PMC:7143804 / 13517-15854 JSONTXT

{"project":"LitCovid_Glycan-Motif-Structure","denotations":[{"id":"T1","span":{"begin":748,"end":751},"obj":"https://glytoucan.org/Structures/Glycans/G00063MO"}],"text":"The microfluidic structure consists of two chambers, i.e., a reaction chamber and a temperature monitor chamber. In Figure 2, a close-up of the final chip is shown. For clarity reasons, the two microfluidic structures are colored with food coloring dye. The reaction chamber is based on the work of Bruijns et al. [36] and its dimensions are chosen in such way that the internal volume of the reaction chamber is the same as the reaction volume of the used Illustra GenomiPhi V2 DNA amplification kit (GE Healthcare Life Sciences, Eindhoven, The Netherlands) together with the EvaGreen dye solution (Biotium, Fremont, CA, USA), while maintaining an as low as possible surface-area-to-volume ratio [44]. Using SolidWorks 2018 computer-aided design (CAD) software (Dassault Systemes, Vélizy-Villacoublay, France), the 3D image of the chip is drawn and with the use of the AutoDesk HSMWorks computer-aided manufacturing (CAM) plug-in (Autodesk Inc., San Rafael, CA, USA), this image is transferred into a computer numerical control (CNC) milling code. The total chip size is 3 cm by 3 cm and contains an inlet and outlet of 1.5 mm diameter. The inlet and outlet are of such size that the reaction chamber can be filled using pipette tips. In between the inlet and outlet, a rectangular reaction chamber of 10 mm by 3 mm is located. Two trapezoid structures are placed in the tapered channels between the inlet/outlet and the chamber. The function of these trapezoids is twofold: First, they minimize the dead volume between the inlet/outlet and the reaction chamber, locating as much as possible of the reaction mixture inside the chamber. Second, they provide support for the chamber closure. A stadium-shaped channel of 1.5 mm wide and 1.0 mm deep is located next to the reaction chamber, in such way that this channel is also covered by the heater. This channel serves as temperature monitor chamber. A thermocouple is inserted in this channel for real-time monitoring of the temperature inside the chip. This way, a more accurate temperature of the reaction mixture inside the chip can be obtained. Via a feedback loop, the input potential can be changed when required. In Figure 3, the SolidWorks design of the chamber-based chip with both chambers is shown. In Figure A1, in Appendix A, the technical drawing of the chip can be found."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T33","span":{"begin":476,"end":478},"obj":"Body_part"},{"id":"T35","span":{"begin":479,"end":482},"obj":"Body_part"},{"id":"T36","span":{"begin":918,"end":921},"obj":"Body_part"},{"id":"T37","span":{"begin":1333,"end":1342},"obj":"Body_part"},{"id":"T38","span":{"begin":1453,"end":1463},"obj":"Body_part"},{"id":"T39","span":{"begin":2271,"end":2273},"obj":"Body_part"},{"id":"T40","span":{"begin":2278,"end":2286},"obj":"Body_part"}],"attributes":[{"id":"A33","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma13443"},{"id":"A34","pred":"fma_id","subj":"T33","obj":"http://purl.org/sig/ont/fma/fma68615"},{"id":"A35","pred":"fma_id","subj":"T35","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A36","pred":"fma_id","subj":"T36","obj":"http://purl.org/sig/ont/fma/fma67214"},{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma23724"},{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma23724"},{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma66592"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma14542"}],"text":"The microfluidic structure consists of two chambers, i.e., a reaction chamber and a temperature monitor chamber. In Figure 2, a close-up of the final chip is shown. For clarity reasons, the two microfluidic structures are colored with food coloring dye. The reaction chamber is based on the work of Bruijns et al. [36] and its dimensions are chosen in such way that the internal volume of the reaction chamber is the same as the reaction volume of the used Illustra GenomiPhi V2 DNA amplification kit (GE Healthcare Life Sciences, Eindhoven, The Netherlands) together with the EvaGreen dye solution (Biotium, Fremont, CA, USA), while maintaining an as low as possible surface-area-to-volume ratio [44]. Using SolidWorks 2018 computer-aided design (CAD) software (Dassault Systemes, Vélizy-Villacoublay, France), the 3D image of the chip is drawn and with the use of the AutoDesk HSMWorks computer-aided manufacturing (CAM) plug-in (Autodesk Inc., San Rafael, CA, USA), this image is transferred into a computer numerical control (CNC) milling code. The total chip size is 3 cm by 3 cm and contains an inlet and outlet of 1.5 mm diameter. The inlet and outlet are of such size that the reaction chamber can be filled using pipette tips. In between the inlet and outlet, a rectangular reaction chamber of 10 mm by 3 mm is located. Two trapezoid structures are placed in the tapered channels between the inlet/outlet and the chamber. The function of these trapezoids is twofold: First, they minimize the dead volume between the inlet/outlet and the reaction chamber, locating as much as possible of the reaction mixture inside the chamber. Second, they provide support for the chamber closure. A stadium-shaped channel of 1.5 mm wide and 1.0 mm deep is located next to the reaction chamber, in such way that this channel is also covered by the heater. This channel serves as temperature monitor chamber. A thermocouple is inserted in this channel for real-time monitoring of the temperature inside the chip. This way, a more accurate temperature of the reaction mixture inside the chip can be obtained. Via a feedback loop, the input potential can be changed when required. In Figure 3, the SolidWorks design of the chamber-based chip with both chambers is shown. In Figure A1, in Appendix A, the technical drawing of the chip can be found."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T20","span":{"begin":748,"end":751},"obj":"Disease"},{"id":"T22","span":{"begin":1030,"end":1033},"obj":"Disease"}],"attributes":[{"id":"A20","pred":"mondo_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/MONDO_0005010"},{"id":"A21","pred":"mondo_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/MONDO_0018922"},{"id":"A22","pred":"mondo_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/MONDO_0015285"},{"id":"A23","pred":"mondo_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/MONDO_0019134"}],"text":"The microfluidic structure consists of two chambers, i.e., a reaction chamber and a temperature monitor chamber. In Figure 2, a close-up of the final chip is shown. For clarity reasons, the two microfluidic structures are colored with food coloring dye. The reaction chamber is based on the work of Bruijns et al. [36] and its dimensions are chosen in such way that the internal volume of the reaction chamber is the same as the reaction volume of the used Illustra GenomiPhi V2 DNA amplification kit (GE Healthcare Life Sciences, Eindhoven, The Netherlands) together with the EvaGreen dye solution (Biotium, Fremont, CA, USA), while maintaining an as low as possible surface-area-to-volume ratio [44]. Using SolidWorks 2018 computer-aided design (CAD) software (Dassault Systemes, Vélizy-Villacoublay, France), the 3D image of the chip is drawn and with the use of the AutoDesk HSMWorks computer-aided manufacturing (CAM) plug-in (Autodesk Inc., San Rafael, CA, USA), this image is transferred into a computer numerical control (CNC) milling code. The total chip size is 3 cm by 3 cm and contains an inlet and outlet of 1.5 mm diameter. The inlet and outlet are of such size that the reaction chamber can be filled using pipette tips. In between the inlet and outlet, a rectangular reaction chamber of 10 mm by 3 mm is located. Two trapezoid structures are placed in the tapered channels between the inlet/outlet and the chamber. The function of these trapezoids is twofold: First, they minimize the dead volume between the inlet/outlet and the reaction chamber, locating as much as possible of the reaction mixture inside the chamber. Second, they provide support for the chamber closure. A stadium-shaped channel of 1.5 mm wide and 1.0 mm deep is located next to the reaction chamber, in such way that this channel is also covered by the heater. This channel serves as temperature monitor chamber. A thermocouple is inserted in this channel for real-time monitoring of the temperature inside the chip. This way, a more accurate temperature of the reaction mixture inside the chip can be obtained. Via a feedback loop, the input potential can be changed when required. In Figure 3, the SolidWorks design of the chamber-based chip with both chambers is shown. In Figure A1, in Appendix A, the technical drawing of the chip can be found."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T92","span":{"begin":59,"end":60},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T93","span":{"begin":82,"end":83},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T94","span":{"begin":123,"end":127},"obj":"http://purl.obolibrary.org/obo/CLO_0001236"},{"id":"T95","span":{"begin":315,"end":317},"obj":"http://purl.obolibrary.org/obo/CLO_0001313"},{"id":"T96","span":{"begin":720,"end":724},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"},{"id":"T97","span":{"begin":1000,"end":1001},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T98","span":{"begin":1030,"end":1033},"obj":"http://purl.obolibrary.org/obo/UBERON_0003099"},{"id":"T99","span":{"begin":1269,"end":1270},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T100","span":{"begin":1691,"end":1692},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T101","span":{"begin":1901,"end":1902},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T102","span":{"begin":2015,"end":2016},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T103","span":{"begin":2104,"end":2105},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T104","span":{"begin":2287,"end":2288},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"The microfluidic structure consists of two chambers, i.e., a reaction chamber and a temperature monitor chamber. In Figure 2, a close-up of the final chip is shown. For clarity reasons, the two microfluidic structures are colored with food coloring dye. The reaction chamber is based on the work of Bruijns et al. [36] and its dimensions are chosen in such way that the internal volume of the reaction chamber is the same as the reaction volume of the used Illustra GenomiPhi V2 DNA amplification kit (GE Healthcare Life Sciences, Eindhoven, The Netherlands) together with the EvaGreen dye solution (Biotium, Fremont, CA, USA), while maintaining an as low as possible surface-area-to-volume ratio [44]. Using SolidWorks 2018 computer-aided design (CAD) software (Dassault Systemes, Vélizy-Villacoublay, France), the 3D image of the chip is drawn and with the use of the AutoDesk HSMWorks computer-aided manufacturing (CAM) plug-in (Autodesk Inc., San Rafael, CA, USA), this image is transferred into a computer numerical control (CNC) milling code. The total chip size is 3 cm by 3 cm and contains an inlet and outlet of 1.5 mm diameter. The inlet and outlet are of such size that the reaction chamber can be filled using pipette tips. In between the inlet and outlet, a rectangular reaction chamber of 10 mm by 3 mm is located. Two trapezoid structures are placed in the tapered channels between the inlet/outlet and the chamber. The function of these trapezoids is twofold: First, they minimize the dead volume between the inlet/outlet and the reaction chamber, locating as much as possible of the reaction mixture inside the chamber. Second, they provide support for the chamber closure. A stadium-shaped channel of 1.5 mm wide and 1.0 mm deep is located next to the reaction chamber, in such way that this channel is also covered by the heater. This channel serves as temperature monitor chamber. A thermocouple is inserted in this channel for real-time monitoring of the temperature inside the chip. This way, a more accurate temperature of the reaction mixture inside the chip can be obtained. Via a feedback loop, the input potential can be changed when required. In Figure 3, the SolidWorks design of the chamber-based chip with both chambers is shown. In Figure A1, in Appendix A, the technical drawing of the chip can be found."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T82","span":{"begin":235,"end":248},"obj":"Chemical"},{"id":"T83","span":{"begin":249,"end":252},"obj":"Chemical"},{"id":"T84","span":{"begin":479,"end":482},"obj":"Chemical"},{"id":"T85","span":{"begin":502,"end":504},"obj":"Chemical"},{"id":"T86","span":{"begin":586,"end":589},"obj":"Chemical"},{"id":"T87","span":{"begin":590,"end":598},"obj":"Chemical"},{"id":"T88","span":{"begin":1030,"end":1033},"obj":"Chemical"},{"id":"T89","span":{"begin":1609,"end":1616},"obj":"Chemical"},{"id":"T90","span":{"begin":2059,"end":2066},"obj":"Chemical"}],"attributes":[{"id":"A82","pred":"chebi_id","subj":"T82","obj":"http://purl.obolibrary.org/obo/CHEBI_77182"},{"id":"A83","pred":"chebi_id","subj":"T83","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"id":"A84","pred":"chebi_id","subj":"T84","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A85","pred":"chebi_id","subj":"T85","obj":"http://purl.obolibrary.org/obo/CHEBI_73801"},{"id":"A86","pred":"chebi_id","subj":"T86","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"id":"A87","pred":"chebi_id","subj":"T87","obj":"http://purl.obolibrary.org/obo/CHEBI_75958"},{"id":"A88","pred":"chebi_id","subj":"T88","obj":"http://purl.obolibrary.org/obo/CHEBI_48390"},{"id":"A89","pred":"chebi_id","subj":"T89","obj":"http://purl.obolibrary.org/obo/CHEBI_60004"},{"id":"A90","pred":"chebi_id","subj":"T90","obj":"http://purl.obolibrary.org/obo/CHEBI_60004"}],"text":"The microfluidic structure consists of two chambers, i.e., a reaction chamber and a temperature monitor chamber. In Figure 2, a close-up of the final chip is shown. For clarity reasons, the two microfluidic structures are colored with food coloring dye. The reaction chamber is based on the work of Bruijns et al. [36] and its dimensions are chosen in such way that the internal volume of the reaction chamber is the same as the reaction volume of the used Illustra GenomiPhi V2 DNA amplification kit (GE Healthcare Life Sciences, Eindhoven, The Netherlands) together with the EvaGreen dye solution (Biotium, Fremont, CA, USA), while maintaining an as low as possible surface-area-to-volume ratio [44]. Using SolidWorks 2018 computer-aided design (CAD) software (Dassault Systemes, Vélizy-Villacoublay, France), the 3D image of the chip is drawn and with the use of the AutoDesk HSMWorks computer-aided manufacturing (CAM) plug-in (Autodesk Inc., San Rafael, CA, USA), this image is transferred into a computer numerical control (CNC) milling code. The total chip size is 3 cm by 3 cm and contains an inlet and outlet of 1.5 mm diameter. The inlet and outlet are of such size that the reaction chamber can be filled using pipette tips. In between the inlet and outlet, a rectangular reaction chamber of 10 mm by 3 mm is located. Two trapezoid structures are placed in the tapered channels between the inlet/outlet and the chamber. The function of these trapezoids is twofold: First, they minimize the dead volume between the inlet/outlet and the reaction chamber, locating as much as possible of the reaction mixture inside the chamber. Second, they provide support for the chamber closure. A stadium-shaped channel of 1.5 mm wide and 1.0 mm deep is located next to the reaction chamber, in such way that this channel is also covered by the heater. This channel serves as temperature monitor chamber. A thermocouple is inserted in this channel for real-time monitoring of the temperature inside the chip. This way, a more accurate temperature of the reaction mixture inside the chip can be obtained. Via a feedback loop, the input potential can be changed when required. In Figure 3, the SolidWorks design of the chamber-based chip with both chambers is shown. In Figure A1, in Appendix A, the technical drawing of the chip can be found."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T7","span":{"begin":479,"end":496},"obj":"http://purl.obolibrary.org/obo/GO_0006277"}],"text":"The microfluidic structure consists of two chambers, i.e., a reaction chamber and a temperature monitor chamber. In Figure 2, a close-up of the final chip is shown. For clarity reasons, the two microfluidic structures are colored with food coloring dye. The reaction chamber is based on the work of Bruijns et al. [36] and its dimensions are chosen in such way that the internal volume of the reaction chamber is the same as the reaction volume of the used Illustra GenomiPhi V2 DNA amplification kit (GE Healthcare Life Sciences, Eindhoven, The Netherlands) together with the EvaGreen dye solution (Biotium, Fremont, CA, USA), while maintaining an as low as possible surface-area-to-volume ratio [44]. Using SolidWorks 2018 computer-aided design (CAD) software (Dassault Systemes, Vélizy-Villacoublay, France), the 3D image of the chip is drawn and with the use of the AutoDesk HSMWorks computer-aided manufacturing (CAM) plug-in (Autodesk Inc., San Rafael, CA, USA), this image is transferred into a computer numerical control (CNC) milling code. The total chip size is 3 cm by 3 cm and contains an inlet and outlet of 1.5 mm diameter. The inlet and outlet are of such size that the reaction chamber can be filled using pipette tips. In between the inlet and outlet, a rectangular reaction chamber of 10 mm by 3 mm is located. Two trapezoid structures are placed in the tapered channels between the inlet/outlet and the chamber. The function of these trapezoids is twofold: First, they minimize the dead volume between the inlet/outlet and the reaction chamber, locating as much as possible of the reaction mixture inside the chamber. Second, they provide support for the chamber closure. A stadium-shaped channel of 1.5 mm wide and 1.0 mm deep is located next to the reaction chamber, in such way that this channel is also covered by the heater. This channel serves as temperature monitor chamber. A thermocouple is inserted in this channel for real-time monitoring of the temperature inside the chip. This way, a more accurate temperature of the reaction mixture inside the chip can be obtained. Via a feedback loop, the input potential can be changed when required. In Figure 3, the SolidWorks design of the chamber-based chip with both chambers is shown. In Figure A1, in Appendix A, the technical drawing of the chip can be found."}

{"project":"LitCovid-sentences","denotations":[{"id":"T114","span":{"begin":0,"end":112},"obj":"Sentence"},{"id":"T115","span":{"begin":113,"end":164},"obj":"Sentence"},{"id":"T116","span":{"begin":165,"end":253},"obj":"Sentence"},{"id":"T117","span":{"begin":254,"end":702},"obj":"Sentence"},{"id":"T118","span":{"begin":703,"end":1048},"obj":"Sentence"},{"id":"T119","span":{"begin":1049,"end":1137},"obj":"Sentence"},{"id":"T120","span":{"begin":1138,"end":1235},"obj":"Sentence"},{"id":"T121","span":{"begin":1236,"end":1328},"obj":"Sentence"},{"id":"T122","span":{"begin":1329,"end":1430},"obj":"Sentence"},{"id":"T123","span":{"begin":1431,"end":1475},"obj":"Sentence"},{"id":"T124","span":{"begin":1476,"end":1636},"obj":"Sentence"},{"id":"T125","span":{"begin":1637,"end":1690},"obj":"Sentence"},{"id":"T126","span":{"begin":1691,"end":1848},"obj":"Sentence"},{"id":"T127","span":{"begin":1849,"end":1900},"obj":"Sentence"},{"id":"T128","span":{"begin":1901,"end":2004},"obj":"Sentence"},{"id":"T129","span":{"begin":2005,"end":2099},"obj":"Sentence"},{"id":"T130","span":{"begin":2100,"end":2170},"obj":"Sentence"},{"id":"T131","span":{"begin":2171,"end":2260},"obj":"Sentence"},{"id":"T132","span":{"begin":2261,"end":2337},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The microfluidic structure consists of two chambers, i.e., a reaction chamber and a temperature monitor chamber. In Figure 2, a close-up of the final chip is shown. For clarity reasons, the two microfluidic structures are colored with food coloring dye. The reaction chamber is based on the work of Bruijns et al. [36] and its dimensions are chosen in such way that the internal volume of the reaction chamber is the same as the reaction volume of the used Illustra GenomiPhi V2 DNA amplification kit (GE Healthcare Life Sciences, Eindhoven, The Netherlands) together with the EvaGreen dye solution (Biotium, Fremont, CA, USA), while maintaining an as low as possible surface-area-to-volume ratio [44]. Using SolidWorks 2018 computer-aided design (CAD) software (Dassault Systemes, Vélizy-Villacoublay, France), the 3D image of the chip is drawn and with the use of the AutoDesk HSMWorks computer-aided manufacturing (CAM) plug-in (Autodesk Inc., San Rafael, CA, USA), this image is transferred into a computer numerical control (CNC) milling code. The total chip size is 3 cm by 3 cm and contains an inlet and outlet of 1.5 mm diameter. The inlet and outlet are of such size that the reaction chamber can be filled using pipette tips. In between the inlet and outlet, a rectangular reaction chamber of 10 mm by 3 mm is located. Two trapezoid structures are placed in the tapered channels between the inlet/outlet and the chamber. The function of these trapezoids is twofold: First, they minimize the dead volume between the inlet/outlet and the reaction chamber, locating as much as possible of the reaction mixture inside the chamber. Second, they provide support for the chamber closure. A stadium-shaped channel of 1.5 mm wide and 1.0 mm deep is located next to the reaction chamber, in such way that this channel is also covered by the heater. This channel serves as temperature monitor chamber. A thermocouple is inserted in this channel for real-time monitoring of the temperature inside the chip. This way, a more accurate temperature of the reaction mixture inside the chip can be obtained. Via a feedback loop, the input potential can be changed when required. In Figure 3, the SolidWorks design of the chamber-based chip with both chambers is shown. In Figure A1, in Appendix A, the technical drawing of the chip can be found."}