Automating incidence and prevalence analysis in open cohorts.

MOTIVATION: Data is increasingly used for improvement and research in public health, especially administrative data such as that collected in electronic health records. Patients enter and exit these typically open-cohort datasets non-uniformly; this can render simple questions about incidence and prevalence time-consuming and with unnecessary variation between analyses. We therefore developed methods to automate analysis of incidence and prevalence in open cohort datasets, to improve transparency, productivity and reproducibility of analyses. IMPLEMENTATION: We provide both a code-free set of rules for incidence and prevalence that can be applied to any open cohort, and a python Command Line Interface implementation of these rules requiring python 3.9 or later. GENERAL FEATURES: The Command Line Interface is used to calculate incidence and point prevalence time series from open cohort data. The ruleset can be used in developing other implementations or can be rearranged to form other analytical questions such as period prevalence. AVAILABILITY: The command line interface is freely available from https://github.com/THINKINGGroup/analogy_publication .

Polypharmacy during pregnancy and associated risk factors: a retrospective analysis of 577 medication exposures among 1.5 million pregnancies in the UK, 2000-2019.

BACKGROUND: The number of medications prescribed during pregnancy has increased over the past few decades. Few studies have described the prevalence of multiple medication use among pregnant women. This study aims to describe the overall prevalence over the last two decades among all pregnant women and those with multimorbidity and to identify risk factors for polypharmacy in pregnancy. METHODS: A retrospective cohort study was conducted between 2000 and 2019 using the Clinical Practice Research Datalink (CPRD) pregnancy register. Prescription records for 577 medication categories were obtained. Prevalence estimates for polypharmacy (ranging from 2+ to 11+ medications) were presented along with the medications commonly prescribed individually and in pairs during the first trimester and the entire pregnancy period. Logistic regression models were performed to identify risk factors for polypharmacy. RESULTS: During the first trimester (812,354 pregnancies), the prevalence of polypharmacy ranged from 24.6% (2+ medications) to 0.1% (11+ medications). During the entire pregnancy period (774,247 pregnancies), the prevalence ranged from 58.7 to 1.4%. Broad-spectrum penicillin (6.6%), compound analgesics (4.5%) and treatment of candidiasis (4.3%) were commonly prescribed. Pairs of medication prescribed to manage different long-term conditions commonly included selective beta 2 agonists or selective serotonin re-uptake inhibitors (SSRIs). Risk factors for being prescribed 2+ medications during the first trimester of pregnancy include being overweight or obese [aOR: 1.16 (1.14-1.18) and 1.55 (1.53-1.57)], belonging to an ethnic minority group [aOR: 2.40 (2.33-2.47), 1.71 (1.65-1.76), 1.41 (1.35-1.47) and 1.39 (1.30-1.49) among women from South Asian, Black, other and mixed ethnicities compared to white women] and smoking or previously smoking [aOR: 1.19 (1.18-1.20) and 1.05 (1.03-1.06)]. Higher and lower age, higher gravidity, increasing number of comorbidities and increasing level of deprivation were also associated with increased odds of polypharmacy. CONCLUSIONS: The prevalence of polypharmacy during pregnancy has increased over the past two decades and is particularly high in younger and older women; women with high BMI, smokers and ex-smokers; and women with multimorbidity, higher gravidity and higher levels of deprivation. Well-conducted pharmaco-epidemiological research is needed to understand the effects of multiple medication use on the developing foetus.

Clinical decision support systems for maternity care: a systematic review and meta-analysis.

Background: The use of Clinical Decision Support Systems (CDSS) is increasing throughout healthcare and may be able to improve safety and outcomes in maternity care, but maternity care has key differences to other disciplines that complicate the use of CDSS. We aimed to identify evaluated CDSS and synthesise evidence of their impact on maternity care. Methods: We conducted a systematic review for articles published before 24th May 2024 that described i) CDSS that ii) investigated the impact of their use iii) in maternity settings. Medline, CINAHL, CENTRAL and HMIC were searched for articles relating to evaluations of CDSS in maternity settings, with forward- and backward-citation tracing conducted for included articles. Risk of bias was assessed using the Mixed Methods Assessment Tool, and CDSS were described according to the clinical problem, purpose, design, and technical environment. Quantitative results from articles reporting appropriate data were meta-analysed to estimate odds of a CDSS achieving its desired outcome using a multi-level random effects model, first by individual CDSS and then across all CDSS. PROSPERO ID: CRD42022348157. Findings: We screened 12,039 papers and included 87 articles describing 47 unique CDSS. 24 articles (28%) described randomised controlled trials, 30 (34%) described non-randomised interventional studies, 10 (11%) described mixed methods studies, 10 (11%) described qualitative studies, 7 (8%) described quantitative descriptive studies, and 7 (8%) described economic evaluations. 49 (56%) were in High-Income Countries and 38 (44%) in Low- and Middle-Income countries, with no CDSS trialled in both income categories. Meta-analysis of 35 included studies found an odds ratio for improved outcomes of 1.69 (95% confidence interval 1.24-2.30). There was substantial variation in effects, aims, CDSS types, context, study designs, and outcomes. Interpretation: Most CDSS evaluations showed improvements in outcomes, but there was heterogeneity in all aspects of design and evaluation of systems. CDSS are increasingly important in delivering healthcare, and Electronic Health Records and mHealth will increase their availability, but traditional epidemiological methods may be limited in guiding design and demonstrating effectiveness due to rapid CDSS development lifecycles and the complex systems in which they are embedded. Development methods that are attentive to context, such as Human Centred Design, will help to meet this need. Funding: None.

Health service readiness to provide care for HIV and cardiovascular disease risk factors in low- and middle-income countries.

Cardiovascular disease risk factors (CVDRF), in particular diabetes and hypertension, are chronic conditions which carry a substantial disease burden in Low- and Middle-Income Countries. Unlike HIV, they were neglected in the Millenium Development Goals along with the health services required to manage them. To inform the level of health service readiness that could be achieved with increased attention, we compared readiness for CVDRF with that for HIV. Using data from national Service Provision Assessments, we describe facility-reported readiness to provide services for CVDRF and HIV, and derive a facility readiness score of observed essential components to manage them. We compared HIV vs CVDRF coverage scores by country, rural or urban location, and facility type, and by whether or not facilities reported readiness to provide care. We assessed the factors associated with coverage scores for CVDRF and HIV in a multivariable analysis. In our results, we include 7522 facilities in 8 countries; 86% of all facilities reported readiness to provide services for CVDRF, ranging from 77-98% in individual countries. For HIV, 30% reported of facilities readiness to provide services, ranging from 3-63%. Median derived facility readiness score for CVDRF was 0.28 (IQR 0.16-0.50), and for HIV was 0.43 (0.32-0.60). Among facilities which reported readiness, this rose to 0.34 (IQR 0.18-0.52) for CVD and 0.68 (0.56-0.76) for HIV. Derived readiness scores were generally significantly lower for CVDRF than for HIV, except in private facilities. In multivariable analysis, odds of a higher readiness score in both CVDRF or HIV care were higher in urban vs rural and secondary vs primary care; facilities with higher CVDRF scores were significantly associated with higher HIV scores. Derived readiness scores for HIV are higher than for CVDRF, and coverage for CVDRF is significantly higher in facilities with higher HIV readiness scores. This suggests possible benefits from leveraging HIV services to provide care for CVDRF, but poor coverage in rural and primary care facilities threatens Sustainable Development Goal 3.8 to provide high quality universal healthcare for all.

Detection and evaluation of signals associated with exposure to individual and combination of medications in pregnancy: a signal detection study protocol.

INTRODUCTION: Considering the high prevalence of polypharmacy in pregnant women and the knowledge gap in the risk-benefit safety profile of their often-complex treatment plan, more research is needed to optimise prescribing. In this study, we aim to detect adverse and protective effect signals of exposure to individual and pairwise combinations of medications during pregnancy. METHODS AND ANALYSIS: Using a range of real-world data sources from the UK, we aim to conduct a pharmacovigilance study to assess the safety of medications prescribed during the preconception period (3 months prior to conception) and first trimester of pregnancy. Women aged between 15 and 49 years with a record of pregnancy within the Clinical Practice Research Datalink (CPRD) Pregnancy Register, the Welsh Secure Anonymised Information Linkage (SAIL), the Scottish Morbidity Record (SMR) data sets and the Northern Ireland Maternity System (NIMATS) will be included. A series of case control studies will be conducted to estimate measures of disproportionality, detecting signals of association between a range of pregnancy outcomes and exposure to individual and combinations of medications. A multidisciplinary expert team will be invited to a signal detection workshop. By employing a structured framework, signals will be transparently assessed by each member of the team using a questionnaire appraising the signals on aspects of temporality, selection, time and measurement-related biases and confounding by underlying disease or comedications. Through group discussion, the expert team will reach consensus on each of the medication exposure-outcome signal, thereby excluding spurious signals, leaving signals suggestive of causal associations for further evaluation. ETHICS AND DISSEMINATION: Ethical approval has been obtained from the Independent Scientific Advisory Committee, SAIL Information Governance Review Panel, University of St. Andrews Teaching and Research Ethics Committee and Office for Research Ethics Committees Northern Ireland (ORECNI) for access and use of CPRD, SAIL, SMR and NIMATS data, respectively.

Maternal and child outcomes for pregnant women with pre-existing multiple long-term conditions: protocol for an observational study in the UK.

INTRODUCTION: One in five pregnant women has multiple pre-existing long-term conditions in the UK. Studies have shown that maternal multiple long-term conditions are associated with adverse outcomes. This observational study aims to compare maternal and child outcomes for pregnant women with multiple long-term conditions to those without multiple long-term conditions (0 or 1 long-term conditions). METHODS AND ANALYSIS: Pregnant women aged 15-49 years old with a conception date between 2000 and 2019 in the UK will be included with follow-up till 2019. The data source will be routine health records from all four UK nations (Clinical Practice Research Datalink (England), Secure Anonymised Information Linkage (Wales), Scotland routine health records and Northern Ireland Maternity System) and the Born in Bradford birth cohort. The exposure of two or more pre-existing, long-term physical or mental health conditions will be defined from a list of health conditions predetermined by women and clinicians. The association of maternal multiple long-term conditions with (a) antenatal, (b) peripartum, (c) postnatal and long-term and (d) mental health outcomes, for both women and their children will be examined. Outcomes of interest will be guided by a core outcome set. Comparisons will be made between pregnant women with and without multiple long-term conditions using modified Poisson and Cox regression. Generalised estimating equation will account for the clustering effect of women who had more than one pregnancy episode. Where appropriate, multiple imputation with chained equation will be used for missing data. Federated analysis will be conducted for each dataset and results will be pooled using random-effects meta-analyses. ETHICS AND DISSEMINATION: Approval has been obtained from the respective data sources in each UK nation. Study findings will be submitted for publications in peer-reviewed journals and presented at key conferences.

Association of pregnancy complications/risk factors with the development of future long-term health conditions in women: overarching protocol for umbrella reviews.

INTRODUCTION: With good medical care, most pregnancy complications like pre-eclampsia, gestational diabetes, etc resolve after childbirth. However, pregnancy complications are known to be associated with an increased risk of new long-term health conditions for women later in life, such as cardiovascular disease. These umbrella reviews aim to summarise systematic reviews evaluating the association between pregnancy complications and five groups of long-term health conditions: autoimmune conditions, cancers, functional disorders, mental health conditions and metabolic health conditions (diabetes and hypertension). METHODS AND ANALYSIS: We will conduct searches in Medline, Embase and the Cochrane database of systematic reviews without any language restrictions. We will include systematic reviews with or without meta-analyses that studied the association between pregnancy complications and the future risk of the five groups of long-term health conditions in women. Pregnancy complications were identified from existing core outcome sets for pregnancy and after consultation with experts. Two reviewers will independently screen the articles. Data will be synthesised with both narrative and quantitative methods. Where a meta-analysis has been carried out, we will report the combined effect size from individual studies. For binary data, pooled ORs with 95% CIs will be presented. For continuous data, we will use the mean difference with 95% CIs. The findings will be presented in forest plots to assess heterogeneity. The methodological quality of the studies will be evaluated with the AMSTAR 2 tool or the Cochrane risk of bias tool. The corrected covered area method will be used to assess the impact of overlap in reviews. The findings will be used to inform the design of prediction models, which will predict the risk of women developing these five group of health conditions following a pregnancy complication. ETHICS AND DISSEMINATION: No ethical approvals required. Findings will be disseminated through publications in peer-reviewed journals and conference presentations.

Symptoms and risk factors for long COVID in non-hospitalized adults.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is associated with a range of persistent symptoms impacting everyday functioning, known as post-COVID-19 condition or long COVID. We undertook a retrospective matched cohort study using a UK-based primary care database, Clinical Practice Research Datalink Aurum, to determine symptoms that are associated with confirmed SARS-CoV-2 infection beyond 12 weeks in non-hospitalized adults and the risk factors associated with developing persistent symptoms. We selected 486,149 adults with confirmed SARS-CoV-2 infection and 1,944,580 propensity score-matched adults with no recorded evidence of SARS-CoV-2 infection. Outcomes included 115 individual symptoms, as well as long COVID, defined as a composite outcome of 33 symptoms by the World Health Organization clinical case definition. Cox proportional hazards models were used to estimate adjusted hazard ratios (aHRs) for the outcomes. A total of 62 symptoms were significantly associated with SARS-CoV-2 infection after 12 weeks. The largest aHRs were for anosmia (aHR 6.49, 95% CI 5.02-8.39), hair loss (3.99, 3.63-4.39), sneezing (2.77, 1.40-5.50), ejaculation difficulty (2.63, 1.61-4.28) and reduced libido (2.36, 1.61-3.47). Among the cohort of patients infected with SARS-CoV-2, risk factors for long COVID included female sex, belonging to an ethnic minority, socioeconomic deprivation, smoking, obesity and a wide range of comorbidities. The risk of developing long COVID was also found to be increased along a gradient of decreasing age. SARS-CoV-2 infection is associated with a plethora of symptoms that are associated with a range of sociodemographic and clinical risk factors.

Ruthenium-catalyzed homo Diels-Alder [2 + 2 + 2] cycloadditions of alkynyl phosphonates with bicyclo[2.2.1]hepta-2,5-diene.

Ruthenium-catalyzed homo Diels-Alder [2 + 2 + 2] cycloadditions between alkynyl phosphonates and bicyclo[2.2.1]hepta-2,5-diene were studied. The observed reactivity was found to be dependent on the presence of the phosphonate moiety. The Ru-catalyzed cycloaddition was compatible with a variety of aromatic and aliphatic substituted alkynyl phosphonates, providing the corresponding phosphonate substituted deltacyclenes in low to good yields (up to 88%).

Rapid translation of clinical guidelines into executable knowledge: A case study of COVID-19 and online demonstration.

Introduction: We report a pathfinder study of AI/knowledge engineering methods to rapidly formalise COVID-19 guidelines into an executable model of decision making and care pathways. The knowledge source for the study was material published by BMJ Best Practice in March 2020. Methods: The PROforma guideline modelling language and OpenClinical.net authoring and publishing platform were used to create a data model for care of COVID-19 patients together with executable models of rules, decisions and plans that interpret patient data and give personalised care advice. Results: PROforma and OpenClinical.net proved to be an effective combination for rapidly creating the COVID-19 model; the Pathfinder 1 demonstrator is available for assessment at https://www.openclinical.net/index.php?id=746. Conclusions: This is believed to be the first use of AI/knowledge engineering methods for disseminating best-practice in COVID-19 care. It demonstrates a novel and promising approach to the rapid translation of clinical guidelines into point of care services, and a foundation for rapid learning systems in many areas of healthcare.

Validation protocol for current good manufacturing practices production of [15O]water for hybrid PET/MR studies.

INTRODUCTION: Oxygen-15 (O; t½ = 122.4 s) has been used for nuclear imaging experiments since the beginning of the field. With the advent of simultaneous hybrid PET/MR technology, [O]water has seen a resurgence and remains the gold standard method for quantitative blood flow studies. The short half-life presents a nontrivial challenge to applying current good manufacturing practices production methods to maintain patient safety. METHODS: A two-vial production method was devised to ensure adequate mixing of [O]water vapour into buffered isotonic saline. For production validation, six batches of [O]water were prepared: sterility, quality control testing and four patient doses. The final dose also underwent quality tested. Routine quality control testing included the following: radiochemical identity and purity, radionuclidic identity and purity, appearance, pH, pyrogenicity, and filter integrity. Sterility was retrospectively confirmed. For validation, breakthrough Pt concentration was also measured. RESULTS: Consistent yields of 10-12 GBq (270-325 mCi) were obtained 3 min after bombardment. Overall, 26 [O]water batches underwent quality control testing under this protocol and all met or exceeded release specifications for clinical use. CONCLUSION: The multiple batch protocol proved to be a safe and effective means for producing [O]water. Furthermore, this protocol could be readily adapted by any facility attempting to produce [O]water for clinical studies. Compared with previous attempts at our site, the protocol outlined here was more consistent and reliable, improved production workflow and led to more available radioactivity for participant injection and QC testing.

Ruthenium-catalyzed [2 + 2] cycloadditions of bicyclic alkenes with alkynyl phosphonates.

Ruthenium-catalyzed [2 + 2] cycloadditions of bicyclic alkenes with alkynyl phosphonates were investigated. The phosphonate moieties were found to be compatible with the Ru-catalyzed cycloadditions giving the corresponding cyclobutene cycloadducts in low to excellent yield (up to 96%). Alkynyl phosphonates showed lower reactivity than other heteroatom-substituted alkynes such as alkynyl halides, ynamides, alkynyl sulfides, and alkynyl sulfones and required a higher reaction temperature and much longer reaction time.

Absolute Cerebral Blood Flow Infarction Threshold for 3-Hour Ischemia Time Determined with CT Perfusion and 18F-FFMZ-PET Imaging in a Porcine Model of Cerebral Ischemia.

CT Perfusion (CTP) derived cerebral blood flow (CBF) thresholds have been proposed as the optimal parameter for distinguishing the infarct core prior to reperfusion. Previous threshold-derivation studies have been limited by uncertainties introduced by infarct expansion between the acute phase of stroke and follow-up imaging, or DWI lesion reversibility. In this study a model is proposed for determining infarction CBF thresholds at 3hr ischemia time by comparing contemporaneously acquired CTP derived CBF maps to 18F-FFMZ-PET imaging, with the objective of deriving a CBF threshold for infarction after 3 hours of ischemia. Endothelin-1 (ET-1) was injected into the brain of Duroc-Cross pigs (n = 11) through a burr hole in the skull. CTP images were acquired 10 and 30 minutes post ET-1 injection and then every 30 minutes for 150 minutes. 370 MBq of 18F-FFMZ was injected ~120 minutes post ET-1 injection and PET images were acquired for 25 minutes starting ~155-180 minutes post ET-1 injection. CBF maps from each CTP acquisition were co-registered and converted into a median CBF map. The median CBF map was co-registered to blood volume maps for vessel exclusion, an average CT image for grey/white matter segmentation, and 18F-FFMZ-PET images for infarct delineation. Logistic regression and ROC analysis were performed on infarcted and non-infarcted pixel CBF values for each animal that developed infarct. Six of the eleven animals developed infarction. The mean CBF value corresponding to the optimal operating point of the ROC curves for the 6 animals was 12.6 ± 2.8 mL·min-1·100g-1 for infarction after 3 hours of ischemia. The porcine ET-1 model of cerebral ischemia is easier to implement then other large animal models of stroke, and performs similarly as long as CBF is monitored using CTP to prevent reperfusion.

Characterization of 5-(2- 18F-fluoroethoxy)-L-tryptophan for PET imaging of the pancreas.

Purpose: In diabetes, pancreatic beta cell mass declines significantly prior to onset of fasting hyperglycemia. This decline may be due to endoplasmic reticulum (ER) stress, and the system L amino acid transporter LAT1 may be a biomarker of this process. In this study, we used 5-(2- 18F-fluoroethoxy)-L-tryptophan ( 18F-L-FEHTP) to target LAT1 as a potential biomarker of beta cell function in diabetes. Procedures: Uptake of 18F-L-FEHTP was determined in wild-type C57BL/6 mice by ex vivo biodistribution. Both dynamic and static positron emission tomography (PET) images were acquired in wild-type and Akita mice, a model of ER stress-induced diabetes, as well as in mice treated with streptozotocin (STZ). LAT1 expression in both groups of mice was evaluated by immunofluorescence microscopy. Results: Uptake of 18F-L-FEHTP was highest in the pancreas, and static PET images showed highly specific pancreatic signal. Time-activity curves showed significantly reduced 18F-L-FEHTP uptake in Akita mice, and LAT1 expression was also reduced. However, mice treated with STZ, in which beta cell mass was reduced by 62%, showed no differences in 18F-L-FEHTP uptake in the pancreas, and there was no significant correlation of 18F-L-FEHTP uptake with beta cell mass. Conclusions:18F-L-FEHTP is highly specific for the pancreas with little background uptake in kidney or liver. We were able to detect changes in LAT1 in a mouse model of diabetes, but these changes did not correlate with beta cell function or mass. Therefore, 18F-L-FEHTP PET is not a suitable method for the noninvasive imaging of changes in beta cell function during the progression of diabetes.