Arnotts Blending Project

Established and supported under the Australian Government’s Cooperative Research Centre Progra

RCandy: an R package for visualizing homologous recombinations in bacterial genomes

SUMMARY: Homologous recombination is an important evolutionary process in bacteria and other prokaryotes, which increases genomic sequence diversity and can facilitate adaptation. Several methods and tools have been developed to detect genomic regions recently affected by recombination. Exploration and visualization of such recombination events can reveal valuable biological insights, but it remains challenging. Here, we present RCandy, a platform-independent R package for rapid, simple and flexible visualization of recombination events in bacterial genomes. AVAILABILITY AND IMPLEMENTATION: RCandy is an R package freely available for use under the MIT license. It is platform-independent and has been tested on Windows, Linux and MacOSX. The source code comes together with a detailed vignette available on GitHub at https://github.com/ChrispinChaguza/RCandy. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

How did a Quality Premium financial incentive influence antibiotic prescribing in primary care? Views of Clinical Commissioning Group and general practice professionals

Background: The Quality Premium (QP) was introduced for Clinical Commissioning Groups (CCGs) in England to optimize antibiotic prescribing, but it remains unclear how it was implemented. Objectives: To understand responses to the QP and how it was perceived to influence antibiotic prescribing. Methods: Semi-structured telephone interviews were conducted with 22 CCG and 19 general practice professionals. Interviews were analysed thematically. Results: The findings were organized into four categories. (i) Communication: this was perceived as unstructured and infrequent, and CCG professionals were unsure whether they received QP funding. (ii) Implementation: this was influenced by available local resources and competing priorities, with multifaceted and tailored strategies seen as most helpful for engaging general practices. Many antimicrobial stewardship (AMS) strategies were implemented independently from the QP, motivated by quality improvement. (iii) Mechanisms: the QP raised the priority of AMS nationally and locally, and provided prescribing targets to aim for and benchmark against, but money was not seen as reinvested into AMS. (iv) Impact and sustainability: the QP was perceived as successful, but targets were considered challenging for a minority of CCGs and practices due to contextual factors (e.g. deprivation, understaffing). CCG professionals were concerned with potential discontinuation of the QP and prescribing rates levelling off. Conclusions: CCG and practice professionals expressed positive views of the QP and associated prescribing targets and feedback. The QP helped influence change mainly by raising the priority of AMS and defining change targets rather than providing additional funding. To maximize impact, behavioural mechanisms of financial incentives should be considered pre-implementation

OPR-PPR, a Computer Program for Assessing Data Importance to Model Predictions Using Linear Statistics

The OPR-PPR program calculates the Observation-Prediction (OPR) and Parameter-Prediction (PPR) statistics that can be used to evaluate the relative importance of various kinds of data to simulated predictions. The data considered fall into three categories: (1) existing observations, (2) potential observations, and (3) potential information about parameters. The first two are addressed by the OPR statistic; the third is addressed by the PPR statistic. The statistics are based on linear theory and measure the leverage of the data, which depends on the location, the type, and possibly the time of the data being considered. For example, in a ground-water system the type of data might be a head measurement at a particular location and time. As a measure of leverage, the statistics do not take into account the value of the measurement. As linear measures, the OPR and PPR statistics require minimal computational effort once sensitivities have been calculated. Sensitivities need to be calculated for only one set of parameter values; commonly these are the values estimated through model calibration. OPR-PPR can calculate the OPR and PPR statistics for any mathematical model that produces the necessary OPR-PPR input files. In this report, OPR-PPR capabilities are presented in the context of using the ground-water model MODFLOW-2000 and the universal inverse program UCODE_2005. The method used to calculate the OPR and PPR statistics is based on the linear equation for prediction standard deviation. Using sensitivities and other information, OPR-PPR calculates (a) the percent increase in the prediction standard deviation that results when one or more existing observations are omitted from the calibration data set; (b) the percent decrease in the prediction standard deviation that results when one or more potential observations are added to the calibration data set; or (c) the percent decrease in the prediction standard deviation that results when potential information on one or more parameters is added

An Alphavirus-Based Adjuvant Enhances Serum and Mucosal Antibodies, T Cells, and Protective Immunity to Influenza Virus in Neonatal Mice

Neonatal immune responses to infection and vaccination are biased toward TH2 at the cost of proinflammatory TH1 responses needed to combat intracellular pathogens. However, upon appropriate stimulation, the neonatal immune system can induce adult-like TH1 responses. Here we report that a new class of vaccine adjuvant is especially well suited to enhance early life immunity. The GVI3000 adjuvant is a safe, nonpropagating, truncated derivative of Venezuelan equine encephalitis virus that targets dendritic cells (DCs) in the draining lymph node (DLN) and produces intracellular viral RNA without propagating to other cells. RNA synthesis strongly activates the innate immune response so that in adult animals, codelivery of soluble protein antigens induces robust humoral, cellular, and mucosal responses. The adjuvant properties of GVI3000 were tested in a neonatal BALB/c mouse model using inactivated influenza virus (iFlu). After a single immunization, mice immunized with iFlu with the GVI3000 adjuvant (GVI3000-adjuvanted iFlu) had significantly higher and sustained influenza virus-specific IgG antibodies, mainly IgG2a (TH1), compared to the mice immunized with antigen only. GVI3000 significantly increased antigen-specific CD4+ and CD8+ T cells, primed mucosal immune responses, and enhanced protection from lethal challenge. As seen in adult mice, the GVI3000 adjuvant increased the DC population in the DLNs, caused activation and maturation of DCs, and induced proinflammatory cytokines and chemokines in the DLNs soon after immunization, including gamma interferon (IFN-γ), tumor necrosis factor alpha (TNF-α), granulocyte colony-stimulating factor (G-CSF), and interleukin 6 (IL-6). In summary, the GVI3000 adjuvant induced an adult-like adjuvant effect with an influenza vaccine and has the potential to improve the immunogenicity and protective efficacy of new and existing neonatal vaccines

Point-of-care tests for infectious diseases: barriers to implementation across three London teaching hospitals.

Existing Point-of-care tests (POCT) to help identify infection-related causes of illness can complement diagnostic and disposition decisions in children attending emergency departments.(1) Evidence-based clinical algorithms can integrate such POCT to aid in the admission and discharge decision process. Paediatric studies validating these tools are scarce, with very few studies conducted in UK centres.(2-5) POCT can be based on host infection markers (e.g. finger prick tests for C-reactive protein (CRP) to help decide if the patient has a bacterial or viral infection) or pathogen detection tests (e.g. throat/nose swabs to rapidly diagnose viral infections such as RSV or influenza). This article is protected by copyright. All rights reserved

Producing polished prokaryotic pangenomes with the Panaroo pipeline

Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here, we introduce Panaroo, a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. Panaroo is available at https://github.com/gtonkinhill/panaroo.Peer reviewe

Patterns and predictors of adherence to statin therapy among older patients: Protocol for a systematic review

Background: The benefits of statin therapy are significantly compromised by noncompliance. Although elderly patients may have particular challenges with medication adherence and persistence, previous reviews on statin adherence have not focused on this population. Additionally, comparisons of adherence and persistence specific to statin indication (primary or secondary prevention) have not been thoroughly explored.Objective: We aim to assess the extent of, and factors associated with, adherence and persistence to statin therapy among older populations (aged ≥65 years).Methods: A systematic review will be undertaken according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses recommendations. Searches will be performed using multiple electronic databases (Ovid MEDLINE, EMBASE, PsycINFO, CINAHL, Cochrane Central Register of Controlled Trials, Database of Abstracts of Reviews of Effects, and the National Health Service Economic Evaluation Database) to identify relevant randomized trials and observational studies that evaluated statin adherence and/or persistence as an outcome. Eligible studies will include those involving community-living or outpatient elderly individuals. The methodological quality of randomized controlled trials (RCTs) will be assessed via the Joanna Briggs Institute's critical appraisal checklist for RCTs, and the quality assessment of observational studies will be undertaken using a set of questions formulated with resort to the National Institute of Health Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. When possible, meta-analyses will be conducted using random-effect modeling and generic inverse variance analyses for adjusted-effect estimates. Heterogeneity across studies will be quantified using the I2 statistic. The presence of publication bias will be assessed using funnel plots and Egger's regression tests. A leave-one-out sensitivity analysis will also be conducted to assess the impact of individual study results on pooled estimates. To explore possible sources of heterogeneity across studies, subgroup analyses will be performed based on covariates such as study design, statin indication, country of study, and length of patient follow-up.Results: The electronic database searches were completed in December 2016. Retrieved articles are currently being screened and the entire study is expected to be completed by June 2017.Conclusions: This systematic review will provide further understanding of the patterns of, and barriers to, statin adherence and persistence among older patients. The findings will inform clinical practice and the design of appropriate interventions

Lithium interactions with non-steroidal anti-inflammatory drugs and diuretics – A review

Background: Lithium is often used in bipolar disorder and occasionally in unipolar depression. Non-steroidal anti-inflammatory drugs (NSAIDs) and diuretics are frequently prescribed and their interaction with lithium is based mainly in few small studies. Objectives: Conduct a review, identify different interaction patterns and discuss treatment options. Methods: Three searches were made in PubMed in January 2016: 1) using the keywords “lithium” [and] “non-steroidal anti-inflammatory”; 2) using the keywords “lithium” [and] “diuretics” and the filter “title/abstract”; 3) using the terms “lithium” [and] “toxicity” and the filters “title” [and] “review”. From the 293 remaining articles, 10 were selected. Another search in Scielo.org was made, using the term “lítio” and the filter “Psiquiatria”. Two articles were selected from the initial 53. Six textbooks were added to expand the evidence, achieving a total of 18 references. Results: The majority of NSAIDs and diuretics rises lithium levels, specially thiazides. However, some show great variability or no interaction at all, and others even decrease lithium levels. Discussion: Lower-doses, shorter durations, lithium adjustments and levels' follow-ups are recommended, especially in elderly and multiple co-morbid patients