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PMC:7019868 / 12956-17051 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
237 50-61 Species denotes Large White Tax:7116
238 88-92 Species denotes PEDV Tax:28295
239 97-101 Species denotes TGEV Tax:11149
240 172-175 Species denotes pig Tax:9823
241 195-199 Species denotes PEDV Tax:28295
242 317-321 Species denotes PEDV Tax:28295
243 330-333 Species denotes pig Tax:9823
244 622-633 Disease denotes weight gain MESH:D015430
245 825-836 Disease denotes weight gain MESH:D015430
247 1008-1012 Species denotes PEDV Tax:28295
253 1644-1647 Gene denotes Rad Gene:6236
254 1060-1064 Species denotes PEDV Tax:28295
255 1187-1191 Chemical denotes DPBS
256 1272-1282 Disease denotes QIAcube HT MESH:D006973
257 1292-1299 Disease denotes QIAcube
264 2243-2246 Species denotes pig Tax:9823
265 2511-2519 Chemical denotes formalin MESH:D005557
266 2527-2535 Chemical denotes paraffin MESH:D010232
267 2592-2603 Chemical denotes hematoxylin MESH:D006416
268 2608-2613 Chemical denotes eosin MESH:D004801
269 2615-2618 Chemical denotes H&E
288 2806-2810 Species denotes PEDV Tax:28295
289 3253-3257 Species denotes goat Tax:9925
290 3417-3421 Species denotes PEDV Tax:28295
291 3478-3482 Species denotes goat Tax:9925
292 3635-3641 Species denotes rabbit Tax:9986
293 3642-3647 Species denotes mouse Tax:10090
294 2829-2837 Chemical denotes formalin MESH:D005557
295 2844-2852 Chemical denotes paraffin MESH:D010232
296 2910-2916 Chemical denotes xylene MESH:D014992
297 2949-2956 Chemical denotes ethanol MESH:D000431
298 3104-3124 Chemical denotes Tris-buffered saline
299 3135-3143 Chemical denotes Tween 20 MESH:D011136
300 3145-3149 Chemical denotes TBST
301 3563-3567 Chemical denotes TBST
302 3673-3676 Chemical denotes DAB
303 3783-3805 Chemical denotes 3, 3′-diaminobenzidine MESH:D015100
304 3807-3810 Chemical denotes DAB
305 3904-3915 Chemical denotes hematoxylin MESH:D006416

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T66 280-285 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T67 286-294 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T68 299-308 Body_part denotes colostrum http://purl.org/sig/ont/fma/fma62101
T69 399-403 Body_part denotes milk http://purl.org/sig/ont/fma/fma62100
T70 1391-1394 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T71 1956-1959 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T72 2095-2098 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T73 2421-2429 Body_part denotes Duodenum http://purl.org/sig/ont/fma/fma7206
T74 2431-2438 Body_part denotes jejunum http://purl.org/sig/ont/fma/fma7207
T75 2440-2445 Body_part denotes ileum http://purl.org/sig/ont/fma/fma7208
T76 2447-2452 Body_part denotes cecum http://purl.org/sig/ont/fma/fma14541
T77 2454-2459 Body_part denotes colon http://purl.org/sig/ont/fma/fma14543
T78 2461-2467 Body_part denotes rectum http://purl.org/sig/ont/fma/fma14544
T79 2472-2494 Body_part denotes mesenteric lymph nodes http://purl.org/sig/ont/fma/fma277405
T80 2862-2869 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T81 3036-3040 Body_part denotes Cell http://purl.org/sig/ont/fma/fma68646
T82 3152-3158 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T83 3258-3263 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T84 3424-3432 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T85 3483-3488 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T86 3648-3662 Body_part denotes immunoglobulin http://purl.org/sig/ont/fma/fma62871

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T5 280-285 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T6 299-308 Body_part denotes colostrum http://purl.obolibrary.org/obo/UBERON_0001914
T7 399-403 Body_part denotes milk http://purl.obolibrary.org/obo/UBERON_0001913
T8 2421-2429 Body_part denotes Duodenum http://purl.obolibrary.org/obo/UBERON_0002114
T9 2431-2438 Body_part denotes jejunum http://purl.obolibrary.org/obo/UBERON_0002115
T10 2440-2445 Body_part denotes ileum http://purl.obolibrary.org/obo/UBERON_0002116
T11 2454-2459 Body_part denotes colon http://purl.obolibrary.org/obo/UBERON_0001155
T12 2461-2467 Body_part denotes rectum http://purl.obolibrary.org/obo/UBERON_0001052
T13 2472-2494 Body_part denotes mesenteric lymph nodes http://purl.obolibrary.org/obo/UBERON_0002509
T14 2483-2488 Body_part denotes lymph http://purl.obolibrary.org/obo/UBERON_0002391
T15 3152-3158 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T16 3258-3263 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977
T17 3483-3488 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T19 200-209 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T147 5-11 http://purl.obolibrary.org/obo/NCBITaxon_33208 denotes Animal
T148 157-158 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T149 526-533 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T150 537-538 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T151 561-564 http://purl.obolibrary.org/obo/CLO_0054060 denotes 102
T152 881-888 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humanly
T153 1080-1083 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T154 1280-1282 http://purl.obolibrary.org/obo/CLO_0004265 denotes HT
T155 1616-1617 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T156 1751-1753 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T157 2215-2220 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T158 2268-2276 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes humanely
T159 2416-2418 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T160 2431-2438 http://purl.obolibrary.org/obo/UBERON_0002115 denotes jejunum
T161 2440-2445 http://purl.obolibrary.org/obo/UBERON_0002116 denotes ileum
T162 2454-2459 http://purl.obolibrary.org/obo/UBERON_0001155 denotes colon
T163 2461-2467 http://purl.obolibrary.org/obo/UBERON_0001052 denotes rectum
T164 2461-2467 http://purl.obolibrary.org/obo/UBERON_0006866 denotes rectum
T165 2472-2494 http://purl.obolibrary.org/obo/UBERON_0002509 denotes mesenteric lymph nodes
T166 3036-3040 http://purl.obolibrary.org/obo/GO_0005623 denotes Cell
T167 3253-3257 http://purl.obolibrary.org/obo/NCBITaxon_9925 denotes goat
T168 3328-3336 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T169 3354-3361 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T170 3437-3442 http://purl.obolibrary.org/obo/CLO_0001757 denotes 1, at
T171 3443-3444 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T172 3478-3482 http://purl.obolibrary.org/obo/NCBITaxon_9925 denotes goat
T173 3642-3647 http://purl.obolibrary.org/obo/CLO_0007836 denotes mouse
T174 4014-4021 http://purl.obolibrary.org/obo/SO_0000418 denotes signals

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T76 578-580 Chemical denotes PI http://purl.obolibrary.org/obo/CHEBI_28874|http://purl.obolibrary.org/obo/CHEBI_53806|http://purl.obolibrary.org/obo/CHEBI_61484|http://purl.obolibrary.org/obo/CHEBI_74790
T80 1224-1236 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T81 1232-1236 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T82 1391-1394 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T83 1582-1587 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T84 2229-2234 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T85 2257-2262 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T86 2592-2603 Chemical denotes hematoxylin http://purl.obolibrary.org/obo/CHEBI_51686
T87 2811-2818 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T88 2910-2916 Chemical denotes xylene http://purl.obolibrary.org/obo/CHEBI_27338
T89 2949-2956 Chemical denotes ethanol http://purl.obolibrary.org/obo/CHEBI_16236
T90 2975-2982 Chemical denotes epitope http://purl.obolibrary.org/obo/CHEBI_53000
T91 3010-3017 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T92 3104-3108 Chemical denotes Tris http://purl.obolibrary.org/obo/CHEBI_9754
T93 3135-3143 Chemical denotes Tween 20 http://purl.obolibrary.org/obo/CHEBI_53424
T94 3187-3195 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T95 3381-3388 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T96 3434-3436 Chemical denotes DE http://purl.obolibrary.org/obo/CHEBI_73828
T97 3673-3676 Chemical denotes DAB http://purl.obolibrary.org/obo/CHEBI_90994
T98 3807-3810 Chemical denotes DAB http://purl.obolibrary.org/obo/CHEBI_90994
T99 3812-3821 Chemical denotes chromogen http://purl.obolibrary.org/obo/CHEBI_75050
T100 3904-3915 Chemical denotes hematoxylin http://purl.obolibrary.org/obo/CHEBI_51686

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T30 1019-1033 http://purl.obolibrary.org/obo/GO_0019076 denotes Viral Shedding
T31 1065-1079 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T32 1415-1436 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T33 1423-1436 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T34 1455-1476 http://purl.obolibrary.org/obo/GO_0001171 denotes Reverse Transcription
T35 1463-1476 http://purl.obolibrary.org/obo/GO_0006351 denotes Transcription
T36 1972-1993 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T37 1980-1993 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T38 3317-3336 http://purl.obolibrary.org/obo/GO_0004601 denotes peroxidase activity

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T93 0-4 Sentence denotes 2.5.
T94 5-22 Sentence denotes Animal Experiment
T95 23-339 Sentence denotes Thirty-seven, six-day-old, Large White × Duroc, crossbred, fecal PEDV and TGEV shedding-negative suckling piglets were purchased from a conventional pig farm devoid of G2b PEDV infection history based on the negative result of our long-term surveillance of serum antibody and colostrum against PEDV in this pig farm.
T96 340-602 Sentence denotes These piglets from different sows were fed with artificial milk and were randomly assigned to five groups, acclimated for one day, and then inoculated orally with indicative recombinant viruses at a dose of 2 mL of 0.5 × 102 TCID50/mL or PI-medium, respectively.
T97 603-654 Sentence denotes Clinical signs and weight gain were recorded daily.
T98 655-716 Sentence denotes Fecal consistency was monitored daily and scored visually as:
T99 717-795 Sentence denotes 0 = normal, 1 = loose, 2 = semi-fluid, and 3 = watery as previously described.
T100 796-900 Sentence denotes Calculation of average daily weight gain was only performed on piglets that were not humanly euthanized.
T101 901-948 Sentence denotes The formula used for calculation is as follows:
T102 949-981 Sentence denotes Weight gained/ surviving period.
T103 983-989 Sentence denotes 2.5.1.
T104 990-1033 Sentence denotes Quantification of PEDV Fecal Viral Shedding
T105 1034-1115 Sentence denotes Methods to quantify fecal PEDV viral shedding has been described previously [19].
T106 1116-1376 Sentence denotes Briefly, fecal samples collected from rectal swabs were resuspended in DPBS and then subjected to automated nucleic acid extraction using Cador Pathogen 96 QIAcube HT Kit with QIAcube (Qiagen Inc., Hilden, Germany) according to the manufacturer’s instructions.
T107 1377-1668 Sentence denotes Complementary DNA was synthesized via reverse transcription using QuantiNova™ Reverse Transcription kit (Qiagen Inc., Hilden, Germany) and proceeded to quantitative real-time PCR analysis using the primer-probe set published previously on a CFX96 Thermal Cycler (Bio-Rad, Hercules, CA, USA).
T108 1669-1806 Sentence denotes The thermal profile comprised an initial denaturation at 95 °C for 2 min and then 45 cycles of 95 °C for 15 s followed by 60 °C for 15 s.
T109 1807-2046 Sentence denotes The detection limit of the assay was determined by generating standard curves from serial 10-fold dilutions of known amounts of in vitro transcribed RNA followed by reverse transcription and real-time PCR quantification as described above.
T110 2047-2113 Sentence denotes The detection limit was calculated as 4.8 log10 RNA copies per mL.
T111 2115-2121 Sentence denotes 2.5.2.
T112 2122-2161 Sentence denotes Histopathology and Immunohistochemistry
T113 2162-2420 Sentence denotes At three days post-inoculation, three pigs from each virus-treated group and one pig from mock group were humanely euthanized by electrocution followed by exsanguination for histopathological and immunohistochemical assessments, as described previously [22].
T114 2421-2738 Sentence denotes Duodenum, jejunum, ileum, cecum, colon, rectum and mesenteric lymph nodes were collected, formalin-fixed, paraffin-embedded, sectioned at 4 μm, and stained routinely with hematoxylin and eosin (H&E) for morphometric analysis by assessing the ratio of villi height to crypt depth blindly by one veterinary pathologist.
T115 2739-2819 Sentence denotes Immunohistochemistry was performed to evaluate the distribution of PEDV antigen.
T116 2820-3067 Sentence denotes Briefly, formalin-fixed paraffin-embedded tissues were sectioned at 4 μm, deparaffined in xylene, rehydrated in serially diluted ethanol, and proceeded to epitope retrieval with the Trilogy antigen retrieval system (Cell Marque, Rocklin, CA, USA).
T117 3068-3376 Sentence denotes After being washed three times with Tris-buffered saline plus 0.1% Tween 20 (TBST), tissue slides were treated with 3% hydrogen peroxidase (KYB, New Taipei City, Taiwan) and 10% normal goat serum (Dako, Carpinteria, CA, USA) to block the endogenous peroxidase activity and non-specific signals, respectively.
T118 3377-3568 Sentence denotes For antigen detection, an in-house anti-PEDV N antibody, DE-1, at a dilution of 1:1000 in 10% normal goat serum was applied to the slides for 1 h at RT followed by three times wash with TBST.
T119 3569-3867 Sentence denotes The first antibodies were then captured using the polyclonal anti-rabbit/mouse immunoglobulin, EnVision-DAB+ system (Agilent Technologies, Santa Clara, CA, USA) at RT for 1 h and color was developed afterward with 3, 3′-diaminobenzidine (DAB) chromogen (Agilent Technologies, Santa Clara, CA, USA).
T120 3868-4004 Sentence denotes The slides were counterstained with hematoxylin (MUTO, Tokyo, Japan), mounted in Entellan (Merck, Darmstadt, Germany) and cover slipped.
T121 4005-4095 Sentence denotes Positive signals were visualized under an inverted light microscope (Nikon, Tokyo, Japan).

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T10 622-633 Phenotype denotes weight gain http://purl.obolibrary.org/obo/HP_0004324
T11 825-836 Phenotype denotes weight gain http://purl.obolibrary.org/obo/HP_0004324
T12 949-962 Phenotype denotes Weight gained http://purl.obolibrary.org/obo/HP_0004324

2_test

Id Subject Object Predicate Lexical cue
31905842-30089548-144353227 2416-2418 30089548 denotes 22