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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
3 38-46 Species denotes Patients Tax:9606
4 0-20 Disease denotes Microvascular Injury MESH:D017566
5 52-60 Disease denotes Covid-19 MESH:C000657245
24 193-201 Species denotes patients Tax:9606
25 547-555 Species denotes patients Tax:9606
26 731-739 Species denotes patients Tax:9606
27 767-775 Species denotes patients Tax:9606
28 851-859 Species denotes patients Tax:9606
29 911-919 Species denotes patients Tax:9606
30 998-1006 Species denotes patients Tax:9606
31 1017-1025 Species denotes patients Tax:9606
32 1162-1170 Species denotes patients Tax:9606
33 207-231 Disease denotes coronavirus disease 2019 MESH:C000657245
34 233-241 Disease denotes Covid-19 MESH:C000657245
35 1059-1067 Disease denotes diabetes MESH:D003920
36 1072-1084 Disease denotes hypertension MESH:D006973
37 1120-1124 Disease denotes died MESH:D003643
38 1211-1219 Disease denotes delirium MESH:D003693
39 1232-1252 Disease denotes respiratory symptoms MESH:D012818
40 1260-1295 Disease denotes acute respiratory distress syndrome MESH:D012128
41 1303-1321 Disease denotes pulmonary embolism MESH:D011655
57 2484-2487 Gene denotes CD8 Gene:925
58 1976-1986 Gene denotes fibrinogen Gene:2244
59 1532-1542 Gene denotes fibrinogen Gene:2244
60 1470-1478 Species denotes patients Tax:9606
61 1818-1826 Species denotes patients Tax:9606
62 1889-1897 Species denotes patients Tax:9606
63 2411-2419 Species denotes patients Tax:9606
64 2573-2581 Species denotes patients Tax:9606
65 2741-2749 Species denotes patients Tax:9606
66 2435-2437 Chemical denotes 1H
67 1507-1527 Disease denotes microvascular injury MESH:D017566
68 2118-2134 Disease denotes microhemorrhages
69 2191-2203 Disease denotes inflammation MESH:D007249
70 2371-2394 Disease denotes hypertrophic astrocytes MESH:D001254
71 2613-2628 Disease denotes vascular injury MESH:D057772
74 3022-3069 Species denotes Severe acute respiratory syndrome coronavirus 2 Tax:2697049
75 3315-3320 Disease denotes death MESH:D003643
84 3424-3432 Species denotes patients Tax:9606
85 3863-3871 Species denotes patients Tax:9606
86 3441-3445 Disease denotes died MESH:D003643
87 3451-3459 Disease denotes Covid-19 MESH:C000657245
88 3472-3492 Disease denotes microvascular injury MESH:D017566
89 3692-3707 Disease denotes viral infection MESH:D001102
90 3877-3885 Disease denotes Covid-19 MESH:C000657245
91 4017-4025 Disease denotes Covid-19 MESH:C000657245
98 4222-4234 Gene denotes USA-WA1/2020
99 4202-4212 Species denotes SARS-CoV-2 Tax:2697049
100 4118-4140 Disease denotes Neurological Disorders MESH:D009422
101 4145-4151 Disease denotes Stroke MESH:D020521
102 4385-4392 Disease denotes Allergy MESH:D004342
103 4397-4416 Disease denotes Infectious Diseases MESH:D003141
120 5045-5053 Species denotes Patients Tax:9606
121 5007-5027 Disease denotes Microvascular Injury MESH:D017566
122 5058-5062 Disease denotes Died MESH:D003643
123 5068-5076 Disease denotes Covid-19 MESH:C000657245
146 5327-5337 Gene denotes fibrinogen Gene:2244
147 5454-5464 Gene denotes fibrinogen Gene:2244
148 6396-6400 Gene denotes CD68 Gene:968
149 6648-6651 Gene denotes CD8 Gene:925
150 6714-6718 Gene denotes IBA1 Gene:199
151 6767-6771 Gene denotes CD68 Gene:968
152 6143-6153 Gene denotes fibrinogen Gene:2244
153 5788-5798 Gene denotes fibrinogen Gene:2244
154 5678-5688 Gene denotes fibrinogen Gene:2244
155 5295-5305 Gene denotes fibrinogen Gene:2244
156 6078-6085 Species denotes Patient Tax:9606
157 6182-6189 Species denotes Patient Tax:9606
158 6257-6264 Species denotes Patient Tax:9606
159 6442-6449 Species denotes Patient Tax:9606
160 6519-6526 Species denotes Patient Tax:9606
161 6591-6598 Species denotes Patient Tax:9606
162 6674-6681 Species denotes Patient Tax:9606
163 6740-6747 Species denotes Patient Tax:9606
164 6829-6836 Species denotes Patient Tax:9606
165 6935-6942 Species denotes Patient Tax:9606
166 6949-6965 Chemical denotes Diaminobenzidine
167 6482-6494 Disease denotes astrocytosis MESH:D005911

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 1072-1084 Phenotype denotes hypertension http://purl.obolibrary.org/obo/HP_0000822
T2 1211-1219 Phenotype denotes delirium http://purl.obolibrary.org/obo/HP_0031258
T3 1266-1286 Phenotype denotes respiratory distress http://purl.obolibrary.org/obo/HP_0002098
T4 1303-1321 Phenotype denotes pulmonary embolism http://purl.obolibrary.org/obo/HP_0002204
T5 2504-2523 Phenotype denotes perivascular spaces http://purl.obolibrary.org/obo/HP_0012520
T6 4145-4151 Phenotype denotes Stroke http://purl.obolibrary.org/obo/HP_0001297
T7 4385-4392 Phenotype denotes Allergy http://purl.obolibrary.org/obo/HP_0012393
T8 6482-6494 Phenotype denotes astrocytosis http://purl.obolibrary.org/obo/HP_0002446

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-60 Sentence denotes Microvascular Injury in the Brains of Patients with Covid-19
T2 62-76 Sentence denotes To the Editor:
T3 77-686 Sentence denotes We conducted postmortem high-resolution magnetic resonance imaging (magnetic resonance microscopy) of the brains of patients with coronavirus disease 2019 (Covid-19) (median age, 50 years) and histopathological examination that focused on microvascular changes in the olfactory bulb and brain stem. (See the Materials and Methods section in the Supplementary Appendix, available with the full text of this letter at NEJM.org.) Images were obtained from the brains of 13 patients with the use of an 11.7-Tesla scanner at a resolution of 25 μm for the olfactory bulb and at a resolution of 100 μm for the brain.
T4 687-740 Sentence denotes Abnormalities were seen in the brains of 10 patients.
T5 741-921 Sentence denotes We examined the brains of patients that showed abnormalities by means of multiplex fluorescence imaging (in 5 patients) and by means of chromogenic immunostaining (in 10 patients).
T6 922-1007 Sentence denotes We performed conventional histopathological examination of the brains of 18 patients.
T7 1008-1151 Sentence denotes Fourteen patients had chronic illnesses, including diabetes and hypertension, and 11 had been found dead or had died suddenly and unexpectedly.
T8 1152-1401 Sentence denotes Of the 16 patients with available medical histories, 1 had delirium, 5 had mild respiratory symptoms, 4 had acute respiratory distress syndrome, 2 had pulmonary embolism, and the symptoms were not known in 3 (Table S1 in the Supplementary Appendix).
T9 1402-1551 Sentence denotes Magnetic resonance microscopy showed punctate hyperintensities in 9 patients, which represented areas of microvascular injury and fibrinogen leakage.
T10 1552-1694 Sentence denotes These features were observed on corresponding histopathological examination performed with the use of fluorescence imaging (Figure 1A and 1B).
T11 1695-1846 Sentence denotes These areas showed thinning of the basal lamina of the endothelial cells, as determined by collagen IV immunostaining in 5 patients (Fig. 1B1 and 1B2).
T12 1847-2065 Sentence denotes Punctate hypointensities on imaging in 10 patients corresponded to congested blood vessels (Figure 1C) with surrounding areas of fibrinogen leakage (Figure 1D and Fig. S1) and relatively intact vasculature (Figure 1E).
T13 2066-2159 Sentence denotes Areas of linear hypointensities were interpreted as microhemorrhages (Figure 1F and Fig. S2).
T14 2160-3021 Sentence denotes There was minimal perivascular inflammation in the specimens examined, but there was no vascular occlusion, as previously described in the Journal.1 Perivascular-activated microglia, macrophage infiltrates, and hypertrophic astrocytes were seen in 13 patients (Figure 1G and 1H, Fig. S3, and Table S4).2 There were CD3+ and CD8+ T cells in the perivascular spaces and in lumens adjacent to endothelial cells in 8 patients, which may have contributed to vascular injury (Figure 1I and 1J), as suggested in a previous report.3 Activated microglia were found adjacent to neurons in 5 patients, which is suggestive of neuronophagia in the olfactory bulb, substantia nigra, dorsal motor nucleus of the vagal nerve, and the pre-Bötzinger complex in the medulla, which is involved in the generation of spontaneous rhythmic breathing (Figure 1K through 1N and Fig. S3).
T15 3022-3257 Sentence denotes Severe acute respiratory syndrome coronavirus 2 was not detected by means of polymerase chain reaction with multiple primer sets, RNA sequencing of several areas of the brain, or RNA in situ hybridization and immunostaining (Table S5).
T16 3258-3396 Sentence denotes It is possible that the virus was cleared by the time of death or that viral copy numbers were below the level of detection by our assays.
T17 3397-3708 Sentence denotes In a convenience sample of patients who had died from Covid-19, multifocal microvascular injury was observed in the brain and olfactory bulbs by means of magnetic resonance microscopy, histopathological evaluation, and immunohistochemical analysis of corresponding sections, without evidence of viral infection.
T18 3709-3886 Sentence denotes These findings may inform the interpretation of changes observed on magnetic resonance imaging of punctate hyperintensities and linear hypointensities in patients with Covid-19.
T19 3887-4026 Sentence denotes Because of the limited clinical information that was available, no conclusions can be drawn in relation to neurologic features of Covid-19.
T20 4028-4152 Sentence denotes Supported by intramural funds (K23NS109284 [to Dr. Hefti]) from the National Institute of Neurological Disorders and Stroke.
T21 4153-4454 Sentence denotes The reagent used in this study (Genomic RNA from SARS-CoV-2, Isolate USA-WA1/2020, NR-52285) was deposited by the Centers for Disease Control and Prevention and obtained through BEI Resources Repository of the National Institute of Allergy and Infectious Diseases of the National Institutes of Health.
T22 4455-4556 Sentence denotes Disclosure forms provided by the authors are available with the full text of this letter at NEJM.org.
T23 4558-4705 Sentence denotes The opinions expressed here are those of the authors and are not necessarily representative of those of the Uniformed Services University, the U.S.
T24 4706-4740 Sentence denotes Department of Defense, or the U.S.
T25 4741-4794 Sentence denotes Army, Navy, or Air Force or any other federal agency.
T26 4795-4855 Sentence denotes This letter was published on December 30, 2020, at NEJM.org.
T27 4857-4879 Sentence denotes Supplementary Appendix
T28 4880-4916 Sentence denotes Click here for additional data file.
T29 4918-4934 Sentence denotes Disclosure Forms
T30 4935-4971 Sentence denotes Click here for additional data file.
T31 4973-5077 Sentence denotes Figure 1 Pathological Studies of Microvascular Injury in the Brains of Patients Who Died from Covid-19.
T32 5078-5185 Sentence denotes Panel A (magnetic resonance microscopy of the olfactory bulb) shows an area of hyperintense signal (arrow).
T33 5186-5419 Sentence denotes Panel B shows the corresponding area on multiplex immunofluorescence imaging, which revealed a focal area of fibrinogen leakage (in the box, fibrinogen is shown in green, collagen IV is shown in yellow, and nuclei are shown in blue).
T34 5420-5576 Sentence denotes Panel B1 shows diffuse leakage of fibrinogen in the parenchyma (an enlarged view showing marked blood vessel staining for collagen IV is shown in Panel B2).
T35 5577-5717 Sentence denotes Panel B2 (collagen IV immunostaining) shows intact (arrowhead) and thinned (arrow) basal lamina with fibrinogen leakage into the parenchyma.
T36 5718-5930 Sentence denotes Panel C shows magnetic resonance microscopy of the pons, and Panel D (fibrinogen staining) shows areas of increased signal intensity corresponding to the vascular leakage visible on magnetic resonance microscopy.
T37 5931-6027 Sentence denotes The arrows and the area within the dashed lines in Panels C and D indicate the vascular leakage.
T38 6028-6090 Sentence denotes Panels A through E represent imaging performed in Patient IA1.
T39 6091-6194 Sentence denotes Panel E (collagen IV immunostaining) shows areas of fibrinogen leakage in blood vessels in Patient IA1.
T40 6195-6269 Sentence denotes Panel F shows magnetic resonance microscopy of the medulla in Patient IA3.
T41 6270-6381 Sentence denotes The yellow arrows indicate linear hypointense signals, and the red arrows indicate linear hyperintense signals.
T42 6382-6454 Sentence denotes Panel G shows CD68+ perivascular macrophages in the pons in Patient NY6.
T43 6455-6531 Sentence denotes Panel H shows perivascular astrocytosis in the basal ganglia in Patient NY5.
T44 6532-6603 Sentence denotes Panel I shows perivascular CD3+ cells in the cerebellum in Patient IA1.
T45 6604-6686 Sentence denotes Panel J shows intraluminal and perivascular CD8+ cells in the pons in Patient NY6.
T46 6687-6752 Sentence denotes Panel K shows perineuronal IBA1 cells in the pons in Patient NY6.
T47 6753-6841 Sentence denotes Panel L shows CD68+ cells in the dorsal motor nucleus of the vagus nerve in Patient IA1.
T48 6842-7007 Sentence denotes Panel M shows a solitary nucleus in the medulla and Panel N shows a pre-Bötzinger complex in Patient IA1. (Diaminobenzidine staining was used in Panels G through N.)