Measuring follow-up time in routinely-collected health datasets: Challenges and solutions

A key requirement for longitudinal studies using routinely-collected health data is to be able to measure what individuals are present in the datasets used, and over what time period. Individuals can enter and leave the covered population of administrative datasets for a variety of reasons, including both life events and characteristics of the datasets themselves. An automated, customizable method of determining individuals' presence was developed for the primary care dataset in Swansea University's SAIL Databank. The primary care dataset covers only a portion of Wales, with 76% of practices participating. The start and end date of the data varies by practice. Additionally, individuals can change practices or leave Wales. To address these issues, a two step process was developed. First, the period for which each practice had data available was calculated by measuring changes in the rate of events recorded over time. Second, the registration records for each individual were simplified. Anomalies such as short gaps and overlaps were resolved by applying a set of rules. The result of these two analyses was a cleaned set of records indicating start and end dates of available primary care data for each individual. Analysis of GP records showed that 91.0% of events occurred within periods calculated as having available data by the algorithm. 98.4% of those events were observed at the same practice of registration as that computed by the algorithm. A standardized method for solving this common problem has enabled faster development of studies using this data set. Using a rigorous, tested, standardized method of verifying presence in the study population will also positively influence the quality of research.

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

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

Programmatically encrypting data linkage fields at a project level within the Secure Anonymised Information Linkage (SAIL) databank

ABSTRACT Introduction/BackgroundThe ability to link datasets within the Secure Anonymised Information Linkage (SAIL) databank provides researchers with a powerful tool to analyse multiple datasets. The ability to combine several datasets also has the adverse effect of potential identification of an individual. Further encrypting linkage fields at a project level limits the links to datasets specific to the project only. This presentation discusses the opensource web based administration tool that programmatically applies project encryption in a consistent and timely manner, logging administrator actions. Objectives1). Identify encryption methodology2). Programme encryption steps and log steps 3). Design and implement web based user administration tool ApproachUtilising existing Secure Anonymised Information Linkage (SAIL) databank security, providing researchers with a view of their data, separating data linkage fields into a separate secure lookup table. Using Python programming language to automate the Structured Query Language (SQL) scripts required to accomplish this, as well as Python packages to interact with the databank and web based administration tool. ResultsProject encrypted views created for several projects and scores of datasets. Encrypted linkage fields unique to each project ensuring views across projects can not be linked either to each other or the original datasets. ConclusionEncryption process is programmable and administered through web tool.

A pharmacological study of slowly adapting mechanoreceptors responsive to cold thermal stimulation

Weber's silver Thaler illusion is the perception that cold objects appear heavier than warm objects. We were interested in studying the pharmacology of mechanoreceptor units that displayed increased spontaneous firing to cold stimuli. An isolated rat sinus hair preparation with intact nerve terminals was used to record the activity of two types of slowly adapting mechanoreceptors (St I and St II) during temperature ramps (0.91-1.73 degrees C/min) from normal bath temperature of 31+/-2 degrees C, cold to 14.5 degrees C and heat to 46 degrees C. Twenty-seven of the 43 mechanoreceptor units displayed marked increases in their spontaneous firing to cold or cooling thermal gradients, and were classified as cold mechanoreceptors. A high proportion (3:1) of St II units were responsive to cold than not, while the ratio was reversed for St I units (1:2). Most cold mechanoreceptor units showed decreases in mechanical responses to cold thermal gradients. Similar to specific cold thermoreceptors, many of the cold mechanoreceptor units briefly displayed increased spontaneous firing at higher (>41 degrees C) temperatures. The spontaneous firing of cold mechanoreceptor units was increased by the transient receptor potential (TRP) channel agonist icilin (30-100 microM) in a dose-dependent manner. Responses to mechanical stimulation were generally unaffected by icilin in these units, although their evoked response latencies were significantly reduced (similar to the effect of K+ channel blocker tetraethylammonium in St II units). TRPM8 channel agonist, (-) menthol 200 microM, had mixed effects on spontaneous firing but consistently enhanced cold responses. Other TRP agonists, cinnamaldehyde 1-2 mM and camphor 0.5-2 microM, reduced spontaneous and evoked responses. TRPA1 agonist allyl isothiocyanate (mustard oil) 50-100 microM and TRPV1 agonist capsaicin 1-3 microM had no effect. A broad spectrum TRP antagonist, Ruthenium Red 30 microM, had no effect. The TRPM8 antagonist, capsazepine 100-200 microM, blocked cold-evoked responses. Although these data generally provide support for the possibility that cooling responses are mediated by TRPM8 channels, the detailed profile of results suggests that another, as yet unidentified TRP channel, is involved. Multiplex coding of mechanical and thermal information by slowly adapting mechanoreceptors may play a functional role in thermal perception, and may explain Weber's silver Thaler illusion.