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PMC:7473770 / 51162-54017 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T318 0-8 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T319 103-107 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T320 108-114 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T321 460-468 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T322 604-608 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T323 653-659 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T324 903-909 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T325 944-948 Body_part denotes V, 1 http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614
T327 1236-1242 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T328 1913-1917 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T329 1918-1924 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T330 2016-2023 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T331 2178-2186 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T332 2225-2229 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T333 2230-2236 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T334 2277-2283 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T335 2477-2488 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T336 2493-2505 Body_part denotes erythrocytes http://purl.org/sig/ont/fma/fma62845
T337 2555-2563 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T338 2643-2649 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T339 2798-2804 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T278 103-107 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T279 108-114 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T280 604-608 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T281 653-659 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T282 903-909 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T283 1236-1242 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T284 1913-1917 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T285 1918-1924 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T286 2225-2229 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T287 2230-2236 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T288 2277-2283 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T289 2455-2461 Body_part denotes septum http://purl.obolibrary.org/obo/UBERON_0003037
T290 2514-2519 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542
T291 2643-2649 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T292 2798-2804 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T293 2839-2844 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T63 2357-2359 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T449 103-107 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T450 103-107 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T451 118-119 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T452 490-491 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T453 537-538 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T454 604-608 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T455 604-608 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T456 895-902 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T457 1603-1604 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T458 1779-1780 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T459 1913-1917 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T460 1913-1917 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T461 2060-2064 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T462 2225-2229 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T463 2225-2229 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T464 2250-2251 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T465 2316-2317 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T466 2445-2446 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T467 2493-2505 http://purl.obolibrary.org/obo/CL_0000232 denotes erythrocytes
T468 2527-2528 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T469 2592-2593 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T470 2670-2671 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T471 2691-2692 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T472 2816-2817 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 937-939 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T2 1087-1089 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T3 1262-1264 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T4 2357-2359 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T426 0-10 Sentence denotes Appendix 3
T427 11-27 Sentence denotes Further datasets
T428 28-37 Sentence denotes Controls:
T429 38-128 Sentence denotes The imaging workflow was also applied to hydrated and/or healthy lung tissue as a control.
T430 129-193 Sentence denotes First, overview scans covering the entire samples were recorded.
T431 194-376 Sentence denotes Then, hydrated 1 mm biopsy punches (two for CTRLI, one for CTRLII and CTRLIII, where CTRLII and CTRLIII are from the same patient) were recorded in (1 - parallel beam) configuration.
T432 377-459 Sentence denotes Biopsy punches from CTRLII and CTRLIII were also examined in (2 - cone beam) mode.
T433 460-660 Sentence denotes Appendix 3—figure 1 presents (a) the rendering of the hydrated control, and (b,c) virtual slices through the reconstruction volume, showing the lung parenchymal architecture in healthy control tissue.
T434 661-680 Sentence denotes UA-stained samples:
T435 681-785 Sentence denotes For all Covid-19 patients, autopsies were also treated by UA-staining in order to increase the contrast.
T436 786-882 Sentence denotes Stitched overview scans in (1 - parallel beam) configuration were recorded, similar to Figure 3.
T437 883-1023 Sentence denotes From the UA-labeled tissue blocks of patients I, III, IV and V, 1 mm, biopsy punches were than scanned in the same configuration (Figure 4).
T438 1024-1177 Sentence denotes Using the (2 - cone beam) setup, these samples from I, III and IV were imaged at 8.0⁢keV x-rays, while V was examined at 13.8⁢keV, as shown for Figure 5.
T439 1178-1212 Sentence denotes Variation of propagation distance:
T440 1213-1400 Sentence denotes Scans of the unstained tissue block from patient II were recorded at different propagation distances (z12=50, 100 and 125keV) and different x-ray energies (13.3, 13.8, 14.3 and 14.8 keV).
T441 1401-1502 Sentence denotes In cone-beam configuration, the unstained biopsy punch from patient I was scanned at 13.8⁢keV x-rays.
T442 1503-1521 Sentence denotes Compact μCT scans:
T443 1522-1880 Sentence denotes Prior to the synchrotron experiment, some of the samples have been examined with a laboratory phase-contrast μCT-setup in large mm2-sized FOV-configuration (Liquid metal jet source, Kα=9.5keV, pxeff=5μm, z12=1.7m, 1200 projections of 1 s exposure time with a flat panel CMOS detector with 150⁢μ⁢m Gadox-scintillator, PerkinElmer, USA) (Bartels et al., 2013).
T444 1881-2090 Sentence denotes Metal-staining (here UA) of the lung tissue helped to achieve sufficient contrast, similar to previous μCT-studies of other biological tissues (Müller et al., 2017; Busse et al., 2018; De Clercq et al., 2019).
T445 2091-2177 Sentence denotes The resulting overview scans could also be correlated well with histological sections.
T446 2178-2198 Sentence denotes Appendix 3—figure 1.
T447 2200-2248 Sentence denotes Illustrations of control lung tissue (hydrated).
T448 2249-2462 Sentence denotes (a) Volume rendering of the tissue block (0.97×1.00×0.73 mm3) and (b) slice through the volume, examined in PB-configuration. (c) Slice from the cone-beam scan, arrows indicating the structure of a healthy septum.
T449 2463-2513 Sentence denotes Particularly, macrophages and erythrocytes emerge.
T450 2514-2554 Sentence denotes Scale bars: (b) 100⁢μ⁢m and (c) 300⁢μ⁢m.
T451 2555-2575 Sentence denotes Appendix 3—figure 2.
T452 2577-2630 Sentence denotes Screening with a laboratory phase-contrast μCT-setup.
T453 2631-2838 Sentence denotes (UA-stained tissue block, patient I). (a) Histological and (b) correlative virtual slice from laboratory phase-contrast tomography. (c) Volume rendering of the entire tissue block from a similar perspective.
T454 2839-2849 Sentence denotes Scale bar:
T455 2850-2855 Sentence denotes 1 mm.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
412 316-323 Species denotes patient Tax:9606
413 698-706 Species denotes patients Tax:9606
414 920-928 Species denotes patients Tax:9606
415 1254-1261 Species denotes patient Tax:9606
416 1461-1468 Species denotes patient Tax:9606
417 1686-1691 Chemical denotes metal MESH:D008670
418 1881-1886 Chemical denotes Metal MESH:D008670
419 689-697 Disease denotes Covid-19 MESH:C000657245
421 2657-2664 Species denotes patient Tax:9606