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PMC:7473770 / 31942-43850 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T223 56-62 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T224 115-119 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T225 176-182 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T226 802-806 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T227 1137-1145 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T228 1530-1536 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T229 1757-1763 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T230 1869-1875 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T231 2448-2452 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T232 2718-2722 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T233 2723-2729 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T234 3111-3115 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T235 3116-3122 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T236 3979-3985 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T237 4081-4087 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T238 4230-4236 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T239 4416-4422 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T240 8986-8994 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T241 9201-9207 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T242 9389-9400 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T243 9413-9419 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T244 9433-9456 Body_part denotes connected to the tissue http://purl.org/sig/ont/fma/fma9640
T245 9450-9456 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T246 9496-9499 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T247 9556-9568 Body_part denotes compartments http://purl.org/sig/ont/fma/fma76577
T248 9603-9609 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T249 9817-9823 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T250 9835-9841 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T251 9896-9902 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T252 9942-9948 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T253 10258-10264 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T254 10291-10302 Body_part denotes compartment http://purl.org/sig/ont/fma/fma76577
T255 10368-10386 Body_part denotes capillary networks http://purl.org/sig/ont/fma/fma45633
T256 10368-10377 Body_part denotes capillary http://purl.org/sig/ont/fma/fma63194
T257 10518-10535 Body_part denotes capillary network http://purl.org/sig/ont/fma/fma45633
T258 10547-10551 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T259 10669-10673 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T260 10700-10711 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T261 10716-10727 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T262 10852-10854 Body_part denotes AG http://purl.org/sig/ont/fma/fma61898
T263 10931-10942 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T264 11111-11122 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T265 11219-11230 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T266 11248-11257 Body_part denotes capillary http://purl.org/sig/ont/fma/fma63194
T267 11315-11326 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T268 11349-11360 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T269 11455-11466 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T270 11511-11522 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T271 11545-11562 Body_part denotes endothelial cells http://purl.org/sig/ont/fma/fma66772
T272 11557-11562 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T273 11580-11591 Body_part denotes capillaries http://purl.org/sig/ont/fma/fma63194
T274 11604-11609 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T275 11760-11771 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T276 11793-11804 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T277 11851-11862 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T278 11874-11878 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T279 11879-11885 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T221 56-62 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T222 115-119 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T223 176-182 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T224 802-806 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T225 1530-1536 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T226 1757-1763 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T227 1869-1875 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T228 2448-2452 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T229 2494-2498 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T230 2593-2597 Body_part denotes tube http://purl.obolibrary.org/obo/UBERON_0000025
T231 2718-2722 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T232 2723-2729 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T233 3111-3115 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T234 3116-3122 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T235 3202-3208 Body_part denotes scales http://purl.obolibrary.org/obo/UBERON_0002542
T236 3979-3985 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T237 4081-4087 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T238 4230-4236 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T239 4416-4422 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T240 9201-9207 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T241 9413-9419 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T242 9450-9456 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T243 9603-9609 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T244 9817-9823 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T245 9835-9841 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T246 9896-9902 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T247 9942-9948 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T248 10258-10264 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T249 10368-10377 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T250 10518-10527 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T251 11248-11257 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T252 11604-11609 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T253 11874-11878 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T254 11879-11885 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T54 466-478 Disease denotes hypertension http://purl.obolibrary.org/obo/MONDO_0005044
T55 700-719 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T56 755-774 Disease denotes respiratory failure http://purl.obolibrary.org/obo/MONDO_0021113
T57 791-796 Disease denotes tumor http://purl.obolibrary.org/obo/MONDO_0005070
T58 852-862 Disease denotes carcinomas http://purl.obolibrary.org/obo/MONDO_0004993

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T321 115-119 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T322 115-119 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T323 174-175 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T324 802-806 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T325 802-806 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T326 880-881 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T327 1269-1273 http://purl.obolibrary.org/obo/CLO_0002983 denotes F 5
T328 1332-1336 http://purl.obolibrary.org/obo/CLO_0007437 denotes M 1
T329 1364-1368 http://purl.obolibrary.org/obo/CLO_0007437 denotes M 1
T330 1444-1448 http://purl.obolibrary.org/obo/CLO_0007437 denotes M 1
T331 1628-1629 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T332 2077-2080 http://purl.obolibrary.org/obo/CLO_0050154 denotes a 8
T333 2087-2088 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T334 2176-2177 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T335 2249-2250 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T336 2321-2322 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T337 2378-2379 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T338 2448-2452 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T339 2448-2452 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T340 2494-2498 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T341 2535-2536 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T342 2581-2582 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T343 2593-2597 http://purl.obolibrary.org/obo/UBERON_0000025 denotes tube
T344 2718-2722 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T345 2718-2722 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T346 2958-2963 http://purl.obolibrary.org/obo/CLO_0007839 denotes m P10
T347 2978-2979 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T348 3111-3115 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T349 3111-3115 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T350 3177-3178 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T351 3296-3297 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T352 3359-3360 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T353 3386-3387 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T354 3510-3511 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T355 3521-3529 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T356 3549-3550 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T357 3569-3571 http://purl.obolibrary.org/obo/CLO_0007074 denotes KB
T358 3569-3571 http://purl.obolibrary.org/obo/CLO_0051988 denotes KB
T359 3625-3626 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T360 3652-3653 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T361 3860-3861 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T362 4027-4028 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T363 4115-4116 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T364 4141-4142 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T365 4347-4348 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T366 5185-5186 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T367 5233-5237 http://purl.obolibrary.org/obo/CLO_0001550 denotes a 10
T368 5261-5270 http://purl.obolibrary.org/obo/BFO_0000030 denotes objective
T369 5276-5277 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T370 5488-5490 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T371 5491-5493 http://purl.obolibrary.org/obo/CLO_0007874 denotes ms
T372 5509-5510 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T373 5683-5691 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T374 5700-5702 http://purl.obolibrary.org/obo/CLO_0007074 denotes KB
T375 5700-5702 http://purl.obolibrary.org/obo/CLO_0051988 denotes KB
T376 6022-6033 http://purl.obolibrary.org/obo/CLO_0009985 denotes was focused
T377 6041-6043 http://purl.obolibrary.org/obo/CLO_0007074 denotes KB
T378 6041-6043 http://purl.obolibrary.org/obo/CLO_0051988 denotes KB
T379 6152-6153 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T380 6278-6279 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T381 6351-6353 http://purl.obolibrary.org/obo/CLO_0007074 denotes KB
T382 6351-6353 http://purl.obolibrary.org/obo/CLO_0051988 denotes KB
T383 6594-6599 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T384 6717-6718 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T385 6794-6795 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T386 6917-6922 http://purl.obolibrary.org/obo/CLO_0009985 denotes focus
T387 6935-6936 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T388 6962-6964 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T389 7081-7082 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T390 8159-8162 http://purl.obolibrary.org/obo/CLO_0051145 denotes Ram
T391 9181-9186 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 × 2
T392 9433-9456 http://purl.obolibrary.org/obo/UBERON_0002384 denotes connected to the tissue
T393 9433-9456 http://www.ebi.ac.uk/efo/EFO_0000952 denotes connected to the tissue
T394 9961-9962 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T395 10109-10110 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T396 10136-10138 http://purl.obolibrary.org/obo/CL_0000453 denotes Lc
T397 10170-10171 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T398 10354-10363 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T399 10500-10509 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T400 10547-10557 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T401 10669-10673 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T402 11069-11070 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T403 11133-11134 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T404 11293-11294 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T405 11545-11562 http://purl.obolibrary.org/obo/CL_0000115 denotes endothelial cells
T406 11604-11609 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T407 11604-11609 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T408 11686-11687 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T409 11874-11878 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T410 11874-11878 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T411 11886-11888 http://purl.obolibrary.org/obo/CLO_0052906 denotes cl

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T42 2796-2803 http://purl.obolibrary.org/obo/GO_0051235 denotes storage
T43 6437-6444 http://purl.obolibrary.org/obo/GO_0051235 denotes storage
T44 7172-7184 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T45 9005-9017 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T46 9267-9279 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T47 9727-9739 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T48 10420-10432 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T49 10879-10891 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T50 11091-11103 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T51 11744-11756 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T241 0-21 Sentence denotes Materials and methods
T242 23-74 Sentence denotes Autopsy, clinical background and tissue preparation
T243 75-173 Sentence denotes In total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020).
T244 174-296 Sentence denotes A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a.
T245 297-438 Sentence denotes Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2.
T246 439-563 Sentence denotes All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs.
T247 564-776 Sentence denotes Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure).
T248 777-892 Sentence denotes Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.
T249 893-901 Sentence denotes Table 2.
T250 903-934 Sentence denotes Sample and medical information.
T251 935-1153 Sentence denotes Age and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.
T252 1154-1164 Sentence denotes Sample no.
T253 1166-1258 Sentence denotes Age group, gender Hospitalization, clinical, radiological, and histological characteristics
T254 1259-1287 Sentence denotes I 60–70, F 5-10d, GGO, DAD
T255 1288-1318 Sentence denotes II 80–90, M 5-10d, C, I, DAD
T256 1319-1352 Sentence denotes III 90–100, M 1-4d, GGO, C, DAD
T257 1353-1392 Sentence denotes IV 70–80, M 1-4d, NIV, S, GGO, C, DAD
T258 1393-1432 Sentence denotes V 60–70, M 5-10d, NIV, S, GGO, C, DAD
T259 1433-1467 Sentence denotes VI 70–80, M 1-4d, S, GGO, C, DAD
T260 1468-1596 Sentence denotes CTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed.
T261 1597-1725 Sentence denotes To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained.
T262 1726-1841 Sentence denotes Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block.
T263 1842-2018 Sentence denotes The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration.
T264 2019-2136 Sentence denotes From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size.
T265 2137-2377 Sentence denotes The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings.
T266 2378-2435 Sentence denotes A sketch of the sample preparation is shown in Figure 1b.
T267 2436-2677 Sentence denotes The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution.
T268 2679-2704 Sentence denotes Phase contrast tomography
T269 2705-2825 Sentence denotes For Covid-19 lung tissue, the scans were recorded at the GINIX endstation of the PETRA III storage ring (DESY, Hamburg).
T270 2826-3028 Sentence denotes The projections were acquired at two different photon energies Eph, 8⁢keV and 13.8⁢keV, using the first and third harmonic of the 5 m P10 undulator and a Si(111) channel-cut monochromator, respectively.
T271 3029-3123 Sentence denotes Data are shown here only for 8⁢keV, which gave highest contrast for the unstained lung tissue.
T272 3124-3209 Sentence denotes Two tomography configurations were combined to cover a larger range of length scales:
T273 3211-3228 Sentence denotes (1–parallel beam)
T274 3229-3409 Sentence denotes Recordings with the unfocused quasi-parallel beam illumination and a high resolution microscope detection system, resulting in in a FOV of 1.6 mm sampled at a pixel size of 650 nm.
T275 3411-3424 Sentence denotes (2–cone beam)
T276 3425-3711 Sentence denotes Holographic recordings with the divergent and coherence filtered beam emanating from a compound focusing system composed of a Kirkpatrick-Baez (KB) mirrors system and an x-ray waveguide, resulting in a FOV of 0.4 mm sampled at a pixel size of about 167 nm (depending on exact geometry).
T277 3712-3859 Sentence denotes Both configurations were implemented side-by-side, using the same fully-motorized tomography stage and mounting, as detailed in Frohn et al., 2020.
T278 3860-3914 Sentence denotes A sketch of both configurations is shown in Figure 1 .
T279 3915-4014 Sentence denotes First, parallel-beam overview scans were acquired of the entire tissue volume embedded in paraffin.
T280 4015-4243 Sentence denotes To this end a 3.5 mm biopsy punch was taken from the multi-sample tissue block, and then scanned in a stitching-mode yielding a large overview reconstruction, composed of up to 20 individual tomograms (depending on tissue size).
T281 4244-4504 Sentence denotes To increase image quality and avoid artifacts related to region-of-interest (ROI) or local tomography, a selected 1 mm punch was then taken from the already scanned larger tissue cylinder, and re-scanned, first in the parallel- and then the cone-beam geometry.
T282 4505-4591 Sentence denotes Experimental and acquisition parameters used for the data shown are listed in Table 3.
T283 4592-4600 Sentence denotes Table 3.
T284 4602-4679 Sentence denotes Data acquisition parameters for x-ray phase-contrast tomography measurements.
T285 4680-4712 Sentence denotes Cone geometry Parallel geometry
T286 4713-4751 Sentence denotes FOV 0.4 mm × 0.35 mm 1.6 mm × 1.4 mm
T287 4752-4778 Sentence denotes Pixel size 167 nm 650 nm
T288 4779-4794 Sentence denotes z 01 125 mm -
T289 4795-4824 Sentence denotes z 12 4975 mm 10 mm − 100 mm
T290 4825-4861 Sentence denotes Regime holographic direct contrast
T291 4862-4894 Sentence denotes Rotation start-stop continuous
T292 4895-4920 Sentence denotes Exposure 2 s 0.035 ⁢ s
T293 4921-4957 Sentence denotes Total exposure ≃ 63 m i n ≃ 75 s
T294 4958-5099 Sentence denotes Volumetric flowrate 1.16 × 10 4 μ m / 3 s 3.75 × 10 7 μ m / 3 s The configuration for (1–parallel beam) is depicted in Figure 1c.
T295 5100-5370 Sentence denotes The high-resolution microscope detection system (Optique Peter, France) was based on a 50⁢μ⁢m thick LuAG:Ce scintillator imaged with a 10× magnifying microscope objective onto a sCMOS sensor (pco.edge 5.5, PCO, Germany), resulting in an effective pixel size of 0.65⁢μ⁢m.
T296 5371-5531 Sentence denotes The high photon flux density allowed for image acquisition with continuous motor movement, short acquisition time of 35 ms per frame, and a framerate of 20 fps.
T297 5532-5661 Sentence denotes Single-distance tomogram recordings with about 1500 projections, and flat images before and after the scan, took less than 2 min.
T298 5662-5859 Sentence denotes For these scans, the focusing optics (KB-mirrors and waveguide) as well as the fastshutter (Cedrat technologies) were moved out of the beam, and beam size was adjusted by the upstream slit systems.
T299 5860-5950 Sentence denotes To avoid detector saturation, the beam was attenuated by 4× single crystal silicon wafers.
T300 5951-6012 Sentence denotes The configuration for (2–cone beam) is depicted in Figure 1d:
T301 6013-6068 Sentence denotes The beam was focused by the KB-mirrors to about 300 nm.
T302 6069-6524 Sentence denotes To further reduce the secondary source size, to increase coherence, and to achieve a smooth wavefront for holographic illumination, an x-ray waveguide formed by 1 mm long lithographic channels in silicon with a cross-section of about 100 nm was positioned in the focal plane of the KB-mirrors, resulting in an exit flux of 1–4⋅109 photon/s (depending on alignment and storage ring), as measured with the single photon counting detector (Pilatus, Dectris).
T303 6525-6661 Sentence denotes The sample was positioned at variable (defocus) distances behind the focus (waveguide exit), typically z01=125mm for the first distance.
T304 6662-6863 Sentence denotes The geometrically magnified holograms were recorded by a fibre-coupled sCMOS sensor (Zyla HF 5.5 detector, Andor Technologies) with a customized 15⁢μ⁢m thick Gadox scintillator, and 6.5⁢μ⁢m pixel size.
T305 6864-7043 Sentence denotes The detector position at about z02=5100mm behind the focus resulted in a magnification of about M=41 (for the first defocus distance), and hence an effective pixel size of 167 nm.
T306 7044-7127 Sentence denotes 1442 projections were recorded, with a typical exposure time of 2 s per projection.
T307 7129-7184 Sentence denotes Phase retrieval, image reconstruction, and segmentation
T308 7186-7220 Sentence denotes Phase retrieval and reconstruction
T309 7221-7569 Sentence denotes Phase retrieval was performed from dark and empty beam corrected holograms, using both linearised single step CTF-approach (Cloetens et al., 1999; Turner et al., 2004), and non-linear generalizations of the CTF-method based on Tikhonov regularization (NL-CTF), using our code package HoloTomoToolbox as described and deposited (Lohse et al., 2020).
T310 7570-7691 Sentence denotes Importantly, both CTF and NL-CTF implementations can be augmented by imposing support and range constraints, when needed.
T311 7692-7850 Sentence denotes When available, projections recorded at several defocus distances were first aligned with sub-pixel accuracy and then used for multi-distance phase retrieval.
T312 7851-8019 Sentence denotes For these purposes, the HoloTomoToolbox provides auxiliary functions, which also help to refine the Fresnel number or to correct for drift in the illumination function.
T313 8020-8324 Sentence denotes After phase reconstruction of all projections, the tomographic reconstruction was carried out with the MATLAB implemented iradon-function (Ram-Lak filter) for the parallel geometry and with the FDK-function of the ASTRA toolbox (van Aarle et al., 2015; van Aarle et al., 2016) for the cone beam geometry.
T314 8325-8652 Sentence denotes Hot pixel and detector sensitivity variations as well as strong phase features in the parallel beam illumination resulting from upstream window materials, which persist after empty beam correction, can all result in ring artifacts in the tomographic reconstruction, in particular as these flaws can increase by phase retrieval.
T315 8653-8821 Sentence denotes To correct for this, the extra information provided by 360° scans was used to mask out the corresponding pixels and replace them with values of the opposing projection.
T316 8822-8929 Sentence denotes Stitching of reconstructions from different tomographic scans was performed using (Miettinen et al., 2019).
T317 8930-8997 Sentence denotes Resolution estimates were obtained by FSC analysis, see Appendix 2.
T318 8999-9036 Sentence denotes Image segmentation and quantification
T319 9037-9138 Sentence denotes For each patient the stitched overview scans were analyzed with regard to structural characteristics.
T320 9139-9361 Sentence denotes The 3D-reconstructions were first binned (2 × 2 × 2), and the tissue was then segmented from the surrounding paraffin using the segmentation software Ilastik (Berg et al., 2019), which was then further refined with MATLAB.
T321 9362-9500 Sentence denotes In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map.
T322 9501-9616 Sentence denotes Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block.
T323 9617-9712 Sentence denotes Individual self-contained areas of paraffin (not connected to air) were excluded from the mask.
T324 9713-9830 Sentence denotes Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel.
T325 9831-9903 Sentence denotes The tissue volume V is given by the sum of all voxels containing tissue.
T326 9904-9994 Sentence denotes The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air.
T327 9995-10100 Sentence denotes From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio.
T328 10101-10209 Sentence denotes Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample.
T329 10210-10345 Sentence denotes Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated.
T330 10346-10484 Sentence denotes Hyaline membranes and capillary networks were extracted using semi-manual segmentation functions in Avizo (Thermo Fisher Scientific, USA).
T331 10485-10640 Sentence denotes Beside hyaline membranes and the capillary network, different cell types can be readily identified based on the 3D reconstructions of the electron density.
T332 10641-10751 Sentence denotes In particular, inflammatory cell subpopulations - that is, macrophages and lymphocytes - can be distinguished.
T333 10752-10865 Sentence denotes To this end, an automatic and parameter-controlled algorithm denoted as BlobFinder was used (arivis AG, Germany).
T334 10866-11009 Sentence denotes Based on its segmentation output, the amount and position of the lymphocytes in the 3D-reconstructions from parallel beam scans was calculated.
T335 11010-11082 Sentence denotes The algorithm is able to identify roundish structures with a given size.
T336 11083-11166 Sentence denotes For the segmentation of the lymphocytes, we chose a characteristic size of 6.5⁢μ⁢m.
T337 11167-11265 Sentence denotes The structures identified in this step also include macrophages and parts of the capillary system.
T338 11266-11414 Sentence denotes For the unbinned datasets, a distinction between lymphocytes and the nuclei of the macrophages was made based on the difference in electron density.
T339 11415-11523 Sentence denotes In the tomographic reconstructions, the lymphocytes appear denser compared to the nuclei of the macrophages.
T340 11524-11664 Sentence denotes Further, nuclei from endothelial cells and parts of the capillaries filled with blood residues were excluded based on their elongated shape.
T341 11665-11730 Sentence denotes Only structures with a sphericity higher than 0.55 were included.
T342 11731-11908 Sentence denotes Based on the segmentation of lymphocytes, the total number of lymphocytes Nl was obtained and the mean concentration of lymphocytes within the lung tissue cl=Nl/V was estimated.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T29 469-481 Phenotype denotes ertension an http://purl.obolibrary.org/obo/HP_0000822
T30 703-722 Phenotype denotes piratory failure in http://purl.obolibrary.org/obo/HP_0002878
T31 758-777 Phenotype denotes piratory failure). http://purl.obolibrary.org/obo/HP_0002878
T32 794-799 Phenotype denotes or-fr http://purl.obolibrary.org/obo/HP_0002664

2_test

Id Subject Object Predicate Lexical cue
32815517-32364264-26997865 167-171 32364264 denotes 2020
32815517-19483813-26997866 7383-7387 19483813 denotes 2004
32815517-32381790-26997867 7563-7567 32381790 denotes 2020
32815517-26057688-26997868 8267-8271 26057688 denotes 2015
32815517-27828452-26997869 8291-8295 27828452 denotes 2016
32815517-31116382-26997870 8923-8927 31116382 denotes 2019
32815517-31570887-26997871 9311-9315 31570887 denotes 2019

MyTest

Id Subject Object Predicate Lexical cue
32815517-32364264-26997865 167-171 32364264 denotes 2020
32815517-19483813-26997866 7383-7387 19483813 denotes 2004
32815517-32381790-26997867 7563-7567 32381790 denotes 2020
32815517-26057688-26997868 8267-8271 26057688 denotes 2015
32815517-27828452-26997869 8291-8295 27828452 denotes 2016
32815517-31116382-26997870 8923-8927 31116382 denotes 2019
32815517-31570887-26997871 9311-9315 31570887 denotes 2019

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
270 142-150 Species denotes patients Tax:9606
271 234-242 Species denotes patients Tax:9606
272 408-416 Species denotes patients Tax:9606
273 443-451 Species denotes patients Tax:9606
274 630-638 Species denotes patients Tax:9606
275 728-735 Species denotes patient Tax:9606
276 737-744 Species denotes patient Tax:9606
277 265-267 Chemical denotes HE
278 525-536 Chemical denotes aldosterone MESH:D000450
279 133-141 Disease denotes Covid-19 MESH:C000657245
280 466-478 Disease denotes hypertension MESH:D006973
281 674-679 Disease denotes death MESH:D003643
282 700-719 Disease denotes respiratory failure MESH:D012131
283 748-774 Disease denotes cardio-respiratory failure MESH:D012131
284 791-796 Disease denotes tumor MESH:D009369
285 842-862 Disease denotes pulmonary carcinomas MESH:D008175
287 1137-1152 Disease denotes alveolar damage MESH:D055370
298 1516-1524 Species denotes patients Tax:9606
299 1619-1626 Species denotes patient Tax:9606
300 1942-1950 Species denotes patients Tax:9606
301 1630-1635 Chemical denotes metal MESH:D008670
302 1654-1669 Chemical denotes uranium acetate MESH:C005460
303 1826-1834 Chemical denotes paraffin MESH:D010232
304 2583-2592 Chemical denotes polyimide
305 2613-2621 Chemical denotes paraffin MESH:D010232
306 1507-1515 Disease denotes Covid-19 MESH:C000657245
307 2006-2017 Disease denotes dehydration MESH:D003681
310 2980-2982 Chemical denotes Si MESH:D012825
311 2709-2717 Disease denotes Covid-19 MESH:C000657245
313 4005-4013 Chemical denotes paraffin MESH:D010232
315 5935-5942 Chemical denotes silicon MESH:D012825
317 6733-6738 Chemical denotes sCMOS
319 8163-8166 Gene denotes Lak Gene:80216
326 9046-9053 Species denotes patient Tax:9606
327 9248-9256 Chemical denotes paraffin MESH:D010232
328 9527-9535 Chemical denotes paraffin MESH:D010232
329 9652-9660 Chemical denotes paraffin MESH:D010232
330 9786-9792 Chemical denotes oxygen MESH:D010100
331 9921-9923 Chemical denotes SA MESH:C012546