PMC:7473770 / 28530-31940
Annnotations
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T211 | 135-139 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T212 | 850-854 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T213 | 976-989 | Body_part | denotes | blood vessels | http://purl.org/sig/ont/fma/fma63183 |
| T214 | 976-981 | Body_part | denotes | blood | http://purl.org/sig/ont/fma/fma9670 |
| T215 | 1071-1075 | Body_part | denotes | hand | http://purl.org/sig/ont/fma/fma9712 |
| T216 | 1347-1355 | Body_part | denotes | Appendix | http://purl.org/sig/ont/fma/fma14542 |
| T217 | 2029-2033 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T218 | 2327-2331 | Body_part | denotes | cell | http://purl.org/sig/ont/fma/fma68646 |
| T219 | 2419-2423 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
| T220 | 2455-2461 | Body_part | denotes | tissue | http://purl.org/sig/ont/fma/fma9637 |
| T221 | 2678-2689 | Body_part | denotes | capillaries | http://purl.org/sig/ont/fma/fma63194 |
| T222 | 3346-3350 | Body_part | denotes | lung | http://purl.org/sig/ont/fma/fma7195 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T205 | 55-60 | Body_part | denotes | scale | http://purl.obolibrary.org/obo/UBERON_0002542 |
| T206 | 135-139 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T207 | 230-236 | Body_part | denotes | scales | http://purl.obolibrary.org/obo/UBERON_0002542 |
| T208 | 976-989 | Body_part | denotes | blood vessels | http://purl.obolibrary.org/obo/UBERON_0001981 |
| T209 | 976-981 | Body_part | denotes | blood | http://purl.obolibrary.org/obo/UBERON_0000178 |
| T210 | 982-989 | Body_part | denotes | vessels | http://purl.obolibrary.org/obo/UBERON_0000055 |
| T211 | 1071-1075 | Body_part | denotes | hand | http://purl.obolibrary.org/obo/UBERON_0002398 |
| T212 | 1709-1715 | Body_part | denotes | scales | http://purl.obolibrary.org/obo/UBERON_0002542 |
| T213 | 1733-1739 | Body_part | denotes | scales | http://purl.obolibrary.org/obo/UBERON_0002542 |
| T214 | 1841-1847 | Body_part | denotes | scales | http://purl.obolibrary.org/obo/UBERON_0002542 |
| T215 | 1992-1998 | Body_part | denotes | scales | http://purl.obolibrary.org/obo/UBERON_0002542 |
| T216 | 2019-2023 | Body_part | denotes | lobe | http://purl.obolibrary.org/obo/UBERON_3010752 |
| T217 | 2029-2033 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T218 | 2419-2423 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
| T219 | 2455-2461 | Body_part | denotes | tissue | http://purl.obolibrary.org/obo/UBERON_0000479 |
| T220 | 3346-3350 | Body_part | denotes | lung | http://purl.obolibrary.org/obo/UBERON_0002048 |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T53 | 356-368 | Disease | denotes | inflammation | http://purl.obolibrary.org/obo/MONDO_0021166 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T299 | 135-139 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T300 | 135-139 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T301 | 187-188 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T302 | 331-340 | http://purl.obolibrary.org/obo/UBERON_0000158 | denotes | membranes |
| T303 | 473-476 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T304 | 477-482 | http://purl.obolibrary.org/obo/UBERON_0001456 | denotes | faced |
| T305 | 547-548 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T306 | 591-592 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T307 | 850-854 | http://purl.obolibrary.org/obo/GO_0005623 | denotes | cell |
| T308 | 976-989 | http://purl.obolibrary.org/obo/UBERON_0001981 | denotes | blood vessels |
| T309 | 976-989 | http://www.ebi.ac.uk/efo/EFO_0000817 | denotes | blood vessels |
| T310 | 2027-2028 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T311 | 2029-2033 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T312 | 2029-2033 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T313 | 2085-2086 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T314 | 2306-2312 | http://purl.obolibrary.org/obo/CLO_0007225 | denotes | labels |
| T315 | 2327-2337 | http://purl.obolibrary.org/obo/CL_0000000 | denotes | cell types |
| T316 | 2419-2423 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T317 | 2419-2423 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
| T318 | 2498-2503 | http://purl.obolibrary.org/obo/CLO_0007225 | denotes | label |
| T319 | 3346-3350 | http://purl.obolibrary.org/obo/UBERON_0002048 | denotes | lung |
| T320 | 3346-3350 | http://www.ebi.ac.uk/efo/EFO_0000934 | denotes | lung |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T36 | 356-368 | http://purl.obolibrary.org/obo/GO_0006954 | denotes | inflammation |
| T37 | 2653-2665 | http://purl.obolibrary.org/obo/GO_0035282 | denotes | segmentation |
| T38 | 2759-2787 | http://purl.obolibrary.org/obo/GO_0002041 | denotes | intussusceptive angiogenesis |
| T39 | 2775-2787 | http://purl.obolibrary.org/obo/GO_0001525 | denotes | angiogenesis |
| T40 | 2983-2995 | http://purl.obolibrary.org/obo/GO_0035282 | denotes | segmentation |
| T41 | 3024-3032 | http://purl.obolibrary.org/obo/GO_0007612 | denotes | learning |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T220 | 0-10 | Sentence | denotes | Discussion |
| T221 | 11-237 | Sentence | denotes | In summary, we have demonstrated that multi-scale x-ray phase contrast tomography can firstly augment pathohistology of the lung to full three dimensions, and secondly provide a link between microscopic and macroscopic scales. |
| T222 | 238-495 | Sentence | denotes | For the first time, characteristic morphological changes associated with DAD such as hyaline membranes and pronounced inflammation have been imaged in three dimensions, in particular in Covid-19, the most severe pandemic which mankind has faced for decades. |
| T223 | 496-628 | Sentence | denotes | Moreover, we conducted our study in FFPE material, a fixation method established for well over a century and ubiquitously available. |
| T224 | 629-806 | Sentence | denotes | The advantage of 3D histology compared to conventional histology relates to the simple fact that features can be visualized and investigated in their full native dimensionality. |
| T225 | 807-990 | Sentence | denotes | This enables the accurate determination of cell densities, the quantification of morphological parameters such as the distance metrics shown in Figure 6, and tracing of blood vessels. |
| T226 | 991-1231 | Sentence | denotes | Standard histology and in particular immunohistochemical staining, on the other hand, can inform us more precisely on the biomolecular origin of the structure, while immunostaining coupled with x-ray contrast agents is not yet within reach. |
| T227 | 1232-1358 | Sentence | denotes | Importantly, since PC-CT is nondestructive, histology can be performed on well-chosen sections after the scan, see Appendix 1. |
| T228 | 1359-1669 | Sentence | denotes | On the side of imaging technology and exploitation, there is still ample room for improvement: higher resolution could be achieved by further geometric zooms, waveguide optics with higher numerical aperture, in combination with pixel detector technology, and further improvements in holographic reconstruction. |
| T229 | 1670-1819 | Sentence | denotes | Equally important to extend the length scales covered to small scales is the further upscaling of the FOV based on stitching different sub-tomograms. |
| T230 | 1820-1961 | Sentence | denotes | At the same time the scales should be extended by including more than two zoom levels, based on different detector and illumination settings. |
| T231 | 1962-2034 | Sentence | denotes | In this way, one could bridge scales to cover the entire lobe of a lung. |
| T232 | 2035-2241 | Sentence | denotes | To this end, optimized recording and data flow is a larger bottleneck than photons and optics, in particular since 4th generation synchrotron radiation sources are about to deliver unprecedented brilliance. |
| T233 | 2242-2412 | Sentence | denotes | Finally, in view of exploitation and information gain, specific labels for different cell types and 3D immunostaining coupled to radiocontrast agents should be developed. |
| T234 | 2413-2516 | Sentence | denotes | Here, lung offers an advantage over other tissue in view of volume accessibility and label diffusivity. |
| T235 | 2517-2666 | Sentence | denotes | Most importantly, efforts have to be directed to exploit the full information contained in the reconstruction volumes based on advanced segmentation. |
| T236 | 2667-2825 | Sentence | denotes | Tracing of capillaries is an obvious important next step, in view of unraveling the role of intussusceptive angiogenesis in Covid-19 (Ackermann et al., 2020). |
| T237 | 2826-3045 | Sentence | denotes | The current data, which are made fully available at https://doi.org/10.5281/zenodo.3892637, are likely to already provide such clues once that more advanced segmentation approaches based on machine learning are applied. |
| T238 | 3046-3180 | Sentence | denotes | More generally, it may advance our understanding of DAD in the particular case of Covid-19, as an intrinsically volumetric phenomenon. |
| T239 | 3181-3306 | Sentence | denotes | Beyond the current data, further studies could shed further light on the differences between moderate and severe progression. |
| T240 | 3307-3410 | Sentence | denotes | Possibly, phase contrast tomography of lung biopsies could in future also help diagnosis and treatment. |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32815517-32437596-26997864 | 2819-2823 | 32437596 | denotes | 2020 |
MyTest
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32815517-32437596-26997864 | 2819-2823 | 32437596 | denotes | 2020 |
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 246 | 356-368 | Disease | denotes | inflammation | MESH:D007249 |
| 247 | 424-432 | Disease | denotes | Covid-19 | MESH:C000657245 |
| 249 | 1251-1256 | CellLine | denotes | PC-CT | CVCL:B848 |
| 252 | 2791-2799 | Disease | denotes | Covid-19 | MESH:C000657245 |
| 253 | 3128-3136 | Disease | denotes | Covid-19 | MESH:C000657245 |