Evaluating the impact of alternative phenotype definitions on incidence rates across a global data network.

Objective: Developing accurate phenotype definitions is critical in obtaining reliable and reproducible background rates in safety research. This study aims to illustrate the differences in background incidence rates by comparing definitions for a given outcome. Materials and Methods: We used 16 data sources to systematically generate and evaluate outcomes for 13 adverse events and their overall background rates. We examined the effect of different modifications (inpatient setting, standardization of code set, and code set changes) to the computable phenotype on background incidence rates. Results: Rate ratios (RRs) of the incidence rates from each computable phenotype definition varied across outcomes, with inpatient restriction showing the highest variation from 1 to 11.93. Standardization of code set RRs ranges from 1 to 1.64, and code set changes range from 1 to 2.52. Discussion: The modification that has the highest impact is requiring inpatient place of service, leading to at least a 2-fold higher incidence rate in the base definition. Standardization showed almost no change when using source code variations. The strength of the effect in the inpatient restriction is highly dependent on the outcome. Changing definitions from broad to narrow showed the most variability by age/gender/database across phenotypes and less than a 2-fold increase in rate compared to the base definition. Conclusion: Characterization of outcomes across a network of databases yields insights into sensitivity and specificity trade-offs when definitions are altered. Outcomes should be thoroughly evaluated prior to use for background rates for their plausibility for use across a global network.

Contextualising adverse events of special interest to characterise the baseline incidence rates in 24 million patients with COVID-19 across 26 databases: a multinational retrospective cohort study.

Background: Adverse events of special interest (AESIs) were pre-specified to be monitored for the COVID-19 vaccines. Some AESIs are not only associated with the vaccines, but with COVID-19. Our aim was to characterise the incidence rates of AESIs following SARS-CoV-2 infection in patients and compare these to historical rates in the general population. Methods: A multi-national cohort study with data from primary care, electronic health records, and insurance claims mapped to a common data model. This study's evidence was collected between Jan 1, 2017 and the conclusion of each database (which ranged from Jul 2020 to May 2022). The 16 pre-specified prevalent AESIs were: acute myocardial infarction, anaphylaxis, appendicitis, Bell's palsy, deep vein thrombosis, disseminated intravascular coagulation, encephalomyelitis, Guillain- Barré syndrome, haemorrhagic stroke, non-haemorrhagic stroke, immune thrombocytopenia, myocarditis/pericarditis, narcolepsy, pulmonary embolism, transverse myelitis, and thrombosis with thrombocytopenia. Age-sex standardised incidence rate ratios (SIR) were estimated to compare post-COVID-19 to pre-pandemic rates in each of the databases. Findings: Substantial heterogeneity by age was seen for AESI rates, with some clearly increasing with age but others following the opposite trend. Similarly, differences were also observed across databases for same health outcome and age-sex strata. All studied AESIs appeared consistently more common in the post-COVID-19 compared to the historical cohorts, with related meta-analytic SIRs ranging from 1.32 (1.05 to 1.66) for narcolepsy to 11.70 (10.10 to 13.70) for pulmonary embolism. Interpretation: Our findings suggest all AESIs are more common after COVID-19 than in the general population. Thromboembolic events were particularly common, and over 10-fold more so. More research is needed to contextualise post-COVID-19 complications in the longer term. Funding: None.

Transforming and evaluating the UK Biobank to the OMOP Common Data Model for COVID-19 research and beyond.

OBJECTIVE: The coronavirus disease 2019 (COVID-19) pandemic has demonstrated the value of real-world data for public health research. International federated analyses are crucial for informing policy makers. Common data models (CDMs) are critical for enabling these studies to be performed efficiently. Our objective was to convert the UK Biobank, a study of 500 000 participants with rich genetic and phenotypic data to the Observational Medical Outcomes Partnership (OMOP) CDM. MATERIALS AND METHODS: We converted UK Biobank data to OMOP CDM v. 5.3. We transformedparticipant research data on diseases collected at recruitment and electronic health records (EHRs) from primary care, hospitalizations, cancer registrations, and mortality from providers in England, Scotland, and Wales. We performed syntactic and semantic validations and compared comorbidities and risk factors between source and transformed data. RESULTS: We identified 502 505 participants (3086 with COVID-19) and transformed 690 fields (1 373 239 555 rows) to the OMOP CDM using 8 different controlled clinical terminologies and bespoke mappings. Specifically, we transformed self-reported noncancer illnesses 946 053 (83.91% of all source entries), cancers 37 802 (70.81%), medications 1 218 935 (88.25%), and prescriptions 864 788 (86.96%). In EHR, we transformed 13 028 182 (99.95%) hospital diagnoses, 6 465 399 (89.2%) procedures, 337 896 333 primary care diagnoses (CTV3, SNOMED-CT), 139 966 587 (98.74%) prescriptions (dm+d) and 77 127 (99.95%) deaths (ICD-10). We observed good concordance across demographic, risk factor, and comorbidity factors between source and transformed data. DISCUSSION AND CONCLUSION: Our study demonstrated that the OMOP CDM can be successfully leveraged to harmonize complex large-scale biobanked studies combining rich multimodal phenotypic data. Our study uncovered several challenges when transforming data from questionnaires to the OMOP CDM which require further research. The transformed UK Biobank resource is a valuable tool that can enable federated research, like COVID-19 studies.

Comparing clinical trial population representativeness to real-world populations: an external validity analysis encompassing 43 895 trials and 5 685 738 individuals across 989 unique drugs and 286 conditions in England.

BACKGROUND: Randomised controlled trials (RCTs) inform prescription guidelines, but stringent eligibility criteria exclude individuals with vulnerable characteristics, which we define as comorbidities, concomitant medication use, and vulnerabilities due to age. Poor external validity can result in inadequate treatment decision information. Our first aim was to quantify the extent of exclusion of individuals with vulnerable characteristics from RCTs for all prescription drugs. Our second aim was to quantify the prevalence of individuals with vulnerable characteristics from population electronic health records who are actively prescribed such drugs. In tandem, these two aims will allow us to assess the representativeness between RCT and real-world populations and identify vulnerable populations potentially at risk of inadequate treatment decision information. When a vulnerable population is highly excluded from RCTs but has a high prevalence of individuals actively being prescribed the same medication, there is likely to be a gap in treatment decision information. Our third aim was to investigate the use of real-world evidence in contributing towards quantifying missing treatment risk or benefit through an observational study. METHODS: We extracted RCTs from ClinicalTrials.gov from its inception to April 28, 2021, and primary care records from the Clinical Practice Research Datalink Gold database from Jan 1, 1998, to Dec 31, 2020. We referred to the British National Formulary to classify prescription drugs into drug categories. We conducted descriptive analyses and quantified RCT exclusion and prevalence of individuals with vulnerable characteristics for comparison to identify populations without treatment decision information. Exclusion and prevalence were assessed separately for different age groups, individual clinical specialities, and for quantities of concomitant conditions by clinical specialities, where multimorbidity was defined as having two or more clinical specialties, and medications prescribed, where polypharmacy was defined as having five or more medications prescribed. Population trends of individuals with multimorbidity or polypharmacy were assessed separately by age group. We conducted an observational cohort study to validate the use of real-world evidence in contributing towards quantifying treatment risk or benefit for patients with dementia on anti-dementia drugs with and without a contraindicated clinical speciality. To do so, we identified the clinical specialities that anti-dementia drug RCTs highly excluded yet had corresponding high prevalence in the real-world population, forming the groups with highest risk of having scarce treatment decision information. Cox regression was used to assess if the risk of mortality outcomes differs between both groups. FINDINGS: 43 895 RCTs from ClinicalTrials.gov and 5 685 738 million individuals from primary care records were used. We considered 989 unique drugs and 286 conditions across 13 drug-category cohorts. For the descriptive analyses, the median RCT exclusion proportion across 13 drug categories was 81·5% (IQR 76·7-85·5) for adolescents (aged <18 years), 26·3% (IQR 21·0-29·5) for individuals older than 60 years, 40·5% (IQR 33·7-43·0) for individuals older than 70 years, and 52·9% (IQR 47·1-56·0) for individuals older than 80 years. Multimorbidity had a median exclusion proportion of 91·1% (IQR 88·9-91·8) and median prevalence of 41·0% (IQR 34·9-46·0). Concomitant medication use had a median exclusion proportion of 52·5% (IQR 50·0-53·7) and a median prevalence of 94·3% (IQR 84·3-97·2), and polypharmacy had a median prevalence of 47·7% (IQR 38·0-56·1). Population trends show increasing multimorbidity with age and consistently high polypharmacy across age groups. Populations with cardiovascular or otorhinolaryngological comorbidities had the highest risk of having scarce treatment decision information. For the observational study, populations with cardiovascular or psychiatric comorbidities had highest risk of having scarce treatment decision information. Patients with dementia with an anti-dementia prescription and contraindicated cardiovascular condition had a higher risk of mortality (hazard ratio [HR] 1·20 [95% CI 1·13-1·28 ; p<0·0001]) compared with patients with dementia without a contraindicated cardiovascular condition. Patients with dementia with comorbid delirium (HR 1·25 [95% CI 1·06-1·48]; p<0·0088), intellectual disability (HR 2·72 [95% CI 1·53-4·81]; p=0·0006), and schizophrenia and schizotypal delusional disorders (HR 1·36 [95% CI 1·02-1·82]; p=0·036) had a higher risk of mortality compared with patients with dementia without these conditions. INTERPRETATION: Overly stringent RCT exclusion criteria do not appropriately account for the heterogeneity of vulnerable characteristics observed in real-world populations. Treatment decision information is scarce for such individuals, which might affect health outcomes. We discuss the challenges facing the inclusivity of such individuals and highlight the strength of real-world evidence as an integrative solution in complementing RCTs and increasing the completeness of evidence-based medicine assessments in evaluating the effectiveness of treatment decisions. FUNDING: Wellcome Trust, National Institute for Health Research (NIHR) University College London Hospitals Biomedical Research Centre, NIHR Great Ormond Street Hospital Biomedical Research Centre, Academy of Medical Sciences, and the University College London Overseas Research Scholarship.

Phenotype Algorithms for the Identification and Characterization of Vaccine-Induced Thrombotic Thrombocytopenia in Real World Data: A Multinational Network Cohort Study.

INTRODUCTION: Vaccine-induced thrombotic thrombocytopenia (VITT) has been identified as a rare but serious adverse event associated with coronavirus disease 2019 (COVID-19) vaccines. OBJECTIVES: In this study, we explored the pre-pandemic co-occurrence of thrombosis with thrombocytopenia (TWT) using 17 observational health data sources across the world. We applied multiple TWT definitions, estimated the background rate of TWT, characterized TWT patients, and explored the makeup of thrombosis types among TWT patients. METHODS: We conducted an international network retrospective cohort study using electronic health records and insurance claims data, estimating background rates of TWT amongst persons observed from 2017 to 2019. Following the principles of existing VITT clinical definitions, TWT was defined as patients with a diagnosis of embolic or thrombotic arterial or venous events and a diagnosis or measurement of thrombocytopenia within 7 days. Six TWT phenotypes were considered, which varied in the approach taken in defining thrombosis and thrombocytopenia in real world data. RESULTS: Overall TWT incidence rates ranged from 1.62 to 150.65 per 100,000 person-years. Substantial heterogeneity exists across data sources and by age, sex, and alternative TWT phenotypes. TWT patients were likely to be men of older age with various comorbidities. Among the thrombosis types, arterial thrombotic events were the most common. CONCLUSION: Our findings suggest that identifying VITT in observational data presents a substantial challenge, as implementing VITT case definitions based on the co-occurrence of TWT results in large and heterogeneous incidence rate and in a cohort of patints with baseline characteristics that are inconsistent with the VITT cases reported to date.

Transforming and evaluating electronic health record disease phenotyping algorithms using the OMOP common data model: a case study in heart failure.

OBJECTIVE: The aim of the study was to transform a resource of linked electronic health records (EHR) to the OMOP common data model (CDM) and evaluate the process in terms of syntactic and semantic consistency and quality when implementing disease and risk factor phenotyping algorithms. MATERIALS AND METHODS: Using heart failure (HF) as an exemplar, we represented three national EHR sources (Clinical Practice Research Datalink, Hospital Episode Statistics Admitted Patient Care, Office for National Statistics) into the OMOP CDM 5.2. We compared the original and CDM HF patient population by calculating and presenting descriptive statistics of demographics, related comorbidities, and relevant clinical biomarkers. RESULTS: We identified a cohort of 502 536 patients with the incident and prevalent HF and converted 1 099 195 384 rows of data from 216 581 914 encounters across three EHR sources to the OMOP CDM. The largest percentage (65%) of unmapped events was related to medication prescriptions in primary care. The average coverage of source vocabularies was >98% with the exception of laboratory tests recorded in primary care. The raw and transformed data were similar in terms of demographics and comorbidities with the largest difference observed being 3.78% in the prevalence of chronic obstructive pulmonary disease (COPD). CONCLUSION: Our study demonstrated that the OMOP CDM can successfully be applied to convert EHR linked across multiple healthcare settings and represent phenotyping algorithms spanning multiple sources. Similar to previous research, challenges mapping primary care prescriptions and laboratory measurements still persist and require further work. The use of OMOP CDM in national UK EHR is a valuable research tool that can enable large-scale reproducible observational research.

Electromagnetic Properties of Steel Fibres for Use in Cementitious Composites, Fibre Detection and Non-Destructive Testing.

This paper deals with the description, measurement, and use of electromagnetic properties of ferromagnetic fibres used as dispersed fibre reinforcement in composite mixtures. Firstly, the fibres' magnetic properties are shown, and a method of measuring the hysteresis loop of fibres is proposed. The results from the measurements are presented and a discussion of the influence of measured parameters on the fibres' orientation in a magnetic field is performed. Furthermore, methods of non-destructive estimation, of their amount and orientation in the composite specimens, are discussed. The main experimental goal of this paper is to show the relationship between this non-destructive method's results and the destructive flexural strength measurements. The method is sensitive enough to provide information related to fibre reinforcement.

An agenda-setting paper on data sharing platforms: euCanSHare workshop.

Various data sharing platforms are being developed to enhance the sharing of cohort data by addressing the fragmented state of data storage and access systems. However, policy challenges in several domains remain unresolved. The euCanSHare workshop was organized to identify and discuss these challenges and to set the future research agenda. Concerns over the multiplicity and long-term sustainability of platforms, lack of resources, access of commercial parties to medical data, credit and recognition mechanisms in academia and the organization of data access committees are outlined. Within these areas, solutions need to be devised to ensure an optimal functioning of platforms.

Simulations of the Behaviour of Steel Ferromagnetic Fibres Commonly Used in Concrete in a Magnetic Field.

The efficiency of fibre reinforcement in concrete can be drastically increased by orienting the fibres using a magnetic field. This orientation occurs immediately after pouring fresh concrete when the fibres can still move. The technique is most relevant for manufacturing prefabricated elements such as beams or columns. However, the parameters of such a field are not immediately apparent, as they depend on the specific fibre reaction to the magnetic field. In this study, a numerical model was created in ANSYS Maxwell to examine the mechanical torque acting on fibres placed in a magnetic field with varying parameters. The model consists of a single fibre placed between two Helmholtz coils. The simulations were verified with an experimental setup as well as theoretical relationships. Ten different fibre types, both straight and hook-ended, were examined. The developed model can be successfully used to study the behaviour of fibres in a magnetic field. The fibre size plays the most important role together with the magnetic saturation of the fibre material. Multiple fibres show significant interactions.

Applying an Archetype-Based Approach to Electroencephalography/Event-Related Potential Experiments in the EEGBase Resource.

PURPOSE: The purpose of this study is to investigate the feasibility of applying openEHR (an archetype-based approach for electronic health records representation) to modeling data stored in EEGBase, a portal for experimental electroencephalography/event-related potential (EEG/ERP) data management. The study evaluates re-usage of existing openEHR archetypes and proposes a set of new archetypes together with the openEHR templates covering the domain. The main goals of the study are to (i) link existing EEGBase data/metadata and openEHR archetype structures and (ii) propose a new openEHR archetype set describing the EEG/ERP domain since this set of archetypes currently does not exist in public repositories. METHODS: The main methodology is based on the determination of the concepts obtained from EEGBase experimental data and metadata that are expressible structurally by the openEHR reference model and semantically by openEHR archetypes. In addition, templates as the third openEHR resource allow us to define constraints over archetypes. Clinical Knowledge Manager (CKM), a public openEHR archetype repository, was searched for the archetypes matching the determined concepts. According to the search results, the archetypes already existing in CKM were applied and the archetypes not existing in the CKM were newly developed. openEHR archetypes support linkage to external terminologies. To increase semantic interoperability of the new archetypes, binding with the existing odML electrophysiological terminology was assured. Further, to increase structural interoperability, also other current solutions besides EEGBase were considered during the development phase. Finally, a set of templates using the selected archetypes was created to meet EEGBase requirements. RESULTS: A set of eleven archetypes that encompassed the domain of experimental EEG/ERP measurements were identified. Of these, six were reused without changes, one was extended, and four were newly created. All archetypes were arranged in the templates reflecting the EEGBase metadata structure. A mechanism of odML terminology referencing was proposed to assure semantic interoperability of the archetypes. The openEHR approach was found to be useful not only for clinical purposes but also for experimental data modeling.

Evaluation of Semantic Web Technologies for Storing Computable Definitions of Electronic Health Records Phenotyping Algorithms.

Electronic Health Records are electronic data generated during or as a byproduct of routine patient care. Structured, semi-structured and unstructured EHR offer researchers unprecedented phenotypic breadth and depth and have the potential to accelerate the development of precision medicine approaches at scale. A main EHR use-case is defining phenotyping algorithms that identify disease status, onset and severity. Phenotyping algorithms utilize diagnoses, prescriptions, laboratory tests, symptoms and other elements in order to identify patients with or without a specific trait. No common standardized, structured, computable format exists for storing phenotyping algorithms. The majority of algorithms are stored as human-readable descriptive text documents making their translation to code challenging due to their inherent complexity and hinders their sharing and re-use across the community. In this paper, we evaluate the two key Semantic Web Technologies, the Web Ontology Language and the Resource Description Framework, for enabling computable representations of EHR-driven phenotyping algorithms.

Software and hardware infrastructure for research in electrophysiology.

As in other areas of experimental science, operation of electrophysiological laboratory, design and performance of electrophysiological experiments, collection, storage and sharing of experimental data and metadata, analysis and interpretation of these data, and publication of results are time consuming activities. If these activities are well organized and supported by a suitable infrastructure, work efficiency of researchers increases significantly. This article deals with the main concepts, design, and development of software and hardware infrastructure for research in electrophysiology. The described infrastructure has been primarily developed for the needs of neuroinformatics laboratory at the University of West Bohemia, the Czech Republic. However, from the beginning it has been also designed and developed to be open and applicable in laboratories that do similar research. After introducing the laboratory and the whole architectural concept the individual parts of the infrastructure are described. The central element of the software infrastructure is a web-based portal that enables community researchers to store, share, download and search data and metadata from electrophysiological experiments. The data model, domain ontology and usage of semantic web languages and technologies are described. Current data publication policy used in the portal is briefly introduced. The registration of the portal within Neuroscience Information Framework is described. Then the methods used for processing of electrophysiological signals are presented. The specific modifications of these methods introduced by laboratory researches are summarized; the methods are organized into a laboratory workflow. Other parts of the software infrastructure include mobile and offline solutions for data/metadata storing and a hardware stimulator communicating with an EEG amplifier and recording software.