The economic imperatives for technology enabled wellness centered healthcare.

A 2020 World Health Organization report underscored the impact of rising healthcare spending globally and questioned the long-term economic sustainability of current funding models. Increases in costs associated with care of late-stage irreversible diseases and the increasing prevalence of debilitating neurodegenerative disorders, coupled with increases in life expectancy are likely to overload the healthcare systems in many nations within the next decade if not addressed. One option for sustainability of the healthcare system is a change in emphasis from illness to wellness centered care. An attractive model is the P4 (Predictive, Preventative, Personalized and Participatory) medicine approach. Recent advances in connected health technology can help accelerate this transition; they offer prediction, diagnosis, and monitoring of health-related parameters. We explain how to integrate such technologies with conventional approaches and guide public health policy toward wellness-based care models and strategies to relieve the escalating economic burdens of managed care.

BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.

Estimates of Within-Subject Biological Variation Derived from Pathology Databases: An Approach to Allow Assessment of the Effects of Age, Sex, Time between Sample Collections, and Analyte Concentration on Reference Change Values.

BACKGROUND: Within-subject biological variation data (CVI) are used to establish quality requirements for assays and allow calculation of the reference change value (RCV) for quantitative clinical laboratory tests. The CVI is generally determined using a large number of samples from a small number of individuals under controlled conditions. The approach presented here is to use a small number of samples (n = 2) that have been collected for routine clinical purposes from a large number of individuals. METHODS: Pairs of sequential results from adult patients were extracted from a routine pathology database for 29 common chemical and hematological tests. Using a statistical process to identify a central gaussian distribution in the ratios of the result pairs, the total result variation for individual results was determined for 26 tests. The CVI was then calculated by removing the effect of analytical variation. RESULTS: This approach produced estimates of CVI that, for most of the analytes in this study, show good agreement with published values. The data demonstrated minimal effect of sex, age, or time between samples. Analyte concentration was shown to affect the distributions with first results more distant from the population mean more likely to be followed by a result closer to the mean. DISCUSSION: The process described here has allowed rapid and simple production of CVI data. The technique requires no patient intervention and replicates the clinical environment, although it may not be universally applicable. Additionally, the effect of regression to the mean described here may allow better interpretation of sequential patient results.

Delivering safe and effective test-result communication, management and follow-up: a mixed-methods study protocol.

INTRODUCTION: The failure to follow-up pathology and medical imaging test results poses patient-safety risks which threaten the effectiveness, quality and safety of patient care. The objective of this project is to: (1) improve the effectiveness and safety of test-result management through the establishment of clear governance processes of communication, responsibility and accountability; (2) harness health information technology (IT) to inform and monitor test-result management; (3) enhance the contribution of consumers to the establishment of safe and effective test-result management systems. METHODS AND ANALYSIS: This convergent mixed-methods project triangulates three multistage studies at seven adult hospitals and one paediatric hospital in Australia.Study 1 adopts qualitative research approaches including semistructured interviews, focus groups and ethnographic observations to gain a better understanding of test-result communication and management practices in hospitals, and to identify patient-safety risks which require quality-improvement interventions.Study 2 analyses linked sets of routinely collected healthcare data to examine critical test-result thresholds and test-result notification processes. A controlled before-and-after study across three emergency departments will measure the impact of interventions (including the use of IT) developed to improve the safety and quality of test-result communication and management processes.Study 3 adopts a consumer-driven approach, including semistructured interviews, and the convening of consumer-reference groups and community forums. The qualitative data will identify mechanisms to enhance the role of consumers in test-management governance processes, and inform the direction of the research and the interpretation of findings. ETHICS AND DISSEMINATION: Ethical approval has been granted by the South Eastern Sydney Local Health District Human Research Ethics Committee and Macquarie University. Findings will be disseminated in academic, industry and consumer journals, newsletters and conferences.

Analytical performance specifications for external quality assessment - definitions and descriptions.

External Quality Assurance (EQA) is vital to ensure acceptable analytical quality in medical laboratories. A key component of an EQA scheme is an analytical performance specification (APS) for each measurand that a laboratory can use to assess the extent of deviation of the obtained results from the target value. A consensus conference held in Milan in 2014 has proposed three models to set APS and these can be applied to setting APS for EQA. A goal arising from this conference is the harmonisation of EQA APS between different schemes to deliver consistent quality messages to laboratories irrespective of location and the choice of EQA provider. At this time there are wide differences in the APS used in different EQA schemes for the same measurands. Contributing factors to this variation are that the APS in different schemes are established using different criteria, applied to different types of data (e.g. single data points, multiple data points), used for different goals (e.g. improvement of analytical quality; licensing), and with the aim of eliciting different responses from participants. This paper provides recommendations from the European Federation of Laboratory Medicine (EFLM) Task and Finish Group on Performance Specifications for External Quality Assurance Schemes (TFG-APSEQA) and on clear terminology for EQA APS. The recommended terminology covers six elements required to understand APS: 1) a statement on the EQA material matrix and its commutability; 2) the method used to assign the target value; 3) the data set to which APS are applied; 4) the applicable analytical property being assessed (i.e. total error, bias, imprecision, uncertainty); 5) the rationale for the selection of the APS; and 6) the type of the Milan model(s) used to set the APS. The terminology is required for EQA participants and other interested parties to understand the meaning of meeting or not meeting APS.

Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent.

The focus of this article is a Bayesian method for inferring both species delimitations and species trees under the multispecies coalescent model using molecular sequences from multiple loci. The species delimitation requires no a priori assignment of individuals to species, and no guide tree. The method is implemented in a package called STACEY for BEAST2, and is a extension of the author's DISSECT package. Here we demonstrate considerable efficiency improvements by using three new operators for sampling from the posterior using the Markov chain Monte Carlo algorithm, and by using a model for the population size parameters along the branches of the species tree which allows these parameters to be integrated out. The correctness of the moves is demonstrated by tests of the implementation. The practice of using a pipeline approach to species delimitation under the multispecies coalescent, has been shown to have major problems on simulated data (Olave et al. in Syst Biol 63:263-271. doi: 10.1093/sysbio/syt106 , 2014). The same simulated data set is used to demonstrate the accuracy and improved convergence of the present method. We also compare performance with *BEAST for a fixed delimitation analysis on a large data set, and again show improved convergence.

Safe reading of chemical pathology reports: the RCPAQAP Report Assessment Survey.

Pathology reports are a vital component of the request-test-report cycle communicating pathology results to doctors to support clinical decision making. This should be done in a comprehensive, safe and time-efficient manner. As doctors may receive reports from different laboratories these goals can be achieved more readily if reports are formatted in the same way. This study evaluates the formatting of paper reports produced by Australian laboratories for numerical biochemistry results. As part of the RCPAQAP Liquid Serum Chemistry program in 2015, laboratories were invited to supply a routine paper report displaying the results. A total of 37 reports were received for analysis. These reports were assessed for variation in a range of components and, where possible, against relevant Australian standards and guidelines. In summary, there was a wide variation in most of the report components assessed including test names, result alignment, result flagging, sequence of data elements on the page, date formatting and patient name formatting. In most components there was also variation from the Standards. In order to ensure safe result transmission by printed reports there is a need to promote the adoption of current reporting standards and monitor compliance with similar external quality assurance programs.

DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent.

MOTIVATION: The multispecies coalescent model provides a formal framework for the assignment of individual organisms to species, where the species are modeled as the branches of the sp tree. None of the available approaches so far have simultaneously co-estimated all the relevant parameters in the model, without restricting the parameter space by requiring a guide tree and/or prior assignment of individuals to clusters or species. RESULTS: We present DISSECT, which explores the full space of possible clusterings of individuals and species tree topologies in a Bayesian framework. It uses an approximation to avoid the need for reversible-jump Markov Chain Monte Carlo, in the form of a prior that is a modification of the birth-death prior for the species tree. It incorporates a spike near zero in the density for node heights. The model has two extra parameters: one controls the degree of approximation and the second controls the prior distribution on the numbers of species. It is implemented as part of BEAST and requires only a few changes from a standard *BEAST analysis. The method is evaluated on simulated data and demonstrated on an empirical dataset. The method is shown to be insensitive to the degree of approximation, but quite sensitive to the second parameter, suggesting that large numbers of sequences are needed to draw firm conclusions. AVAILABILITY AND IMPLEMENTATION: http://tree.bio.ed.ac.uk/software/beast/, http://www.indriid.com/dissectinbeast.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bias Assessment of General Chemistry Analytes using Commutable Samples.

Harmonisation of reference intervals for routine general chemistry analytes has been a goal for many years. Analytical bias may prevent this harmonisation. To determine if analytical bias is present when comparing methods, the use of commutable samples, or samples that have the same properties as the clinical samples routinely analysed, should be used as reference samples to eliminate the possibility of matrix effect. The use of commutable samples has improved the identification of unacceptable analytical performance in the Netherlands and Spain. The International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) has undertaken a pilot study using commutable samples in an attempt to determine not only country specific reference intervals but to make them comparable between countries. Australia and New Zealand, through the Australasian Association of Clinical Biochemists (AACB), have also undertaken an assessment of analytical bias using commutable samples and determined that of the 27 general chemistry analytes studied, 19 showed sufficiently small between method biases as to not prevent harmonisation of reference intervals. Application of evidence based approaches including the determination of analytical bias using commutable material is necessary when seeking to harmonise reference intervals.

Mass or molar? Recommendations for reporting concentrations of therapeutic drugs.

A working party (WP) from the Australasian Association of Clinical Biochemists, Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists, Royal College of Pathologists of Australasia and Royal Australasian College of Physicians recommends the following: *mass units should be used for reporting therapeutic drug concentrations in Australia and New Zealand; and the litre (L) should be used as the denominator when expressing concentration. Examples of these units are mg/L and µg/L Exceptions to these principles include: *drugs for which there is current uniformity of reporting and supporting information using molar units, notably lithium (mmol/L) and methotrexate (µmol/L); *drugs that are also present as endogenous substances, where the units used routinely should continue to be used. This applies to many substances, including minerals (eg, iron; µmol/L), vitamins (eg, vitamin D; nmol/L) and hormones (eg, thyroxine; pmol/L). *drugs for which the denominator is not a 198 of fluid and there is international uniformity of reporting (eg, thiopurine metabolites; per 109 red blood cells). These recommendations relate to drugs that are used therapeutically, whether measured for therapeutic drug monitoring purposes or for assessment of overdose. Other substances, such as drugs of misuse, heavy metals or environmental toxins, were not considered by the WP and are thus not covered by this document. These recommendations should also be applied to other supporting documentation such as published guidelines, journal articles and websites. The implementation of these recommendations in New Zealand is subject to local confirmation.

Chemical and biological characterisation of solvent extracts and essential oils from leaves and fruit of two Australian species of Pittosporum (Pittosporaceae) used in aboriginal medicinal practice.

ETHNOPHARMACOLOGICAL SIGNIFICANCE: Although no known medicinal use for Pittosporum undulatum Vent. (Pittosporaceae) has been recorded, anecdotal evidence suggests that Australian Aboriginal people used Pittosporum angustifolium Lodd., G. Lodd. & W. Lodd. topically for eczema, pruritis or to induce lactation in mothers following child-birth and internally for coughs, colds or cramps. AIMS OF THE STUDY: Essential oil composition and bioactivity as well as differential solvent extract antimicrobial activity from Pittosporum angustifolium are investigated here first, to partially describe the composition of volatiles released in traditional applications of Pittosporum angustifolium for colds or as a lactagogue, and second to investigate antibacterial activity related to topical applications. Essential oils were also investigated from Pittosporum undulatum Vent., first to enhance essential oil data produced in previous studies, and second as a comparison to Pittosporum angustifolium. MATERIALS AND METHODS: Essential oils were hydrodistilled from fruit and leaves of both species using a modified approach to lessen the negative (frothing) effect of saponins. This was achieved by floating pumice or pearlite obsidian over the mixture to crush the suds formed while boiling. Essential oil extracts were analysed using GC-MS, quantified using GC-FID then screened for antimicrobial activity using a micro-titre plate broth dilution assay (MIC). Using dichloromethane, methanol, hexane and H(2)O as solvents, extracts were produced from leaves and fruit of Pittosporum angustifolium and screened for antimicrobial activity and qualitative phytochemical character. RESULTS: Although the essential oil from leaves and fruit of Pittosporum undulatum demonstrated some component variation, the essential oil from fruits of Pittosporum angustifolium had major constituents that strongly varied according to the geographical location of collection, suggesting the existence of at least two chemotypes; one with high abundance of acetic acid decyl ester. This chemotype had high antimicrobial activity whilst the other chemotype had only moderate antimicrobial activity against the three microbial species investigated here. This result may support the occurrence of geographical specificity with regard to ethnopharmacological use. Antimicrobial activity screening of the solvent extracts from Pittosporum angustifolium revealed the leaves to be superior to fruit, with water being the most suitable extraction solvent. CONCLUSION: To the best of our knowledge, this study constitutes the first time essential oils, and solvent extracts from the fruits of Pittosporum angustifolium, have been examined employing comprehensive chemical and biological analysis. The essential oil composition presented in this paper, includes components with structural similarity as chemosemiotic compounds involved in mother-infant identification, which may have significance with regard to traditional applications as a lactagogue.

Proficiency testing/external quality assessment: current challenges and future directions.

BACKGROUND: Proficiency testing (PT), or external quality assessment (EQA), is intended to verify on a recurring basis that laboratory results conform to expectations for the quality required for patient care. CONTENT: Key factors for interpreting PT/EQA results are knowledge of the commutability of the samples used and the process used for target value assignment. A commutable PT/EQA sample demonstrates the same numeric relationship between different measurement procedures as that expected for patients' samples. Noncommutable PT/EQA samples frequently have a matrix-related bias of unknown magnitude that limits interpretation of results. PT/EQA results for commutable samples can be used to assess accuracy against a reference measurement procedure or a designated comparison method. In addition, the agreement of the results between different measurement procedures for commutable samples reflects that which would be seen for patients' samples. PT/EQA results for noncommutable samples must be compared to a peer group mean/median of results from participants who use measurement procedures that are expected to have the same or very similar matrix-related bias. Peer group evaluation is used to asses whether a laboratory is using a measurement procedure in conformance to the manufacturer's specifications and/or in conformance to other laboratories using the same technology. A noncommutable PT/EQA sample does not give meaningful information about the relationship of results for patients' samples between different measurement procedures. SUMMARY: PT/EQA provides substantial value to the practice of laboratory medicine by assessing the performance of individual laboratories and, when commutable samples are used, the status of standardization or harmonization among different measurement procedures.

Therapeutic monitoring of vancomycin in adult patients: a consensus review of the American Society of Health-System Pharmacists, the Infectious Diseases Society of America, and the Society Of Infectious Diseases Pharmacists.

The Review is a welcome and up-to-date consensus statement on the use of vancomycin. Although many of the points are pertinent to Australasian practice, the clinical context may be subtly different such that different recommendations apply here. It is thus an apt time for clinical, biochemical, pharmacological and pathology staff in Australasia to collaborate and discuss the literature with particular relevance to establishing guidelines for an Australasian context. The new TG (Version 14) will be an interesting update in the antibiotic TDM area and we hope it will be used as a springboard for Australasian clinical research into this area.

Study Protocol--accurate assessment of kidney function in Indigenous Australians: aims and methods of the eGFR study.

BACKGROUND: There is an overwhelming burden of cardiovascular disease, type 2 diabetes and chronic kidney disease among Indigenous Australians. In this high risk population, it is vital that we are able to measure accurately kidney function. Glomerular filtration rate is the best overall marker of kidney function. However, differences in body build and body composition between Indigenous and non-Indigenous Australians suggest that creatinine-based estimates of glomerular filtration rate derived for European populations may not be appropriate for Indigenous Australians. The burden of kidney disease is borne disproportionately by Indigenous Australians in central and northern Australia, and there is significant heterogeneity in body build and composition within and amongst these groups. This heterogeneity might differentially affect the accuracy of estimation of glomerular filtration rate between different Indigenous groups. By assessing kidney function in Indigenous Australians from Northern Queensland, Northern Territory and Western Australia, we aim to determine a validated and practical measure of glomerular filtration rate suitable for use in all Indigenous Australians. METHODS/DESIGN: A cross-sectional study of Indigenous Australian adults (target n = 600, 50% male) across 4 sites: Top End, Northern Territory; Central Australia; Far North Queensland and Western Australia. The reference measure of glomerular filtration rate was the plasma disappearance rate of iohexol over 4 hours. We will compare the accuracy of the following glomerular filtration rate measures with the reference measure: Modification of Diet in Renal Disease 4-variable formula, Chronic Kidney Disease Epidemiology Collaboration equation, Cockcroft-Gault formula and cystatin C- derived estimates. Detailed assessment of body build and composition was performed using anthropometric measurements, skinfold thicknesses, bioelectrical impedance and a sub-study used dual-energy X-ray absorptiometry. A questionnaire was performed for socio-economic status and medical history. DISCUSSION: We have successfully managed several operational challenges within this multi-centre complex clinical research project performed across remote North, Western and Central Australia. It seems unlikely that a single correction factor (similar to that for African-Americans) to the equation for estimated glomerular filtration rate will prove appropriate or practical for Indigenous Australians. However, it may be that a modification of the equation in Indigenous Australians would be to include a measure of fat-free mass.