3758 arg2Of hours,for
R2981 T3760 T3759 arg1Of hours,16
R2982 T3760 T3761 arg2Of hours,after
R2983 T3760 T3762 arg1Of hours,which
R2984 T3763 T3764 arg1Of they,were
R2985 T3763 T3765 arg2Of they,stimulated
R2986 T3763 T3773 arg1Of they,left
R2987 T3765 T3764 arg2Of stimulated,were
R2988 T3765 T3766 arg1Of stimulated,with
R2989 T3765 T3772 arg1Of stimulated,or
R2990 T3771 T3766 arg2Of lysate,with
R2991 T3771 T3767 arg1Of lysate,10
R2992 T3771 T3768 arg1Of lysate,µg/ml
R2993 T3771 T3769 arg1Of lysate,MTb
R2994 T3771 T3770 arg1Of lysate,CDC1551
R2995 T3772 T3761 arg1Of or,after
R2996 T3773 T3772 arg2Of left,or
R2997 T3773 T3775 arg1Of left,for
R2998 T3774 T3773 arg2Of unstimulated,left
R2999 T3777 T3775 arg2Of hours,for
R3000 T3777 T3776 arg1Of hours,8
R3001 T3780 T3778 arg1Of expression,Reporter
R3002 T3780 T3779 arg1Of expression,gene
R3003 T3780 T3781 arg1Of expression,was
R3004 T3780 T3782 arg2Of expression,quantitated
R3005 T3782 T3781 arg2Of quantitated,was
R3006 T3782 T3787 arg1Of quantitated,according
R3007 T3786 T3782 arg1Of assay,quantitated
R3008 T3786 T3783 arg2Of assay,by
R3009 T3786 T3784 arg1Of assay,dual-luciferase
R3010 T3786 T3785 arg1Of assay,reporter
R3011 T3788 T3787 arg2Of to,according
R3012 T3790 T3789 arg1Of manufacturer,the
R3013 T3790 T3791 arg2Of manufacturer,'s
R3014 T3792 T3788 arg2Of protocol,to
R3015 T3792 T3791 arg1Of protocol,'s
R3016 T3792 T3793 arg1Of protocol,(
R3017 T3794 T3793 arg2Of Promega,(
R3018 T3794 T3795 arg1Of Promega,;
R3019 T3796 T3795 arg2Of www.promega.com,;
R3020 T3797 T3793 arg3Of ),(

bionlp-st-ge-2016-test-proteins

Id Subject Object Predicate Lexical cue
T3598 1041-1051 Protein denotes luciferase
T3597 992-1005 Protein denotes Reporter gene
T3596 752-762 Protein denotes luciferase

bionlp-st-ge-2016-uniprot

Id Subject Object Predicate Lexical cue
T3800 1041-1051 http://www.uniprot.org/uniprot/P08659 denotes luciferase
T3799 752-762 http://www.uniprot.org/uniprot/P08659 denotes luciferase
T3798 496-501 http://www.uniprot.org/uniprot/O94916 denotes NFAT5

GO-BP

Id Subject Object Predicate Lexical cue
T3600 1001-1016 http://purl.obolibrary.org/obo/GO_0010467 denotes gene expression
T3599 92-107 http://purl.obolibrary.org/obo/GO_0006351 denotes transcriptional

GO-MF

Id Subject Object Predicate Lexical cue
T3601 502-509 http://purl.obolibrary.org/obo/GO_0005488 denotes binding

GO-CC

Id Subject Object Predicate Lexical cue
T3602 614-619 http://purl.obolibrary.org/obo/GO_0005623 denotes cells

sentences

Id Subject Object Predicate Lexical cue
T3591 992-1135 Sentence denotes Reporter gene expression was quantitated by dual-luciferase reporter assay according to the manufacturer's protocol (Promega; www.promega.com).
T3590 850-991 Sentence denotes Cells were incubated at 37°C for 16 hours after which they were stimulated with 10 µg/ml MTb CDC1551 lysate or left unstimulated for 8 hours.
T3589 608-849 Sentence denotes THP-1 cells (0.8×106/ml) were transfected with 0.3 µg/ml LTR wild-type (WT) or mutated reporter plasmids in combination with 0.03 µg/ml Renilla luciferase (pRL-TK) control vector using Effectene transfection reagent (Qiagen; www.qiagen.com).
T3588 483-607 Sentence denotes The HIV-1Lai NFAT5 binding site-mutant (N5-Mut) reporter plasmid was created by standard PCR-based mutagenesis methods [34].
T3587 405-482 Sentence denotes Sequences were aligned and analyzed with CLUSTAL W (www.ebi.ac.uk/clustalw/).
T3586 0-404 Sentence denotes LTR reporter plasmids were constructed by inserting nucleotides −208 to +64 relative to the transcriptional initiation site of HIV-1Lai, HIV-1Bal (B subtype), HIV-198IN17, HIV-198IN22, HIV-198CH01, HIV-1CM9 (C subtype), HIV-193TH64, HIV-192TH53, HIV-192TH51, and HIV-1KR25 (E subtype) into the reporter vector pGL3 (Promega BioSciences, www.promega.com) using Xho I and Hind III restriction enzyme sites.
T48 0-404 Sentence denotes LTR reporter plasmids were constructed by inserting nucleotides −208 to +64 relative to the transcriptional initiation site of HIV-1Lai, HIV-1Bal (B subtype), HIV-198IN17, HIV-198IN22, HIV-198CH01, HIV-1CM9 (C subtype), HIV-193TH64, HIV-192TH53, HIV-192TH51, and HIV-1KR25 (E subtype) into the reporter vector pGL3 (Promega BioSciences, www.promega.com) using Xho I and Hind III restriction enzyme sites.
T49 405-482 Sentence denotes Sequences were aligned and analyzed with CLUSTAL W (www.ebi.ac.uk/clustalw/).
T50 483-607 Sentence denotes The HIV-1Lai NFAT5 binding site-mutant (N5-Mut) reporter plasmid was created by standard PCR-based mutagenesis methods [34].
T51 608-849 Sentence denotes THP-1 cells (0.8×106/ml) were transfected with 0.3 µg/ml LTR wild-type (WT) or mutated reporter plasmids in combination with 0.03 µg/ml Renilla luciferase (pRL-TK) control vector using Effectene transfection reagent (Qiagen; www.qiagen.com).
T52 850-991 Sentence denotes Cells were incubated at 37°C for 16 hours after which they were stimulated with 10 µg/ml MTb CDC1551 lysate or left unstimulated for 8 hours.
T53 992-1135 Sentence denotes Reporter gene expression was quantitated by dual-luciferase reporter assay according to the manufacturer's protocol (Promega; www.promega.com).

simple1

Id Subject Object Predicate Lexical cue
T3605 1041-1051 Protein denotes luciferase
T3604 992-1005 Protein denotes Reporter gene
T3603 752-762 Protein denotes luciferase

BioNLP16_DUT

Id Subject Object Predicate Lexical cue
T4044 1006-1016 Gene_expression denotes expression
T4043 1041-1051 Protein denotes luciferase
T4042 992-1005 Protein denotes Reporter gene
T4041 752-762 Protein denotes luciferase
R3236 T4042 T4044 themeOf Reporter gene,expression

BioNLP16_Messiy

Id Subject Object Predicate Lexical cue
T3808 752-762 Protein denotes luciferase
T3811 1006-1016 Gene_expression denotes expression
T3810 1041-1051 Protein denotes luciferase
T3809 992-1005 Protein denotes Reporter gene
R3022 T3809 T3811 themeOf Reporter gene,expression

DLUT931

Id Subject Object Predicate Lexical cue
T3807 1006-1016 Gene_expression denotes expression
T3806 1041-1051 Protein denotes luciferase
T3805 992-1005 Protein denotes Reporter gene
T3804 752-762 Protein denotes luciferase
R3021 T3805 T3807 themeOf Reporter gene,expression

bionlp-st-ge-2016-test-ihmc

Id Subject Object Predicate Lexical cue
T4055 930-942 Protein denotes 10 µg/ml MTb
T4054 764-770 Protein denotes pRL-TK
T4053 793-823 Entity denotes Effectene transfection reagent
T4052 523-529 Entity denotes N5-Mut
T4051 496-530 Entity denotes NFAT5 binding site-mutant (N5-Mut)
T4050 379-397 Protein denotes restriction enzyme
T4049 744-771 Protein denotes Renilla luciferase (pRL-TK)
T4048 523-529 Protein denotes N5-Mut
T4047 370-403 Entity denotes Hind III restriction enzyme sites
T4046 52-63 Entity denotes nucleotides
T4045 850-855 Entity denotes Cells

bionlp-st-ge-2016-spacy-parsed

Id Subject Object Predicate Lexical cue
T4040 1134-1135 . denotes .
T4039 1133-1134 -RRB- denotes )
T4038 1118-1133 NN denotes www.promega.com
T4037 1116-1117 : denotes ;
T4036 1109-1116 JJ denotes Promega
T4035 1108-1109 -LRB- denotes (
T4034 1099-1107 NN denotes protocol
T4033 1096-1098 POS denotes 's
T4032 1084-1096 NN denotes manufacturer
T4031 1080-1083 DT denotes the
T4030 1077-1079 TO denotes to
T4029 1067-1076 VBG denotes according
T4028 1061-1066 NN denotes assay
T4027 1052-1060 NN denotes reporter
T4026 1036-1051 JJ denotes dual-luciferase
T4025 1033-1035 IN denotes by
T4024 1021-1032 VBN denotes quantitated
T4023 1017-1020 VBD denotes was
T4022 1006-1016 NN denotes expression
T4021 1001-1005 NN denotes gene
T4020 992-1000 NN denotes Reporter
T4019 990-991 . denotes .
T4018 985-990 NNS denotes hours
T4017 983-984 CD denotes 8
T4016 979-982 IN denotes for
T4015 966-978 JJ denotes unstimulated
T4014 961-965 VBD denotes left
T4013 958-960 CC denotes or
T4012 951-957 VBP denotes lysate
T4011 943-950 NNP denotes CDC1551
T4010 939-942 NNP denotes MTb
T4009 936-938 NN denotes ml
T4008 935-936 NN denotes /
T4007 933-935 NN denotes µg
T4006 930-932 CD denotes 10
T4005 925-929 IN denotes with
T4004 914-924 VBN denotes stimulated
T4003 909-913 VBD denotes were
T4002 904-908 PRP denotes they
T4001 898-903 WDT denotes which
T3983 816-823 NN denotes reagent
T3982 803-815 NN denotes transfection
T3981 793-802 NNP denotes Effectene
T3980 787-792 VBG denotes using
T3979 780-786 NN denotes vector
T3978 772-779 NN denotes control
T3977 770-771 -RRB- denotes )
T3976 764-770 JJ denotes pRL-TK
T3975 763-764 -LRB- denotes (
T3974 752-762 NN denotes luciferase
T3973 744-751 NN denotes Renilla
T3972 741-743 NN denotes ml
T3971 740-741 NN denotes /
T3970 738-740 NN denotes µg
T3969 733-737 CD denotes 0.03
T3968 728-732 IN denotes with
T3967 716-727 NN denotes combination
T3966 713-715 IN denotes in
T3965 704-712 NNS denotes plasmids
T3964 695-703 NN denotes reporter
T3963 687-694 VBN denotes mutated
T3962 684-686 CC denotes or
T3961 682-683 -RRB- denotes )
T3960 680-682 NNP denotes WT
T3959 679-680 -LRB- denotes (
T3958 669-678 JJ denotes wild-type
T3957 665-668 NNP denotes LTR
T3956 662-664 NN denotes ml
T3955 661-662 NN denotes /
T3954 659-661 NN denotes µg
T3953 655-658 CD denotes 0.3
T3952 650-654 IN denotes with
T3951 638-649 VBN denotes transfected
T3950 633-637 VBD denotes were
T3949 631-632 -RRB- denotes )
T3948 625-631 CD denotes 106/ml
T3947 624-625 NN denotes ×
T3946 621-624 CD denotes 0.8
T3945 620-621 -LRB- denotes (
T3944 614-619 NNS denotes cells
T3943 608-613 CD denotes THP-1
T3942 606-607 . denotes .
T3941 605-606 NNP denotes ]
T3940 603-605 CD denotes 34
T3939 602-603 NNP denotes [
T3938 594-601 NNS denotes methods
T3937 582-593 NN denotes mutagenesis
T3936 572-581 JJ denotes PCR-based
T3935 563-571 JJ denotes standard
T3934 560-562 IN denotes by
T3933 552-559 VBN denotes created
T3932 548-551 VBD denotes was
T3931 540-547 NN denotes plasmid
T3930 531-539 NN denotes reporter
T3929 529-530 -RRB- denotes )
T3928 523-529 JJ denotes N5-Mut
T3927 522-523 -LRB- denotes (
T3926 510-521 JJ denotes site-mutant
T3925 502-509 JJ denotes binding
T3924 496-501 CD denotes NFAT5
T3923 487-495 JJ denotes HIV-1Lai
T3922 483-486 DT denotes The
T3921 481-482 . denotes .
T3920 480-481 -RRB- denotes )
T3919 457-480 NNP denotes www.ebi.ac.uk/clustalw/
T3918 456-457 -LRB- denotes (
T3917 454-455 NNP denotes W
T3916 446-453 NNP denotes CLUSTAL
T3915 441-445 IN denotes with
T3914 432-440 VBN denotes analyzed
T3913 428-431 CC denotes and
T3912 420-427 VBN denotes aligned
T3911 415-419 VBD denotes were
T3910 405-414 NNS denotes Sequences
T3909 403-404 . denotes .
T3908 398-403 NNS denotes sites
T3907 391-397 NN denotes enzyme
T3906 379-390 NN denotes restriction
T3905 375-378 NNP denotes III
T3904 370-374 NNP denotes Hind
T3903 366-369 CC denotes and
T3902 364-365 PRP denotes I
T3901 360-363 NNP denotes Xho
T3900 354-359 VBG denotes using
T3899 352-353 -RRB- denotes )
T3898 337-352 NN denotes www.promega.com
T3897 335-336 , denotes ,
T3896 324-335 NNP denotes BioSciences
T3895 316-323 NNP denotes Promega
T3894 315-316 -LRB- denotes (
T3893 310-314 NNP denotes pGL3
T3892 303-309 NN denotes vector
T3891 294-302 NN denotes reporter
T3890 290-293 DT denotes the
T3889 285-289 IN denotes into
T3888 283-284 -RRB- denotes )
T3887 276-283 NN denotes subtype
T3886 274-275 NNP denotes E
T3885 273-274 -LRB- denotes (
T3884 263-272 NNP denotes HIV-1KR25
T3883 259-262 CC denotes and
T3882 257-258 , denotes ,
T3881 246-257 NNP denotes HIV-192TH51
T3880 244-245 , denotes ,
T3879 233-244 NNP denotes HIV-192TH53
T3878 231-232 , denotes ,
T3877 220-231 NNP denotes HIV-193TH64
T3876 218-219 , denotes ,
T3875 217-218 -RRB- denotes )
T3874 210-217 NN denotes subtype
T3873 208-209 NNP denotes C
T3872 207-208 -LRB- denotes (
T4000 892-897 IN denotes after
T3999 886-891 NNS denotes hours
T3998 883-885 CD denotes 16
T3997 879-882 IN denotes for
T3996 877-878 NNP denotes C
T3995 876-877 CD denotes °
T3994 874-876 CD denotes 37
T3993 871-873 IN denotes at
T3992 861-870 VBN denotes incubated
T3991 856-860 VBD denotes were
T3990 850-855 NNS denotes Cells
T3989 848-849 . denotes .
T3988 847-848 -RRB- denotes )
T3987 833-847 NN denotes www.qiagen.com
T3986 831-832 : denotes ;
T3985 825-831 NNP denotes Qiagen
T3984 824-825 -LRB- denotes (
T3871 198-206 NNP denotes HIV-1CM9
T3870 196-197 , denotes ,
T3869 185-196 NNP denotes HIV-198CH01
T3868 183-184 , denotes ,
T3867 172-183 NNP denotes HIV-198IN22
T3866 170-171 , denotes ,
T3865 159-170 NNP denotes HIV-198IN17
T3864 157-158 , denotes ,
T3863 156-157 -RRB- denotes )
T3862 149-156 NN denotes subtype
T3861 147-148 NNP denotes B
T3860 146-147 -LRB- denotes (
T3859 137-145 JJ denotes HIV-1Bal
T3858 135-136 , denotes ,
T3857 127-135 JJ denotes HIV-1Lai
T3856 124-126 IN denotes of
T3855 119-123 NN denotes site
T3854 108-118 NN denotes initiation
T3853 92-107 JJ denotes transcriptional
T3852 88-91 DT denotes the
T3851 85-87 TO denotes to
T3850 76-84 JJ denotes relative
T3849 72-75 CD denotes +64
T3848 69-71 TO denotes to
T3847 65-68 CD denotes 208
T3846 64-65 VBP denotes −
T3845 52-63 NNS denotes nucleotides
T3844 42-51 VBG denotes inserting
T3843 39-41 IN denotes by
T3842 27-38 VBN denotes constructed
T3841 22-26 VBD denotes were
T3840 13-21 NNS denotes plasmids
T3839 4-12 NN denotes reporter
T3838 0-3 NNP denotes LTR
R3033 T3838 T3839 compound LTR,reporter
R3034 T3839 T3840 compound reporter,plasmids
R3036 T3841 T3842 auxpass were,constructed
R3037 T3842 T3842 ROOT constructed,constructed
R3038 T3843 T3842 prep by,constructed
R3039 T3844 T3843 pcomp inserting,by
R3040 T3845 T3844 dobj nucleotides,inserting
R3041 T3846 T3849 quantmod −,+64
R3042 T3847 T3849 quantmod 208,+64
R3043 T3848 T3849 quantmod to,+64
R3044 T3849 T3850 npadvmod +64,relative
R3045 T3850 T3842 advmod relative,constructed
R3046 T3851 T3850 prep to,relative
R3047 T3852 T3855 det the,site
R3048 T3853 T3855 amod transcriptional,site
R3049 T3854 T3855 compound initiation,site
R3050 T3855 T3851 pobj site,to
R3051 T3856 T3855 prep of,site
R3052 T3857 T3900 nsubj HIV-1Lai,using
R3053 T3858 T3857 punct ",",HIV-1Lai
R3054 T3859 T3857 conj HIV-1Bal,HIV-1Lai
R3055 T3860 T3862 punct (,subtype
R3056 T3861 T3862 compound B,subtype
R3057 T3862 T3859 appos subtype,HIV-1Bal
R3058 T3863 T3862 punct ),subtype
R3059 T3864 T3859 punct ",",HIV-1Bal
R3060 T3865 T3859 conj HIV-198IN17,HIV-1Bal
R3061 T3866 T3865 punct ",",HIV-198IN17
R3062 T3867 T3865 conj HIV-198IN22,HIV-198IN17
R3063 T3868 T3867 punct ",",HIV-198IN22
R3064 T3869 T3867 conj HIV-198CH01,HIV-198IN22
R3065 T3870 T3869 punct ",",HIV-198CH01
R3066 T3871 T3869 conj HIV-1CM9,HIV-198CH01
R3067 T3872 T3874 punct (,subtype
R3068 T3873 T3874 compound C,subtype
R3069 T3874 T3871 parataxis subtype,HIV-1CM9
R3070 T3875 T3874 punct ),subtype
R3071 T3876 T3871 punct ",",HIV-1CM9
R3072 T3877 T3871 conj HIV-193TH64,HIV-1CM9
R3073 T3878 T3877 punct ",",HIV-193TH64
R3074 T3879 T3877 conj HIV-192TH53,HIV-193TH64
R3075 T3880 T3879 punct ",",HIV-192TH53
R3076 T3881 T3879 conj HIV-192TH51,HIV-192TH53
R3077 T3882 T3881 punct ",",HIV-192TH51
R3078 T3883 T3881 cc and,HIV-192TH51
R3079 T3884 T3881 conj HIV-1KR25,HIV-192TH51
R3080 T3885 T3887 punct (,subtype
R3081 T3886 T3887 compound E,subtype
R3082 T3887 T3884 appos subtype,HIV-1KR25
R3083 T3888 T3887 punct ),subtype
R3084 T3889 T3857 prep into,HIV-1Lai
R3085 T3890 T3892 det the,vector
R3086 T3891 T3892 compound reporter,vector
R3087 T3892 T3889 pobj vector,into
R3088 T3893 T3892 appos pGL3,vector
R3089 T3894 T3896 punct (,BioSciences
R3090 T3895 T3896 compound Promega,BioSciences
R3091 T3896 T3892 appos BioSciences,vector
R3092 T3897 T3896 punct ",",BioSciences
R3093 T3898 T3896 appos www.promega.com,BioSciences
R3094 T3899 T3896 punct ),BioSciences
R3095 T3900 T3856 pcomp using,of
R3096 T3901 T3900 dobj Xho,using
R3097 T3902 T3900 npadvmod I,using
R3098 T3903 T3902 cc and,I
R3099 T3904 T3905 compound Hind,III
R3100 T3905 T3906 compound III,restriction
R3101 T3906 T3908 compound restriction,sites
R3102 T3907 T3908 compound enzyme,sites
R3103 T3908 T3902 conj sites,I
R3104 T3909 T3842 punct .,constructed
R3105 T3910 T3912 nsubjpass Sequences,aligned
R3106 T3911 T3912 auxpass were,aligned
R3107 T3912 T3912 ROOT aligned,aligned
R3108 T3913 T3912 cc and,aligned
R3109 T3914 T3912 conj analyzed,aligned
R3110 T3915 T3914 prep with,analyzed
R3111 T3916 T3917 compound CLUSTAL,W
R3112 T3917 T3915 pobj W,with
R3113 T3918 T3917 punct (,W
R3114 T3919 T3917 appos www.ebi.ac.uk/clustalw/,W
R3115 T3920 T3917 punct ),W
R3116 T3921 T3912 punct .,aligned
R3117 T3922 T3931 det The,plasmid
R3118 T3923 T3931 amod HIV-1Lai,plasmid
R3119 T3924 T3926 nummod NFAT5,site-mutant
R3120 T3925 T3926 amod binding,site-mutant
R3121 T3926 T3931 amod site-mutant,plasmid
R3122 T3927 T3930 punct (,reporter
R3123 T3928 T3930 amod N5-Mut,reporter
R3124 T3929 T3930 punct ),reporter
R3125 T3930 T3931 compound reporter,plasmid
R3126 T3931 T3933 nsubjpass plasmid,created
R3127 T3932 T3933 auxpass was,created
R3128 T3933 T3933 ROOT created,created
R3129 T3934 T3933 agent by,created
R3130 T3935 T3938 amod standard,methods
R3131 T3936 T3938 amod PCR-based,methods
R3132 T3937 T3938 compound mutagenesis,methods
R3133 T3938 T3934 pobj methods,by
R3134 T3939 T3941 nmod [,]
R3135 T3940 T3941 nummod 34,]
R3136 T3941 T3938 appos ],methods
R3137 T3942 T3933 punct .,created
R3138 T3943 T3944 nummod THP-1,cells
R3139 T3944 T3951 nsubjpass cells,transfected
R3140 T3945 T3947 punct (,×
R3141 T3946 T3947 nummod 0.8,×
R3142 T3947 T3944 appos ×,cells
R3143 T3948 T3947 nummod 106/ml,×
R3144 T3949 T3947 punct ),×
R3145 T3950 T3951 auxpass were,transfected
R3146 T3951 T3951 ROOT transfected,transfected
R3147 T3952 T3951 prep with,transfected
R3148 T3953 T3954 nummod 0.3,µg
R3149 T3954 T3987 amod µg,www.qiagen.com
R3150 T3955 T3987 ccomp /,www.qiagen.com
R3151 T3956 T3987 dep ml,www.qiagen.com
R3152 T3957 T3958 compound LTR,wild-type
R3153 T3958 T3956 appos wild-type,ml
R3154 T3959 T3960 punct (,WT
R3155 T3960 T3958 appos WT,wild-type
R3156 T3961 T3960 punct ),WT
R3157 T3962 T3958 cc or,wild-type
R3158 T3963 T3958 conj mutated,wild-type
R3159 T3964 T3965 compound reporter,plasmids
R3160 T3965 T3963 dobj plasmids,mutated
R3161 T3966 T3963 prep in,mutated
R3162 T3967 T3966 pobj combination,in
R3163 T3968 T3963 prep with,mutated
R3164 T3969 T3970 nummod 0.03,µg
R3165 T3970 T3979 nmod µg,vector
R3166 T3971 T3974 nmod /,luciferase
R3167 T3972 T3974 nmod ml,luciferase
R3168 T3973 T3974 compound Renilla,luciferase
R3169 T3974 T3979 nmod luciferase,vector
R3170 T3975 T3976 punct (,pRL-TK
R3171 T3976 T3974 appos pRL-TK,luciferase
R3172 T3977 T3976 punct ),pRL-TK
R3173 T3978 T3979 compound control,vector
R3174 T3979 T3980 nsubj vector,using
R3175 T3980 T3968 pcomp using,with
R3176 T3981 T3983 nmod Effectene,reagent
R3177 T3982 T3983 compound transfection,reagent
R3178 T3983 T3980 dobj reagent,using
R3179 T3984 T3985 punct (,Qiagen
R3180 T3985 T3983 appos Qiagen,reagent
R3181 T3986 T3987 punct ;,www.qiagen.com
R3182 T3987 T3952 pobj www.qiagen.com,with
R3183 T3988 T3987 punct ),www.qiagen.com
R3184 T3989 T3951 punct .,transfected
R3185 T3990 T3992 nsubjpass Cells,incubated
R3186 T3991 T3992 auxpass were,incubated
R3187 T3992 T3992 ROOT incubated,incubated
R3188 T3993 T3992 prep at,incubated
R3189 T3994 T3995 nummod 37,°
R3190 T3995 T3996 nummod °,C
R3191 T3996 T3993 pobj C,at
R3192 T3997 T3992 prep for,incubated
R3193 T3998 T3999 nummod 16,hours
R3194 T3999 T3997 pobj hours,for
R3195 T4000 T4004 prep after,stimulated
R3196 T4001 T4000 pobj which,after
R3197 T4002 T4004 nsubjpass they,stimulated
R3198 T4003 T4004 auxpass were,stimulated
R3199 T4004 T3992 advcl stimulated,incubated
R3200 T4005 T4004 prep with,stimulated
R3201 T4006 T4007 nummod 10,µg
R3202 T4007 T4011 compound µg,CDC1551
R3203 T4008 T4009 compound /,ml
R3204 T4009 T4011 compound ml,CDC1551
R3205 T4010 T4011 compound MTb,CDC1551
R3206 T4011 T4005 pobj CDC1551,with
R3207 T4012 T4004 advmod lysate,stimulated
R3208 T4013 T4004 cc or,stimulated
R3209 T4014 T4004 conj left,stimulated
R3210 T4015 T4014 oprd unstimulated,left
R3211 T4016 T4015 prep for,unstimulated
R3212 T4017 T4018 nummod 8,hours
R3213 T4018 T4016 pobj hours,for
R3214 T4019 T3992 punct .,incubated
R3215 T4020 T4022 compound Reporter,expression
R3216 T4021 T4022 compound gene,expression
R3217 T4022 T4024 nsubjpass expression,quantitated
R3218 T4023 T4024 auxpass was,quantitated
R3219 T4024 T4024 ROOT quantitated,quantitated
R3220 T4025 T4024 agent by,quantitated
R3221 T4026 T4028 amod dual-luciferase,assay
R3222 T4027 T4028 compound reporter,assay
R3223 T4028 T4025 pobj assay,by
R3224 T4029 T4024 prep according,quantitated
R3225 T4030 T4029 prep to,according
R3226 T4031 T4032 det the,manufacturer
R3227 T4032 T4034 poss manufacturer,protocol
R3228 T4033 T4032 case 's,manufacturer
R3229 T4034 T4030 pobj protocol,to
R3230 T4035 T4036 punct (,Promega
R3231 T4036 T4034 appos Promega,protocol
R3232 T4037 T4038 punct ;,www.promega.com
R3233 T4038 T4038 ROOT www.promega.com,www.promega.com
R3234 T4039 T4038 punct ),www.promega.com
R3235 T4040 T4024 punct .,quantitated

bionlp-st-ge-2016-test-tees

Id Subject Object Predicate Lexical cue
T3823 1041-1051 Protein denotes luciferase
T3822 768-770 Protein denotes TK
T3821 764-767 Protein denotes pRL
T3820 744-762 Protein denotes Renilla luciferase
T3819 496-501 Protein denotes NFAT5
T3818 354-359 Positive_regulation denotes using
T3817 370-378 Protein denotes Hind III
T3816 360-365 Protein denotes Xho I
R3025 T3816 T3818 themeOf Xho I,using

testone

Id Subject Object Predicate Lexical cue
T3578 1041-1051 Protein denotes luciferase
T3577 992-1005 Protein denotes Reporter gene
T3576 752-762 Protein denotes luciferase

test3

Id Subject Object Predicate Lexical cue
T3584 1041-1051 Protein denotes luciferase
T3583 992-1005 Protein denotes Reporter gene
T3582 752-762 Protein denotes luciferase
T3581 1041-1051 Protein denotes luciferase
T3580 992-1005 Protein denotes Reporter gene
T3579 752-762 Protein denotes luciferase