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PMC:7784824 / 1891-7434 JSONTXT

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LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 62-71 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T2 1788-1797 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T3 2344-2363 Phenotype denotes shortness of breath http://purl.obolibrary.org/obo/HP_0002098
T4 2365-2370 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T5 2375-2386 Phenotype denotes muscle pain http://purl.obolibrary.org/obo/HP_0003326
T6 2472-2483 Phenotype denotes lymphopenia http://purl.obolibrary.org/obo/HP_0001888
T7 2661-2678 Phenotype denotes elevated D-dimers http://purl.obolibrary.org/obo/HP_0033106
T8 3393-3418 Phenotype denotes respiratory insufficiency http://purl.obolibrary.org/obo/HP_0002093
T9 3689-3694 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T10 3703-3714 Phenotype denotes muscle pain http://purl.obolibrary.org/obo/HP_0003326
T11 3716-3721 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T12 3723-3734 Phenotype denotes sore throat http://purl.obolibrary.org/obo/HP_0033050
T13 3736-3744 Phenotype denotes headache http://purl.obolibrary.org/obo/HP_0002315
T14 3749-3756 Phenotype denotes fatigue http://purl.obolibrary.org/obo/HP_0012378
T15 3794-3799 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T16 3967-3972 Phenotype denotes shock http://purl.obolibrary.org/obo/HP_0031273
T17 4002-4013 Phenotype denotes hypotension http://purl.obolibrary.org/obo/HP_0002615
T18 4034-4049 Phenotype denotes cardiac failure http://purl.obolibrary.org/obo/HP_0001635
T19 4122-4133 Phenotype denotes lymphopenia http://purl.obolibrary.org/obo/HP_0001888
T20 4313-4330 Phenotype denotes elevated D-dimers http://purl.obolibrary.org/obo/HP_0033106
T21 4453-4462 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
41 203-218 Species denotes new coronavirus Tax:2697049
42 294-309 Species denotes betacoronavirus Tax:694002
43 365-374 Species denotes 2019-nCOV Tax:2697049
44 439-486 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
45 488-498 Species denotes SARS-CoV-2 Tax:2697049
46 62-71 Disease denotes pneumonia MESH:D011014
47 341-363 Disease denotes novel coronavirus 2019 MESH:C000657245
52 1099-1109 Species denotes SARS-CoV-2 Tax:2697049
53 1752-1760 Species denotes patients Tax:9606
54 1589-1598 Disease denotes infection MESH:D007239
55 1779-1797 Disease denotes COVID-19 pneumonia MESH:C000657245
61 2026-2034 Species denotes patients Tax:9606
62 2186-2196 Species denotes SARS-CoV-2 Tax:2697049
63 1927-1935 Disease denotes COVID-19 MESH:C000657245
64 2100-2108 Disease denotes COVID-19 MESH:C000657245
65 2109-2118 Disease denotes infection MESH:D007239
80 2723-2741 Gene denotes C-reactive protein Gene:1401
81 3254-3259 Gene denotes Prima Gene:145270
82 3088-3098 Species denotes SARS-CoV-2 Tax:2697049
83 3321-3328 Species denotes patient Tax:9606
84 3420-3423 Chemical denotes pO2 MESH:C093415
85 2344-2363 Disease denotes shortness of breath MESH:D004417
86 2365-2370 Disease denotes fever MESH:D005334
87 2375-2386 Disease denotes muscle pain MESH:D063806
88 2421-2433 Disease denotes thrombopenia MESH:D013921
89 2472-2483 Disease denotes lymphopenia MESH:D008231
90 2882-2890 Disease denotes COVID-19 MESH:C000657245
91 2948-2956 Disease denotes COVID-19 MESH:C000657245
92 3393-3418 Disease denotes respiratory insufficiency MESH:D012131
93 3600-3608 Disease denotes COVID-19 MESH:C000657245
119 4371-4389 Gene denotes C-reactive protein Gene:1401
120 4773-4778 Gene denotes Prima Gene:145270
121 3635-3640 Species denotes child Tax:9606
122 3762-3766 Species denotes girl Tax:9606
123 3862-3870 Species denotes patients Tax:9606
124 4664-4674 Species denotes SARS-CoV-2 Tax:2697049
125 3689-3694 Disease denotes fever MESH:D005334
126 3703-3714 Disease denotes muscle pain MESH:D063806
127 3716-3721 Disease denotes cough MESH:D003371
128 3723-3734 Disease denotes sore throat MESH:D010608
129 3736-3744 Disease denotes headache MESH:D006261
130 3749-3756 Disease denotes fatigue MESH:D005221
131 3794-3799 Disease denotes fever MESH:D005334
132 3804-3824 Disease denotes respiratory symptoms MESH:D012818
133 3853-3861 Disease denotes COVID-19 MESH:C000657245
134 3967-3972 Disease denotes shock MESH:D012769
135 3977-3996 Disease denotes multi-organ failure MESH:D009102
136 4002-4013 Disease denotes hypotension MESH:D007022
137 4034-4049 Disease denotes cardiac failure MESH:D006333
138 4071-4083 Disease denotes thrombopenia MESH:D013921
139 4122-4133 Disease denotes lymphopenia MESH:D008231
140 4447-4462 Disease denotes viral pneumonia
141 4490-4525 Disease denotes decreased left ventricular function MESH:D018487
142 4841-4861 Disease denotes multisystem syndrome MESH:D012791
143 4889-4897 Disease denotes COVID-19 MESH:C000657245
145 5015-5023 Disease denotes COVID-19 MESH:C000657245

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T27 0-10 Sentence denotes Background
T28 11-113 Sentence denotes In December 2019, several cases of an unidentified pneumonia occurred in the province of Hubei, China.
T29 114-250 Sentence denotes With the use of next-generation sequencing, the Wuhan Institute of Virology identified a new coronavirus as the etiological agent [1,2].
T30 251-380 Sentence denotes This new virus, which belongs to the genus betacoronavirus, was initially acknowledged as novel coronavirus 2019 (2019-nCOV) [3].
T31 381-558 Sentence denotes On 11 February 2020, the virus was officially renamed the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the International Committee on Taxonomy of Viruses [4].
T32 559-714 Sentence denotes Since then the virus has rapidly spread and on the 18th of July 2020, over 14 million confirmed cases and 600 000 direct casualties have been reported [5].
T33 715-880 Sentence denotes So far, implementation of strict quarantine measures have contained further exponential spreading of the virus in Europe and have flattened the first epidemic curve.
T34 881-1051 Sentence denotes Considering the extent of the pandemic, its socio-economic impact, and the effect on healthcare systems worldwide, there is a high need to extend the diagnostic capacity.
T35 1052-1227 Sentence denotes So far, the gold standard for the diagnosis of SARS-CoV-2, implemented at the start of the outbreak, is real-time reverse transcriptase polymerase chain reaction (RT-PCR) [6].
T36 1228-1378 Sentence denotes In contrast with a high specificity up to 98.8% [7], RT-PCR suffers from a rather long turnaround time when performed in batch testing (2 to 6 hours).
T37 1379-1456 Sentence denotes Continuous PCR testing has a faster turnaround time (1 u) but a low capacity.
T38 1457-1619 Sentence denotes False negative results in both the very early as well as the late phase of the disease due to low virus shedding at these stages of infection are reported [8–10].
T39 1620-1725 Sentence denotes Studies have shown discrepant results between RT-PCR and chest computed tomography (CT) findings [11,12].
T40 1726-1896 Sentence denotes CT imaging findings in 30 patients with suspicion of COVID-19 pneumonia were shown to have a sensitivity of 97.2% compared to 83.3% of initial nasopharyngeal RT-PCR [13].
T41 1897-2008 Sentence denotes Establishing the diagnosis of COVID-19 is sometimes very challenging and does not only rely on molecular tests.
T42 2009-2171 Sentence denotes We report on two patients who presented at the emergency department with high suspicion of COVID-19 infection based on clinical findings and/or chest-CT findings.
T43 2172-2288 Sentence denotes Nevertheless, SARS-CoV-2 RT-PCR testing was repeatedly negative on repetitive nasopharyngeal, throat and anal swabs.
T44 2289-2400 Sentence denotes Case 1 was a 66 year old male experiencing symptoms of shortness of breath, fever and muscle pain since 8 days.
T45 2401-2450 Sentence denotes Lab findings showed thrombopenia (87,000/µL, ref.
T46 2451-2497 Sentence denotes 149,000–31,9000/µL), lymphopenia (930/µL, ref.
T47 2498-2554 Sentence denotes 1,133–3,105/µL), normal neutrophil count (2,980/µL, ref.
T48 2555-2603 Sentence denotes 1,573–6,100/µL) low eosinophil count (0/µL, ref.
T49 2604-2650 Sentence denotes 28–273/µL), normal basophil count (10/µL, ref.
T50 2651-2765 Sentence denotes 6–50/µL), elevated D-dimers (1,480 ng/mL, ref. <500 ng/mL) and elevated C-reactive protein (29 mg/L, ref <5 mg/L).
T51 2766-2965 Sentence denotes Chest CT on the day of admission showed bilateral ground glass opacities with a crazy paving pattern suspicious for COVID-19 (CT severity score of 10 or CO-RADS classification of 4: COVID-19 likely).
T52 2966-3173 Sentence denotes Repetitive nasopharyngeal swabs on day 8, 9, 12 and 13 as well as anal swabs on day 9 and 13 after symptom onset were all SARS-CoV-2 RT-PCR negative using the protocol described by Corman and colleagues [6].
T53 3174-3305 Sentence denotes Serology on day 13 after symptom onset indicated negative IgM but positive IgG (Prima Professional®, Point-Of-Care antibody Tests).
T54 3306-3437 Sentence denotes On day 13, the patient was admitted to the intensive care unit (ICU) because of type 1 respiratory insufficiency (pO2 60 mmHg, ref.
T55 3438-3470 Sentence denotes 83–108 mm Hg; pCO2 31 mmHg, ref.
T56 3471-3497 Sentence denotes 35–45 mm Hg; pH 7.46, ref.
T57 3498-3509 Sentence denotes 7.35–7.45).
T58 3510-3552 Sentence denotes He did not require mechanical ventilation.
T59 3553-3609 Sentence denotes Based on these findings, he was diagnosed with COVID-19.
T60 3610-3757 Sentence denotes Case 2 was a 14 year old child presenting at the emergency room with 3 days of fever > 39°C, muscle pain, cough, sore throat, headache and fatigue.
T61 3758-3887 Sentence denotes The girl’s father had suffered from fever and respiratory symptoms after contact with multiple COVID-19 patients 4 weeks earlier.
T62 3888-4050 Sentence denotes On day 4 after symptom onset, there was a clinical deterioration to refractory shock and multi-organ failure with hypotension and respiratory and cardiac failure.
T63 4051-4100 Sentence denotes Lab findings showed thrombopenia (89,000/µL, ref.
T64 4101-4147 Sentence denotes 154,000–452,000/µL), lymphopenia (162/µL, ref.
T65 4148-4204 Sentence denotes 1,500–6,500/µL), normal neutrophil count (7,564/µL, ref.
T66 4205-4256 Sentence denotes 2,500–8,000), normal eosinophil count (283/µL, ref.
T67 4257-4300 Sentence denotes 100–500/µL), low basophil count (0/µL, ref.
T68 4301-4415 Sentence denotes 10–100/µL), elevated D-dimers (4,420 ng/mL, ref. <500 ng/mL) and high C-reactive protein (308 mg/L, ref. <5 mg/L).
T69 4416-4463 Sentence denotes Chest CT did not show signs of viral pneumonia.
T70 4464-4526 Sentence denotes Echocardiography revealed decreased left ventricular function.
T71 4527-4597 Sentence denotes She responded well to supportive therapy and corticosteroid treatment.
T72 4598-4691 Sentence denotes Throat swabs on day 3 and 5 after symptom onset were negative for SARS-CoV-2 with RT-PCR [6].
T73 4692-4794 Sentence denotes Serology on day 8 after symptom onset was negative for IgM but positive for IgG (Prima Professional®).
T74 4795-4908 Sentence denotes She was diagnosed with pediatric inflammatory multisystem syndrome temporally associated with COVID-19 (PIMS-TS).
T75 4909-5024 Sentence denotes The case reports mentioned above point out the potential of serological assays to add to the diagnosis of COVID-19.
T76 5025-5130 Sentence denotes So far, a large number of serological assays have been developed in response to the diagnostic need [14].
T77 5131-5247 Sentence denotes Data on the validation and comparison of the performance of these assays are emerging but are still limited [15–18].
T78 5248-5424 Sentence denotes Since antibody production by the specific immune system is subject to delay, a lower diagnostic performance of serological assays in the early phase of the disease is expected.
T79 5425-5543 Sentence denotes So far, studies have revealed that antibodies could be detected as early as 3–6 days after symptom onset [9,10,19,20].