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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1289 1787-1809 Species denotes Listeria monocytogenes Tax:1639
1290 1811-1827 Species denotes L. monocytogenes Tax:1639
1291 1975-1998 Species denotes human influenza A virus Tax:11320
1292 1698-1702 Chemical denotes TiO2
1293 1872-1879 Chemical denotes silicon MESH:D012825
1297 2732-2753 Species denotes cucumber mosaic virus Tax:12305
1298 2053-2060 Chemical denotes polymer MESH:D011108
1299 2252-2259 Chemical denotes Polymer MESH:D011108
1301 3332-3339 Chemical denotes silicon MESH:D012825
1306 5339-5347 Gene denotes Fe(CN)63 Gene:2960
1307 5272-5279 Species denotes E. coli Tax:562
1308 5114-5116 Chemical denotes Au MESH:D006046
1309 5208-5211 Disease denotes CIP MESH:D010259
1317 5764-5772 Gene denotes Fe(CN)63 Gene:2960
1318 5594-5608 Species denotes S. typhimurium Tax:90371
1319 5708-5715 Species denotes E. coli Tax:562
1320 5720-5731 Species denotes V. cholerae Tax:666
1321 5898-5905 Species denotes E. coli Tax:562
1322 5910-5919 Species denotes S. aureus Tax:1280
1323 5540-5542 Chemical denotes Au MESH:D006046
1328 4939-4966 Species denotes Japanese encephalitis virus Tax:11072
1329 4446-4448 Chemical denotes Au MESH:D006046
1330 4788-4794 Chemical denotes carbon MESH:D002244
1331 4811-4817 Chemical denotes carbon MESH:D002244
1337 6761-6776 Species denotes West Nile virus Tax:11082
1338 6296-6298 Chemical denotes Au MESH:D006046
1339 6343-6362 Chemical denotes gold (III) chloride
1340 6711-6718 Chemical denotes alumina MESH:D000537
1341 6726-6728 Chemical denotes Pt MESH:D010984

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T112 4577-4580 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T113 4746-4750 Body_part denotes Chin http://purl.org/sig/ont/fma/fma46495
T114 4968-4972 Body_part denotes Chin http://purl.org/sig/ont/fma/fma46495
T115 5184-5188 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T8 2448-2453 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T9 4746-4750 Body_part denotes Chin http://purl.obolibrary.org/obo/UBERON_0008199
T10 4968-4972 Body_part denotes Chin http://purl.obolibrary.org/obo/UBERON_0008199

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T58 1981-1990 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T59 4939-4960 Disease denotes Japanese encephalitis http://purl.obolibrary.org/obo/MONDO_0019209
T60 4948-4960 Disease denotes encephalitis http://purl.obolibrary.org/obo/MONDO_0019956
T61 5208-5211 Disease denotes CIP http://purl.obolibrary.org/obo/MONDO_0009459|http://purl.obolibrary.org/obo/MONDO_0015364

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T336 136-137 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T337 478-480 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T338 478-480 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T339 578-579 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T340 665-668 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T341 876-877 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T342 999-1000 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T343 1141-1142 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T344 1732-1733 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T345 1912-1913 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T346 1975-1980 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T347 1991-1992 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T348 1993-1998 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T349 2472-2473 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T350 2503-2504 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T351 2748-2753 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T352 2905-2908 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T353 3401-3402 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T354 3633-3636 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T355 4015-4016 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T356 4475-4476 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T357 4603-4604 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T358 4688-4689 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T359 4735-4736 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T360 4961-4966 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T361 5094-5098 http://purl.obolibrary.org/obo/CLO_0001627 denotes a) A
T362 5181-5188 http://purl.obolibrary.org/obo/CL_0000236 denotes b) Cell
T363 5494-5495 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T364 5510-5516 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T365 5633-5634 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T366 5778-5780 http://purl.obolibrary.org/obo/CLO_0001022 denotes Li
T367 5778-5780 http://purl.obolibrary.org/obo/CLO_0007314 denotes Li
T368 5811-5812 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T369 5826-5832 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T370 5851-5866 http://purl.obolibrary.org/obo/BFO_0000006 denotes spatial regions
T371 6279-6280 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T372 6528-6529 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T373 6771-6776 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T374 7378-7379 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T375 7399-7405 http://purl.obolibrary.org/obo/OBI_0000968 denotes device
T376 7409-7415 http://purl.obolibrary.org/obo/OBI_0000968 denotes device

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T873 478-480 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145
T874 1194-1202 Chemical denotes nanowire http://purl.obolibrary.org/obo/CHEBI_52593
T875 1339-1347 Chemical denotes nanowire http://purl.obolibrary.org/obo/CHEBI_52593
T876 1582-1590 Chemical denotes nanowire http://purl.obolibrary.org/obo/CHEBI_52593
T877 1681-1689 Chemical denotes nanowire http://purl.obolibrary.org/obo/CHEBI_52593
T878 1698-1702 Chemical denotes TiO2 http://purl.obolibrary.org/obo/CHEBI_32234
T879 1872-1879 Chemical denotes silicon http://purl.obolibrary.org/obo/CHEBI_27573
T880 1880-1888 Chemical denotes nanowire http://purl.obolibrary.org/obo/CHEBI_52593
T881 2053-2060 Chemical denotes polymer http://purl.obolibrary.org/obo/CHEBI_33839|http://purl.obolibrary.org/obo/CHEBI_60027
T883 2217-2228 Chemical denotes application http://purl.obolibrary.org/obo/CHEBI_33232
T884 2252-2259 Chemical denotes Polymer http://purl.obolibrary.org/obo/CHEBI_60027
T885 2659-2661 Chemical denotes Au http://purl.obolibrary.org/obo/CHEBI_29287
T886 2698-2709 Chemical denotes polypyrrole http://purl.obolibrary.org/obo/CHEBI_38077|http://purl.obolibrary.org/obo/CHEBI_53263
T888 3323-3328 Chemical denotes PEDOT http://purl.obolibrary.org/obo/CHEBI_53228|http://purl.obolibrary.org/obo/CHEBI_60622
T890 3332-3339 Chemical denotes silicon http://purl.obolibrary.org/obo/CHEBI_27573
T8928 3607-3615 Chemical denotes nanowire http://purl.obolibrary.org/obo/CHEBI_52593
T10559 3905-3918 Chemical denotes nanoparticles http://purl.obolibrary.org/obo/CHEBI_50803
T35760 4446-4448 Chemical denotes Au http://purl.obolibrary.org/obo/CHEBI_29287
T53769 4577-4580 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T37781 4788-4794 Chemical denotes carbon http://purl.obolibrary.org/obo/CHEBI_27594|http://purl.obolibrary.org/obo/CHEBI_33415
T56418 4811-4817 Chemical denotes carbon http://purl.obolibrary.org/obo/CHEBI_27594|http://purl.obolibrary.org/obo/CHEBI_33415
T32697 4818-4831 Chemical denotes nanoparticles http://purl.obolibrary.org/obo/CHEBI_50803
T26618 4845-4853 Chemical denotes electron http://purl.obolibrary.org/obo/CHEBI_10545
T5809 5114-5116 Chemical denotes Au http://purl.obolibrary.org/obo/CHEBI_29287
T47439 5199-5206 Chemical denotes polymer http://purl.obolibrary.org/obo/CHEBI_33839|http://purl.obolibrary.org/obo/CHEBI_60027
T81022 5326-5329 Chemical denotes EIS http://purl.obolibrary.org/obo/CHEBI_73498
T16800 5339-5341 Chemical denotes Fe http://purl.obolibrary.org/obo/CHEBI_18248
T75529 5358-5363 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T57023 5540-5542 Chemical denotes Au http://purl.obolibrary.org/obo/CHEBI_29287
T53521 5647-5660 Chemical denotes nanoparticles http://purl.obolibrary.org/obo/CHEBI_50803
T23103 5764-5766 Chemical denotes Fe http://purl.obolibrary.org/obo/CHEBI_18248
T20 5778-5780 Chemical denotes Li http://purl.obolibrary.org/obo/CHEBI_30145
T45528 6296-6298 Chemical denotes Au http://purl.obolibrary.org/obo/CHEBI_29287
T67953 6343-6362 Chemical denotes gold (III) chloride http://purl.obolibrary.org/obo/CHEBI_30076
T82273 6343-6347 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T60058 6354-6362 Chemical denotes chloride http://purl.obolibrary.org/obo/CHEBI_17996
T11281 6363-6371 Chemical denotes hydrates http://purl.obolibrary.org/obo/CHEBI_35505
T16339 6711-6718 Chemical denotes alumina http://purl.obolibrary.org/obo/CHEBI_30187
T78755 6726-6728 Chemical denotes Pt http://purl.obolibrary.org/obo/CHEBI_33364|http://purl.obolibrary.org/obo/CHEBI_75318

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T47165 2454-2463 http://purl.obolibrary.org/obo/GO_0009058 denotes synthesis
T48052 4845-4862 http://purl.obolibrary.org/obo/GO_0022904 denotes electron transfer
T32260 5003-5015 http://purl.obolibrary.org/obo/GO_0009293 denotes transduction

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T8 4948-4960 Phenotype denotes encephalitis http://purl.obolibrary.org/obo/HP_0002383

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T365 0-32 Sentence denotes 2.1.5 Electrode nanostructuring
T366 33-190 Sentence denotes Transducers with physical dimensions comparable to the target species have been widely investigated as a means of creating sensitive biosensors (Gupta et al.
T367 191-210 Sentence denotes 2004; Pumera et al.
T368 211-229 Sentence denotes 2007; Singh et al.
T369 230-246 Sentence denotes 2010; Wei et al.
T370 247-253 Sentence denotes 2009).
T371 254-356 Sentence denotes Thus, electrodes ranging from micrometers to nanometers have been investigated for pathogen detection.
T372 357-463 Sentence denotes While nanoscale planar electrodes are among the most commonly examined for pathogen detection (Hong et al.
T373 464-774 Sentence denotes 2015; Peh and Li, 2013), the fabrication of nanoscale structures of conducting and semiconducting materials using a wide range of bottom-up and top-down nanomanufacturing processes, such as nanowires, has led to the investigation of nanostructured electrodes for pathogen detection (Patolsky and Lieber, 2005).
T374 775-945 Sentence denotes Nanostructuring can be performed simultaneously with bottom-up electrode fabrication processes or as a post-processing step with top-down electrode fabrication processes.
T375 946-1106 Sentence denotes Nanowire-based electrodes have been fabricated using a variety of engineering materials using both bottom-up and top-down nanomanufacturing processes (Hu et al.
T376 1107-1140 Sentence denotes 1999; Yogeswaran and Chen, 2008).
T377 1141-1248 Sentence denotes A detailed review of nanomanufacturing processes for nanowire fabrication can be found elsewhere (Hu et al.
T378 1249-1255 Sentence denotes 1999).
T379 1256-1334 Sentence denotes Nanowires can exhibit circular, hexagonal, and even triangular cross-sections.
T380 1335-1456 Sentence denotes The nanowire aspect ratio, defined as the ratio of the length to width, often ranges from 1 to greater than 10 (Hu et al.
T381 1457-1517 Sentence denotes 1999; Vaseashta and Dimova-Malinovska, 2005; Wanekaya et al.
T382 1518-1524 Sentence denotes 2006).
T383 1525-1650 Sentence denotes As shown in Table 1, metallic and ceramic microwire- and nanowire-based electrodes have been examined for pathogen detection.
T384 1651-1841 Sentence denotes For example, Wang et al. used nanowire-bundled TiO2 electrodes synthesized using a bottom-up wet chemistry process for the detection of Listeria monocytogenes (L. monocytogenes) (Wang et al.
T385 1842-1848 Sentence denotes 2008).
T386 1849-2036 Sentence denotes Shen et al. fabricated silicon nanowire-based electrodes using a chemical vapor deposition process for the rapid detection of human influenza A virus in an array-based format (Shen et al.
T387 2037-2043 Sentence denotes 2012).
T388 2044-2169 Sentence denotes Although polymer nanowires have been relatively more applied to the detection of non-pathogenic species (Travas-Sejdic et al.
T389 2170-2251 Sentence denotes 2014), there appears to be potential for their application to pathogen detection.
T390 2252-2495 Sentence denotes Polymer nanowires are also synthesized via bottom-up and top-down nanomanufacturing processes, including hard template methods, soft template methods, or physical approaches, but efficient, large-scale synthesis remains a challenge (Xia et al.
T391 2496-2502 Sentence denotes 2010).
T392 2503-2619 Sentence denotes A comprehensive summary of studies using micro- and nano-wire electrodes for pathogen detection is shown in Table 1.
T393 2620-2775 Sentence denotes For example, Chartuprayoon et al. used Au microelectrode arrays modified with polypyrrole nanoribbons to detect cucumber mosaic virus (Chartuprayoon et al.
T394 2776-2782 Sentence denotes 2013).
T395 2783-2955 Sentence denotes The topographical modification of electrode surfaces with micro- and nano-structured features beyond wire-like structures has also been investigated for pathogen detection.
T396 2956-3171 Sentence denotes Electrode nanostructuring increases the electrode surface area without significantly increasing the electrode volume, thereby increasing the ratio of electrode surface area to fluid volume analyzed (Soleymani et al.
T397 3172-3178 Sentence denotes 2009).
T398 3179-3279 Sentence denotes Topographical modification of electrodes can also affect their mechanical and electrical properties.
T399 3280-3524 Sentence denotes For example, electrochemical deposition of PEDOT on silicon electrodes reduces the electrode electrical impedance across a wide frequency range, which offers measurement advantages for neural monitoring and recording applications (Ludwig et al.
T400 3525-3531 Sentence denotes 2006).
T401 3532-3734 Sentence denotes Electrode nanostructuring for pathogen detection beyond the fabrication of nanowire-based electrodes has been accomplished primarily using bottom-up wet chemistry approaches and electrochemical methods.
T402 3735-3817 Sentence denotes Among the wet chemistry approaches for electrode nanostructuring (Eftekhari et al.
T403 3818-3940 Sentence denotes 2008), nanostructured electrodes are often fabricated by the deposition or coupling of nanoparticles to planar electrodes.
T404 3941-4082 Sentence denotes For example, AuNPs are commonly deposited on planar electrodes to provide a nanostructured surface for biorecognition element immobilization.
T405 4083-4195 Sentence denotes In such studies, the particles are bound to the planar electrode via physical adsorption processes (Attar et al.
T406 4196-4234 Sentence denotes 2016) or chemical methods (Wang et al.
T407 4235-4241 Sentence denotes 2013).
T408 4242-4389 Sentence denotes In addition to AuNPs, CNTs have also been extensively investigated as potentially useful nanomaterials for electrode nanostructuring (see Table 1).
T409 4390-4706 Sentence denotes De Luna et al. found that high-curvature nanostructured Au microelectrodes exhibited a reduced extent of biorecognition element aggregation relative to that found on planar electrodes in DNA sensing studies using a combination of experimental studies and molecular dynamics simulations (see Fig. 3 a) (De Luna et al.
T410 4707-4727 Sentence denotes 2017; Mahshid et al.
T411 4728-4734 Sentence denotes 2016).
T412 4735-4979 Sentence denotes A study by Chin et al. found that nanostructuring of carbon electrodes with carbon nanoparticles enhanced the electron transfer kinetics and current intensity of the electrode by 63% for the detection of Japanese encephalitis virus (Chin et al.
T413 4980-4986 Sentence denotes 2017).
T414 4987-5173 Sentence denotes Fig. 3 Emerging transduction approaches associated with electrochemical biosensors for pathogen detection. a) A nanostructured Au microelectrode array with high curvature (De Luna et al.
T415 5174-5378 Sentence denotes 2017). b) Cell-imprinted polymer (CIP) with ‘artificial’ biorecognition elements for detection of E. coli using electrochemical impedance spectroscopy (EIS) and the Fe(CN)63-/4- redox probe (Jafari et al.
T416 5379-5385 Sentence denotes 2019).
T417 5386-5625 Sentence denotes Fig. 4 Measurement settings associated with electrochemical biosensor-based multiplexed pathogen detection. a) Microfluidic device with an interdigitated Au microelectrode array for continuous measurement of S. typhimurium (Dastider et al.
T418 5626-5787 Sentence denotes 2015). b) Conjugated nanoparticles with two different biorecognition elements for E. coli and V. cholerae detection via voltammetry using Fe(CN)63-/4- (Li et al.
T419 5788-5932 Sentence denotes 2017). c) Schematic of a microfluidic device with two separate spatial regions of biorecognition elements for E. coli and S. aureus (Tian et al.
T420 5933-5939 Sentence denotes 2016).
T421 5940-6242 Sentence denotes In addition to fabricating nanostructured electrodes by coupling already processed nanomaterials to planar electrodes, electrochemical methods are also commonly used for bottom-up electrode nanostructuring processes and have been leveraged to fabricate nanostructured electrodes for pathogen detection.
T422 6243-6435 Sentence denotes For example, Hong et al. fabricated a nanostructured Au electrode via electrochemical deposition of gold (III) chloride hydrates for the detection of norovirus in lettuce extracts (Hong et al.
T423 6436-6442 Sentence denotes 2015).
T424 6443-6663 Sentence denotes While the physical or chemical deposition of materials on planar electrodes provides a useful nanostructuring approach, introducing porosity to the electrode, such as nanoporosity, also enables electrode nanostructuring.
T425 6664-6791 Sentence denotes For example, Nguyen et al. utilized nanoporous alumina-coated Pt microwires for the detection of West Nile virus (Nguyen et al.
T426 6792-6798 Sentence denotes 2009).
T427 6799-7045 Sentence denotes While studies have reported improved biosensor performance using electrode nanostructuring, such as improved sensitivity and LOD, it is prudent to consider the effect of nanostructuring on biorecognition element immobilization and target binding.
T428 7046-7313 Sentence denotes For example, nanostructured electrodes that exhibit high-aspect-ratio structures and other three-dimensional structures have also been shown to enhance biomolecular steric hindrance effects, which may have implications for pathogen detection applications (Hong et al.
T429 7314-7330 Sentence denotes 2015; Lam et al.
T430 7331-7351 Sentence denotes 2012; Mahshid et al.
T431 7352-7358 Sentence denotes 2017).
T432 7359-7482 Sentence denotes There also remains a need to understand device-to-device and batch-to-batch variation in electrode nanostructuring quality.
T433 7483-7693 Sentence denotes For example, it is presently unclear how the structure (e.g., topography, crystal structure) and material properties (e.g., electrical properties) of nanostructured surfaces vary among mass-produced electrodes.
T434 7694-7809 Sentence denotes It is also unclear how such variance in nanostructuring quality affects the repeatability of biosensor performance.

2_test

Id Subject Object Predicate Lexical cue
32364936-20419506-7713035 230-234 20419506 denotes 2010
32364936-19606287-7713036 247-251 19606287 denotes 2009
32364936-25254625-7713037 464-468 25254625 denotes 2015
32364936-23220066-7713038 482-486 23220066 denotes 2013
32364936-27879709-7713039 1134-1138 27879709 denotes 2008
32364936-18715043-7713040 1842-1846 18715043 denotes 2008
32364936-22731392-7713041 2037-2041 22731392 denotes 2012
32364936-32262272-7713042 2170-2174 32262272 denotes 2014
32364936-19837415-7713043 2496-2500 19837415 denotes 2010
32364936-19893517-7713044 3172-3176 19893517 denotes 2009
32364936-16510943-7713045 3525-3529 16510943 denotes 2006
32364936-23811484-7713046 4235-4239 23811484 denotes 2013
32364936-28075594-7713047 4707-4711 28075594 denotes 2017
32364936-28075594-7713048 5174-5178 28075594 denotes 2017
32364936-28382165-7713049 5788-5792 28382165 denotes 2017
32364936-25254625-7713050 6436-6440 25254625 denotes 2015
32364936-19663392-7713051 6792-6796 19663392 denotes 2009
32364936-25254625-7713052 7314-7318 25254625 denotes 2015
32364936-22142422-7713053 7331-7335 22142422 denotes 2012
32364936-28829912-7713054 7352-7356 28829912 denotes 2017