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PMC:7473770 / 43852-54017 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T280 2460-2464 Body_part denotes Lung http://purl.org/sig/ont/fma/fma7195
T281 2465-2471 Body_part denotes Tissue http://purl.org/sig/ont/fma/fma9637
T282 2566-2574 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T283 2659-2665 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T284 2787-2795 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T285 2960-2968 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T286 3332-3340 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T287 3359-3367 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T288 3505-3517 Body_part denotes Artery lumen http://purl.org/sig/ont/fma/fma14163
T289 3505-3511 Body_part denotes Artery http://purl.org/sig/ont/fma/fma50720
T290 3519-3530 Body_part denotes artery wall http://purl.org/sig/ont/fma/fma14155
T291 3519-3525 Body_part denotes artery http://purl.org/sig/ont/fma/fma50720
T292 3532-3544 Body_part denotes erythrocytes http://purl.org/sig/ont/fma/fma62845
T293 3556-3564 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T294 3648-3656 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T295 3806-3818 Body_part denotes Erythrocytes http://purl.org/sig/ont/fma/fma62845
T296 3844-3847 Body_part denotes eye http://purl.org/sig/ont/fma/fma54448
T297 4024-4029 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T298 4078-4095 Body_part denotes blood capillaries http://purl.org/sig/ont/fma/fma63194
T299 4078-4083 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T300 4103-4111 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T301 4256-4264 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T302 4277-4285 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T303 4393-4405 Body_part denotes Artery lumen http://purl.org/sig/ont/fma/fma14163
T304 4393-4399 Body_part denotes Artery http://purl.org/sig/ont/fma/fma50720
T305 4407-4418 Body_part denotes artery wall http://purl.org/sig/ont/fma/fma14155
T306 4407-4413 Body_part denotes artery http://purl.org/sig/ont/fma/fma50720
T307 4420-4432 Body_part denotes erythrocytes http://purl.org/sig/ont/fma/fma62845
T308 4444-4452 Body_part denotes alveolar http://purl.org/sig/ont/fma/fma264783
T309 4461-4471 Body_part denotes macrophage http://purl.org/sig/ont/fma/fma63261
T310 4699-4707 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T311 4940-4952 Body_part denotes erythrocytes http://purl.org/sig/ont/fma/fma62845
T312 5133-5141 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T313 5196-5202 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T314 6463-6469 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T315 6565-6573 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T316 7066-7074 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T317 7112-7120 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T318 7310-7318 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T319 7413-7417 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T320 7418-7424 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T321 7770-7778 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T322 7914-7918 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T323 7963-7969 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T324 8213-8219 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T325 8254-8258 Body_part denotes V, 1 http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614
T327 8546-8552 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T328 9223-9227 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T329 9228-9234 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T330 9326-9333 Body_part denotes tissues http://purl.org/sig/ont/fma/fma9637
T331 9488-9496 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T332 9535-9539 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T333 9540-9546 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T334 9587-9593 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T335 9787-9798 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T336 9803-9815 Body_part denotes erythrocytes http://purl.org/sig/ont/fma/fma62845
T337 9865-9873 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T338 9953-9959 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T339 10108-10114 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T255 2460-2464 Body_part denotes Lung http://purl.obolibrary.org/obo/UBERON_0002048
T256 2465-2471 Body_part denotes Tissue http://purl.obolibrary.org/obo/UBERON_0000479
T257 2659-2665 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T258 3182-3187 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542
T259 3228-3250 Body_part denotes morphological features http://purl.obolibrary.org/obo/UBERON_0034768
T260 3505-3511 Body_part denotes Artery http://purl.obolibrary.org/obo/UBERON_0001637
T261 3519-3530 Body_part denotes artery wall http://purl.obolibrary.org/obo/UBERON_0000415
T262 3519-3525 Body_part denotes artery http://purl.obolibrary.org/obo/UBERON_0001637
T263 3565-3571 Body_part denotes septum http://purl.obolibrary.org/obo/UBERON_0003037
T264 3844-3847 Body_part denotes eye http://purl.obolibrary.org/obo/UBERON_0000970
T265 4024-4029 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T266 4078-4083 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T267 4112-4118 Body_part denotes septum http://purl.obolibrary.org/obo/UBERON_0003037
T268 4313-4335 Body_part denotes morphological features http://purl.obolibrary.org/obo/UBERON_0034768
T269 4393-4399 Body_part denotes Artery http://purl.obolibrary.org/obo/UBERON_0001637
T270 4407-4418 Body_part denotes artery wall http://purl.obolibrary.org/obo/UBERON_0000415
T271 4407-4413 Body_part denotes artery http://purl.obolibrary.org/obo/UBERON_0001637
T272 4453-4459 Body_part denotes septum http://purl.obolibrary.org/obo/UBERON_0003037
T273 4658-4663 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542
T274 5112-5117 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542
T275 5196-5202 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T276 5333-5338 Body_part denotes shell http://purl.obolibrary.org/obo/UBERON_0006612
T277 6463-6469 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T278 7413-7417 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T279 7418-7424 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T280 7914-7918 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T281 7963-7969 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T282 8213-8219 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T283 8546-8552 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T284 9223-9227 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T285 9228-9234 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T286 9535-9539 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T287 9540-9546 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T288 9587-9593 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T289 9765-9771 Body_part denotes septum http://purl.obolibrary.org/obo/UBERON_0003037
T290 9824-9829 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542
T291 9953-9959 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T292 10108-10114 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T293 10149-10154 Body_part denotes Scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T59 3546-3554 Disease denotes thrombus http://purl.obolibrary.org/obo/MONDO_0000831
T60 3622-3633 Disease denotes anthracosis http://purl.obolibrary.org/obo/MONDO_0006654
T61 4011-4019 Disease denotes thrombus http://purl.obolibrary.org/obo/MONDO_0000831
T62 4434-4442 Disease denotes thrombus http://purl.obolibrary.org/obo/MONDO_0000831
T63 9667-9669 Disease denotes PB http://purl.obolibrary.org/obo/MONDO_0019035

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T412 162-168 http://purl.obolibrary.org/obo/CLO_0001914 denotes to Tim
T413 325-328 http://purl.obolibrary.org/obo/CLO_0001914 denotes Tim
T414 430-436 http://purl.obolibrary.org/obo/CLO_0001914 denotes to Tim
T415 761-776 http://purl.obolibrary.org/obo/OBI_0000968 denotes instrumentation
T416 1966-1971 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes Human
T417 2401-2402 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T418 2460-2464 http://purl.obolibrary.org/obo/UBERON_0002048 denotes Lung
T419 2460-2464 http://www.ebi.ac.uk/efo/EFO_0000934 denotes Lung
T420 2773-2774 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T421 3388-3389 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T422 3505-3511 http://purl.obolibrary.org/obo/UBERON_0001637 denotes Artery
T423 3505-3511 http://www.ebi.ac.uk/efo/EFO_0000814 denotes Artery
T424 3519-3525 http://purl.obolibrary.org/obo/UBERON_0001637 denotes artery
T425 3519-3525 http://www.ebi.ac.uk/efo/EFO_0000814 denotes artery
T426 3532-3544 http://purl.obolibrary.org/obo/CL_0000232 denotes erythrocytes
T427 3593-3601 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T428 3718-3726 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T429 3806-3818 http://purl.obolibrary.org/obo/CL_0000232 denotes Erythrocytes
T430 3844-3847 http://www.ebi.ac.uk/efo/EFO_0000827 denotes eye
T431 3975-3976 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T432 4024-4029 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T433 4024-4029 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T434 4048-4049 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T435 4078-4083 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T436 4078-4083 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T437 4393-4399 http://purl.obolibrary.org/obo/UBERON_0001637 denotes Artery
T438 4393-4399 http://www.ebi.ac.uk/efo/EFO_0000814 denotes Artery
T439 4407-4413 http://purl.obolibrary.org/obo/UBERON_0001637 denotes artery
T440 4407-4413 http://www.ebi.ac.uk/efo/EFO_0000814 denotes artery
T441 4420-4432 http://purl.obolibrary.org/obo/CL_0000232 denotes erythrocytes
T442 4481-4489 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membrane
T443 4940-4952 http://purl.obolibrary.org/obo/CL_0000232 denotes erythrocytes
T444 5492-5493 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T445 6212-6213 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T446 6276-6277 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T447 6358-6359 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T448 6727-6728 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T449 7413-7417 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T450 7413-7417 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T451 7428-7429 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T452 7800-7801 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T453 7847-7848 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T454 7914-7918 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T455 7914-7918 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T456 8205-8212 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T457 8913-8914 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T458 9089-9090 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T459 9223-9227 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T460 9223-9227 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T461 9370-9374 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T462 9535-9539 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T463 9535-9539 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T464 9560-9561 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T465 9626-9627 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T466 9755-9756 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T467 9803-9815 http://purl.obolibrary.org/obo/CL_0000232 denotes erythrocytes
T468 9837-9838 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T469 9902-9903 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T470 9980-9981 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T471 10001-10002 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T472 10126-10127 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 8247-8249 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T2 8397-8399 Chemical denotes IV http://purl.obolibrary.org/obo/CHEBI_74327
T3 8572-8574 Chemical denotes II http://purl.obolibrary.org/obo/CHEBI_74067
T4 9667-9669 Chemical denotes PB http://purl.obolibrary.org/obo/CHEBI_53319|http://purl.obolibrary.org/obo/CHEBI_60686

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T52 812-824 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T53 3792-3804 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T343 0-19 Sentence denotes Funding Information
T344 20-69 Sentence denotes This paper was supported by the following grants:
T345 70-177 Sentence denotes http://dx.doi.org/10.13039/501100002347Bundesministerium für Bildung und Forschung 05K19MG2 to Tim Salditt.
T346 178-269 Sentence denotes http://dx.doi.org/10.13039/100010663H2020 European Research Council 771883 to Danny Jonigk.
T347 270-337 Sentence denotes Max-Planck Schools Matter to Life to Marius Reichardt, Tim Salditt.
T348 338-445 Sentence denotes http://dx.doi.org/10.13039/501100001659Deutsche Forschungsgemeinschaft EXC 2067/1-390729940 to Tim Salditt.
T349 446-513 Sentence denotes Botnar Research Center for Child Health BRCCH to Alexandar Tzankov.
T350 515-531 Sentence denotes Acknowledgements
T351 532-825 Sentence denotes We thank Maximilian Ackermann and Florian Länger for their helpful suggestions, Patrick Zardo for providing control specimen, Emily Brouwer for help in sample preparation, Bastian Hartmann and Jan Goemann for technical help with instrumentation and IT, and Jakob Koch for help in segmentation.
T352 826-940 Sentence denotes It is also our pleasure to acknowledge DESY photon science management for the Covid-19 beamtime call and beamtime.
T353 942-964 Sentence denotes Additional information
T354 965-984 Sentence denotes Competing interests
T355 985-1017 Sentence denotes No competing interests declared.
T356 1018-1038 Sentence denotes Author contributions
T357 1039-1166 Sentence denotes Data curation, Software, Formal analysis, Investigation, Visualization, Writing - original draft, Writing - review and editing.
T358 1167-1294 Sentence denotes Data curation, Software, Formal analysis, Investigation, Visualization, Writing - original draft, Writing - review and editing.
T359 1295-1422 Sentence denotes Data curation, Software, Formal analysis, Investigation, Visualization, Writing - original draft, Writing - review and editing.
T360 1423-1490 Sentence denotes Software, Investigation, Methodology, Writing - review and editing.
T361 1491-1514 Sentence denotes Resources, Methodology.
T362 1515-1538 Sentence denotes Resources, Methodology.
T363 1539-1561 Sentence denotes Resources, Validation.
T364 1562-1603 Sentence denotes Validation, Investigation, Visualisation.
T365 1604-1652 Sentence denotes Resources, Validation, Writing - original draft.
T366 1653-1754 Sentence denotes Conceptualization, Resources, Supervision, Funding acquisition, Validation, Writing - original draft.
T367 1755-1958 Sentence denotes Conceptualization, Resources, Data curation, Formal analysis, Supervision, Funding acquisition, Investigation, Methodology, Writing - original draft, Project administration, Writing - review and editing.
T368 1959-1965 Sentence denotes Ethics
T369 1966-1981 Sentence denotes Human subjects:
T370 1982-2113 Sentence denotes The study was approved by and conducted according to requirements of the ethics committees at the Hannover Medical School (vote Nr.
T371 2114-2130 Sentence denotes 9022 BO K 2020).
T372 2132-2148 Sentence denotes Additional files
T373 2149-2175 Sentence denotes Transparent reporting form
T374 2177-2194 Sentence denotes Data availability
T375 2195-2272 Sentence denotes All datasets were uploaded to zenodo: https://doi.org/10.5281/zenodo.3892637.
T376 2273-2309 Sentence denotes The following dataset was generated:
T377 2310-2564 Sentence denotes Salditt T Frohn J Eckermann M Reichardt M Osterhoff M Westermeier F Sprung M Tzankov A Kühnel M Jonigk D 2020 3d Virtual Patho-Histology of Lung Tissue from Covid19 Patients based on Phase Contrast X-ray Tomography Zenodo 10.5281/zenodo.3892637
T378 2566-2576 Sentence denotes Appendix 1
T379 2577-2622 Sentence denotes Medical information and correlative histology
T380 2623-2786 Sentence denotes Before recording tomographic scans, tissue sections of 2.5⁢μ⁢m thickness were cut from the top, stained by HE (hematoxylin and eosin) and imaged with a microscope.
T381 2787-2851 Sentence denotes Appendix 1—figure 1 shows the histological slice of each sample.
T382 2852-2959 Sentence denotes The imaged section is just above the upper plane of the 3D PC-CT reconstruction volume, but not part of it.
T383 2960-2980 Sentence denotes Appendix 1—figure 1.
T384 2982-3059 Sentence denotes Microscopic images of HE-stained histological sections of all samples (I–VI).
T385 3060-3181 Sentence denotes Histological slices show comparable morphologies to the virtual slices in Figure 3, which represent different z-position.
T386 3182-3193 Sentence denotes Scale bars:
T387 3194-3202 Sentence denotes 400⁢μ⁢m.
T388 3203-3427 Sentence denotes An overview of different morphological features identified by conventional HE histology and virtual 3D histology is presented in Appendix 1—figure 2, while Appendix 1—figure 3 presents a direct comparison for the same slice.
T389 3428-3504 Sentence denotes For this purpose, the sample was sectioned and stained after the PC-CT scan.
T390 3505-3693 Sentence denotes Artery lumen, artery wall, erythrocytes, thrombus, alveolar septum, marcophage, hyaline membrane and black granules (anthracosis) are shown in Appendix 1—figure 2 for both imaging methods.
T391 3694-3805 Sentence denotes Contrast of the hyaline membrane is homogenous in both modalities, facilitating idetification and segmentation.
T392 3806-3958 Sentence denotes Erythrocytes are easily recognized by eye in the conventional histology image, due to the HE staining, but less well distinguished by virtual histology.
T393 3959-4119 Sentence denotes This results in a difficult differentiation between thrombus and blood stasis as well as a difficult identification of blood capillaries in the alveolar septum.
T394 4120-4276 Sentence denotes Importantly, however, feature identification can be confirmed by correlative 2d and 3D histology on the same section, as exemplified by Appendix 1—figure 3.
T395 4277-4297 Sentence denotes Appendix 1—figure 2.
T396 4299-4392 Sentence denotes Comparison of morphological features between conventional HE histology and virtual histology.
T397 4393-4657 Sentence denotes Artery lumen, artery wall, erythrocytes, thrombus, alveolar septum, macrophage, hyaline membrane and anthracotic pigments (i.e. the black granules) are presented on exemplary slices of different samples (I–VI) for conventional (left) and virtual histology (right).
T398 4658-4698 Sentence denotes Scale bars: left 200⁢μ⁢m, right 100⁢μ⁢m.
T399 4699-4719 Sentence denotes Appendix 1—figure 3.
T400 4721-4798 Sentence denotes Direct comparison of virtual and HE histology for an identical slice/section.
T401 4799-4927 Sentence denotes (top left) Region of interest of the parallel beam tomogram (Sample II). (bottom left) Corresponding HE stained histology slice.
T402 4928-4998 Sentence denotes Thrombi and erythrocytes can be identified in both imaging modalities.
T403 4999-5111 Sentence denotes The red square marks the position of the zoom tomogram, for which the corresponding slice is shown on the right.
T404 5112-5123 Sentence denotes Scale bars:
T405 5124-5131 Sentence denotes 50⁢μ⁢m.
T406 5133-5143 Sentence denotes Appendix 2
T407 5144-5154 Sentence denotes Resolution
T408 5155-5286 Sentence denotes Resolution estimates are challenging for tissue reconstructions due to the absence of sharp edges or features of well defined size.
T409 5287-5357 Sentence denotes Here, we follow the approach known as Fourier-shell correlation (FSC).
T410 5358-5521 Sentence denotes Accordingly, an upper bound for the resolution is be obtained in the following way: the CT scan is split into two, and from each half a 3D volume is reconstructed.
T411 5522-5701 Sentence denotes After registry, that is, mutual alignment of the volumes, the correlation between the two independent reconstructions in Fourier space is plotted as function of spatial frequency.
T412 5702-5857 Sentence denotes This correlation must not necessarily reflect the pure system resolution, but instead the range of spatial frequencies over which the results are reliable.
T413 5858-5982 Sentence denotes As such it is not only affected by the system resolution but also by the sample contrast and the noise of the specific scan.
T414 5983-6155 Sentence denotes Further, it represents an average over all structures, not taking into account that features with stronger/weaker contrast can correspondingly show higher/lower resolution.
T415 6156-6247 Sentence denotes Here the Fourier operation for FSC was implemented with a Kaiser-Bessel window of 7 pixels.
T416 6248-6393 Sentence denotes For the parallel-beam data, a central volume of 650 × 650 × 650 voxels was correlated, for the cone-beam data a volume of 685 × 680 × 250 voxels.
T417 6394-6528 Sentence denotes These sub-volumes were selected to obtain the average values for the tissue while minimizing contributions from paraffin-filled holes.
T418 6529-6585 Sentence denotes The correlation curves are shown in Appendix 2—figure 1.
T419 6586-6709 Sentence denotes The intersection of the curve with the half-bit threshold yields the resolution estimate, indicated with dashed black line.
T420 6710-6854 Sentence denotes Correspondingly, a half-period resolution of 0.71⁢μ⁢m and 0.39⁢μ⁢m (or better) is obtained for the parallel and cone beam dataset, respectively.
T421 6855-7065 Sentence denotes However, since the splitted dataset resulted in only 721 angles for the reconstruction, i.e. the resolution estimate is severely affected by under-sampling artifacts, and hence can only serve as an upper bound.
T422 7066-7111 Sentence denotes Appendix 2—figure 1 illustrates the analysis.
T423 7112-7132 Sentence denotes Appendix 2—figure 1.
T424 7134-7198 Sentence denotes Quantification of the 3D-resolution for the example of sample V.
T425 7199-7308 Sentence denotes FSC analysis was carried out for two independent reconstructions, each from half the projections of the scan.
T426 7310-7320 Sentence denotes Appendix 3
T427 7321-7337 Sentence denotes Further datasets
T428 7338-7347 Sentence denotes Controls:
T429 7348-7438 Sentence denotes The imaging workflow was also applied to hydrated and/or healthy lung tissue as a control.
T430 7439-7503 Sentence denotes First, overview scans covering the entire samples were recorded.
T431 7504-7686 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 7687-7769 Sentence denotes Biopsy punches from CTRLII and CTRLIII were also examined in (2 - cone beam) mode.
T433 7770-7970 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 7971-7990 Sentence denotes UA-stained samples:
T435 7991-8095 Sentence denotes For all Covid-19 patients, autopsies were also treated by UA-staining in order to increase the contrast.
T436 8096-8192 Sentence denotes Stitched overview scans in (1 - parallel beam) configuration were recorded, similar to Figure 3.
T437 8193-8333 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 8334-8487 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 8488-8522 Sentence denotes Variation of propagation distance:
T440 8523-8710 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 8711-8812 Sentence denotes In cone-beam configuration, the unstained biopsy punch from patient I was scanned at 13.8⁢keV x-rays.
T442 8813-8831 Sentence denotes Compact μCT scans:
T443 8832-9190 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 9191-9400 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 9401-9487 Sentence denotes The resulting overview scans could also be correlated well with histological sections.
T446 9488-9508 Sentence denotes Appendix 3—figure 1.
T447 9510-9558 Sentence denotes Illustrations of control lung tissue (hydrated).
T448 9559-9772 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 9773-9823 Sentence denotes Particularly, macrophages and erythrocytes emerge.
T450 9824-9864 Sentence denotes Scale bars: (b) 100⁢μ⁢m and (c) 300⁢μ⁢m.
T451 9865-9885 Sentence denotes Appendix 3—figure 2.
T452 9887-9940 Sentence denotes Screening with a laboratory phase-contrast μCT-setup.
T453 9941-10148 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 10149-10159 Sentence denotes Scale bar:
T455 10160-10165 Sentence denotes 1 mm.

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
333 165-168 Gene denotes Tim Gene:7984
335 325-328 Gene denotes Tim Gene:7984
337 433-436 Gene denotes Tim Gene:7984
339 1966-1971 Species denotes Human Tax:9606
341 2535-2541 Chemical denotes Zenodo
386 2730-2732 Chemical denotes HE
387 2734-2745 Chemical denotes hematoxylin MESH:D006416
388 2750-2755 Chemical denotes eosin MESH:D004801
389 2911-2916 CellLine denotes PC-CT CVCL:B848
391 3004-3006 Chemical denotes HE
396 3896-3898 Chemical denotes HE
397 3546-3554 Disease denotes thrombus MESH:D013927
398 4011-4019 Disease denotes thrombus MESH:D013927
399 3493-3498 CellLine denotes PC-CT CVCL:B848
401 4434-4442 Disease denotes thrombus MESH:D013927
403 6506-6514 Chemical denotes paraffin MESH:D010232
412 7626-7633 Species denotes patient Tax:9606
413 8008-8016 Species denotes patients Tax:9606
414 8230-8238 Species denotes patients Tax:9606
415 8564-8571 Species denotes patient Tax:9606
416 8771-8778 Species denotes patient Tax:9606
417 8996-9001 Chemical denotes metal MESH:D008670
418 9191-9196 Chemical denotes Metal MESH:D008670
419 7999-8007 Disease denotes Covid-19 MESH:C000657245
421 9967-9974 Species denotes patient Tax:9606