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PMC:7558914 / 8438-14868 JSONTXT

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LitCovid_Glycan-Motif-Structure

Id Subject Object Predicate Lexical cue
T5 5156-5163 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T6 5156-5163 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T7 5203-5210 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T8 5203-5210 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T9 5259-5266 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T10 5259-5266 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T11 5380-5387 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T12 5380-5387 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T13 5620-5627 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T14 5620-5627 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T15 5786-5793 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T16 5786-5793 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T17 5870-5877 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T18 5870-5877 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin
T19 6033-6040 https://glytoucan.org/Structures/Glycans/G00021MO denotes heparin
T20 6033-6040 https://glytoucan.org/Structures/Glycans/G54161DR denotes heparin

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
156 177-185 Species denotes patients Tax:9606
157 54-63 Disease denotes infection MESH:D007239
158 136-144 Disease denotes COVID-19 MESH:C000657245
159 202-221 Disease denotes respiratory illness MESH:D012140
187 330-338 Species denotes patients Tax:9606
188 406-414 Species denotes patients Tax:9606
189 458-466 Species denotes Patients Tax:9606
190 1402-1410 Species denotes patients Tax:9606
191 1512-1519 Species denotes patient Tax:9606
192 507-525 Chemical denotes hydroxychloroquine MESH:D006886
193 529-548 Chemical denotes lopinavir/ritonavir MESH:C558899
194 568-586 Chemical denotes hydroxychloroquine MESH:D006886
195 592-604 Chemical denotes azithromycin MESH:D017963
196 608-627 Chemical denotes lopinavir/ritonavir MESH:C558899
197 652-670 Chemical denotes hydroxychloroquine MESH:D006886
198 672-684 Chemical denotes azithromycin MESH:D017963
199 690-709 Chemical denotes lopinavir/ritonavir MESH:C558899
200 711-729 Chemical denotes Hydroxychloroquine MESH:D006886
201 776-795 Chemical denotes lopinavir/ritonavir MESH:C558899
202 940-952 Chemical denotes Azithromycin MESH:D017963
203 1062-1080 Chemical denotes hydroxychloroquine MESH:D006886
204 1095-1107 Chemical denotes azithromycin MESH:D017963
205 1129-1147 Chemical denotes hydroxychloroquine MESH:D006886
206 1203-1222 Chemical denotes lopinavir/ritonavir MESH:C558899
207 1257-1269 Chemical denotes azithromycin MESH:D017963
208 1289-1300 Chemical denotes Chloroquine MESH:D002738
209 1361-1379 Chemical denotes hydroxychloroquine MESH:D006886
210 1440-1459 Chemical denotes lopinavir/ritonavir MESH:C558899
211 1494-1504 Chemical denotes remdesivir MESH:C000606551
212 355-374 Disease denotes respiratory illness MESH:D012140
213 447-456 Disease denotes pneumonia MESH:D011014
240 1666-1674 Species denotes patients Tax:9606
241 2773-2781 Species denotes patients Tax:9606
242 2881-2889 Species denotes patients Tax:9606
243 1773-1791 Chemical denotes hydroxychloroquine MESH:D006886
244 1883-1901 Chemical denotes hydroxychloroquine MESH:D006886
245 1917-1929 Chemical denotes azithromycin MESH:D017963
246 1974-1992 Chemical denotes hydroxychloroquine MESH:D006886
247 1998-2010 Chemical denotes azithromycin MESH:D017963
248 2014-2033 Chemical denotes lopinavir/ritonavir MESH:C558899
249 2213-2231 Chemical denotes hydroxychloroquine MESH:D006886
250 2237-2249 Chemical denotes azithromycin MESH:D017963
251 2273-2291 Chemical denotes hydroxychloroquine MESH:D006886
252 2297-2316 Chemical denotes lopinavir/ritonavir MESH:C558899
253 2403-2421 Chemical denotes hydroxychloroquine MESH:D006886
254 2452-2471 Chemical denotes lopinavir/ritonavir MESH:C558899
255 2558-2576 Chemical denotes hydroxychloroquine MESH:D006886
256 2581-2600 Chemical denotes lopinavir/ritonavir MESH:C558899
257 2639-2657 Chemical denotes hydroxychloroquine MESH:D006886
258 2673-2685 Chemical denotes azithromycin MESH:D017963
259 2690-2709 Chemical denotes lopinavir/ritonavir MESH:C558899
260 1643-1662 Disease denotes respiratory illness MESH:D012140
261 2145-2154 Disease denotes pneumonia MESH:D011014
262 2392-2401 Disease denotes pneumonia MESH:D011014
263 2794-2803 Disease denotes pneumonia MESH:D011014
264 2895-2904 Disease denotes pneumonia MESH:D011014
265 2963-2971 Disease denotes COVID-19 MESH:C000657245
272 3308-3319 Chemical denotes Amoxicillin MESH:D000658
273 3325-3340 Chemical denotes clavulanic acid MESH:D019818
274 3344-3355 Chemical denotes ceftriaxone MESH:D002443
275 3095-3104 Disease denotes infection MESH:D007239
276 3220-3229 Disease denotes pneumonia MESH:D011014
277 3287-3306 Disease denotes bacterial infection MESH:D001424
297 3519-3532 Gene denotes interleukin-6 Gene:3569
298 3534-3544 Gene denotes fibrinogen Gene:2244
299 3559-3577 Gene denotes C-reactive protein Gene:1401
300 4493-4500 Species denotes patient Tax:9606
301 4040-4053 Chemical denotes dexamethasone MESH:D003907
302 4055-4073 Chemical denotes methylprednisolone MESH:D008775
303 4078-4088 Chemical denotes prednisone MESH:D011241
304 4090-4103 Chemical denotes Dexamethasone MESH:D003907
305 4216-4234 Chemical denotes Methylprednisolone MESH:D008775
306 4375-4385 Chemical denotes prednisone MESH:D011241
307 4523-4534 Chemical denotes Tocilizumab MESH:C502936
308 4837-4846 Chemical denotes sarilumab MESH:C000592401
309 4848-4859 Chemical denotes baricitinib MESH:C000596027
310 4861-4871 Chemical denotes colchicine MESH:D003078
311 4873-4886 Chemical denotes ciclosporin A MESH:D016572
312 4888-4897 Chemical denotes sirolimus MESH:D020123
313 4899-4909 Chemical denotes tacrolimus MESH:D016559
314 4915-4924 Chemical denotes vitamin D MESH:D014807
315 3445-3449 Disease denotes ARDS MESH:D012128
330 5156-5163 Chemical denotes heparin MESH:D006493
331 5203-5210 Chemical denotes heparin MESH:D006493
332 5259-5266 Chemical denotes heparin MESH:D006493
333 5380-5387 Chemical denotes heparin MESH:D006493
334 5620-5627 Chemical denotes heparin MESH:D006493
335 5786-5793 Chemical denotes heparin MESH:D006493
336 5870-5877 Chemical denotes heparin MESH:D006493
337 6033-6040 Chemical denotes heparin MESH:D006493
338 5306-5314 Disease denotes COVID-19 MESH:C000657245
339 5430-5440 Disease denotes thrombosis MESH:D013927
340 5449-5457 Disease denotes COVID-19 MESH:C000657245
341 5511-5533 Disease denotes venous thromboembolism MESH:D054556
342 5537-5566 Disease denotes acute ischemic artery disease MESH:D014715
343 5819-5841 Disease denotes venous thromboembolism MESH:D054556
345 6257-6272 Disease denotes QT prolongation MESH:D008133

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T14 202-221 Phenotype denotes respiratory illness http://purl.obolibrary.org/obo/HP_0002086
T15 355-374 Phenotype denotes respiratory illness http://purl.obolibrary.org/obo/HP_0002086
T16 447-456 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T17 1643-1662 Phenotype denotes respiratory illness http://purl.obolibrary.org/obo/HP_0002086
T18 2145-2154 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T19 2392-2401 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T20 2794-2803 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T21 2895-2904 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T22 3220-3229 Phenotype denotes pneumonia http://purl.obolibrary.org/obo/HP_0002090
T23 3464-3489 Phenotype denotes cytokine release syndrome http://purl.obolibrary.org/obo/HP_0033041
T24 5475-5500 Phenotype denotes cytokine release syndrome http://purl.obolibrary.org/obo/HP_0033041
T25 5518-5533 Phenotype denotes thromboembolism http://purl.obolibrary.org/obo/HP_0001907
T26 5826-5841 Phenotype denotes thromboembolism http://purl.obolibrary.org/obo/HP_0001907

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T52 0-2 Sentence denotes 3.
T53 3-10 Sentence denotes Results
T54 11-289 Sentence denotes Symptomatic treatment, recommendations for infection prevention and control, and recommendations for early identification of COVID-19 alarm symptoms were adopted for patients with mild upper respiratory illness without clinical risk factors and confirmed cases without symptoms.
T55 290-457 Sentence denotes Antiviral treatment was recommended for patients with mild upper respiratory illness with clinical risk factors and patients with mild, moderate, and severe pneumonia.
T56 458-710 Sentence denotes Patients could be treated with monotherapy using hydroxychloroquine or lopinavir/ritonavir; dual therapy with hydroxychloroquine plus azithromycin or lopinavir/ritonavir; or triple therapy with hydroxychloroquine, azithromycin, and lopinavir/ritonavir.
T57 711-939 Sentence denotes Hydroxychloroquine could be used in four different regimens, and lopinavir/ritonavir could be used in two different regimens, with varied dosages and duration of treatment—either a short (5-day) regimen or long (10-day) regimen.
T58 940-1014 Sentence denotes Azithromycin was recommended at the same dosage and duration of treatment.
T59 1015-1108 Sentence denotes Protocols included the combination of all four hydroxychloroquine regimens with azithromycin.
T60 1109-1288 Sentence denotes Regimens 1 and 3 of hydroxychloroquine were combined in dual therapy with the two regimens of lopinavir/ritonavir, which in turn were combined with azithromycin in triple therapy.
T61 1289-1398 Sentence denotes Chloroquine 500 mg twice per day was recommended as an alternative when hydroxychloroquine was not available.
T62 1399-1553 Sentence denotes In patients with three antiviral agents, lopinavir/ritonavir could be replaced with once-daily remdesivir if the patient was enrolled in a clinical trial.
T63 1554-1624 Sentence denotes The dosage and durations of antiviral treatments are shown in Table 1.
T64 1625-1742 Sentence denotes For treating mild respiratory illness in patients with clinical risk factors, up to six antiviral options were found.
T65 1743-1942 Sentence denotes Monotherapy with regimen 1 of hydroxychloroquine was the most frequent antiviral treatment recommended (5/15 protocols, 33.3%), followed by hydroxychloroquine regimen 1 plus azithromycin (3/15, 20%).
T66 1943-2079 Sentence denotes Dual antiviral treatment using hydroxychloroquine with azithromycin or lopinavir/ritonavir in combination was found in 40% of protocols.
T67 2080-2126 Sentence denotes No treatment was recommended in two protocols.
T68 2127-2317 Sentence denotes In regard to mild pneumonia, 14 protocols recommended dual therapy: seven recommended hydroxychloroquine plus azithromycin, and seven recommended hydroxychloroquine plus lopinavir/ritonavir.
T69 2318-2378 Sentence denotes Only one protocol did not recommend any antiviral treatment.
T70 2379-2531 Sentence denotes For moderate pneumonia, hydroxychloroquine regimen 1 in combination with lopinavir/ritonavir regimen 2 was the most recommended treatment (5/15, 33.3%).
T71 2532-2804 Sentence denotes Different combinations of hydroxychloroquine and lopinavir/ritonavir (7/15, 46.7%) and triple therapy with hydroxychloroquine regimen 3, and azithromycin and lopinavir/ritonavir regimen 2 (6/15, 40%) were the most recommended treatments for patients with severe pneumonia.
T72 2805-2905 Sentence denotes Most protocols showed a preference for dual or triple antiviral therapy for patients with pneumonia.
T73 2906-2998 Sentence denotes Further details about recommended antiviral treatment of COVID-19 are summarized in Table 2.
T74 2999-3172 Sentence denotes All protocols recommended initiating empirical antibacterial treatment when secondary bacterial infection was suspected, according to local antibacterial therapy guidelines.
T75 3173-3307 Sentence denotes Empirical antibiotics were also indicated when pneumonia was diagnosed in seven protocols regardless of suspected bacterial infection.
T76 3308-3402 Sentence denotes Amoxicillin plus clavulanic acid or ceftriaxone were the main antibiotics recommended for use.
T77 3403-3589 Sentence denotes All protocol considered the management of ARDS with signs of cytokine release syndrome, which included elevation of interleukin-6, fibrinogen, D-dimer, and C-reactive protein levels [9].
T78 3590-3743 Sentence denotes The therapies (corticosteroids, anticytokine or immunomodulatory agents, and immunoglobulin therapy) were recommended once these syndromes were observed.
T79 3744-3843 Sentence denotes The choice of which therapy to use was made by physicians according to their own clinical judgment.
T80 3844-3977 Sentence denotes Corticosteroids were widely included in all protocols; indeed, only 2 out of 15 hospitals did not include any corticosteroid regimen.
T81 3978-4089 Sentence denotes There was a total of five corticosteroid regimens, which used dexamethasone, methylprednisolone, or prednisone.
T82 4090-4167 Sentence denotes Dexamethasone was recommended in eight protocols with two different regimens:
T83 4168-4215 Sentence denotes 20 mg (5/8, 62.5%) or 40 mg (3/8, 37.5%) daily.
T84 4216-4290 Sentence denotes Methylprednisolone was included in 13 protocols with 2 different regimens:
T85 4291-4347 Sentence denotes 125–250 mg (8/13, 61.5%) or 1 mg/kg (5/13, 38.5%) daily.
T86 4348-4423 Sentence denotes Only one protocol included prednisone with a single regimen of 40 mg daily.
T87 4424-4522 Sentence denotes The duration of treatment varied from 3 to 10 days, depending on the patient’s clinical condition.
T88 4523-4630 Sentence denotes Tocilizumab was recommended in all protocols with the same dosage (400 or 600 mg) according to body weight.
T89 4631-4700 Sentence denotes Anakinra was included in seven protocols with six different regimens.
T90 4701-4770 Sentence denotes Immunoglobulins were included as possible therapy in three protocols.
T91 4771-4955 Sentence denotes In six protocols, other optional therapies were included, such as sarilumab, baricitinib, colchicine, ciclosporin A, sirolimus, tacrolimus, and vitamin D, according to clinical trials.
T92 4956-5086 Sentence denotes Dosage and durations of corticosteroids, anticytokine or immunomodulatory agents, and immunoglobulin therapy are shown in Table 3.
T93 5087-5290 Sentence denotes All protocols included anticoagulant treatment (low-molecular-weight heparin as the first option and unfractionated heparin as an alternative) and recommended prophylactic heparin during hospitalization.
T94 5291-5592 Sentence denotes In 8 of the 15 COVID-19 protocols (53.3%), the dose of prophylactic low-molecular-weight heparin was increased if there was a high risk of thrombosis (severe COVID-19 with evidence of cytokine release syndrome, previous venous thromboembolism or acute ischemic artery disease, or D-dimer >3000 ng/mL).
T95 5593-5750 Sentence denotes In five protocols (33.3%), heparin was increased to therapeutic doses if the condition was critical or if there was a progressive increase in D-dimer levels.
T96 5751-5842 Sentence denotes All protocols included therapeutic heparin if there was evidence of venous thromboembolism.
T97 5843-6017 Sentence denotes At discharge, prophylactic heparin was recommended if D-dimer >1500-3000 ng/dL for 7 days or during the time of the expected severe immobilization in seven protocols (46.6%).
T98 6018-6090 Sentence denotes Adjustments of heparin doses were indicated in the respective protocols.
T99 6091-6195 Sentence denotes Supportive care, hospital circuits, ward organization, and care planning were included in all protocols.
T100 6196-6430 Sentence denotes Drug side effects (including follow-up electrocardiogram for QT prolongation), interactions, nonrecommended treatment, or recommendation for other drugs were included in 11 protocols (73,3%), and discharge recommendations in 12 (80%).