rEHR: An R package for manipulating and analysing Electronic Health Record data

Research with structured Electronic Health Records (EHRs) is expanding as data becomes more accessible; analytic methods advance; and the scientific validity of such studies is increasingly accepted. However, data science methodology to enable the rapid searching/extraction, cleaning and analysis of these large, often complex, datasets is less well developed. In addition, commonly used software is inadequate, resulting in bottlenecks in research workflows and in obstacles to increased transparency and reproducibility of the research. Preparing a research-ready dataset from EHRs is a complex and time consuming task requiring substantial data science skills, even for simple designs. In addition, certain aspects of the workflow are computationally intensive, for example extraction of longitudinal data and matching controls to a large cohort, which may take days or even weeks to run using standard software. The rEHR package simplifies and accelerates the process of extracting ready-for-analysis datasets from EHR databases. It has a simple import function to a database backend that greatly accelerates data access times. A set of generic query functions allow users to extract data efficiently without needing detailed knowledge of SQL queries. Longitudinal data extractions can also be made in a single command, making use of parallel processing. The package also contains functions for cutting data by time-varying covariates, matching controls to cases, unit conversion and construction of clinical code lists. There are also functions to synthesise dummy EHR. The package has been tested with one for the largest primary care EHRs, the Clinical Practice Research Datalink (CPRD), but allows for a common interface to other EHRs. This simplified and accelerated work flow for EHR data extraction results in simpler, cleaner scripts that are more easily debugged, shared and reproduced

Modelling Conditions and Health Care Processes in Electronic Health Records : An Application to Severe Mental Illness with the Clinical Practice Research Datalink

BACKGROUND: The use of Electronic Health Records databases for medical research has become mainstream. In the UK, increasing use of Primary Care Databases is largely driven by almost complete computerisation and uniform standards within the National Health Service. Electronic Health Records research often begins with the development of a list of clinical codes with which to identify cases with a specific condition. We present a methodology and accompanying Stata and R commands (pcdsearch/Rpcdsearch) to help researchers in this task. We present severe mental illness as an example. METHODS: We used the Clinical Practice Research Datalink, a UK Primary Care Database in which clinical information is largely organised using Read codes, a hierarchical clinical coding system. Pcdsearch is used to identify potentially relevant clinical codes and/or product codes from word-stubs and code-stubs suggested by clinicians. The returned code-lists are reviewed and codes relevant to the condition of interest are selected. The final code-list is then used to identify patients. RESULTS: We identified 270 Read codes linked to SMI and used them to identify cases in the database. We observed that our approach identified cases that would have been missed with a simpler approach using SMI registers defined within the UK Quality and Outcomes Framework. CONCLUSION: We described a framework for researchers of Electronic Health Records databases, for identifying patients with a particular condition or matching certain clinical criteria. The method is invariant to coding system or database and can be used with SNOMED CT, ICD or other medical classification code-lists

Ultrafast band structure control of a two-dimensional heterostructure

The electronic structure of two-dimensional (2D) semiconductors can be signicantly altered by screening effects, either from free charge carriers in the material itself, or by environmental screening from the surrounding medium. The physical properties of 2D semiconductors placed in a heterostructure with other 2D materials are therefore governed by a complex interplay of both intra- and inter-layer interactions. Here, using time- and angle-resolved photoemission, we are able to isolate both the layer-resolved band structure and, more importantly, the transient band structure evolution of a model 2D heterostructure formed of a single layer of MoS 2 on graphene. Our results reveal a pronounced renormalization of the quasiparticle gap of the MoS 2 layer. Following optical excitation, the band gap is reduced by up to ∼400 meV on femtosecond timescales due to a persistence of strong electronic interactions despite the environmental screening by the n-doped graphene. This points to a large degree of tuneability of both the electronic structure and electron dynamics for 2D semiconductors embedded in a van der Waals-bonded heterostructure.PostprintPeer reviewe

Global perspectives and transdisciplinary opportunities for locust and grasshopper pest management and research

Locusts and other migratory grasshoppers are transboundary pests. Monitoring and control, therefore, involve a complex system made up of social, ecological, and technological factors. Researchers and those involved in active management are calling for more integration between these siloed but often interrelated sectors. In this paper, we bring together 38 coauthors from six continents and 34 unique organizations, representing much of the social-ecological-technological system (SETS) related to grasshopper and locust management and research around the globe, to introduce current topics of interest and review recent advancements. Together, the paper explores the relationships, strengths, and weaknesses of the organizations responsible for the management of major locust-affected regions. The authors cover topics spanning humanities, social science, and the history of locust biological research and offer insights and approaches for the future of collaborative sustainable locust management. These perspectives will help support sustainable locust management, which still faces immense challenges such as fluctuations in funding, focus, isolated agendas, trust, communication, transparency, pesticide use, and environmental and human health standards. Arizona State University launched the Global Locust Initiative (GLI) in 2018 as a response to some of these challenges. The GLI welcomes individuals with interests in locusts and grasshoppers, transboundary pests, integrated pest management, landscape-level processes, food security, and/or cross-sectoral initiatives

A Re-Analysis of the Cochrane Library Data: The Dangers of Unobserved Heterogeneity in Meta-Analyses

BACKGROUND: Heterogeneity has a key role in meta-analysis methods and can greatly affect conclusions. However, true levels of heterogeneity are unknown and often researchers assume homogeneity. We aim to: a) investigate the prevalence of unobserved heterogeneity and the validity of the assumption of homogeneity; b) assess the performance of various meta-analysis methods; c) apply the findings to published meta-analyses. METHODS AND FINDINGS: We accessed 57,397 meta-analyses, available in the Cochrane Library in August 2012. Using simulated data we assessed the performance of various meta-analysis methods in different scenarios. The prevalence of a zero heterogeneity estimate in the simulated scenarios was compared with that in the Cochrane data, to estimate the degree of unobserved heterogeneity in the latter. We re-analysed all meta-analyses using all methods and assessed the sensitivity of the statistical conclusions. Levels of unobserved heterogeneity in the Cochrane data appeared to be high, especially for small meta-analyses. A bootstrapped version of the DerSimonian-Laird approach performed best in both detecting heterogeneity and in returning more accurate overall effect estimates. Re-analysing all meta-analyses with this new method we found that in cases where heterogeneity had originally been detected but ignored, 17–20% of the statistical conclusions changed. Rates were much lower where the original analysis did not detect heterogeneity or took it into account, between 1% and 3%. CONCLUSIONS: When evidence for heterogeneity is lacking, standard practice is to assume homogeneity and apply a simpler fixed-effect meta-analysis. We find that assuming homogeneity often results in a misleading analysis, since heterogeneity is very likely present but undetected. Our new method represents a small improvement but the problem largely remains, especially for very small meta-analyses. One solution is to test the sensitivity of the meta-analysis conclusions to assumed moderate and large degrees of heterogeneity. Equally, whenever heterogeneity is detected, it should not be ignored