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pmc-enju-pas

bionlp-st-ge-2016-test-proteins

{"project":"bionlp-st-ge-2016-test-proteins","denotations":[{"id":"T2770","span":{"begin":1450,"end":1454},"obj":"Protein"},{"id":"T2769","span":{"begin":1059,"end":1066},"obj":"Protein"},{"id":"T2768","span":{"begin":970,"end":974},"obj":"Protein"},{"id":"T2767","span":{"begin":926,"end":933},"obj":"Protein"},{"id":"T2766","span":{"begin":917,"end":921},"obj":"Protein"},{"id":"T2765","span":{"begin":819,"end":826},"obj":"Protein"},{"id":"T2764","span":{"begin":798,"end":817},"obj":"Protein"},{"id":"T2763","span":{"begin":778,"end":796},"obj":"Protein"},{"id":"T2762","span":{"begin":678,"end":682},"obj":"Protein"},{"id":"T2761","span":{"begin":18,"end":22},"obj":"Protein"},{"id":"T2772","span":{"begin":1503,"end":1510},"obj":"Protein"},{"id":"T2771","span":{"begin":1490,"end":1494},"obj":"Protein"}],"namespaces":[{"prefix":"_base","uri":"http://bionlp.dbcls.jp/ontology/ge.owl#"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

bionlp-st-ge-2016-uniprot

{"project":"bionlp-st-ge-2016-uniprot","denotations":[{"id":"T3383","span":{"begin":1503,"end":1510},"obj":"http://www.uniprot.org/uniprot/P60709"},{"id":"T3382","span":{"begin":1059,"end":1066},"obj":"http://www.uniprot.org/uniprot/P60709"},{"id":"T3381","span":{"begin":926,"end":933},"obj":"http://www.uniprot.org/uniprot/P60709"},{"id":"T3380","span":{"begin":819,"end":826},"obj":"http://www.uniprot.org/uniprot/P60709"},{"id":"T3379","span":{"begin":1490,"end":1494},"obj":"http://www.uniprot.org/uniprot/O00206"},{"id":"T3378","span":{"begin":1450,"end":1454},"obj":"http://www.uniprot.org/uniprot/O00206"},{"id":"T3377","span":{"begin":970,"end":974},"obj":"http://www.uniprot.org/uniprot/O00206"},{"id":"T3376","span":{"begin":917,"end":921},"obj":"http://www.uniprot.org/uniprot/O00206"},{"id":"T3375","span":{"begin":678,"end":682},"obj":"http://www.uniprot.org/uniprot/O00206"},{"id":"T3374","span":{"begin":18,"end":22},"obj":"http://www.uniprot.org/uniprot/O00206"}],"namespaces":[{"prefix":"_base","uri":"http://www.uniprot.org/uniprot/"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

GO-BP

{"project":"GO-BP","denotations":[{"id":"T2775","span":{"begin":548,"end":557},"obj":"http://purl.obolibrary.org/obo/GO_0009058"},{"id":"T2774","span":{"begin":566,"end":568},"obj":"http://purl.obolibrary.org/obo/GO_0003964"},{"id":"T2773","span":{"begin":45,"end":47},"obj":"http://purl.obolibrary.org/obo/GO_0003964"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

GO-MF

{"project":"GO-MF","denotations":[{"id":"T2777","span":{"begin":566,"end":568},"obj":"http://purl.obolibrary.org/obo/GO_0003964"},{"id":"T2776","span":{"begin":45,"end":47},"obj":"http://purl.obolibrary.org/obo/GO_0003964"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

sentences

simple1

{"project":"simple1","denotations":[{"id":"T2815","span":{"begin":1503,"end":1510},"obj":"Protein"},{"id":"T2814","span":{"begin":1490,"end":1494},"obj":"Protein"},{"id":"T2813","span":{"begin":1450,"end":1454},"obj":"Protein"},{"id":"T2812","span":{"begin":1059,"end":1066},"obj":"Protein"},{"id":"T2811","span":{"begin":970,"end":974},"obj":"Protein"},{"id":"T2810","span":{"begin":926,"end":933},"obj":"Protein"},{"id":"T2809","span":{"begin":917,"end":921},"obj":"Protein"},{"id":"T2808","span":{"begin":819,"end":826},"obj":"Protein"},{"id":"T2807","span":{"begin":798,"end":817},"obj":"Protein"},{"id":"T2806","span":{"begin":778,"end":796},"obj":"Protein"},{"id":"T2805","span":{"begin":678,"end":682},"obj":"Protein"},{"id":"T2804","span":{"begin":18,"end":22},"obj":"Protein"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

BioNLP16_DUT

{"project":"BioNLP16_DUT","denotations":[{"id":"T3473","span":{"begin":1437,"end":1446},"obj":"Transcription"},{"id":"T3472","span":{"begin":1503,"end":1510},"obj":"Protein"},{"id":"T3471","span":{"begin":1490,"end":1494},"obj":"Protein"},{"id":"T3470","span":{"begin":1450,"end":1454},"obj":"Protein"},{"id":"T3469","span":{"begin":1059,"end":1066},"obj":"Protein"},{"id":"T3468","span":{"begin":970,"end":974},"obj":"Protein"},{"id":"T3467","span":{"begin":926,"end":933},"obj":"Protein"},{"id":"T3466","span":{"begin":917,"end":921},"obj":"Protein"},{"id":"T3465","span":{"begin":819,"end":826},"obj":"Protein"},{"id":"T3464","span":{"begin":798,"end":817},"obj":"Protein"},{"id":"T3463","span":{"begin":778,"end":796},"obj":"Protein"},{"id":"T3462","span":{"begin":678,"end":682},"obj":"Protein"},{"id":"T3461","span":{"begin":18,"end":22},"obj":"Protein"}],"relations":[{"id":"R2753","pred":"themeOf","subj":"T3470","obj":"T3473"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

BioNLP16_Messiy

{"project":"BioNLP16_Messiy","denotations":[{"id":"T3396","span":{"begin":1464,"end":1473},"obj":"Transcription"},{"id":"T3395","span":{"begin":1503,"end":1510},"obj":"Protein"},{"id":"T3394","span":{"begin":1490,"end":1494},"obj":"Protein"},{"id":"T3393","span":{"begin":1450,"end":1454},"obj":"Protein"},{"id":"T3392","span":{"begin":1059,"end":1066},"obj":"Protein"},{"id":"T3391","span":{"begin":970,"end":974},"obj":"Protein"},{"id":"T3390","span":{"begin":926,"end":933},"obj":"Protein"},{"id":"T3389","span":{"begin":917,"end":921},"obj":"Protein"},{"id":"T3388","span":{"begin":819,"end":826},"obj":"Protein"},{"id":"T3387","span":{"begin":798,"end":817},"obj":"Protein"},{"id":"T3386","span":{"begin":778,"end":796},"obj":"Protein"},{"id":"T3385","span":{"begin":678,"end":682},"obj":"Protein"},{"id":"T3384","span":{"begin":18,"end":22},"obj":"Protein"}],"relations":[{"id":"R2741","pred":"themeOf","subj":"T3393","obj":"T3396"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

DLUT931

{"project":"DLUT931","denotations":[{"id":"T3413","span":{"begin":1495,"end":1499},"obj":"Transcription"},{"id":"T3412","span":{"begin":1455,"end":1459},"obj":"Transcription"},{"id":"T3411","span":{"begin":1437,"end":1446},"obj":"Transcription"},{"id":"T3410","span":{"begin":23,"end":27},"obj":"Transcription"},{"id":"T3409","span":{"begin":5,"end":14},"obj":"Transcription"},{"id":"T3408","span":{"begin":1503,"end":1510},"obj":"Protein"},{"id":"T3407","span":{"begin":1490,"end":1494},"obj":"Protein"},{"id":"T3406","span":{"begin":1450,"end":1454},"obj":"Protein"},{"id":"T3405","span":{"begin":1059,"end":1066},"obj":"Protein"},{"id":"T3404","span":{"begin":970,"end":974},"obj":"Protein"},{"id":"T3403","span":{"begin":926,"end":933},"obj":"Protein"},{"id":"T3402","span":{"begin":917,"end":921},"obj":"Protein"},{"id":"T3401","span":{"begin":819,"end":826},"obj":"Protein"},{"id":"T3400","span":{"begin":798,"end":817},"obj":"Protein"},{"id":"T3399","span":{"begin":778,"end":796},"obj":"Protein"},{"id":"T3398","span":{"begin":678,"end":682},"obj":"Protein"},{"id":"T3397","span":{"begin":18,"end":22},"obj":"Protein"},{"id":"T3414","span":{"begin":1511,"end":1515},"obj":"Transcription"}],"relations":[{"id":"R2745","pred":"themeOf","subj":"T3406","obj":"T3412"},{"id":"R2746","pred":"themeOf","subj":"T3407","obj":"T3413"},{"id":"R2747","pred":"themeOf","subj":"T3408","obj":"T3414"},{"id":"R2742","pred":"themeOf","subj":"T3397","obj":"T3409"},{"id":"R2743","pred":"themeOf","subj":"T3397","obj":"T3410"},{"id":"R2744","pred":"themeOf","subj":"T3406","obj":"T3411"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

bionlp-st-ge-2016-test-ihmc

{"project":"bionlp-st-ge-2016-test-ihmc","denotations":[{"id":"T3491","span":{"begin":1299,"end":1302},"obj":"Protein"},{"id":"T3490","span":{"begin":819,"end":826},"obj":"Protein"},{"id":"T3489","span":{"begin":961,"end":964},"obj":"Protein"},{"id":"T3488","span":{"begin":798,"end":827},"obj":"Protein"},{"id":"T3487","span":{"begin":1031,"end":1066},"obj":"Protein"},{"id":"T3486","span":{"begin":15,"end":27},"obj":"Protein"},{"id":"T3485","span":{"begin":970,"end":974},"obj":"Protein"},{"id":"T3484","span":{"begin":674,"end":716},"obj":"Protein"},{"id":"T3483","span":{"begin":67,"end":70},"obj":"Protein"},{"id":"T3482","span":{"begin":865,"end":868},"obj":"Protein"},{"id":"T3481","span":{"begin":705,"end":708},"obj":"Protein"},{"id":"T3480","span":{"begin":678,"end":682},"obj":"Protein"},{"id":"T3479","span":{"begin":18,"end":22},"obj":"Protein"},{"id":"T3478","span":{"begin":365,"end":369},"obj":"Entity"},{"id":"T3477","span":{"begin":419,"end":426},"obj":"Protein"},{"id":"T3476","span":{"begin":523,"end":561},"obj":"Protein"},{"id":"T3475","span":{"begin":165,"end":168},"obj":"Protein"},{"id":"T3474","span":{"begin":775,"end":796},"obj":"Entity"},{"id":"T3460","span":{"begin":1490,"end":1494},"obj":"Protein"},{"id":"T3459","span":{"begin":913,"end":921},"obj":"Protein"},{"id":"T3458","span":{"begin":1487,"end":1499},"obj":"Protein"},{"id":"T3457","span":{"begin":1447,"end":1459},"obj":"Protein"},{"id":"T3456","span":{"begin":374,"end":379},"obj":"Entity"},{"id":"T3455","span":{"begin":1500,"end":1515},"obj":"Protein"},{"id":"T3454","span":{"begin":1450,"end":1454},"obj":"Protein"},{"id":"T3453","span":{"begin":775,"end":796},"obj":"Protein"},{"id":"T3452","span":{"begin":1341,"end":1352},"obj":"Entity"},{"id":"T3451","span":{"begin":674,"end":716},"obj":"Protein"},{"id":"T3450","span":{"begin":926,"end":968},"obj":"Protein"},{"id":"T3449","span":{"begin":747,"end":751},"obj":"Entity"},{"id":"T3448","span":{"begin":1341,"end":1348},"obj":"Entity"},{"id":"T3447","span":{"begin":566,"end":586},"obj":"Protein"},{"id":"T3446","span":{"begin":1500,"end":1515},"obj":"Protein"},{"id":"T3445","span":{"begin":454,"end":457},"obj":"Protein"},{"id":"T3444","span":{"begin":157,"end":182},"obj":"Protein"},{"id":"T3443","span":{"begin":263,"end":275},"obj":"Protein"},{"id":"T3442","span":{"begin":961,"end":968},"obj":"Protein"},{"id":"T3441","span":{"begin":42,"end":51},"obj":"Protein"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

bionlp-st-ge-2016-spacy-parsed

bionlp-st-ge-2016-test-tees

{"project":"bionlp-st-ge-2016-test-tees","denotations":[{"id":"T2803","span":{"begin":1481,"end":1486},"obj":"Positive_regulation"},{"id":"T2802","span":{"begin":1437,"end":1446},"obj":"Positive_regulation"},{"id":"T2801","span":{"begin":1503,"end":1515},"obj":"Protein"},{"id":"T2800","span":{"begin":1490,"end":1499},"obj":"Protein"},{"id":"T2799","span":{"begin":1450,"end":1459},"obj":"Protein"},{"id":"T2798","span":{"begin":1059,"end":1066},"obj":"Protein"},{"id":"T2797","span":{"begin":961,"end":968},"obj":"Protein"},{"id":"T2796","span":{"begin":926,"end":933},"obj":"Protein"},{"id":"T2795","span":{"begin":917,"end":921},"obj":"Protein"},{"id":"T2794","span":{"begin":819,"end":826},"obj":"Protein"},{"id":"T2793","span":{"begin":778,"end":796},"obj":"Protein"},{"id":"T2792","span":{"begin":566,"end":586},"obj":"Protein"},{"id":"T2791","span":{"begin":5,"end":14},"obj":"Transcription"},{"id":"T2790","span":{"begin":18,"end":27},"obj":"Protein"}],"relations":[{"id":"R2184","pred":"themeOf","subj":"T2790","obj":"T2791"},{"id":"R2185","pred":"themeOf","subj":"T2799","obj":"T2802"},{"id":"R2186","pred":"themeOf","subj":"T2800","obj":"T2803"},{"id":"R2187","pred":"causeOf","subj":"T2801","obj":"T2803"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

testone

{"project":"testone","denotations":[{"id":"T2703","span":{"begin":1464,"end":1473},"obj":"Gene_expression"},{"id":"T2702","span":{"begin":1503,"end":1510},"obj":"Protein"},{"id":"T2701","span":{"begin":1490,"end":1494},"obj":"Protein"},{"id":"T2700","span":{"begin":1450,"end":1454},"obj":"Protein"},{"id":"T2699","span":{"begin":1059,"end":1066},"obj":"Protein"},{"id":"T2698","span":{"begin":970,"end":974},"obj":"Protein"},{"id":"T2697","span":{"begin":926,"end":933},"obj":"Protein"},{"id":"T2696","span":{"begin":917,"end":921},"obj":"Protein"},{"id":"T2695","span":{"begin":819,"end":826},"obj":"Protein"},{"id":"T2694","span":{"begin":798,"end":817},"obj":"Protein"},{"id":"T2693","span":{"begin":778,"end":796},"obj":"Protein"},{"id":"T2692","span":{"begin":678,"end":682},"obj":"Protein"},{"id":"T2691","span":{"begin":18,"end":22},"obj":"Protein"}],"relations":[{"id":"R2180","pred":"equivalentTo","subj":"T2695","obj":"T2694"},{"id":"R2181","pred":"themeOf","subj":"T2701","obj":"T2703"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

test3

{"project":"test3","denotations":[{"id":"T2728","span":{"begin":1503,"end":1510},"obj":"Protein"},{"id":"T2727","span":{"begin":1490,"end":1494},"obj":"Protein"},{"id":"T2725","span":{"begin":1450,"end":1454},"obj":"Protein"},{"id":"T2724","span":{"begin":1059,"end":1066},"obj":"Protein"},{"id":"T2723","span":{"begin":970,"end":974},"obj":"Protein"},{"id":"T2722","span":{"begin":926,"end":933},"obj":"Protein"},{"id":"T2721","span":{"begin":917,"end":921},"obj":"Protein"},{"id":"T2720","span":{"begin":819,"end":826},"obj":"Protein"},{"id":"T2719","span":{"begin":798,"end":817},"obj":"Protein"},{"id":"T2718","span":{"begin":778,"end":796},"obj":"Protein"},{"id":"T2717","span":{"begin":678,"end":682},"obj":"Protein"},{"id":"T2716","span":{"begin":18,"end":22},"obj":"Protein"},{"id":"T2715","span":{"begin":1503,"end":1510},"obj":"Protein"},{"id":"T2714","span":{"begin":1490,"end":1494},"obj":"Protein"},{"id":"T2713","span":{"begin":1450,"end":1454},"obj":"Protein"},{"id":"T2712","span":{"begin":1059,"end":1066},"obj":"Protein"},{"id":"T2711","span":{"begin":970,"end":974},"obj":"Protein"},{"id":"T2710","span":{"begin":926,"end":933},"obj":"Protein"},{"id":"T2709","span":{"begin":917,"end":921},"obj":"Protein"},{"id":"T2708","span":{"begin":819,"end":826},"obj":"Protein"},{"id":"T2707","span":{"begin":798,"end":817},"obj":"Protein"},{"id":"T2706","span":{"begin":778,"end":796},"obj":"Protein"},{"id":"T2705","span":{"begin":678,"end":682},"obj":"Protein"},{"id":"T2704","span":{"begin":18,"end":22},"obj":"Protein"},{"id":"T2726","span":{"begin":1464,"end":1473},"obj":"Transcription"}],"relations":[{"id":"R2182","pred":"equivalentTo","subj":"T2720","obj":"T2719"}],"text":"2.3. Detection of TLR4 mRNA by the Method of RT-PCR\nBriefly, total RNA samples were isolated from peri-hemorrhage regions in left basal ganglia using Simply P Total RNA isolation Kit (BioFlux, HZ, China) according to the manufacturer's instructions. The quantity of total RNA was determined on a Nanodrop (ND-1000 Spectrophotometer) by measuring optical density at A260 and A280 nm wavelength. Then, the concentrations of mRNA were adjusted to 1.0 g/mL. RNA was reverse-transcribed into cDNA in 20 μL reaction system using Superscript First-Strand Synthesis Kit for RT-PCR (promega Inc) under conditions described by the supplier. One microliter of cDNA was used to amplify the TLR4 gene fragment with 1× PCR buffer, 1.5 mM MgCl2, 200 μM of each dNTP, 200 μM of primers, and 2u Taq DNA polymerase. The house keep gene (β-actin) was used as an internal control. The PCR primer sequences were designed according to the TLR4 and β-actin gene sequences reported in GenBank. TLR4 (145 bp): forward: 5′-AGCTTTGGTCAGTTGGCTCT-3′; reverse: 5′-CAGGATGACACCATTGAAGC-3′; β-actin (701 bp): forward: 5′-GCCAACCGTGAAAAAGATG-3′; reverse: 5′-CCAGGATAGAGCCACCAAT-3′. Reaction cycles were performed at the following condition: 94°C 2 min, 94°C 40 s, 55°C 40 s, and 72°C 60 s. The reaction was stopped after 31 cycles. PCR products were electrophoresed through agarose gel. Image Acquisition and Analysis software were used to determine band densities. The abundance of TLR4 mRNA was expressed as the ratio of TLR4 mRNA to β-actin mRNA."}

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