Chen A, Jonnagaddala J, Nekkantti C, Liaw ST. Generation of surrogates for de-identification of electronic health records. Paper presentation. Medinfo 2019: Health and Wellbeing e-Networks for All. L. Ohno-Machado & B. Séroussi (Eds) © 2019 International Medical Informatics Association (IMIA) and IOS Press. doi:10.3233/SHTI190185

Unstructured electronic health records are valuable resources for research. Before they are shared with researchers, protected health information needs to be removed from these unstructured documents to protect patient privacy. The main steps involved in removing protected health information are accurately identifying sensitive information in the documents and removing the identified information. To keep the

Williamson D, Kirk M, Sintchenko V, Howden B. The importance of public health genomics to ensure health security for Australia. Medical Journal of Australia 2019;210(7):295-297.e1.

Coordination is required to future‐proof Australia’s capacity and leadership in public health genomics. Infectious diseases are an ever‐present risk to society, particularly because of globalisation and the threat of antimicrobial‐resistant organisms. Recently, a World Health Organization (WHO) team conducted a joint external evaluation of Australia’s core capacities under the International Health Regulations. The evaluation gave

Moynihan R, Sanders S, Michaleff ZA, Scott A, Clark J, To EJ, Jones M, Kitchener E, Fox M, Johansson M, Lang E, Duggan A, Scott I, Albarqouni L. Pandemic impacts on healthcare utilisation: a systematic review. medRxiv. 2020:2020.10.26.20219352.

Objectives: To determine the extent and nature of changes in utilisation of healthcare services during COVID-19 pandemic. Design: Systematic review. Eligibility: Eligible studies compared utilisation of services during COVID-19 pandemic to at least one comparable period in prior years. Services included visits, admissions, diagnostics, and therapeutics. Studies were excluded if from single-centres or studied only

Byambasuren O, Dobler CC, Bell K, Rojas DP, Clark J, McLaws M-L, Glasziou P. Comparison of seroprevalence of SARS-CoV-2 infections with cumulative and imputed COVID-19 cases: systematic review. medRxiv. 2020:2020.07.13.20153163. preprint

Background. Accurate seroprevalence estimates of SARS-CoV-2 in different populations could clarify the extent to which current testing strategies are identifying all active infection, and hence the true magnitude and spread of the infection. Our primary objective was to identify valid seroprevalence studies of SARS-CoV-2 infection and compare their estimates with the reported and imputed COVID-19

Byambasuren O, Cardona M, Bell K, Clark J, McLaws M-L, Glasziou P. Estimating the extent of asymptomatic COVID-19 and its potential for community transmission: systematic review and meta-analysis. medRxiv. 2020:2020.05.10.20097543.

Background: The prevalence of true asymptomatic COVID-19 cases is critical to policy makers considering the effectiveness of mitigation measures against the SARS-CoV-2 pandemic. We aimed to synthesize all available research on the asymptomatic rates and transmission rates where possible. Methods: We searched PubMed, Embase, Cochrane COVID-19 trials, and Europe PMC (which covers pre-print platforms such

Bakhit M, Krzyzaniak N, Scott AM, Clark J, Glasziou P, Del Mar C. Downsides of face masks and possible mitigation strategies: a systematic review and meta-analysis. medRxiv. 2020:2020.06.16.20133207.

Objective To identify, appraise, and synthesise studies evaluating the downsides of wearing facemasks in any setting. We also discuss potential strategies to mitigate these downsides. Methods PubMed, Embase, CENTRAL, EuropePMC were searched (inception-18/5/2020), and clinical registries were searched via CENTRAL. We also did forward-backward citation search of the included studies. We included randomised controlled trials

Albarqouni L, Byambasuren, O., Clark, J., Scott, A.M., Looke, DGlasziou, P. Does Copper treating of commonly touched surfaces reduce healthcare acquired infections? A Systematic Review and meta-analysis. Journal of Hospital Infection. (106/4) p765-773, 2020

Background Healthcare-acquired infections (HAIs) cause substantial morbidity and mortality. Copper appears to have strong antimicrobial properties under laboratory conditions. Aim To examine the potential effect of copper treatment of commonly touched surfaces in healthcare facilities. Methods Controlled trials comparing the effect of copper-treated surfaces (furniture or bed linens) in hospital rooms compared with standard rooms

Scott AM, Clark J, Del Mar C, Glasziou P, Increased fluid intake to prevent urinary tract infections: systematic review and meta-analysis. British Journal of General Practice, 70(692), pp.e200-e207.

Background Approximately 15% of community-prescribed antibiotics are used in treating urinary tract infections (UTIs). Increase in antibiotic resistance necessitates considering alternatives. Aim To assess the impact of increased fluid intake in individuals at risk for UTIs, for impact on UTI recurrence (primary outcome), antimicrobial use, and UTI symptoms (secondary outcomes). Design and setting A systematic

Akhtyamova L, Martínez P, Verspoor K, Cardiff J. (2020) Testing Contextualized Word Embeddings to Improve NER in Spanish Clinical Case Narratives. IEEE Access.

In the Big Data era, there is an increasing need to fully exploit and analyze the huge quantity of information available about health. Natural Language Processing (NLP) technologies can contribute by extracting relevant information from unstructured data contained in Electronic Health Records (EHR) such as clinical notes, patients’ discharge summaries and radiology reports. The extracted

Wilson DJ, and The CRyPTIC Consortium. GenomeMap: Within-species genome-wide dn/ds estimation from over 10,000 genomes. Molecular Biology and Evolution 2020;37(8):2450-2460.

The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN/dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating

Staccini P, Lau AYS; Social Media, Research, and Ethics: Does Participant Willingness Matter?. Section Editors for the IMIA Yearbook Section on Consumer Health Informatics and Education. Yearb Med Inform. 2020 Aug;29(1):176-183. doi: 10.1055/s-0040-1702022. Epub 2020 Aug 21.

Objective : To summarise the state of the art published in 2019 in consumer health informatics and education, with a special emphasis on “Ethics and Health Informatics”. Methods : We conducted a systematic search of articles published in PubMed using a predefined set of queries, which identified 368 potential articles for review. These articles were

Sittig DF, Wright A, Coiera E, et al. Current challenges in health information technology-related patient safety. Health Informatics J 2020;26(1):181-89 doi: 10.1177/1460458218814893[published Online First: Epub Date]

We identify and describe nine key, short-term, challenges to help healthcare organizations, health information technology developers, researchers, policymakers, and funders focus their efforts on health information technology-related patient safety. Categorized according to the stage of the health information technology lifecycle where they appear, these challenges relate to (1) developing models, methods, and tools to enable