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PMC:7143804 / 3449-9317 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
69 2024-2032 Chemical denotes polymers MESH:D011108
70 2584-2589 Chemical denotes metal MESH:D008670
71 2620-2622 Chemical denotes Cu MESH:D003300
76 3832-3852 Chemical denotes polydimethylsiloxane MESH:C013830
77 3854-3858 Chemical denotes PDMS MESH:C013830
78 4269-4292 Chemical denotes cyclic olefin copolymer
79 4294-4297 Chemical denotes COC
86 4769-4774 Chemical denotes metal MESH:D008670
87 4908-4913 Chemical denotes metal MESH:D008670
88 4966-4969 Chemical denotes COC
89 4978-4983 Chemical denotes metal MESH:D008670
90 5103-5108 Chemical denotes metal MESH:D008670
91 5766-5771 Chemical denotes metal MESH:D008670

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T13 54-57 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T14 62-65 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 176-179 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T16 1194-1197 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T17 2120-2123 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T18 3320-3323 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T19 3327-3330 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T20 5016-5022 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 4235-4240 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T17 3075-3078 Disease denotes PID http://purl.obolibrary.org/obo/MONDO_0000922
T18 3109-3112 Disease denotes PID http://purl.obolibrary.org/obo/MONDO_0000922

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T32 80-87 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T33 333-334 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 365-370 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T35 695-696 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 873-874 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 880-887 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T38 1185-1190 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T39 1541-1542 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 1580-1581 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 1947-1948 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 2085-2086 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 2092-2099 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T44 2196-2197 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 2765-2766 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 2873-2874 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 3039-3040 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 3171-3172 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 3301-3302 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 3308-3315 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T51 3378-3381 http://purl.obolibrary.org/obo/CLO_0050884 denotes ten
T52 3468-3475 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T53 3509-3510 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 3953-3954 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 4153-4155 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T56 4470-4477 http://purl.obolibrary.org/obo/OBI_0000968 denotes devices
T57 4554-4556 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T58 4651-4652 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 4742-4744 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T60 4787-4788 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 4868-4869 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T62 4996-4997 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 5016-5022 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T64 5034-5041 http://purl.obolibrary.org/obo/OBI_0100026 denotes organic
T65 5034-5041 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organic
T66 5319-5322 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T67 5323-5324 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T19 54-57 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T20 62-65 Chemical denotes RNA http://purl.obolibrary.org/obo/CHEBI_33697
T21 176-179 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T22 1194-1197 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T23 2024-2032 Chemical denotes polymers http://purl.obolibrary.org/obo/CHEBI_33839
T24 2120-2123 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T25 2620-2622 Chemical denotes Cu http://purl.obolibrary.org/obo/CHEBI_28694
T26 3075-3078 Chemical denotes PID http://purl.obolibrary.org/obo/CHEBI_8066
T27 3109-3112 Chemical denotes PID http://purl.obolibrary.org/obo/CHEBI_8066
T28 3320-3323 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T29 3327-3330 Chemical denotes RNA http://purl.obolibrary.org/obo/CHEBI_33697
T30 3382-3390 Chemical denotes polymers http://purl.obolibrary.org/obo/CHEBI_33839
T31 3415-3421 Chemical denotes metals http://purl.obolibrary.org/obo/CHEBI_33521
T32 3832-3852 Chemical denotes polydimethylsiloxane http://purl.obolibrary.org/obo/CHEBI_31498|http://purl.obolibrary.org/obo/CHEBI_48137|http://purl.obolibrary.org/obo/CHEBI_61466|http://purl.obolibrary.org/obo/CHEBI_61468
T36 3854-3858 Chemical denotes PDMS http://purl.obolibrary.org/obo/CHEBI_31498|http://purl.obolibrary.org/obo/CHEBI_61468
T38 4269-4282 Chemical denotes cyclic olefin http://purl.obolibrary.org/obo/CHEBI_33642
T39 4276-4282 Chemical denotes olefin http://purl.obolibrary.org/obo/CHEBI_32878|http://purl.obolibrary.org/obo/CHEBI_33641
T41 4283-4292 Chemical denotes copolymer http://purl.obolibrary.org/obo/CHEBI_53310|http://purl.obolibrary.org/obo/CHEBI_60804
T43 4294-4297 Chemical denotes COC http://purl.obolibrary.org/obo/CHEBI_53310
T44 4578-4581 Chemical denotes COC http://purl.obolibrary.org/obo/CHEBI_53310
T45 4789-4792 Chemical denotes COC http://purl.obolibrary.org/obo/CHEBI_53310
T46 4966-4969 Chemical denotes COC http://purl.obolibrary.org/obo/CHEBI_53310
T47 5042-5049 Chemical denotes solvent http://purl.obolibrary.org/obo/CHEBI_46787
T48 5118-5121 Chemical denotes COC http://purl.obolibrary.org/obo/CHEBI_53310
T49 5202-5205 Chemical denotes COC http://purl.obolibrary.org/obo/CHEBI_53310
T50 5222-5224 Chemical denotes Au http://purl.obolibrary.org/obo/CHEBI_29287
T51 5315-5318 Chemical denotes COC http://purl.obolibrary.org/obo/CHEBI_53310
T52 5355-5357 Chemical denotes Tg http://purl.obolibrary.org/obo/CHEBI_9516
T53 5375-5378 Chemical denotes COC http://purl.obolibrary.org/obo/CHEBI_53310
T54 5604-5607 Chemical denotes COC http://purl.obolibrary.org/obo/CHEBI_53310
T55 5672-5679 Chemical denotes mixture http://purl.obolibrary.org/obo/CHEBI_60004

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T3 176-193 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T4 1194-1211 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T5 2120-2137 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T28 0-4 Sentence denotes 1.1.
T29 5-21 Sentence denotes State-of-the-Art
T30 22-101 Sentence denotes In the past, several chip-based DNA and RNA amplification devices are reported.
T31 102-209 Sentence denotes It goes beyond the scope of this paper to discuss the state-of-the-art of DNA amplification chips in-depth.
T32 210-298 Sentence denotes There are several good review papers written on this topic [12,13,14,15,16,17,18,19,20].
T33 299-371 Sentence denotes Readers are referred to these for a comprehensive overview of the field.
T34 372-562 Sentence denotes In this paper, the state-of-the-art is divided into several discussion points, i.e., the heating method, the temperature control method, and the substrate material and fabrication technique.
T35 563-605 Sentence denotes These points will be discussed separately.
T36 606-672 Sentence denotes With respect to heat supply, different methods have been employed.
T37 673-785 Sentence denotes Almassian et al. give a comprehensive overview of different possible heating methods in their review paper [12].
T38 786-935 Sentence denotes Not all of the mentioned methods are easy to implement in low-cost and portable lab-on-a-chip devices due to their bulkiness or implementation costs.
T39 936-1045 Sentence denotes Examples of these rather difficult methods are using heating via induction, infrared, or microwave radiation.
T40 1046-1173 Sentence denotes Others are not useful due ot their challenging temperature control, like with heating up the system using exothermic reactions.
T41 1174-1257 Sentence denotes Within the field of DNA amplification, different mechanisms of amplification exist.
T42 1258-1343 Sentence denotes Some are based on thermo cycling processes, e.g., PCR, whereas others are isothermal.
T43 1344-1431 Sentence denotes The use of an isothermal amplification technique puts less requirements on the heaters.
T44 1432-1625 Sentence denotes Isothermal processes are either truly isothermal or consisting of three different temperatures, as they have a thermal denaturation step before and a termination step after the elongation step.
T45 1626-1775 Sentence denotes The switching between these temperature steps does not have to be as fast as with thermal cycling steps in, for example, PCR amplification reactions.
T46 1776-1908 Sentence denotes The use of less temperature variations makes it easier to maintain the set temperature as there is less heating an cooling involved.
T47 1909-2033 Sentence denotes Furthermore, it eliminates the use of a continuous flow approach in systems with low thermal conductivities, e.g., polymers.
T48 2034-2108 Sentence denotes Therefore, it is easier to implement within lab-on-a-chip devices [17,21].
T49 2109-2266 Sentence denotes Isothermal DNA amplification reactions can already be performed by putting the chip on a commercially available hotplate [22,23] or Peltier elements [24,25].
T50 2267-2328 Sentence denotes However, these heating systems are bulky and power-consuming.
T51 2329-2416 Sentence denotes Therefore, they are not useful for portable equipment or operation at remote locations.
T52 2417-2482 Sentence denotes Miniaturizing heaters lowers the bulkiness and power consumption.
T53 2483-2671 Sentence denotes Miniaturized heaters can be integrated as integrated resistive heaters, e.g., as deposited thin-film metal [26,27,28,29] or as laminated Cu foil [30], or as micro-Peltier elements [31,32].
T54 2672-2851 Sentence denotes These miniaturized heaters can be implemented directly onto the microfluidic chip [28] or on a different substrate and leter incorporated onto the microfluidic chip [33,34,35,36].
T55 2852-2975 Sentence denotes The geometry of such a heater contributes significantly to the uniformity of the heat distribution within the chip [26,37].
T56 2976-3102 Sentence denotes One method to accurately control the temperature is the use of a proportional-integral-derivative (PID) controlled thermostat.
T57 3103-3235 Sentence denotes These PID controllers are coupled to the electrical heaters and use a thermocouple as feedback-loop to the controller [22,23,24,25].
T58 3236-3345 Sentence denotes There are various materials that can be used to fabricate lab-on-a-chip devices for DNA or RNA amplification.
T59 3346-3481 Sentence denotes In the past 15 years, more than ten polymers, ceramic materials, and metals have successfully been used to fabricate such devices [15].
T60 3482-3561 Sentence denotes The major property playing a role here is the biocompatibility of the material.
T61 3562-3650 Sentence denotes The surface of the microfluidic structure should not inhibit the amplification reaction.
T62 3651-3804 Sentence denotes This biocompatibility can be an intrinsic property of the material or the surface can be modified or coated to achieve this [12,13,14,15,16,17,18,19,20].
T63 3805-3935 Sentence denotes One often used material is polydimethylsiloxane (PDMS) [22,23,31,32,34,35,38], which can be processed using soft lithography [39].
T64 3936-4053 Sentence denotes However, this is a fabrication technology used in academia and is not suitable for upscaling to mass production [40].
T65 4054-4157 Sentence denotes Fabrication methods suitable for mass production are thermoforming/embossing or injection molding [41].
T66 4158-4377 Sentence denotes One of the materials which is biocompatible and suitable for both industrial scale fabrication technologies is cyclic olefin copolymer (COC) [42], which is one of the materials used in the past as well [28,36,43,44,45].
T67 4378-4558 Sentence denotes Guckenberger et al. estimates the costs of injection molding of only 50 simple microfluidic devices on $47, but this becomes cheaper when the mass production stage is reached [41].
T68 4559-4632 Sentence denotes Another benefit of COC is the possibility to shape it using micromilling.
T69 4633-4746 Sentence denotes This technique is a rapid prototyping technology and therefore very useful within proof-of-concept projects [41].
T70 4747-4835 Sentence denotes Integrating resistive metal tracks onto a COC substrate have also been done in the past.
T71 4836-5055 Sentence denotes Some papers describe the use of a surface modification step done before metal deposition in order to enhance adhesion between the COC and the metal layer, like a pretreatment with plasma [46] or an organic solvent [47].
T72 5056-5138 Sentence denotes Other papers describe the direct deposition of metal onto the COC surface [28,48].
T73 5139-5238 Sentence denotes Chung et al. specifically, fabricated an amplification chip in COC with integrated Au heaters [28].
T74 5239-5369 Sentence denotes However, their system required heating from both sides as the used grade of COC has a glass transition temperature (Tg) of 130 °C.
T75 5370-5473 Sentence denotes This COC could not withstand the required heater temperatures to have enough heat flux into the system.
T76 5474-5608 Sentence denotes They had to heat up the heater to temperatures above 130 °C, which caused cracking of the heater tracks due to deformation of the COC.
T77 5609-5713 Sentence denotes With their double-sided heating they ensured that the reaction mixture had the desired PCR temperatures.
T78 5714-5868 Sentence denotes However, double-sided heating doubles the amount of metal required, increases the amount of fabrication steps, and therefore increases the price per chip.

2_test

Id Subject Object Predicate Lexical cue
32106462-24030680-69893274 270-272 24030680 denotes 12
32106462-19327449-69893275 279-281 19327449 denotes 15
32106462-21387067-69893276 285-287 21387067 denotes 17
32106462-17553097-69893277 288-290 17553097 denotes 18
32106462-22704369-69893278 294-296 22704369 denotes 20
32106462-24030680-69893279 781-783 24030680 denotes 12
32106462-21387067-69893280 2101-2103 21387067 denotes 17
32106462-22592150-69893281 2104-2106 22592150 denotes 21
32106462-21479543-69893282 2231-2233 21479543 denotes 22
32106462-23610705-69893283 2234-2236 23610705 denotes 23
32106462-21267083-69893284 2259-2261 21267083 denotes 24
32106462-22038328-69893285 2262-2264 22038328 denotes 25
32106462-15269812-69893286 2838-2840 15269812 denotes 33
32106462-18975094-69893287 2841-2843 18975094 denotes 34
32106462-21479543-69893288 3222-3224 21479543 denotes 22
32106462-23610705-69893289 3225-3227 23610705 denotes 23
32106462-21267083-69893290 3228-3230 21267083 denotes 24
32106462-22038328-69893291 3231-3233 22038328 denotes 25
32106462-19327449-69893292 3477-3479 19327449 denotes 15
32106462-24030680-69893293 3776-3778 24030680 denotes 12
32106462-19327449-69893294 3785-3787 19327449 denotes 15
32106462-21387067-69893295 3791-3793 21387067 denotes 17
32106462-17553097-69893296 3794-3796 17553097 denotes 18
32106462-22704369-69893297 3800-3802 22704369 denotes 20
32106462-21479543-69893298 3861-3863 21479543 denotes 22
32106462-23610705-69893299 3864-3866 23610705 denotes 23
32106462-18975094-69893300 3873-3875 18975094 denotes 34
32106462-20218572-69893301 3879-3881 20218572 denotes 38
32106462-28281349-69893302 4049-4051 28281349 denotes 40
32106462-25906246-69893303 4153-4155 25906246 denotes 41
32106462-20066496-69893304 4367-4369 20066496 denotes 43
32106462-31277382-69893305 4373-4375 31277382 denotes 45
32106462-25906246-69893306 4554-4556 25906246 denotes 41
32106462-25906246-69893307 4742-4744 25906246 denotes 41
32106462-24957952-69893308 5134-5136 24957952 denotes 48