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PMC:1186732 / 56372-57413 JSONTXT

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craft-sa-dev

Id Subject Object Predicate Lexical cue
T12883 0-2 FW denotes In
T12884 3-7 FW denotes Situ
T12885 8-21 NN denotes hybridization
T12886 21-22 . denotes .
T12887 22-172 sentence denotes Section in situ hybridization was performed as previously described [61] using 20-μm cryosections from OCT-embedded tissue or 4-μm paraffin sections.
T12888 23-30 NN denotes Section
T12889 39-52 NN denotes hybridization
T12890 31-33 FW denotes in
T12891 34-38 FW denotes situ
T12892 57-66 VBN denotes performed
T12893 53-56 VBD denotes was
T12894 67-69 IN denotes as
T12895 81-90 VBN denotes described
T12896 70-80 RB denotes previously
T12897 91-92 -LRB- denotes [
T12898 92-94 CD denotes 61
T12899 94-95 -RRB- denotes ]
T12900 96-101 VBG denotes using
T12901 102-104 CD denotes 20
T12902 105-107 NN denotes μm
T12903 104-105 HYPH denotes -
T12904 108-120 NNS denotes cryosections
T12905 121-125 IN denotes from
T12906 126-129 NN denotes OCT
T12907 130-138 VBN denotes embedded
T12908 129-130 HYPH denotes -
T12909 139-145 NN denotes tissue
T12910 146-148 CC denotes or
T12911 149-150 CD denotes 4
T12912 151-153 NN denotes μm
T12913 150-151 HYPH denotes -
T12914 163-171 NNS denotes sections
T12915 154-162 NN denotes paraffin
T12916 171-172 . denotes .
T12917 172-286 sentence denotes All in situ hybridizations were performed with the mutant and wild-type control sections on the same glass slide.
T12918 173-176 DT denotes All
T12919 185-199 NNS denotes hybridizations
T12920 177-179 FW denotes in
T12921 180-184 FW denotes situ
T12922 205-214 VBN denotes performed
T12923 200-204 VBD denotes were
T12924 215-219 IN denotes with
T12925 220-223 DT denotes the
T12926 253-261 NNS denotes sections
T12927 224-230 NN denotes mutant
T12928 231-234 CC denotes and
T12929 235-239 JJ denotes wild
T12930 240-244 NN denotes type
T12931 239-240 HYPH denotes -
T12932 245-252 NN denotes control
T12933 262-264 IN denotes on
T12934 265-268 DT denotes the
T12935 280-285 NN denotes slide
T12936 269-273 JJ denotes same
T12937 274-279 NN denotes glass
T12938 285-286 . denotes .
T12939 286-434 sentence denotes Riboprobes labeled with digoxygenin-tagged UTP (Roche, Basel, Switzerland) were detected with NBT/BCIP (Sigma, St. Louis, Missouri, United States).
T12940 287-297 NNS denotes Riboprobes
T12941 367-375 VBN denotes detected
T12942 298-305 VBN denotes labeled
T12943 306-310 IN denotes with
T12944 311-322 NN denotes digoxygenin
T12945 323-329 VBN denotes tagged
T12946 322-323 HYPH denotes -
T12947 330-333 NN denotes UTP
T12948 334-335 -LRB- denotes (
T12949 335-340 NNP denotes Roche
T12950 340-342 , denotes ,
T12951 342-347 NNP denotes Basel
T12952 347-349 , denotes ,
T12953 349-360 NNP denotes Switzerland
T12954 360-361 -RRB- denotes )
T12955 362-366 VBD denotes were
T12956 376-380 IN denotes with
T12957 381-384 NN denotes NBT
T12958 385-389 NN denotes BCIP
T12959 384-385 HYPH denotes /
T12960 390-391 -LRB- denotes (
T12961 391-396 NNP denotes Sigma
T12962 396-398 , denotes ,
T12963 398-401 NNP denotes St.
T12964 402-407 NNP denotes Louis
T12965 407-409 , denotes ,
T12966 409-417 NNP denotes Missouri
T12967 417-419 , denotes ,
T12968 419-425 NNP denotes United
T12969 426-432 NNP denotes States
T12970 432-433 -RRB- denotes )
T12971 433-434 . denotes .
T12972 434-529 sentence denotes The sources of the individual riboprobes used in this study are described in Tables S1 and S2.
T12973 435-438 DT denotes The
T12974 439-446 NNS denotes sources
T12975 499-508 VBN denotes described
T12976 447-449 IN denotes of
T12977 450-453 DT denotes the
T12978 465-475 NNS denotes riboprobes
T12979 454-464 JJ denotes individual
T12980 476-480 VBN denotes used
T12981 481-483 IN denotes in
T12982 484-488 DT denotes this
T12983 489-494 NN denotes study
T12984 495-498 VBP denotes are
T12985 509-511 IN denotes in
T12986 512-518 NNS denotes Tables
T12987 519-521 NN denotes S1
T12988 522-525 CC denotes and
T12989 526-528 NN denotes S2
T12990 528-529 . denotes .
T12991 529-700 sentence denotes Dissociated cell in situ hybridization was performed as described previously [62] using the same S-opsin digoxygenin-labeled probe used for section in situ hybridization.
T12992 530-541 VBN denotes Dissociated
T12993 555-568 NN denotes hybridization
T12994 542-546 NN denotes cell
T12995 547-549 FW denotes in
T12996 550-554 FW denotes situ
T12997 573-582 VBN denotes performed
T12998 569-572 VBD denotes was
T12999 583-585 IN denotes as
T13000 586-595 VBN denotes described
T13001 596-606 RB denotes previously
T13002 607-608 -LRB- denotes [
T13003 608-610 CD denotes 62
T13004 610-611 -RRB- denotes ]
T13005 612-617 VBG denotes using
T13006 618-621 DT denotes the
T13007 655-660 NN denotes probe
T13008 622-626 JJ denotes same
T13009 627-628 NN denotes S
T13010 629-634 NN denotes opsin
T13011 628-629 HYPH denotes -
T13012 635-646 JJ denotes digoxygenin
T13013 647-654 JJ denotes labeled
T13014 646-647 HYPH denotes -
T13015 661-665 VBN denotes used
T13016 666-669 IN denotes for
T13017 670-677 NN denotes section
T13018 686-699 NN denotes hybridization
T13019 678-680 FW denotes in
T13020 681-685 FW denotes situ
T13021 699-700 . denotes .
T13022 700-825 sentence denotes All images were captured on a compound microscope (Eclipse e1000; Nikon, Tokyo, Japan) using a CCD camera (DXM1200F, Nikon).
T13023 701-704 DT denotes All
T13024 705-711 NNS denotes images
T13025 717-725 VBN denotes captured
T13026 712-716 VBD denotes were
T13027 726-728 IN denotes on
T13028 729-730 DT denotes a
T13029 740-750 NN denotes microscope
T13030 731-739 NN denotes compound
T13031 751-752 -LRB- denotes (
T13032 760-765 NN denotes e1000
T13033 752-759 NN denotes Eclipse
T13034 765-766 : denotes ;
T13035 767-772 NNP denotes Nikon
T13036 772-774 , denotes ,
T13037 774-779 NNP denotes Tokyo
T13038 779-781 , denotes ,
T13039 781-786 NNP denotes Japan
T13040 786-787 -RRB- denotes )
T13041 788-793 VBG denotes using
T13042 794-795 DT denotes a
T13043 800-806 NN denotes camera
T13044 796-799 NN denotes CCD
T13045 807-808 -LRB- denotes (
T13046 808-816 NN denotes DXM1200F
T13047 816-818 , denotes ,
T13048 818-823 NNP denotes Nikon
T13049 823-824 -RRB- denotes )
T13050 824-825 . denotes .
T13051 825-937 sentence denotes S-opsin positive cells were quantitated on dissociated cell in situ hybridization as previously described [62].
T13052 826-827 NN denotes S
T13053 828-833 NN denotes opsin
T13054 827-828 HYPH denotes -
T13055 834-842 JJ denotes positive
T13056 843-848 NNS denotes cells
T13057 854-865 VBN denotes quantitated
T13058 849-853 VBD denotes were
T13059 866-868 IN denotes on
T13060 869-880 VBN denotes dissociated
T13061 894-907 NN denotes hybridization
T13062 881-885 NN denotes cell
T13063 886-888 FW denotes in
T13064 889-893 FW denotes situ
T13065 908-910 IN denotes as
T13066 922-931 VBN denotes described
T13067 911-921 RB denotes previously
T13068 932-933 -LRB- denotes [
T13069 933-935 CD denotes 62
T13070 935-936 -RRB- denotes ]
T13071 936-937 . denotes .
T13072 937-1041 sentence denotes Twenty fields were quantitated in this manner at 200× magnification for both rd7 and wild-type retinas.
T13073 938-944 CD denotes Twenty
T13074 945-951 NNS denotes fields
T13075 957-968 VBN denotes quantitated
T13076 952-956 VBD denotes were
T13077 969-971 IN denotes in
T13078 972-976 DT denotes this
T13079 977-983 NN denotes manner
T13080 984-986 IN denotes at
T13081 987-990 CD denotes 200
T13082 992-1005 NN denotes magnification
T13083 990-991 SYM denotes ×
T13084 1006-1009 IN denotes for
T13085 1010-1014 CC denotes both
T13086 1033-1040 NNS denotes retinas
T13087 1015-1018 NN denotes rd7
T13088 1019-1022 CC denotes and
T13089 1023-1027 JJ denotes wild
T13090 1028-1032 NN denotes type
T13091 1027-1028 HYPH denotes -
T13092 1040-1041 . denotes .
R8609 T12883 T12884 advmod In,Situ
R8610 T12884 T12885 amod Situ,hybridization
R8611 T12886 T12885 punct .,hybridization
R8612 T12888 T12889 nmod Section,hybridization
R8613 T12889 T12892 nsubjpass hybridization,performed
R8614 T12890 T12891 advmod in,situ
R8615 T12891 T12889 amod situ,hybridization
R8616 T12893 T12892 auxpass was,performed
R8617 T12894 T12895 mark as,described
R8618 T12895 T12892 advcl described,performed
R8619 T12896 T12895 advmod previously,described
R8620 T12897 T12898 punct [,61
R8621 T12898 T12892 parataxis 61,performed
R8622 T12899 T12898 punct ],61
R8623 T12900 T12892 advcl using,performed
R8624 T12901 T12902 nummod 20,μm
R8625 T12902 T12904 compound μm,cryosections
R8626 T12903 T12902 punct -,μm
R8627 T12904 T12900 dobj cryosections,using
R8628 T12905 T12904 prep from,cryosections
R8629 T12906 T12907 npadvmod OCT,embedded
R8630 T12907 T12909 amod embedded,tissue
R8631 T12908 T12907 punct -,embedded
R8632 T12909 T12905 pobj tissue,from
R8633 T12910 T12904 cc or,cryosections
R8634 T12911 T12912 nummod 4,μm
R8635 T12912 T12914 compound μm,sections
R8636 T12913 T12912 punct -,μm
R8637 T12914 T12904 conj sections,cryosections
R8638 T12915 T12914 compound paraffin,sections
R8639 T12916 T12892 punct .,performed
R8640 T12918 T12919 det All,hybridizations
R8641 T12919 T12922 nsubjpass hybridizations,performed
R8642 T12920 T12921 advmod in,situ
R8643 T12921 T12919 amod situ,hybridizations
R8644 T12923 T12922 auxpass were,performed
R8645 T12924 T12922 prep with,performed
R8646 T12925 T12926 det the,sections
R8647 T12926 T12924 pobj sections,with
R8648 T12927 T12926 nmod mutant,sections
R8649 T12928 T12927 cc and,mutant
R8650 T12929 T12930 amod wild,type
R8651 T12930 T12927 conj type,mutant
R8652 T12931 T12930 punct -,type
R8653 T12932 T12926 compound control,sections
R8654 T12933 T12926 prep on,sections
R8655 T12934 T12935 det the,slide
R8656 T12935 T12933 pobj slide,on
R8657 T12936 T12935 amod same,slide
R8658 T12937 T12935 compound glass,slide
R8659 T12938 T12922 punct .,performed
R8660 T12940 T12941 nsubjpass Riboprobes,detected
R8661 T12942 T12940 acl labeled,Riboprobes
R8662 T12943 T12942 prep with,labeled
R8663 T12944 T12945 npadvmod digoxygenin,tagged
R8664 T12945 T12947 amod tagged,UTP
R8665 T12946 T12945 punct -,tagged
R8666 T12947 T12943 pobj UTP,with
R8667 T12948 T12949 punct (,Roche
R8668 T12949 T12947 parataxis Roche,UTP
R8669 T12950 T12949 punct ", ",Roche
R8670 T12951 T12949 npadvmod Basel,Roche
R8671 T12952 T12949 punct ", ",Roche
R8672 T12953 T12949 npadvmod Switzerland,Roche
R8673 T12954 T12949 punct ),Roche
R8674 T12955 T12941 auxpass were,detected
R8675 T12956 T12941 prep with,detected
R8676 T12957 T12958 compound NBT,BCIP
R8677 T12958 T12956 pobj BCIP,with
R8678 T12959 T12958 punct /,BCIP
R8679 T12960 T12961 punct (,Sigma
R8680 T12961 T12958 parataxis Sigma,BCIP
R8681 T12962 T12961 punct ", ",Sigma
R8682 T12963 T12964 compound St.,Louis
R8683 T12964 T12961 npadvmod Louis,Sigma
R8684 T12965 T12961 punct ", ",Sigma
R8685 T12966 T12961 npadvmod Missouri,Sigma
R8686 T12967 T12961 punct ", ",Sigma
R8687 T12968 T12969 compound United,States
R8688 T12969 T12961 npadvmod States,Sigma
R8689 T12970 T12961 punct ),Sigma
R8690 T12971 T12941 punct .,detected
R8691 T12973 T12974 det The,sources
R8692 T12974 T12975 nsubjpass sources,described
R8693 T12976 T12974 prep of,sources
R8694 T12977 T12978 det the,riboprobes
R8695 T12978 T12976 pobj riboprobes,of
R8696 T12979 T12978 amod individual,riboprobes
R8697 T12980 T12978 acl used,riboprobes
R8698 T12981 T12980 prep in,used
R8699 T12982 T12983 det this,study
R8700 T12983 T12981 pobj study,in
R8701 T12984 T12975 auxpass are,described
R8702 T12985 T12975 prep in,described
R8703 T12986 T12987 compound Tables,S1
R8704 T12987 T12985 pobj S1,in
R8705 T12988 T12987 cc and,S1
R8706 T12989 T12987 conj S2,S1
R8707 T12990 T12975 punct .,described
R8708 T12992 T12993 amod Dissociated,hybridization
R8709 T12993 T12997 nsubjpass hybridization,performed
R8710 T12994 T12993 nmod cell,hybridization
R8711 T12995 T12996 advmod in,situ
R8712 T12996 T12993 amod situ,hybridization
R8713 T12998 T12997 auxpass was,performed
R8714 T12999 T13000 mark as,described
R8715 T13000 T12997 advcl described,performed
R8716 T13001 T13000 advmod previously,described
R8717 T13002 T13003 punct [,62
R8718 T13003 T12997 parataxis 62,performed
R8719 T13004 T13003 punct ],62
R8720 T13005 T12997 advcl using,performed
R8721 T13006 T13007 det the,probe
R8722 T13007 T13005 dobj probe,using
R8723 T13008 T13007 amod same,probe
R8724 T13009 T13010 nmod S,opsin
R8725 T13010 T13007 nmod opsin,probe
R8726 T13011 T13010 punct -,opsin
R8727 T13012 T13013 amod digoxygenin,labeled
R8728 T13013 T13007 amod labeled,probe
R8729 T13014 T13013 punct -,labeled
R8730 T13015 T13007 acl used,probe
R8731 T13016 T13015 prep for,used
R8732 T13017 T13018 nmod section,hybridization
R8733 T13018 T13016 pobj hybridization,for
R8734 T13019 T13020 advmod in,situ
R8735 T13020 T13018 amod situ,hybridization
R8736 T13021 T12997 punct .,performed
R8737 T13023 T13024 det All,images
R8738 T13024 T13025 nsubjpass images,captured
R8739 T13026 T13025 auxpass were,captured
R8740 T13027 T13025 prep on,captured
R8741 T13028 T13029 det a,microscope
R8742 T13029 T13027 pobj microscope,on
R8743 T13030 T13029 compound compound,microscope
R8744 T13031 T13032 punct (,e1000
R8745 T13032 T13029 parataxis e1000,microscope
R8746 T13033 T13032 compound Eclipse,e1000
R8747 T13034 T13032 punct ;,e1000
R8748 T13035 T13032 npadvmod Nikon,e1000
R8749 T13036 T13032 punct ", ",e1000
R8750 T13037 T13032 npadvmod Tokyo,e1000
R8751 T13038 T13032 punct ", ",e1000
R8752 T13039 T13032 npadvmod Japan,e1000
R8753 T13040 T13032 punct ),e1000
R8754 T13041 T13025 advcl using,captured
R8755 T13042 T13043 det a,camera
R8756 T13043 T13041 dobj camera,using
R8757 T13044 T13043 compound CCD,camera
R8758 T13045 T13046 punct (,DXM1200F
R8759 T13046 T13043 parataxis DXM1200F,camera
R8760 T13047 T13046 punct ", ",DXM1200F
R8761 T13048 T13046 npadvmod Nikon,DXM1200F
R8762 T13049 T13046 punct ),DXM1200F
R8763 T13050 T13025 punct .,captured
R8764 T13052 T13053 compound S,opsin
R8765 T13053 T13055 npadvmod opsin,positive
R8766 T13054 T13053 punct -,opsin
R8767 T13055 T13056 amod positive,cells
R8768 T13056 T13057 nsubjpass cells,quantitated
R8769 T13058 T13057 auxpass were,quantitated
R8770 T13059 T13057 prep on,quantitated
R8771 T13060 T13061 amod dissociated,hybridization
R8772 T13061 T13059 pobj hybridization,on
R8773 T13062 T13061 nmod cell,hybridization
R8774 T13063 T13064 advmod in,situ
R8775 T13064 T13061 amod situ,hybridization
R8776 T13065 T13066 mark as,described
R8777 T13066 T13057 advcl described,quantitated
R8778 T13067 T13066 advmod previously,described
R8779 T13068 T13069 punct [,62
R8780 T13069 T13057 parataxis 62,quantitated
R8781 T13070 T13069 punct ],62
R8782 T13071 T13057 punct .,quantitated
R8783 T13073 T13074 nummod Twenty,fields
R8784 T13074 T13075 nsubjpass fields,quantitated
R8785 T13076 T13075 auxpass were,quantitated
R8786 T13077 T13075 prep in,quantitated
R8787 T13078 T13079 det this,manner
R8788 T13079 T13077 pobj manner,in
R8789 T13080 T13075 prep at,quantitated
R8790 T13081 T13082 nummod 200,magnification
R8791 T13082 T13080 pobj magnification,at
R8792 T13083 T13081 punct ×,200
R8793 T13084 T13075 prep for,quantitated
R8794 T13085 T13086 preconj both,retinas
R8795 T13086 T13084 pobj retinas,for
R8796 T13087 T13086 nmod rd7,retinas
R8797 T13088 T13087 cc and,rd7
R8798 T13089 T13090 amod wild,type
R8799 T13090 T13087 conj type,rd7
R8800 T13091 T13090 punct -,type
R8801 T13092 T13075 punct .,quantitated

craft-ca-core-ex-dev

Below, discontinuous spans are shown in the bag model. You can change it to the chain model.

Id Subject Object Predicate Lexical cue
T12856 8-21 GO:0097617 denotes hybridization
T12857 39-52 GO:0097617 denotes hybridization
T12858 139-145 UBERON:0000479 denotes tissue
T12859 185-199 GO:0097617 denotes hybridizations
T12860 224-230 SO_EXT:sequence_altered_entity_or_alteration_process denotes mutant
T12861 235-244 SO_EXT:wild_type_entity_or_quality denotes wild-type
T12862 287-297 CHEBI_SO_EXT:riboprobe denotes Riboprobes
T12863 298-305 CHEBI_SO_EXT:molecular_label_or_mark_or_tag_process denotes labeled
T12864 311-322 CHEBI:42098 denotes digoxygenin
T12865 323-329 CHEBI_SO_EXT:molecular_label_or_mark_or_tag_process denotes tagged
T12866 330-333 CHEBI_EXT:UTP denotes UTP
T12867 381-384 CHEBI:7586 denotes NBT
T12868 385-389 CHEBI:75508 denotes BCIP
T12869 465-475 CHEBI_SO_EXT:riboprobe denotes riboprobes
T12870 542-546 CL_GO_EXT:cell denotes cell
T12871 555-568 GO:0097617 denotes hybridization
T12872 627-634 PR_EXT:000001195 denotes S-opsin
T12873 635-646 CHEBI:42098 denotes digoxygenin
T12874 647-654 CHEBI_SO_EXT:molecular_label_or_mark_or_tag_process denotes labeled
T12875 655-660 CHEBI_SO_EXT:molecular_probe denotes probe
T12876 686-699 GO:0097617 denotes hybridization
T12877 826-833 PR_EXT:000001195 denotes S-opsin
T12878 843-848 CL_GO_EXT:cell denotes cells
T12879 881-885 CL_GO_EXT:cell denotes cell
T12880 894-907 GO:0097617 denotes hybridization
T12881 1023-1032 SO_EXT:wild_type_entity_or_quality denotes wild-type
T12882 1033-1040 UBERON:0000966 denotes retinas

craft-ca-core-dev

Below, discontinuous spans are shown in the bag model. You can change it to the chain model.

Id Subject Object Predicate Lexical cue
T12851 635-646 CHEBI:42098 denotes digoxygenin
T12852 686-699 GO:0097617 denotes hybridization
T12853 826-833 PR:000001195 denotes S-opsin
T12854 894-907 GO:0097617 denotes hybridization
T12855 1033-1040 UBERON:0000966 denotes retinas
T12842 8-21 GO:0097617 denotes hybridization
T12843 39-52 GO:0097617 denotes hybridization
T12844 139-145 UBERON:0000479 denotes tissue
T12845 185-199 GO:0097617 denotes hybridizations
T12846 311-322 CHEBI:42098 denotes digoxygenin
T12847 381-384 CHEBI:7586 denotes NBT
T12848 385-389 CHEBI:75508 denotes BCIP
T12849 555-568 GO:0097617 denotes hybridization
T12850 627-634 PR:000001195 denotes S-opsin

2_test

Id Subject Object Predicate Lexical cue
16110338-9925646-85798574 92-94 9925646 denotes 61
16110338-15226823-85798575 608-610 15226823 denotes 62
16110338-15226823-85798576 933-935 15226823 denotes 62
T45653 92-94 9925646 denotes 61
T61849 608-610 15226823 denotes 62
T5184 933-935 15226823 denotes 62