> top > docs > PMC:7276972 > annotations

PMC:7276972 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T1 29-35 UBERON:0001969 denotes plasma
T2 57-67 SP_7 denotes SARS CoV-2
T3 77-85 SP_7 denotes COVID-19
T4 206-212 UBERON:0001969 denotes plasma
T5 231-236 UBERON:0007023 denotes adult
T6 259-263 UBERON:0000104 denotes life
T7 276-284 SP_7 denotes COVID-19
T8 305-309 UBERON:0007221 denotes care
T9 377-381 UBERON:0000104 denotes life
T10 394-402 SP_7 denotes COVID-19
T11 563-579 PR:000000017 denotes interferon-gamma
T12 584-611 PR:000000134 denotes tumor necrosis factor-alpha
T13 689-697 SP_7 denotes COVID-19
T14 874-883 CL:0002211 denotes intensive
T15 884-888 UBERON:0007221;CL:0002486 denotes care
T16 889-893 CL:0002486 denotes unit
T17 929-933 UBERON:0000104 denotes life
T18 946-954 SP_7 denotes COVID-19
T19 1012-1022 SP_7 denotes SARS-CoV-2
T20 1273-1279 UBERON:0001969 denotes plasma
T21 1315-1329 CHEBI:53258;CHEBI:53258 denotes sodium citrate
T22 1377-1387 SP_7 denotes SARS-CoV-2
T23 1421-1429 SP_7 denotes COVID-19
T24 1862-1870 SP_7 denotes COVID-19
T25 2034-2040 UBERON:0001969 denotes plasma
T26 2066-2072 UBERON:0001969 denotes plasma
T27 2191-2195 CHEBI:37527;CHEBI:37527 denotes acid
T28 2241-2247 UBERON:0002113 denotes Kidney
T29 2307-2313 UBERON:0001969 denotes Plasma
T30 2358-2364 UBERON:0001969 denotes plasma
T31 2382-2394 GO:0050817 denotes coagulopathy
T32 2507-2517 GO:0005577 denotes fibrinogen
T33 2703-2711 SP_7 denotes COVID-19
T34 2927-2931 UBERON:0000104 denotes life
T35 2944-2952 SP_7 denotes COVID-19
T36 3121-3125 CHEBI:33290;CHEBI:33290 denotes Food
T37 3130-3134 CHEBI:23888;CHEBI:23888 denotes Drug
T38 3216-3221 UBERON:0000062 denotes Organ
T39 3294-3299 UBERON:0001977 denotes serum
T40 3300-3318 PR:000005897 denotes C-reactive protein
T41 3320-3327 CHEBI:24996;CHEBI:24996 denotes lactate
T42 3366-3379 PR:000001393 denotes interleukin-6
T43 4240-4244 UBERON:0000104 denotes life
T44 4257-4265 SP_7 denotes COVID-19

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 29-35 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T2 206-212 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T3 537-551 Body_part denotes interleukins-3 http://purl.org/sig/ont/fma/fma264832
T4 537-549 Body_part denotes interleukins http://purl.org/sig/ont/fma/fma86578
T5 637-645 Body_part denotes cytokine http://purl.org/sig/ont/fma/fma84050
T6 1273-1279 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T7 2034-2040 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T8 2066-2072 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T9 2241-2247 Body_part denotes Kidney http://purl.org/sig/ont/fma/fma7203
T10 2307-2313 Body_part denotes Plasma http://purl.org/sig/ont/fma/fma62970
T11 2358-2364 Body_part denotes plasma http://purl.org/sig/ont/fma/fma62970
T12 3216-3221 Body_part denotes Organ http://purl.org/sig/ont/fma/fma67498
T13 3294-3299 Body_part denotes serum http://purl.org/sig/ont/fma/fma63083
T14 3311-3318 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T15 3366-3379 Body_part denotes interleukin-6 http://purl.org/sig/ont/fma/fma264829

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 2241-2247 Body_part denotes Kidney http://purl.obolibrary.org/obo/UBERON_0002113
T2 3216-3221 Body_part denotes Organ http://purl.obolibrary.org/obo/UBERON_0000062
T3 3294-3299 Body_part denotes serum http://purl.obolibrary.org/obo/UBERON_0001977

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2 57-75 Disease denotes SARS CoV-2 disease MESH:C000657245
3 77-85 Disease denotes COVID-19 MESH:C000657245
10 563-611 Gene denotes interferon-gamma and tumor necrosis factor-alpha Gene:3458
11 237-245 Species denotes patients Tax:9606
12 276-284 Disease denotes COVID-19 MESH:C000657245
13 354-363 Disease denotes mortality MESH:D003643
14 394-402 Disease denotes COVID-19 MESH:C000657245
15 689-697 Disease denotes COVID-19 MESH:C000657245
18 946-954 Disease denotes COVID-19 MESH:C000657245
19 1012-1032 Disease denotes SARS-CoV-2 infection MESH:C000657245
25 1377-1387 Species denotes SARS-CoV-2 Tax:2697049
26 1480-1488 Species denotes patients Tax:9606
27 1315-1329 Chemical denotes sodium citrate MESH:D000077559
28 1252-1269 Disease denotes allergic reaction MESH:D004342
29 1421-1429 Disease denotes COVID-19 MESH:C000657245
37 2507-2517 Gene denotes fibrinogen Gene:2244
38 2368-2376 Species denotes patients Tax:9606
39 2191-2212 Chemical denotes acid-citrate dextrose MESH:C002113
40 1862-1870 Disease denotes COVID-19 MESH:C000657245
41 2241-2255 Disease denotes Kidney Disease MESH:D007674
42 2382-2394 Disease denotes coagulopathy MESH:D001778
43 2703-2711 Disease denotes COVID-19 MESH:C000657245
48 3300-3318 Gene denotes C-reactive protein Gene:1401
49 3366-3379 Gene denotes interleukin-6 Gene:3569
50 2881-2890 Disease denotes mortality MESH:D003643
51 2944-2952 Disease denotes COVID-19 MESH:C000657245
55 3474-3482 Species denotes patients Tax:9606
56 3666-3674 Species denotes patients Tax:9606
57 3746-3754 Species denotes patients Tax:9606
63 4211-4219 Species denotes patients Tax:9606
64 4290-4298 Species denotes patients Tax:9606
65 4416-4424 Species denotes patients Tax:9606
66 4489-4501 Species denotes participants Tax:9606
67 4257-4265 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 57-61 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T2 77-85 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 276-284 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 394-402 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 584-589 Disease denotes tumor http://purl.obolibrary.org/obo/MONDO_0005070
T6 689-697 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T7 946-954 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T8 1012-1020 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 1023-1032 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T10 1252-1269 Disease denotes allergic reaction http://purl.obolibrary.org/obo/MONDO_0000605|http://purl.obolibrary.org/obo/MONDO_0005271
T12 1252-1260 Disease denotes allergic http://purl.obolibrary.org/obo/MONDO_0004980
T13 1377-1385 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 1421-1429 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T15 1862-1870 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 2241-2255 Disease denotes Kidney Disease http://purl.obolibrary.org/obo/MONDO_0001343|http://purl.obolibrary.org/obo/MONDO_0005240
T18 2382-2394 Disease denotes coagulopathy http://purl.obolibrary.org/obo/MONDO_0001531
T19 2703-2711 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T20 2944-2952 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 4257-4265 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 0-1 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T2 29-35 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T3 88-89 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T4 112-113 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 157-167 http://purl.obolibrary.org/obo/BFO_0000030 denotes Objectives
T6 206-212 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T7 537-551 http://purl.obolibrary.org/obo/PR_000001387 denotes interleukins-3
T8 563-579 http://purl.obolibrary.org/obo/PR_000000017 denotes interferon-gamma
T9 584-611 http://purl.obolibrary.org/obo/PR_000000134 denotes tumor necrosis factor-alpha
T10 748-753 http://purl.obolibrary.org/obo/CLO_0007225 denotes label
T11 842-844 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T12 1147-1148 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T13 1273-1279 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T14 1367-1372 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T15 2034-2040 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T16 2066-2072 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T17 2241-2247 http://purl.obolibrary.org/obo/UBERON_0002113 denotes Kidney
T18 2241-2247 http://www.ebi.ac.uk/efo/EFO_0000927 denotes Kidney
T19 2241-2247 http://www.ebi.ac.uk/efo/EFO_0000929 denotes Kidney
T20 2307-2313 http://purl.obolibrary.org/obo/UBERON_0001969 denotes Plasma
T21 2358-2364 http://purl.obolibrary.org/obo/UBERON_0001969 denotes plasma
T22 2396-2407 http://purl.obolibrary.org/obo/PR_000007299 denotes prothrombin
T23 2461-2470 http://purl.obolibrary.org/obo/CLO_0001658 denotes activated
T24 3216-3221 http://purl.obolibrary.org/obo/UBERON_0003103 denotes Organ
T25 3366-3379 http://purl.obolibrary.org/obo/PR_000001393 denotes interleukin-6
T26 3499-3502 http://purl.obolibrary.org/obo/CLO_0053733 denotes 1:1
T27 3676-3677 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T28 4187-4188 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T29 4444-4447 http://purl.obolibrary.org/obo/CLO_0001577 denotes a 3
T30 4474-4475 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 4694-4696 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T32 4961-4964 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T33 5004-5005 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 537-549 Chemical denotes interleukins http://purl.obolibrary.org/obo/CHEBI_52998
T2 563-573 Chemical denotes interferon http://purl.obolibrary.org/obo/CHEBI_52999
T3 574-579 Chemical denotes gamma http://purl.obolibrary.org/obo/CHEBI_30212
T4 606-611 Chemical denotes alpha http://purl.obolibrary.org/obo/CHEBI_30216
T5 748-753 Chemical denotes label http://purl.obolibrary.org/obo/CHEBI_35209
T6 1149-1154 Chemical denotes Light http://purl.obolibrary.org/obo/CHEBI_30212
T7 1315-1329 Chemical denotes sodium citrate http://purl.obolibrary.org/obo/CHEBI_53258
T8 1315-1321 Chemical denotes sodium http://purl.obolibrary.org/obo/CHEBI_26708
T9 1322-1329 Chemical denotes citrate http://purl.obolibrary.org/obo/CHEBI_133748|http://purl.obolibrary.org/obo/CHEBI_16947|http://purl.obolibrary.org/obo/CHEBI_50744
T12 1811-1816 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T13 1916-1918 Chemical denotes TM http://purl.obolibrary.org/obo/CHEBI_55460|http://purl.obolibrary.org/obo/CHEBI_74861
T15 2157-2159 Chemical denotes TM http://purl.obolibrary.org/obo/CHEBI_55460|http://purl.obolibrary.org/obo/CHEBI_74861
T17 2191-2195 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T18 2196-2203 Chemical denotes citrate http://purl.obolibrary.org/obo/CHEBI_133748|http://purl.obolibrary.org/obo/CHEBI_16947|http://purl.obolibrary.org/obo/CHEBI_50744
T21 2204-2212 Chemical denotes dextrose http://purl.obolibrary.org/obo/CHEBI_17634
T22 2213-2226 Chemical denotes anticoagulant http://purl.obolibrary.org/obo/CHEBI_50249
T23 3311-3318 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T24 3320-3327 Chemical denotes lactate http://purl.obolibrary.org/obo/CHEBI_24996
T25 4328-4333 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T26 4433-4438 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 584-589 Phenotype denotes tumor http://purl.obolibrary.org/obo/HP_0002664
T2 637-662 Phenotype denotes cytokine release syndrome http://purl.obolibrary.org/obo/HP_0033041
T3 2241-2255 Phenotype denotes Kidney Disease http://purl.obolibrary.org/obo/HP_0000112
T4 2382-2394 Phenotype denotes coagulopathy http://purl.obolibrary.org/obo/HP_0003256

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 36-44 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange
T2 213-221 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange
T3 590-598 http://purl.obolibrary.org/obo/GO_0070265 denotes necrosis
T4 590-598 http://purl.obolibrary.org/obo/GO_0019835 denotes necrosis
T5 590-598 http://purl.obolibrary.org/obo/GO_0008219 denotes necrosis
T6 590-598 http://purl.obolibrary.org/obo/GO_0001906 denotes necrosis
T7 1280-1291 http://purl.obolibrary.org/obo/GO_0015297 denotes exchange or

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-87 Sentence denotes A pilot study of therapeutic plasma exchange for serious SARS CoV-2 disease (COVID-19):
T2 88-156 Sentence denotes A structured summary of a randomized controlled trial study protocol
T3 157-167 Sentence denotes Objectives
T4 168-364 Sentence denotes To evaluate the safety of therapeutic plasma exchange (TPE) in adult patients with serious/life-threatening COVID-19 requiring intensive care unit (ICU) admission, and associated 28-day mortality.
T5 365-499 Sentence denotes Serious and life threatening COVID-19 are defined as per published literature (please, refer to the full protocol, Additional file 1).
T6 500-612 Sentence denotes The rationale is that TPE can remove interleukins-3, 6, 8, 10, interferon-gamma and tumor necrosis factor-alpha.
T7 613-706 Sentence denotes Thus, it may reduce the cytokine release syndrome associated with fulminant COVID-19 disease.
T8 707-719 Sentence denotes Trial design
T9 720-795 Sentence denotes Pilot, interventional, open-label, randomized controlled multicenter trial.
T10 796-808 Sentence denotes Participants
T11 809-832 Sentence denotes Inclusion criteria are:
T12 833-1011 Sentence denotes 1) age ≥ 18 years old; 2) intubation and intensive care unit (ICU) admission; 3) serious and/or life-threatening COVID-19 (please, refer to the full protocol, Additional file 1).
T13 1012-1215 Sentence denotes SARS-CoV-2 infection is confirmed by Real-Time-Polymerase-Chain-Reaction (RT-PCR) assays using QuantiNova Probe RT-PCR kit (Qiagen) in a Light-Cycler 480 real-time PCR system (Roche, Basel, Switzerland).
T14 1216-1239 Sentence denotes Exclusion criteria are:
T15 1240-1515 Sentence denotes 1) previous allergic reaction to plasma exchange or its ingredients (i.e., sodium citrate), 2) two consecutive negative RT-PCR tests for SARS-CoV-2 at least 24 hours apart, 3) mild COVID-19 not requiring ICU admission and 4) terminally ill patients receiving palliative care.
T16 1516-1610 Sentence denotes The primary site will be King Saud Medical City (KSMC), Riyadh, Kingdom of Saudi Arabia (KSA).
T17 1611-1764 Sentence denotes Also, the study will run in ICUs (Ministry of Health Cluster 1; Riyadh) and other centers in KSA pending their institutional review board (IRB) approval.
T18 1765-1793 Sentence denotes Interventions and comparator
T19 1794-1871 Sentence denotes The intervention group will receive TPE, plus empiric treatment for COVID-19.
T20 1872-2011 Sentence denotes TPE is administered using the Spectra Optia TM Apheresis System equipped with the Depuro D2000 Adsorption Cartridge (Terumo BCT Inc., USA).
T21 2012-2142 Sentence denotes The first dose is 1.5 plasma volumes, followed by one plasma volume on alternate days or daily for five to seven total treatments.
T22 2143-2306 Sentence denotes Spectra Optia TM Apheresis System operates with acid-citrate dextrose anticoagulant (ACDA) as per Kidney Disease Improving Global Outcomes (KDIGO) 2019 guidelines.
T23 2307-2535 Sentence denotes Plasma is replaced with albumin 5% or fresh frozen plasma in patients with coagulopathy (prothrombin time >37 seconds; international normalized ratio >3; activated partial thromboplastin time >100 or fibrinogen level <100 mg/d).
T24 2536-2623 Sentence denotes TPE sessions are performed daily over four hours and laboratory markers measured daily.
T25 2624-2777 Sentence denotes The comparators are controls not receiving TPE but usual empiric treatment for COVID-19 as per institutional, national and international recommendations.
T26 2778-2832 Sentence denotes Both groups will receive standard ICU supportive care.
T27 2833-2846 Sentence denotes Main outcomes
T28 2847-2953 Sentence denotes Primary study end-point is 28-day mortality and safety of TPE in serious and/or life-threatening COVID-19.
T29 2954-3162 Sentence denotes Safety will be evaluated by the documentation of any pertinent adverse and/or serious adverse effects related to TPE as per institutional, national and international (Food and Drug Administration) guidelines.
T30 3163-3440 Sentence denotes Secondary outcomes are: i) improvement in Sequential Organ Function Assessment (SOFA) score ; ii) changes in inflammatory markers: serum C-reactive protein, lactate dehydrogenase, ferritin, d-dimers and interleukin-6; iii) days on mechanical ventilation and ICU length of stay.
T31 3441-3454 Sentence denotes Randomization
T32 3455-3603 Sentence denotes Eligible consented patients are randomized (1:1 allocation) after stratification by ICU center and two PaO2/FIO2 ratio categories (> 150 and ≤ 150).
T33 3604-3675 Sentence denotes Randomization occurs in variable block sizes of four to eight patients.
T34 3676-3827 Sentence denotes A web-based randomization service, randomize.net, is used to allocate patients to their respective strata prior to the intervention or control therapy.
T35 3828-3846 Sentence denotes Blinding (masking)
T36 3847-3973 Sentence denotes Given the visibility of TPE machinery, the intervention will be unblinded; hence, no enrollment concealment will be expedited.
T37 3974-4103 Sentence denotes The lack of allocation concealment will be mitigated by several measures (please, refer to the full protocol, Additional file 1).
T38 4104-4142 Sentence denotes Numbers to be randomized (sample size)
T39 4143-4266 Sentence denotes This pilot randomized trial aims to recruit a convenience sample of patients with serious and/or life-threatening COVID-19.
T40 4267-4359 Sentence denotes Therefore, at least 20 patients are to be randomized to each group per participating center.
T41 4360-4502 Sentence denotes We are hoping to consent and randomize approximately 60 patients in each group over a 3 to 6 months period giving a total of 120 participants.
T42 4503-4515 Sentence denotes Trial Status
T43 4516-4563 Sentence denotes The protocol version 1 was approved 29/04/2020.
T44 4564-4612 Sentence denotes Recruitment is ongoing, and began on 01/05/2020.
T45 4613-4650 Sentence denotes We estimate completion by 29/10/2020.
T46 4651-4669 Sentence denotes Trial registration
T47 4670-4751 Sentence denotes Registered at ISRCTN on 18/05/2020 (ISRCTN21363594; doi.10.1186/ ISRCTN21363594).
T48 4752-4765 Sentence denotes Full protocol
T49 4766-4874 Sentence denotes The full protocol is attached as an additional file, accessible from the Trials website (Additional file 1).
T50 4875-5055 Sentence denotes In the interest of expediting dissemination of this material, the familiar formatting has been eliminated; this letter serves as a summary of the key elements of the full protocol.