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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 3797-3812 Body_part denotes coronary artery http://purl.org/sig/ont/fma/fma49893
T2 9475-9481 Body_part denotes Mental http://purl.org/sig/ont/fma/fma264279
T3 15269-15274 Body_part denotes heart http://purl.org/sig/ont/fma/fma7088

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 3797-3812 Body_part denotes coronary artery http://purl.obolibrary.org/obo/UBERON_0001621
T2 3806-3812 Body_part denotes artery http://purl.obolibrary.org/obo/UBERON_0001637
T3 15269-15274 Body_part denotes heart http://purl.obolibrary.org/obo/UBERON_0000948

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 15-23 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T2 108-116 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 1512-1520 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 1954-1962 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 1964-2011 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T6 1964-1997 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T7 2669-2677 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T8 3331-3339 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 3695-3711 Disease denotes coronary disease http://purl.obolibrary.org/obo/MONDO_0005010
T10 3933-3941 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 4190-4206 Disease denotes coronary disease http://purl.obolibrary.org/obo/MONDO_0005010
T12 4688-4696 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 4942-4950 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T14 5752-5760 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T15 6037-6045 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 7500-7508 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 7884-7892 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T18 8172-8180 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 8340-8348 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T20 10030-10038 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 11058-11066 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T22 11356-11364 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 12829-12837 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 13901-13909 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 14524-14532 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 14779-14787 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T27 14895-14903 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T28 15640-15648 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 198-199 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 293-294 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 551-554 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T4 689-690 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 1081-1082 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 1420-1421 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T7 1916-1917 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 2032-2033 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T9 2151-2154 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T10 2626-2632 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T11 2701-2704 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T12 2736-2739 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T13 2788-2791 http://purl.obolibrary.org/obo/CLO_0001000 denotes 3–5
T14 3806-3812 http://purl.obolibrary.org/obo/UBERON_0001637 denotes artery
T15 3806-3812 http://www.ebi.ac.uk/efo/EFO_0000814 denotes artery
T16 4025-4028 http://purl.obolibrary.org/obo/CLO_0001755 denotes ask
T17 4229-4232 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T18 4295-4296 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 4844-4845 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T20 4902-4903 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 5563-5564 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 5766-5767 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T23 5876-5877 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T24 6177-6178 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T25 6255-6258 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T26 6715-6716 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T27 6796-6797 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T28 7115-7117 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T29 7124-7125 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T30 7182-7183 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T31 7225-7226 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 8377-8380 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T33 8513-8514 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 8549-8550 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 8731-8732 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 9033-9034 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 9723-9724 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T38 10384-10385 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 10775-10776 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 10841-10842 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T41 10857-10858 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 11080-11087 http://purl.obolibrary.org/obo/OBI_0100026 denotes organic
T43 11080-11087 http://purl.obolibrary.org/obo/UBERON_0000468 denotes organic
T44 11379-11380 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 11581-11583 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T46 11859-11862 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T47 12230-12233 http://purl.obolibrary.org/obo/PR_000001343 denotes aim
T48 12400-12401 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 12502-12503 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 12643-12644 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 13095-13096 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T52 13165-13166 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T53 13174-13181 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T54 13407-13408 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 13456-13462 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T56 13473-13474 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 13917-13920 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T58 13928-13929 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 14094-14095 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 15269-15274 http://purl.obolibrary.org/obo/UBERON_0000948 denotes heart
T61 15269-15274 http://purl.obolibrary.org/obo/UBERON_0007100 denotes heart
T62 15269-15274 http://purl.obolibrary.org/obo/UBERON_0015228 denotes heart
T63 15269-15274 http://www.ebi.ac.uk/efo/EFO_0000815 denotes heart
T64 15348-15350 http://purl.obolibrary.org/obo/CLO_0007029 denotes JM
T65 15348-15350 http://purl.obolibrary.org/obo/CLO_0050993 denotes JM
T66 15393-15395 http://purl.obolibrary.org/obo/CLO_0008812 denotes RH
T67 15405-15406 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 15572-15573 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 15713-15714 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 15904-15906 http://purl.obolibrary.org/obo/CLO_0007029 denotes JM
T71 15904-15906 http://purl.obolibrary.org/obo/CLO_0050993 denotes JM
T72 16057-16059 http://purl.obolibrary.org/obo/CLO_0007029 denotes JM
T73 16057-16059 http://purl.obolibrary.org/obo/CLO_0050993 denotes JM
T74 16132-16133 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 16342-16346 http://purl.obolibrary.org/obo/CLO_0008416 denotes peer
T76 16342-16346 http://purl.obolibrary.org/obo/CLO_0050081 denotes peer
T77 16384-16388 http://purl.obolibrary.org/obo/CLO_0008416 denotes peer
T78 16384-16388 http://purl.obolibrary.org/obo/CLO_0050081 denotes peer

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 2272-2276 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T3 3783-3787 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T5 4592-4596 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T7 4759-4763 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T9 5804-5808 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T11 5973-5977 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T13 6491-6493 Chemical denotes WD http://purl.obolibrary.org/obo/CHEBI_74868
T14 6744-6752 Chemical denotes medicine http://purl.obolibrary.org/obo/CHEBI_23888
T15 7364-7368 Chemical denotes Gold http://purl.obolibrary.org/obo/CHEBI_29287
T16 7697-7702 Chemical denotes bases http://purl.obolibrary.org/obo/CHEBI_22695
T17 7812-7816 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T19 7958-7962 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T21 8040-8044 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T23 10207-10211 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T25 14159-14163 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T27 14431-14435 Chemical denotes gold http://purl.obolibrary.org/obo/CHEBI_29287|http://purl.obolibrary.org/obo/CHEBI_30050
T29 15348-15350 Chemical denotes JM http://purl.obolibrary.org/obo/CHEBI_31739
T30 15355-15357 Chemical denotes SM http://purl.obolibrary.org/obo/CHEBI_17076|http://purl.obolibrary.org/obo/CHEBI_74817
T32 15393-15395 Chemical denotes RH http://purl.obolibrary.org/obo/CHEBI_18310
T33 15904-15906 Chemical denotes JM http://purl.obolibrary.org/obo/CHEBI_31739
T34 15911-15913 Chemical denotes SM http://purl.obolibrary.org/obo/CHEBI_17076|http://purl.obolibrary.org/obo/CHEBI_74817
T36 16057-16059 Chemical denotes JM http://purl.obolibrary.org/obo/CHEBI_31739

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 2169-2175 http://purl.obolibrary.org/obo/GO_0098739 denotes uptake
T2 2169-2175 http://purl.obolibrary.org/obo/GO_0098657 denotes uptake

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-97 Sentence denotes Surgery during COVID-19 crisis conditions: can we protect our ethical integrity against the odds?
T2 99-107 Sentence denotes Abstract
T3 108-253 Sentence denotes COVID-19 is reducing the ability to perform surgical procedures worldwide, giving rise to a multitude of ethical, practical and medical dilemmas.
T4 254-403 Sentence denotes Adapting to crisis conditions requires a rethink of traditional best practices in surgical management, delving into an area of unknown risk profiles.
T5 404-547 Sentence denotes Key challenging areas include cancelling elective operations, modifying procedures to adapt local services and updating the consenting process.
T6 548-650 Sentence denotes We aim to provide an ethical rationale to support change in practice and guide future decision-making.
T7 651-799 Sentence denotes Using the four principles approach as a structure, Medline was searched for existing ethical frameworks aimed at resolving conflicting moral duties.
T8 800-895 Sentence denotes Where insufficient data were available, best guidance was sought from educational institutions:
T9 896-962 Sentence denotes National Health Service England and The Royal College of Surgeons.
T10 963-1066 Sentence denotes Multiple papers presenting high-quality, reasoned, ethical theory and practice guidance were collected.
T11 1067-1231 Sentence denotes Using this as a basis to assess current practice, multiple requirements were generated to ensure preservation of ethical integrity when making management decisions.
T12 1232-1419 Sentence denotes Careful consideration of ethical principles must guide production of local guidance ensuring consistent patient selection thus preserving equality as well as quality of clinical services.
T13 1420-1554 Sentence denotes A critical issue is balancing the benefit of surgery against the unknown risk of developing COVID-19 and its associated complications.
T14 1555-1732 Sentence denotes As such, the need for surgery must be sufficiently pressing to proceed with conventional or non-conventional operative management; otherwise, delaying intervention is justified.
T15 1733-1898 Sentence denotes For delayed operations, it is our duty to quantify the long-term impact on patients’ outcome within the constraints of pandemic management and its long-term outlook.
T16 1900-1912 Sentence denotes Introduction
T17 1913-2103 Sentence denotes As a surgical department operating under COVID-19 (severe acute respiratory syndrome coronavirus 2) crisis conditions, a multitude of ethical, practical and medical dilemmas are encountered.
T18 2104-2246 Sentence denotes Instruction to halt all elective surgical work has received high uptake across centres nationwide; however, urgent surgical cases are ongoing.
T19 2247-2390 Sentence denotes Conventional thinking of gold standard management must be updated to consider possible consequences of operating in this high-risk environment.
T20 2391-2475 Sentence denotes This directly impacts what procedure is performed, when and where it is carried out.
T21 2476-2551 Sentence denotes Each change presents ethical dilemmas that requires careful considerations.
T22 2553-2588 Sentence denotes What procedure should be performed?
T23 2589-2722 Sentence denotes Working in cardiac surgery within an active tertiary care centre, the impact of COVID-19 on our working pattern has been significant.
T24 2723-2823 Sentence denotes The caseload has now reduced from an average of 15 cases/week to 3–5 cases/week after 30 March 2020.
T25 2824-3051 Sentence denotes Although this is primarily due to the aforementioned cancellation of elective work, procurement of theatres as intensive treatment unit (ITU) bed spaces and modification of the required interventions have also reduced caseload.
T26 3052-3236 Sentence denotes With the resultant limitation to operative facilities, careful case selection is imperative to minimise harm: only the most urgent patients with no feasible alternatives can be listed.
T27 3237-3512 Sentence denotes The Royal College of Surgeons published guidelines on good practice for surgical teams during COVID-19 on 31 March.1 The recommended changes are in keeping with those outlined above; however, advice on operation selection when more than one procedure is available is lacking.
T28 3513-3836 Sentence denotes National Health Service (NHS) England also published specific guidelines for cardiothoracic surgery which does not address these issues clearly.2 Emergency patients with multivessel coronary disease are receiving percutaneous coronary intervention (PCI) rather than the gold standard coronary artery bypass grafting (CABG).
T29 3837-4010 Sentence denotes The short-term benefits are clear: with reduced recovery time and systemic insult, the risks of COVID-19 exposure and associated complications will be significantly reduced.
T30 4011-4070 Sentence denotes One must also ask; how does this affect long-term outcomes?
T31 4071-4127 Sentence denotes Does the short-term benefit outweigh the long-term risk?
T32 4128-4659 Sentence denotes Extrapolating the situation of PCI versus CABG in multivessel coronary disease, the 5-year mortality has been shown to be 14.6% versus 9.2%, respectively; equating to a 58.7% increased risk of death at 5 years with PCI.3 Although there is some conflicting evidence, it is undoubtable that, for some patients, CABG provides better long-term outcomes.4 Similar situations exist across other surgical specialities.5 With consideration of the above, is delivering the gold standard surgery safely possible through alternative pathways?
T33 4661-4723 Sentence denotes How else could we minimise COVID-19 risk to surgical patients?
T34 4724-4836 Sentence denotes Other opportunities to deliver the gold standard surgery safely are changing the location or time of procedures.
T35 4837-4956 Sentence denotes Having a ‘clean’ hospital that performs operations would provide a safe space, theoretically eliminating COVID-19 risk.
T36 4957-5049 Sentence denotes To implement this, both private hospitals and designated surgical units have been suggested.
T37 5050-5270 Sentence denotes Given the persistent viral spread despite nationwide lockdown, and widespread personal protective equipment shortages, keeping any hospital clean for an extended period of time would be very demanding, if not impossible.
T38 5271-5551 Sentence denotes To stratify patients who can be delayed until infective risk declines, scoring tools such as the HEART6 and EUROSCORE 2 (The European System for Cardiac Operative Risk Evaluation 2) tools7 can be used, but clinical judgement plays an essential role under such unprecedented times.
T39 5552-5714 Sentence denotes Indeed, in a high-risk population, triaging and potential delay of patients’ management adds to the unpredictably of the long-term consequences of such decisions.
T40 5715-5926 Sentence denotes Coupling the unclear risk profile of COVID-19 with a lack of alternatives to provide the gold standard surgery, what is the ethical justification for performing a substitute procedure on this cohort of patients?
T41 5928-6053 Sentence denotes How can we ethically provide the traditional gold standard, or alternative, operation to patients during the COVID-19 crisis?
T42 6054-6164 Sentence denotes In times of dissonance with moral norms, it is essential to use an ethical framework to guide decision-making.
T43 6165-6235 Sentence denotes This allows a structured method of resolving conflicting moral duties.
T44 6236-6457 Sentence denotes One such framework has formed the basis of healthcare ethics: initially proposed by Beauchamp and Childress in 1979, the four principles of patient care are beneficence, non-maleficence, respect for autonomy and justice.8
T45 6459-6490 Sentence denotes Beneficence and non-maleficence
T46 6491-7007 Sentence denotes WD Ross established the concept of prima facie duties, acts that are morally obligatory unless overridden by another.9 Beneficence is one such duty defined as an act done to benefit.8 It is often paired with non-maleficence a principal engrained within medicine as primum non nocere—physician do no harm, a phrase with unclear origins.10 As all interventions confer risk, it is important to distinguish the difference between the weighed risks of positive intervention within beneficence and physically causing harm.
T47 7008-7252 Sentence denotes The theory of utilitarianism holds that whatever maximises population benefit is the most ethical decision.11 It is a form of consequentialism; in principle, one can perform a minor harmful process in order to create a major beneficial process.
T48 7253-7363 Sentence denotes This raises questions in regards to how we determine ‘an optimal outcome’ as discussed in the Justice section.
T49 7364-7635 Sentence denotes Gold standard operations are those with the best evidence-based outcomes and lowest risk profiles.12 Historic research does not reflect COVID-19-related mortality or the current limitations within the NHS, as such operative risk will be considerably higher than previous.
T50 7636-7786 Sentence denotes Less invasive procedures, such as PCI, have smaller evidence bases than surgery3; hence, they have not been first-line treatment options historically.
T51 7787-7909 Sentence denotes Their inferiority to the gold standard should be weighed up against the possible protection from COVID-19-associated risk.
T52 7910-8233 Sentence denotes Does the current climate mean we can change the gold standard regardless of the challenge around quantifying risk?13 Although the gold standard will remain unknown we can, at the very least, meet the obligations of beneficence and non-maleficence, without clear COVID-19 data, through only performing lifesaving operations.
T53 8234-8349 Sentence denotes Multiple operations across the UK are being delayed to open space in hospitals for possible patients with COVID-19.
T54 8350-8492 Sentence denotes This governmental decision has determined that the viral risk to the population is greater than the risk of cancelling all routine procedures.
T55 8493-8633 Sentence denotes As described above, a maleficent act can be accepted if a largely beneficent act is the result; thus, the prima facie duty can be overruled.
T56 8634-8773 Sentence denotes The net morbidity and mortality from delaying all NHS procedures are uncalculatable, resultantly a utilitarian argument becomes impossible.
T57 8774-8893 Sentence denotes Locally, it is necessary to make projected mortality-based decisions in relation to the safest way to delay procedures.
T58 8895-8915 Sentence denotes Respect for autonomy
T59 8916-9470 Sentence denotes Kantian ethics traditionally described respecting autonomy through individual importance: each person is an end, not a means, in themselves, holding their own categorical imperative and should be treated accordingly.14 Beauchamp and Childress expanded on this by presenting two prerequisites for autonomy: (1) liberty (freedom from influencing factors) and (2) agency (capacity for intentional action).8 These influential pieces have shaped our modern view of respecting autonomy, whereby an individual is deemed to have capacity unless proven otherwise.
T60 9471-9664 Sentence denotes The Mental Capacity Act 2019 enforces this principle and describes the ability to understand, weigh up, retain and communicate information as the fundamental requirements for decision-making.15
T61 9665-9781 Sentence denotes To ensure compliance with set legal standards when making a decision regarding surgery, written consent is obtained.
T62 9782-9873 Sentence denotes The validity of this consent relies on the accuracy of information provided to the patient.
T63 9874-10039 Sentence denotes Operating in current crisis conditions, previously modelled mortality rates are not accurate as they do not account for the increased risk from contracting COVID-19.
T64 10040-10186 Sentence denotes Update to quoted mortality statistics must be increased in line with local experience to the best of provider ability, to ensure informed consent.
T65 10187-10329 Sentence denotes With regards to the gold standard procedure, one could argue that in the midst of unclear risk profiles patient choice should take precedence.
T66 10330-10465 Sentence denotes Taking this ‘fully autonomous’ approach as opposed to a more guided approach to management decisions yields some negative consequences.
T67 10466-10784 Sentence denotes Patients lacking confidence, who will be significant in number during crisis conditions, feel abandoned when presented with management options without clinician recommendation.16 In addition, Davies and Elwyn16 showed that these patients suffer lasting feelings of guilt should negative consequences arise as a result.
T68 10785-10881 Sentence denotes As such, it should be remembered that patient choice is a right and not a mandatory requirement.
T69 10882-10960 Sentence denotes Another issue with patient autonomy arises when exploring patient perceptions.
T70 10961-11067 Sentence denotes Take the example of the man who refuses to undergo urgent surgery due to the fear of contracting COVID-19.
T71 11068-11156 Sentence denotes There is no organic reason for him to lack capacity and his decision could be respected.
T72 11157-11424 Sentence denotes It is for this reason that Walker argued in 2008 that current frameworks do not sufficiently account for internal control factors.17 In following, surgeons must explore patient perceptions regarding COVID-19 to facilitate a fully informed decision in the current era.
T73 11426-11433 Sentence denotes Justice
T74 11434-11685 Sentence denotes The alignment of institutional policy with principles of justice is of fundamental importance to maintain citizen, employee and governmental trust.18 These requirements at least persist, if not amplify, through crisis conditions with scarce resources.
T75 11686-11935 Sentence denotes Indeed, no situation exists where all alternative choices are equally unjust.19 It follows that when the question ‘who should we operate on during this crisis when capacity has been significantly reduced?’ is asked, an optimal answer may be derived.
T76 11936-12079 Sentence denotes Three principles are primarily used to resolve microallocation problems such as this; these are needs, maximising and egalitarian principles.20
T77 12080-12207 Sentence denotes According to needs principles, patients who are most acutely unwell should be operated on regardless of potential for recovery.
T78 12208-12313 Sentence denotes Maximising principles aim to increase population health by intervening on those who can benefit the most.
T79 12314-12450 Sentence denotes Egalitarian principles advise that all people should be given an equal opportunity to a long life of health, favouring younger patients.
T80 12451-12624 Sentence denotes Although clinicians are generally stated to favour a needs principle for patient selection,20 surgeons ensure sufficient benefit from operating to justify the incurred risk.
T81 12625-12692 Sentence denotes This demonstrates a combination of needs and maximising principles.
T82 12693-12820 Sentence denotes The current practice of delaying elective surgery and operating on emergency cases is in keeping with this rationing principle.
T83 12821-12988 Sentence denotes Despite COVID-19’s primary tendency to envelop ITU and ward areas, acute surgical cases may still overload departmental capacity necessitating complex decision-making.
T84 12989-13164 Sentence denotes Clinicians in these situations undoubtedly judge each case individually, however, must carefully act with a consistent balance of needs, maximising and egalitarian principles.
T85 13165-13217 Sentence denotes A simple testing method is presented for this below.
T86 13218-13589 Sentence denotes The standard, proposed by Beauchamp and Childress, to judge systemic alignment with just principles is whether two cases of similar presentation are treated differently.8 Achieving this in a realm of guideline-deficient practice requires active planning: a lack of evidence to guide decisions exacerbates the existing natural variation in management21 between clinicians.
T87 13590-13758 Sentence denotes Indeed, local protocols must be devised early to reduce these otherwise inevitable management discrepancies, maintaining essential equality of opportunity for patients.
T88 13759-13876 Sentence denotes It is only through such grounded actions that we may act justly and therefore withstand any possible future scrutiny.
T89 13878-13888 Sentence denotes Conclusion
T90 13889-13984 Sentence denotes The current COVID-19 crisis has placed a new type of demand on the healthcare system in the UK.
T91 13985-14123 Sentence denotes The pandemic results in unknown variables being pushed to the forefront of clinical decision-making, raising a plethora of ethical issues.
T92 14124-14235 Sentence denotes As such, to continue providing the gold standard surgical procedures ethically, certain conditions must be met.
T93 14236-14349 Sentence denotes First, we can continue operating as long as there is clear net benefit to the patients, that is, emergency cases.
T94 14350-14555 Sentence denotes For those patients requiring acute treatment, an alternative to the conventional gold standard can be performed if its known inferiority is outweighed by the reduced risk of COVID-19-related complications.
T95 14556-14696 Sentence denotes Given these options structured local protocols must be devised to reduce variability and therefore preserve patient equality of opportunity.
T96 14697-14808 Sentence denotes The decision to operate must involve the patient; capacity and perceptions around COVID-19 need to be explored.
T97 14809-14922 Sentence denotes In addition, for valid consent to be obtained, operative risk discussion must include COVID-19-related mortality.
T98 14923-15087 Sentence denotes If withholding the decision to operate, we should consider the harm caused: detailed effects of this harm need to be quantified to guide future disaster management.
T99 15088-15332 Sentence denotes Altogether, whether the conscientious clinician opts for conventional, non-conventional or non-operative management during this crisis, retaining the patient’s best interest at the heart of our practice will preserve our professional integrity.
T100 15334-15392 Sentence denotes Contributors: JM and SM contributed equally to this paper.
T101 15393-15465 Sentence denotes RH provided a supervisory role in editing and finalising the manuscript.
T102 15466-15608 Sentence denotes They have extensive expertise in arranging cardiac surgery, specifically with patient interaction forming a crucial portion of daily workload.
T103 15609-15757 Sentence denotes It was initially drafted after COVID-19 drastically cut down our departments operating capacity raising a variety of ethical issues to be addressed.
T104 15758-15903 Sentence denotes The lack of clear guidance lead to discussion in regards to how we treat urgent cardiac surgery patients to the best of our department’s ability.
T105 15904-15985 Sentence denotes JM and SM wrote, edited and reviewed the manuscript and approved the final draft.
T106 15986-16056 Sentence denotes Sources were found via analysing key ethical texts, found via Medline.
T107 16057-16092 Sentence denotes JM is the guarantor of the article.
T108 16093-16101 Sentence denotes Funding:
T109 16102-16243 Sentence denotes The authors have not declared a specific grant for this research from any funding agency in the public, commercial or not-for-profit sectors.
T110 16244-16264 Sentence denotes Competing interests:
T111 16265-16279 Sentence denotes None declared.
T112 16280-16312 Sentence denotes Patient consent for publication:
T113 16313-16326 Sentence denotes Not required.
T114 16327-16354 Sentence denotes Provenance and peer review:
T115 16355-16398 Sentence denotes Not commissioned; internally peer reviewed.
T116 16399-16427 Sentence denotes Data availability statement:
T117 16428-16459 Sentence denotes There are no data in this work.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 3695-3711 Phenotype denotes coronary disease http://purl.obolibrary.org/obo/HP_0001677
T2 4190-4206 Phenotype denotes coronary disease http://purl.obolibrary.org/obo/HP_0001677
T3 14096-14104 Phenotype denotes plethora http://purl.obolibrary.org/obo/HP_0001050

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
1 15-23 Disease denotes COVID-19 MESH:C000657245
6 1336-1343 Species denotes patient Tax:9606
7 1808-1816 Species denotes patients Tax:9606
8 108-116 Disease denotes COVID-19 MESH:C000657245
9 1512-1520 Disease denotes COVID-19 MESH:C000657245
12 1964-2011 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
13 1954-1962 Disease denotes COVID-19 MESH:C000657245
16 3183-3191 Species denotes patients Tax:9606
17 2669-2677 Disease denotes COVID-19 MESH:C000657245
26 3669-3677 Species denotes patients Tax:9606
27 4427-4435 Species denotes patients Tax:9606
28 3331-3339 Disease denotes COVID-19 MESH:C000657245
29 3695-3711 Disease denotes coronary disease MESH:D003324
30 3933-3941 Disease denotes COVID-19 MESH:C000657245
31 4190-4206 Disease denotes coronary disease MESH:D003324
32 4219-4228 Disease denotes mortality MESH:D003643
33 4321-4326 Disease denotes death MESH:D003643
36 4714-4722 Species denotes patients Tax:9606
37 4688-4696 Disease denotes COVID-19 MESH:C000657245
39 4942-4950 Disease denotes COVID-19 MESH:C000657245
42 5283-5291 Species denotes patients Tax:9606
43 5619-5627 Species denotes patients Tax:9606
46 5917-5925 Species denotes patients Tax:9606
47 5752-5760 Disease denotes COVID-19 MESH:C000657245
50 6017-6025 Species denotes patients Tax:9606
51 6037-6045 Disease denotes COVID-19 MESH:C000657245
53 6376-6383 Species denotes patient Tax:9606
55 6526-6531 Gene denotes prima Gene:145270
60 7500-7508 Disease denotes COVID-19 MESH:C000657245
61 7517-7526 Disease denotes mortality MESH:D003643
62 7884-7892 Disease denotes COVID-19 MESH:C000657245
63 8172-8180 Disease denotes COVID-19 MESH:C000657245
69 8599-8604 Gene denotes prima Gene:145270
70 8326-8334 Species denotes patients Tax:9606
71 8340-8348 Disease denotes COVID-19 MESH:C000657245
72 8656-8665 Disease denotes mortality MESH:D003643
73 8817-8826 Disease denotes mortality MESH:D003643
78 9865-9872 Species denotes patient Tax:9606
79 9934-9943 Disease denotes mortality MESH:D003643
80 10030-10038 Disease denotes COVID-19 MESH:C000657245
81 10057-10066 Disease denotes mortality MESH:D003643
86 10291-10298 Species denotes patient Tax:9606
87 10466-10474 Species denotes Patients Tax:9606
88 10695-10703 Species denotes patients Tax:9606
89 10823-10830 Species denotes patient Tax:9606
95 10901-10908 Species denotes patient Tax:9606
96 10940-10947 Species denotes patient Tax:9606
97 11326-11333 Species denotes patient Tax:9606
98 11058-11066 Disease denotes COVID-19 MESH:C000657245
99 11356-11364 Disease denotes COVID-19 MESH:C000657245
105 12111-12119 Species denotes patients Tax:9606
106 12353-12359 Species denotes people Tax:9606
107 12441-12449 Species denotes patients Tax:9606
108 12524-12531 Species denotes patient Tax:9606
109 12829-12837 Disease denotes COVID-19 MESH:C000657245
111 13749-13757 Species denotes patients Tax:9606
113 13901-13909 Disease denotes COVID-19 MESH:C000657245
118 14314-14322 Species denotes patients Tax:9606
119 14360-14368 Species denotes patients Tax:9606
120 14664-14671 Species denotes patient Tax:9606
121 14524-14532 Disease denotes COVID-19 MESH:C000657245
126 14738-14745 Species denotes patient Tax:9606
127 14779-14787 Disease denotes COVID-19 MESH:C000657245
128 14895-14903 Disease denotes COVID-19 MESH:C000657245
129 14912-14921 Disease denotes mortality MESH:D003643
131 15238-15245 Species denotes patient Tax:9606
135 15544-15551 Species denotes patient Tax:9606
136 15854-15862 Species denotes patients Tax:9606
137 15640-15648 Disease denotes COVID-19 MESH:C000657245
139 16280-16287 Species denotes Patient Tax:9606

2_test

Id Subject Object Predicate Lexical cue
32532825-24849105-61943082 4347-4348 24849105 denotes 3
32532825-28760214-61943083 4477-4478 28760214 denotes 4
32532825-23892941-61943084 5373-5374 23892941 denotes 6
32532825-22378855-61943085 5458-5459 22378855 denotes 7
32532825-15778417-61943086 6826-6828 15778417 denotes 10
32532825-24849105-61943087 7715-7716 24849105 denotes 3
32532825-8044100-61943088 8024-8026 8044100 denotes 13
32532825-17975729-61943089 10642-10644 17975729 denotes 16
32532825-17975729-61943090 10674-10676 17975729 denotes 16
32532825-19109530-61943091 11287-11289 19109530 denotes 17
32532825-11055033-61943092 12077-12079 11055033 denotes 20
32532825-11055033-61943093 12542-12544 11055033 denotes 20
32532825-20436026-61943094 13567-13569 20436026 denotes 21