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Bailey JA, Morton AJ, Jones J, Chapman CJ, Oliver S, Morling JR, Patel H, Humes DJ, Banerjea A. 'Low' faecal immunochemical test (FIT) colorectal cancer: a 4-year comparison of the Nottingham '4F' protocol with FIT10 in symptomatic patients. Colorectal Dis 2024; 26:309-316. [PMID: 38173125 DOI: 10.1111/codi.16848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
AIM The aim of this work was to evaluate colorectal cancer (CRC) outcomes after 'low' (sub-threshold) faecal immunochemical test (FIT) results in symptomatic patients tested in primary care. METHOD This work comprised a retrospective audit of 35 289 patients with FIT results who had consulted their general practitioner with lower gastrointestinal symptoms and had subsequent CRC diagnoses. The Rapid Colorectal Cancer Diagnosis pathway was introduced in November 2017 to allow incorporation of FIT into clinical practice. The local '4F' protocol combined FIT results with blood tests and digital rectal examination (DRE): FIT, full blood count, ferritin and finger [DRE]. The outcome used was detection rates of CRC, missed CRC and time to diagnosis in local 4F protocols for patients with a subthreshold faecal haemoglobin (fHb) result compared with thresholds of 10 and 20 μg Hb/g faeces. RESULTS A single threshold of 10 μg Hb/g faeces identifies a population in whom the risk of CRC is 0.2%, but this would have missed 63 (10.5%) of 599 CRCs in this population. The Nottingham 4F protocol would have missed fewer CRCs [42 of 599 (7%)] despite using a threshold of 20 μg Hb/g faeces for patients with normal blood tests. Subthreshold FIT results in patients subsequently diagnosed with a palpable rectal tumour yielded the longest delays in diagnosis. CONCLUSION A combination of FIT with blood results and DRE (the 4F protocol) reduced the risk of missed or delayed diagnosis. Further studies on the impact of such protocols on the diagnostic accuracy of FIT are expected. The value of adding blood tests to FIT may be restricted to specific parts of the fHb results spectrum.
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Kasim MF, Watson-Parris D, Deaconu L, Oliver S, Hatfield P, Froula DH, Gregori G, Jarvis M, Khatiwala S, Korenaga J, Topp-Mugglestone J, Viezzer E, Vinko SM. Building high accuracy emulators for scientific simulations with deep neural architecture search. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1088/2632-2153/ac3ffa] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Computer simulations are invaluable tools for scientific discovery. However, accurate simulations are often slow to execute, which limits their applicability to extensive parameter exploration, large-scale data analysis, and uncertainty quantification. A promising route to accelerate simulations by building fast emulators with machine learning requires large training datasets, which can be prohibitively expensive to obtain with slow simulations. Here we present a method based on neural architecture search to build accurate emulators even with a limited number of training data. The method successfully emulates simulations in 10 scientific cases including astrophysics, climate science, biogeochemistry, high energy density physics, fusion energy, and seismology, using the same super-architecture, algorithm, and hyperparameters. Our approach also inherently provides emulator uncertainty estimation, adding further confidence in their use. We anticipate this work will accelerate research involving expensive simulations, allow more extensive parameters exploration, and enable new, previously unfeasible computational discovery.
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Fusama M, Oliver S, Nakahara H, Van Eijk-Hustings Y, Kuroe Y. AB0894-HPR THE JOURNEY OF PATIENTS WITH RHEUMATOID ARTHRITIS. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.3029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:The course of rheumatoid arthritis (RA) differs from patient to patient, and each patient has a unique story. The disease condition affects psychological and social aspects, greatly affecting the quality of life. The disease course is unpredictable, and each patient’s story can be seen as a lifelong journey, full of ups and downs. Therefore, it is crucial to know what kind of support is required during the course of their life.Objectives:The aim of this study is to examine the life story of patients with RA and clarify a common situation in their stories in order to consider what kind of support is needed.Methods:This is a qualitative study using life story interview for patients with RA in Japan. Interview included disease history, patients’ behaviors, effects on daily life, the patients’ perspectives regarding psychological considerations and useful support. Data were analyzed using content analysis. This study was approved by the ethics committee and informed consent was obtained.Results:Eight patients participated in this study. They were all females and the average age was 57 years old. As a result of the categorization, we extracted the following eight situations: (1) Emergence of symptom; patients thought joint pain would go away, however, the symptom did not improve and began to affect their daily life and work, (2) Choose a hospital to visit; pain and anxiety have continued and decided to visit a hospital, (3) Encounter with their doctors; patients expected their doctor to relieve their pain, while they were afraid of being told that they were suffering from a serious disease. (4) Diagnosis of RA; patients were shocked when diagnosed and anxious about what would happen and wondered why they had such a disease, (5) Choice of treatment; patients were afraid of the side effects. They wanted to make a decision discussing with their doctor, but they could not understand the explanation about drugs well and, therefore, followed the doctor’s opinion. (6) Change of treatment; a biological agent was often recommended. Patients were also worried about side effects and the financial burden. (7) Remission or stable phase; they felt better mentally too, however, they often felt anxiety about disease flare, side effect of drugs and financial burden, and (8) Flare and remission; patients felt shocked and disappointed when RA flared, and then, they noticed that patients with RA had alternating periods of relapse and remission and they had to live with RA.These interviews revealed repeated worsening and improvement of symptoms and many similar repeated psychological reactions such as anxiety, shock, denial, conflict, acceptance, giving up and relief. To cope with these fluctuating disease and mental conditions, patients were supported by educational and psychological assistance, timely consultations, social life help from nurses and support from their family. The patients considered a trusting relationship with their doctors is necessary. The patients had also realized through their experience the importance of enhancing their own abilities, such as decision-making, prevention of infections and self-management skills. Moreover, they noticed that it is important to have their own goals including hobbies and work.Conclusion:This study elucidated the common behaviors of patients with RA, the impact of RA on their psychological state and daily and social life, and the required support. The psychological condition and daily and social life also had a great influence on medical behavior. Therefore, psychosocial support and establishment of trust between healthcare professionals and patients are crucial. In addition, improving patients’ self-management skills including self-efficacy and empowerment is also necessary. As patients with RA often feel anxious in various situations and expect nurses’ support, nurses should listen to patients, pay attention to their concerns and anxieties, and show a solution-oriented attitude. In order for patients to feel at ease in their Patient Journey, nurses should sail with them while maintaining a patient-centered perspective.Disclosure of Interests:None declared
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Marinkovich M, Forte S, Oliver S, Dolorito J, Sridhar K, Liu H, Reitze N, Sarma N, Krishnan S. 155 Assessment of safety in repeat dosing of an in vivo topical gene therapy for the treatment of recessive dystrophic epidermolysis bullosa (RDEB) in a phase I/II trial. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.02.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Bailey JA, Khawaja A, Andrews H, Weller J, Chapman C, Morling JR, Oliver S, Castle S, Simpson JA, Humes DJ, Banerjea A. GP access to FIT increases the proportion of colorectal cancers detected on urgent pathways in symptomatic patients in Nottingham. Surgeon 2021; 19:93-102. [PMID: 32327303 DOI: 10.1016/j.surge.2020.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/13/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Service evaluation of GP access to Faecal Immunochemical Test (FIT) for colorectal cancer (CRC) detection in Nottinghamshire and use of FIT for "rule out", "rule in" and "first test selection". DESIGN Retrospective audit of FIT results, CRC outcomes and resource utilisation before and after introduction of FIT in Primary Care in November 2017. Data from the new pathway up to December 2018 was compared with previous experience. RESULTS Between November 2017 and December 2018, 6747 GP FIT test requests yielded 5733 FIT results, of which 4082 (71.2%) were <4.0 μg Hb/g faeces, 579 (10.1%) were 4.0-9.9 μg Hb/g faeces, 836 (14.6%) were 10.0-149.9 μg Hb/g faeces, and 236 (4.1%) were ≥150.0 μg Hb/g faeces. The proportion of "rule out" results <4.0 μg Hb/g faeces was significantly higher than in the Getting FIT cohort (71.2% vs 60.4%, Chi squared 42.8, p < 0.0001) and the proportion of "rule in" results ≥150.0 μg Hb/g faeces was significantly lower (4.1% vs 8.1%, Chi squared 27.3,P < 0.0001). There was a 33% rise in urgent referrals across Nottingham overall during the evaluation period. 2 CRC diagnoses were made in 4082 patients who had FIT<4.0 μg Hb/g faeces. 58.4% of new CRC diagnoses associated with a positive FIT were early stage cancers (Stage I and II). The proportion of all CRC diagnoses that follow an urgent referral s rose after introduction of FIT. CONCLUSIONS FIT allows GP's to select a more appropriate cohort for urgent investigation without a large number of missed diagnoses. FIT appears to promise a "stage migration" effect which may ultimately improve CRC outcomes.
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Bailey JA, Weller J, Chapman CJ, Ford A, Hardy K, Oliver S, Morling JR, Simpson JA, Humes DJ, Banerjea A. Faecal immunochemical testing and blood tests for prioritization of urgent colorectal cancer referrals in symptomatic patients: a 2-year evaluation. BJS Open 2021; 5:6162967. [PMID: 33693553 PMCID: PMC7947575 DOI: 10.1093/bjsopen/zraa056] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/15/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND A novel pathway incorporating faecal immunochemical testing (FIT) for rapid colorectal cancer diagnosis (RCCD) was introduced in 2017. This paper reports on the service evaluation after 2 years of pathway implementation. METHODS The RCCD protocol was based on FIT, blood results and symptoms to stratify adult patients in primary care. Two-week-wait (2WW) investigation was indicated for patients with rectal bleeding, rectal mass and faecal haemoglobin (fHb) level of 10 µg Hb/g faeces or above or 4 µg Hb/g faeces or more in the presence of anaemia, low ferritin or thrombocytosis, in all other symptom groups. Patients with 100 µg Hb/g faeces or above had expedited investigation . A retrospective audit of colorectal cancer detected between 2017 and 2019 was conducted, fHb thresholds were reviewed and critically assessed for cancer diagnoses. RESULTS In 2 years, 14788 FIT tests were dispatched with 13361 (90.4 per cent) completed returns. Overall, fHb was less than 4 µg Hb/g faeces in 9208 results (68.9 per cent), 4-9.9 µg Hb/g in 1583 (11.8 per cent), 10-99.9 µg Hb/g in 1850 (13.8 per cent) and 100 µg Hb/g faeces or above in 720 (5.4 per cent). During follow-up (median 10.4 months), 227 colorectal cancers were diagnosed. The cancer detection rate was 0.1 per cent in patients with fHb below 4 µg Hb/g faeces, 0.6 per cent in those with fHb 4-9.9 µg Hb/g faeces, 3.3 per cent for fHb 10-99.9 µg Hb/g faeces and 20.7 per cent for fHb 100 µg Hb/g faeces or above. The detection rate in the cohort with 10-19.9 µg Hb/g faeces was 1.4 per cent, below the National Institute for Health and Care Excellence threshold for urgent referral. The colorectal cancer rate in patients with fHb below 20 µg Hb/g faeces was less than 0.3 per cent. CONCLUSION Use of FIT to "rule out" urgent referral from primary care misses a small number of cases. The threshold for referral may be adjusted with blood results to improve stratification .
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Ford E, Sheppard J, Oliver S, Rooney P, Banerjee S, Cassell JA. Automated detection of patients with dementia whose symptoms have been identified in primary care but have no formal diagnosis: a retrospective case-control study using electronic primary care records. BMJ Open 2021; 11:e039248. [PMID: 33483436 PMCID: PMC7831719 DOI: 10.1136/bmjopen-2020-039248] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
OBJECTIVES UK statistics suggest only two-thirds of patients with dementia get a diagnosis recorded in primary care. General practitioners (GPs) report barriers to formally diagnosing dementia, so some patients may be known by GPs to have dementia but may be missing a diagnosis in their patient record. We aimed to produce a method to identify these 'known but unlabelled' patients with dementia using data from primary care patient records. DESIGN Retrospective case-control study using routinely collected primary care patient records from Clinical Practice Research Datalink. SETTING UK general practice. PARTICIPANTS English patients aged >65 years, with a coded diagnosis of dementia recorded in 2000-2012 (cases), matched 1:1 with patients with no diagnosis code for dementia (controls). INTERVENTIONS Eight coded and nine keyword concepts indicating symptoms, screening tests, referrals and care for dementia recorded in the 5 years before diagnosis. We trialled machine learning classifiers to discriminate between cases and controls (logistic regression, naïve Bayes, random forest). PRIMARY AND SECONDARY OUTCOMES The outcome variable was dementia diagnosis code; the accuracy of classifiers was assessed using area under the receiver operating characteristic curve (AUC); the order of features contributing to discrimination was examined. RESULTS 93 426 patients were included; the median age was 83 years (64.8% women). Three classifiers achieved high discrimination and performed very similarly. AUCs were 0.87-0.90 with coded variables, rising to 0.90-0.94 with keywords added. Feature prioritisation was different for each classifier; commonly prioritised features were Alzheimer's prescription, dementia annual review, memory loss and dementia keywords. CONCLUSIONS It is possible to detect patients with dementia who are known to GPs but unlabelled with a diagnostic code, with a high degree of accuracy in electronic primary care record data. Using keywords from clinic notes and letters improves accuracy compared with coded data alone. This approach could improve identification of dementia cases for record-keeping, service planning and delivery of good quality care.
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Ford E, Starlinger J, Rooney P, Oliver S, Banerjee S, van Marwijk H, Cassell J. Could dementia be detected from UK primary care patients' records by simple automated methods earlier than by the treating physician? A retrospective case-control study. Wellcome Open Res 2020; 5:120. [PMID: 32766457 PMCID: PMC7385545 DOI: 10.12688/wellcomeopenres.15903.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2020] [Indexed: 12/18/2022] Open
Abstract
Background: Timely diagnosis of dementia is a policy priority in the United Kingdom (UK). Primary care physicians receive incentives to diagnose dementia; however, 33% of patients are still not receiving a diagnosis. We explored automating early detection of dementia using data from patients' electronic health records (EHRs). We investigated: a) how early a machine-learning model could accurately identify dementia before the physician; b) if models could be tuned for dementia subtype; and c) what the best clinical features were for achieving detection. Methods: Using EHRs from Clinical Practice Research Datalink in a case-control design, we selected patients aged >65y with a diagnosis of dementia recorded 2000-2012 (cases) and matched them 1:1 to controls; we also identified subsets of Alzheimer's and vascular dementia patients. Using 77 coded concepts recorded in the 5 years before diagnosis, we trained random forest classifiers, and evaluated models using Area Under the Receiver Operating Characteristic Curve (AUC). We examined models by year prior to diagnosis, subtype, and the most important features contributing to classification. Results: 95,202 patients (median age 83y; 64.8% female) were included (50% dementia cases). Classification of dementia cases and controls was poor 2-5 years prior to physician-recorded diagnosis (AUC range 0.55-0.65) but good in the year before (AUC: 0.84). Features indicating increasing cognitive and physical frailty dominated models 2-5 years before diagnosis; in the final year, initiation of the dementia diagnostic pathway (symptoms, screening and referral) explained the sudden increase in accuracy. No substantial differences were seen between all-cause dementia and subtypes. Conclusions: Automated detection of dementia earlier than the treating physician may be problematic, if using only primary care data. Future work should investigate more complex modelling, benefits of linking multiple sources of healthcare data and monitoring devices, or contextualising the algorithm to those cases that the GP would need to investigate.
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Fusama M, Uda M, Matsumura H, Van Eijk-Hustings Y, Oliver S, Nakahara H. THU0646-HPR EXPLORING THE ROLE OF NURSE IN RHEUMATIC CARE AND FEASIBILITY OF ENHANCING TREAT TO TARGET STRATEGIES IN JAPAN. Ann Rheum Dis 2020. [DOI: 10.1136/annrheumdis-2020-eular.5315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:The role of rheumatology nurses is considered important for the implementation of T2T [1]. For nurses’ contribution to implementation of the T2T strategy, it is necessary to explore the nurses’ opinion on their roles in real clinical practice.Objectives:The aim of this study is to evaluate what is required for nurses to implement T2T in real clinical practice in Japan.Methods:Registered nurses engaged in rheumatic care in clinical practice in Japan were enrolled. Focus group interviews were conducted exploring ‘What is necessary for RA nurses to implement T2T’using semi-structured interviews. Data analysis was used with Krippendorff’s content analysis method.Results:24 nurses (all females) from 10 hospitals were enrolled in this study. The results of the qualitative analysis were categorized in 10 main categories, derived from 37 subcategories based on 64 different codes: (1) provide basic knowledge of RA, (2) provide knowledge of RA drugs, (3) provide knowledge and skills of self-monitoring, (4) enhance self-efficacy and support self-management, (5) support decision-making, (6) psychological and social support, (7) understand the diversity and feelings of patients and their families, (8) support based on individual needs, (9) ensure continuing educational opportunities for nurses to enable the provision of high quality care, (10) collaborate with multidisciplinary teams.These categories are mostly covered in the contents of the 2018 updated EULAR recommendations for the role of nurses except “evidence-based rheumatic care”, “telehealth” and “comprehensive participation in disease management”.Conclusion:These findings indicate the areas of exploration including further educational and training needs, attitudes and the professional scope for nurses to extend their roles to provide greater value to patient care.In Japan, evidence-based RA nursing and telehealth systems have not yet been established. In addition, therapeutic intervention by nurses and nurse-led clinic are not permitted. Our results might reflect this situation and possibly elucidates the gap between EULAR’s evidence-based recommendations and opinions of Japanese nurses working in daily clinical practice. As evidence-based nursing is considered to be crucial from both cost-effectiveness and improvement of patients QOL, this result also might shed light on what we need for future better rheumatic nursing in Japan.References:[1]van Eijk- Hustings Y, et al. Ann Rheum Dis 2012;71: 13–19.Disclosure of Interests:MIE FUSAMA: None declared, Miyabi Uda: None declared, Harumi Matsumura: None declared, Yvonne van Eijk-Hustings Grant/research support from: grand from sanofi and UCB, Consultant of: fee from amgen, Susan Oliver: None declared, Hideko Nakahara: None declared
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Chapman C, Thomas C, Morling J, Tangri A, Oliver S, Simpson JA, Humes DJ, Banerjea A. Early clinical outcomes of a rapid colorectal cancer diagnosis pathway using faecal immunochemical testing in Nottingham. Colorectal Dis 2020; 22:679-688. [PMID: 31876975 DOI: 10.1111/codi.14944] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 11/29/2019] [Indexed: 12/29/2022]
Abstract
AIM We introduced primary care access to faecal immunochemical testing (FIT) as a stratification tool for symptomatic patients considered to be at risk of colorectal cancer (CRC) prior to urgent referral. We aimed to evaluate clinical and pathway outcomes during the first 6 months of this novel approach. METHOD FIT was recommended for all patients who consulted their general practitioner with lower gastrointestinal symptoms other than rectal bleeding and rectal mass. We undertook a retrospective audit of the results of FIT, related clinical outcomes and resource utilization on prospectively logged cases between November 2017 and May 2018. RESULTS Of the 1862 FIT kits dispatched by post 91.4% were returned, with a median return time of 7 days (range 2-110 days); however, 1.3% of returned kits could not be analysed. FIT results ≥ 150.0 μg haemoglobin (Hb)/g faeces identified patients with a significantly higher risk of CRC (30.9% vs 1.4%, chi-square 167.1, P < 0.0001). FIT results ≥ 10.0 μg Hb/g faeces identified patients with significantly higher risk of significant noncancer bowel pathology (24.1% vs 4.9%, chi-square 73.6, P < 0.0001) and FIT results < 4.0 μg Hb/g faeces identified a group more likely to have non-CRC pathology (5.1% vs 2.4%, chi-square 3.9, P < 0.05). The CRC detection rate in 531 patients investigated after a FIT result of < 4.0 μg Hb/g faeces was 0.2%. In 899 investigated patients, a FIT result with a threshold of 4.0 μg Hb/g faeces had sensitivity 97.2% (85.5-99.9% CI), specificity 61.4% (58.1-64.7% CI), negative predictive value 99.8% (98.7-100.0% CI) and positive predictive value 9.5% (8.7-10.4% CI). CONCLUSION A symptomatic pathway incorporating FIT is feasible and appears more clinically effective than pathways based on age and symptoms alone.
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Nielsen N, White P, Smith R, Smith N, Sykes J, Alpugan G, Oliver S, Power R, Asmutaite J, Gebbett C, Northfield F. Using CSP hip fracture standards to review quality of hip fracture rehabilitation in a central London hospital trust. Physiotherapy 2020. [DOI: 10.1016/j.physio.2020.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Ford E, Rooney P, Hurley P, Oliver S, Bremner S, Cassell J. Can the Use of Bayesian Analysis Methods Correct for Incompleteness in Electronic Health Records Diagnosis Data? Development of a Novel Method Using Simulated and Real-Life Clinical Data. Front Public Health 2020; 8:54. [PMID: 32211363 PMCID: PMC7066995 DOI: 10.3389/fpubh.2020.00054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/14/2020] [Indexed: 01/21/2023] Open
Abstract
Background: Patient health information is collected routinely in electronic health records (EHRs) and used for research purposes, however, many health conditions are known to be under-diagnosed or under-recorded in EHRs. In research, missing diagnoses result in under-ascertainment of true cases, which attenuates estimated associations between variables and results in a bias toward the null. Bayesian approaches allow the specification of prior information to the model, such as the likely rates of missingness in the data. This paper describes a Bayesian analysis approach which aimed to reduce attenuation of associations in EHR studies focussed on conditions characterized by under-diagnosis. Methods: Study 1: We created synthetic data, produced to mimic structured EHR data where diagnoses were under-recorded. We fitted logistic regression (LR) models with and without Bayesian priors representing rates of misclassification in the data. We examined the LR parameters estimated by models with and without priors. Study 2: We used EHR data from UK primary care in a case-control design with dementia as the outcome. We fitted LR models examining risk factors for dementia, with and without generic prior information on misclassification rates. We examined LR parameters estimated by models with and without the priors, and estimated classification accuracy using Area Under the Receiver Operating Characteristic. Results: Study 1: In synthetic data, estimates of LR parameters were much closer to the true parameter values when Bayesian priors were added to the model; with no priors, parameters were substantially attenuated by under-diagnosis. Study 2: The Bayesian approach ran well on real life clinic data from UK primary care, with the addition of prior information increasing LR parameter values in all cases. In multivariate regression models, Bayesian methods showed no improvement in classification accuracy over traditional LR. Conclusions: The Bayesian approach showed promise but had implementation challenges in real clinical data: prior information on rates of misclassification was difficult to find. Our simple model made a number of assumptions, such as diagnoses being missing at random. Further development is needed to integrate the method into studies using real-life EHR data. Our findings nevertheless highlight the importance of developing methods to address missing diagnoses in EHR data.
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Ford E, Rooney P, Oliver S, Hoile R, Hurley P, Banerjee S, van Marwijk H, Cassell J. Identifying undetected dementia in UK primary care patients: a retrospective case-control study comparing machine-learning and standard epidemiological approaches. BMC Med Inform Decis Mak 2019; 19:248. [PMID: 31791325 PMCID: PMC6889642 DOI: 10.1186/s12911-019-0991-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Identifying dementia early in time, using real world data, is a public health challenge. As only two-thirds of people with dementia now ultimately receive a formal diagnosis in United Kingdom health systems and many receive it late in the disease process, there is ample room for improvement. The policy of the UK government and National Health Service (NHS) is to increase rates of timely dementia diagnosis. We used data from general practice (GP) patient records to create a machine-learning model to identify patients who have or who are developing dementia, but are currently undetected as having the condition by the GP. METHODS We used electronic patient records from Clinical Practice Research Datalink (CPRD). Using a case-control design, we selected patients aged >65y with a diagnosis of dementia (cases) and matched them 1:1 by sex and age to patients with no evidence of dementia (controls). We developed a list of 70 clinical entities related to the onset of dementia and recorded in the 5 years before diagnosis. After creating binary features, we trialled machine learning classifiers to discriminate between cases and controls (logistic regression, naïve Bayes, support vector machines, random forest and neural networks). We examined the most important features contributing to discrimination. RESULTS The final analysis included data on 93,120 patients, with a median age of 82.6 years; 64.8% were female. The naïve Bayes model performed least well. The logistic regression, support vector machine, neural network and random forest performed very similarly with an AUROC of 0.74. The top features retained in the logistic regression model were disorientation and wandering, behaviour change, schizophrenia, self-neglect, and difficulty managing. CONCLUSIONS Our model could aid GPs or health service planners with the early detection of dementia. Future work could improve the model by exploring the longitudinal nature of patient data and modelling decline in function over time.
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Chapman C, Bunce J, Oliver S, Ng O, Tangri A, Rogers R, Logan RF, Humes DJ, Banerjea A. Service evaluation of faecal immunochemical testing and anaemia for risk stratification in the 2-week-wait pathway for colorectal cancer. BJS Open 2019; 3:395-402. [PMID: 31183456 PMCID: PMC6551399 DOI: 10.1002/bjs5.50131] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 11/19/2018] [Indexed: 12/21/2022] Open
Abstract
Background New national guidance on urgent referral for investigation of colorectal cancer included faecal occult blood testing in 2015. A service evaluation of faecal immunochemical testing (FIT) and anaemia as risk stratification tools in symptomatic patients suspected of having CRC was undertaken. Methods Postal FIT was incorporated into the colorectal cancer 2-week wait (2WW) pathway for all patients without rectal bleeding in 2016. Patients were investigated in the 2WW pathway as normal, and outcomes of investigations were recorded prospectively. Anaemia was defined as a haemoglobin level below 120 g/l in women and 130 g/l in men. Results FIT kits were sent to 1106 patients, with an 80·9 per cent return rate; 810 patients completed investigations and 40 colorectal cancers were diagnosed (4·9 per cent). FIT results were significantly higher in patients with anaemia (median (i.q.r.) 4·8 (0·8-34·1) versus 1·2 (0-6·4) μg Hb/g faeces in those without anaemia; P < 0·001). Some 60·4 per cent of patients (538 of 891) had a result lower than 4 μg haemoglobin (Hb) per g faeces (limit of detectability), and 69·7 per cent (621 of 891) had less than 10 μg Hb/g faeces. Some 60 per cent of patients with colorectal cancer had a FIT reading of 150 μg Hb/g faeces or more. For five colorectal cancers diagnosed in patients with a FIT value below 10 μg Hb/g faeces, there was either a palpable rectal mass or the patient was anaemic. A FIT result of more than 4 μg Hb/g faeces had 97·5 per cent sensitivity and 64·5 per cent specificity for a diagnosis of colorectal cancer. A FIT result above 4 μg Hb/g faeces and/or anaemia had a 100 per cent sensitivity and 45·3 per cent specificity for colorectal cancer diagnosis. Conclusion FIT is most useful at the extremes of detectability; strongly positive readings predict high rates of colorectal cancer and other significant pathology, whereas very low readings in the absence of anaemia or a palpable rectal mass identify a group with very low risk. High return rates for FIT within this 2WW pathway indicate its acceptability.
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Hurley PD, Oliver S, Mehta A. Creating longitudinal datasets and cleaning existing data identifiers in a cystic fibrosis registry using a novel Bayesian probabilistic approach from astronomy. PLoS One 2018; 13:e0199815. [PMID: 29985939 PMCID: PMC6037350 DOI: 10.1371/journal.pone.0199815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 06/14/2018] [Indexed: 11/18/2022] Open
Abstract
Patient registry data are commonly collected as annual snapshots that need to be amalgamated to understand the longitudinal progress of each patient. However, patient identifiers can either change or may not be available for legal reasons when longitudinal data are collated from patients living in different countries. Here, we apply astronomical statistical matching techniques to link individual patient records that can be used where identifiers are absent or to validate uncertain identifiers. We adopt a Bayesian model framework used for probabilistically linking records in astronomy. We adapt this and validate it across blinded, annually collected data. This is a high-quality (Danish) sub-set of data held in the European Cystic Fibrosis Society Patient Registry (ECFSPR). Our initial experiments achieved a precision of 0.990 at a recall value of 0.987. However, detailed investigation of the discrepancies uncovered typing errors in 27 of the identifiers in the original Danish sub-set. After fixing these errors to create a new gold standard our algorithm correctly linked individual records across years achieving a precision of 0.997 at a recall value of 0.987 without recourse to identifiers. Our Bayesian framework provides the probability of whether a pair of records belong to the same patient. Unlike other record linkage approaches, our algorithm can also use physical models, such as body mass index curves, as prior information for record linkage. We have shown our framework can create longitudinal samples where none existed and validate pre-existing patient identifiers. We have demonstrated that in this specific case this automated approach is better than the existing identifiers.
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Ford E, Greenslade N, Paudyal P, Bremner S, Smith HE, Banerjee S, Sadhwani S, Rooney P, Oliver S, Cassell J. Predicting dementia from primary care records: A systematic review and meta-analysis. PLoS One 2018; 13:e0194735. [PMID: 29596471 PMCID: PMC5875793 DOI: 10.1371/journal.pone.0194735] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 03/08/2018] [Indexed: 01/11/2023] Open
Abstract
INTRODUCTION Possible dementia is usually identified in primary care by general practitioners (GPs) who refer to specialists for diagnosis. Only two-thirds of dementia cases are currently recorded in primary care, so increasing the proportion of cases diagnosed is a strategic priority for the UK and internationally. Variables in the primary care record may indicate risk of developing dementia, and could be combined in a predictive model to help find patients who are missing a diagnosis. We conducted a meta-analysis to identify clinical entities with potential for use in such a predictive model for dementia in primary care. METHODS AND FINDINGS We conducted a systematic search in PubMed, Web of Science and primary care database bibliographies. We included cohort or case-control studies which used routinely collected primary care data, to measure the association between any clinical entity and dementia. Meta-analyses were performed to pool odds ratios. A sensitivity analysis assessed the impact of non-independence of cases between studies. From a sift of 3836 papers, 20 studies, all European, were eligible for inclusion, comprising >1 million patients. 75 clinical entities were assessed as risk factors for all cause dementia, Alzheimer's (AD) and Vascular dementia (VaD). Data included were unexpectedly heterogeneous, and assumptions were made about definitions of clinical entities and timing as these were not all well described. Meta-analysis showed that neuropsychiatric symptoms including depression, anxiety, and seizures, cognitive symptoms, and history of stroke, were positively associated with dementia. Cardiovascular risk factors such as hypertension, heart disease, dyslipidaemia and diabetes were positively associated with VaD and negatively with AD. Sensitivity analyses showed similar results. CONCLUSIONS These findings are of potential value in guiding feature selection for a risk prediction tool for dementia in primary care. Limitations include findings being UK-focussed. Further predictive entities ascertainable from primary care data, such as changes in consulting patterns, were absent from the literature and should also be explored in future studies.
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Favaloro EJ, Mohammed S, Oliver S. The increasing maturity of the von Willebrand factor collagen binding in von Willebrand disease diagnosis. Haemophilia 2017; 24:20-23. [DOI: 10.1111/hae.13369] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2017] [Indexed: 12/29/2022]
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Favaloro EJ, Oliver S, Mohammed S, Ahuja M, Grzechnik E, Azimulla S, McDonald J, Lima-Oliveira G, Lippi G. Potential misdiagnosis of von Willebrand disease and haemophilia caused by ineffective mixing of thawed plasma. Haemophilia 2017; 23:e436-e443. [DOI: 10.1111/hae.13305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2017] [Indexed: 12/15/2022]
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Favaloro EJ, Oliver S. Evaluation of a new commercial von Willebrand factor multimer assay. Haemophilia 2017; 23:e373-e377. [PMID: 28497866 DOI: 10.1111/hae.13261] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2017] [Indexed: 12/21/2022]
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Martin P, Gillen M, Ritter J, Mathews D, Brealey C, Surry D, Oliver S, Holmes V, Severin P, Elsby R. Effects of Fostamatinib on the Pharmacokinetics of Oral Contraceptive, Warfarin, and the Statins Rosuvastatin and Simvastatin: Results From Phase I Clinical Studies. Drugs R D 2016; 16:93-107. [PMID: 26748647 PMCID: PMC4767723 DOI: 10.1007/s40268-015-0120-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Fostamatinib is a spleen tyrosine kinase inhibitor that has been investigated as therapy for rheumatoid arthritis and immune thrombocytopenic purpura. The present studies assessed the potential for pharmacokinetic interaction between fostamatinib and the commonly prescribed medications oral contraceptive (OC), warfarin, and statins (rosuvastatin, simvastatin) in healthy subjects. METHODS The OC study was a crossover study over two 28-day treatment periods (Microgynon(®) 30 plus placebo or fostamatinib). Concentrations of OC constituents (ethinyl estradiol/levonorgestrel) were measured. Effects on warfarin pharmacokinetics and pharmacodynamics were assessed (21-day study). Warfarin was administered on days 1 and 14, fostamatinib on days 8-20. The statin study was a two-period, fixed-sequence study of the effects of fostamatinib on exposure to rosuvastatin or simvastatin (single doses). Safety was assessed throughout. RESULTS Fostamatinib co-administration with OC increased exposure to ethinyl estradiol [area under the plasma concentration-time curve at steady state (AUCss) 28% [confidence interval (CI 90%) 21-36]; maximum plasma concentration (Cmax) at steady state (Cmax,ss) 34% (CI 26-43)], but not levonorgestrel (AUCss 5%; Cmax,ss -3%), while exposure to luteinizing hormone and follicle-stimulating hormone decreased (≈ 20%). Fostamatinib did not affect the pharmacokinetics/pharmacodynamics of warfarin to a clinically relevant extent, but caused an upward trend in AUC for both R- and S-warfarin [18% (CI 13-23) and 13% (CI 7-19)]. Fostamatinib increased rosuvastatin AUC by 96% (CI 78-115) and Cmax by 88% (CI 69-110), and increased simvastatin acid AUC by 74% (CI 50-102) and Cmax by 83% (CI 57-113). CONCLUSION Fostamatinib exhibits drug-drug interactions when co-administered with OC, simvastatin, or rosuvastatin, with the AUC of statins almost doubling. Fostamatinib did not exhibit a clinically relevant DDI on warfarin.
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González-Pérez V, Arana E, Bartrés A, Oliver S, Pellicer B, Cruz J, Barrios M, Rubio L. EP-2050: The assessment of fractal dimension with Dual Energy CT gives information on lung cancer biomarkers. Radiother Oncol 2016. [DOI: 10.1016/s0167-8140(16)33301-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Goldenberg SD, Brown S, Edwards L, Gnanarajah D, Howard P, Jenkins D, Nayar D, Pasztor M, Oliver S, Planche T, Sandoe JAT, Wade P, Whitney L. The impact of the introduction of fidaxomicin on the management of Clostridium difficile infection in seven NHS secondary care hospitals in England: a series of local service evaluations. Eur J Clin Microbiol Infect Dis 2015; 35:251-9. [PMID: 26661400 PMCID: PMC4724367 DOI: 10.1007/s10096-015-2538-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 11/09/2015] [Indexed: 11/24/2022]
Abstract
Clostridium difficile infection (CDI) is associated with high mortality. Reducing incidence is a priority for patients, clinicians, the National Health Service (NHS) and Public Health England alike. In June 2012, fidaxomicin (FDX) was launched for the treatment of adults with CDI. The objective of this evaluation was to collect robust real-world data to understand the effectiveness of FDX in routine practice. In seven hospitals introducing FDX between July 2012 and July 2013, data were collected retrospectively from medical records on CDI episodes occurring 12 months before/after the introduction of FDX. All hospitalised patients aged ≥18 years with primary CDI (diarrhoea with presence of toxin A/B without a previous CDI in the previous 3 months) were included. Recurrence was defined as in-patient diarrhoea re-emergence requiring treatment any time within 3 months after the first episode. Each hospital had a different protocol for the use of FDX. In hospitals A and B, where FDX was used first line for all primary and recurrent episodes, the recurrence rate reduced from 10.6 % to 3.1 % and from 16.3 % to 3.1 %, with a significant difference in 28-day mortality from 18.2 % to 3.1 % (p < 0.05) and 17.3 % to 6.3 % (p < 0.05) for hospitals A and B, respectively. In hospitals using FDX in selected patients only, the changes in recurrence rates and mortality were less marked. The pattern of adoption of FDX appears to affect its impact on CDI outcome, with maximum reduction in recurrence and all-cause mortality where it is used as first-line treatment.
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Gossec L, Smolen JS, Ramiro S, de Wit M, Cutolo M, Dougados M, Emery P, Landewé R, Oliver S, Aletaha D, Betteridge N, Braun J, Burmester G, Cañete JD, Damjanov N, FitzGerald O, Haglund E, Helliwell P, Kvien TK, Lories R, Luger T, Maccarone M, Marzo-Ortega H, McGonagle D, McInnes IB, Olivieri I, Pavelka K, Schett G, Sieper J, van den Bosch F, Veale DJ, Wollenhaupt J, Zink A, van der Heijde D. European League Against Rheumatism (EULAR) recommendations for the management of psoriatic arthritis with pharmacological therapies: 2015 update. Ann Rheum Dis 2015; 75:499-510. [PMID: 26644232 DOI: 10.1136/annrheumdis-2015-208337] [Citation(s) in RCA: 620] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/30/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Since the publication of the European League Against Rheumatism recommendations for the pharmacological treatment of psoriatic arthritis (PsA) in 2012, new evidence and new therapeutic agents have emerged. The objective was to update these recommendations. METHODS A systematic literature review was performed regarding pharmacological treatment in PsA. Subsequently, recommendations were formulated based on the evidence and the expert opinion of the 34 Task Force members. Levels of evidence and strengths of recommendations were allocated. RESULTS The updated recommendations comprise 5 overarching principles and 10 recommendations, covering pharmacological therapies for PsA from non-steroidal anti-inflammatory drugs (NSAIDs), to conventional synthetic (csDMARD) and biological (bDMARD) disease-modifying antirheumatic drugs, whatever their mode of action, taking articular and extra-articular manifestations of PsA into account, but focusing on musculoskeletal involvement. The overarching principles address the need for shared decision-making and treatment objectives. The recommendations address csDMARDs as an initial therapy after failure of NSAIDs and local therapy for active disease, followed, if necessary, by a bDMARD or a targeted synthetic DMARD (tsDMARD). The first bDMARD would usually be a tumour necrosis factor (TNF) inhibitor. bDMARDs targeting interleukin (IL)12/23 (ustekinumab) or IL-17 pathways (secukinumab) may be used in patients for whom TNF inhibitors are inappropriate and a tsDMARD such as a phosphodiesterase 4-inhibitor (apremilast) if bDMARDs are inappropriate. If the first bDMARD strategy fails, any other bDMARD or tsDMARD may be used. CONCLUSIONS These recommendations provide stakeholders with an updated consensus on the pharmacological treatment of PsA and strategies to reach optimal outcomes in PsA, based on a combination of evidence and expert opinion.
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Wilman E, Megone C, Oliver S, Duley L, Gyte G, Wright JM. The ethical issues regarding consent to clinical trials with pre-term or sick neonates: a systematic review (framework synthesis) of the empirical research. Trials 2015; 16:502. [PMID: 26537492 PMCID: PMC4634156 DOI: 10.1186/s13063-015-0957-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/14/2015] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Conducting clinical trials with pre-term or sick infants is important if care for this population is to be underpinned by sound evidence. Yet approaching parents at this difficult time raises challenges for the obtaining of valid informed consent to such research. This study asked: what light does the empirical literature cast on an ethically defensible approach to the obtaining of informed consent in perinatal clinical trials? METHODS A systematic search identified 49 studies. Analysis began by applying philosophical frameworks which were then refined in light of the concepts emerging from empirical studies to present a coherent picture of a broad literature. RESULTS Between them, studies addressed the attitudes of both parents and clinicians concerning consent in neonatal trials; the validity of the consent process in the neonatal research context; and different possible methods of obtaining consent. CONCLUSIONS Despite a variety of opinions among parents and clinicians there is a strongly and widely held view that it is important that parents do give or decline consent for neonatal participation in trials. However, none of the range of existing consent processes reviewed by the research is satisfactory. A significant gap is evaluation of the widespread practice of emergency 'assent', in which parents assent or refuse their baby's participation as best they can during the emergency and later give full consent to ongoing participation and follow-up. Emergency assent has not been evaluated for its acceptability, how such a process would deal with bad outcomes such as neonatal death between assent and consent, or the extent to which late parental refusal might bias results. This review of a large number of empirical papers, while not making fundamental changes, has refined and developed the conceptual framework from philosophy for examining informed consent in this context.
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MESH Headings
- Attitude of Health Personnel
- Clinical Trials as Topic/ethics
- Emergencies
- Emotions
- Gestational Age
- Health Knowledge, Attitudes, Practice
- Humans
- Infant, Newborn
- Infant, Newborn, Diseases/diagnosis
- Infant, Newborn, Diseases/mortality
- Infant, Newborn, Diseases/therapy
- Infant, Premature
- Motivation
- Parental Consent/ethics
- Parents/psychology
- Research Design
- Risk Assessment
- Volition
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