Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles.

Island populations often experience different ecological and demographic conditions than their counterparts on the continent, resulting in divergent evolutionary forces affecting their genomes. Random genetic drift and selection both may leave their imprints on island populations, although the relative impact depends strongly on the specific conditions. Here we address their contributions to the island syndrome in a rodent with an unusually clear history of isolation. Common voles (Microtus arvalis) were introduced by humans on the Orkney archipelago north of Scotland >5000 years ago and rapidly evolved to exceptionally large size. Our analyses show that the genomes of Orkney voles were dominated by genetic drift, with extremely low diversity, variable Tajima's D, and very high divergence from continental conspecifics. Increased d N/d S ratios over a wide range of genes in Orkney voles indicated genome-wide relaxation of purifying selection. We found evidence of hard sweeps on key genes of the lipid metabolism pathway only in continental voles. The marked increase of body size in Orkney-a typical phenomenon of the island syndrome-may thus be associated to the relaxation of positive selection on genes related to this pathway. On the other hand, a hard sweep on immune genes of Orkney voles likely reflects the divergent ecological conditions and possibly the history of human introduction. The long-term isolated Orkney voles show that adaptive changes may still impact the evolutionary trajectories of such populations despite the pervasive consequences of genetic drift at the genome level.

Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK.

There are longstanding questions about the origins and ancestry of the Picts of early medieval Scotland (ca. 300-900 CE), prompted in part by exotic medieval origin myths, their enigmatic symbols and inscriptions, and the meagre textual evidence. The Picts, first mentioned in the late 3rd century CE resisted the Romans and went on to form a powerful kingdom that ruled over a large territory in northern Britain. In the 9th and 10th centuries Gaelic language, culture and identity became dominant, transforming the Pictish realm into Alba, the precursor to the medieval kingdom of Scotland. To date, no comprehensive analysis of Pictish genomes has been published, and questions about their biological relationships to other cultural groups living in Britain remain unanswered. Here we present two high-quality Pictish genomes (2.4 and 16.5X coverage) from central and northern Scotland dated from the 5th-7th century which we impute and co-analyse with >8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the genomes within the Iron Age gene pool in Britain and demonstrate regional biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-By-Descent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland-where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of direct common female ancestors, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and present-day groups of the UK.

Rates and causes of death after release from incarceration among 1 471 526 people in eight high-income and middle-income countries: an individual participant data meta-analysis.

BACKGROUND: Formerly incarcerated people have exceptionally poor health profiles and are at increased risk of preventable mortality when compared with their general population peers. However, not enough is known about the epidemiology of mortality in this population-specifically the rates, causes, and timing of death in specific subgroups and regions-to inform the development of targeted, evidence-based responses. We aimed to document the incidence, timing, causes, and risk factors for mortality after release from incarceration. METHODS: We analysed linked administrative data from the multi-national Mortality After Release from Incarceration Consortium (MARIC) study. We examined mortality outcomes for 1 471 526 people released from incarceration in eight countries (Australia, Brazil, Canada, New Zealand, Norway, Scotland, Sweden, and the USA) from 1980 to 2018, across 10 534 441 person-years of follow-up (range 0-24 years per person). We combined data from 18 cohort studies using two-step individual participant data meta-analyses to estimate pooled all-cause and cause-specific crude mortality rates (CMRs) per 100 000 person-years, for specific time periods (first, daily from days 1-14; second, weekly from weeks 3-12; third, weeks 13-52 combined; fourth, weeks 53 and over combined; and fifth, total follow-up) after release, overall and stratified by age, sex, and region. FINDINGS: 75 427 deaths were recorded. The all-cause CMR during the first week following release (1612 [95% CI 1048-2287]) was higher than during all other time periods (incidence rate ratio [IRR] compared with week 2: 1·5 [95% CI 1·2-1·8], I2=26·0%, weeks 3-4: 2·0 [1·5-2·6], I2=53·0%, and weeks 9-12: 2·2 [1·6-3·0], I2=70·5%). The highest cause-specific mortality rates during the first week were due to alcohol and other drug poisoning (CMR 657 [95% CI 332-1076]), suicide (135 [36-277]), and cardiovascular disease (71 [16-153]). We observed considerable variation in cause-specific CMRs over time since release and across regions. Pooled all-cause CMRs were similar between males (731 [95% CI 630-839]) and females (660 [560-767]) and were higher in older age groups. INTERPRETATION: The markedly elevated rate of death in the first week post-release underscores an urgent need for investment in evidence-based, coordinated transitional healthcare, including treatment for mental illness and substance use disorders to prevent post-release deaths due to suicide and overdose. Temporal variations in rates and causes of death highlight the need for routine monitoring of post-release mortality. FUNDING: Australia's National Health and Medical Research Council.

Undervaccination and severe COVID-19 outcomes: meta-analysis of national cohort studies in England, Northern Ireland, Scotland, and Wales.

BACKGROUND: Undervaccination (receiving fewer than the recommended number of SARS-CoV-2 vaccine doses) could be associated with increased risk of severe COVID-19 outcomes-ie, COVID-19 hospitalisation or death-compared with full vaccination (receiving the recommended number of SARS-CoV-2 vaccine doses). We sought to determine the factors associated with undervaccination, and to investigate the risk of severe COVID-19 outcomes in people who were undervaccinated in each UK nation and across the UK. METHODS: We used anonymised, harmonised electronic health record data with whole population coverage to carry out cohort studies in England, Northern Ireland, Scotland, and Wales. Participants were required to be at least 5 years of age to be included in the cohorts. We estimated adjusted odds ratios for undervaccination as of June 1, 2022. We also estimated adjusted hazard ratios (aHRs) for severe COVID-19 outcomes during the period June 1 to Sept 30, 2022, with undervaccination as a time-dependent exposure. We combined results from nation-specific analyses in a UK-wide fixed-effect meta-analysis. We estimated the reduction in severe COVID-19 outcomes associated with a counterfactual scenario in which everyone in the UK was fully vaccinated on June 1, 2022. FINDINGS: The numbers of people undervaccinated on June 1, 2022 were 26 985 570 (45·8%) of 58 967 360 in England, 938 420 (49·8%) of 1 885 670 in Northern Ireland, 1 709 786 (34·2%) of 4 992 498 in Scotland, and 773 850 (32·8%) of 2 358 740 in Wales. People who were younger, from more deprived backgrounds, of non-White ethnicity, or had a lower number of comorbidities were less likely to be fully vaccinated. There was a total of 40 393 severe COVID-19 outcomes in the cohorts, with 14 156 of these in undervaccinated participants. We estimated the reduction in severe COVID-19 outcomes in the UK over 4 months of follow-up associated with a counterfactual scenario in which everyone was fully vaccinated on June 1, 2022 as 210 (95% CI 94-326) in the 5-15 years age group, 1544 (1399-1689) in those aged 16-74 years, and 5426 (5340-5512) in those aged 75 years or older. aHRs for severe COVID-19 outcomes in the meta-analysis for the age group of 75 years or older were 2·70 (2·61-2·78) for one dose fewer than recommended, 3·13 (2·93-3·34) for two fewer, 3·61 (3·13-4·17) for three fewer, and 3·08 (2·89-3·29) for four fewer. INTERPRETATION: Rates of undervaccination against COVID-19 ranged from 32·8% to 49·8% across the four UK nations in summer, 2022. Undervaccination was associated with an elevated risk of severe COVID-19 outcomes. FUNDING: UK Research and Innovation National Core Studies: Data and Connectivity.

Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney.

Orkney was a major cultural center during the Neolithic, 3800 to 2500 BC. Farming flourished, permanent stone settlements and chambered tombs were constructed, and long-range contacts were sustained. From ∼3200 BC, the number, density, and extravagance of settlements increased, and new ceremonial monuments and ceramic styles, possibly originating in Orkney, spread across Britain and Ireland. By ∼2800 BC, this phenomenon was waning, although Neolithic traditions persisted to at least 2500 BC. Unlike elsewhere in Britain, there is little material evidence to suggest a Beaker presence, suggesting that Orkney may have developed along an insular trajectory during the second millennium BC. We tested this by comparing new genomic evidence from 22 Bronze Age and 3 Iron Age burials in northwest Orkney with Neolithic burials from across the archipelago. We identified signals of inward migration on a scale unsuspected from the archaeological record: As elsewhere in Bronze Age Britain, much of the population displayed significant genome-wide ancestry deriving ultimately from the Pontic-Caspian Steppe. However, uniquely in northern and central Europe, most of the male lineages were inherited from the local Neolithic. This suggests that some male descendants of Neolithic Orkney may have remained distinct well into the Bronze Age, although there are signs that this had dwindled by the Iron Age. Furthermore, although the majority of mitochondrial DNA lineages evidently arrived afresh with the Bronze Age, we also find evidence for continuity in the female line of descent from Mesolithic Britain into the Bronze Age and even to the present day.

Respiratory Syncytial Virus-Associated Hospital Admissions by Deprivation Levels Among Children and Adults in Scotland.

BACKGROUND: Socioeconomic deprivation may predispose individuals to respiratory tract infections. We estimated RSV-associated hospitalizations by socioeconomic deprivation in Scotland. METHODS: Using national routine health care records and virological surveillance from 2010 to 2016, we used a time-series linear regression model and a direct measurement based on ICD-10 coded diagnoses to estimate RSV-associated hospitalizations by Scottish Index of Multiple Deprivation (SIMD) quintile and age in comparison to influenza-associated hospitalizations. RESULTS: We estimated an annual average rate per 1000 people of 0.76 (95% CI: 0.43-0.90) in the least deprived group to 1.51 (1.03-1.79) for the most deprived group using model-based approach. The rate ratio (RR) was 1.96 (1.23-3.25), 1.60 (1.0-2.66), 1.35 (0.85-2.25), and 1.12 (0.7-1.85) in the 1st to 4th quintile versus the least deprived group. The pattern of RSV-associated hospitalization rates variation with SIMD was most pronounced in children 0-2y. The ICD-10 approach provided much lower rates than the model-based approach but yielded similar RR estimates between SIMD. Influenza-associated hospitalization rate generally increased with higher deprivation levels among individuals 1y+. CONCLUSIONS: Higher RSV and influenza hospitalization rates are related to higher deprivation levels. Differences between deprivation levels are most pronounced in infants and young children for RSV, and are more apparent among individuals 1y+ for influenza.

Testing and Treatment Interventions in Community Settings Key to Controlling a Recent Human Immunodeficiency Virus Outbreak Among People Who Inject Drugs in Glasgow: A Modeling Study.

BACKGROUND: A human immunodeficiency virus (HIV) outbreak was identified among people who inject drugs (PWID) in Glasgow in 2015, with >150 diagnoses by the end of 2019. The outbreak response involved scaling up HIV testing and improving HIV treatment initiation and retention. METHODS: We parameterized and calibrated a dynamic, deterministic model of HIV transmission among PWID in Glasgow to epidemiological data. We use this model to evaluate HIV testing and treatment interventions. We present results in terms of relative changes in HIV prevalence, incidence, and cases averted. RESULTS: If the improvements in both testing and treatment had not occurred, we predict that HIV prevalence would have reached 17.8% (95% credible interval [CrI], 14.1%-22.6%) by the beginning of 2020, compared to 5.9% (95% CrI, 4.7%-7.4%) with the improvements. If the improvements had been made on detection of the outbreak in 2015, we predict that peak incidence would have been 26.2% (95% CrI, 8.8%-49.3%) lower and 62.7% (95% CrI, 43.6%-76.6%) of the outbreak cases could have been averted. The outbreak could have been avoided if the improvements had already been in place. CONCLUSIONS: Our modeling suggests that the HIV testing and treatment interventions successfully brought the HIV outbreak in Glasgow under control by the beginning of 2020.

Clinical Impact of Serious Respiratory Disease in Children Under the Age of 2 Years During the 2021-2022 Bronchiolitis Season in England, Scotland, and Ireland.

BACKGROUND: Interventions introduced to reduce the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to a widespread reduction in childhood infections. However, from spring 2021 onwards the United Kingdom and Ireland experienced an unusual out-of-season epidemic of respiratory disease. METHODS: We conducted a prospective observational study (BronchStart), enrolling children 0-23 months of age presenting with bronchiolitis, lower respiratory tract infection, or first episode of wheeze to 59 emergency departments across England, Scotland, and Ireland from May 2021 to April 2022. We combined testing data with national admissions datasets to infer the impact of respiratory syncytial virus (RSV) disease. RESULTS: The BronchStart study collected data on 17 899 presentations for 17 164 children. Risk factors for admission and escalation of care included prematurity and congenital heart disease, but most admissions were for previously healthy term-born children. Of those aged 0-11 months who were admitted and tested for RSV, 1907 of 3912 (48.7%) tested positive. We estimate that every year in England and Scotland 28 561 (95% confidence interval, 27 637-29 486) infants are admitted with RSV infection. CONCLUSIONS: RSV infection was the main cause of hospitalizations in this cohort, but 51.3% of admissions in infants were not associated with the virus. The majority of admissions were in previously healthy term-born infants.

Clinical benefit, reimbursement outcomes, and prices of FDA-approved cancer drugs reviewed through Project Orbis in the USA, Canada, England, and Scotland: a retrospective, comparative analysis.

BACKGROUND: Project Orbis is a global initiative that aims to streamline regulatory review processes across international regulators in the USA, Canada, Australia, UK, Israel, Brazil, Singapore, and Switzerland to bring promising cancer drugs to patients earlier. We explored the clinical benefit, time to regulatory approval and health technology assessment recommendations, reimbursement outcomes, and monthly treatment prices of cancer drugs reviewed through this initiative. METHODS: For this retrospective, comparative analysis, we identified cancer drug approvals reviewed through Project Orbis in the USA, Canada, and the UK between May 1, 2019, and Nov 1, 2023. Approvals of cancer drugs reviewed Project Orbis were extracted from the Food and Drug Administration (FDA) Oncology Centre of Excellence and all other FDA approvals from the Drugs@FDA database. The co-primary outcomes were time of regulatory review, time from regulatory approval to health technology assessment recommendation (England, Scotland, and Canada), reimbursement outcomes, clinical benefit (defined as median gains in progression-free survival and overall survival) between cancer drug approvals reviewed by Project Orbis and other FDA approval processes, and monthly treatment prices. The Wilcoxon rank-sum and Fisher's Exact tests were used to examine statistical significance between approvals reviewed through Project Orbis and other FDA approvals during the same period. FINDINGS: Between May 1, 2019 and Nov 1, 2023, 81 (33%) of 244 cancer drugs approved by the FDA were reviewed through Project Orbis. The median overall survival gains were 4·1 months (IQR 3·3-5·1) compared with 2·7 months (2·1-3·9) for other FDA approvals. Similarly, progression-free survival gains were 2·6 months (IQR 1·7-4·9) for Project Orbis compared with 2·6 months (0·6-5·1) for other FDA approvals. Neither overall survival (p=0·11) nor progression-free survival (p=0·44) gains were significantly different between the two cohorts of approvals. Of the 14 UK Medicines and Healthcare products Regulatory Agency (MHRA) approvals reviewed by the Scottish Medicines Consortium (SMC), the agency gave positive recommendations for all 14 (100%). Of the 15 MHRA approvals reviewed by the National Institute for Health and Care Excellence (NICE), the agency gave positive recommendations for six (40%). Of the 49 approvals reviewed by the Canadian Agency for Drugs and Technologies in Health (CADTH), the agency conditionally recommended 44 (90%). The time between regulatory approval to NICE recommendation increased from a median of 137 days (IQR 102-172) in 2021 to 302 days (184-483) in 2023, SMC recommendation increased from 185 days (in 2021 for one drug only) to 368 days (IQR 313-476) in 2023, and CADTH decision increased from 97 days (in 2020 for one drug only) to 202 days (IQR 153-304) in 2023. The median monthly price of approvals reviewed through Project Orbis was US$20 000 per month (IQR 13 000-37 000). INTERPRETATION: Clinical outcomes of Project Orbis were no different than other FDA approvals during the same time, and access, after a successful health technology assessment, was considerably delayed or absent, raising questions about whether Project Orbis participation translates into faster patient access to medicines with high clinical benefit and sustainable costs. Although future challenges might benefit from regulatory harmonisation, the advantages are currently unclear. FUNDING: None.

Trajectories of clinical characteristics, complications and treatment choices in data-driven subgroups of type 2 diabetes.

AIMS/HYPOTHESIS: This study aimed to explore the added value of subgroups that categorise individuals with type 2 diabetes by k-means clustering for two primary care registries (the Netherlands and Scotland), inspired by Ahlqvist's novel diabetes subgroups and previously analysed by Slieker et al. METHODS: We used two Dutch and Scottish diabetes cohorts (N=3054 and 6145; median follow-up=11.2 and 12.3 years, respectively) and defined five subgroups by k-means clustering with age at baseline, BMI, HbA1c, HDL-cholesterol and C-peptide. We investigated differences between subgroups by trajectories of risk factor values (random intercept models), time to diabetes-related complications (logrank tests and Cox models) and medication patterns (multinomial logistic models). We also compared directly using the clustering indicators as predictors of progression vs the k-means discrete subgroups. Cluster consistency over follow-up was assessed. RESULTS: Subgroups' risk factors were significantly different, and these differences remained generally consistent over follow-up. Among all subgroups, individuals with severe insulin resistance faced a significantly higher risk of myocardial infarction both before (HR 1.65; 95% CI 1.40, 1.94) and after adjusting for age effect (HR 1.72; 95% CI 1.46, 2.02) compared with mild diabetes with high HDL-cholesterol. Individuals with severe insulin-deficient diabetes were most intensively treated, with more than 25% prescribed insulin at 10 years of diagnosis. For severe insulin-deficient diabetes relative to mild diabetes, the relative risks for using insulin relative to no common treatment would be expected to increase by a factor of 3.07 (95% CI 2.73, 3.44), holding other factors constant. Clustering indicators were better predictors of progression variation relative to subgroups, but prediction accuracy may improve after combining both. Clusters were consistent over 8 years with an accuracy ranging from 59% to 72%. CONCLUSIONS/INTERPRETATION: Data-driven subgroup allocations were generally consistent over follow-up and captured significant differences in risk factor trajectories, medication patterns and complication risks. Subgroups serve better as a complement rather than as a basis for compressing clustering indicators.

Cardiovascular risk management among individuals with type 2 diabetes and severe mental illness: a cohort study.

AIMS/HYPOTHESIS: The aim of this study was to compare cardiovascular risk management among people with type 2 diabetes according to severe mental illness (SMI) status. METHODS: We used linked electronic data to perform a retrospective cohort study of adults diagnosed with type 2 diabetes in Scotland between 2004 and 2020, ascertaining their history of SMI from hospital admission records. We compared total cholesterol, systolic BP and HbA1c target level achievement 1 year after diabetes diagnosis, and receipt of a statin prescription at diagnosis and 1 year thereafter, by SMI status using logistic regression, adjusting for sociodemographic factors and clinical history. RESULTS: We included 291,644 individuals with type 2 diabetes, of whom 1.0% had schizophrenia, 0.5% had bipolar disorder and 3.3% had major depression. People with SMI were less likely to achieve cholesterol targets, although this difference did not reach statistical significance for all disorders. However, people with SMI were more likely to achieve systolic BP targets compared to those without SMI, with effect estimates being largest for schizophrenia (men: adjusted OR 1.72; 95% CI 1.49, 1.98; women: OR 1.64; 95% CI 1.38, 1.96). HbA1c target achievement differed by SMI disorder and sex. Among people without previous CVD, statin prescribing was similar or better in those with vs those without SMI at diabetes diagnosis and 1 year later. In people with prior CVD, SMI was associated with lower odds of statin prescribing at diabetes diagnosis (schizophrenia: OR 0.54; 95% CI 0.43, 0.68, bipolar disorder: OR 0.75; 95% CI 0.56, 1.01, major depression: OR 0.92; 95% CI 0.83, 1.01), with this difference generally persisting 1 year later. CONCLUSIONS/INTERPRETATION: We found disparities in cholesterol target achievement and statin prescribing by SMI status. This reinforces the importance of clinical review of statin prescribing for secondary prevention of CVD, particularly among people with SMI.

Circulating 25-hydroxyvitamin D and survival outcomes of colorectal cancer: evidence from population-based prospective cohorts and Mendelian randomisation.

BACKGROUND: To investigate the association between circulating 25-hydroxyvitamin D (25-OHD) and colorectal cancer (CRC) survival outcomes. METHODS: We conducted analyses among the Study of Colorectal Cancer in Scotland (SOCCS) and the UK Biobank (UKBB). Both cancer-specific survival (CSS) and overall survival (OS) outcomes were examined. The 25-OHD levels were categorised into three groups, and multi-variable Cox-proportional hazard models were applied to estimate hazard ratios (HRs). We performed individual-level Mendelian randomisation (MR) through the generated polygenic risk scores (PRS) of 25-OHD and summary-level MR using the inverse-variance weighted (IVW) method. RESULTS: We observed significantly poorer CSS (HR = 0.65,95%CI = 0.55-0.76,P = 1.03 × 10-7) and OS (HR = 0.66,95%CI = 0.58-0.75,P = 8.15 × 10-11) in patients with the lowest compared to those with the highest 25-OHD after adjusting for covariates. These associations remained across patients with varied tumour sites and stages. However, we found no significant association between 25-OHD PRS and either CSS (HR = 0.98,95%CI = 0.80-1.19,P = 0.83) or OS (HR = 1.07,95%CI = 0.91-1.25,P = 0.42). Furthermore, we found no evidence for causal effects by conducting summary-level MR analysis for either CSS (IVW:HR = 1.04,95%CI = 0.85-1.28,P = 0.70) or OS (IVW:HR = 1.10,95%CI = 0.93-1.31,P = 0.25). CONCLUSION: This study supports the observed association between lower circulating 25-OHD and poorer survival outcomes for CRC patients. Whilst the genotype-specific association between better outcomes and higher 25-OHD is intriguing, we found no support for causality using MR approaches.

Smallpox vaccination campaigns resulted in age-associated population cross-immunity against monkeypox virus.

Increased human-to-human transmission of monkeypox virus (MPXV) is cause for concern, and antibodies directed against vaccinia virus (VACV) are known to confer cross-protection against Mpox. We used 430 serum samples derived from the Scottish patient population to investigate antibody-mediated cross-neutralization against MPXV. By combining electrochemiluminescence immunoassays with live-virus neutralization assays, we show that people born when smallpox vaccination was routinely offered in the United Kingdom have increased levels of antibodies that cross-neutralize MPXV. Our results suggest that age is a risk factor of Mpox infection, and people born after 1971 are at higher risk of infection upon exposure.

Distinguishing pedigree relationships via multi-way identity by descent sharing and sex-specific genetic maps.

The proportion of samples with one or more close relatives in a genetic dataset increases rapidly with sample size, necessitating relatedness modeling and enabling pedigree-based analyses. Despite this, relatives are generally unreported and current inference methods typically detect only the degree of relatedness of sample pairs and not pedigree relationships. We developed CREST, an accurate and fast method that identifies the pedigree relationships of close relatives. CREST utilizes identity by descent (IBD) segments shared between a pair of samples and their mutual relatives, leveraging the fact that sharing rates among these individuals differ across pedigree configurations. Furthermore, CREST exploits the profound differences in sex-specific genetic maps to classify pairs as maternally or paternally related-e.g., paternal half-siblings-using the locations of autosomal IBD segments shared between the pair. In simulated data, CREST correctly classifies 91.5%-100% of grandparent-grandchild (GP) pairs, 80.0%-97.5% of avuncular (AV) pairs, and 75.5%-98.5% of half-siblings (HS) pairs compared to PADRE's rates of 38.5%-76.0% of GP, 60.5%-92.0% of AV, 73.0%-95.0% of HS pairs. Turning to the real 20,032 sample Generation Scotland (GS) dataset, CREST identified seven pedigrees with incorrect relationship types or maternal/paternal parent sexes, five of which we confirmed as mistakes, and two with uncertain relationships. After correcting these, CREST correctly determines relationship types for 93.5% of GP, 97.7% of AV, and 92.2% of HS pairs that have sufficient mutual relative data; the parent sex in 100% of HS and 99.6% of GP pairs; and it completes this analysis in 2.8 h including IBD detection in eight threads.

Using the Doughnut Economics framework to structure whole-system thinking in socioecological wellbeing with multidisciplinary stakeholders: an applied case study in Glasgow, Scotland.

BACKGROUND: Human and environmental health are inseparable and interdependent. Doughnut Economics is a conceptual framework combining the Sustainable Development Goals with Planetary Boundaries, thereby simultaneously considering human and planetary wellbeing. The vision is to "meet the needs of all people within the means of the living planet, for the benefit of both current and future generations". Glasgow City Council has committed to becoming a Green Wellbeing Economy, with a socially just transition to Net Zero by 2030. Through our City-University partnership, we are exploring whether Doughnut Economics can drive transformative action towards a sustainable, healthy, and equitable future. METHODS: Glasgow is a pilot site for the C40 Cities' Thriving City Portrait methodology that downscales Doughnut Economics to cities. The Portrait process combined desk-based research and policy review (from January to April, 2022) with participatory workshops to enrich initial findings. The five participatory workshops took place between April, 2022, and February, 2023, and involved about 130 stakeholders. Participants included civil servants, politicians, scientists, community representatives, employees and representatives of private and third-sector organisations, and social enterprises, identified through an iterative stakeholder mapping process with City Council partners. Workshop aims were to create pluralistic definitions of what thriving means for each of the Doughnut's social and ecological dimensions. Ethics approval for the study was granted by The University of Glasgow, College of Medical Veterinary and Life Sciences. FINDINGS: The workshops produced a shared, holistic vision for Glasgow's future as a thriving city. The Doughnut demonstrated potential as a tool for both understanding the city's socioecological impacts, and as a compass by which the city might set its policy agenda. It allows the multiple goals and priorities of a city system to congregate around a cohesive goal. The Portrait process led to a widening of stakeholders' perspectives, applying systems thinking to policy priorities, cross-sector discussion and collaboration, and significant buy-in from a diverse range of changemakers. INTERPRETATION: The Doughnut framework offered a starting point for Public and Planetary Health researchers to understand connections, co-benefits and trade-offs across different parts of the policy and intervention system. Applying this framework in cities could generate support for whole-system interventions and sustainable solutions to the complex and interconnected climate and social challenges we face. One of the limitations is that we do not yet know whether stakeholders can translate support for this co-created framework into tangible whole-systems action. FUNDING: UKRI Natural Environment Research Council and University of Glasgow.

Evaluating the impact of alcohol minimum unit pricing on deaths and hospitalisations in Scotland: a controlled interrupted time series study.

BACKGROUND: Since May 1, 2018, every alcoholic drink sold in Scotland has had minimum unit pricing (MUP) of £0·50 per unit. Previous studies have indicated that the introduction of this policy reduced alcohol sales by 3%. We aimed to assess whether this has led to reductions in alcohol-attributable deaths and hospitalisations. METHODS: Study outcomes, wholly attributable to alcohol consumption, were defined using routinely collected data on deaths and hospitalisations. Controlled interrupted time series regression was used to assess the legislation's impact in Scotland, and any effect modification across demographic and socioeconomic deprivation groups. The pre-intervention time series ran from Jan 1, 2012, to April 30, 2018, and for 32 months after the policy was implemented (until Dec 31, 2020). Data from England, a part of the UK where the intervention was not implemented, were used to form a control group. FINDINGS: MUP in Scotland was associated with a significant 13·4% reduction (95% CI -18·4 to -8·3; p=0·0004) in deaths wholly attributable to alcohol consumption. Hospitalisations wholly attributable to alcohol consumption decreased by 4·1% (-8·3 to 0·3; p=0·064). Effects were driven by significant improvements in chronic outcomes, particularly alcoholic liver disease. Furthermore, MUP legislation was associated with a reduction in deaths and hospitalisations wholly attributable to alcohol consumption in the four most socioeconomically deprived deciles in Scotland. INTERPRETATION: The implementation of MUP legislation was associated with significant reductions in deaths, and reductions in hospitalisations, wholly attributable to alcohol consumption. The greatest improvements were in the four most socioeconomically deprived deciles, indicating that the policy is positively tackling deprivation-based inequalities in alcohol-attributable health harm. FUNDING: Scottish Government.

Evaluating the impact of minimum unit pricing for alcohol in Scotland: a theory-based synthesis of the evidence.

BACKGROUND: In May 2018, the Scottish Government set a minimum unit price (MUP) of £0·50 per unit of alcohol sold in Scotland to reduce alcohol-related health harms. We synthesised evidence to establish the effects of MUP on alcohol-related health and social harms, at population level and within specific societal groups. METHODS: We did a theory-based synthesis of academic and grey research evidence about impacts of MUP in Scotland, including compliance, price, consumption, health outcomes, social outcomes, public attitudes, and the alcoholic drinks industry. We searched the Public Health Scotland's MUP evaluation portfolio and relevant grey and academic literature for studies published between Jan 1, 2018, and Jan 31, 2023. We conducted systematic searches and screening of bibliographic databases (Scopus, Public Health Database, EconLit, MEDLINE, ProQuest Public Health, Social Policy and Practice, NHS Scotland Knowledge Network Library Search, medRxiv, bioRxiv, SSRN, Idox Knowledge Exchange, Social Policy & Practice, and Google Search). Search terms were tailored to specific databases but included variants of the terms "minimum unit pricing", "alcohol", and "policy". Eligibility literature included English-language research into impacts of MUP on either the population of Scotland or a specific subpopulation. We excluded conference abstracts, literature reviews, articles that did not report research, and research based solely on data from before the introduction of MUP. FINDINGS: We included 40 reports in our analysis. On the balance of evidence, MUP improved population-level health outcomes, demonstrated most starkly by a 13·4% reduction in alcohol-attributable deaths in Scotland compared with England. There was no evidence of substantial negative effects on the alcoholic drinks industry or social harms at the population level. While population-level outcomes were predominantly positive, some qualitative evidence suggests that MUP might have exacerbated health and social harms for some individuals or groups, especially those with alcohol dependence who were financially vulnerable. INTERPRETATION: MUP in Scotland has been effective in reducing alcohol-related health harms, with little evidence of any effect on social harms. If MUP continues, policymakers should consider raising the £0·50 per unit threshold and supplementing the intervention with policies or services to address any unintended negative effects experienced by specific groups. The synthesis is persuasive due to the prospective, theory-based design of the evaluation portfolio and the quality and comprehensiveness of the evidence. FUNDING: Scottish Government.

Association between care experience and mental health hospitalisation among children in Scotland, with a focus on chronic conditions (CHiCS): a population-wide longitudinal study using administrative data.

BACKGROUND: Chronic conditions in children are associated with an increased risk of mental health problems. However, not much is known about the nature of this association among care experienced children. We explore the association between three chronic conditions (epilepsy, asthma, and diabetes) and mental health hospitalisation in children with or without care experience. METHODS: The Children's Health in Care in Scotland (CHiCS) is a population-wide longitudinal study that links health and social care data for 13 830 care-experienced children (6274 [45%] female, 7556 [55%] male) and 649 771 general population children (319 438 [49%] female, 330 333 [51%] male). Hospitalisations were followed up from birth between 1990 and 2004, up to July 31, 2016 (when children were aged 12-27 years). We used Cox proportional hazards models with age as timescale to estimate hazard ratios (HR) and 95% CIs for first mental health hospitalisation separately among care-experienced children and general population children. FINDINGS: Among general population children, 3152 (0·49%) children had epilepsy, 94 700 (14·57%) had asthma, and 5501 (0·85%) had diabetes. In comparison, among care-experienced children, 160 (1·16%) children had epilepsy, 2242 (16·21%) had asthma, and 142 (1·03%) had diabetes. Care-experienced children were more likely to have mental health hospitalisations than general population children, with 701 cases (5·1%) versus 5225 cases (0·8%), respectively. Among general population children, out of all three chronic conditions, epilepsy showed the highest risk (HR 2·61, 95% CI 2·20-3·09) for first mental health hospitalisation, followed by diabetes (1·93, 1·62-2·31), and asthma (1·25, 1·16-1·34). Among care-experienced children, asthma showed an HR of 1·43 (1·17-1·74) for first mental health hospitalisation, whereas epilepsy (1·33, 0·70-2·52) and diabetes (1·71, 0·96-3·05) had no association with first mental health hospitalisation in this subgroup. INTERPRETATION: The study highlights the associations between chronic conditions and risk of mental health hospitalisation among children with or without care experience. One limitation of the study is the small number of care experienced children with a chronic condition and mental health hospitalisation, which might have contributed to the lack of association found among care-experienced children between epilepsy and mental health, and diabetes and mental health. Nevertheless, one of its strengths is contributing to the limited knowledge regarding this association. FUNDING: Economic and Social Research Council, Medical Research Council, Scottish Government Chief Scientist Office.

Exploring the experiences of junior doctors who were shielding during the COVID-19 pandemic: a qualitative study of semi-structured interviews.

BACKGROUND: The term "Shielding" was introduced in the UK during the COVID-19 pandemic to protect approximately 4 million people at highest risk from infection. Shielding was characterised by extreme isolation and applied to those with certain illnesses, disabilities, and during pregnancy. For the estimated 1300 high-risk doctors, shielding meant abrupt departure from the clinical environment. We aimed to understand the impact of shielding on junior doctors (JDs) by interviewing them and their consultants. METHODS: This qualitative study used individual semi-structured interviews and reflexive thematic analysis. Virtual interviews were conducted between Sept 2, and Nov 30, 2022, using an interview guide, including open questions around impacts on training, career, and health. 11 JDs and 2 consultants were recruited via Scotland-wide purposive and snowball sampling. Written informed consent was obtained. 12 of 13 participants were women. Eight JDs were shielding because of health issues, and three because of pregnancy. Participant specialties included primary care, secondary care, and foundation and specialty training. Interview transcripts were coded by the lead author and the second author acted as a critical friend. FINDINGS: Despite making important contributions working from home, most JDs (73%, eight of 11) felt that their work was undervalued during shielding. They felt forgotten, feeling they had to "pester" supervisors to be allocated work. All participants reported inadequate support at Occupational Health and workplace levels, including limited supervision or information about training impacts. Negative attitudes towards JDs were experienced by 82% (nine of 11) of JDs, including being denied reasonable adjustments and threatened with dismissal if not following shielding advice. Consultants described supervisory challenges including not receiving guidance or resources and ongoing issues supporting disabled and pregnant JDs beyond the pandemic. INTERPRETATION: These findings offer novel qualitative insight into the impacts of shielding on JDs in Scotland. Findings indicated that support infrastructure was not fit for purpose. Given the significant number of JDs that take prolonged leave from the clinical environment, and the JDs working with disabilities and during pregnancy, these findings are of ongoing concern. Although the sample size was small and the study was set in a specific region, these findings suggest there is potential to improve support infrastructure and move towards a more inclusive clinical environment that recognises, celebrates, and benefits from the value of a diverse workforce. FUNDING: Scottish Medical Education Research Consortium.

Oesophageal cell collection device and biomarker testing to identify high-risk Barrett's patients requiring endoscopic investigation.

BACKGROUND: Barrett's oesophagus surveillance places significant burden on endoscopy services yet is vital to detect early cancerous change. Oesophageal cell collection device (OCCD) testing was introduced across Scotland for Barrett's surveillance in response to the COVID-19 pandemic. This national pragmatic retrospective study presents the CytoSCOT programme results and evaluates whether OCCD testing is successfully identifying high-risk Barrett's patients requiring urgent endoscopy. METHODS: All patients undergoing OCCD testing for Barrett's surveillance across 11 Scottish health boards over a 32-month period were identified. Patients who underwent endoscopy within 12 months of OCCD test were included. Individual patient records were interrogated to record clinical information and OCCD test result to categorize patients into risk groups. Endoscopic histopathology results were analysed according to risk group and segment length. Patients were deemed high risk if the OCCD test demonstrated atypia and/or p53 positivity. RESULTS: 4204 OCCD tests were performed in 3745 patients: 608 patients underwent endoscopy within 12 months and were included in this analysis. Patients with longer Barrett's segments were significantly more likely to have an abnormal OCCD test. 50/608 patients (8.2%) had high-grade dysplasia or cancer on endoscopic biopsies: this equates to 1.3% of the total group (50/3745). 46/50 patients (92.0%) were deemed high risk, triggering urgent endoscopy: this rose to 100% with insufficient tests removed. There were no cancers diagnosed within 12 months post-OCCD in the low-risk group. CONCLUSION: OCCD testing is an effective triage tool to identify high-risk patients with Barrett's oesophagus requiring further investigation with endoscopy within the real-world setting.