Secure and safe water supplies in remote Australian and rural Sri Lankan regions : common issues and emerging responses

Most urban dwelling Australians take secure and safe water supplies for granted. That is, they have an adequate quantity of water at a quality that can be used by people without harm from human and animal wastes, salinity and hardness or pollutants from agriculture and manufacturing industries. Australia wide urban and peri-urban dwellers use safe water for all domestic as well as industrial purposes. However, this is not the situation remote regions in Australia where availability and poor quality water can be a development constraint. Nor is it the case in Sri Lanka where people in rural regions are struggling to obtain a secure supply of water, irrespective of it being safe because of the impact of faecal and other contaminants. The purposes of this paper are to overview: the population and environmental health challenges arising from the lack of safe water in rural and remote communities; response pathways to address water quality issues; and the status of and need for integrated catchment management (ICM) in selected remote regions of Australia and vulnerable and lagging rural regions in Sri Lanka. Conclusions are drawn that focus on the opportunity for inter-regional collaborations between Australia and Sri Lanka for the delivery of safe water through ICM.

How to sequence and annotate insect mitochondrial genomes for systematic and comparative genomics research

Over the past decade the mitochondrial (mt) genome has become the most widely used genomic resource available for systematic entomology. While the availability of other types of ‘–omics’ data – in particular transcriptomes – is increasing rapidly, mt genomes are still vastly cheaper to sequence and are far less demanding of high quality templates. Furthermore, almost all other ‘–omics’ approaches also sequence the mt genome, and so it can form a bridge between legacy and contemporary datasets. Mitochondrial genomes have now been sequenced for all insect orders, and in many instances representatives of each major lineage within orders (suborders, series or superfamilies depending on the group). They have also been applied to systematic questions at all taxonomic scales from resolving interordinal relationships (e.g. Cameron et al., 2009; Wan et al., 2012; Wang et al., 2012), through many intraordinal (e.g. Dowton et al., 2009; Timmermans et al., 2010; Zhao et al. 2013a) and family-level studies (e.g. Nelson et al., 2012; Zhao et al., 2013b) to population/biogeographic studies (e.g. Ma et al., 2012). Methodological issues around the use of mt genomes in insect phylogenetic analyses and the empirical results found to date have recently been reviewed by Cameron (2014), yet the technical aspects of sequencing and annotating mt genomes were not covered. Most papers which generate new mt genome report their methods in a simplified form which can be difficult to replicate without specific knowledge of the field. Published studies utilize a sufficiently wide range of approaches, usually without justification for the one chosen, that confusion about commonly used jargon such as ‘long PCR’ and ‘primer walking’ could be a serious barrier to entry. Furthermore, sequenced mt genomes have been annotated (gene locations defined) to wildly varying standards and improving data quality through consistent annotation procedures will benefit all downstream users of these datasets. The aims of this review are therefore to: 1. Describe in detail the various sequencing methods used on insect mt genomes; 2. Explore the strengths/weakness of different approaches; 3. Outline the procedures and software used for insect mt genome annotation, and; 4. Highlight quality control steps used for new annotations, and to improve the re-annotation of previously sequenced mt genomes used in systematic or comparative research.

An analytical framework for quantifying aquifer response time scales associated with transient boundary conditions

A major challenge in studying coupled groundwater and surface-water interactions arises from the considerable difference in the response time scales of groundwater and surface-water systems affected by external forcings. Although coupled models representing the interaction of groundwater and surface-water systems have been studied for over a century, most have focused on groundwater quantity or quality issues rather than response time. In this study, we present an analytical framework, based on the concept of mean action time (MAT), to estimate the time scale required for groundwater systems to respond to changes in surface-water conditions. MAT can be used to estimate the transient response time scale by analyzing the governing mathematical model. This framework does not require any form of transient solution (either numerical or analytical) to the governing equation, yet it provides a closed form mathematical relationship for the response time as a function of the aquifer geometry, boundary conditions, and flow parameters. Our analysis indicates that aquifer systems have three fundamental time scales: (i) a time scale that depends on the intrinsic properties of the aquifer; (ii) a time scale that depends on the intrinsic properties of the boundary condition, and; (iii) a time scale that depends on the properties of the entire system. We discuss two practical scenarios where MAT estimates provide useful insights and we test the MAT predictions using new laboratory-scale experimental data sets.

BIM - Implications for government (Case Study No. 5 [2004-032-A + Case study no. 5])

BIM as a suite of technologies has been enabled by the significant improvements in IT infrastructure, the capabilities of computer hardware and software, the increasing adoption of BIM, and the development of Industry Foundation Classes (IFC) which facilitate the sharing of information between firms. The report highlights the advantages of BIM, particularly the increased utility and speed, better data quality and enhanced fault finding in all construction phases. Additionally BIM promotes enhanced collaborations and visualisation of data mainly in the design and construction phase. There are a number of barriers to the effective implementation of BIM. These include, somewhat paradoxically, a single detailed model (which precludes scenarios and development of detailed alternative designs); the need for three different interoperability standards for effective implementation; added work for the designer which needs to be recognised and remunerated; the size and complexity of BIM, which requires significant investment in human capital to enable the realisation of its full potential. There are also a number of challenges to implementing BIM. The report has identified these as a range of issues concerning: IP, liability, risks and contracts, and the authenticity of users. Additionally, implementing BIM requires investment in new technology, skills training and development of news ways of collaboration. Finally, there are likely to be Trade Practices concerns as requiring certain technology owned by relatively few firms may limit

Machine learning approaches to analysing textual injury surveillance data: A systematic review

Objective To synthesise recent research on the use of machine learning approaches to mining textual injury surveillance data. Design Systematic review. Data sources The electronic databases which were searched included PubMed, Cinahl, Medline, Google Scholar, and Proquest. The bibliography of all relevant articles was examined and associated articles were identified using a snowballing technique. Selection criteria For inclusion, articles were required to meet the following criteria: (a) used a health-related database, (b) focused on injury-related cases, AND used machine learning approaches to analyse textual data. Methods The papers identified through the search were screened resulting in 16 papers selected for review. Articles were reviewed to describe the databases and methodology used, the strength and limitations of different techniques, and quality assurance approaches used. Due to heterogeneity between studies meta-analysis was not performed. Results Occupational injuries were the focus of half of the machine learning studies and the most common methods described were Bayesian probability or Bayesian network based methods to either predict injury categories or extract common injury scenarios. Models were evaluated through either comparison with gold standard data or content expert evaluation or statistical measures of quality. Machine learning was found to provide high precision and accuracy when predicting a small number of categories, was valuable for visualisation of injury patterns and prediction of future outcomes. However, difficulties related to generalizability, source data quality, complexity of models and integration of content and technical knowledge were discussed. Conclusions The use of narrative text for injury surveillance has grown in popularity, complexity and quality over recent years. With advances in data mining techniques, increased capacity for analysis of large databases, and involvement of computer scientists in the injury prevention field, along with more comprehensive use and description of quality assurance methods in text mining approaches, it is likely that we will see a continued growth and advancement in knowledge of text mining in the injury field.

Sharing of clinical data in a maternity setting: How do paper hand-held records and electronic health records compare for completeness?

Background Historically, the paper hand-held record (PHR) has been used for sharing information between hospital clinicians, general practitioners and pregnant women in a maternity shared-care environment. Recently in alignment with a National e-health agenda, an electronic health record (EHR) was introduced at an Australian tertiary maternity service to replace the PHR for collection and transfer of data. The aim of this study was to examine and compare the completeness of clinical data collected in a PHR and an EHR. Methods We undertook a comparative cohort design study to determine differences in completeness between data collected from maternity records in two phases. Phase 1 data were collected from the PHR and Phase 2 data from the EHR. Records were compared for completeness of best practice variables collected The primary outcome was the presence of best practice variables and the secondary outcomes were the differences in individual variables between the records. Results Ninety-four percent of paper medical charts were available in Phase 1 and 100% of records from an obstetric database in Phase 2. No PHR or EHR had a complete dataset of best practice variables. The variables with significant improvement in completeness of data documented in the EHR, compared with the PHR, were urine culture, glucose tolerance test, nuchal screening, morphology scans, folic acid advice, tobacco smoking, illicit drug assessment and domestic violence assessment (p = 0.001). Additionally the documentation of immunisations (pertussis, hepatitis B, varicella, fluvax) were markedly improved in the EHR (p = 0.001). The variables of blood pressure, proteinuria, blood group, antibody, rubella and syphilis status, showed no significant differences in completeness of recording. Conclusion This is the first paper to report on the comparison of clinical data collected on a PHR and EHR in a maternity shared-care setting. The use of an EHR demonstrated significant improvements to the collection of best practice variables. Additionally, the data in an EHR were more available to relevant clinical staff with the appropriate log-in and more easily retrieved than from the PHR. This study contributes to an under-researched area of determining data quality collected in patient records.

Provisioning a 3.3 MW PhotoVoltaic generation system onto a distribution authority’s 11 kV rural feeder

This paper describes part of an engineering study that was undertaken to demonstrate that a multi-megawatt Photovoltaic (PV) generation system could be connected to a rural 11 kV feeder without creating power quality issues for other consumers. The paper concentrates solely on the voltage regulation aspect of the study as this was the most innovative part of the study. The study was carried out using the time-domain software package, PSCAD/EMTDC. The software model included real time data input of actual measured load and scaled PV generation data, along with real-time substation voltage regulator and PV inverter reactive power control. The outputs from the model plot real-time voltage, current and power variations throughout the daily load and PV generation variations. Other aspects of the study not described in the paper include the analysis of harmonics, voltage flicker, power factor, voltage unbalance and system losses.

A principled experimental design approach to Big Data analysis

Big Datasets are endemic, but they are often notoriously difficult to analyse because of their size, heterogeneity, history and quality. The purpose of this paper is to open a discourse on the use of modern experimental design methods to analyse Big Data in order to answer particular questions of interest. By appealing to a range of examples, it is suggested that this perspective on Big Data modelling and analysis has wide generality and advantageous inferential and computational properties. In particular, the principled experimental design approach is shown to provide a flexible framework for analysis that, for certain classes of objectives and utility functions, delivers near equivalent answers compared with analyses of the full dataset under a controlled error rate. It can also provide a formalised method for iterative parameter estimation, model checking, identification of data gaps and evaluation of data quality. Finally, it has the potential to add value to other Big Data sampling algorithms, in particular divide-and-conquer strategies, by determining efficient sub-samples.

Constructing a traditional Chinese medicine data warehouse application

The explosive growth in the development of Traditional Chinese Medicine (TCM) has resulted in the continued increase in clinical and research data. The lack of standardised terminology, flaws in data quality planning and management of TCM informatics are preventing clinical decision-making, drug discovery and education. This paper argues that the introduction of data warehousing technologies to enhance the effectiveness and durability in TCM is paramount. To showcase the role of data warehousing in the improvement of TCM, this paper presents a practical model for data warehousing with detailed explanation, which is based on the structured electronic records, for TCM clinical researches and medical knowledge discovery.

Chronicling the patient journey: Co-creating value with digital health ecosystems

With the introduction of the PCEHR (Personally Controlled Electronic Health Record), the Australian public is being asked to accept greater responsibility for the management of their health information. However, the implementation of the PCEHR has occasioned poor adoption rates underscored by criticism from stakeholders with concerns about transparency, accountability, privacy, confidentiality, governance, and limited capabilities. This study adopts an ethnographic lens to observe how information is created and used during the patient journey and the social factors impacting on the adoption of the PCEHR at the micro-level in order to develop a conceptual model that will encourage the sharing of patient information within the cycle of care. Objective: This study aims to firstly, establish a basic understanding of healthcare professional attitudes toward a national platform for sharing patient summary information in the form of a PCEHR. Secondly, the studies aims to map the flow of patient related information as it traverses a patient’s personal cycle of care. Thus, an ethnographic approach was used to bring a “real world” lens to information flow in a series of case studies in the Australian healthcare system to discover themes and issues that are important from the patient’s perspective. Design: Qualitative study utilising ethnographic case studies. Setting: Case studies were conducted at primary and allied healthcare professionals located in Brisbane Queensland between October 2013 and July 2014. Results: In the first dimension, it was identified that healthcare professionals’ concerns about trust and medico-legal issues related to patient control and information quality, and the lack of clinical value available with the PCEHR emerged as significant barriers to use. The second dimension of the study which attempted to map patient information flow identified information quality issues, clinical workflow inefficiencies and interoperability misconceptions resulting in duplication of effort, unnecessary manual processes, data quality and integrity issues and an over reliance on the understanding and communication skills of the patient. Conclusion: Opportunities for process efficiencies, improved data quality and increased patient safety emerge with the adoption of an appropriate information sharing platform. More importantly, large scale eHealth initiatives must be aligned with the value proposition of individual stakeholders in order to achieve widespread adoption. Leveraging an Australian national eHealth infrastructure and the PCEHR we offer a practical example of a service driven digital ecosystem suitable for co-creating value in healthcare.

Evaluating the specificity of community injury hospitalization data over time

This study identified the areas of poor specificity in national injury hospitalization data and the areas of improvement and deterioration in specificity over time. A descriptive analysis of ten years of national hospital discharge data for Australia from July 2002-June 2012 was performed. Proportions and percentage change of defined/undefined codes over time was examined. At the intent block level, accidents and assault were the most poorly defined with over 11% undefined in each block. The mechanism blocks for accidents showed a significant deterioration in specificity over time with up to 20% more undefined codes in some mechanisms. Place and activity were poorly defined at the broad block level (43% and 72% undefined respectively). Private hospitals and hospitals in very remote locations recorded the highest proportion of undefined codes. Those aged over 60 years and females had the higher proportion of undefined code usage. This study has identified significant, and worsening, deficiencies in the specificity of coded injury data in several areas. Focal attention is needed to improve the quality of injury data, especially on those identified in this study, to provide the evidence base needed to address the significant burden of injury in the Australian community.

Causes of injuries resulting in hospitalisation in Australia : assessing coder agreement on external causes

Objective: To assess extent of coder agreement for external causes of injury using ICD-10-AM for injury-related hospitalisations in Australian public hospitals. Methods: A random sample of 4850 discharges from 2002 to 2004 was obtained from a stratified random sample of 50 hospitals across four states in Australia. On-site medical record reviews were conducted and external cause codes were assigned blinded to the original coded data. Code agreement levels were grouped into the following agreement categories: block level, 3-character level, 4-character level, 5th-character level, and complete code level. Results: At a broad block level, code agreement was found in over 90% of cases for most mechanisms (eg, transport, fall). Percentage disagreement was 26.0% at the 3-character level; agreement for the complete external cause code was 67.6%. For activity codes, the percentage of disagreement at the 3-character level was 7.3% and agreement for the complete activity code was 68.0%. For place of occurrence codes, the percentage of disagreement at the 4-character level was 22.0%; agreement for the complete place code was 75.4%. Conclusions: With 68% agreement for complete codes and 74% agreement for 3-character codes, as well as variability in agreement levels across different code blocks, place and activity codes, researchers need to be aware of the reliability of their specific data of interest when they wish to undertake trend analyses or case selection for specific causes of interest.

Economic evaluation and catheter-related bloodstream infections

Catheter-related bloodstream infections are a serious problem. Many interventions reduce risk, and some have been evaluated in cost-effectiveness studies. We review the usefulness and quality of these economic studies. Evidence is incomplete, and data required to inform a coherent policy are missing. The cost-effectiveness studies are characterized by a lack of transparency, short time-horizons, and narrow economic perspectives. Data quality is low for some important model parameters. Authors of future economic evaluations should aim to model the complete policy and not just single interventions. They should be rigorous in developing the structure of the economic model, include all relevant economic outcomes, use a systematic approach for selecting data sources for model parameters, and propagate the effect of uncertainty in model parameters on conclusions. This will inform future data collection and improve our understanding of the economics of preventing these infections.

Building Information Modelling for FM at Sydney Opera House

“SOH see significant benefit in digitising its drawings and operation and maintenance manuals. Since SOH do not currently have digital models of the Opera House structure or other components, there is an opportunity for this national case study to promote the application of Digital Facility Modelling using standardized Building Information Models (BIM)”. The digital modelling element of this project examined the potential of building information models for Facility Management focusing on the following areas: • The re-usability of building information for FM purposes • BIM as an Integrated information model for facility management • Extendibility of the BIM to cope with business specific requirements • Commercial facility management software using standardised building information models • The ability to add (organisation specific) intelligence to the model • A roadmap for SOH to adopt BIM for FM The project has established that BIM – building information modelling - is an appropriate and potentially beneficial technology for the storage of integrated building, maintenance and management data for SOH. Based on the attributes of a BIM, several advantages can be envisioned: consistency in the data, intelligence in the model, multiple representations, source of information for intelligent programs and intelligent queries. The IFC – open building exchange standard – specification provides comprehensive support for asset and facility management functions, and offers new management, collaboration and procurement relationships based on sharing of intelligent building data. The major advantages of using an open standard are: information can be read and manipulated by any compliant software, reduced user “lock in” to proprietary solutions, third party software can be the “best of breed” to suit the process and scope at hand, standardised BIM solutions consider the wider implications of information exchange outside the scope of any particular vendor, information can be archived as ASCII files for archival purposes, and data quality can be enhanced as the now single source of users’ information has improved accuracy, correctness, currency, completeness and relevance. SOH current building standards have been successfully drafted for a BIM environment and are confidently expected to be fully developed when BIM is adopted operationally by SOH. There have been remarkably few technical difficulties in converting the House’s existing conventions and standards to the new model based environment. This demonstrates that the IFC model represents world practice for building data representation and management (see Sydney Opera House – FM Exemplar Project Report Number 2005-001-C-3, Open Specification for BIM: Sydney Opera House Case Study). Availability of FM applications based on BIM is in its infancy but focussed systems are already in operation internationally and show excellent prospects for implementation systems at SOH. In addition to the generic benefits of standardised BIM described above, the following FM specific advantages can be expected from this new integrated facilities management environment: faster and more effective processes, controlled whole life costs and environmental data, better customer service, common operational picture for current and strategic planning, visual decision-making and a total ownership cost model. Tests with partial BIM data – provided by several of SOH’s current consultants – show that the creation of a SOH complete model is realistic, but subject to resolution of compliance and detailed functional support by participating software applications. The showcase has demonstrated successfully that IFC based exchange is possible with several common BIM based applications through the creation of a new partial model of the building. Data exchanged has been geometrically accurate (the SOH building structure represents some of the most complex building elements) and supports rich information describing the types of objects, with their properties and relationships.

Cost effectiveness of antimicrobial catheters in the intensive care unit : Addressing uncertainty in the decision

Introduction: Some types of antimicrobial-coated central venous catheters (A-CVC) have been shown to be cost-effective in preventing catheter-related bloodstream infection (CR-BSI). However, not all types have been evaluated, and there are concerns over the quality and usefulness of these earlier studies. There is uncertainty amongst clinicians over which, if any, antimicrobial-coated central venous catheters to use. We re-evaluated the cost-effectiveness of all commercially available antimicrobialcoated central venous catheters for prevention of catheter-related bloodstream infection in adult intensive care unit (ICU) patients. Methods: We used a Markov decision model to compare the cost-effectiveness of antimicrobial-coated central venous catheters relative to uncoated catheters. Four catheter types were evaluated; minocycline and rifampicin (MR)-coated catheters; silver, platinum and carbon (SPC)-impregnated catheters; and two chlorhexidine and silver sulfadiazine-coated catheters, one coated on the external surface (CH/SSD (ext)) and the other coated on both surfaces (CH/SSD (int/ext)). The incremental cost per qualityadjusted life-year gained and the expected net monetary benefits were estimated for each. Uncertainty arising from data estimates, data quality and heterogeneity was explored in sensitivity analyses. Results: The baseline analysis, with no consideration of uncertainty, indicated all four types of antimicrobial-coated central venous catheters were cost-saving relative to uncoated catheters. Minocycline and rifampicin-coated catheters prevented 15 infections per 1,000 catheters and generated the greatest health benefits, 1.6 quality-adjusted life-years, and cost-savings, AUD $130,289. After considering uncertainty in the current evidence, the minocycline and rifampicin-coated catheters returned the highest incremental monetary net benefits of $948 per catheter; but there was a 62% probability of error in this conclusion. Although the minocycline and rifampicin-coated catheters had the highest monetary net benefits across multiple scenarios, the decision was always associated with high uncertainty. Conclusions: Current evidence suggests that the cost-effectiveness of using antimicrobial-coated central venous catheters within the ICU is highly uncertain. Policies to prevent catheter-related bloodstream infection amongst ICU patients should consider the cost-effectiveness of competing interventions in the light of this uncertainty. Decision makers would do well to consider the current gaps in knowledge and the complexity of producing good quality evidence in this area.