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PMC:7473770 / 40941-43850 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T241 202-208 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T242 390-401 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T243 414-420 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T244 434-457 Body_part denotes connected to the tissue http://purl.org/sig/ont/fma/fma9640
T245 451-457 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T246 497-500 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T247 557-569 Body_part denotes compartments http://purl.org/sig/ont/fma/fma76577
T248 604-610 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T249 818-824 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T250 836-842 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T251 897-903 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T252 943-949 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T253 1259-1265 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637
T254 1292-1303 Body_part denotes compartment http://purl.org/sig/ont/fma/fma76577
T255 1369-1387 Body_part denotes capillary networks http://purl.org/sig/ont/fma/fma45633
T256 1369-1378 Body_part denotes capillary http://purl.org/sig/ont/fma/fma63194
T257 1519-1536 Body_part denotes capillary network http://purl.org/sig/ont/fma/fma45633
T258 1548-1552 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T259 1670-1674 Body_part denotes cell http://purl.org/sig/ont/fma/fma68646
T260 1701-1712 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T261 1717-1728 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T262 1853-1855 Body_part denotes AG http://purl.org/sig/ont/fma/fma61898
T263 1932-1943 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T264 2112-2123 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T265 2220-2231 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T266 2249-2258 Body_part denotes capillary http://purl.org/sig/ont/fma/fma63194
T267 2316-2327 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T268 2350-2361 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T269 2456-2467 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T270 2512-2523 Body_part denotes macrophages http://purl.org/sig/ont/fma/fma63261
T271 2546-2563 Body_part denotes endothelial cells http://purl.org/sig/ont/fma/fma66772
T272 2558-2563 Body_part denotes cells http://purl.org/sig/ont/fma/fma68646
T273 2581-2592 Body_part denotes capillaries http://purl.org/sig/ont/fma/fma63194
T274 2605-2610 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T275 2761-2772 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T276 2794-2805 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T277 2852-2863 Body_part denotes lymphocytes http://purl.org/sig/ont/fma/fma62863
T278 2875-2879 Body_part denotes lung http://purl.org/sig/ont/fma/fma7195
T279 2880-2886 Body_part denotes tissue http://purl.org/sig/ont/fma/fma9637

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T240 202-208 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T241 414-420 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T242 451-457 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T243 604-610 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T244 818-824 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T245 836-842 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T246 897-903 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T247 943-949 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T248 1259-1265 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479
T249 1369-1378 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T250 1519-1528 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T251 2249-2258 Body_part denotes capillary http://purl.obolibrary.org/obo/UBERON_0001982
T252 2605-2610 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T253 2875-2879 Body_part denotes lung http://purl.obolibrary.org/obo/UBERON_0002048
T254 2880-2886 Body_part denotes tissue http://purl.obolibrary.org/obo/UBERON_0000479

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T391 182-187 http://purl.obolibrary.org/obo/CLO_0050507 denotes 2 × 2
T392 434-457 http://purl.obolibrary.org/obo/UBERON_0002384 denotes connected to the tissue
T393 434-457 http://www.ebi.ac.uk/efo/EFO_0000952 denotes connected to the tissue
T394 962-963 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T395 1110-1111 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T396 1137-1139 http://purl.obolibrary.org/obo/CL_0000453 denotes Lc
T397 1171-1172 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T398 1355-1364 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T399 1501-1510 http://purl.obolibrary.org/obo/UBERON_0000158 denotes membranes
T400 1548-1558 http://purl.obolibrary.org/obo/CL_0000000 denotes cell types
T401 1670-1674 http://purl.obolibrary.org/obo/GO_0005623 denotes cell
T402 2070-2071 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T403 2134-2135 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T404 2294-2295 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T405 2546-2563 http://purl.obolibrary.org/obo/CL_0000115 denotes endothelial cells
T406 2605-2610 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T407 2605-2610 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T408 2687-2688 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T409 2875-2879 http://purl.obolibrary.org/obo/UBERON_0002048 denotes lung
T410 2875-2879 http://www.ebi.ac.uk/efo/EFO_0000934 denotes lung
T411 2887-2889 http://purl.obolibrary.org/obo/CLO_0052906 denotes cl

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T45 6-18 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T46 268-280 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T47 728-740 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T48 1421-1433 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T49 1880-1892 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T50 2092-2104 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation
T51 2745-2757 http://purl.obolibrary.org/obo/GO_0035282 denotes segmentation

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T318 0-37 Sentence denotes Image segmentation and quantification
T319 38-139 Sentence denotes For each patient the stitched overview scans were analyzed with regard to structural characteristics.
T320 140-362 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 363-501 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 502-617 Sentence denotes Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block.
T323 618-713 Sentence denotes Individual self-contained areas of paraffin (not connected to air) were excluded from the mask.
T324 714-831 Sentence denotes Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel.
T325 832-904 Sentence denotes The tissue volume V is given by the sum of all voxels containing tissue.
T326 905-995 Sentence denotes The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air.
T327 996-1101 Sentence denotes From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio.
T328 1102-1210 Sentence denotes Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample.
T329 1211-1346 Sentence denotes Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated.
T330 1347-1485 Sentence denotes Hyaline membranes and capillary networks were extracted using semi-manual segmentation functions in Avizo (Thermo Fisher Scientific, USA).
T331 1486-1641 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 1642-1752 Sentence denotes In particular, inflammatory cell subpopulations - that is, macrophages and lymphocytes - can be distinguished.
T333 1753-1866 Sentence denotes To this end, an automatic and parameter-controlled algorithm denoted as BlobFinder was used (arivis AG, Germany).
T334 1867-2010 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 2011-2083 Sentence denotes The algorithm is able to identify roundish structures with a given size.
T336 2084-2167 Sentence denotes For the segmentation of the lymphocytes, we chose a characteristic size of 6.5⁢μ⁢m.
T337 2168-2266 Sentence denotes The structures identified in this step also include macrophages and parts of the capillary system.
T338 2267-2415 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 2416-2524 Sentence denotes In the tomographic reconstructions, the lymphocytes appear denser compared to the nuclei of the macrophages.
T340 2525-2665 Sentence denotes Further, nuclei from endothelial cells and parts of the capillaries filled with blood residues were excluded based on their elongated shape.
T341 2666-2731 Sentence denotes Only structures with a sphericity higher than 0.55 were included.
T342 2732-2909 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
32815517-31570887-26997871 312-316 31570887 denotes 2019

MyTest

Id Subject Object Predicate Lexical cue
32815517-31570887-26997871 312-316 31570887 denotes 2019

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
326 47-54 Species denotes patient Tax:9606
327 249-257 Chemical denotes paraffin MESH:D010232
328 528-536 Chemical denotes paraffin MESH:D010232
329 653-661 Chemical denotes paraffin MESH:D010232
330 787-793 Chemical denotes oxygen MESH:D010100
331 922-924 Chemical denotes SA MESH:C012546