PMC:7473770 / 31965-34619 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T223","span":{"begin":33,"end":39},"obj":"Body_part"},{"id":"T224","span":{"begin":92,"end":96},"obj":"Body_part"},{"id":"T225","span":{"begin":153,"end":159},"obj":"Body_part"},{"id":"T226","span":{"begin":779,"end":783},"obj":"Body_part"},{"id":"T227","span":{"begin":1114,"end":1122},"obj":"Body_part"},{"id":"T228","span":{"begin":1507,"end":1513},"obj":"Body_part"},{"id":"T229","span":{"begin":1734,"end":1740},"obj":"Body_part"},{"id":"T230","span":{"begin":1846,"end":1852},"obj":"Body_part"},{"id":"T231","span":{"begin":2425,"end":2429},"obj":"Body_part"}],"attributes":[{"id":"A223","pred":"fma_id","subj":"T223","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A224","pred":"fma_id","subj":"T224","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A225","pred":"fma_id","subj":"T225","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A226","pred":"fma_id","subj":"T226","obj":"http://purl.org/sig/ont/fma/fma7195"},{"id":"A227","pred":"fma_id","subj":"T227","obj":"http://purl.org/sig/ont/fma/fma264783"},{"id":"A228","pred":"fma_id","subj":"T228","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A229","pred":"fma_id","subj":"T229","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A230","pred":"fma_id","subj":"T230","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A231","pred":"fma_id","subj":"T231","obj":"http://purl.org/sig/ont/fma/fma7195"}],"text":"Autopsy, clinical background and tissue preparation\nIn total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020). A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a. Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2. All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs. Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure). Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.\nTable 2. Sample and medical information.\nAge and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.\nSample no. Age group, gender Hospitalization, clinical, radiological, and histological characteristics\nI 60–70, F 5-10d, GGO, DAD\nII 80–90, M 5-10d, C, I, DAD\nIII 90–100, M 1-4d, GGO, C, DAD\nIV 70–80, M 1-4d, NIV, S, GGO, C, DAD\nV 60–70, M 5-10d, NIV, S, GGO, C, DAD\nVI 70–80, M 1-4d, S, GGO, C, DAD\nCTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed. To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained. Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block. The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration. From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size. The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings. A sketch of the sample preparation is shown in Figure 1b. The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T221","span":{"begin":33,"end":39},"obj":"Body_part"},{"id":"T222","span":{"begin":92,"end":96},"obj":"Body_part"},{"id":"T223","span":{"begin":153,"end":159},"obj":"Body_part"},{"id":"T224","span":{"begin":779,"end":783},"obj":"Body_part"},{"id":"T225","span":{"begin":1507,"end":1513},"obj":"Body_part"},{"id":"T226","span":{"begin":1734,"end":1740},"obj":"Body_part"},{"id":"T227","span":{"begin":1846,"end":1852},"obj":"Body_part"},{"id":"T228","span":{"begin":2425,"end":2429},"obj":"Body_part"},{"id":"T229","span":{"begin":2471,"end":2475},"obj":"Body_part"},{"id":"T230","span":{"begin":2570,"end":2574},"obj":"Body_part"}],"attributes":[{"id":"A221","pred":"uberon_id","subj":"T221","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A222","pred":"uberon_id","subj":"T222","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A223","pred":"uberon_id","subj":"T223","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A224","pred":"uberon_id","subj":"T224","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A225","pred":"uberon_id","subj":"T225","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A226","pred":"uberon_id","subj":"T226","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A227","pred":"uberon_id","subj":"T227","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A228","pred":"uberon_id","subj":"T228","obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"A229","pred":"uberon_id","subj":"T229","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"A230","pred":"uberon_id","subj":"T230","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"}],"text":"Autopsy, clinical background and tissue preparation\nIn total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020). A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a. Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2. All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs. Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure). Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.\nTable 2. Sample and medical information.\nAge and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.\nSample no. Age group, gender Hospitalization, clinical, radiological, and histological characteristics\nI 60–70, F 5-10d, GGO, DAD\nII 80–90, M 5-10d, C, I, DAD\nIII 90–100, M 1-4d, GGO, C, DAD\nIV 70–80, M 1-4d, NIV, S, GGO, C, DAD\nV 60–70, M 5-10d, NIV, S, GGO, C, DAD\nVI 70–80, M 1-4d, S, GGO, C, DAD\nCTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed. To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained. Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block. The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration. From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size. The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings. A sketch of the sample preparation is shown in Figure 1b. The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T54","span":{"begin":443,"end":455},"obj":"Disease"},{"id":"T55","span":{"begin":677,"end":696},"obj":"Disease"},{"id":"T56","span":{"begin":732,"end":751},"obj":"Disease"},{"id":"T57","span":{"begin":768,"end":773},"obj":"Disease"},{"id":"T58","span":{"begin":829,"end":839},"obj":"Disease"}],"attributes":[{"id":"A54","pred":"mondo_id","subj":"T54","obj":"http://purl.obolibrary.org/obo/MONDO_0005044"},{"id":"A55","pred":"mondo_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/MONDO_0021113"},{"id":"A56","pred":"mondo_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/MONDO_0021113"},{"id":"A57","pred":"mondo_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/MONDO_0005070"},{"id":"A58","pred":"mondo_id","subj":"T58","obj":"http://purl.obolibrary.org/obo/MONDO_0004993"}],"text":"Autopsy, clinical background and tissue preparation\nIn total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020). A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a. Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2. All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs. Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure). Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.\nTable 2. Sample and medical information.\nAge and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.\nSample no. Age group, gender Hospitalization, clinical, radiological, and histological characteristics\nI 60–70, F 5-10d, GGO, DAD\nII 80–90, M 5-10d, C, I, DAD\nIII 90–100, M 1-4d, GGO, C, DAD\nIV 70–80, M 1-4d, NIV, S, GGO, C, DAD\nV 60–70, M 5-10d, NIV, S, GGO, C, DAD\nVI 70–80, M 1-4d, S, GGO, C, DAD\nCTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed. To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained. Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block. The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration. From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size. The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings. A sketch of the sample preparation is shown in Figure 1b. The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T321","span":{"begin":92,"end":96},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T322","span":{"begin":92,"end":96},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T323","span":{"begin":151,"end":152},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T324","span":{"begin":779,"end":783},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T325","span":{"begin":779,"end":783},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T326","span":{"begin":857,"end":858},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T327","span":{"begin":1246,"end":1250},"obj":"http://purl.obolibrary.org/obo/CLO_0002983"},{"id":"T328","span":{"begin":1309,"end":1313},"obj":"http://purl.obolibrary.org/obo/CLO_0007437"},{"id":"T329","span":{"begin":1341,"end":1345},"obj":"http://purl.obolibrary.org/obo/CLO_0007437"},{"id":"T330","span":{"begin":1421,"end":1425},"obj":"http://purl.obolibrary.org/obo/CLO_0007437"},{"id":"T331","span":{"begin":1605,"end":1606},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T332","span":{"begin":2054,"end":2057},"obj":"http://purl.obolibrary.org/obo/CLO_0050154"},{"id":"T333","span":{"begin":2064,"end":2065},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T334","span":{"begin":2153,"end":2154},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T335","span":{"begin":2226,"end":2227},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T336","span":{"begin":2298,"end":2299},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T337","span":{"begin":2355,"end":2356},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T338","span":{"begin":2425,"end":2429},"obj":"http://purl.obolibrary.org/obo/UBERON_0002048"},{"id":"T339","span":{"begin":2425,"end":2429},"obj":"http://www.ebi.ac.uk/efo/EFO_0000934"},{"id":"T340","span":{"begin":2471,"end":2475},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"T341","span":{"begin":2512,"end":2513},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T342","span":{"begin":2558,"end":2559},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T343","span":{"begin":2570,"end":2574},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"}],"text":"Autopsy, clinical background and tissue preparation\nIn total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020). A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a. Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2. All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs. Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure). Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.\nTable 2. Sample and medical information.\nAge and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.\nSample no. Age group, gender Hospitalization, clinical, radiological, and histological characteristics\nI 60–70, F 5-10d, GGO, DAD\nII 80–90, M 5-10d, C, I, DAD\nIII 90–100, M 1-4d, GGO, C, DAD\nIV 70–80, M 1-4d, NIV, S, GGO, C, DAD\nV 60–70, M 5-10d, NIV, S, GGO, C, DAD\nVI 70–80, M 1-4d, S, GGO, C, DAD\nCTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed. To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained. Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block. The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration. From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size. The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings. A sketch of the sample preparation is shown in Figure 1b. The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution."}

{"project":"LitCovid-sentences","denotations":[{"id":"T242","span":{"begin":0,"end":51},"obj":"Sentence"},{"id":"T243","span":{"begin":52,"end":150},"obj":"Sentence"},{"id":"T244","span":{"begin":151,"end":273},"obj":"Sentence"},{"id":"T245","span":{"begin":274,"end":415},"obj":"Sentence"},{"id":"T246","span":{"begin":416,"end":540},"obj":"Sentence"},{"id":"T247","span":{"begin":541,"end":753},"obj":"Sentence"},{"id":"T248","span":{"begin":754,"end":869},"obj":"Sentence"},{"id":"T249","span":{"begin":870,"end":878},"obj":"Sentence"},{"id":"T250","span":{"begin":880,"end":911},"obj":"Sentence"},{"id":"T251","span":{"begin":912,"end":1130},"obj":"Sentence"},{"id":"T252","span":{"begin":1131,"end":1141},"obj":"Sentence"},{"id":"T253","span":{"begin":1143,"end":1235},"obj":"Sentence"},{"id":"T254","span":{"begin":1236,"end":1264},"obj":"Sentence"},{"id":"T255","span":{"begin":1265,"end":1295},"obj":"Sentence"},{"id":"T256","span":{"begin":1296,"end":1329},"obj":"Sentence"},{"id":"T257","span":{"begin":1330,"end":1369},"obj":"Sentence"},{"id":"T258","span":{"begin":1370,"end":1409},"obj":"Sentence"},{"id":"T259","span":{"begin":1410,"end":1444},"obj":"Sentence"},{"id":"T260","span":{"begin":1445,"end":1573},"obj":"Sentence"},{"id":"T261","span":{"begin":1574,"end":1702},"obj":"Sentence"},{"id":"T262","span":{"begin":1703,"end":1818},"obj":"Sentence"},{"id":"T263","span":{"begin":1819,"end":1995},"obj":"Sentence"},{"id":"T264","span":{"begin":1996,"end":2113},"obj":"Sentence"},{"id":"T265","span":{"begin":2114,"end":2354},"obj":"Sentence"},{"id":"T266","span":{"begin":2355,"end":2412},"obj":"Sentence"},{"id":"T267","span":{"begin":2413,"end":2654},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Autopsy, clinical background and tissue preparation\nIn total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020). A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a. Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2. All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs. Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure). Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.\nTable 2. Sample and medical information.\nAge and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.\nSample no. Age group, gender Hospitalization, clinical, radiological, and histological characteristics\nI 60–70, F 5-10d, GGO, DAD\nII 80–90, M 5-10d, C, I, DAD\nIII 90–100, M 1-4d, GGO, C, DAD\nIV 70–80, M 1-4d, NIV, S, GGO, C, DAD\nV 60–70, M 5-10d, NIV, S, GGO, C, DAD\nVI 70–80, M 1-4d, S, GGO, C, DAD\nCTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed. To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained. Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block. The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration. From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size. The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings. A sketch of the sample preparation is shown in Figure 1b. The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution."}

{"project":"LitCovid-PD-HP","denotations":[{"id":"T29","span":{"begin":446,"end":458},"obj":"Phenotype"},{"id":"T30","span":{"begin":680,"end":699},"obj":"Phenotype"},{"id":"T31","span":{"begin":735,"end":754},"obj":"Phenotype"},{"id":"T32","span":{"begin":771,"end":776},"obj":"Phenotype"}],"attributes":[{"id":"A29","pred":"hp_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/HP_0000822"},{"id":"A30","pred":"hp_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/HP_0002878"},{"id":"A31","pred":"hp_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/HP_0002878"},{"id":"A32","pred":"hp_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/HP_0002664"}],"text":"Autopsy, clinical background and tissue preparation\nIn total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020). A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a. Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2. All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs. Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure). Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.\nTable 2. Sample and medical information.\nAge and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.\nSample no. Age group, gender Hospitalization, clinical, radiological, and histological characteristics\nI 60–70, F 5-10d, GGO, DAD\nII 80–90, M 5-10d, C, I, DAD\nIII 90–100, M 1-4d, GGO, C, DAD\nIV 70–80, M 1-4d, NIV, S, GGO, C, DAD\nV 60–70, M 5-10d, NIV, S, GGO, C, DAD\nVI 70–80, M 1-4d, S, GGO, C, DAD\nCTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed. To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained. Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block. The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration. From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size. The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings. A sketch of the sample preparation is shown in Figure 1b. The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution."}

{"project":"2_test","denotations":[{"id":"32815517-32364264-26997865","span":{"begin":144,"end":148},"obj":"32364264"}],"text":"Autopsy, clinical background and tissue preparation\nIn total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020). A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a. Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2. All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs. Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure). Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.\nTable 2. Sample and medical information.\nAge and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.\nSample no. Age group, gender Hospitalization, clinical, radiological, and histological characteristics\nI 60–70, F 5-10d, GGO, DAD\nII 80–90, M 5-10d, C, I, DAD\nIII 90–100, M 1-4d, GGO, C, DAD\nIV 70–80, M 1-4d, NIV, S, GGO, C, DAD\nV 60–70, M 5-10d, NIV, S, GGO, C, DAD\nVI 70–80, M 1-4d, S, GGO, C, DAD\nCTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed. To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained. Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block. The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration. From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size. The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings. A sketch of the sample preparation is shown in Figure 1b. The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution."}

{"project":"MyTest","denotations":[{"id":"32815517-32364264-26997865","span":{"begin":144,"end":148},"obj":"32364264"}],"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":"Autopsy, clinical background and tissue preparation\nIn total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020). A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a. Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2. All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs. Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure). Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.\nTable 2. Sample and medical information.\nAge and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.\nSample no. Age group, gender Hospitalization, clinical, radiological, and histological characteristics\nI 60–70, F 5-10d, GGO, DAD\nII 80–90, M 5-10d, C, I, DAD\nIII 90–100, M 1-4d, GGO, C, DAD\nIV 70–80, M 1-4d, NIV, S, GGO, C, DAD\nV 60–70, M 5-10d, NIV, S, GGO, C, DAD\nVI 70–80, M 1-4d, S, GGO, C, DAD\nCTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed. To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained. Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block. The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration. From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size. The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings. A sketch of the sample preparation is shown in Figure 1b. The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution."}

{"project":"LitCovid-PubTator","denotations":[{"id":"270","span":{"begin":119,"end":127},"obj":"Species"},{"id":"271","span":{"begin":211,"end":219},"obj":"Species"},{"id":"272","span":{"begin":385,"end":393},"obj":"Species"},{"id":"273","span":{"begin":420,"end":428},"obj":"Species"},{"id":"274","span":{"begin":607,"end":615},"obj":"Species"},{"id":"275","span":{"begin":705,"end":712},"obj":"Species"},{"id":"276","span":{"begin":714,"end":721},"obj":"Species"},{"id":"277","span":{"begin":242,"end":244},"obj":"Chemical"},{"id":"278","span":{"begin":502,"end":513},"obj":"Chemical"},{"id":"279","span":{"begin":110,"end":118},"obj":"Disease"},{"id":"280","span":{"begin":443,"end":455},"obj":"Disease"},{"id":"281","span":{"begin":651,"end":656},"obj":"Disease"},{"id":"282","span":{"begin":677,"end":696},"obj":"Disease"},{"id":"283","span":{"begin":725,"end":751},"obj":"Disease"},{"id":"284","span":{"begin":768,"end":773},"obj":"Disease"},{"id":"285","span":{"begin":819,"end":839},"obj":"Disease"},{"id":"287","span":{"begin":1114,"end":1129},"obj":"Disease"},{"id":"298","span":{"begin":1493,"end":1501},"obj":"Species"},{"id":"299","span":{"begin":1596,"end":1603},"obj":"Species"},{"id":"300","span":{"begin":1919,"end":1927},"obj":"Species"},{"id":"301","span":{"begin":1607,"end":1612},"obj":"Chemical"},{"id":"302","span":{"begin":1631,"end":1646},"obj":"Chemical"},{"id":"303","span":{"begin":1803,"end":1811},"obj":"Chemical"},{"id":"304","span":{"begin":2560,"end":2569},"obj":"Chemical"},{"id":"305","span":{"begin":2590,"end":2598},"obj":"Chemical"},{"id":"306","span":{"begin":1484,"end":1492},"obj":"Disease"},{"id":"307","span":{"begin":1983,"end":1994},"obj":"Disease"}],"attributes":[{"id":"A270","pred":"tao:has_database_id","subj":"270","obj":"Tax:9606"},{"id":"A271","pred":"tao:has_database_id","subj":"271","obj":"Tax:9606"},{"id":"A272","pred":"tao:has_database_id","subj":"272","obj":"Tax:9606"},{"id":"A273","pred":"tao:has_database_id","subj":"273","obj":"Tax:9606"},{"id":"A274","pred":"tao:has_database_id","subj":"274","obj":"Tax:9606"},{"id":"A275","pred":"tao:has_database_id","subj":"275","obj":"Tax:9606"},{"id":"A276","pred":"tao:has_database_id","subj":"276","obj":"Tax:9606"},{"id":"A278","pred":"tao:has_database_id","subj":"278","obj":"MESH:D000450"},{"id":"A279","pred":"tao:has_database_id","subj":"279","obj":"MESH:C000657245"},{"id":"A280","pred":"tao:has_database_id","subj":"280","obj":"MESH:D006973"},{"id":"A281","pred":"tao:has_database_id","subj":"281","obj":"MESH:D003643"},{"id":"A282","pred":"tao:has_database_id","subj":"282","obj":"MESH:D012131"},{"id":"A283","pred":"tao:has_database_id","subj":"283","obj":"MESH:D012131"},{"id":"A284","pred":"tao:has_database_id","subj":"284","obj":"MESH:D009369"},{"id":"A285","pred":"tao:has_database_id","subj":"285","obj":"MESH:D008175"},{"id":"A287","pred":"tao:has_database_id","subj":"287","obj":"MESH:D055370"},{"id":"A298","pred":"tao:has_database_id","subj":"298","obj":"Tax:9606"},{"id":"A299","pred":"tao:has_database_id","subj":"299","obj":"Tax:9606"},{"id":"A300","pred":"tao:has_database_id","subj":"300","obj":"Tax:9606"},{"id":"A301","pred":"tao:has_database_id","subj":"301","obj":"MESH:D008670"},{"id":"A302","pred":"tao:has_database_id","subj":"302","obj":"MESH:C005460"},{"id":"A303","pred":"tao:has_database_id","subj":"303","obj":"MESH:D010232"},{"id":"A305","pred":"tao:has_database_id","subj":"305","obj":"MESH:D010232"},{"id":"A306","pred":"tao:has_database_id","subj":"306","obj":"MESH:C000657245"},{"id":"A307","pred":"tao:has_database_id","subj":"307","obj":"MESH:D003681"}],"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":"Autopsy, clinical background and tissue preparation\nIn total we investigated six postmortem lung samples from Covid-19 patients (Menter et al., 2020). A tissue micro-array paraffin block with samples of all six patients and the corresponding HE stain is shown in Figure 1a. Information about age, gender, hospitalization, clinical, radiological and histological characteristics of all patients are shown in Table 2. All patients suffered from hypertension and were treated with RAAS (renin-angiotensin-aldosterone-system) interacting drugs. Heterogeneous ground glass and consolidation were observed in all patients clinical CT scans and the cause of death was also related to respiratory failure in each patient (patient IV cardio-respiratory failure). Additionally, tumor-free lung samples from partial resections of pulmonary carcinomas were analyzed as a reference.\nTable 2. Sample and medical information.\nAge and gender, clinical presentation with hospitalization and treatment; NIV: non-invasive ventilation, I: immunosuppression, S: smoker, GGO: ground-glass opacification, C: consolidation, DAD: diffuse alveolar damage.\nSample no. Age group, gender Hospitalization, clinical, radiological, and histological characteristics\nI 60–70, F 5-10d, GGO, DAD\nII 80–90, M 5-10d, C, I, DAD\nIII 90–100, M 1-4d, GGO, C, DAD\nIV 70–80, M 1-4d, NIV, S, GGO, C, DAD\nV 60–70, M 5-10d, NIV, S, GGO, C, DAD\nVI 70–80, M 1-4d, S, GGO, C, DAD\nCTRL 20–30, M - From each of the six Covid-19 patients, two tissue samples with edge lengths of about 4 mm each were analyzed. To one sample of each patient, a metal containing stain (uranium acetate, UA) was applied, the other samples remained unstained. Separated for their stain, six tissue samples were dehydrated and embedded in the same multi-sample paraffin block. The size of the postmortem tissue samples made available for the study varied between the different patients (I-VI), with maximum cross-section of about 4 mm after dehydration. From all six samples, biopsy punches were taken by either a 8 mm or a 3.5 mm punch, depending on the individual size. The punches were then transferred onto a holder for the parallel-beam local tomography acquisition, followed by a further reduction in size (after measurement of the entire sample) to a 1 mm biopsy punch, for further tomographic recordings. A sketch of the sample preparation is shown in Figure 1b. The control lung sample was first mounted in an Eppendorf tube for parallel beam acquisitions, and a 1 mm biopsy punch was then transferred into a polyimide tube similar to the paraffin-embedded ones, but scanned in fixative buffer solution."}