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PMC:7574920 / 27234-30181 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T122 1579-1582 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T70 1819-1821 Disease denotes OD http://purl.obolibrary.org/obo/MONDO_0017178

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T243 0-7 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T244 390-397 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T245 507-513 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T246 609-615 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T247 671-677 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T248 796-799 http://purl.obolibrary.org/obo/CLO_0001387 denotes 4°C
T249 961-962 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T250 1008-1009 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T251 1097-1098 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T252 1133-1134 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T253 1292-1293 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T254 1361-1362 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T255 1400-1401 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T256 1559-1560 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T257 1571-1572 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T258 1950-1951 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T259 2065-2066 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T260 2140-2141 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T261 2424-2431 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T262 2691-2693 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T263 2697-2699 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T264 2711-2713 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T265 2721-2723 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T266 2725-2727 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T267 2850-2855 http://purl.obolibrary.org/obo/CLO_0001046 denotes 1 16
T268 2866-2868 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T269 2876-2878 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T270 2890-2892 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T271 2935-2937 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T65 2381-2383 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388
T66 2519-2521 Chemical denotes S3 http://purl.obolibrary.org/obo/CHEBI_29388

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T158 42-44 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T159 188-190 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T160 258-260 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T161 450-452 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T162 558-560 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T163 638-640 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T164 837-839 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T165 884-886 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T166 938-940 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T167 1068-1070 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T168 1197-1199 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T169 1507-1509 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T170 1645-1647 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T171 1795-1797 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T172 1850-1852 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T173 2024-2026 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T174 2301-2303 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T175 2350-2352 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T176 2404-2406 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T177 2416-2418 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T178 2605-2607 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T179 2616-2618 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T180 2645-2647 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T181 2784-2786 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T182 2795-2797 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T183 2824-2826 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T197 0-55 Sentence denotes Testing clinical samples with the swab–to–RT-LAMP assay
T198 56-273 Sentence denotes On the basis of these preliminary experiments, we decided to use swab samples either directly without any treatment (direct swab–to–RT-LAMP assay) or after heat treatment for 5 min at 95°C (hot swab–to–RT-LAMP assay).
T199 274-385 Sentence denotes As an additional precaution, we kept the samples in the cold (using an ice-cold metal block) whenever possible.
T200 386-493 Sentence denotes For testing large numbers of clinical samples, we performed the RT-LAMP assay using several 96-well plates.
T201 494-652 Sentence denotes In total, we tested 209 different samples using the hot swab–to–RT-LAMP assay, and of these, 131 samples also were tested by the direct swab–to–RT-LAMP assay.
T202 653-800 Sentence denotes Many samples were tested twice but using aliquots withdrawn at different time points (usually within 24 hours) from the swab samples stored at 4°C.
T203 801-921 Sentence denotes This resulted in 235 direct swab–to–RT-LAMP assay measurements and 343 hot swab–to–RT-LAMP assay measurements (Fig. 5A).
T204 922-1164 Sentence denotes The hot swab–to–RT-LAMP assay detected a color change in the majority of samples with a CT < 30 with high sensitivity, whereas the direct swab–to–RT-LAMP assay only exhibited a high sensitivity for samples with a CT < 25 (Fig. 5 and Table 3).
T205 1165-1309 Sentence denotes The heat treatment rendered the RT-LAMP assay more stringent as it reduced false positives and more sensitive for samples with a CT of 25 to 30.
T206 1310-1414 Sentence denotes We found that some positive samples did not induce a color change but did so when assayed a second time.
T207 1415-1490 Sentence denotes We therefore would recommend running this assay using technical duplicates.
T208 1491-1557 Sentence denotes Fig. 5 Swab–to–RT-LAMP assay of clinical pharyngeal swab samples.
T209 1558-1731 Sentence denotes (A) Skipping a prior RNA isolation step, pharyngeal swab samples were subjected to the RT-LAMP assay either directly (left) or after 5 min of heat treatment at 95°C (right).
T210 1732-1870 Sentence denotes For each sample, scatter plots are used to compare the swab–to–RT-LAMP assay results (ΔOD values) with the results of RT-qPCR (CT values).
T211 1871-2143 Sentence denotes The measurement time point was 30 min after the start of the 65°C incubation. (B) Shown is the sensitivity (right) and specificity (left) of the swab–to–RT-LAMP assay [derived from the data in (A)] using the decision threshold indicated by the horizontal gray line in (A).
T212 2144-2385 Sentence denotes Specificity and sensitivity values (thick lines) are shown with their 95% confidence intervals (boxes) as in Fig. 3, with blue indicating the direct swab–to–RT-LAMP assay and red indicating the hot swab–to–RT-LAMP assay. (Also see table S3).
T213 2386-2500 Sentence denotes Table 3 Shown is RT-qPCR and RT-LAMP testing of 592 clinical samples stratified into CT value bins (see Fig. 5A).
T214 2501-2592 Sentence denotes Fig. 5A and table S3 show specificity and sensitivity values calculated from these numbers.
T215 2593-2623 Sentence denotes Hot swab–to–RT-LAMP RT-LAMP
T216 2624-2644 Sentence denotes CT Pos Neg Sum
T217 2645-2676 Sentence denotes RT-qPCR Pos 0–25 38 4 42
T218 2677-2693 Sentence denotes 25–30 17 5 22
T219 2694-2710 Sentence denotes 30–35 5 23 28
T220 2711-2727 Sentence denotes 35–40 0 36 36
T221 2728-2750 Sentence denotes Neg Neg 1 214 215
T222 2751-2768 Sentence denotes Sum 61 282 343
T223 2769-2802 Sentence denotes Direct swab–to–RT-LAMP RT-LAMP
T224 2803-2823 Sentence denotes CT Pos Neg Sum
T225 2824-2855 Sentence denotes RT-qPCR Pos 0–25 15 1 16
T226 2856-2872 Sentence denotes 25–30 6 11 17
T227 2873-2889 Sentence denotes 30–35 2 21 23
T228 2890-2906 Sentence denotes 35–40 3 23 26
T229 2907-2929 Sentence denotes Neg Neg 9 144 153
T230 2930-2947 Sentence denotes Sum 35 200 235