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LitCovid-PubTator

LitCovid_Glycan-Motif-Structure

{"project":"LitCovid_Glycan-Motif-Structure","denotations":[{"id":"T2","span":{"begin":1546,"end":1549},"obj":"https://glytoucan.org/Structures/Glycans/G00063MO"}],"text":"Acknowledgments\nThe authors would like to thank Brigitte Bruijns from Micronit Microtechnologies for her help during the brainstorm sessions. Jörg Strack from TOPAS Advanced Polymers and Thomas Wagenknecht from KUZ Leipzig are thanked for their information on COC. Pieter Post, Rob Dierink, and Sip Jan Boorsma of TCO (Technical Center for Education and Research of the University of Twente) are thanked for their work in the milling and laser cutting processes, Christian Bruinink for his assistance in the transparency measurements, Daniel Monteiro Cunha, M.Sc. for his assistance in the AFM measurements, and Nikki Stroot for her assistance with the initial amplification reactions. Sample Availability: Samples of the amplification chips are available from the authors.\n\nAuthor Contributions\nConceived and designed the experiments: H.-W.V., F.A.M., and R.S.; developed the measurement setup and software, and provided technical help: R.S.; developed the methodology: H.-W.V. and F.A.M.; performed the experiments: F.A.M.; visualized the results: H.-W.V. and F.A.M.; wrote the first draft of the paper: H.-W.V.; reviewed and edited the first draft of the paper: H.-W.V., F.A.M., R.S., R.W. and J.L.; supervised the project: H.-W.V. All authors have read and agreed to the published version of the manuscript.\n\nFunding\nThis work is financed with institutional funding.\n\nConflicts of Interest\nThe authors declare no conflict of interest. Abbreviations\nThe following abbreviations are used in this manuscript: AFM atomic force microscopy\nAu gold\nCAD computer-aided design\nCAM computer-aided manufacturing\nCNC computer numerical control\nCOC cyclic olefin copolymer\nDC direct current\nDI de-ionized\nDNA deoxyribonucleic acid\ndsDNA double stranded DNA\nH2O water\nHDA helicase-dependent amplification\nLAMP loop-mediated isothermal amplification\nMDA multiple displacement amplification\nMo molybdenum\nN2 nitrogen\nNTC non template control\nPCR polymerase chain reaction\nPDMS polydimethylsiloxane\nPID proportional-integral-derivative\nPt platinum\nPVD physical vapor deposition\nRNA ribonucleic acid\nSEM scanning electron microscopy\nssDNA single stranded DNA\nSDI Sexually Transmitted Diseases Diagnostics Initiative\nTCR temperature coefficient of resistance\nTg glass transition temperature\nWGA whole genome amplification\nWHO World Health Organization\n\nAppendix A. Technical Drawing Chip\nFigure A1 Technical drawing of the DNA amplification chip. All dimensions are in mm. The total chip size is 3 mm by 3 mm.\n\nAppendix B. Equations and Values Used in the COMSOL Multiphysics Study\n\nAppendix B.1. Water\nFor H2O, the build-in temperature-dependent equations for the density (ρH2O, see equations in Equation (A1)), heat capacity at constant pressure (CP,H2O, see equations in Equation (A2)), and thermal conductivity (κH2O, see equations in Equation (A3)) are used. The ratio (γH2O) of the specific heats at constant pressure (CP,H2O) and constant volume (CV,H2O) is calculated manually according to the table from the Engineering Toolbox website [81] and Equation (A4). The values for γH2O are listed in Table A1. (A1) ρH2O(T)=972.7584+0.2084T−4×10−4T2for273≤T\u003c283345.28+5.749816T−0.0157244T2+1.264375×10−5T3for283≤T\u003c373 (A2) CP,H2O(T)=12010.1471−80.4072879T+0.309866854T2for273.15≤T\u003c553.75−5.38186884×10−4T3+3.62536437×10−7T4 (A3) κH2O(T)=−0.869083936+0.00894880345T−1.58366345×10−5T2for273.15≤T\u003c553.75+7.97543259×10−9T3 (A4) γH2O=CP,H2OCV,H2O\nTable A1 The ratio of specific heats of water.\nT γH2O T γH2O\n[K] [-] [K] [-]\n273.16 1.000592782 393.15 1.157465496\n283.15 1.001073729 413.15 1.199809492\n293.15 1.006591292 433.15 1.246234334\n298.15 1.010560913 453.15 1.297534537\n303.15 1.015203400 473.15 1.355013713\n313.15 1.025996023 493.15 1.420794975\n323.15 1.038520763 513.15 1.498241758\n333.15 1.052405261 533.15 1.592792563\n343.15 1.067512483 553.15 1.714447794\n353.15 1.083658241 573.15 1.883524402\n363.15 1.100748613 593.15 2.148448797\n373.15 1.118756966 613.15 2.666580033\n383.15 1.137648990 633.15 4.550527720\n\nAppendix B.2. Cyclic Olefin Copolymer\nValues for the density (ρCOC = 1020 kg m−3), specific heat (cCOC, see Table A2), and thermal conductivity (κCOC,23°C = 0.17 W m−1 K−1 and κCOC,320°C = 0.24 W m−1 K−1, linear fit in between these point) of TOPAS 6017 COC are obtained via TOPAS Advanced Polymers (TOPAS Advanced Polymers, Farmington Hills, MI, USA). The heat capacity at constant pressure (CP,COC) is calculated assuming a homogeneous body of mass m, via Equation (A5), where COMSOL interpolated linearly in between the points. (A5) CP,COC=cCOC×m\nTable A2 The specific heat of TOPAS 6017 COC.\nT c T c\n[°C] [W m−1 K−1] [°C] [W m−1 K−1]\n30 1333 180 2298\n70 1538 210 2412\n110 1754 250 2539\n150 1968 290 2645\n160 2047 330 2758 Convective heat loss to the air is also taken into account with Equation (A6), which is often used in simulations [56]. (A6) h=10Wm−2K−1\n\nAppendix C. TCR Measurements\nThe two subsections below show two effects on the TCR measurements, i.e., the effect of thermal annealing during the first temperature cycle and the effect of aging.\n\nAppendix C.1. Thermal Annealing\nThe graph below is an example of the measured thermal annealing of a metal layer on COC. Here, only the graph for evaporated Au is shown, but all except evaporated Pt show this behavior. Evaporated Pt had some contaminants in the metal track. This is most probably caused by the shadow mask.\nFigure A2 Thermal annealing of an evaporated 100 nm Au layer.\n\nAppendix C.2. Aging\nThe layer analyzed in Figure A2 is stored for two weeks in ambient conditions and the TCR is analyzed again. From the graph it is visible that the aging has some effect on the TCR of the metal layer.\nFigure A3 The effect of two weeks aging in ambient conditions on a 100 nm Au layer. The TCR of the as deposited layer is 0.00161 K−1 and the TCR of the two week old layer is 0.00224 K−1.\n\nAppendix D. MDA Reaction Mixture\nThe reaction mixture for the on-chip MDA reaction consisted of the following.\nTable A3 On-chip MDA reaction mixtures.\nSample Reaction Buffer Sample Buffer DNA MilliQ DI Water EG Enzyme\n[μL] [μL] [μL] [μL] [μL] [μL]\nTube with DNA 9 9 1 - 4 1\nTube NTC 9 9 - 1 4 1\nChip with DNA 9 9 1 - 4 1\nChip NTC 9 9 - 1 4 1\n\nAppendix E. Background Signal Fluorescence Measurements\nAll fluorescence measurements in the Horiba Scientific FluoroMax+ spectrofluorometer are normalized by subtracting the background signal. This background signal is measured using the mixture in Table A4.\nTable A4 Mixture used for background signal measurement.\nSample Reaction Buffer Sample Buffer DNA MilliQ DI Water EG Enzyme\n[μL] [μL] [μL] [μL] [μL] [μL]\nBackground 9 9 1 1 4 -\nFigure A4 The background signal of the mixture in Table A4."}

LitCovid-PD-FMA-UBERON

LitCovid-PD-UBERON

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T18","span":{"begin":6191,"end":6195},"obj":"Body_part"},{"id":"T19","span":{"begin":6223,"end":6227},"obj":"Body_part"}],"attributes":[{"id":"A18","pred":"uberon_id","subj":"T18","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"A19","pred":"uberon_id","subj":"T19","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"}],"text":"Acknowledgments\nThe authors would like to thank Brigitte Bruijns from Micronit Microtechnologies for her help during the brainstorm sessions. Jörg Strack from TOPAS Advanced Polymers and Thomas Wagenknecht from KUZ Leipzig are thanked for their information on COC. Pieter Post, Rob Dierink, and Sip Jan Boorsma of TCO (Technical Center for Education and Research of the University of Twente) are thanked for their work in the milling and laser cutting processes, Christian Bruinink for his assistance in the transparency measurements, Daniel Monteiro Cunha, M.Sc. for his assistance in the AFM measurements, and Nikki Stroot for her assistance with the initial amplification reactions. Sample Availability: Samples of the amplification chips are available from the authors.\n\nAuthor Contributions\nConceived and designed the experiments: H.-W.V., F.A.M., and R.S.; developed the measurement setup and software, and provided technical help: R.S.; developed the methodology: H.-W.V. and F.A.M.; performed the experiments: F.A.M.; visualized the results: H.-W.V. and F.A.M.; wrote the first draft of the paper: H.-W.V.; reviewed and edited the first draft of the paper: H.-W.V., F.A.M., R.S., R.W. and J.L.; supervised the project: H.-W.V. All authors have read and agreed to the published version of the manuscript.\n\nFunding\nThis work is financed with institutional funding.\n\nConflicts of Interest\nThe authors declare no conflict of interest. Abbreviations\nThe following abbreviations are used in this manuscript: AFM atomic force microscopy\nAu gold\nCAD computer-aided design\nCAM computer-aided manufacturing\nCNC computer numerical control\nCOC cyclic olefin copolymer\nDC direct current\nDI de-ionized\nDNA deoxyribonucleic acid\ndsDNA double stranded DNA\nH2O water\nHDA helicase-dependent amplification\nLAMP loop-mediated isothermal amplification\nMDA multiple displacement amplification\nMo molybdenum\nN2 nitrogen\nNTC non template control\nPCR polymerase chain reaction\nPDMS polydimethylsiloxane\nPID proportional-integral-derivative\nPt platinum\nPVD physical vapor deposition\nRNA ribonucleic acid\nSEM scanning electron microscopy\nssDNA single stranded DNA\nSDI Sexually Transmitted Diseases Diagnostics Initiative\nTCR temperature coefficient of resistance\nTg glass transition temperature\nWGA whole genome amplification\nWHO World Health Organization\n\nAppendix A. Technical Drawing Chip\nFigure A1 Technical drawing of the DNA amplification chip. All dimensions are in mm. The total chip size is 3 mm by 3 mm.\n\nAppendix B. Equations and Values Used in the COMSOL Multiphysics Study\n\nAppendix B.1. Water\nFor H2O, the build-in temperature-dependent equations for the density (ρH2O, see equations in Equation (A1)), heat capacity at constant pressure (CP,H2O, see equations in Equation (A2)), and thermal conductivity (κH2O, see equations in Equation (A3)) are used. The ratio (γH2O) of the specific heats at constant pressure (CP,H2O) and constant volume (CV,H2O) is calculated manually according to the table from the Engineering Toolbox website [81] and Equation (A4). The values for γH2O are listed in Table A1. (A1) ρH2O(T)=972.7584+0.2084T−4×10−4T2for273≤T\u003c283345.28+5.749816T−0.0157244T2+1.264375×10−5T3for283≤T\u003c373 (A2) CP,H2O(T)=12010.1471−80.4072879T+0.309866854T2for273.15≤T\u003c553.75−5.38186884×10−4T3+3.62536437×10−7T4 (A3) κH2O(T)=−0.869083936+0.00894880345T−1.58366345×10−5T2for273.15≤T\u003c553.75+7.97543259×10−9T3 (A4) γH2O=CP,H2OCV,H2O\nTable A1 The ratio of specific heats of water.\nT γH2O T γH2O\n[K] [-] [K] [-]\n273.16 1.000592782 393.15 1.157465496\n283.15 1.001073729 413.15 1.199809492\n293.15 1.006591292 433.15 1.246234334\n298.15 1.010560913 453.15 1.297534537\n303.15 1.015203400 473.15 1.355013713\n313.15 1.025996023 493.15 1.420794975\n323.15 1.038520763 513.15 1.498241758\n333.15 1.052405261 533.15 1.592792563\n343.15 1.067512483 553.15 1.714447794\n353.15 1.083658241 573.15 1.883524402\n363.15 1.100748613 593.15 2.148448797\n373.15 1.118756966 613.15 2.666580033\n383.15 1.137648990 633.15 4.550527720\n\nAppendix B.2. Cyclic Olefin Copolymer\nValues for the density (ρCOC = 1020 kg m−3), specific heat (cCOC, see Table A2), and thermal conductivity (κCOC,23°C = 0.17 W m−1 K−1 and κCOC,320°C = 0.24 W m−1 K−1, linear fit in between these point) of TOPAS 6017 COC are obtained via TOPAS Advanced Polymers (TOPAS Advanced Polymers, Farmington Hills, MI, USA). The heat capacity at constant pressure (CP,COC) is calculated assuming a homogeneous body of mass m, via Equation (A5), where COMSOL interpolated linearly in between the points. (A5) CP,COC=cCOC×m\nTable A2 The specific heat of TOPAS 6017 COC.\nT c T c\n[°C] [W m−1 K−1] [°C] [W m−1 K−1]\n30 1333 180 2298\n70 1538 210 2412\n110 1754 250 2539\n150 1968 290 2645\n160 2047 330 2758 Convective heat loss to the air is also taken into account with Equation (A6), which is often used in simulations [56]. (A6) h=10Wm−2K−1\n\nAppendix C. TCR Measurements\nThe two subsections below show two effects on the TCR measurements, i.e., the effect of thermal annealing during the first temperature cycle and the effect of aging.\n\nAppendix C.1. Thermal Annealing\nThe graph below is an example of the measured thermal annealing of a metal layer on COC. Here, only the graph for evaporated Au is shown, but all except evaporated Pt show this behavior. Evaporated Pt had some contaminants in the metal track. This is most probably caused by the shadow mask.\nFigure A2 Thermal annealing of an evaporated 100 nm Au layer.\n\nAppendix C.2. Aging\nThe layer analyzed in Figure A2 is stored for two weeks in ambient conditions and the TCR is analyzed again. From the graph it is visible that the aging has some effect on the TCR of the metal layer.\nFigure A3 The effect of two weeks aging in ambient conditions on a 100 nm Au layer. The TCR of the as deposited layer is 0.00161 K−1 and the TCR of the two week old layer is 0.00224 K−1.\n\nAppendix D. MDA Reaction Mixture\nThe reaction mixture for the on-chip MDA reaction consisted of the following.\nTable A3 On-chip MDA reaction mixtures.\nSample Reaction Buffer Sample Buffer DNA MilliQ DI Water EG Enzyme\n[μL] [μL] [μL] [μL] [μL] [μL]\nTube with DNA 9 9 1 - 4 1\nTube NTC 9 9 - 1 4 1\nChip with DNA 9 9 1 - 4 1\nChip NTC 9 9 - 1 4 1\n\nAppendix E. Background Signal Fluorescence Measurements\nAll fluorescence measurements in the Horiba Scientific FluoroMax+ spectrofluorometer are normalized by subtracting the background signal. This background signal is measured using the mixture in Table A4.\nTable A4 Mixture used for background signal measurement.\nSample Reaction Buffer Sample Buffer DNA MilliQ DI Water EG Enzyme\n[μL] [μL] [μL] [μL] [μL] [μL]\nBackground 9 9 1 1 4 -\nFigure A4 The background signal of the mixture in Table A4."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T38","span":{"begin":314,"end":317},"obj":"Disease"},{"id":"T39","span":{"begin":1546,"end":1549},"obj":"Disease"},{"id":"T41","span":{"begin":1605,"end":1608},"obj":"Disease"},{"id":"T43","span":{"begin":1682,"end":1684},"obj":"Disease"},{"id":"T44","span":{"begin":1986,"end":1989},"obj":"Disease"},{"id":"T45","span":{"begin":2149,"end":2178},"obj":"Disease"},{"id":"T46","span":{"begin":4392,"end":4394},"obj":"Disease"},{"id":"T47","span":{"begin":6135,"end":6137},"obj":"Disease"},{"id":"T48","span":{"begin":6680,"end":6682},"obj":"Disease"}],"attributes":[{"id":"A38","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0011312"},{"id":"A39","pred":"mondo_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/MONDO_0005010"},{"id":"A40","pred":"mondo_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/MONDO_0018922"},{"id":"A41","pred":"mondo_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/MONDO_0015285"},{"id":"A42","pred":"mondo_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/MONDO_0019134"},{"id":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0018849"},{"id":"A44","pred":"mondo_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/MONDO_0000922"},{"id":"A45","pred":"mondo_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/MONDO_0021681"},{"id":"A46","pred":"mondo_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/MONDO_0005068"},{"id":"A47","pred":"mondo_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/MONDO_0018849"},{"id":"A48","pred":"mondo_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/MONDO_0018849"}],"text":"Acknowledgments\nThe authors would like to thank Brigitte Bruijns from Micronit Microtechnologies for her help during the brainstorm sessions. Jörg Strack from TOPAS Advanced Polymers and Thomas Wagenknecht from KUZ Leipzig are thanked for their information on COC. Pieter Post, Rob Dierink, and Sip Jan Boorsma of TCO (Technical Center for Education and Research of the University of Twente) are thanked for their work in the milling and laser cutting processes, Christian Bruinink for his assistance in the transparency measurements, Daniel Monteiro Cunha, M.Sc. for his assistance in the AFM measurements, and Nikki Stroot for her assistance with the initial amplification reactions. Sample Availability: Samples of the amplification chips are available from the authors.\n\nAuthor Contributions\nConceived and designed the experiments: H.-W.V., F.A.M., and R.S.; developed the measurement setup and software, and provided technical help: R.S.; developed the methodology: H.-W.V. and F.A.M.; performed the experiments: F.A.M.; visualized the results: H.-W.V. and F.A.M.; wrote the first draft of the paper: H.-W.V.; reviewed and edited the first draft of the paper: H.-W.V., F.A.M., R.S., R.W. and J.L.; supervised the project: H.-W.V. All authors have read and agreed to the published version of the manuscript.\n\nFunding\nThis work is financed with institutional funding.\n\nConflicts of Interest\nThe authors declare no conflict of interest. Abbreviations\nThe following abbreviations are used in this manuscript: AFM atomic force microscopy\nAu gold\nCAD computer-aided design\nCAM computer-aided manufacturing\nCNC computer numerical control\nCOC cyclic olefin copolymer\nDC direct current\nDI de-ionized\nDNA deoxyribonucleic acid\ndsDNA double stranded DNA\nH2O water\nHDA helicase-dependent amplification\nLAMP loop-mediated isothermal amplification\nMDA multiple displacement amplification\nMo molybdenum\nN2 nitrogen\nNTC non template control\nPCR polymerase chain reaction\nPDMS polydimethylsiloxane\nPID proportional-integral-derivative\nPt platinum\nPVD physical vapor deposition\nRNA ribonucleic acid\nSEM scanning electron microscopy\nssDNA single stranded DNA\nSDI Sexually Transmitted Diseases Diagnostics Initiative\nTCR temperature coefficient of resistance\nTg glass transition temperature\nWGA whole genome amplification\nWHO World Health Organization\n\nAppendix A. Technical Drawing Chip\nFigure A1 Technical drawing of the DNA amplification chip. All dimensions are in mm. The total chip size is 3 mm by 3 mm.\n\nAppendix B. Equations and Values Used in the COMSOL Multiphysics Study\n\nAppendix B.1. Water\nFor H2O, the build-in temperature-dependent equations for the density (ρH2O, see equations in Equation (A1)), heat capacity at constant pressure (CP,H2O, see equations in Equation (A2)), and thermal conductivity (κH2O, see equations in Equation (A3)) are used. The ratio (γH2O) of the specific heats at constant pressure (CP,H2O) and constant volume (CV,H2O) is calculated manually according to the table from the Engineering Toolbox website [81] and Equation (A4). The values for γH2O are listed in Table A1. (A1) ρH2O(T)=972.7584+0.2084T−4×10−4T2for273≤T\u003c283345.28+5.749816T−0.0157244T2+1.264375×10−5T3for283≤T\u003c373 (A2) CP,H2O(T)=12010.1471−80.4072879T+0.309866854T2for273.15≤T\u003c553.75−5.38186884×10−4T3+3.62536437×10−7T4 (A3) κH2O(T)=−0.869083936+0.00894880345T−1.58366345×10−5T2for273.15≤T\u003c553.75+7.97543259×10−9T3 (A4) γH2O=CP,H2OCV,H2O\nTable A1 The ratio of specific heats of water.\nT γH2O T γH2O\n[K] [-] [K] [-]\n273.16 1.000592782 393.15 1.157465496\n283.15 1.001073729 413.15 1.199809492\n293.15 1.006591292 433.15 1.246234334\n298.15 1.010560913 453.15 1.297534537\n303.15 1.015203400 473.15 1.355013713\n313.15 1.025996023 493.15 1.420794975\n323.15 1.038520763 513.15 1.498241758\n333.15 1.052405261 533.15 1.592792563\n343.15 1.067512483 553.15 1.714447794\n353.15 1.083658241 573.15 1.883524402\n363.15 1.100748613 593.15 2.148448797\n373.15 1.118756966 613.15 2.666580033\n383.15 1.137648990 633.15 4.550527720\n\nAppendix B.2. Cyclic Olefin Copolymer\nValues for the density (ρCOC = 1020 kg m−3), specific heat (cCOC, see Table A2), and thermal conductivity (κCOC,23°C = 0.17 W m−1 K−1 and κCOC,320°C = 0.24 W m−1 K−1, linear fit in between these point) of TOPAS 6017 COC are obtained via TOPAS Advanced Polymers (TOPAS Advanced Polymers, Farmington Hills, MI, USA). The heat capacity at constant pressure (CP,COC) is calculated assuming a homogeneous body of mass m, via Equation (A5), where COMSOL interpolated linearly in between the points. (A5) CP,COC=cCOC×m\nTable A2 The specific heat of TOPAS 6017 COC.\nT c T c\n[°C] [W m−1 K−1] [°C] [W m−1 K−1]\n30 1333 180 2298\n70 1538 210 2412\n110 1754 250 2539\n150 1968 290 2645\n160 2047 330 2758 Convective heat loss to the air is also taken into account with Equation (A6), which is often used in simulations [56]. (A6) h=10Wm−2K−1\n\nAppendix C. TCR Measurements\nThe two subsections below show two effects on the TCR measurements, i.e., the effect of thermal annealing during the first temperature cycle and the effect of aging.\n\nAppendix C.1. Thermal Annealing\nThe graph below is an example of the measured thermal annealing of a metal layer on COC. Here, only the graph for evaporated Au is shown, but all except evaporated Pt show this behavior. Evaporated Pt had some contaminants in the metal track. This is most probably caused by the shadow mask.\nFigure A2 Thermal annealing of an evaporated 100 nm Au layer.\n\nAppendix C.2. Aging\nThe layer analyzed in Figure A2 is stored for two weeks in ambient conditions and the TCR is analyzed again. From the graph it is visible that the aging has some effect on the TCR of the metal layer.\nFigure A3 The effect of two weeks aging in ambient conditions on a 100 nm Au layer. The TCR of the as deposited layer is 0.00161 K−1 and the TCR of the two week old layer is 0.00224 K−1.\n\nAppendix D. MDA Reaction Mixture\nThe reaction mixture for the on-chip MDA reaction consisted of the following.\nTable A3 On-chip MDA reaction mixtures.\nSample Reaction Buffer Sample Buffer DNA MilliQ DI Water EG Enzyme\n[μL] [μL] [μL] [μL] [μL] [μL]\nTube with DNA 9 9 1 - 4 1\nTube NTC 9 9 - 1 4 1\nChip with DNA 9 9 1 - 4 1\nChip NTC 9 9 - 1 4 1\n\nAppendix E. Background Signal Fluorescence Measurements\nAll fluorescence measurements in the Horiba Scientific FluoroMax+ spectrofluorometer are normalized by subtracting the background signal. This background signal is measured using the mixture in Table A4.\nTable A4 Mixture used for background signal measurement.\nSample Reaction Buffer Sample Buffer DNA MilliQ DI Water EG Enzyme\n[μL] [μL] [μL] [μL] [μL] [μL]\nBackground 9 9 1 1 4 -\nFigure A4 The background signal of the mixture in Table A4."}

LitCovid-PD-CLO

LitCovid-PD-CHEBI

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T26","span":{"begin":2409,"end":2426},"obj":"http://purl.obolibrary.org/obo/GO_0006277"},{"id":"T27","span":{"begin":5126,"end":5131},"obj":"http://purl.obolibrary.org/obo/GO_0007568"},{"id":"T28","span":{"begin":5343,"end":5351},"obj":"http://purl.obolibrary.org/obo/GO_0007610"},{"id":"T29","span":{"begin":5536,"end":5541},"obj":"http://purl.obolibrary.org/obo/GO_0007568"},{"id":"T30","span":{"begin":5689,"end":5694},"obj":"http://purl.obolibrary.org/obo/GO_0007568"},{"id":"T31","span":{"begin":5777,"end":5782},"obj":"http://purl.obolibrary.org/obo/GO_0007568"}],"text":"Acknowledgments\nThe authors would like to thank Brigitte Bruijns from Micronit Microtechnologies for her help during the brainstorm sessions. Jörg Strack from TOPAS Advanced Polymers and Thomas Wagenknecht from KUZ Leipzig are thanked for their information on COC. Pieter Post, Rob Dierink, and Sip Jan Boorsma of TCO (Technical Center for Education and Research of the University of Twente) are thanked for their work in the milling and laser cutting processes, Christian Bruinink for his assistance in the transparency measurements, Daniel Monteiro Cunha, M.Sc. for his assistance in the AFM measurements, and Nikki Stroot for her assistance with the initial amplification reactions. Sample Availability: Samples of the amplification chips are available from the authors.\n\nAuthor Contributions\nConceived and designed the experiments: H.-W.V., F.A.M., and R.S.; developed the measurement setup and software, and provided technical help: R.S.; developed the methodology: H.-W.V. and F.A.M.; performed the experiments: F.A.M.; visualized the results: H.-W.V. and F.A.M.; wrote the first draft of the paper: H.-W.V.; reviewed and edited the first draft of the paper: H.-W.V., F.A.M., R.S., R.W. and J.L.; supervised the project: H.-W.V. All authors have read and agreed to the published version of the manuscript.\n\nFunding\nThis work is financed with institutional funding.\n\nConflicts of Interest\nThe authors declare no conflict of interest. Abbreviations\nThe following abbreviations are used in this manuscript: AFM atomic force microscopy\nAu gold\nCAD computer-aided design\nCAM computer-aided manufacturing\nCNC computer numerical control\nCOC cyclic olefin copolymer\nDC direct current\nDI de-ionized\nDNA deoxyribonucleic acid\ndsDNA double stranded DNA\nH2O water\nHDA helicase-dependent amplification\nLAMP loop-mediated isothermal amplification\nMDA multiple displacement amplification\nMo molybdenum\nN2 nitrogen\nNTC non template control\nPCR polymerase chain reaction\nPDMS polydimethylsiloxane\nPID proportional-integral-derivative\nPt platinum\nPVD physical vapor deposition\nRNA ribonucleic acid\nSEM scanning electron microscopy\nssDNA single stranded DNA\nSDI Sexually Transmitted Diseases Diagnostics Initiative\nTCR temperature coefficient of resistance\nTg glass transition temperature\nWGA whole genome amplification\nWHO World Health Organization\n\nAppendix A. Technical Drawing Chip\nFigure A1 Technical drawing of the DNA amplification chip. All dimensions are in mm. The total chip size is 3 mm by 3 mm.\n\nAppendix B. Equations and Values Used in the COMSOL Multiphysics Study\n\nAppendix B.1. Water\nFor H2O, the build-in temperature-dependent equations for the density (ρH2O, see equations in Equation (A1)), heat capacity at constant pressure (CP,H2O, see equations in Equation (A2)), and thermal conductivity (κH2O, see equations in Equation (A3)) are used. The ratio (γH2O) of the specific heats at constant pressure (CP,H2O) and constant volume (CV,H2O) is calculated manually according to the table from the Engineering Toolbox website [81] and Equation (A4). The values for γH2O are listed in Table A1. (A1) ρH2O(T)=972.7584+0.2084T−4×10−4T2for273≤T\u003c283345.28+5.749816T−0.0157244T2+1.264375×10−5T3for283≤T\u003c373 (A2) CP,H2O(T)=12010.1471−80.4072879T+0.309866854T2for273.15≤T\u003c553.75−5.38186884×10−4T3+3.62536437×10−7T4 (A3) κH2O(T)=−0.869083936+0.00894880345T−1.58366345×10−5T2for273.15≤T\u003c553.75+7.97543259×10−9T3 (A4) γH2O=CP,H2OCV,H2O\nTable A1 The ratio of specific heats of water.\nT γH2O T γH2O\n[K] [-] [K] [-]\n273.16 1.000592782 393.15 1.157465496\n283.15 1.001073729 413.15 1.199809492\n293.15 1.006591292 433.15 1.246234334\n298.15 1.010560913 453.15 1.297534537\n303.15 1.015203400 473.15 1.355013713\n313.15 1.025996023 493.15 1.420794975\n323.15 1.038520763 513.15 1.498241758\n333.15 1.052405261 533.15 1.592792563\n343.15 1.067512483 553.15 1.714447794\n353.15 1.083658241 573.15 1.883524402\n363.15 1.100748613 593.15 2.148448797\n373.15 1.118756966 613.15 2.666580033\n383.15 1.137648990 633.15 4.550527720\n\nAppendix B.2. Cyclic Olefin Copolymer\nValues for the density (ρCOC = 1020 kg m−3), specific heat (cCOC, see Table A2), and thermal conductivity (κCOC,23°C = 0.17 W m−1 K−1 and κCOC,320°C = 0.24 W m−1 K−1, linear fit in between these point) of TOPAS 6017 COC are obtained via TOPAS Advanced Polymers (TOPAS Advanced Polymers, Farmington Hills, MI, USA). The heat capacity at constant pressure (CP,COC) is calculated assuming a homogeneous body of mass m, via Equation (A5), where COMSOL interpolated linearly in between the points. (A5) CP,COC=cCOC×m\nTable A2 The specific heat of TOPAS 6017 COC.\nT c T c\n[°C] [W m−1 K−1] [°C] [W m−1 K−1]\n30 1333 180 2298\n70 1538 210 2412\n110 1754 250 2539\n150 1968 290 2645\n160 2047 330 2758 Convective heat loss to the air is also taken into account with Equation (A6), which is often used in simulations [56]. (A6) h=10Wm−2K−1\n\nAppendix C. TCR Measurements\nThe two subsections below show two effects on the TCR measurements, i.e., the effect of thermal annealing during the first temperature cycle and the effect of aging.\n\nAppendix C.1. Thermal Annealing\nThe graph below is an example of the measured thermal annealing of a metal layer on COC. Here, only the graph for evaporated Au is shown, but all except evaporated Pt show this behavior. Evaporated Pt had some contaminants in the metal track. This is most probably caused by the shadow mask.\nFigure A2 Thermal annealing of an evaporated 100 nm Au layer.\n\nAppendix C.2. Aging\nThe layer analyzed in Figure A2 is stored for two weeks in ambient conditions and the TCR is analyzed again. From the graph it is visible that the aging has some effect on the TCR of the metal layer.\nFigure A3 The effect of two weeks aging in ambient conditions on a 100 nm Au layer. The TCR of the as deposited layer is 0.00161 K−1 and the TCR of the two week old layer is 0.00224 K−1.\n\nAppendix D. MDA Reaction Mixture\nThe reaction mixture for the on-chip MDA reaction consisted of the following.\nTable A3 On-chip MDA reaction mixtures.\nSample Reaction Buffer Sample Buffer DNA MilliQ DI Water EG Enzyme\n[μL] [μL] [μL] [μL] [μL] [μL]\nTube with DNA 9 9 1 - 4 1\nTube NTC 9 9 - 1 4 1\nChip with DNA 9 9 1 - 4 1\nChip NTC 9 9 - 1 4 1\n\nAppendix E. Background Signal Fluorescence Measurements\nAll fluorescence measurements in the Horiba Scientific FluoroMax+ spectrofluorometer are normalized by subtracting the background signal. This background signal is measured using the mixture in Table A4.\nTable A4 Mixture used for background signal measurement.\nSample Reaction Buffer Sample Buffer DNA MilliQ DI Water EG Enzyme\n[μL] [μL] [μL] [μL] [μL] [μL]\nBackground 9 9 1 1 4 -\nFigure A4 The background signal of the mixture in Table A4."}

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