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PubMed:18525076 JSONTXT

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PMID_GLOBAL

Id Subject Object Predicate Lexical cue mondo_id
T1 403-405 DiseaseOrPhenotypicFeature denotes BA 0003024
T2 667-674 DiseaseOrPhenotypicFeature denotes abscess 0005227
T3 877-884 DiseaseOrPhenotypicFeature denotes abscess 0005227
T4 1228-1230 DiseaseOrPhenotypicFeature denotes LS 0009723
T5 1259-1261 DiseaseOrPhenotypicFeature denotes BA 0003024
T6 1821-1823 DiseaseOrPhenotypicFeature denotes DM 0005015|0016367
T8 2359-2379 DiseaseOrPhenotypicFeature denotes bacterial infections 0005113

sentences

Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-83 Sentence denotes Characteristics of carbohydrate antigen binding to the presentation protein HLA-DR.
TextSentencer_T2 84-439 Sentence denotes Zwitterionic polysaccharide antigens (ZPSs) were recently shown to activate T cells in a class II major histocompatibility complex (MHCII)-dependent fashion requiring antigen presenting cell (APC)-mediated oxidative processing although little is known about the mechanism or affinity of carbohydrate presentation (Cobb BA, Wang Q, Tzianabos AO, Kasper DL.
TextSentencer_T3 440-445 Sentence denotes 2004.
TextSentencer_T4 446-510 Sentence denotes Polysaccharide processing and presentation by the MHCII pathway.
TextSentencer_T5 511-516 Sentence denotes Cell.
TextSentencer_T6 517-530 Sentence denotes 117:677-687).
TextSentencer_T7 531-636 Sentence denotes A recent study showed that the helical conformation of ZPSs (Wang Y, Kalka-Moll WM, Roehrl MH, Kasper DL.
TextSentencer_T8 637-642 Sentence denotes 2000.
TextSentencer_T9 643-730 Sentence denotes Structural basis of the abscess-modulating polysaccharide A2 from Bacteroides fragilis.
TextSentencer_T10 731-754 Sentence denotes Proc Natl Acad Sci USA.
TextSentencer_T11 755-810 Sentence denotes 97:13478-13483; Choi YH, Roehrl MH, Kasper DL, Wang JY.
TextSentencer_T12 811-816 Sentence denotes 2002.
TextSentencer_T13 817-925 Sentence denotes A unique structural pattern shared by T-cell-activating and abscess-regulating zwitterionic polysaccharides.
TextSentencer_T14 926-939 Sentence denotes Biochemistry.
TextSentencer_T15 940-1062 Sentence denotes 41:15144-15151) is closely linked with immunogenic activity (Tzianabos AO, Onderdonk AB, Rosner B, Cisneros RL, Kasper DL.
TextSentencer_T16 1063-1068 Sentence denotes 1993.
TextSentencer_T17 1069-1146 Sentence denotes Structural features of polysaccharides that induce intra-abdominal abscesses.
TextSentencer_T18 1147-1155 Sentence denotes Science.
TextSentencer_T19 1156-1262 Sentence denotes 262:416-419) and is stabilized by a zwitterionic charge motif (Kreisman LS, Friedman JH, Neaga A, Cobb BA.
TextSentencer_T20 1263-1268 Sentence denotes 2007.
TextSentencer_T21 1269-1375 Sentence denotes Structure and function relations with a T-cell-activating polysaccharide antigen using circular dichroism.
TextSentencer_T22 1376-1389 Sentence denotes Glycobiology.
TextSentencer_T23 1390-1466 Sentence denotes 17:46-55), suggesting a strong carbohydrate structure-function relationship.
TextSentencer_T24 1467-1647 Sentence denotes In this study, we show that PSA, the ZPS from Bacteroides fragilis, associates with MHCII at high affinity and 1:1 stoichiometry through a mechanism mirroring peptide presentation.
TextSentencer_T25 1648-1788 Sentence denotes Interestingly, PSA binding was mutually exclusive with common MHCII antigens and showed significant allelic differences in binding affinity.
TextSentencer_T26 1789-1994 Sentence denotes The antigen exchange factor HLA-DM that catalyzes peptide antigen association with MHCII also increased the rate of ZPS association and was required for APC presentation and ZPS-mediated T cell activation.
TextSentencer_T27 1995-2170 Sentence denotes Finally, the zwitterionic nature of these antigens was required only for MHCII binding, and not endocytosis, processing, or vesicular trafficking to MHCII-containing vesicles.
TextSentencer_T28 2171-2380 Sentence denotes This report is the first quantitative analysis of the binding mechanism of carbohydrate antigens with MHCII and leads to a novel model for nontraditional MHCII antigen presentation during bacterial infections.
T1 0-83 Sentence denotes Characteristics of carbohydrate antigen binding to the presentation protein HLA-DR.
T2 84-439 Sentence denotes Zwitterionic polysaccharide antigens (ZPSs) were recently shown to activate T cells in a class II major histocompatibility complex (MHCII)-dependent fashion requiring antigen presenting cell (APC)-mediated oxidative processing although little is known about the mechanism or affinity of carbohydrate presentation (Cobb BA, Wang Q, Tzianabos AO, Kasper DL.
T3 440-445 Sentence denotes 2004.
T4 446-510 Sentence denotes Polysaccharide processing and presentation by the MHCII pathway.
T5 511-530 Sentence denotes Cell. 117:677-687).
T6 531-636 Sentence denotes A recent study showed that the helical conformation of ZPSs (Wang Y, Kalka-Moll WM, Roehrl MH, Kasper DL.
T7 637-642 Sentence denotes 2000.
T8 643-730 Sentence denotes Structural basis of the abscess-modulating polysaccharide A2 from Bacteroides fragilis.
T9 731-754 Sentence denotes Proc Natl Acad Sci USA.
T10 755-810 Sentence denotes 97:13478-13483; Choi YH, Roehrl MH, Kasper DL, Wang JY.
T11 811-816 Sentence denotes 2002.
T12 817-925 Sentence denotes A unique structural pattern shared by T-cell-activating and abscess-regulating zwitterionic polysaccharides.
T13 926-1062 Sentence denotes Biochemistry. 41:15144-15151) is closely linked with immunogenic activity (Tzianabos AO, Onderdonk AB, Rosner B, Cisneros RL, Kasper DL.
T14 1063-1068 Sentence denotes 1993.
T15 1069-1146 Sentence denotes Structural features of polysaccharides that induce intra-abdominal abscesses.
T16 1147-1262 Sentence denotes Science. 262:416-419) and is stabilized by a zwitterionic charge motif (Kreisman LS, Friedman JH, Neaga A, Cobb BA.
T17 1263-1268 Sentence denotes 2007.
T18 1269-1375 Sentence denotes Structure and function relations with a T-cell-activating polysaccharide antigen using circular dichroism.
T19 1376-1466 Sentence denotes Glycobiology. 17:46-55), suggesting a strong carbohydrate structure-function relationship.
T20 1467-1647 Sentence denotes In this study, we show that PSA, the ZPS from Bacteroides fragilis, associates with MHCII at high affinity and 1:1 stoichiometry through a mechanism mirroring peptide presentation.
T21 1648-1788 Sentence denotes Interestingly, PSA binding was mutually exclusive with common MHCII antigens and showed significant allelic differences in binding affinity.
T22 1789-1994 Sentence denotes The antigen exchange factor HLA-DM that catalyzes peptide antigen association with MHCII also increased the rate of ZPS association and was required for APC presentation and ZPS-mediated T cell activation.
T23 1995-2170 Sentence denotes Finally, the zwitterionic nature of these antigens was required only for MHCII binding, and not endocytosis, processing, or vesicular trafficking to MHCII-containing vesicles.
T24 2171-2380 Sentence denotes This report is the first quantitative analysis of the binding mechanism of carbohydrate antigens with MHCII and leads to a novel model for nontraditional MHCII antigen presentation during bacterial infections.
T1 0-83 Sentence denotes Characteristics of carbohydrate antigen binding to the presentation protein HLA-DR.
T2 84-439 Sentence denotes Zwitterionic polysaccharide antigens (ZPSs) were recently shown to activate T cells in a class II major histocompatibility complex (MHCII)-dependent fashion requiring antigen presenting cell (APC)-mediated oxidative processing although little is known about the mechanism or affinity of carbohydrate presentation (Cobb BA, Wang Q, Tzianabos AO, Kasper DL.
T3 440-445 Sentence denotes 2004.
T4 446-510 Sentence denotes Polysaccharide processing and presentation by the MHCII pathway.
T5 511-516 Sentence denotes Cell.
T6 517-530 Sentence denotes 117:677-687).
T7 531-636 Sentence denotes A recent study showed that the helical conformation of ZPSs (Wang Y, Kalka-Moll WM, Roehrl MH, Kasper DL.
T8 637-642 Sentence denotes 2000.
T9 643-730 Sentence denotes Structural basis of the abscess-modulating polysaccharide A2 from Bacteroides fragilis.
T10 731-754 Sentence denotes Proc Natl Acad Sci USA.
T11 755-810 Sentence denotes 97:13478-13483; Choi YH, Roehrl MH, Kasper DL, Wang JY.
T12 811-816 Sentence denotes 2002.
T13 817-925 Sentence denotes A unique structural pattern shared by T-cell-activating and abscess-regulating zwitterionic polysaccharides.
T14 926-939 Sentence denotes Biochemistry.
T15 940-1062 Sentence denotes 41:15144-15151) is closely linked with immunogenic activity (Tzianabos AO, Onderdonk AB, Rosner B, Cisneros RL, Kasper DL.
T16 1063-1068 Sentence denotes 1993.
T17 1069-1146 Sentence denotes Structural features of polysaccharides that induce intra-abdominal abscesses.
T18 1147-1155 Sentence denotes Science.
T19 1156-1262 Sentence denotes 262:416-419) and is stabilized by a zwitterionic charge motif (Kreisman LS, Friedman JH, Neaga A, Cobb BA.
T20 1263-1268 Sentence denotes 2007.
T21 1269-1375 Sentence denotes Structure and function relations with a T-cell-activating polysaccharide antigen using circular dichroism.
T22 1376-1389 Sentence denotes Glycobiology.
T23 1390-1466 Sentence denotes 17:46-55), suggesting a strong carbohydrate structure-function relationship.
T24 1467-1647 Sentence denotes In this study, we show that PSA, the ZPS from Bacteroides fragilis, associates with MHCII at high affinity and 1:1 stoichiometry through a mechanism mirroring peptide presentation.
T25 1648-1788 Sentence denotes Interestingly, PSA binding was mutually exclusive with common MHCII antigens and showed significant allelic differences in binding affinity.
T26 1789-1994 Sentence denotes The antigen exchange factor HLA-DM that catalyzes peptide antigen association with MHCII also increased the rate of ZPS association and was required for APC presentation and ZPS-mediated T cell activation.
T27 1995-2170 Sentence denotes Finally, the zwitterionic nature of these antigens was required only for MHCII binding, and not endocytosis, processing, or vesicular trafficking to MHCII-containing vesicles.
T28 2171-2380 Sentence denotes This report is the first quantitative analysis of the binding mechanism of carbohydrate antigens with MHCII and leads to a novel model for nontraditional MHCII antigen presentation during bacterial infections.

ICD10

Id Subject Object Predicate Lexical cue
T1 173-214 http://purl.bioontology.org/ontology/ICD10/D81.7 denotes class II major histocompatibility complex
T2 2359-2379 http://purl.bioontology.org/ontology/ICD10/A49.9 denotes bacterial infections

uniprot-human

Id Subject Object Predicate Lexical cue
T1 276-279 http://www.uniprot.org/uniprot/P25054 denotes APC
T2 1942-1945 http://www.uniprot.org/uniprot/P25054 denotes APC
T3 425-427 http://www.uniprot.org/uniprot/Q06278 denotes AO
T4 1011-1013 http://www.uniprot.org/uniprot/Q06278 denotes AO
T5 436-438 http://www.uniprot.org/uniprot/Q9UNE0 denotes DL
T6 633-635 http://www.uniprot.org/uniprot/Q9UNE0 denotes DL
T7 798-800 http://www.uniprot.org/uniprot/Q9UNE0 denotes DL
T8 1059-1061 http://www.uniprot.org/uniprot/Q9UNE0 denotes DL
T9 1495-1498 http://www.uniprot.org/uniprot/Q9Y617 denotes PSA
T10 1663-1666 http://www.uniprot.org/uniprot/Q9Y617 denotes PSA
T11 1495-1498 http://www.uniprot.org/uniprot/P55786 denotes PSA
T12 1663-1666 http://www.uniprot.org/uniprot/P55786 denotes PSA
T13 1495-1498 http://www.uniprot.org/uniprot/P07288 denotes PSA
T14 1663-1666 http://www.uniprot.org/uniprot/P07288 denotes PSA

uniprot-mouse

Id Subject Object Predicate Lexical cue
T1 276-279 http://www.uniprot.org/uniprot/Q61315 denotes APC
T2 1942-1945 http://www.uniprot.org/uniprot/Q61315 denotes APC
T3 731-735 http://www.uniprot.org/uniprot/P33587 denotes Proc
T4 741-745 http://www.uniprot.org/uniprot/Q07417 denotes Acad
T5 1495-1498 http://www.uniprot.org/uniprot/Q11011 denotes PSA
T6 1663-1666 http://www.uniprot.org/uniprot/Q11011 denotes PSA

GlycoBiology-NCBITAXON

Id Subject Object Predicate Lexical cue
T1 162-167 http://purl.bioontology.org/ontology/STY/T025 denotes cells
T2 346-355 http://purl.bioontology.org/ontology/NCBITAXON/127244 denotes mechanism
T3 562-569 http://purl.bioontology.org/ontology/NCBITAXON/53324 denotes helical
T4 709-720 http://purl.bioontology.org/ontology/NCBITAXON/816 denotes Bacteroides
T5 709-720 http://purl.bioontology.org/ontology/NCBITAXON/200643 denotes Bacteroides
T6 1292-1301 http://purl.bioontology.org/ontology/NCBITAXON/353209 denotes relations
T7 1513-1524 http://purl.bioontology.org/ontology/NCBITAXON/200643 denotes Bacteroides
T8 1513-1524 http://purl.bioontology.org/ontology/NCBITAXON/816 denotes Bacteroides
T9 1606-1615 http://purl.bioontology.org/ontology/NCBITAXON/127244 denotes mechanism
T10 2119-2128 http://purl.bioontology.org/ontology/NCBITAXON/246680 denotes vesicular
T11 2233-2242 http://purl.bioontology.org/ontology/NCBITAXON/127244 denotes mechanism

GO-BP

Id Subject Object Predicate Lexical cue
T1 151-167 http://purl.obolibrary.org/obo/GO_0032393 denotes activate T cells
T2 151-167 http://purl.obolibrary.org/obo/GO_0032394 denotes activate T cells
T3 151-167 http://purl.obolibrary.org/obo/GO_0032395 denotes activate T cells
T4 855-872 http://purl.obolibrary.org/obo/GO_0032393 denotes T-cell-activating
T5 855-872 http://purl.obolibrary.org/obo/GO_0032394 denotes T-cell-activating
T6 855-872 http://purl.obolibrary.org/obo/GO_0032395 denotes T-cell-activating
T7 1309-1326 http://purl.obolibrary.org/obo/GO_0032393 denotes T-cell-activating
T8 1309-1326 http://purl.obolibrary.org/obo/GO_0032394 denotes T-cell-activating
T9 1309-1326 http://purl.obolibrary.org/obo/GO_0032395 denotes T-cell-activating
T10 1976-1993 http://purl.obolibrary.org/obo/GO_0032393 denotes T cell activation
T11 1976-1993 http://purl.obolibrary.org/obo/GO_0032394 denotes T cell activation
T12 1976-1993 http://purl.obolibrary.org/obo/GO_0032395 denotes T cell activation
T13 151-167 http://purl.obolibrary.org/obo/GO_0042110 denotes activate T cells
T14 855-872 http://purl.obolibrary.org/obo/GO_0042110 denotes T-cell-activating
T15 1309-1326 http://purl.obolibrary.org/obo/GO_0042110 denotes T-cell-activating
T16 1976-1993 http://purl.obolibrary.org/obo/GO_0042110 denotes T cell activation
T17 151-167 http://purl.obolibrary.org/obo/GO_0045582 denotes activate T cells
T18 855-872 http://purl.obolibrary.org/obo/GO_0045582 denotes T-cell-activating
T19 1309-1326 http://purl.obolibrary.org/obo/GO_0045582 denotes T-cell-activating
T20 1976-1993 http://purl.obolibrary.org/obo/GO_0045582 denotes T cell activation
T21 151-167 http://purl.obolibrary.org/obo/GO_0050798 denotes activate T cells
T22 855-872 http://purl.obolibrary.org/obo/GO_0050798 denotes T-cell-activating
T23 1309-1326 http://purl.obolibrary.org/obo/GO_0050798 denotes T-cell-activating
T24 1976-1993 http://purl.obolibrary.org/obo/GO_0050798 denotes T cell activation
T25 151-167 http://purl.obolibrary.org/obo/GO_0050863 denotes activate T cells
T26 855-872 http://purl.obolibrary.org/obo/GO_0050863 denotes T-cell-activating
T27 1309-1326 http://purl.obolibrary.org/obo/GO_0050863 denotes T-cell-activating
T28 1976-1993 http://purl.obolibrary.org/obo/GO_0050863 denotes T cell activation
T29 151-167 http://purl.obolibrary.org/obo/GO_0051132 denotes activate T cells
T30 855-872 http://purl.obolibrary.org/obo/GO_0051132 denotes T-cell-activating
T31 1309-1326 http://purl.obolibrary.org/obo/GO_0051132 denotes T-cell-activating
T32 1976-1993 http://purl.obolibrary.org/obo/GO_0051132 denotes T cell activation
T33 151-167 http://purl.obolibrary.org/obo/GO_1903905 denotes activate T cells
T34 855-872 http://purl.obolibrary.org/obo/GO_1903905 denotes T-cell-activating
T35 1309-1326 http://purl.obolibrary.org/obo/GO_1903905 denotes T-cell-activating
T36 1976-1993 http://purl.obolibrary.org/obo/GO_1903905 denotes T cell activation
T37 151-167 http://purl.obolibrary.org/obo/GO_0042102 denotes activate T cells
T38 855-872 http://purl.obolibrary.org/obo/GO_0042102 denotes T-cell-activating
T39 1309-1326 http://purl.obolibrary.org/obo/GO_0042102 denotes T-cell-activating
T40 1976-1993 http://purl.obolibrary.org/obo/GO_0042102 denotes T cell activation
T41 251-269 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen presenting
T42 2331-2351 http://purl.obolibrary.org/obo/GO_0019882 denotes antigen presentation
T43 398-402 http://purl.obolibrary.org/obo/GO_0042242 denotes Cobb
T44 398-402 http://purl.obolibrary.org/obo/GO_0043802 denotes Cobb
T45 1254-1258 http://purl.obolibrary.org/obo/GO_0042242 denotes Cobb
T46 1254-1258 http://purl.obolibrary.org/obo/GO_0043802 denotes Cobb
T47 741-745 http://purl.obolibrary.org/obo/GO_0070238 denotes Acad
T48 857-872 http://purl.obolibrary.org/obo/GO_0001775 denotes cell-activating
T49 1311-1326 http://purl.obolibrary.org/obo/GO_0001775 denotes cell-activating
T50 1978-1993 http://purl.obolibrary.org/obo/GO_0001775 denotes cell activation
T51 885-895 http://purl.obolibrary.org/obo/GO_0065007 denotes regulating
T52 1228-1230 http://purl.obolibrary.org/obo/GO_0016992 denotes LS
T53 1679-1687 http://purl.obolibrary.org/obo/GO_0085030 denotes mutually
T54 1801-1809 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange
T55 2091-2102 http://purl.obolibrary.org/obo/GO_0006897 denotes endocytosis

GO-MF

Id Subject Object Predicate Lexical cue
T1 32-47 http://purl.obolibrary.org/obo/GO_0003823 denotes antigen binding
T2 40-47 http://purl.obolibrary.org/obo/GO_0070026 denotes binding
T3 1667-1674 http://purl.obolibrary.org/obo/GO_0070026 denotes binding
T4 1771-1778 http://purl.obolibrary.org/obo/GO_0070026 denotes binding
T5 2074-2081 http://purl.obolibrary.org/obo/GO_0070026 denotes binding
T6 2225-2232 http://purl.obolibrary.org/obo/GO_0070026 denotes binding
T7 40-47 http://purl.obolibrary.org/obo/GO_0003680 denotes binding
T8 1667-1674 http://purl.obolibrary.org/obo/GO_0003680 denotes binding
T9 1771-1778 http://purl.obolibrary.org/obo/GO_0003680 denotes binding
T10 2074-2081 http://purl.obolibrary.org/obo/GO_0003680 denotes binding
T11 2225-2232 http://purl.obolibrary.org/obo/GO_0003680 denotes binding
T12 40-47 http://purl.obolibrary.org/obo/GO_0017091 denotes binding
T13 1667-1674 http://purl.obolibrary.org/obo/GO_0017091 denotes binding
T14 1771-1778 http://purl.obolibrary.org/obo/GO_0017091 denotes binding
T15 2074-2081 http://purl.obolibrary.org/obo/GO_0017091 denotes binding
T16 2225-2232 http://purl.obolibrary.org/obo/GO_0017091 denotes binding
T17 40-47 http://purl.obolibrary.org/obo/GO_0005488 denotes binding
T18 1667-1674 http://purl.obolibrary.org/obo/GO_0005488 denotes binding
T19 1771-1778 http://purl.obolibrary.org/obo/GO_0005488 denotes binding
T20 2074-2081 http://purl.obolibrary.org/obo/GO_0005488 denotes binding
T21 2225-2232 http://purl.obolibrary.org/obo/GO_0005488 denotes binding

GO-CC

Id Subject Object Predicate Lexical cue
T1 162-167 http://purl.obolibrary.org/obo/GO_0005623 denotes cells
T2 270-274 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T3 857-861 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T4 1311-1315 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T5 511-515 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T6 276-279 http://purl.obolibrary.org/obo/GO_0005680 denotes APC
T7 1942-1945 http://purl.obolibrary.org/obo/GO_0005680 denotes APC
T8 2161-2169 http://purl.obolibrary.org/obo/GO_0031982 denotes vesicles

Lectin

Id Subject Object Predicate Lexical cue
Lectin_T1 1495-1498 https://acgg.asia/db/lfdb/LfDB0181 denotes PSA
Lectin_T2 1663-1666 https://acgg.asia/db/lfdb/LfDB0181 denotes PSA

mondo_disease

Id Subject Object Predicate Lexical cue mondo_id
T1 667-674 Disease denotes abscess http://purl.obolibrary.org/obo/MONDO_0005227
T2 877-884 Disease denotes abscess http://purl.obolibrary.org/obo/MONDO_0005227
T3 1136-1145 Disease denotes abscesses http://purl.obolibrary.org/obo/MONDO_0005227
T4 2359-2379 Disease denotes bacterial infections http://purl.obolibrary.org/obo/MONDO_0005113

NCBITAXON

Id Subject Object Predicate Lexical cue db_id
T1 709-729 OrganismTaxon denotes Bacteroides fragilis 817
T2 1513-1533 OrganismTaxon denotes Bacteroides fragilis 817

Anatomy-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 855-861 Body_part denotes T-cell http://purl.obolibrary.org/obo/CL_0000084
T2 1309-1315 Body_part denotes T-cell http://purl.obolibrary.org/obo/CL_0000084
T3 1976-1982 Body_part denotes T cell http://purl.obolibrary.org/obo/CL_0000084

HP-phenotype

Id Subject Object Predicate Lexical cue hp_id
T1 667-674 Phenotype denotes abscess HP:0025615
T2 877-884 Phenotype denotes abscess HP:0025615

CL-cell

Id Subject Object Predicate Lexical cue cl_id
T1 160-167 Cell denotes T cells http://purl.obolibrary.org/obo/CL:0000084
T2 855-861 Cell denotes T-cell http://purl.obolibrary.org/obo/CL:0000084
T3 1309-1315 Cell denotes T-cell http://purl.obolibrary.org/obo/CL:0000084
T4 1976-1982 Cell denotes T cell http://purl.obolibrary.org/obo/CL:0000084