Model choice problems using approximate Bayesian computation with applications to pathogen transmission data sets

Analytically or computationally intractable likelihood functions can arise in complex statistical inferential problems making them inaccessible to standard Bayesian inferential methods. Approximate Bayesian computation (ABC) methods address such inferential problems by replacing direct likelihood evaluations with repeated sampling from the model. ABC methods have been predominantly applied to parameter estimation problems and less to model choice problems due to the added difficulty of handling multiple model spaces. The ABC algorithm proposed here addresses model choice problems by extending Fearnhead and Prangle (2012, Journal of the Royal Statistical Society, Series B 74, 1–28) where the posterior mean of the model parameters estimated through regression formed the summary statistics used in the discrepancy measure. An additional stepwise multinomial logistic regression is performed on the model indicator variable in the regression step and the estimated model probabilities are incorporated into the set of summary statistics for model choice purposes. A reversible jump Markov chain Monte Carlo step is also included in the algorithm to increase model diversity for thorough exploration of the model space. This algorithm was applied to a validating example to demonstrate the robustness of the algorithm across a wide range of true model probabilities. Its subsequent use in three pathogen transmission examples of varying complexity illustrates the utility of the algorithm in inferring preference of particular transmission models for the pathogens.

Thought balloon : Dr Christy Dena

In this interview, we discuss the basics of transmedia storytelling and lessons for creatives considering making the jump to a transmedia project.

The effects of exercise and adipose tissue lipolysis on plasma adiponectin concentration and adiponectin receptor expression in human skeletal muscle

Objective It has been suggested that adiponectin regulates plasma free fatty acid (FFA) clearance by stimulating FFA uptake and/or oxidation in muscle. We aimed to determine changes in plasma adiponectin concentration and adiponectin receptor 1 and 2 mRNA expression in skeletal muscle during and after prolonged exercise under normal, fasting conditions (high FFA trial; HFA) and following pharmacological inhibition of adipose tissue lipolysis (low FFA trial; LFA). Furthermore, we aimed to detect and locate adiponectin in skeletal muscle tissue. Methods Ten subjects performed two exercise trials (120 min at 50% VO2max). Indirect calorimetry was used to determine total fat oxidation rate. Plasma samples were collected at rest, during exercise and during post-exercise recovery to determine adiponectin, FFA and glycerol concentrations. Muscle biopsies were taken to determine adiponectin protein and adiponectin receptor 1 and 2 mRNA expression and to localise intramyocellular adiponectin. Results Basal plasma adiponectin concentrations averaged 6.57±0.7 and 6.63±0.8 mg/l in the HFA and LFA trials respectively, and did not change significantly during or after exercise. In the LFA trial, plasma FFA concentrations and total fat oxidation rates were substantially reduced. However, plasma adiponectin and muscle adiponectin receptor 1 and 2 mRNA expression did not differ between trials. Immunohistochemical staining of muscle cross-sections showed the presence of adiponectin in the sarcolemma of individual muscle fibres and within the interfibrillar arterioles. Conclusion Plasma adiponectin concentrations and adiponectin receptor 1 and 2 mRNA expression in muscle are not acutely regulated by changes in adipose tissue lipolysis and/or plasma FFA concentrations. Adiponectin is abundantly expressed in muscle, and, for the first time, it has been shown to be present in/on the sarcolemma of individual muscle fibres.

Trait resilience fosters adaptive coping when control opportunities are high : implications for the motivating potential of active work

Purpose: We examine the interaction between trait resilience and control in predicting coping and performance. Drawing on a person–environment fit perspective, we hypothesized resilient individuals would cope and perform better in demanding work situations when control was high. In contrast, those low in resilience would cope and perform better when control was low. Recognizing the relationship between trait resilience and performance also could be indirect, adaptive coping was examined as a mediating mechanism through which high control enables resilient individuals to demonstrate better performance. Methodology: In Study 1 (N = 78) and Study 2 (N = 94), participants completed a demanding inbox task in which trait resilience was measured and high and low control was manipulated. Study 3 involved surveying 368 employees on their trait resilience, control, and demand at work (at Time 1), and coping and performance 1 month later at Time 2. Findings: For more resilient individuals, high control facilitated problem-focused coping (Study 1, 2, and 3), which was indirectly associated with higher subjective performance (Study 1), mastery (Study 2), adaptive, and proficient performance (Study 3). For more resilient individuals, high control also facilitated positive reappraisal (Study 2 and 3), which was indirectly associated with higher adaptive and proficient performance (Study 3). Implications: Individuals higher in resilience benefit from high control because it enables adaptive coping. Originality/value: This research makes two contributions: (1) an experimental investigation into the interaction of trait resilience and control, and (2) investigation of coping as the mechanism explaining better performance.

Evaluation of the potential impact of the global economic crisis on HIV epidemics in Southeast Asia

Economic conditions around the world are likely to deteriorate in the short to medium term. The potential impact of this crisis on the spread of HIV is not clear. Government revenues and aid flows from international donors may face constraints, possibly leading to reductions in funding for HIV programs. Economic conditions (leading to increases in unemployment, for example) may also have an indirect impact on HIV epidemics by affecting the behaviour of individual people. Some behavioural changes may influence the rate of HIV transmission. This report presents findings from a study that investigates the potential impact of the economic crisis on HIV epidemics through the use of mathematical modelling. The potential epidemiological impacts of changes in the economy are explored for two distinctly characterised HIV epidemics: (i) a well-defined, established, and generalised HIV epidemic (specifically Cambodia, where incidence is declining); (ii) an HIV epidemic in its early expansion phase (specifically Papua New Guinea, where incidence has not yet peaked). Country-specific data are used for both settings and the models calibrated to accurately reflect the unique HIV epidemics in each population in terms of both incidence and prevalence. Models calibrated to describe the past and present epidemics are then used to forecast epidemic trajectories over the next few years under assumptions that behavioural or program conditions may change due to economic conditions. It should be noted that there are very limited solid data on how HIV/AIDS program funds may decrease or how social determinants related to HIV risk may change due to the economic crisis. Potential changes in key relevant factors were explored, along with sensitivity ranges around these assumptions, based on extensive discussions with in-country and international experts and stakeholders. As with all mathematical models, assumptions should be reviewed critically and results interpreted cautiously.

Volunteering and recent governance reforms

The regulatory reforms touching volunteer governs over the last 25 years are identified and analysed. BOth direct reforms such as the Australian Charities and Not-for-profits Commission's (ACNC) governance standards and society--wide indirect reforms to workplace health and safety, civil liability and deemed liability provisions are discussed in this chapter.

Just what the doctor ordered? Investigating the impact of health service quality on consumer misbehaviour

The growth in demand and expenditure currently being experienced in the Australian health sector is also accompanied by a rise in dysfunctional customer behaviour, such as verbal abuse and physical violence, perpetrated against health service providers. While service failure and poor recovery are known to trigger consumer misbehaviour, this study investigates whether lower than expected perceived service quality generates cognitive and emotional appraisals that trigger two common forms of misbehaviour: refusal to participate and verbal abuse. Data were collected using a 2 × 2 between-subjects experiment administered via online written survey and analysed using path modelling. The findings indicate that perceptions of service encounter quality have an indirect effect on whether consumers refuse to participate in the service and/or verbally abuse the service provider through the mediating effect of anger.

Sexual selection in true fruit flies (Diptera: Tephritidae) : transcriptome and experimental evidences for phytochemicals increasing male competitive ability

In male tephritid fruit flies of the genus Bactrocera, feeding on secondary plant compounds (sensu lato male lures = methyl eugenol, raspberry ketone and zingerone) increases male mating success. Ingested male lures alter the male pheromonal blend, normally making it more attractive to females and this is considered the primary mechanism for the enhanced mating success. However, the male lures raspberry ketone and zingerone are known, across a diverse range of other organisms, to be involved in increasing energy metabolism. If this also occurs in Bactrocera, then this may represent an additional benefit to males as courtship is metabolically expensive and lure feeding may increase a fly's short-term energy. We tested this hypothesis by performing comparative RNA-seq analysis between zingerone-fed and unfed males of Bactrocera tryoni. We also carried out behavioural assays with zingerone- and cuelure-fed males to test whether they became more active. RNA-seq analysis revealed, in zingerone-fed flies, up-regulation of 3183 genes with homologues transcripts to those known to regulate intermale aggression, pheromone synthesis, mating and accessory gland proteins, along with significant enrichment of several energy metabolic pathways and gene ontology terms. Behavioural assays show significant increases in locomotor activity, weight reduction and successful mating after mounting; all direct/indirect measures of increased activity. These results suggest that feeding on lures leads to complex physiological changes, which result in more competitive males. These results do not negate the pheromone effect, but do strongly suggest that the phytochemical-induced sexual selection is governed by both female preference and male competitive mechanisms.

Measuring reliability and validity of the ActiGraph GT3X accelerometer for children with cerebral palsy : a feasibility study

PURPOSE The purposes of this study were to: 1) establish inter-instrument reliability between left and right hip accelerometer placement; 2) examine procedural reliability of a walking protocol used to measure physical activity (PA), and; 3) confirm concurrent validity of accelerometers in measuring PA intensity as compared to the gold standard of oxygen consumption measured by indirect calorimetry. METHODS Eight children (mean age: 11.9; SD: 3.2, 75% male) with CP (GMFCS levels I-III) wore ActiGraph GT3X accelerometers on each hip and the Cosmed K4b^{2} portable indirect calorimeter during two measurement sessions in which they performed the six minute walk test (6MWT) at three self-selected speeds (comfortable/slow, brisk, fast). Oxygen consumption (VO2) and accelerometer step and activity count data were recorded. RESULTS Inter-instrument reliability of ActiGraph GT3X accelerometers placed on left and right hips was excellent (ICC=0.96-0.99, CI_{95}: 0.81-0.99). Reproducibility of the protocol was good/excellent (ICC=0.75-0.95, CI_{95}: 0.75-0.98). Concurrent validity of accelerometer count data and VO2 was fair/good (rho=0.67, p< 0.001). The correlation between step count and VO2 was not significant (rho=0.29, p=0.2). CONCLUSION This preliminary research suggests that ActiGraph GT3X accelerometers are reliable and valid devices to monitor PA during walking in children with CP and may be appropriate in rehabilitation research and clinical practice. ActiGraph GTX3 step counts were not valid for this sample and further research is warranted.

Children's advertising literacy for advergames : perception of the game as advertising

This study examined whether children recognized advergames as a type of advertising and the efficacy of an advertising literacy program. Results indicated that without the advertising literacy education, about three-quarters of the children did not recognize advergames as a type of advertising. However, those with advertising literacy education showed a significantly enhanced understanding. Also, a series of mediation tests showed that recognition of advertising was an indirect-only mediator between the advertising literacy and skeptical attitudes toward advertising. Only those who viewed the advergame as a type of advertising demonstrated more skeptical attitudes toward it.

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.

What keeps nurses busy in the mental health setting?

The foundation of mental health nursing has historically been grounded in an interpersonal, person-centred process of health care, yet recent evidence suggests that the interactional work of mental health nursing is being eroded. Literature emphasizes the importance of person-centred care on consumer outcomes, a model reliant upon the intimate engagement of nurses and consumers. Yet, the arrival of medical interventions in psychiatry has diverted nursing work from the therapeutic nursing role to task-based roles delegated by medicine, distancing nurses from consumers. This study used work sampling methodology to observe the proportion of time nurses working in an inpatient mental health setting spend in the activities of direct care, indirect care and service-related activities. Nurses spent 32 of their time in direct care, 52% in indirect care and 17% in service-related activities. Mental health nurses need to re-establish their therapeutic availability to maximize consumer experiences and outcomes.

Cold water immersion enhances recovery of submaximal muscle function after resistance exercise

We investigated the effect of cold water immersion (CWI) on the recovery of muscle function and physiological responses following high-intensity resistance exercise. Using a randomized, cross-over design, 10 physically active men performed high-intensity resistance exercise, followed by one of two recovery interventions: 10 min of cold water immersion at 10°C, or 10 min active recovery (low-intensity cycling). After the recovery interventions, maximal muscle function was assessed after 2 h and 4 h by measuring jump height and isometric squat strength. Submaximal muscle function was assessed after 6 h by measuring the average load lifted during six sets of 10 squats at 80% 1RM. Intramuscular temperature (1 cm) was also recorded, and venous blood samples were analyzed for markers of metabolism, vasoconstriction and muscle damage. CWI did not enhance recovery of maximal muscle function. However, during the final three sets of the submaximal muscle function test, the participants lifted a greater load (p<0.05; 38%; Cohen’s d 1.3) following CWI compared with active recovery. During CWI, muscle temperature decreased 6°C below post-exercise values, and remained below pre-exercise values for another 35 min. Venous blood O2 saturation decreased below pre-exercise values for 1.5 h after CWI. Serum endothelin-1 concentration did not change after CWI, whereas it decreased after active recovery. Plasma myoglobin concentration was lower, whereas plasma interleukin-6 concentration was higher after CWI compared with active recovery. These results suggest that cold water immersion after resistance exercise allow athletes to complete more work during subsequent training sessions, which could enhance long-term training adaptations.

Statistical methods for electromyography data and associated problems

This thesis proposes three novel models which extend the statistical methodology for motor unit number estimation, a clinical neurology technique. Motor unit number estimation is important in the treatment of degenerative muscular diseases and, potentially, spinal injury. Additionally, a recent and untested statistic to enable statistical model choice is found to be a practical alternative for larger datasets. The existing methods for dose finding in dual-agent clinical trials are found to be suitable only for designs of modest dimensions. The model choice case-study is the first of its kind containing interesting results using so-called unit information prior distributions.

Pre-processing for approximate Bayesian computation in image analysis

Most of the existing algorithms for approximate Bayesian computation (ABC) assume that it is feasible to simulate pseudo-data from the model at each iteration. However, the computational cost of these simulations can be prohibitive for high dimensional data. An important example is the Potts model, which is commonly used in image analysis. Images encountered in real world applications can have millions of pixels, therefore scalability is a major concern. We apply ABC with a synthetic likelihood to the hidden Potts model with additive Gaussian noise. Using a pre-processing step, we fit a binding function to model the relationship between the model parameters and the synthetic likelihood parameters. Our numerical experiments demonstrate that the precomputed binding function dramatically improves the scalability of ABC, reducing the average runtime required for model fitting from 71 hours to only 7 minutes. We also illustrate the method by estimating the smoothing parameter for remotely sensed satellite imagery. Without precomputation, Bayesian inference is impractical for datasets of that scale.