Exact and approximate Bayesian inference for low count time series models with intractable likelihoods

In this paper we present a new simulation methodology in order to obtain exact or approximate Bayesian inference for models for low-valued count time series data that have computationally demanding likelihood functions. The algorithm fits within the framework of particle Markov chain Monte Carlo (PMCMC) methods. The particle filter requires only model simulations and, in this regard, our approach has connections with approximate Bayesian computation (ABC). However, an advantage of using the PMCMC approach in this setting is that simulated data can be matched with data observed one-at-a-time, rather than attempting to match on the full dataset simultaneously or on a low-dimensional non-sufficient summary statistic, which is common practice in ABC. For low-valued count time series data we find that it is often computationally feasible to match simulated data with observed data exactly. Our particle filter maintains $N$ particles by repeating the simulation until $N+1$ exact matches are obtained. Our algorithm creates an unbiased estimate of the likelihood, resulting in exact posterior inferences when included in an MCMC algorithm. In cases where exact matching is computationally prohibitive, a tolerance is introduced as per ABC. A novel aspect of our approach is that we introduce auxiliary variables into our particle filter so that partially observed and/or non-Markovian models can be accommodated. We demonstrate that Bayesian model choice problems can be easily handled in this framework.

A bridge over troubling waters : a snapshot of teacher graduates' perceptions of their ongoing professional learning needs

For graduating teachers, the bridging period between formal teacher preparation and joining the profession is a time of high anxiety and great excitement. While this transition influences efficacy, job satisfaction, career length and future teaching quality, it is widely recognized to be inconsistent, poorly planned and resourced and largely unsupported (DEST, 2002; Herrington & Herrington, 2004). In Australia, the transition to teaching remains largely a school-based affair. However, individual schools may not have the resources to support a comprehensive and cohesive transition program. This paper discusses a pilot university program of extended teacher preparation. It reports on the perceived professional learning needs of a group of graduates as they transition to teaching. The key findings indicate that these graduates are seeking ongoing support as they develop confidence in their canonical skills of teaching. We argue that university-based programs are one way of providing professional learning and support for beginning teachers.

Contemporaneous correlations within individuals in an automated web-based walking program (Walk@Work) over a six week period (three phases) of time

Introduction: Participants may respond to phases of a workplace walking program at different rates. This study evaluated the factors that contribute to the number of steps through phases of the program. The intervention was automated through a web-based program designed to increase workday walking. Methods: The study reviewed independent variable influences throughout phases I–III. A convenience sample of university workers (n=56; 43.6±1.7 years; BMI 27.44±.2.15 kg/m2; 48 female) were recruited at worksites in Australia. These workers were given a pedometer (Yamax SW 200) and access to the website program. For analyses, step counts entered by workers into the website were downloaded and mean workday steps were compared using a seemingly unrelated regression. This model was employed to capture the contemporaneous correlation within individuals in the study across observed time periods. Results: The model predicts that the 36 subjects with complete information took an average 7460 steps in the baseline two week period. After phase I, statistically significance increases in steps (from baseline) were explained by age, working status (full or part time), occupation (academic or professional), and self reported public transport (PT) use (marginally significant). Full time workers walked more than part time workers by about 440 steps, professionals walked about 300 steps more than academics, and PT users walked about 400 steps more than non-PT users. The ability to differentiate steps after two weeks among participants suggests a differential affect of the program after only two weeks. On average participants increased steps from week two to four by about 525 steps, but regular auto users had nearly 750 steps less than non-auto users at week four. The effect of age was diminished in the 4th week of observation and accounted for 34 steps per year of age. In phase III, discriminating between participants became more difficult, with only age effects differentiating their increase over baseline. The marginal effect of age by phase III compared to phase I, increased from 36 to 50, suggesting a 14 step per year increase from the 2nd to 6th week. Discussion: The findings suggest that participants responded to the program at different rates, with uniformity of effect achieved by the 6th week. Participants increased steps, however a tapering off occurred over time. Age played the most consistent role in predicting steps over the program. PT use was associated with increased step counts, while Auto use was associated with decreased step counts.

A reliable real-time transport protocol for networked control systems over wireless networks

Deploying wireless networks in networked control systems (NCSs) has become more and more popular during the last few years. As a typical type of real-time control systems, an NCS is sensitive to long and nondeterministic time delay and packet losses. However, the nature of the wireless channel has the potential to degrade the performance of NCS networks in many aspects, particularly in time delay and packet losses. Transport layer protocols could play an important role in providing both reliable and fast transmission service to fulfill NCS’s real-time transmission requirements. Unfortunately, none of the existing transport protocols, including the Transport Control Protocol (TCP) and the User Datagram Protocol (UDP), was designed for real-time control applications. Moreover, periodic data and sporadic data are two types of real-time data traffic with different priorities in an NCS. Due to the lack of support for prioritized transmission service, the real-time performance for periodic and sporadic data in an NCS network is often degraded significantly, particularly under congested network conditions. To address these problems, a new transport layer protocol called Reliable Real-Time Transport Protocol (RRTTP) is proposed in this thesis. As a UDP-based protocol, RRTTP inherits UDP’s simplicity and fast transmission features. To improve the reliability, a retransmission and an acknowledgement mechanism are designed in RRTTP to compensate for packet losses. They are able to avoid unnecessary retransmission of the out-of-date packets in NCSs, and collisions are unlikely to happen, and small transmission delay can be achieved. Moreover, a prioritized transmission mechanism is also designed in RRTTP to improve the real-time performance of NCS networks under congested traffic conditions. Furthermore, the proposed RRTTP is implemented in the Network Simulator 2 for comprehensive simulations. The simulation results demonstrate that RRTTP outperforms TCP and UDP in terms of real-time transmissions in an NCS over wireless networks.

On the time spent preparing grant proposals : an observational study of Australian researchers

Objective: To estimate the time spent by the researchers for preparing grant proposals, and to examine whether spending more time increase the chances of success. Design: Observational study. Setting: The National Health and Medical Research Council (NHMRC) of Australia. Participants: Researchers who submitted one or more NHMRC Project Grant proposals in March 2012. Main outcome measures: Total researcher time spent preparing proposals; funding success as predicted by the time spent. Results: The NHMRC received 3727 proposals of which 3570 were reviewed and 731 (21%) were funded. Among our 285 participants who submitted 632 proposals, 21% were successful. Preparing a new proposal took an average of 38 working days of researcher time and a resubmitted proposal took 28 working days, an overall average of 34 days per proposal. An estimated 550 working years of researchers' time (95% CI 513 to 589) was spent preparing the 3727 proposals, which translates into annual salary costs of AU$66 million. More time spent preparing a proposal did not increase the chances of success for the lead researcher (prevalence ratio (PR) of success for 10 day increase=0.91, 95% credible interval 0.78 to 1.04) or other researchers (PR=0.89, 95% CI 0.67 to 1.17). Conclusions: Considerable time is spent preparing NHMRC Project Grant proposals. As success rates are historically 20–25%, much of this time has no immediate benefit to either the researcher or society, and there are large opportunity costs in lost research output. The application process could be shortened so that only information relevant for peer review, not administration, is collected. This would have little impact on the quality of peer review and the time saved could be reinvested into research.

The time course of in vivo recovery of transverse strain in high-stress tendons following exercise

Objective To evaluate the time course of the recovery of transverse strain in the Achilles and patellar tendon following a bout of resistance exercise. Methods Seventeen healthy adults underwent sonographic examination of the right patellar (n=9) and Achilles (n=8) tendons immediately prior to and following 90 repetitions of weight-bearing quadriceps and gastrocnemius-resistance exercise performed against an effective resistance of 175% and 250% body weight, respectively. Sagittal tendon thickness was determined 20 mm from the enthesis and transverse strain, as defined by the stretch ratio, was repeatedly monitored over a 24 h recovery period. Results Resistance exercise resulted in an immediate decrease in Achilles (t7=10.6, p<0.01) and patellar (t8=8.9, p<0.01) tendon thickness, resulting in an average transverse stretch ratio of 0.86±0.04 and 0.82±0.05, which was not significantly different between tendons. The magnitude of the immediate transverse strain response, however, was reduced with advancing age (r=0.63, p<0.01). Recovery in transverse strain was prolonged compared with the duration of loading and exponential in nature. The average primary recovery time was not significantly different between the Achilles (6.5±3.2 h) and patellar (7.1±3.2 h) tendons. Body weight accounted for 62% and 64% of the variation in recovery time, respectively. Conclusions Despite structural and biochemical differences between the Achilles and patellar tendon, the mechanisms underlying transverse creep recovery in vivo appear similar and are highly time dependent. These novel findings have important implications concerning the time required for the mechanical recovery of high-stress tendons following an acute bout of exercise.

The interplay between chondrocyte redifferentiation pellet size and oxygen concentration

Chondrocytes dedifferentiate during ex vivo expansion on 2-dimensional surfaces. Aggregation of the expanded cells into 3-dimensional pellets, in the presence of induction factors, facilitates their redifferentiation and restoration of the chondrogenic phenotype. Typically 1×105–5×105 chondrocytes are aggregated, resulting in “macro” pellets having diameters ranging from 1–2 mm. These macropellets are commonly used to study redifferentiation, and recently macropellets of autologous chondrocytes have been implanted directly into articular cartilage defects to facilitate their repair. However, diffusion of metabolites over the 1–2 mm pellet length-scales is inefficient, resulting in radial tissue heterogeneity. Herein we demonstrate that the aggregation of 2×105 human chondrocytes into micropellets of 166 cells each, rather than into larger single macropellets, enhances chondrogenic redifferentiation. In this study, we describe the development of a cost effective fabrication strategy to manufacture a microwell surface for the large-scale production of micropellets. The thousands of micropellets were manufactured using the microwell platform, which is an array of 360×360 µm microwells cast into polydimethylsiloxane (PDMS), that has been surface modified with an electrostatic multilayer of hyaluronic acid and chitosan to enhance micropellet formation. Such surface modification was essential to prevent chondrocyte spreading on the PDMS. Sulfated glycosaminoglycan (sGAG) production and collagen II gene expression in chondrocyte micropellets increased significantly relative to macropellet controls, and redifferentiation was enhanced in both macro and micropellets with the provision of a hypoxic atmosphere (2% O2). Once micropellet formation had been optimized, we demonstrated that micropellets could be assembled into larger cartilage tissues. Our results indicate that micropellet amalgamation efficiency is inversely related to the time cultured as discreet microtissues. In summary, we describe a micropellet production platform that represents an efficient tool for studying chondrocyte redifferentiation and demonstrate that the micropellets could be assembled into larger tissues, potentially useful in cartilage defect repair.

Integrating real time positioning systems to improve blind lifting and loading crane operations

Mobile/tower cranes are the most essential forms of construction plant in use in the construction industry but are also the subject of several safety issues. Of these, blind lifting has been found to be one of the most hazardous of crane operations. To improve the situation, a real-time monitoring system that integrates the use of a Global Positioning System (GPS) and Radio Frequency Identification (RFID) is developed. This system aims to identify unauthorized work or entrance of personnel within a pre-defined risk zone by obtaining positioning data of both site workers and the crane. The system alerts to the presence of unauthorized workers within a risk zone——currently defined as 3m from the crane. When this happens, the system suspends the power of the crane and a warning signal is generated to the safety management team. In this way the system assists the safety management team to manage the safety of hundreds of workers simultaneously. An onsite trial with debriefing interviews is presented to illustrate and validate the system in use.

Over time assessment data analysis tracking a school's on-going performance

In Australia, as in some other western nations, governments impose accountability measures on educational institutions (Earl, 2005). One such accountability measure is the National Assessment Program - Literacy and Numeracy (NAPLAN) from which high-stakes assessment data is generated. In this article, a practical method of data analysis known as the Over Time Assessment Data Analysis (OTADA) is offered as an analytical process by which schools can monitor their current and over time performances. This analysis developed by the author, is currently used extensively in schools throughout Queensland. By Analysing in this way, teachers, and in particular principals, can obtain a quick and insightful performance overview. For those seeking to track the achievements and progress of year level cohorts, the OTADA should be considered.

Assessment of precision timing and real-time data networks for digital substation automation

This project researched the performance of emerging digital technology for high voltage electricity substations that significantly improves safety for staff and reduces the potential impact on the environment of equipment failure. The experimental evaluation used a scale model of a substation control system that incorporated real substation control and networking equipment with real-time simulation of the power system. The outcomes confirm that it is possible to implement Ethernet networks in high voltage substations that meet the needs of utilities; however component-level testing of devices is necessary to achieve this. The assessment results have been used to further develop international standards for substation communication and precision timing.

Demanding a change : time to act on statutory demands

The statutory demand procedure has been a part of our corporate law from its earliest modern formulations and it has been suggested, albeit anecdotally, that under the current regime, it gives rise to more litigation than any other part of the Corporations Act. Despite this there has been a lack of consideration of the underlying policy behind the procedure in both the case law and literature; both of which are largely centred on the technical aspects of the process. The purpose of this article is to examine briefly the process of the statutory demand in the context of the current insolvency law in Australia.

Cerebral cortex activation mapping upon electrical muscle stimulation by 32-channel time-domain functional near-infrared spectroscopy

The application of different EMS current thresholds on muscle activates not only the muscle but also peripheral sensory axons that send proprioceptive and pain signals to the cerebral cortex. A 32-channel time-domain fNIRS instrument was employed to map regional cortical activities under varied EMS current intensities applied on the right wrist extensor muscle. Eight healthy volunteers underwent four EMS at different current thresholds based on their individual maximal tolerated intensity (MTI), i.e., 10 % < 50 % < 100 % < over 100 % MTI. Time courses of the absolute oxygenated and deoxygenated hemoglobin concentrations primarily over the bilateral sensorimotor cortical (SMC) regions were extrapolated, and cortical activation maps were determined by general linear model using the NIRS-SPM software. The stimulation-induced wrist extension paradigm significantly increased activation of the contralateral SMC region according to the EMS intensities, while the ipsilateral SMC region showed no significant changes. This could be due in part to a nociceptive response to the higher EMS current intensities and result also from increased sensorimotor integration in these cortical regions.

Health complaints commissions in Australia : Time for a national approach to data collection

Health complaint commissions in Australia: Time for a national approach • There is considerable variation between jurisdictions in the ways complaint data are defined, collected and recorded by the Health complaint commissions. • Complaints from the public are an important accountability mechanism and an indicator of service quality. • The lack of a consistent approach leads to fragmentation of complaint data and a lost opportunity to use national data to assist policy development and identify the main areas causing consumers to complain. • We need a national approach to complaints data collection by the Health complaints commissions in order to better respond to patients’ concerns

Strategies for improved disease resistance in micro-propagated bananas

Bananas (Musa sp) are one of the most important food crops in the world and provide a staple food and source of income in many households especially in Africa. Diseases are a major constraint to production with bunchy top, caused by Banana bunchy top virus (BBTV) generally considered the most important virus disease of bananas worldwide. Of the fungal diseases, Fusarium wilt, caused by the Fusarium oxysporum f.sp cubense (Foc), and black Sigatoka, caused by Mycosphaerella fijiensis, are arguably two of the most important and cause significant yield losses. The low fertility of commercially important banana cultivars has hampered efforts to generate disease resistance using conventional breeding. Possible alternative strategies to generate or increase disease resistance are through genetic engineering or by manipulation of the innate plant defence mechanisms, namely systemic acquired resistance (SAR). The first research component of this thesis describes attempts to generate BBTV-resistant banana plants using a genetic modification approach. The second research component of the thesis focused on the identification of a potential marker gene associated with SAR in banana plants and a comparison of the expression levels of the marker gene in response to biotic and abiotic stresses, and chemical inducers. Previous research at QUT CTCB showed that replication of BBTV DNA components in banana embryogenic cell suspensions (ECS) was abolished following co-bombardment with 1.1mers of mutated BBTV DNA-R. BBTV DNA-R encodes the master replication protein (Rep) and is the only viral protein essential for BBTV replication. In this study, ECS of banana were stably transformed with the same constructs, each containing a different mutation in BBTV DNA-R, namely H41G, Y79F and K187M, to examine the effect on virus replication in stably transformed plants. Cells were also transformed with a construct containing a native BBTV Rep. A total of 16, 16, 11 and five lines of stably transformed banana plants containing the Y79F, H41G, K187M and native Rep constructs, respectively, were generated. Of these, up to nine replicates from Y79F lines, four H41G lines, seven K187M lines and three native Rep lines were inoculated with BBTV by exposure to viruliferous aphids in two separate experiments. At least one replicate from each of the nine Y79F lines developed typical bunchy top symptoms and all tested positive for BBTV using PCR. Of the four H41G lines tested, at least one replicate from three of the lines showed symptoms of bunchy top and tested positive using PCR. However, none of the five replicates of one H41G line (H41G-3) developed symptoms of bunchy top and none of the plants tested positive for BBTV using PCR. Of the seven K187M lines, at least one replicate of all lines except one (K187M-1) developed symptoms of bunchy top and tested positive for BBTV. Importantly, none of the four replicates of line K187M-1 showed symptoms or tested positive for BBTV. At least one replicate from each of the three native Rep lines developed symptoms and tested positive for BBTV. The H41G-3 and K187M-1 lines possibly represent the first transgenic banana plants generated using a mutated Rep strategy. The second research component of this thesis focused on the identification of SAR-associated genes in banana and their expression levels in response to biotic and abiotic stresses and chemical inducers. The impetus for this research was the observation that tissue-cultured (TC) banana plants were more susceptible to Fusarium wilt disease (and possibly bunchy top disease) than plants grown from field-derived suckers, possibly due to decreased levels of SAR gene expression in the former. In this study, the pathogenesis-related protein 1 (PR-1) gene was identified as a potential marker for SAR gene expression in banana. A quantitative real-time PCR assay was developed and optimised in order to determine the expression of PR-1, with polyubiquitin (Ubi-1) found to be the most suitable reference gene to enable relative quantification. The levels of PR-1 expression were subsequently compared in Lady Finger and Cavendish (cv. Williams) banana plants grown under three different environmental conditions, namely in the field, the glass house and in tissue-culture. PR-1 was shown to be expressed in both cultivars growing under different conditions. While PR-1 expression was highest in the field grown bananas and lowest in the TC bananas in Lady Finger cultivar, this was not the case in the Cavendish cultivar with glass house plants exhibiting the lowest PR-1 expression compared with tissue culture and field grown plants. The important outcomes of this work were the establishment of a qPCR-based assay to monitor PR-1 expression levels in banana and a preliminary assessment of the baseline PR-1 expression levels in two banana cultivars under three different growing conditions. After establishing the baseline PR-1 expression levels in Cavendish bananas, a study was done to determine whether PR-1 levels could be increased in these plants by exposure to known banana pathogens and non-pathogens, and a known chemical inducer of SAR. Cavendish banana plants were exposed to pathogenic Foc subtropical race 4 (FocSR4) and non-pathogenic Foc race 1 (Foc1), as well as two putative inducers of resistance, Fusarium lycopersici (Fol) and the chemical, acibenzolar-S-methyl (BION®). Tissue culture bananas were acclimatised under either glass house (TCS) or field (TCH) conditions and treatments were carried out in a randomised complete block design. PR-1 expression was determined using qPCR for both TCS and TCH samples for the period 12-72h post-exposure. Treatment of TCH plants using Foc1 and FocSR4 resulted in 120 and 80 times higher PR-1 expression than baseline levels, respectively. For TCS plants treated with Foc1, PR-1 expression was 30 times higher than baseline levels at 12h post-exposure, while TCS plants treated with FocSR4 showed the highest PR-1 expression (20 times higher than baseline levels) at 72h post-exposure. Interestingly, when TCS plants were treated with Fol there was a marked increase of PR-1 expression at 12 h and 48 h following treatment which was 4 and 8 times higher than the levels observed when TCS plants were treated with Foc1 and FocSR4, respectively. In contrast, when TCH plants were treated with Fol only a slight increase in PR-1 expression was observed at 12 h, which eventually returned to baseline levels. Exposure of both TCS and TCH plants to BION® resulted in no effect on PR-1 expression levels at any time-point. The major outcome of the SAR study was that the glass house acclimatised tissue culture bananas exhibited lower PR-1 gene expression compared to field acclimatised tissue culture plants and the identification of Fol as a good candidate for SAR induction in banana plants exhibiting low PR-1 levels. A number of outcomes that foster understanding of both pathogen-derived and plant innate resistance strategies in order to potentially improve banana resistance to diseases were explored in this study and include identification of potential inducers of systemic acquired resistance and a promising mutated Rep approach for BBTV resistance. The work presented in this thesis is the first report on the generation of potential BBTV resistant bananas using the mutated Rep approach. In addition, this is the first report on the status of SAR in banana grown under different conditions of exposure to the biotic and abiotic environment. Further, a robust qPCR assay for the study of gene expression using banana leaf samples was developed and a potential inducer of SAR in tissue culture bananas identified which could be harnessed to increase resistance in tissue culture bananas.

Using real-time authentic online learning scenarios to teach criminal intelligence

Criminal intelligence is an area of expertise highly sought-after internationally and within a variety of justice-related professions; however, producing university graduates with the requisite professional knowledge, as well as analytical, organisational and technical skills presents a pedagogical and technical challenge to university educators. The situation becomes even more challenging when students are undertaking their studies by distance education. This best practice session showcases the design of an online undergraduate unit for final year justice students which uses an evolving real-time criminal scenario as the focus of authentic learning activities in order to prepare students for graduate roles within the criminal intelligence and justice professions. Within the unit, students take on the role of criminal intelligence analysts, applying relevant theories, models and strategies to solve a complex but realistic crime and complete briefings and documentation to industry standards as their major summative assessment task. The session will demonstrate how the design of the online unit corresponds to authentic learning principles, and will specifically map the elements of the unit design to Herrington & Oliver’s instructional design framework for authentic learning (2000; Herrington & Herrington 2006). The session will show how a range of technologies was used to create a rich learning experience for students that could be easily maintained over multiple unit iterations without specialist technical support. The session will also discuss the unique pedagogical affordances and challenges implicated in the location of the unit within an online learning environment, and will reflect on some of the lessons learned from the development which may be relevant to other authentic online learning contexts.