Linear models for endocytic transformations from live cell imaging

Endocytosis is the process by which cells internalise molecules including nutrient proteins from the extracellular media. In one form, macropinocytosis, the membrane at the cell surface ruffles and folds over to give rise to an internalised vesicle. Negatively charged phospholipids within the membrane called phosphoinositides then undergo a series of transformations that are critical for the correct trafficking of the vesicle within the cell, and which are often pirated by pathogens such as Salmonella. Advanced fluorescent video microscopy imaging now allows the detailed observation and quantification of these events in live cells over time. Here we use these observations as a basis for building differential equation models of the transformations. An initial investigation of these interactions was modelled with reaction rates proportional to the sum of the concentrations of the individual constituents. A first order linear system for the concentrations results. The structure of the system enables analytical expressions to be obtained and the problem becomes one of determining the reaction rates which generate the observed data plots. We present results with reaction rates which capture the general behaviour of the reactions so that we now have a complete mathematical model of phosphoinositide transformations that fits the experimental observations. Some excellent fits are obtained with modulated exponential functions; however, these are not solutions of the linear system. The question arises as to how the model may be modified to obtain a system whose solution provides a more accurate fit.

Quantifying in-plane deformation of plate elements using vibration characteristics

Plate elements are used in many engineering applications. In-plane loads and deformations have significant influence on the vibration characteristics of plate elements. Numerous methods have been developed to quantify the effects of in-plane loads and deformations of individual plate elements with different boundary conditions based on their natural frequencies. However, these developments cannot be applied to the plate elements in a structural system as the natural frequency is a global parameter for the entire structure. This highlights the need for a method to quantify in-plane deformations of plate elements in structural framing systems. Motivated by this gap in knowledge, this research has developed a comprehensive vibration based procedure to quantify in-plane deformation of plate elements in a structural framing system. This procedure with its unique capabilities to capture the influence of load migration, boundary conditions and different tributary areas is presented herein and illustrated through examples.

Capturing affective experiences using the SMS experience sampling (SMS-ES) method

This paper reports the feasibility and methodological considerations of using the Short Message System Experience Sampling (SMS-ES) Method, which is an experience sampling research method developed to assist researchers to collect repeat measures of consumers’ affective experiences. The method combines SMS with web-based technology in a simple yet effective way. It is described using a practical implementation study that collected consumers’ emotions in response to using mobile phones in everyday situations. The method is further evaluated in terms of the quality of data collected in the study, as well as against the methodological considerations for experience sampling studies. These two evaluations suggest that the SMS-ES Method is both a valid and reliable approach for collecting consumers’ affective experiences. Moreover, the method can be applied across a range of for-profit and not-for-profit contexts where researchers want to capture repeated measures of consumers’ affective experiences occurring over a period of time. The benefits of the method are discussed to assist researchers who wish to apply the SMS-ES Method in their own research designs.

Aircraft emission reduction through multi-disciplinary flight path optimisation

There is worldwide interest in reducing aircraft emissions. The difficulty of reducing emissions including water vapour, carbon dioxide (CO2) and oxides of nitrogen (NOx) is mainly due from the fact that a commercial aircraft is usually designed for a particular optimal cruise altitude but may be requested or required to operate and deviate at different altitude and speeds to archive a desired or commanded flight plan, resulting in increased emissions. This is a multi- disciplinary problem with multiple trade-offs such as optimising engine efficiency, minimising fuel burnt, minimise emissions while maintaining aircraft separation and air safety. This project presents the coupling of an advanced optimisation technique with mathematical models and algorithms for aircraft emission reduction through flight optimisation. Numerical results show that the method is able to capture a set of useful trade-offs between aircraft range and NOx, and mission fuel consumption and NOx. In addition, alternative cruise operating conditions including Mach and altitude that produce minimum NOx and CO2 (minimum mission fuel weight) are suggested.

Accelerated leap methods for simulating discrete stochastic chemical kinetics

Biologists are increasingly conscious of the critical role that noise plays in cellular functions such as genetic regulation, often in connection with fluctuations in small numbers of key regulatory molecules. This has inspired the development of models that capture this fundamentally discrete and stochastic nature of cellular biology - most notably the Gillespie stochastic simulation algorithm (SSA). The SSA simulates a temporally homogeneous, discrete-state, continuous-time Markov process, and of course the corresponding probabilities and numbers of each molecular species must all remain positive. While accurately serving this purpose, the SSA can be computationally inefficient due to very small time stepping so faster approximations such as the Poisson and Binomial τ-leap methods have been suggested. This work places these leap methods in the context of numerical methods for the solution of stochastic differential equations (SDEs) driven by Poisson noise. This allows analogues of Euler-Maruyuma, Milstein and even higher order methods to be developed through the Itô-Taylor expansions as well as similar derivative-free Runge-Kutta approaches. Numerical results demonstrate that these novel methods compare favourably with existing techniques for simulating biochemical reactions by more accurately capturing crucial properties such as the mean and variance than existing methods.

Cross likelihood ratio based speaker clustering using eigenvoice models

This paper proposes the use of eigenvoice modeling techniques with the Cross Likelihood Ratio (CLR) as a criterion for speaker clustering within a speaker diarization system. The CLR has previously been shown to be a robust decision criterion for speaker clustering using Gaussian Mixture Models. Recently, eigenvoice modeling techniques have become increasingly popular, due to its ability to adequately represent a speaker based on sparse training data, as well as an improved capture of differences in speaker characteristics. This paper hence proposes that it would be beneficial to capitalize on the advantages of eigenvoice modeling in a CLR framework. Results obtained on the 2002 Rich Transcription (RT-02) Evaluation dataset show an improved clustering performance, resulting in a 35.1% relative improvement in the overall Diarization Error Rate (DER) compared to the baseline system.

Phenomenological modeling of cell-to-cell and beat-to-beat variability in isolated Guinea Pig ventricular myocytes

Experimental action potential (AP) recordings in isolated ventricular myoctes display significant temporal beat-to-beat variability in morphology and duration. Furthermore, significant cell-to-cell differences in AP also exist even for isolated cells originating from the same region of the same heart. However, current mathematical models of ventricular AP fail to replicate the temporal and cell-to-cell variability in AP observed experimentally. In this study, we propose a novel mathematical framework for the development of phenomenological AP models capable of capturing cell-to-cell and temporal variabilty in cardiac APs. A novel stochastic phenomenological model of the AP is developed, based on the deterministic Bueno-Orovio/Fentonmodel. Experimental recordings of AP are fit to the model to produce AP models of individual cells from the apex and the base of the guinea-pig ventricles. Our results show that the phenomenological model is able to capture the considerable differences in AP recorded from isolated cells originating from the location. We demonstrate the closeness of fit to the available experimental data which may be achieved using a phenomenological model, and also demonstrate the ability of the stochastic form of the model to capture the observed beat-to-beat variablity in action potential duration.

Peer state assessment of TxDOT maintenance program and practices : workshop and road rally findings

In an effort to evaluate and improve their practices to ensure the future excellence of the Texas highway system, the Texas Department of Transportation (TxDOT) sought a forum in which experts from other state departments of transportation could share their expertise. Thus, the Peer State Review of TxDOT Maintenance Practices project was organized and conducted for TxDOT by the Center for Transportation Research (CTR) at The University of Texas at Austin. The goal of the project was to conduct a workshop at CTR and in the Austin District that would educate the visiting peers on TxDOT’s maintenance practices and invite their feedback. CTR and TxDOT arranged the participation of the following directors of maintenance: Steve Takigawa, CA; Roy Rissky, KS; Eric Pitts, GA; Jim Carney, MO; Jennifer Brandenburg, NC; and David Bierschbach, WA. One of the means used to capture the peer reviewers’ opinions was a carefully designed booklet of 15 questions. The peers provided TxDOT with written responses to these questions, and the oral comments made during the workshop were also captured. This information was then compiled and summarized in the following report. An examination of the peers’ comments suggests that TxDOT should use a more holistic, statewide approach to funding and planning rather than funding and planning for each district separately. Additionally, the peers stressed the importance of allocating funds based on the actual conditions of the roadways instead of on inventory. The visiting directors of maintenance also recommended continuing and proliferating programs that enhance communication, such as peer review workshops.

Arterial traffic congestion analysis using Bluetooth duration data

The aim of this study is to assess the potential use of Bluetooth data for traffic monitoring of arterial road networks. Bluetooth data provides the direct measurement of travel time between pairs of scanners, and intensive research has been reported on this topic. Bluetooth data includes “Duration” data, which represents the time spent by Bluetooth devices to pass through the detection range of Bluetooth scanners. If the scanners are located at signalised intersections, this Duration can be related to intersection performance, and hence represents valuable information for traffic monitoring. However the use of Duration has been ignored in previous analyses. In this study, the Duration data as well as travel time data is analysed to capture the traffic condition of a main arterial route in Brisbane. The data consists of one week of Bluetooth data provided by Brisbane City Council. As well, micro simulation analysis is conducted to further investigate the properties of Duration. The results reveal characteristics of Duration, and address future research needs to utilise this valuable data source.

An accessible method for teaching doctors about death certification

The World Health Organization recommends that data on mortality in its member countries are collected utilising the Medical Certificate of Cause of Death published in the instruction volume of the ICD-10. However, investment in health information processes necessary to promote the use of this certificate and improve mortality information is lacking in many countries. An appeal for support to make improvements has been launched through the Health Metrics Network’s MOVE-IT strategy (Monitoring of Vital Events – Information Technology) [World Health Organization, 2011]. Despite this international spotlight on the need for capture of mortality data and in the use of the ICD-10 to code the data reported on such certificates, there is little cohesion in the way that certifiers of deaths receive instruction in how to complete the death certificate, which is the main source document for mortality statistics. Complete and accurate documentation of the immediate, underlying and contributory causes of death of the decedent on the death certificate is a requirement to produce standardised statistical information and to the ability to produce cause-specific mortality statistics that can be compared between populations and across time. This paper reports on a research project conducted to determine the efficacy and accessibility of the certification module of the WHO’s newly-developed web based training tool for coders and certifiers of deaths. Involving a population of medical students from the Fiji School of Medicine and a pre and post research design, the study entailed completion of death certificates based on vignettes before and after access to the training tool. The ability of the participants to complete the death certificates and analysis of the completeness and specificity of the ICD-10 coding of the reported causes of death were used to measure the effect of the students’ learning from the training tool. The quality of death certificate completion was assessed using a Quality Index before and after the participants accessed the training tool. In addition, the views of the participants about accessibility and use of the training tool were elicited using a supplementary questionnaire. The results of the study demonstrated improvement in the ability of the participants to complete death certificates completely and accurately according to best practice. The training tool was viewed very positively and its implementation in the curriculum for medical students was encouraged. Participants also recommended that interactive discussions to examine the certification exercises would be an advantage.

An exploration of the technical, social and macro-societal pressures influencing the adoption of online social networking services by organisations

Measuring the business value that Internet technologies deliver for organisations has proven to be a difficult and elusive task, given their complexity and increased embeddedness within the value chain. Yet, despite the lack of empirical evidence that links the adoption of Information Technology (IT) with increased financial performance, many organisations continue to adopt new technologies at a rapid rate. This is evident in the widespread adoption of Web 2.0 online Social Networking Services (SNSs) such as Facebook, Twitter and YouTube. These new Internet based technologies, widely used for social purposes, are being employed by organisations to enhance their business communication processes. However, their use is yet to be correlated with an increase in business performance. Owing to the conflicting empirical evidence that links prior IT applications with increased business performance, IT, Information Systems (IS), and E-Business Model (EBM) research has increasingly looked to broader social and environmental factors as a means for examining and understanding the broader influences shaping IT, IS and E-Business (EB) adoption behaviour. Findings from these studies suggest that organisations adopt new technologies as a result of strong external pressures, rather than a clear measure of enhanced business value. In order to ascertain if this is the case with the adoption of SNSs, this study explores how organisations are creating value (and measuring that value) with the use of SNSs for business purposes, and the external pressures influencing their adoption. In doing so, it seeks to address two research questions: 1. What are the external pressures influencing organisations to adopt SNSs for business communication purposes? 2. Are SNSs providing increased business value for organisations, and if so, how is that value being captured and measured? Informed by the background literature fields of IT, IS, EBM, and Web 2.0, a three-tiered theoretical framework is developed that combines macro-societal, social and technological perspectives as possible causal mechanisms influencing the SNS adoption event. The macro societal view draws on the concept of Castells. (1996) network society and the behaviour of crowds, herds and swarms, to formulate a new explanatory concept of the network vortex. The social perspective draws on key components of institutional theory (DiMaggio & Powell, 1983, 1991), and the technical view draws from the organising vision concept developed by Swanson and Ramiller (1997). The study takes a critical realist approach, and conducts four stages of data collection and one stage of data coding and analysis. Stage 1 consisted of content analysis of websites and SNSs of many organisations, to identify the types of business purposes SNSs are being used for. Stage 2 also involved content analysis of organisational websites, in order to identify suitable sample organisations in which to conduct telephone interviews. Stage 3 consisted of conducting 18 in-depth, semi-structured telephone interviews within eight Australian organisations from the Media/Publishing and Galleries, Libraries, Archives and Museum (GLAM) industries. These sample organisations were considered leaders in the use of SNSs technologies. Stage 4 involved an SNS activity count of the organisations interviewed in Stage 3, in order to rate them as either Advanced Innovator (AI) organisations, or Learning Focussed (LF) organisations. A fifth stage of data coding and analysis of all four data collection stages was conducted, based on the theoretical framework developed for the study, and using QSR NVivo 8 software. The findings from this study reveal that SNSs have been adopted by organisations for the purpose of increasing business value, and as a result of strong social and macro-societal pressures. SNSs offer organisations a wide range of value enhancing opportunities that have broader benefits for customers and society. However, measuring the increased business value is difficult with traditional Return On Investment (ROI) mechanisms, ascertaining the need for new value capture and measurement rationales, to support the accountability of SNS adoption practices. The study also identified the presence of technical, social and macro-societal pressures, all of which influenced SNS adoption by organisations. These findings contribute important theoretical insight into the increased complexity of pressures influencing technology adoption rationales by organisations, and have important practical implications for practice, by reflecting the expanded global online networks in which organisations now operate. The limitations of the study include the small number of sample organisations in which interviews were conducted, its limited generalisability, and the small range of SNSs selected for the study. However, these were compensated in part by the expertise of the interviewees, and the global significance of the SNSs that were chosen. Future research could replicate the study to a larger sample from different industries, sectors and countries. It could also explore the life cycle of SNSs in a longitudinal study, and map how the technical, social and macro-societal pressures are emphasised through stages of the life cycle. The theoretical framework could also be applied to other social fad technology adoption studies.

Constructing tag ontology from folksonomy based on WordNet

With the emergence of Web 2.0, Web users can classify Web items of their interest by using tags. Tags reflect users’ understanding to the items collected in each tag. Exploring user tagging behavior provides a promising way to understand users’ information needs. However, free and relatively uncontrolled vocabulary has its drawback in terms of lack of standardization and semantic ambiguity. Moreover, the relationships among tags have not been explored even there exist rich relationships among tags which could provide valuable information for us to better understand users. In this paper, we propose a novel approach to construct tag ontology based on the widely used general ontology WordNet to capture the semantics and the structural relationships of tags. Ambiguity of tags is a challenging problem to deal with in order to construct high quality tag ontology. We propose strategies to find the semantic meanings of tags and a strategy to disambiguate the semantics of tags based on the opinion of WordNet lexicographers. In order to evaluate the usefulness of the constructed tag ontology, in this paper we apply the extracted tag ontology in a tag recommendation experiment. We believe this is the first application of tag ontology for recommendation making. The initial result shows that by using the tag ontology to re-rank the recommended tags, the accuracy of the tag recommendation can be improved.

Development of an autonomous unmanned aerial system to collect time-stamped samples from the atmosphere and localize potential pathogen sources

This paper presents the hardware development and testing of a new concept for air sampling via the integration of a prototype spore trap onboard an unmanned aerial system (UAS).We propose the integration of a prototype spore trap onboard a UAS to allow multiple capture of spores of pathogens in single remote locations at high or low altitude, otherwise not possible with stationary sampling devices.We also demonstrate the capability of this system for the capture of multiple time-stamped samples during a single mission.Wind tunnel testing was followed by simulation, and flight testing was conducted to measure and quantify the spread during simulated airborne air sampling operations. During autonomous operations, the onboard autopilot commands the servo to rotate the sampling device to a new indexed location once the UAS vehicle reaches the predefined waypoint or set of waypoints (which represents the region of interest). Time-stamped UAS data are continuously logged during the flight to assist with analysis of the particles collected. Testing and validation of the autopilot and spore trap integration, functionality, and performance is described. These tools may enhance the ability to detect new incursions of spores

Performance load testing and structural adequacy evaluation of road bridge decks

Many ageing road bridges, particularly timber bridges, require urgent improvement due to the demand imposed by the recent version of the Australian bridge loading code, AS 5100. As traffic volume plays a key role in the decision of budget allocations for bridge refurbishment/ replacement, many bridges in low volume traffic network remain in poor condition with axle load and/ or speed restrictions, thus disadvantaging many rural communities. This thesis examines an economical and environmentally sensible option of incorporating disused flat rail wagons (FRW) in the construction of bridges in low volume, high axle load road network. The constructability, economy and structural adequacy of the FRW road bridge is reported in the thesis with particular focus of a demonstration bridge commissioned in regional Queensland. The demonstration bridge comprises of a reinforced concrete slab (RCS) pavement resting on two FRWs with custom designed connection brackets at regular intervals along the span of the bridge. The FRW-RC bridge deck assembly is supported on elastomeric rubber pads resting on the abutment. As this type of bridge replacement technology is new and its structural design is not covered in the design standards, the in-service structural performance of the FRW bridge subjected to the high axle loadings prescribed in AS 5100 is examined through performance load testing. Both the static and the moving load tests are carried out using a fully laden commonly available three-axle tandem truck. The bridge deck is extensively strain gauged and displacement at several key locations is measured using linear variable displacement transducers (LVDTs). A high speed camera is used in the performance test and the digital image data are analysed using proprietary software to capture the locations of the wheel positions on the bridge span accurately. The wheel location is thus synchronised with the displacement and strain time series to infer the structural response of the FRW bridge. Field test data are used to calibrate a grillage model, developed for further analysis of the FRW bridge to various sets of high axle loads stipulated in the bridge design standard. Bridge behaviour predicted by the grillage model has exemplified that the live load stresses of the FRW bridge is significantly lower than the yield strength of steel and the deflections are well below the serviceability limit state set out in AS 5100. Based on the results reported in this thesis, it is concluded that the disused FRWs are competent to resist high axle loading prescribed in AS 5100 and are a viable alternative structural solution of bridge deck in the context of the low volume road networks.

Quantification of particle emission characteristics and development of an emission model for use in transport microenvironments affected by traffic emissions

Vehicle emitted particles are of significant concern based on their potential to influence local air quality and human health. Transport microenvironments usually contain higher vehicle emission concentrations compared to other environments, and people spend a substantial amount of time in these microenvironments when commuting. Currently there is limited scientific knowledge on particle concentration, passenger exposure and the distribution of vehicle emissions in transport microenvironments, partially due to the fact that the instrumentation required to conduct such measurements is not available in many research centres. Information on passenger waiting time and location in such microenvironments has also not been investigated, which makes it difficult to evaluate a passenger’s spatial-temporal exposure to vehicle emissions. Furthermore, current emission models are incapable of rapidly predicting emission distribution, given the complexity of variations in emission rates that result from changes in driving conditions, as well as the time spent in driving condition within the transport microenvironment. In order to address these scientific gaps in knowledge, this work conducted, for the first time, a comprehensive statistical analysis of experimental data, along with multi-parameter assessment, exposure evaluation and comparison, and emission model development and application, in relation to traffic interrupted transport microenvironments. The work aimed to quantify and characterise particle emissions and human exposure in the transport microenvironments, with bus stations and a pedestrian crossing identified as suitable research locations representing a typical transport microenvironment. Firstly, two bus stations in Brisbane, Australia, with different designs, were selected to conduct measurements of particle number size distributions, particle number and PM2.5 concentrations during two different seasons. Simultaneous traffic and meteorological parameters were also monitored, aiming to quantify particle characteristics and investigate the impact of bus flow rate, station design and meteorological conditions on particle characteristics at stations. The results showed higher concentrations of PN20-30 at the station situated in an open area (open station), which is likely to be attributed to the lower average daily temperature compared to the station with a canyon structure (canyon station). During precipitation events, it was found that particle number concentration in the size range 25-250 nm decreased greatly, and that the average daily reduction in PM2.5 concentration on rainy days compared to fine days was 44.2 % and 22.6 % at the open and canyon station, respectively. The effect of ambient wind speeds on particle number concentrations was also examined, and no relationship was found between particle number concentration and wind speed for the entire measurement period. In addition, 33 pairs of average half-hourly PN7-3000 concentrations were calculated and identified at the two stations, during the same time of a day, and with the same ambient wind speeds and precipitation conditions. The results of a paired t-test showed that the average half-hourly PN7-3000 concentrations at the two stations were not significantly different at the 5% confidence level (t = 0.06, p = 0.96), which indicates that the different station designs were not a crucial factor for influencing PN7-3000 concentrations. A further assessment of passenger exposure to bus emissions on a platform was evaluated at another bus station in Brisbane, Australia. The sampling was conducted over seven weekdays to investigate spatial-temporal variations in size-fractionated particle number and PM2.5 concentrations, as well as human exposure on the platform. For the whole day, the average PN13-800 concentration was 1.3 x 104 and 1.0 x 104 particle/cm3 at the centre and end of the platform, respectively, of which PN50-100 accounted for the largest proportion to the total count. Furthermore, the contribution of exposure at the bus station to the overall daily exposure was assessed using two assumed scenarios of a school student and an office worker. It was found that, although the daily time fraction (the percentage of time spend at a location in a whole day) at the station was only 0.8 %, the daily exposure fractions (the percentage of exposures at a location accounting for the daily exposure) at the station were 2.7% and 2.8 % for exposure to PN13-800 and 2.7% and 3.5% for exposure to PM2.5 for the school student and the office worker, respectively. A new parameter, “exposure intensity” (the ratio of daily exposure fraction and the daily time fraction) was also defined and calculated at the station, with values of 3.3 and 3.4 for exposure to PN13-880, and 3.3 and 4.2 for exposure to PM2.5, for the school student and the office worker, respectively. In order to quantify the enhanced emissions at critical locations and define the emission distribution in further dispersion models for traffic interrupted transport microenvironments, a composite line source emission (CLSE) model was developed to specifically quantify exposure levels and describe the spatial variability of vehicle emissions in traffic interrupted microenvironments. This model took into account the complexity of vehicle movements in the queue, as well as different emission rates relevant to various driving conditions (cruise, decelerate, idle and accelerate), and it utilised multi-representative segments to capture the accurate emission distribution for real vehicle flow. This model does not only helped to quantify the enhanced emissions at critical locations, but it also helped to define the emission source distribution of the disrupted steady flow for further dispersion modelling. The model then was applied to estimate particle number emissions at a bidirectional bus station used by diesel and compressed natural gas fuelled buses. It was found that the acceleration distance was of critical importance when estimating particle number emission, since the highest emissions occurred in sections where most of the buses were accelerating and no significant increases were observed at locations where they idled. It was also shown that emissions at the front end of the platform were 43 times greater than at the rear of the platform. The CLSE model was also applied at a signalled pedestrian crossing, in order to assess increased particle number emissions from motor vehicles when forced to stop and accelerate from rest. The CLSE model was used to calculate the total emissions produced by a specific number and mix of light petrol cars and diesel passenger buses including 1 car travelling in 1 direction (/1 direction), 14 cars / 1 direction, 1 bus / 1 direction, 28 cars / 2 directions, 24 cars and 2 buses / 2 directions, and 20 cars and 4 buses / 2 directions. It was found that the total emissions produced during stopping on a red signal were significantly higher than when the traffic moved at a steady speed. Overall, total emissions due to the interruption of the traffic increased by a factor of 13, 11, 45, 11, 41, and 43 for the above 6 cases, respectively. In summary, this PhD thesis presents the results of a comprehensive study on particle number and mass concentration, together with particle size distribution, in a bus station transport microenvironment, influenced by bus flow rates, meteorological conditions and station design. Passenger spatial-temporal exposure to bus emitted particles was also assessed according to waiting time and location along the platform, as well as the contribution of exposure at the bus station to overall daily exposure. Due to the complexity of the interrupted traffic flow within the transport microenvironments, a unique CLSE model was also developed, which is capable of quantifying emission levels at critical locations within the transport microenvironment, for the purpose of evaluating passenger exposure and conducting simulations of vehicle emission dispersion. The application of the CLSE model at a pedestrian crossing also proved its applicability and simplicity for use in a real-world transport microenvironment.