Genetic influences on epilepsy outcomes: A whole-exome sequencing and health care records data linkage study

OBJECTIVE

This study was undertaken to develop a novel pathway linking genetic data with routinely collected data for people with epilepsy, and to analyze the influence of rare, deleterious genetic variants on epilepsy outcomes.

METHODS

We linked whole-exome sequencing (WES) data with routinely collected primary and secondary care data and natural language processing (NLP)-derived seizure frequency information for people with epilepsy within the Secure Anonymised Information Linkage Databank. The study participants were adults who had consented to participate in the Swansea Neurology Biobank, Wales, between 2016 and 2018. DNA sequencing was carried out as part of the Epi25 collaboration. For each individual, we calculated the total number and cumulative burden of rare and predicted deleterious genetic variants and the total of rare and deleterious variants in epilepsy and drug metabolism genes. We compared these measures with the following outcomes: (1) no unscheduled hospital admissions versus unscheduled admissions for epilepsy, (2) antiseizure medication (ASM) monotherapy versus polytherapy, and (3) at least 1 year of seizure freedom versus <1 year of seizure freedom.

RESULTS

We linked genetic data for 107 individuals with epilepsy (52% female) to electronic health records. Twenty-six percent had unscheduled hospital admissions, and 70% were prescribed ASM polytherapy. Seizure frequency information was linked for 100 individuals, and 10 were seizure-free. There was no significant difference between the outcome groups in terms of the exome-wide and gene-based burden of rare and deleterious genetic variants.

SIGNIFICANCE

We successfully uploaded, annotated, and linked genetic sequence data and NLP-derived seizure frequency data to anonymized health care records in this proof-of-concept study. We did not detect a genetic influence on real-world epilepsy outcomes, but our study was limited by a small sample size. Future studies will require larger (WES) data to establish genetic variant contribution to epilepsy outcomes.

Clinical outcome of open ankle fractures in patients above 70 years of age

BACKGROUND

Open fractures of the ankle are complex injuries requiring multidisciplinary input and are associated with significant morbidity and mortality. However, data on the clinical outcomes of open ankle fracture management in patients older than 70 is minimal.

AIM

To evaluate the clinical outcomes following open ankle fracture management in patients older than 70. Our secondary aim is to look at predictors of poor outcomes.

METHODS

Following local research and audit department registration, 22 years of prospectively collated data from an electronic database in a district general hospital were assessed. All patients older than 70 years of age with an open ankle fracture requiring surgical intervention were identified. Demographic information, the nature, and the number of surgical interventions were collated. Complications, including surgical site infection (SSI), venous thromboembolic events (VTEs) during hospital stay, and mortality rate, were reviewed.

RESULTS

A total of 37 patients were identified (median age: 84 years, range: 70-98); n = 30 females median age: 84 years, range: 70-97); n = 7 males median age: 74 years, range: 71-98)) who underwent surgical intervention after an open ankle fracture. Sixteen patients developed SSIs (43%). Superficial SSIs (n = 8) were managed without surgical intervention and treated with antibiotics and regular dressing changes. Deep SSIs (n = 8; 20%) required a median of 3 (range: 2-9) surgical interventions, with four patients requiring multiple washouts and one patient having metalwork removed. VTE incidence was 5% during the hospital stay. Eight patients died within 30 d, and mortality at one year was 19%. The 10-year mortality rate was 57%. The presence of a history of stroke, cancer, or prolonged inpatient stay was found to be predictive of lower survivorship in this population (log-rank test: cancer P = 0.008, stroke P = 0.001, length of stay > 33 d P = 0.015). The presence of a cardiac history was predictive of wound complications (logistic regression, P = 0.045). Age, number of operations, and diabetic history were found to be predictive of an increase in the length of stay (general linear model; age P < 0.001, number of operations P < 0.001, diabetes P = 0.041).

CONCLUSION

An open ankle fracture in a patient older than 70 years has at least a 20% chance of requiring repeated surgical intervention due to deep SSIs. The presence of a cardiac history appears to be the main predictor for wound complications.

Use of zinc deposited in deciduous teeth as a retrospective measurement of dietary zinc exposure during early development

Purpose

We proposed that zinc (Zn) deposition in deciduous teeth would be a timed record of exposure to this essential micronutrient over very early life. We tested this hypothesis by gathering information on the maternal and child's diet during pregnancy and early infancy and measuring mineral deposition in the dentine at points during deciduous tooth development.

Methods

We developed a short food frequency questionnaire (S-FFQ) to record consumption of food containing Zn during pregnancy and over the first year of life of the child in an Indonesian population. Zn, Sr and Ca were measured by laser ablation ICP-MS in a series of points across the developmental timeline in deciduous teeth extracted from 18 children undergoing the process as part of dental treatment whose mothers completed the SFFQ. Mothers and children were classified into either high Zn or low Zn groups according to calculated daily Zn intake.

Results

The Zn/Sr ratio in dentine deposited over late pregnancy and 0-3 months post-partum was higher (p < 0.001, 2-way ANOVA; p < 0.05 by Holm-Sidak post hoc test) in the teeth of children of mothers classified as high Zn consumers (n = 10) than in children of mothers classified as low Zn consumers (n = 8).

Conclusion

The S-FFQ was validated internally as adequately accurate to measure zinc intake retrospectively during pregnancy and post-partum (∼7 years prior) by virtue of the correlation with measurements of zinc in deciduous teeth. The ratio of Zn/Sr in deciduous teeth appears to be a biomarker of exposure to zinc nutrition during early development and offers promise for use as a record of prior exposure along a timeline for research studies and, potentially, to identify individuals at heightened risk of detrimental impacts of poor early life zinc nutrition on health in later life and to implement preventative interventions.

Effect of a test-and-treat approach to vitamin D supplementation on risk of all cause acute respiratory tract infection and covid-19: phase 3 randomised controlled trial (CORONAVIT)

OBJECTIVE

To determine the effect of population level implementation of a test-and-treat approach to correction of suboptimal vitamin D status (25-hydroxyvitamin D (25(OH)D) <75 nmol/L) on risk of all cause acute respiratory tract infection and covid 19.

DESIGN

Phase 3 open label randomised controlled trial.

SETTING

United Kingdom.

PARTICIPANTS

6200 people aged ≥16 years who were not taking vitamin D supplements at baseline.

INTERVENTIONS

Offer of a postal finger prick test of blood 25(OH)D concentration with provision of a six month supply of lower dose vitamin D (800 IU/day, n=1550) or higher dose vitamin D (3200 IU/day, n=1550) to those with blood 25(OH)D concentration <75 nmol/L, compared with no offer of testing or supplementation (n=3100). Follow-up was for six months.

MAIN OUTCOME MEASURES

The primary outcome was the proportion of participants with at least one swab test or doctor confirmed acute respiratory tract infection of any cause. A secondary outcome was the proportion of participants with swab test confirmed covid-19. Logistic regression was used to calculate odds ratios and associated 95% confidence intervals. The primary analysis was conducted by intention to treat.

RESULTS

Of 3100 participants offered a vitamin D test, 2958 (95.4%) accepted and 2674 (86.3%) had 25(OH)D concentrations <75 nmol/L and received vitamin D supplements (n=1328 lower dose, n=1346 higher dose). Compared with 136/2949 (4.6%) participants in the no offer group, at least one acute respiratory tract infection of any cause occurred in 87/1515 (5.7%) in the lower dose group (odds ratio 1.26, 95% confidence interval 0.96 to 1.66) and 76/1515 (5.0%) in the higher dose group (1.09, 0.82 to 1.46). Compared with 78/2949 (2.6%) participants in the no offer group, 55/1515 (3.6%) developed covid-19 in the lower dose group (1.39, 0.98 to 1.97) and 45/1515 (3.0%) in the higher dose group (1.13, 0.78 to 1.63).

CONCLUSIONS

Among people aged 16 years and older with a high baseline prevalence of suboptimal vitamin D status, implementation of a population level test-and-treat approach to vitamin D supplementation was not associated with a reduction in risk of all cause acute respiratory tract infection or covid-19.

TRIAL REGISTRATION

ClinicalTrials.gov NCT04579640.

A population-level study into health vulnerabilities of mothers and fathers involved in public law care proceedings in Wales, UK

ObjectivesUnder section 31 (s.31) of the UK Children Act 1989, public law care proceedings can be issued if there is concern a child is subject to, or at risk of significant harm. We examined health vulnerabilities of parents involved in public law care proceedings in the two-year period prior to involvement. ApproachOur study created an anonymised individual-level population-based cohort, with a matched comparison group of parents in Wales who were not subject to care proceedings, matched on age, sex and deprivation. Family court data provided by Cafcass Cymru were linked to population-level healthcare records held within the Secure Anonymised Information Linkage (SAIL) Databank. Demographic characteristics, overall health service use and health profiles of parents of children subject to s.31 care proceedings between 2011 and 2019 were examined. ResultsData were available for 8,821 parents involved in care proceedings between 2011 and 2019, with a comparison group of 32,006 parents. Nearly half (47.6%) of cohort parents resided in the most deprived quintile. Higher levels of healthcare use were found for cohort mothers and fathers compared to the comparison group across multiple healthcare settings, with the most pronounced differences for emergency department attendances (59.3% vs 37.0%). Health conditions with the largest variation between groups were related to mental health (43.6% vs 16.0%), substance use (19.4% vs 1.6%) and injuries (41.5% vs 23.6%). ConclusionThis study highlights the heightened socioeconomic and health vulnerabilities of parents who experience care proceedings concerning a child. Better understanding of the needs and vulnerabilities of this population may provide opportunities to improve a range of support and preventative interventions that respond to crises in the community.

BREATHE: The Health Data Research Hub for Respiratory Health

ObjectivesThe BREATHE Health Data Research Hub for Respiratory Health was formed in October 2019 as a multi-site academic consortium with multiple industrial partners via an Industry Forum and across its wider network. BREATHE’s main mission is enhancing data services within respiratory science, funded by the UKRI Industrial Strategy Challenge Fund. ApproachBREATHE leveraged expertise across its founding sites and industrial partners to create data services which could be used by multiple sectors of collaborator. Across the founding sites, BREATHE was able to mobilise datasets housed within national TREs to form real-world evidence eCohorts for rapid and efficient respiratory study (Asthma, COPD, ILD), and has worked with specialists in cohort study and genomic data to house and supply these from within our partner TRE, SAIL Databank. As well as data assets, BREATHE is able to provide clinical and data expertise to collaborators for grant submissions and on bespoke respiratory science projects. ResultsIncluding a significant period of work during the pandemic supporting COVID-19 research and also focusing on other respiratory disease science support, BREATHE is now well-placed to move towards a sustainable operating plan post-grant from March 2023. Due to the approach taken in maximising data services for multiple sectors, BREATHE is positioned to provide data linkage and sharing services (making use of its TRE, SAIL Databank), providing analytic and clinical support to respiratory research projects for customers in multiple sectors (Pharma, SMEs, Academia, NHS, Charities), and advancing synthetic data and software development, again in partnership with SAIL and our wider industry partners. ConclusionAs of March 2022, BREATHE has established a portfolio of data services and projects interfacing with multiple sectors of collaborator in enhancing respiratory science projects across the UK. With population-level data assets representing Wales, Scotland, and England and the ability to work with the Northern Ireland infrastructure housed at Swansea University, BREATHE supports 4-nation respiratory science in RWE data, and provides clinical and data linkage expertise to studies such as longitudinal cohorts, pharma companies, and contract research organisations.

051 The capture of a UK minimum data set for MS

Background

The UK Multiple Sclerosis Register (UKMSR) was established in 2011 to capture ‘real world’ data from people with MS (pwMS) and the NHS. Capturing clinical data from the NHS for research is time consuming for clinical staff, can involve complicated governance, security and data quality issues. UKMSR has implemented quality controls, validation rules, new capture systems and site reporting to improve this.

Method

Compare the Minimum Data Set (MDS) consisting of 7 items including demographics and EDSS for quality and quantity in the first 3 years (pilot phase) to the most recent 3 years of data capture

Results

Completion of MDS (100% valid and completed values) (2011–2014) 4 sites, n=884. MDS received= 159 (17.9%), Time to add site ~3 Months (2017–2020) 48 Sites, n= 8836. MDS received = 5791 (65.5%), Time to add site ~6 Weeks

Conclusion

The UKMSR has improved the clinical capture of MDS from a vastly increased number of patients and clinical sites. Improved validation standards and systems have increased data quality. Sites are added more quickly and rapidly notified of data quality issues for correction, making the data more useful to the site and ultimately of more utility to researchers.

richard.nicholas@btinternet.com

Data Resource: Children Receiving Care and Support and Children in Need, administrative records in Wales

Introduction

In Wales, the Children in Need (CIN) dataset includes information relating to needs of children and social care support. Before the Social Services and Well-being (Wales) Act 2014 came into force in April 2016, this data collection was named the Children in Need census, changing to Children Receiving Care and Support (CRCS) after this date to reflect better the children eligible for inclusion. This paper describes these datasets, their potential for research and their limitations. We describe data that researchers can access via the Secure Anonymised Information Linkage (SAIL) Databank and exploratory linkages made to health records.

Methods

CIN and CRCS data were transferred to the SAIL Databank using a standardised approach to provide de-identified data with Anonymised Linking Fields (ALF) for successfully matched records. The linkage method relies on the use of Unique Pupil Numbers (UPN). As such, no records are currently available for children without a UPN, which includes most under age three. ALFs enabled linkage to individual-level health data within SAIL. Health service use was compared to non-CIN/CRCS populations.

Results

CRCS data held within the SAIL Databank comprises 25,972 records, 81% of the total number of records reported by the Welsh Government. The CIN data contains 108,449 records, 79% of the Welsh Government’s records for this data collection. Health service use of children in need, and children receiving care and support, was roughly equal to that of the non-CIN/CRCS population, except GP visits, where children in need had fewer consultations, and children receiving care and support had more consultations than the comparison population.

Conclusion

Researchers can access Welsh CIN and CRCS datasets through the SAIL Databank, enabling research opportunities. Work is ongoing to improve records and to understand better the health and health service use among children captured by CIN and CRCS censuses.

Mechanistic Investigation of Granzyme A inhibitory effects on intracellular Mycobacterium tuberculosis

One fourth of the world population is infected with Tuberculosis (TB). Our lab has identified γ9δ2 T cells that secrete Granzyme A (GzmA) with TB protective effects. In this study, we investigated the mechanism(s) by which human GzmA inhibits the intracellular replication of mycobacteria within infected human primary monocytes.

GzmA was added to mycobacteria-infected monocytes for downstream analyses using 2D-DIGE and shotgun proteomics. We generated WT, enzymatically inactive (S195A), and monomeric only (C93S) recombinant GzmA and performed: flow cytometry studies using viable mycobacteria; intracellular inhibition assays neutralizing CD14, TLR4 and TLR2; and GzmA immunoprecipitation experiments.

The 2D-DIGE proteomic analyses found the ER-stress response and ATP metabolism pathways as important for GzmA-mediated inhibition. Separately, shotgun proteomics uncovered the upregulation of Rab11FIP1 (important for phagocytosis). Both GzmA-WT and S195A proteins inhibited intracellular mycobacteria, but C93S did not. Neutralization of CD14 and TLR4, but not TLR2, reversed GzmA-inhibitory activity. GzmA-WT, S195A, and C93S all bound mycobacteria. However, GzmA-WT and S195A, but not GzmA-C93S, stably bound to TLR4 and CD14.

Collectively, these studies demonstrate key structural, functional, and inter-/intra-molecular features required for GzmA-mediated inhibition of intracellular mycobacteria including interactions between GzmA, mycobacteria, TLR4 and CD14. These interactions result in the ER stress response, altered ATP metabolism, enhanced phagocytosis, and inhibition of mycobacteria. Thus, GzmA’s potential role as opsonin could lead to novel host-directed therapeutics for TB infections.

Supported by grants from NIH (F30HL151136-01, R01AI048391-12)

A Cohort Comparison Study on Women in Threatened Preterm Labor Given Nifedipine or Nifedipine and Salbutamol Tocolysis in Air Medical Retrieval

OBJECTIVE

Women with threatened preterm labor in remote Australia often require tocolysis in the prevention of in-flight birth during air medical retrieval. However, debate exists over the tocolytic choice.

METHODS

A retrospective analysis was undertaken on data containing women who required air medical retrieval for threatened preterm labor within Western Australia between the years 2013 and 2018.

RESULTS

A total number of 236 air medical retrievals were deemed suitable for inclusion; 141 received nifedipine, and 95 women received salbutamol + nifedipine. Tocolytic efficaciousness was reported in 151 cases, proportionally more (P < .05) from the women who received salbutamol + nifedipine (n = 68, 71.6%) compared with the women who received nifedipine only (n = 83, 58.9%). Those receiving salbutamol + nifedipine were more likely to suffer maternal tachycardia (n = 87 [91.6%] vs. n = 62 [44.0%]), fetal tachycardia (n = 26 [27.4%] vs. n = 13 [9.2%]), nausea (n = 17 [17.9] vs. n = 5 [3.55%]), and vomiting (n = 12 [12.6%] vs. n = 2 [1.4%]). Three women who received salbutamol + nifedipine had serious side effects including echocardiographic changes, chest pain, and metabolic and lactic acidosis.

CONCLUSION

Salbutamol + nifedipine tocolysis was proven to be more effective than nifedipine only. Although salbutamol + nifedipine had increased temporary side effects, most were nonsevere and managed in-flight.

A population level study into health vulnerabilities of mothers and fathers involved in public law care proceedings in Wales, UK between 2011 and 2019

IntroductionUnder section 31 of the Children Act 1989, public law care proceedings can be issued if there is concern a child is subject to, or at risk of significant harm, which can lead to removal of a child from parents. Appropriate and effective health and social support are required to potentially prevent some of the need for these proceedings. More comprehensive evidence of the health needs and vulnerabilities of parents will enable enhanced response from family courts and integrated other services. ObjectiveTo examine health vulnerabilities of parents involved in care proceedings in the two-year period prior to involvement. MethodsFamily court data provided by Cafcass Cymru were linked to population-based health records held within the Secure Anonymised Information Linkage Databank. Linked data were available for 8,821 parents of children involved in care proceedings between 2011 and 2019. Findings were benchmarked with reference to a comparison group of parents matched on sex, age, and deprivation (n = 32,006), not subject to care proceedings. Demographic characteristics, overall health service use, and health profiles of parents were examined. Descriptive and statistical tests of independence were used. ResultsNearly half of cohort parents (47.6%) resided in the most deprived quintile. They had higher levels of healthcare use compared to the comparison group across multiple healthcare settings, with the most pronounced differences for emergency department attendances (59.3% vs 37.0%). Health conditions with the largest variation between groups were related to mental health (43.6% vs 16.0%), substance use (19.4% vs 1.6%) and injuries (41.5% vs 23.6%). ConclusionThis study highlights the heightened socioeconomic and health vulnerabilities of parents who experience care proceedings concerning a child. Better understanding of the needs and vulnerabilities of this population may provide opportunities to improve a range of support and preventative interventions that respond to crises in the community.

An emic-etic-emic research cycle for understanding context in under-researched countries

Given the importance of understanding the context of management issues in the world, this article discusses the role of both emic (developing culture-specific concepts) and etic (applying concepts across cultures) research in the international management literature. This paper proposes a more comprehensive mixed methods research cycle that can provide researchers with a deeper understanding of the context in under-researched countries. Using a decolonial lens, this theoretical paper proposes that an emic-etic-emic cycle is the best way to disaggregate contextual issues in organizational research, particularly when dealing with human issues in management. By examining a research project on leadership in Africa and the African diaspora from decolonial perspective, our proposed emic-etic-emic cycle (1) stresses the importance of using an emic approach in addition to the dominant etic approach in cross-cultural management; (2) provides researchers with a deeper understanding of context in under-researched countries; and (3) contributes to decolonial approaches to management, which call for a symmetrical dialogue across borders which decentralizes the dominant Western approach, and provides a deeper understanding of management from an indigenous and local perspective. Contextualizing research using the emic-etic-emic cycle can enhance rigor and relevance of the research.

Investigating the uptake, effectiveness and safety of COVID-19 vaccines: protocol for an observational study using linked UK national data

INTRODUCTION

The novel coronavirus SARS-CoV-2, which emerged in December 2019, has caused millions of deaths and severe illness worldwide. Numerous vaccines are currently under development of which a few have now been authorised for population-level administration by several countries. As of 20 September 2021, over 48 million people have received their first vaccine dose and over 44 million people have received their second vaccine dose across the UK. We aim to assess the uptake rates, effectiveness, and safety of all currently approved COVID-19 vaccines in the UK.

METHODS AND ANALYSIS

We will use prospective cohort study designs to assess vaccine uptake, effectiveness and safety against clinical outcomes and deaths. Test-negative case-control study design will be used to assess vaccine effectiveness (VE) against laboratory confirmed SARS-CoV-2 infection. Self-controlled case series and retrospective cohort study designs will be carried out to assess vaccine safety against mild-to-moderate and severe adverse events, respectively. Individual-level pseudonymised data from primary care, secondary care, laboratory test and death records will be linked and analysed in secure research environments in each UK nation. Univariate and multivariate logistic regression models will be carried out to estimate vaccine uptake levels in relation to various population characteristics. VE estimates against laboratory confirmed SARS-CoV-2 infection will be generated using a generalised additive logistic model. Time-dependent Cox models will be used to estimate the VE against clinical outcomes and deaths. The safety of the vaccines will be assessed using logistic regression models with an offset for the length of the risk period. Where possible, data will be meta-analysed across the UK nations.

ETHICS AND DISSEMINATION

We obtained approvals from the National Research Ethics Service Committee, Southeast Scotland 02 (12/SS/0201), the Secure Anonymised Information Linkage independent Information Governance Review Panel project number 0911. Concerning English data, University of Oxford is compliant with the General Data Protection Regulation and the National Health Service (NHS) Digital Data Security and Protection Policy. This is an approved study (Integrated Research Application ID 301740, Health Research Authority (HRA) Research Ethics Committee 21/HRA/2786). The Oxford-Royal College of General Practitioners Clinical Informatics Digital Hub meets NHS Digital's Data Security and Protection Toolkit requirements. In Northern Ireland, the project was approved by the Honest Broker Governance Board, project number 0064. Findings will be made available to national policy-makers, presented at conferences and published in peer-reviewed journals.

First dose ChAdOx1 and BNT162b2 COVID-19 vaccinations and cerebral venous sinus thrombosis: A pooled self-controlled case series study of 11.6 million individuals in England, Scotland, and Wales

BACKGROUND

Several countries restricted the administration of ChAdOx1 to older age groups in 2021 over safety concerns following case reports and observed versus expected analyses suggesting a possible association with cerebral venous sinus thrombosis (CVST). Large datasets are required to precisely estimate the association between Coronavirus Disease 2019 (COVID-19) vaccination and CVST due to the extreme rarity of this event. We aimed to accomplish this by combining national data from England, Scotland, and Wales.

METHODS AND FINDINGS

We created data platforms consisting of linked primary care, secondary care, mortality, and virological testing data in each of England, Scotland, and Wales, with a combined cohort of 11,637,157 people and 6,808,293 person years of follow-up. The cohort start date was December 8, 2020, and the end date was June 30, 2021. The outcome measure we examined was incident CVST events recorded in either primary or secondary care records. We carried out a self-controlled case series (SCCS) analysis of this outcome following first dose vaccination with ChAdOx1 and BNT162b2. The observation period consisted of an initial 90-day reference period, followed by a 2-week prerisk period directly prior to vaccination, and a 4-week risk period following vaccination. Counts of CVST cases from each country were tallied, then expanded into a full dataset with 1 row for each individual and observation time period. There was a combined total of 201 incident CVST events in the cohorts (29.5 per million person years). There were 81 CVST events in the observation period among those who a received first dose of ChAdOx1 (approximately 16.34 per million doses) and 40 for those who received a first dose of BNT162b2 (approximately 12.60 per million doses). We fitted conditional Poisson models to estimate incidence rate ratios (IRRs). Vaccination with ChAdOx1 was associated with an elevated risk of incident CVST events in the 28 days following vaccination, IRR = 1.93 (95% confidence interval (CI) 1.20 to 3.11). We did not find an association between BNT162b2 and CVST in the 28 days following vaccination, IRR = 0.78 (95% CI 0.34 to 1.77). Our study had some limitations. The SCCS study design implicitly controls for variables that are constant over the observation period, but also assumes that outcome events are independent of exposure. This assumption may not be satisfied in the case of CVST, firstly because it is a serious adverse event, and secondly because the vaccination programme in the United Kingdom prioritised the clinically extremely vulnerable and those with underlying health conditions, which may have caused a selection effect for individuals more prone to CVST. Although we pooled data from several large datasets, there was still a low number of events, which may have caused imprecision in our estimates.

CONCLUSIONS

In this study, we observed a small elevated risk of CVST events following vaccination with ChAdOx1, but not BNT162b2. Our analysis pooled information from large datasets from England, Scotland, and Wales. This evidence may be useful in risk-benefit analyses of vaccine policies and in providing quantification of risks associated with vaccination to the general public.

A Rare Presentation of a Solitary Melanoma Bone Metastasis

A 74-year-old woman presented with sudden onset pain and swelling in her right wrist. Plain radiographs showed a pathological fracture through a lytic lesion. The patient had a past medical history of melanoma on her right thigh, which had been excised two years previously. She was referred to the bone cancer unit to undergo a series of investigations that included a magnetic resonance imaging scan, bone scintigraphy and a computed tomography-guided biopsy. Collectively, all investigations revealed a solitary bone metastasis from her previous melanoma in the right distal radius. The patient was treated symptomatically and underwent internal fixation with cement augmentation for symptom control. With the incidence of melanoma increasing, this case demonstrates the importance of being vigilant of unusual presentations. 

Mobile digital x-ray and portable cartridge based nucleic acid amplification test machines for point-of-care diagnosis of TB in rural India

BACKGROUND

There is no experience of point-of-care (POC) microbiological confirmation for TB in India in field settings.

METHODS

Under the TB-Free Haryana project, a mobile van-mounted digital x-ray and portable GeneXpert system screened all presumptive TB patients with strong clinic-radiological suspicion for TB.

RESULTS

Of 1673 x-rays, 215 (13%) had findings suggestive of TB, 109 had strong clinical suspicion and were eligible for POC GeneXpert, in whom a test was performed in 82 (75%) cases; 59 (72%) tested positive and were initiated on treatment within 24 h.

CONCLUSIONS

A mobile van equipped with digital x-ray and POC GeneXpert is feasible and has a good success rate with potential for replication.

How a Pandemic Changes Trauma: Epidemiology and Management of Trauma Admissions in the UK during COVID-19 Lockdown

Introduction:

On June 24 in the United Kingdom, there were 277,989 cases of COVID-19 and 39,369 deaths recorded. The government enforced a complete lockdown on March 23 that resulted in cessation of all elective admissions on 24^th onward, with only acute trauma cases being admitted to hospital. This study aims to characterize the changes in trauma admissions during the first 5-week lockdown period. The hypothesis states that there would be a significant reduction in overall orthopedic trauma admissions, polytrauma, and high-energy outdoor trauma during this COVID-19 period.

Methods:

All trauma admissions over nearly a 5-week period from March 23, 2020, to April 26, 2020, were collated as the “COVID cohort” and compared to the “control” group of patients from the same hospitals 1 year before between March 23, 2019, and April 26, 2019. Spinal admissions and pediatrics were excluded from the study as they were managed in other regional units.

Results:

There was a 56% reduction in trauma admissions during the COVID-19 lockdown (133 vs. 304). A majority of the COVID cohort were admitted with fractures (89 vs. 164, P = 0.017, Chi-square test) from home with low-energy falls. Overall, fewer operations were performed than the year before. However, a greater proportion of admitted patients had a surgical orthopedic intervention rather than admission and nonoperative management.

Conclusions:

There was a reduction in admissions as well as reductions in high energy and occupational injuries. Elderly patients continued to fall at home or in care, sustaining hip fractures. This vulnerable group requires beds, orthogeriatric management followed by surgical intervention and social care. Orthogeriatric services must be maintained to ensure the best clinical outcomes for this group.

Interim findings from first-dose mass COVID-19 vaccination roll-out and COVID-19 hospital admissions in Scotland: a national prospective cohort study

BACKGROUND

The BNT162b2 mRNA (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca) COVID-19 vaccines have shown high efficacy against disease in phase 3 clinical trials and are now being used in national vaccination programmes in the UK and several other countries. Studying the real-world effects of these vaccines is an urgent requirement. The aim of our study was to investigate the association between the mass roll-out of the first doses of these COVID-19 vaccines and hospital admissions for COVID-19.

METHODS

We did a prospective cohort study using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19-EAVE II-database comprising linked vaccination, primary care, real-time reverse transcription-PCR testing, and hospital admission patient records for 5·4 million people in Scotland (about 99% of the population) registered at 940 general practices. Individuals who had previously tested positive were excluded from the analysis. A time-dependent Cox model and Poisson regression models with inverse propensity weights were fitted to estimate effectiveness against COVID-19 hospital admission (defined as 1-adjusted rate ratio) following the first dose of vaccine.

FINDINGS

Between Dec 8, 2020, and Feb 22, 2021, a total of 1 331 993 people were vaccinated over the study period. The mean age of those vaccinated was 65·0 years (SD 16·2). The first dose of the BNT162b2 mRNA vaccine was associated with a vaccine effect of 91% (95% CI 85-94) for reduced COVID-19 hospital admission at 28-34 days post-vaccination. Vaccine effect at the same time interval for the ChAdOx1 vaccine was 88% (95% CI 75-94). Results of combined vaccine effects against hospital admission due to COVID-19 were similar when restricting the analysis to those aged 80 years and older (83%, 95% CI 72-89 at 28-34 days post-vaccination).

INTERPRETATION

Mass roll-out of the first doses of the BNT162b2 mRNA and ChAdOx1 vaccines was associated with substantial reductions in the risk of hospital admission due to COVID-19 in Scotland. There remains the possibility that some of the observed effects might have been due to residual confounding.

FUNDING

UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK.

Interim findings from first-dose mass COVID-19 vaccination roll-out and COVID-19 hospital admissions in Scotland: a national prospective cohort study

BACKGROUND

The BNT162b2 mRNA (Pfizer-BioNTech) and ChAdOx1 nCoV-19 (Oxford-AstraZeneca) COVID-19 vaccines have shown high efficacy against disease in phase 3 clinical trials and are now being used in national vaccination programmes in the UK and several other countries. Studying the real-world effects of these vaccines is an urgent requirement. The aim of our study was to investigate the association between the mass roll-out of the first doses of these COVID-19 vaccines and hospital admissions for COVID-19.

METHODS

We did a prospective cohort study using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19-EAVE II-database comprising linked vaccination, primary care, real-time reverse transcription-PCR testing, and hospital admission patient records for 5·4 million people in Scotland (about 99% of the population) registered at 940 general practices. Individuals who had previously tested positive were excluded from the analysis. A time-dependent Cox model and Poisson regression models with inverse propensity weights were fitted to estimate effectiveness against COVID-19 hospital admission (defined as 1-adjusted rate ratio) following the first dose of vaccine.

FINDINGS

Between Dec 8, 2020, and Feb 22, 2021, a total of 1 331 993 people were vaccinated over the study period. The mean age of those vaccinated was 65·0 years (SD 16·2). The first dose of the BNT162b2 mRNA vaccine was associated with a vaccine effect of 91% (95% CI 85-94) for reduced COVID-19 hospital admission at 28-34 days post-vaccination. Vaccine effect at the same time interval for the ChAdOx1 vaccine was 88% (95% CI 75-94). Results of combined vaccine effects against hospital admission due to COVID-19 were similar when restricting the analysis to those aged 80 years and older (83%, 95% CI 72-89 at 28-34 days post-vaccination).

INTERPRETATION

Mass roll-out of the first doses of the BNT162b2 mRNA and ChAdOx1 vaccines was associated with substantial reductions in the risk of hospital admission due to COVID-19 in Scotland. There remains the possibility that some of the observed effects might have been due to residual confounding.

FUNDING

UK Research and Innovation (Medical Research Council), Research and Innovation Industrial Strategy Challenge Fund, Health Data Research UK.

British Columbia’s Health Data Platform: Unleashing the Power of a Data Environment Commons for Health and Health System Improvement

IntroductionThere is no power for change greater than a community discovering what it cares about.1 The Health Data Platform (HDP) will democratize British Columbia’s (population of approximately 4.6 million) health sector data by creating common enabling infrastructure that supports cross-organization analytics and research used by both decision makers and cademics. HDP will provide streamlined, proportionate processes that provide timelier access to data with increased transparency for the data consumer and provide shared data related services that elevate best practices by enabling consistency across data contributors, while maintaining continued stewardship of their data. HDP will be built in collaboration with Swansea University following an agile pragmatic approach starting with a minimum viable product. Objectives and ApproachBuild a data sharing environment that harnesses the data and the understanding and expertise about health data across academe, decision makers, and clinicians in the province by: Enabling a common harmonized approach across the sector on: Data stewardship Data access Data security and privacy Data management Data standards To: Enhance data consumer data access experience Increase process consistency and transparency Reduce burden of liberating data from a data source Build trust in the data and what it is telling us and therefore the decisions made Increase data accessibility safely and responsibly Working within the jurisdiction’s existing legislation, the Five Safes Privacy and Security Framework will be implemented, tailored to address the requirements of data contributors. ResultsThe minimum viable product will provide the necessary enabling infrastructure including governance to enable timelier access, safely to administrative data to a limited set of data consumers. The MVP will be expanded with another release planned for early 2021. Conclusion / ImplicationsCollaboration with Swansea University has enabled BC to accelerate its journey to increasing timelier access to data, safely and increasing the maturity of analytics by creating the enabling infrastructure that promotes collaboration and sharing of data and data approaches. 1 Margaret Wheatley

Unifying the UK’S Data for Respiratory Science: BREATHE, The Health Data Research UK (HDR UK) Respiratory Health Data Research Hub

IntroductionThe BREATHE Health Data Research Hub is a consortium of five academic institutions and several industry partners seeking to facilitate and accelerate respiratory science initiatives and outcomes. Unlocking organisational, jurisdictional, and scientific challenges, such as differing and inherent complexities with data standards, incongruous governance, and disparate data access mechanisms for over 100 diverse UK datasets are key aims. Objectives and ApproachCentral to the data effort is the UK Secure eResearch Platform (SeRP UK), and its flagship tenancy, the SAIL Databank. Onboarding datasets, making them remotely available to the respiratory research community, is a key approach. Datasets targeted range from population cohort studies, to respiratory trials data, routine healthcare datasets, and specialist ‘omics data. Partnerships with national safe havens and providers such as eDRIS and NHS Digital will enable BREATHE to expedite and improve wider sharing of datasets for the respiratory science. Data improvements focus on datasets from primary, secondary, and tertiary care from national healthcare systems, ‘respiratorising’ these datasets and increasing utility for academic and industry respiratory scientists. Incorporating dataset metadata and access permutations into national cataloguing systems at HDR UK, standardising metadata, and interoperability for in-scope datasets form a concerted data quality improvement effort. ResultsFacilitating data sharing through initiatives such as BREATHE will increase visibility and accessibility for datasets within respiratory science, whilst addressing national cultural and governance issues to data sharing. BREATHE data sharing processes will allow for team science to be undertaken in a highly collaborative manner and allow for best practise in data collection and sharing to flow to nationwide datasets in respiratory science. Conclusion / ImplicationsCollaborative hubs with scientific domain expertise can be created and leveraged to accelerate data sharing and data science within the scientific area. These collaborative efforts can however be translated to other disease-specific efforts, and indeed disease agnostic platform solutions.

The Role of Partnership in The Integration of Intersectoral Data

IntroductionThe importance of the determinants of health to health outcomes has long been established. Historically, data from each of these sectors has been captured in disparate, often siloed, sources. Attempts to integrate these data have faced a number of challenges including technical, legislative and interpretative barriers, creating inefficiencies and inhibiting knowledge sharing. Despite this, there have been notable successes where intersectoral data and health data have been brought together in a meaningful way. The establishment of strong partnerships, with academia, governments, privacy and legal sectors, and other bodies, across sectors has been key to this success. These partnerships ensure data are integrated, analyzed, and interpreted accurately and appropriately, while also leveraging existing investments and expertise. Objectives and ApproachThe objective of this session is to explore the role of partnerships throughout the data integration life cycle, from initial discussions, to data integration, through to connecting research output to policy impact. Each of the presenters will discuss the successes, barriers and mitigation strategies they have experienced across different jurisdictions using real world examples. ResultsHealth research institutes globally are increasingly able to access routinely collected intersectoral data from non-health sectors. In each institute, data are unique, complex and have been collected in a manner consistent with the needs of the sector. As health research institutes work to understand the data structures and determine the best way to link, use and interpret the information according to national and international best practice guidelines, it has become clear that it is critical to undertake this in partnership with experts from each sector, who understand how the data was collected and can guide appropriate interpretation. In addition, these partnerships have enabled the connection of policy priorities in other sectors with research done in the health sector using intersectoral data. For example, in addition to supporting government health departments, health research institutes have collaborated with other government ministries including immigration, social services, and education. This session will present real world examples from local (provincial), national and international contexts, and highlight a novel data platform, being developed to minimize barriers to data access and use across sectors and jurisdictions. Conclusion / ImplicationsThe participants on this panel will demonstrate the importance of partnership throughout the data integration life cycle when working with intersectoral data using real world examples. Collaboration increases the value of integrated data to both health and non-health sectors, through the connection of policy priorities and support of research across the determinants of health.

Long-term clinical, virological and immunological outcomes following planned treatment interruption in HIV-infected children

OBJECTIVES

Planned treatment interruption (PTI) of antiretroviral therapy (ART) in adults is associated with adverse outcomes. The PENTA 11 trial randomized HIV-infected children to continuous ART (CT) vs. CD4-driven PTIs. We report 5 years' follow-up after the end of main trial.

METHODS

Post-trial, all children resumed ART. Clinical, immunological, virological and treatment data were collected annually. A sub-study investigated more detailed immunophenotype. CT and PTI arms were compared using intention-to-treat. Laboratory parameters were compared using linear regression, adjusting for baseline values; mixed models were used to include all data over time.

RESULTS

In all, 101 children (51 CT, 50 PTI) contributed a median of 7.6 years, including 5.1 years of post-trial follow-up. Post-trial, there were no deaths, one pulmonary tuberculosis and no other CDC stage B/C events. At 5 years post-trial, 90% of children in the CT vs. 82% in the PTI arm had HIV RNA < 50 copies/mL (P = 0.26). A persistent increase in CD8 cells was observed in the PTI arm. The sub-study (54 children) suggested that both naïve and memory populations contributed to higher CD8 cells following PTI. Mean CD4/CD8 ratios at 5 years post-trial were 1.22 and 1.08 in CT and PTI arms, respectively [difference (CT - PTI) = -0.15; 95% CI: -0.34-0.05), P = 0.14]. The sub-study also suggested that during the trial and at early timepoints after the end of the trial, reduction in CD4 in the PTI arm was mainly from loss of CD4 memory cells.

CONCLUSIONS

Children tolerated PTI with few long-term clinical, virological or immunological consequences.

Linking pre- and post-adoption records for research in anonymised form in a data safe haven: legal implications and support for a social licence

INTRODUCTION

The long-term health and wellbeing of adoptees is under-researched. One reason for this has been limited data accessibility regarding the adoption process, and another is a practice common in some UK jurisdictions of changing the National Health Service (NHS) number (or equivalent) at adoption, as part of creating the new identity. The SAIL Databank holds data on child and family court cases from Cafcass Cymru, together with children's social care data, and can link these with routine health and administrative data in anonymised form. However, because the linkage key at SAIL is based on an encryption of the NHS number, working with pre- and post-adoption records for longitudinal research remains a major challenge. We set out to explore the legal implications of, and social support for, linking these records for use in anonymised form for longitudinal research.

METHODS

We reviewed the main legislation and regulations governing the use of data about adoptees in England and Wales. We gauged support for a social licence in Wales by carrying out interviews with individuals who had been involved in the adoptions process, and by engaging with general public groups for their views. We drew out the main emerging themes and, in combination with the review, propose a way forward.

RESULTS

The legal review indicated that there are provisions in the Family Procedure Rules (England and Wales) and the General Data Protection Regulation that can be relied upon for the lawful processing of adoption data into anonymised form for research. The main points of concern about linking pre- and post-adoption records were privacy, data security, the need to limit the number of organisations involved in data sharing, and re-identification risk. The over-riding message was favourable with longitudinal research seen as strongly beneficial.

CONCLUSION

This study has indicated that in Wales, there is no legal impediment, nor major objection from individuals involved in the adoptions process, or members of the general public, for the use of adoption data in anonymised form in a data safe haven. This includes the linkage of pre- and post-adoption records to enable novel longitudinal research to take place. The provisos were that robust safeguards must be in place, and that the research should aim to benefit adoptees and to improve policy and practice. We conclude that it is reasonable to proceed with caution to develop practical ways to link pre- and post-adoption records in a data safe haven.

Lessons for test and treat in an antiretroviral programme after decentralisation in Uganda: a retrospective analysis of outcomes in public healthcare facilities within the Lablite project

BACKGROUND

We describe the decentralisation of antiretroviral therapy (ART) alongside Option B+ roll-out in public healthcare facilities in the Lablite project in Uganda. Lessons learned will inform programmes now implementing universal test and treat (UTT).

METHODS

Routine data were retrospectively extracted from ART registers between October 2012 and March 2015 for all adults and children initiating ART at two primary care facilities (spokes) and their corresponding district hospitals (hubs) in northern and central Uganda. We describe ART initiation over time and retention and use of Cox models to explore risk factors for attrition due to mortality and loss to follow-up. Results from tracing of patients lost to follow-up were used to correct retention estimates.

RESULTS

Of 2100 ART initiations, 1125 were in the north, including 944 (84%) at the hub and 181 (16%) at the spokes; children comprised 95 (10%) initiations at the hubs and 14 (8%) at the spokes. Corresponding numbers were 642 (66%) at the hub and 333 (34%) at the spokes in the central region (77 [12%] and 22 [7%], respectively, in children). Children <3 y of age comprised the minority of initiations in children at all sites. Twenty-three percent of adult ART initiations at the north hub were Option B+ compared with 45% at the spokes (25% and 65%, respectively, in the central region). Proportions retained in care in the north hub at 6 and 12 mo were 92% (95% CI 90 to 93) and 89% (895% CI 7 to 91), respectively. Corresponding corrected estimates in the north spokes were 87% (95% CI 78 to 93) and 82% (95% CI 72 to 89), respectively. In the central hub, corrected estimates were 84% (95% CI 80 to 87) and 78% (95% CI 74 to 82), and were 89% (95% CI 77.9 to 95.1) and 83% (95% CI 64.1 to 92.9) at the spokes, respectively. Among adults newly initiating ART, being older was independently associated with a lower risk of attrition (adjusted hazard ratio [aHR] 0.93 per 5 y [95% CI 0.88 to 0.97]). Other independent risk factors included initiating with a tenofovir-based regimen vs zidovudine (aHR 0.60 [95% CI 0.46 to 0.77]), year of ART initiation (2013 aHR 1.55 [95% CI 1.21 to 1.97], ≥2014 aHR 1.41 [95% CI 1.06 to 1.87]) vs 2012, hub vs spoke (aHR 0.35 [95% CI 0.29 to 0.43]) and central vs north (aHR 2.28 [95% CI 1.86 to 2.81]). Independently, patient type was associated with retention.

CONCLUSIONS

After ART decentralisation, people living with human immunodeficiency virus (HIV) were willing to initiate ART in rural primary care facilities. Retention on ART was variable across facilities and attrition was higher among some groups, including younger adults and women initiating ART during pregnancy/breastfeeding. Interventions to support these groups are required to optimise benefits of expanded access to HIV services under UTT.

Public involvement & engagement in the work of a data safe haven: a case study of the SAIL Databank

BACKGROUND

The SAIL Databank is a data safe haven established in 2007 at Swansea University (Wales). It was set up to create new opportunities for research using routinely-collected health and other public service datasets in linkable anonymised form. SAIL forms the bedrock of other Population Data Science initiatives made possible by the data and safe haven environment.

AIM

The aim of this paper is to provide an overview of public involvement & engagement in connection with the SAIL Databank and related Population Data Science initiatives.

APPROACH

We have a public involvement & engagement policy for SAIL in the context of Population Data Science. We established a Consumer Panel to provide advice on the work of SAIL and associated initiatives, including on proposed uses of SAIL data. We reviewed the topics discussed and provide examples of advice to researchers. We carried out a survey with members on their experiences of being on the Panel and their perceptions of the work of SAIL. We have a programme of wider public engagement and provide illustrations of this work.

DISCUSSION

We summarise what this paper adds and some lessons learned. In the rapidly developing area of Population Data Science it is important that people feel welcome, that they are encouraged to ask questions and are provided with digestible information and adequate consideration time. Citizens have provided us with valuable anticipated and unanticipated opinions and novel viewpoints. We seek to take a pragmatic approach, prioritising the communication modes that allow maximum public input commensurate with the purpose of the activity.

CONCLUSION

This paper has set out our policy, rationale, scope and practical approaches to public involvement & engagement for SAIL and our related Population Data Science initiatives. Although there will be jurisdictional, cultural and organizational differences, we believe that the material covered in this paper will be of interest to other data focused enterprises across the world.

Implementing upfront mobile digital chest x-ray for tuberculosis diagnosis in India—feasibility and benefits

Background

The Tuberculosis (TB) Control Program in India changed the TB diagnostic algorithm and recommended sputum testing and chest x-ray (CXR) for presumptive TB up front. There is no experience of testing this algorithm in routine field settings.

Methods

In a public–private partnership (PPP), a private hospital provided mobile digital CXR services (mounted on a van) to complement the existing diagnostic services of sputum microscopy and GeneXpert testing. All presumptive TB patients (cough &gt;2 weeks) underwent CXR and sputum microscopy, and GeneXpert testing if eligible (smear-negative CXR suggestive of TB).

Results

All 2973 presumptive TB patients underwent CXR and sputum microscopy; 471 (15.8%) had abnormal CXR findings suggestive of TB, 129 (4.3%) were smear positive and 17 were extrapulmonary TB. Of the remaining 325 with smear-negative and CXR suggestive of TB, 147 (45.2%) underwent GeneXpert testing, yielding 32 positives (21.8%). Of the remaining 178 with no GeneXpert test done, 106 (60.0%) had CXR definitely suggesting TB (clinically diagnosed TB). Thus a total of 284 cases of TB (161 microbiologically confirmed, 106 clinically diagnosed, 17 extrapulmonary TB) were identified, giving a potential diagnostic yield of 19.6%.

Conclusions

Systematic screening with mobile digital X-ray service via a PPP model integrated into the national program is feasible and scalable with a high yield.

Born into Care: characterising newborn babies and infants in care proceedings in England and Wales

Background/rationaleNations with advanced child protection systems place considerable emphasis on the developmental salience of infancy. However, this emphasis is not matched by any differentiated analysis of the timing of family court intervention in the lives of infants or the final legal order outcomes of these cases. This presentation shares findings from the first ever population profiling study of infants subject to care proceedings within the family justice system in England and Wales. AimTo estimate the proportion of all infant care proceedings cases issued within 7 days and 4 weeks of birth and describe case and infant characteristics; to calculate incidence rates over time and by local authority and family court region; to describe and compare legal order outcomes according to age. Methods/approachData was extracted from case management records produced by the Children and Family Court Advisory and Support Service (Cafcass) England and Wales. Records were first restructured to link infants to legal order outcome data and birth mother records. Incidence rates were calculated using ONS mid-year population estimates and annual live births. Within the SAIL Databank, Welsh infant records were linked to birth registration and community child health data to produce a fuller picture of infant characteristics in Wales. ResultsThe cohort we created comprised all infants recorded as subjects within care proceedings in England (2007/08-2016/17) and Wales (2011/12-2018/19). The study captured the high proportion of infant cases that are issued at/close to birth, but also marked regional and local authority variation in incidence rates. ConclusionHigh rates of adoption, particularly for babies born to mothers without a previous family court history, have prompted calls for new preventative solutions. The President of the Family (Court) Division in England has initiated a review of legal proceedings at birth.

The Nuffield Family Justice Observatory Data Partnership

Background Not enough is known about how the family justice system is working, the children and families using these services, and their wider outcomes beyond their involvement with the family court. The Nuffield Family Justice Observatory (FJO) Data Partnership, comprising a bespoke analysis platform hosted within the Secure Anonymised Information Linkage (SAIL) Databank and analytical teams at Lancaster and Swansea Universities, has been established to address this knowledge deficit. MethodsFamily justice data is being deposited in the SAIL Databank. Data are acquired using a standardised split-file approach, stored in an anonymised format and made available to projects as linked data using a unique encrypted project anonymised linkage field. These data can be augmented with a wealth of available health, education and other governmental/social routinely collected datasets, and future data acquired from other sources, for a range of research projects. ResultsChildren and Family Court Advisory and Support Service (Cafcass) Cymru data has been transferred to the SAIL Databank, and agreements to transfer the Cafcass England data are being finalised. Applications are now welcomed to use these data to enhance understanding of the family justice system and children and families involved with the family courts in public and private law. Access will be facilitated through the SAIL Databank, subject to relevant governance procedures. ConclusionWe will discuss the rationale of the Nuffield FJO Data Partnership, and how it aims to a) increase capacity and capability of researchers and data scientists utilising family justice and other relevant administrative datasets, b) improve understanding about the family justice system using data from the Cafcass in England and Wales, c) demonstrate the complexities and value of data linkage, and d) assist future policy and practice development. We will discuss matching rates for the Cafcass Cymru data and linkages that have been made to other datasets within the SAIL Databank. We will also set out the support available from the partnership to those wishing to access and utilise family justice data.

Repeatable Research Infrastructure Enabling Administrative Data Analysis

Background/RationaleLinked administrative datasets offer great potential for research, but also present major challenges—including the preparation of operational data into a form suitable for efficient research, complex and computationally demanding analysis, and the need to capture and share information about dataset contents and research methods. Main AimThe analytical services team in the Secure Anonymised Information Linkage (SAIL) Databank is creating interconnected tools and systems to automate the preparation and analysis of research data and to curate information about datasets and research methods. Our underlying goal is to make linked data research orders of magnitude faster and cheaper, as well as improve its consistency and quality. MethodsSeveral key developments are ongoing: Automation of data quality checking. Management of dataset metadata. Processing of raw source datasets into cleaned, research-ready data assets. The Concept Library, an application for creating, using, and sharing knowledge about research definitions and methods. A suite of R packages for analysis. Web Application Programming Interfaces will allow these pieces to work together as an integrated system enabling efficient research. ResultsInitial versions of dataset quality checking, cleaned datasets, and R code to implement common tasks are already in day-to-day use by researchers within SAIL. An advisory group has been convened to help guide the work. For example, shared library code that flags conditions within health data has been used across multiple projects; a cleaned dataset measuring follow-up within primary care has been used by more than 100 projects. ConclusionOur proof-of-concept work demonstrates the ability of shared code and cleaned data to meet needs across multiple projects, saving effort and standardizing results. Ongoing work to develop and integrate these tools should further streamline the research process, increasing the output and public benefit of SAIL and other data sources.

LINKAGE: Factors in selecting a data linkage approach

Background The great benefits of linking health datasets for research in the public interest have long been demonstrated. More recently, we are seeing an increase in the availability of wider administrative data, such as employment, education and housing, to add new opportunities for population data science. However, there are challenges to be overcome in selecting a data linkage approach. Main Aim We set out to examine various data linkage approaches, and to formulate some high level questions to inform decision-making. Methods We used published literature to review various data linkage methods in theory and in practical settings. The study was commissioned by the UK Government Statistical Service and a key focus was privacy and confidentiality in data linkage. Results The questions we formulated are based on: Legislative position; Information systems; Nature of datasets; Knowledge-base; Aims and purposes; Ground truth; and Environment. Conclusion There are many factors influencing the selection of a data linkage approach. While not exhaustive, our set of questions covers some of the major ones. The findings of the study are being taken forward by UK Government Statistical Service and government departments to inform decision-making on options for data linkage research and the greater availability of their datasets.

The Influence of Temperature and Community Structure on Light Absorption by Phytoplankton in the North Atlantic

We present a model that estimates the spectral phytoplankton absorption coefficient (aph(λ)) of four phytoplankton groups (picophytoplankton, nanophytoplankton, dinoflagellates, and diatoms) as a function of the total chlorophyll-a concentration (C) and sea surface temperature (SST). Concurrent data on aph(λ) (at 12 visible wavelengths), C and SST, from the surface layer (<20 m depth) of the North Atlantic Ocean, were partitioned into training and independent validation data, the validation data being matched with satellite ocean-colour observations. Model parameters (the chlorophyll-specific phytoplankton absorption coefficients of the four groups) were tuned using the training data and found to compare favourably (in magnitude and shape) with results of earlier studies. Using the independent validation data, the new model was found to retrieve total aph(λ) with a similar performance to two earlier models, using either in situ or satellite data as input. Although more complex, the new model has the advantage of being able to determine aph(λ) for four phytoplankton groups and of incorporating the influence of SST on the composition of the four groups. We integrate the new four-population absorption model into a simple model of ocean colour, to illustrate the influence of changes in SST on phytoplankton community structure, and consequently, the blue-to-green ratio of remote-sensing reflectance. We also present a method of propagating error through the model and illustrate the technique by mapping errors in group-specific aph(λ) using a satellite image. We envisage the model will be useful for ecosystem model validation and assimilation exercises and for investigating the influence of temperature change on ocean colour.

Fifth year of a public-private partnership to improve the case detection of tuberculosis in India: A role model for future action?

BACKGROUND

There is limited access to radiology facilities in most parts of India leading to significant under diagnosis and underreporting of smear negative clinically diagnosed tuberculosis (CDTB). Public Private Partnership (PPP) has a lot to contribute towards addressing this gap through providing access to chest x-ray (CXR) in far-off locations.

METHOD

Mobile vans equipped with digital CXR equipment and support staff were provided by a Corporate Hospital working closely with government, with scheduled visits to government peripheral health institutes. Patients received upfront CXR and sputum microscopy along with GeneXpert in accordance with the revised TB diagnostic algorithm prescribed by the national program, Following a successful pilot in 2014 in district Rewari, "TB free Haryana" was launched in November 2015 with a phased roll out in 16 districts by 2018.

RESULTS

The pilot initiative in 2014 confirmed practical and clinical feasibility and revealed a high rate (30% of people screened) of CDTB i.e. symptomatic cases with radiologic abnormalities compatible with Pulmonary TB. In the first year (2016), 5 districts were covered and a total of 3340 CXRs were carried out. There was an increase in the case notification rates of new CDTB (smear negative) in 2016 compared to 2015 (p = 0.036); yielding an additional 180 cases and an 11.67% increase in case detection. Scale up to a total of 13 and 16 districts took place successfully in 2017 and 2018 respectively; with 6268 CXRs and 8021 CXRs done in the respective years.

CONCLUSION

PPP can involve Corporate Hospitals to improve the existing diagnostic infrastructure and provides access to CXR in a not-for-profit sustainable collaboration, with scale-up to the state level; and potential to replicate this initiative in other states.

Phosgene inhalation causes hemolysis and acute lung injury

Phosgene (Carbonyl Chloride, COCl₂) remains an important chemical intermediate in many industrial processes such as combustion of chlorinated hydrocarbons and synthesis of solvents (degreasers, cleaners). It is a sweet smelling gas, and therefore does not prompt escape by the victim upon exposure. Supplemental oxygen and ventilation are the only available management strategies. This study was aimed to delineate the pathogenesis and identify novel biomarkers of acute lung injury post exposure to COCl₂ gas. Adult male and female C57BL/6 mice (20-25 g), exposed to COCl₂ gas (10 or 20 ppm) for 10 min in environmental chambers, had a dose dependent reduction in P_aO₂ and an increase in P_aCO₂, 1 day post exposure. However, mortality increased only in mice exposed to 20 ppm of COCl₂ for 10 min. Correspondingly, these mice (20 ppm) also had severe acute lung injury as indicated by an increase in lung wet to dry weight ratio, extravasation of plasma proteins and neutrophils into the bronchoalveolar lavage fluid, and an increase in total lung resistance. The increase in acute lung injury parameters in COCl₂ (20 ppm, 10 min) exposed mice correlated with simultaneous increase in oxidation of red blood cells (RBC) membrane, RBC fragility, and plasma levels of cell-free heme. In addition, these mice had decreased plasmalogen levels (plasmenylethanolamine) and elevated levels of their breakdown product, polyunsaturated lysophosphatidylethanolamine, in the circulation suggesting damage to cellular plasma membranes. This study highlights the importance of free heme in the pathogenesis of COCl₂ lung injury and identifies plasma membrane breakdown product as potential biomarkers of COCl₂ toxicity.

GooD4Mum: A general practice-based quality improvement collaborative for diabetes prevention in women with previous gestational diabetes

AIMS

Gestational diabetes (GDM) and Type 2 diabetes pose tremendous health and economic burdens as worldwide incidence increases. Primary care-based systematic diabetes screening and prevention programs could be effective in women with previous GDM. GooD4Mum aimed to determine whether a Quality Improvement Collaborative (QIC) would improve postpartum diabetes screening and prevention planning in women with previous GDM in general practice.

METHODS

Fifteen general practices within Victoria (Australia) participated in a 12-month QIC, consisting of baseline and four quarterly audits, guideline-led workshops and Plan-Do-Study-Act feedback cycles after each audit. The primary outcome measures were the proportion of women on local GDM registers completing a diabetes screening test and a diabetes prevention planning consultation within the previous 15 months.

RESULTS

Diabetes screening increased with rates more than doubled from 26% to 61% and postpartum screening increased from 43%-60%. Diabetes prevention planning consultations did not show the same level of increase (0%-10%). The recording of body mass index improved overall (51%-69%) but the number of women with normal body mass index did not.

CONCLUSIONS

GooD4Mum supported increased diabetes screening and the monitoring of high risk women with previous GDM in general practice.

Comparison of clinical and cost-effectiveness of two strategies using mobile digital x-ray to detect pulmonary tuberculosis in rural India

BACKGROUND

Medanta - The Medicity, a multi-super specialty corporate hospital in Gurugram, Haryana launched a "TB-Free Haryana" Campaign; mobile van equipped with a digital CXR machine to screen patients with presumptive Tuberculosis (TB).

OBJECTIVES

In this study, we aimed to assess the (1) yield and cost analysis of two strategies using mobile digital x-ray to detect Pulmonary TB in rural Haryana.

METHODS

An observational study was conducted on all individuals screened by either of the two case finding strategies using a mobile x-ray unit (MXU) mounted on a mobile van in District Mewat, Haryana during Jan-March 2016.

RESULTS

Strategy 1: Out of 121 smear negative cases, x-rays were suggestive of TB in 39(32%), of which 24 were started on TB treatment. Cost of identifying a smear negative TB was US$ 32. Strategy 2: Out of 596 presumptive TB, chest x-rays were suggestive of TB in 108 (18%), of which 67 were started on TB treatment (56 were smear negative TB). Cost of detecting any case of TB was US$ 08 (1 USD = 64 INR).

CONCLUSION

The study reports a new initiative within a PPM model to improve the diagnosis of PTB by filling the gap in the current diagnostic infrastructure. We believe there is potential for replication of strategy 2 model in other states, although further evidence is required.

Code List Library: A Solution to Improve Research Repeatability, Transparency, and Efficiency by Curating Lists of Clinical Codes

IntroductionSets of clinical codes that define conditions and events of interest are a key knowledge product in health data research. Documenting such lists is essential for transparency and repeatability, and there is great potential benefit in their sharing and reuse. We designed and implemented software to address these goals. Objectives and ApproachOur goals were threefold: Provide a graphical user interface (GUI) to allow easier creation of code lists, for less technical users. Allow clear documentation of code lists, preserving the history of their creation and capturing metadata about their meaning, provenance, and use. Facilitate programmatic access, so that the software is not just documentation but can be integrated into data preparation and analysis. To these ends, we developed a web application using Python and PostgreSQL that allows creating, editing, and accessing via a GUI, as well as a REST API for integration into SQL, R, and other environments. ResultsThe software allows users to view and create lists through a familiar web paradigm. Lists can be built by identifying codes in a variety of ways, including keyword searches, regular expressions, and more complex rules. A change history is stored. Information such as a description, whether there was clinical reviewed, and relevant publications is captured. The REST API allows access and use in a variety of settings. We have implemented a DB2 SQL interface to enable code lists to be used within database queries, and other interfaces such as an R package are planned for the future. It will be used within the SAIL Databank initially, with a public version for sharing across institutions planned. The code will be open source to enable further development. Conclusion/ImplicationsWe expect this tool to facilitate faster, higher-quality, more reproducible research in Wales and beyond. Hopefully it will be not just a standalone effort, but one small piece in a set of better tools and methods that will enable our field to truly realized the benefit of large linked datasets.

Secure data analysis environments: can we agree on criteria for “Appropriate secure access” to linked health data?

Overall objectives or goalMany health data linkage ecosystems across the world have designed and implemented secure data analysis environments as one of their controls to protect patient privacy and confidentiality. These have been shaped by local legislation and data governance policies, available IT infrastructure and resources, and the skills and imagination of their architects. However, at present their various features and functionalities have not been reviewed, synthesised or contrasted. Burton et al [1] have proposed 12 criteria for Data Safe Havens in health and healthcare, which they conceptualise broadly as encompassing data governance and ethics, quality and curation of data repositories, and data security. Under this definition, secure analysis environments, which may or may not be integrated with data repositories, are a component of a Data Safe Haven, addressing the criterion “Appropriate secure access to individually identifying data”. To guide those building and operating these environments, and data custodians and stewards who need to assess their fitness-for-purpose, it would be of great value to discuss and agree an aggregate term (e.g. “Secure Data Lab”) that describes them, and to develop a more detailed set of criteria for what entails “Appropriate secure access” to linked health data. The goal of this session is to describe and document the approaches that have been taken by flagship secure data analysis environments internationally, including their approaches to authentication, assigning permissions, managing the ingress and egress of files and auditing transactions, and their responses to emerging opportunities, including cloud computing and national and international data sharing. We will explore how the interplay of physical, technical and procedural controls have been combined to create existing models, and the extent to which these can balance each other and be applied with flexibility depending on perceived risk and regimes. Session structurePrior to the session, we will develop a draft set of criteria for “Appropriate secure access” to linked health data. The session will comprise presentations describing existing secure analysis environments against the draft criteria, followed by a facilitated discussion. The secure data analysis environments that will be presented include: UNSW Sydney E-Research Institutional Cloud Architecture (ERICA) PopData BC Secure Research Environment (SRE) Institute for Clinical Evaluative Sciences (ICES) Data and Analytic Virtual Environment (IDAVE) Secure Anonymised Information Linkage (SAIL) Gateway Intended output or outcomeWe will write up the outcomes of the session as a scientific paper that proposes an aggregate term for secure data analysis environments for linked health data and a set of criteria for what entails “Appropriate secure access” to linked health data. Presenters and Facilitators Professor Louisa Jorm, Centre for Big Data Research in Health, UNSW Sydney, Australia Dr Tim Churches, South Western Sydney Clinical School, UNSW Sydney, Australia Professor Kim McGrail, Population Data BC, The University of British Columbia, Vancouver, Canada J. Charles Victor, Institute for Clinical Evaluative Sciences, Toronto, Canada Dr Kerina Jones, Swansea University Medical School, Wales, United Kingdom Professor David Ford, Swansea University Medical School, Wales, United Kingdom 1. Burton PR, Murtagh MJ, Boyd A, et al. Data Safe Havens in health research and healthcare. Bioinformatics 2015; 31(20): 3241–3248

Data Services for Cohort Studies: Increasing the impact of existing research studies and epidemiological readiness

IntroductionThe Dementias Platform UK (DPUK) Data Portal is a secure, accessible environment facilitating provision of rich data towards the largest Dementia, cognition and ageing community of cohort studies in the world. DPUK is also providing services for cohort studies and researchers to maximise the research potential of the programme’s community. Objectives and ApproachAs part of the engagement of DPUK cohorts with the Data Portal, cohorts will upload data onto the DPUK instance of UK Secure eResearch Platform infrastructure. The Data Portal allows access to a collaborative working space that allows cohorts to enrich their own data, perform their own analysis, and enhance the research potential of their data whilst making use of expertise at various DPUK sites, such as data linking, curation and multi-modal specialism. Cohort data divided into ontologies allows researchers to access data specific to their study needs and can be requested from multiple cohorts simultaneously. ResultsBy utilising the Data Portal researchers have access to cohort data that has been prepared for dementia epidemiology using the agreed ontologies, providing more rapid access to cohort data that otherwise may be large and complex. The knowledge and experience of DPUK staff and collaborators can also help to guide nascent cohorts and feasibility studies into producing research-ready datasets, enabling them to achieve greater impact with their data. A range of analytical tools are provided on the Data Portal making analysis of a cohort’s own data or multiple independent datasets more accessible. Alongside data curation, DPUK also facilitates data linkage to routine sources, beginning with a Wales-wide use case that will expand to the UK over the course of the project. Conclusion/ImplicationsData from international sources accessible using a central platform permits international collaboration, with ontologies allowing previously disparate data to be combined and analysed to build knowledge and research impact. DPUK projects create policy leading results and operational research standards, enhancing cohort impact and discovery of benefits for Dementia patients.

Dementias Platform UK (DPUK) Data Portal - World-leading infrastructure facilitating innovative multi-modal research

IntroductionModern team science requires effective sharing of data and skills. The DPUK Data Portal is a collection of tools, datasets and networks that allows for epidemiologists and specialist researchers alike to access, analyse and investigate cohort and different modalities of routine data across UK and international sources. Objectives and ApproachThe Portal is housed on an instance of UKSeRP (UK Secure eResearch Platform), that allows customisable infrastructure to be used for multi-modal research (thus far live in genetics, imaging and clinical data) for researchers across the world using remote access technology whilst allowing governance to remain with the data provider. A central team at Swansea University is responsible for data curation and processing, and runs an access procedure for researchers to apply to use data from multiple sources to be analysed in a central analysis environment. Other modalities are similarly hosted, with input from partner sites in Cardiff and Oxford. ResultsDPUK facilitates data access and research on 49 cohorts, 40 UK-based and 9 international. The centralised repository model including remote access and ability to store and make available different modalities of data, from phenotypic data, to genetic and imaging data, has allowed DPUK to begin to support research of varying topics, from those studying cognitive decline and Dementia as a disease, to those maturing analytical models. By providing access to data platforms specialising in genetics, imaging and routine clinical data, as well as to specialists in disease and biology to aid with its understanding, DPUK has realised a large-scale research exercise combining major data modalities on a central platform, and allow access to such rich data across the world under an umbrella of robust governance. Conclusion/ImplicationsGlobally, cohorts are pooling data, expertise and desire to enrich their own aims in partnership with a federated research community to enable in-depth scrutiny of the biological origins of dementia and the development and evaluation of novel approach to disease prevention and cure.

Using natural language processing to extract structured epilepsy data from unstructured clinic letters

IntroductionElectronic health records (EHR) are a powerful resource in enabling large-scale healthcare research. EHRs often lack detailed disease-specific information that is collected in free text within clinical settings. This challenge can be addressed by using Natural Language Processing (NLP) to derive and extract detailed clinical information from free text. Objectives and ApproachUsing a training sample of 40 letters, we used the General Architecture for Text Engineering (GATE) framework to build custom rule sets for nine categories of epilepsy information as well as clinic date and date of birth. We used a validation set of 200 clinic letters to compare the results of our algorithm to a separate manual review by a clinician, where we evaluated a “per item” and a “per letter” approach for each category. ResultsThe “per letter” approach identified 1,939 items of information with overall precision, recall and F1-score of 92.7%, 77.7% and 85.6%. Precision and recall for epilepsy specific categories were: diagnosis (85.3%,92.4%),  type (93.7%,83.2%), focal seizure (99.0%,68.3%), generalised seizure (92.5%,57.0%), seizure frequency (92.0%,52.3%), medication (96.1%,94.0%), CT (66.7%,47.1%), MRI (96.6%,51.4%) and EEG (95.8%,40.6%). By combining all items per category, per letter we were able to achieve higher precision, recall and F1-scores of 94.6%, 84.2% and 89.0% across all categories. Conclusion/ImplicationsOur results demonstrate that NLP techniques can be used to accurately extract rich phenotypic details from clinic letters that is often missing from routinely-collected data. Capturing these new data types provides a platform for conducting novel precision neurology research, in addition to potential applicability to other disease areas.

Towards an ethically-founded framework for the use of mobile phone CDRs in health research

IntroductionCall Detail Records (CDRs) are collected by mobile network operators in the course of service provision, and they are increasingly being used in health research. It has been identified that further work is needed to show that CDRs can be used within an ethically-founded framework that meets with social acceptability. Objectives and ApproachThe published research literature was reviewed to identify data governance arrangements, challenges and potential opportunities for the greater use of the location element of CDRs in health research. A series of 3 workshops with members of the public (N=61) were conducted to gain views on the use of CDRs for health research. Data use scenarios of CDRs for health research were constructed to consider risk and mitigating controls. The findings were drawn together against a backdrop of legislative and regulatory requirements. ResultsThe majority of published studies focused on low and middle income countries, often modelling the transmission of infectious diseases, and population movement following natural disasters. CDRs were used in anonymised or aggregated form, and gaining regulatory approvals varied with data provider and by jurisdiction. Only 2 people knew CDR data was being used for health research, but ultimately, most (N=49) were happy for their anonymised CDRs to be used, provided that safeguards were in place. Recommendations towards an ethically-founded framework for using CDR locations in health research are proposed, including the need for greater transparency, accountability, and the incorporation of public views for social acceptability. Conclusion/ImplicationsDespite limitations inherent in the data, mobile phone CDRs have been used successfully in health research. People are generally amenable to the use of anonymised CDR data, but they want to be properly informed. The proposed recommendations should be taken into consideration to contribute towards a consistent, socially-acceptable, ethically founded framework.