PMC:7473770 / 40979-42287 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T241","span":{"begin":164,"end":170},"obj":"Body_part"},{"id":"T242","span":{"begin":352,"end":363},"obj":"Body_part"},{"id":"T243","span":{"begin":376,"end":382},"obj":"Body_part"},{"id":"T244","span":{"begin":396,"end":419},"obj":"Body_part"},{"id":"T245","span":{"begin":413,"end":419},"obj":"Body_part"},{"id":"T246","span":{"begin":459,"end":462},"obj":"Body_part"},{"id":"T247","span":{"begin":519,"end":531},"obj":"Body_part"},{"id":"T248","span":{"begin":566,"end":572},"obj":"Body_part"},{"id":"T249","span":{"begin":780,"end":786},"obj":"Body_part"},{"id":"T250","span":{"begin":798,"end":804},"obj":"Body_part"},{"id":"T251","span":{"begin":859,"end":865},"obj":"Body_part"},{"id":"T252","span":{"begin":905,"end":911},"obj":"Body_part"},{"id":"T253","span":{"begin":1221,"end":1227},"obj":"Body_part"},{"id":"T254","span":{"begin":1254,"end":1265},"obj":"Body_part"}],"attributes":[{"id":"A241","pred":"fma_id","subj":"T241","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A242","pred":"fma_id","subj":"T242","obj":"http://purl.org/sig/ont/fma/fma63261"},{"id":"A243","pred":"fma_id","subj":"T243","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A244","pred":"fma_id","subj":"T244","obj":"http://purl.org/sig/ont/fma/fma9640"},{"id":"A245","pred":"fma_id","subj":"T245","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A246","pred":"fma_id","subj":"T246","obj":"http://purl.org/sig/ont/fma/fma67847"},{"id":"A247","pred":"fma_id","subj":"T247","obj":"http://purl.org/sig/ont/fma/fma76577"},{"id":"A248","pred":"fma_id","subj":"T248","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A249","pred":"fma_id","subj":"T249","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A250","pred":"fma_id","subj":"T250","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A251","pred":"fma_id","subj":"T251","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A252","pred":"fma_id","subj":"T252","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A253","pred":"fma_id","subj":"T253","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A254","pred":"fma_id","subj":"T254","obj":"http://purl.org/sig/ont/fma/fma76577"}],"text":"For each patient the stitched overview scans were analyzed with regard to structural characteristics. 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. In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map. Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block. Individual self-contained areas of paraffin (not connected to air) were excluded from the mask. Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel. The tissue volume V is given by the sum of all voxels containing tissue. The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air. From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio. Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample. Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T240","span":{"begin":164,"end":170},"obj":"Body_part"},{"id":"T241","span":{"begin":376,"end":382},"obj":"Body_part"},{"id":"T242","span":{"begin":413,"end":419},"obj":"Body_part"},{"id":"T243","span":{"begin":566,"end":572},"obj":"Body_part"},{"id":"T244","span":{"begin":780,"end":786},"obj":"Body_part"},{"id":"T245","span":{"begin":798,"end":804},"obj":"Body_part"},{"id":"T246","span":{"begin":859,"end":865},"obj":"Body_part"},{"id":"T247","span":{"begin":905,"end":911},"obj":"Body_part"},{"id":"T248","span":{"begin":1221,"end":1227},"obj":"Body_part"}],"attributes":[{"id":"A240","pred":"uberon_id","subj":"T240","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A241","pred":"uberon_id","subj":"T241","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A242","pred":"uberon_id","subj":"T242","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A243","pred":"uberon_id","subj":"T243","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A244","pred":"uberon_id","subj":"T244","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A245","pred":"uberon_id","subj":"T245","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A246","pred":"uberon_id","subj":"T246","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A247","pred":"uberon_id","subj":"T247","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A248","pred":"uberon_id","subj":"T248","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"}],"text":"For each patient the stitched overview scans were analyzed with regard to structural characteristics. 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. In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map. Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block. Individual self-contained areas of paraffin (not connected to air) were excluded from the mask. Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel. The tissue volume V is given by the sum of all voxels containing tissue. The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air. From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio. Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample. Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T391","span":{"begin":144,"end":149},"obj":"http://purl.obolibrary.org/obo/CLO_0050507"},{"id":"T392","span":{"begin":396,"end":419},"obj":"http://purl.obolibrary.org/obo/UBERON_0002384"},{"id":"T393","span":{"begin":396,"end":419},"obj":"http://www.ebi.ac.uk/efo/EFO_0000952"},{"id":"T394","span":{"begin":924,"end":925},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T395","span":{"begin":1072,"end":1073},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T396","span":{"begin":1099,"end":1101},"obj":"http://purl.obolibrary.org/obo/CL_0000453"},{"id":"T397","span":{"begin":1133,"end":1134},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"For each patient the stitched overview scans were analyzed with regard to structural characteristics. 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. In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map. Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block. Individual self-contained areas of paraffin (not connected to air) were excluded from the mask. Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel. The tissue volume V is given by the sum of all voxels containing tissue. The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air. From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio. Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample. Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T46","span":{"begin":230,"end":242},"obj":"http://purl.obolibrary.org/obo/GO_0035282"},{"id":"T47","span":{"begin":690,"end":702},"obj":"http://purl.obolibrary.org/obo/GO_0035282"}],"text":"For each patient the stitched overview scans were analyzed with regard to structural characteristics. 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. In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map. Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block. Individual self-contained areas of paraffin (not connected to air) were excluded from the mask. Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel. The tissue volume V is given by the sum of all voxels containing tissue. The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air. From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio. Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample. Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated."}

{"project":"LitCovid-sentences","denotations":[{"id":"T319","span":{"begin":0,"end":101},"obj":"Sentence"},{"id":"T320","span":{"begin":102,"end":324},"obj":"Sentence"},{"id":"T321","span":{"begin":325,"end":463},"obj":"Sentence"},{"id":"T322","span":{"begin":464,"end":579},"obj":"Sentence"},{"id":"T323","span":{"begin":580,"end":675},"obj":"Sentence"},{"id":"T324","span":{"begin":676,"end":793},"obj":"Sentence"},{"id":"T325","span":{"begin":794,"end":866},"obj":"Sentence"},{"id":"T326","span":{"begin":867,"end":957},"obj":"Sentence"},{"id":"T327","span":{"begin":958,"end":1063},"obj":"Sentence"},{"id":"T328","span":{"begin":1064,"end":1172},"obj":"Sentence"},{"id":"T329","span":{"begin":1173,"end":1308},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"For each patient the stitched overview scans were analyzed with regard to structural characteristics. 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. In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map. Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block. Individual self-contained areas of paraffin (not connected to air) were excluded from the mask. Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel. The tissue volume V is given by the sum of all voxels containing tissue. The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air. From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio. Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample. Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated."}

{"project":"2_test","denotations":[{"id":"32815517-31570887-26997871","span":{"begin":274,"end":278},"obj":"31570887"}],"text":"For each patient the stitched overview scans were analyzed with regard to structural characteristics. 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. In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map. Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block. Individual self-contained areas of paraffin (not connected to air) were excluded from the mask. Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel. The tissue volume V is given by the sum of all voxels containing tissue. The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air. From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio. Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample. Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated."}

{"project":"MyTest","denotations":[{"id":"32815517-31570887-26997871","span":{"begin":274,"end":278},"obj":"31570887"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"For each patient the stitched overview scans were analyzed with regard to structural characteristics. 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. In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map. Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block. Individual self-contained areas of paraffin (not connected to air) were excluded from the mask. Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel. The tissue volume V is given by the sum of all voxels containing tissue. The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air. From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio. Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample. Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated."}

{"project":"LitCovid-PubTator","denotations":[{"id":"326","span":{"begin":9,"end":16},"obj":"Species"},{"id":"327","span":{"begin":211,"end":219},"obj":"Chemical"},{"id":"328","span":{"begin":490,"end":498},"obj":"Chemical"},{"id":"329","span":{"begin":615,"end":623},"obj":"Chemical"},{"id":"330","span":{"begin":749,"end":755},"obj":"Chemical"},{"id":"331","span":{"begin":884,"end":886},"obj":"Chemical"}],"attributes":[{"id":"A326","pred":"tao:has_database_id","subj":"326","obj":"Tax:9606"},{"id":"A327","pred":"tao:has_database_id","subj":"327","obj":"MESH:D010232"},{"id":"A328","pred":"tao:has_database_id","subj":"328","obj":"MESH:D010232"},{"id":"A329","pred":"tao:has_database_id","subj":"329","obj":"MESH:D010232"},{"id":"A330","pred":"tao:has_database_id","subj":"330","obj":"MESH:D010100"},{"id":"A331","pred":"tao:has_database_id","subj":"331","obj":"MESH:C012546"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"For each patient the stitched overview scans were analyzed with regard to structural characteristics. 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. In order to exclude single macrophages or detached tissue, only voxels connected to the tissue block were considered for the distance map. Further, the areas of the paraffin which represent air compartments were linked to the outside of the tissue block. Individual self-contained areas of paraffin (not connected to air) were excluded from the mask. Based on this segmentation, the distance to the nearest voxel containing oxygen was calculated for each tissue voxel. The tissue volume V is given by the sum of all voxels containing tissue. The surface area SA is defined by all tissue voxels with a distance of 1 pixel to the air. From this information we calculated the specific surface(2) SV=SA/Vwith S⁢A/V surface area volume -ratio. Further a characteristic length(3) Lc=V/SA⋅vxwith v⁢x edge length of a voxel was determined for each sample. Additionally, the mean distance (dO2¯) from all tissue voxels to the closest air compartment and its standard deviation was calculated."}