Comparison of genomic DNA extraction techniques from whole blood samples : a time, cost and quality evaluation study

Genomic DNA obtained from patient whole blood samples is a key element for genomic research. Advantages and disadvantages, in terms of time-efficiency, cost-effectiveness and laboratory requirements, of procedures available to isolate nucleic acids need to be considered before choosing any particular method. These characteristics have not been fully evaluated for some laboratory techniques, such as the salting out method for DNA extraction, which has been excluded from comparison in different studies published to date. We compared three different protocols (a traditional salting out method, a modified salting out method and a commercially available kit method) to determine the most cost-effective and time-efficient method to extract DNA. We extracted genomic DNA from whole blood samples obtained from breast cancer patient volunteers and compared the results of the product obtained in terms of quantity (concentration of DNA extracted and DNA obtained per ml of blood used) and quality (260/280 ratio and polymerase chain reaction product amplification) of the obtained yield. On average, all three methods showed no statistically significant differences between the final result, but when we accounted for time and cost derived for each method, they showed very significant differences. The modified salting out method resulted in a seven- and twofold reduction in cost compared to the commercial kit and traditional salting out method, respectively and reduced time from 3 days to 1 hour compared to the traditional salting out method. This highlights a modified salting out method as a suitable choice to be used in laboratories and research centres, particularly when dealing with a large number of samples.

SettleMEN-2: Displaced twice? Impact of the Queensland floods on men from refugee backgrounds living in Brisbane and Toowoomba. Broadsheet No. 1: Exposure to and impact of the floods

Between 2008 and 2010, the SettleMEN study followed a group of 233 recently arrived men from refugee backgrounds living in urban and regional Southeast Queensland with the aim of documenting their health and settlement experiences. The study found that overall, these men bring important resources that may help them to cope better with the challenges of settlement: good levels of subjective health status, mental health and wellbeing; good family and social support; and good levels of engagement in tertiary/trade education in Australia. Over time, however, their levels of wellbeing decreased as they experienced barriers to social participation and inclusion within their host community, including: unemployment and difficulties securing good jobs (even for those with tertiary/trade qualifications obtained in Australia), financial stress, difficulties accessing housing, limited interactions with neighbours, and experiences of racism and discrimination. Importantly, although men living in the Toowoomba acknowledged some of the benefits of regional settlement, they faced greater barriers to participation in the labour market, reported lower job satisfaction, and were more likely to experience social exclusion overall. In 2012 method approach and a peer interviewer model, we were able to conduct a follow 141 (61%) of the original 233 SettleMEN participants to document the impact of the January 2011 Queensland floods on their health and settlement. This broadsheet focuses on participants’ degree of exposure to and impact of the floods, their perceptions of safety and security, and their vulnerability and adaptive capacity to extreme weather events.

"Talking with lips" : settlement, transnationalism and identity of Karen people from Burma living in Brisbane, Australia

This thesis explores, from an anthropological perspective, the settlement of Karen people from Burma now living in Brisbane. It critiques settlement constructs reified by public policy and settlement model-building using narratives of the lived experience of settlement. It gives voice to a typically voiceless group of people and challenges traditional conceptions of people with refugee backgrounds as passive and vulnerable, by bringing their experiences from the periphery to the centre. It explores transnationalism, identity work and Karen organisations to demonstrate how settlement can be done both to people through policy and by people through agency and self-determination.

Standard preanalytical coding for biospecimens: Review and implementation of the Sample PREanalytical Code (SPREC)

The first version of the Standard PREanalytical Code (SPREC) was developed in 2009 by the International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group to facilitate documentation and communication of the most important preanalytical quality parameters of different types of biospecimens used for research. This same Working Group has now updated the SPREC to version 2.0, presented here, so that it contains more options to allow for recent technological developments. Existing elements have been fine tuned. An interface to the Biospecimen Reporting for Improved Study Quality (BRISQ) has been defined, and informatics solutions for SPREC implementation have been developed. A glossary with SPRECrelated definitions has also been added.

Environments For Healthy Living (EFHL) Griffith birth cohort study : characteristics of sample and profile of antenatal exposures

Background The Environments for Healthy Living (EFHL) study is a repeated sample, longitudinal birth cohort in South East Queensland, Australia. We describe the sample characteristics and profile of maternal, household, and antenatal exposures. Variation and data stability over recruitment years were examined. Methods Four months each year from 2006, pregnant women were recruited to EFHL at routine antenatal visits on or after 24 weeks gestation, from three public maternity hospitals. Participating mothers completed a baseline questionnaire on individual, familial, social and community exposure factors. Perinatal data were extracted from hospital birth records. Descriptive statistics and measures of association were calculated comparing the EFHL birth sample with regional and national reference populations. Data stability of antenatal exposure factors was assessed across five recruitment years (2006–2010 inclusive) using the Gamma statistic for ordinal data and chi-squared for nominal data. Results Across five recruitment years 2,879 pregnant women were recruited which resulted in 2904 live births with 29 sets of twins. EFHL has a lower representation of early gestational babies, fewer still births and a lower percentage of low birth weight babies, when compared to regional data. The majority of women (65%) took a multivitamin supplement during pregnancy, 47% consumed alcohol, and 26% reported having smoked cigarettes. There were no differences in rates of a range of antenatal exposures across five years of recruitment, with the exception of increasing maternal pre-pregnancy weight (p=0.0349), decreasing rates of high maternal distress (p=0.0191) and decreasing alcohol consumption (p<0.0001). Conclusions The study sample is broadly representative of births in the region and almost all factors showed data stability over time. This study, with repeated sampling of birth cohorts over multiple years, has the potential to make important contributions to population health through evaluating longitudinal follow-up and within cohort temporal effects.

Cost and environmental efficiency of rice farms in South Korea

We examine cost and nutrient use efficiency of farms and determine the cost to move farms to nutrient-efficient operation using Data Envelopment Analysis (DEA) with a dataset of 96 rice farms in Gangwon province of South Korea from 2003 to 2007. Our findings show that improvements in technical efficiency would result in both lower production costs and better environmental performance. It is, however, not costless for farms to move from their current operation to the environmentally efficient operation. On average, this movement would increase production costs by 119% but benefit the water system through an approximately 69% reduction in eutrofying power (EP). The average estimated cost of each EP kg of aggregate nutrient reduction is approximately one thousand two hundred won. For technically efficient farms, there is a trade-off between cost and environmental efficiency. We also find that the environmental performance of farms varies across farms and regions. We suggest that agri-environmental policies should be (re)designed to improve both cost and environmental performance of rice farms.

The innovation potential of living-labs to strengthen small and medium enterprises in regional Australia

The small and medium enterprise (SME) sector has been the major source of well-being and employment opportunities in regional Australia. Consequently, fostering the innovative capacity of SMEs in regions that are struggling to grow their economies and distribute the growth fairly while not degrading the environment has never been more important. While SMEs generally face more uncertainties in relation to resources (e.g. financial, human and social capital) when compared to larger businesses, collaborative, cuttingedge mechanisms to enhance innovation capabilities of regional SMEs are lacking. This paper responds to this gap and proposes a Living Laboratory – an open, multi-disciplinary and multi-stakeholder action research platform where innovations can be co-created, tested and evaluated in the every-day environment of SMEs – as a way to strengthen the SME sector in regional Australia.

The increasing cost of the basic foods required to promote health in Queensland

Objective: To assess changes in the cost and availability of a standard basket of healthy food items (the Healthy Food Access Basket [HFAB]) in Queensland over time. Design and participants: A series of four cross-sectional surveys (in 1998, 2000, 2001 and 2004) describing the cost and availability of foods in the HFAB over time. In the latest survey, 97 Queensland food stores across the five Australian Bureau of Statistics remoteness categories were compared. Main outcome measures: Cost comparisons for HFAB items by remoteness category for the 97 stores surveyed in 2004; changes in cost and availability of foods in the 81 stores surveyed since 2000; comparisons of food prices in the 56 stores surveyed in 1998, 2000, 2001 and 2004. Results: In 2004, the Queensland mean cost of the HFAB was $395.28 a fortnight. The cost of the HFAB was 29.6%($113.89) higher in “very remote” areas than in “major cities” (P<0.001). Between 2001 and 2004, the Queensland mean cost of the HFAB increased by 14.0% ($48.45), while in very remote areas the cost increased by 18.0% ($76.93) (P<0.001). Since 2000, the annualised per cent increase in cost of the HFAB has been higher than the increase in Consumer Price Index for food in Brisbane. The cost of healthy foods has risen more than the cost of some less nutritious foods, so that the latter are now relatively more affordable. Conclusions: Consumers, particularly those in very remote locations, need to pay substantially more for basic healthy foods than they did a few years ago. Higher prices are likely to be a barrier to good health among people of low socioeconomic status and other vulnerable groups. Interventions to make basic healthy food affordable and accessible to all would help reduce the high burden of chronic disease.

Mobility and out-of-home activities of older people living in suburban environments : ‘Because I'm a driver, I don't have a problem'

Governments are challenged by the need to ensure that ageing populations stay active and engaged as they age. Therefore, it is critical to investigate the role of mobility in older people's engagement in out-of-home activities, and to identify the experiences they have within their communities. This research investigates the use of transportation by older people and its implications for their out-of-home activities within suburban environments. The qualitative, mixed-method approach employs data collection methods which include a daily travel diary (including a questionnaire), Global Positioning System (GPS) tracking and semi-structured interviews with older people living in suburban environments in Brisbane, Australia. Results show that older people are mobile throughout the city, and their car provides them with that opportunity to access desired destinations. This ability to drive allows older people to live independently and to assist others who do not drive, particularly where transport alternatives are not as accessible. The ability to transport goods and other people is a significant advantage of the private car over other transport options. People with no access to private transportation who live in low-density environments are disadvantaged when it comes to participation within the community. Further research is needed to better understand the relationship between transportation and participation within the community environment, to assist policy makers and city and transportation planners to develop strategies for age-friendly environments within the community.

A rapid and cost-effective method of producing recombinant proBNP and NT-proBNP variants in Escherichia coli for immunoassay of heart failure

The measurements of plasma natriuretic peptides (NT-proBNP, proBNP and BNP) are used to diagnose heart failure but these are expensive to produce. We describe a rapid, cheap and facile production of proteins for immunoassays of heart failure. DNA encoding N-terminally His-tagged NT-proBNP and proBNP were cloned into the pJexpress404 vector. ProBNP and NT-proBNP peptides were expressed in Escherichia coli, purified and refolded in vitro. The analytical performance of these peptides were comparable with commercial analytes (NT-proBNP EC50 for the recombinant is 2.6 ng/ml and for the commercial material is 5.3 ng/ml) and the EC50 for recombinant and commercial proBNP, are 3.6 and 5.7 ng/ml respectively). Total yield of purified refolded NT-proBNP peptide was 1.75 mg/l and proBNP was 0.088 mg/l. This approach may also be useful in expressing other protein analytes for immunoassay applications. To develop a cost effective protein expression method in E. coli to obtain high yields of NT-proBNP (1.75 mg/l) and proBNP (0.088 mg/l) peptides for immunoassay use.

Adverse breast cancer treatment effects: The economic case for making rehabilitative programs standard of care

Purpose: The purpose of this work was to evaluate the patient-borne financial cost of common, adverse breast cancer treatment-associated effects, comparing cost across women with or without these side-effects. Methods: 287 Australian women diagnosed with early-stage breast cancer were prospectively followed starting at six months post-surgery for 12 months, with three-monthly assessment of detailed treatment-related side effects and their direct and indirect patient costs attributable to breast cancer. Bootstrapping statistics were used to analyze cost data and adjusted logistic regression was used to evaluate the association between costs and adverse events from breast cancer. Costs were inflated and converted from 2002 Australian to 2014 US dollars. Results: More than 90% of women experienced at least one adverse effect (i.e. post-surgical issue, reaction to radiotherapy, upper-body symptoms or reduced function, lymphedema, fatigue or weight gain). On average, women paid $5,636 (95%CI: $4,694, $6,577) in total costs. Women with any one of the following symptoms (fatigue, reduced upper-body function, upper-body symptoms) or women who report ≥4 adverse treatment-related effects, have 1.5 to nearly 4 times the odds of having higher healthcare costs than women who do not report these complaints (p<0.05). Conclusions: Women face substantial economic burden due to a range of treatment-related health problems, which may persist beyond the treatment period. Improving breast cancer care by incorporating prospective surveillance of treatment-related side effects, and strategies for prevention and treatment of concerns (e.g., exercise) has real potential for reducing patient-borne costs.

Factors influencing robustness and effectiveness of conditional random fields in active learning frameworks

Active learning approaches reduce the annotation cost required by traditional supervised approaches to reach the same effectiveness by actively selecting informative instances during the learning phase. However, effectiveness and robustness of the learnt models are influenced by a number of factors. In this paper we investigate the factors that affect the effectiveness, more specifically in terms of stability and robustness, of active learning models built using conditional random fields (CRFs) for information extraction applications. Stability, defined as a small variation of performance when small variation of the training data or a small variation of the parameters occur, is a major issue for machine learning models, but even more so in the active learning framework which aims to minimise the amount of training data required. The factors we investigate are a) the choice of incremental vs. standard active learning, b) the feature set used as a representation of the text (i.e., morphological features, syntactic features, or semantic features) and c) Gaussian prior variance as one of the important CRFs parameters. Our empirical findings show that incremental learning and the Gaussian prior variance lead to more stable and robust models across iterations. Our study also demonstrates that orthographical, morphological and contextual features as a group of basic features play an important role in learning effective models across all iterations.

Characterization and Mapping of Patterned Ground in the Saginaw Lowlands, Michigan: Possible Evidence for Late-Wisconsin Permafrost

We identified, mapped, and characterized a widespread area (gt;1,020 km2) of patterned ground in the Saginaw Lowlands of Michigan, a wet, flat plain composed of waterlain tills, lacustrine deposits, or both. The polygonal patterned ground is interpreted as a possible relict permafrost feature, formed in the Late Wisconsin when this area was proximal to the Laurentide ice sheet. Cold-air drainage off the ice sheet might have pooled in the Saginaw Lowlands, which sloped toward the ice margin, possibly creating widespread but short-lived permafrost on this glacial lake plain. The majority of the polygons occur between the Glacial Lake Warren strandline (~14.8 cal. ka) and the shoreline of Glacial Lake Elkton (~14.3 cal. ka), providing a relative age bracket for the patterned ground. Most of the polygons formed in dense, wet, silt loam soils on flat-lying sites and take the form of reticulate nets with polygon long axes of 150 to 160 m and short axes of 60 to 90 m. Interpolygon swales, often shown as dark curvilinears on aerial photographs, are typically slightly lower than are the polygon centers they bound. Some portions of these interpolygon swales are infilled with gravel-free, sandy loam sediments. The subtle morphology and sedimentological characteristics of the patterned ground in the Saginaw Lowlands suggest that thermokarst erosion, rather than ice-wedge replacement, was the dominant geomorphic process associated with the degradation of the Late-Wisconsin permafrost in the study area and, therefore, was primarily responsible for the soil patterns seen there today.

On Merging Business Process Management and Geographic Information Systems : Modeling and Execution of Ecological Concerns in Processes

Business Process Management describes a holistic management approach for the systematic design, modeling, execution, validation, monitoring and improvement of organizational business processes. Traditionally, most attention within this community has been given to control-flow aspects, i.e., the ordering and sequencing of business activities, oftentimes in isolation with regards to the context in which these activities occur. In this paper, we propose an approach that allows executable process models to be integrated with Geographic Information Systems. This approach enables process models to take geospatial and other geographic aspects into account in an explicit manner both during the modeling phase and the execution phase. We contribute a structured modeling methodology, based on the well-known Business Process Model and Notation standard, which is formalized by means of a mapping to executable Colored Petri nets. We illustrate the feasibility of our approach by means of a sustainability-focused case example of a process with important ecological concerns.

Cost-effective suppression and eradication of invasive predators

Introduced predators can have pronounced effects on naïve prey species; thus, predator control is often essential for conservation of threatened native species. Complete eradication of the predator, although desirable, may be elusive in budget-limited situations, whereas predator suppression is more feasible and may still achieve conservation goals. We used a stochastic predator-prey model based on a Lotka-Volterra system to investigate the cost-effectiveness of predator control to achieve prey conservation. We compared five control strategies: immediate eradication, removal of a constant number of predators (fixed-number control), removal of a constant proportion of predators (fixed-rate control), removal of predators that exceed a predetermined threshold (upper-trigger harvest), and removal of predators whenever their population falls below a lower predetermined threshold (lower-trigger harvest). We looked at the performance of these strategies when managers could always remove the full number of predators targeted by each strategy, subject to budget availability. Under this assumption immediate eradication reduced the threat to the prey population the most. We then examined the effect of reduced management success in meeting removal targets, assuming removal is more difficult at low predator densities. In this case there was a pronounced reduction in performance of the immediate eradication, fixed-number, and lower-trigger strategies. Although immediate eradication still yielded the highest expected minimum prey population size, upper-trigger harvest yielded the lowest probability of prey extinction and the greatest return on investment (as measured by improvement in expected minimum population size per amount spent). Upper-trigger harvest was relatively successful because it operated when predator density was highest, which is when predator removal targets can be more easily met and the effect of predators on the prey is most damaging. This suggests that controlling predators only when they are most abundant is the "best" strategy when financial resources are limited and eradication is unlikely. © 2008 Society for Conservation Biology.