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PMC:7473770 / 39071-43850 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T240 1857-1865 Body_part denotes Appendix http://purl.org/sig/ont/fma/fma14542
T241 2072-2078 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T242 2260-2271 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T243 2284-2290 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T244 2304-2327 Body_part denotes connected to the tissue http://purl.org/sig/ont/fma/fma9640
T245 2321-2327 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T246 2367-2370 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T247 2427-2439 Body_part denotes compartments http://purl.org/sig/ont/fma/fma76577
T248 2474-2480 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T249 2688-2694 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T250 2706-2712 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T251 2767-2773 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T252 2813-2819 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T253 3129-3135 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T254 3162-3173 Body_part denotes compartment http://purl.org/sig/ont/fma/fma76577
T255 3239-3257 Body_part denotes capillary networks http://purl.org/sig/ont/fma/fma45633
T256 3239-3248 Body_part denotes capillary http://purl.org/sig/ont/fma/fma63194
T257 3389-3406 Body_part denotes capillary network http://purl.org/sig/ont/fma/fma45633
T258 3418-3422 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T259 3540-3544 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T260 3571-3582 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T261 3587-3598 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T262 3723-3725 Body_part denotes AG http://purl.org/sig/ont/fma/fma61898
T263 3802-3813 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T264 3982-3993 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T265 4090-4101 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T266 4119-4128 Body_part denotes capillary http://purl.org/sig/ont/fma/fma63194
T267 4186-4197 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T268 4220-4231 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T269 4326-4337 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T270 4382-4393 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T271 4416-4433 Body_part denotes endothelial cells http://purl.org/sig/ont/fma/fma66772
T272 4428-4433 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T273 4451-4462 Body_part denotes capillaries http://purl.org/sig/ont/fma/fma63194
T274 4475-4480 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T275 4631-4642 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T276 4664-4675 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T277 4722-4733 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T278 4745-4749 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T279 4750-4756 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T240 2072-2078 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T241 2284-2290 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T242 2321-2327 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T243 2474-2480 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T244 2688-2694 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T245 2706-2712 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T246 2767-2773 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T247 2813-2819 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T248 3129-3135 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T249 3239-3248 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T250 3389-3398 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T251 4119-4128 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T252 4475-4480 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T253 4745-4749 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T254 4750-4756 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T390 1030-1033 http://purl.obolibrary.org/obo/CLO_0051145 denotes Ram
T391 2052-2057 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 × 2
T392 2304-2327 http://purl.obolibrary.org/obo/UBERON_0002384 denotes connected to the tissue
T393 2304-2327 http://www.ebi.ac.uk/efo/EFO_0000952 denotes connected to the tissue
T394 2832-2833 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T395 2980-2981 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T396 3007-3009 http://purl.obolibrary.org/obo/CL_0000453 denotes Lc
T397 3041-3042 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T398 3225-3234 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T399 3371-3380 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T400 3418-3428 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T401 3540-3544 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T402 3940-3941 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T403 4004-4005 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T404 4164-4165 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T405 4416-4433 http://purl.obolibrary.org/obo/CL_0000115 denotes endothelial cells
T406 4475-4480 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T407 4475-4480 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T408 4557-4558 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T409 4745-4749 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T410 4745-4749 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T411 4757-4759 http://purl.obolibrary.org/obo/CLO_0052906 denotes cl

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T44 43-55 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T45 1876-1888 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T46 2138-2150 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T47 2598-2610 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T48 3291-3303 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T49 3750-3762 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T50 3962-3974 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T51 4615-4627 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T307 0-55 Sentence denotes Phase retrieval, image reconstruction, and segmentation
T308 57-91 Sentence denotes Phase retrieval and reconstruction
T309 92-440 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 441-562 Sentence denotes Importantly, both CTF and NL-CTF implementations can be augmented by imposing support and range constraints, when needed.
T311 563-721 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 722-890 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 891-1195 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 1196-1523 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 1524-1692 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 1693-1800 Sentence denotes Stitching of reconstructions from different tomographic scans was performed using (Miettinen et al., 2019).
T317 1801-1868 Sentence denotes Resolution estimates were obtained by FSC analysis, see Appendix 2.
T318 1870-1907 Sentence denotes Image segmentation and quantification
T319 1908-2009 Sentence denotes For each patient the stitched overview scans were analyzed with regard to structural characteristics.
T320 2010-2232 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 2233-2371 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 2372-2487 Sentence denotes Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block.
T323 2488-2583 Sentence denotes Individual self-contained areas of paraffin (not connected to air) were excluded from the mask.
T324 2584-2701 Sentence denotes Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel.
T325 2702-2774 Sentence denotes The tissue volume V is given by the sum of all voxels containing tissue.
T326 2775-2865 Sentence denotes The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air.
T327 2866-2971 Sentence denotes From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio.
T328 2972-3080 Sentence denotes Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample.
T329 3081-3216 Sentence denotes Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated.
T330 3217-3355 Sentence denotes Hyaline membranes and capillary networks were extracted using semi-manual segmentation functions in Avizo (Thermo Fisher Scientific, USA).
T331 3356-3511 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 3512-3622 Sentence denotes In particular, inflammatory cell subpopulations - that is, macrophages and lymphocytes - can be distinguished.
T333 3623-3736 Sentence denotes To this end, an automatic and parameter-controlled algorithm denoted as BlobFinder was used (arivis AG, Germany).
T334 3737-3880 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 3881-3953 Sentence denotes The algorithm is able to identify roundish structures with a given size.
T336 3954-4037 Sentence denotes For the segmentation of the lymphocytes, we chose a characteristic size of 6.5⁢μ⁢m.
T337 4038-4136 Sentence denotes The structures identified in this step also include macrophages and parts of the capillary system.
T338 4137-4285 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 4286-4394 Sentence denotes In the tomographic reconstructions, the lymphocytes appear denser compared to the nuclei of the macrophages.
T340 4395-4535 Sentence denotes Further, nuclei from endothelial cells and parts of the capillaries filled with blood residues were excluded based on their elongated shape.
T341 4536-4601 Sentence denotes Only structures with a sphericity higher than 0.55 were included.
T342 4602-4779 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.

2_test

Id Subject Object Predicate Lexical cue
32815517-19483813-26997866 254-258 19483813 denotes 2004
32815517-32381790-26997867 434-438 32381790 denotes 2020
32815517-26057688-26997868 1138-1142 26057688 denotes 2015
32815517-27828452-26997869 1162-1166 27828452 denotes 2016
32815517-31116382-26997870 1794-1798 31116382 denotes 2019
32815517-31570887-26997871 2182-2186 31570887 denotes 2019

MyTest

Id Subject Object Predicate Lexical cue
32815517-19483813-26997866 254-258 19483813 denotes 2004
32815517-32381790-26997867 434-438 32381790 denotes 2020
32815517-26057688-26997868 1138-1142 26057688 denotes 2015
32815517-27828452-26997869 1162-1166 27828452 denotes 2016
32815517-31116382-26997870 1794-1798 31116382 denotes 2019
32815517-31570887-26997871 2182-2186 31570887 denotes 2019

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
319 1034-1037 Gene denotes Lak Gene:80216
326 1917-1924 Species denotes patient Tax:9606
327 2119-2127 Chemical denotes paraffin MESH:D010232
328 2398-2406 Chemical denotes paraffin MESH:D010232
329 2523-2531 Chemical denotes paraffin MESH:D010232
330 2657-2663 Chemical denotes oxygen MESH:D010100
331 2792-2794 Chemical denotes SA MESH:C012546