Effect of female sex hormones on Chlamydia trachomatis growth and gene expression

Transmissible diseases are re-emerging as a global problem, with Sexually Transmitted Diseases (STDs) becoming endemic. Chlamydia trachomatis is the leading cause of bacterially-acquired STD worldwide, with the Australian cost of infection estimated at $90 - $160 million annually. Studies using animal models of genital tract Chlamydia infection suggested that the hormonal status of the genital tract epithelium at the time of exposure may influence the outcome of infection. Oral contraceptive use also increased the risk of contracting chlamydial infections compared to women not using contraception. Generally it was suggested that the outcome of chlamydial infection is determined in part by the hormonal status of the epithelium at the time of exposure. Using the human endolmetrial cell line ECC-1 this study investigated the effects of C. trachomatis serovar D infection, in conjunction with the female sex hormones, 17β-estradiol and progesterone, on chlamydial gene expression. While previous studies have examined the host response, this is the first study to examine C.trachomatis gene expression under different hormonal conditions. We have highlighted a basic model of C. trachomatis gene regulation in the presence of steroid hormones by identifying 60 genes that were regulated by addition of estradiol and/or progesterone. In addition, the third chapter of this thesis discussed and compared the significance of the current findings in the context of data from other research groups to improve our understanding of the molecular basis of chlamydial persistence under hormonal different conditions. In addition, this study analysed the effects of these female sex hormones and C. trachomatis Serovar D infection, on host susceptibility and bacterial growth. Our results clearly demonstrated that addition of steroid hormones not only had a great impact on the level of infectivity of epithelial cells with C.trachomatis serovar D, but also the morphology of chlamydial inclusions was affected by hormone supplementation.

The effect of language models on phonetic decoding for spoken term detection

Spoken term detection (STD) popularly involves performing word or sub-word level speech recognition and indexing the result. This work challenges the assumption that improved speech recognition accuracy implies better indexing for STD. Using an index derived from phone lattices, this paper examines the effect of language model selection on the relationship between phone recognition accuracy and STD accuracy. Results suggest that language models usually improve phone recognition accuracy but their inclusion does not always translate to improved STD accuracy. The findings suggest that using phone recognition accuracy to measure the quality of an STD index can be problematic, and highlight the need for an alternative that is more closely aligned with the goals of the specific detection task.

Spoken term detection using fast phonetic decoding

While spoken term detection (STD) systems based on word indices provide good accuracy, there are several practical applications where it is infeasible or too costly to employ an LVCSR engine. An STD system is presented, which is designed to incorporate a fast phonetic decoding front-end and be robust to decoding errors whilst still allowing for rapid search speeds. This goal is achieved through mono-phone open-loop decoding coupled with fast hierarchical phone lattice search. Results demonstrate that an STD system that is designed with the constraint of a fast and simple phonetic decoding front-end requires a compromise to be made between search speed and search accuracy.

CTA1-DD is an effective adjuvant for targeting anti-chlamydial immunity to the murine genital mucosa

Chlamydia trachomatis is a significant human pathogen with potentially severe disease sequelae in the genital tract, including infertility. A successful vaccine will need to effectively target immunity to the genital mucosa. Intranasal immunisation with cholera toxin (CT) can target immunity to the genital tract, but has the potential to cause neurological side effects. CTA1-DD is a non-toxic potent mucosal adjuvant which combines the enzymatic properties of CT, with a B cell targeting moiety. Here, we demonstrate that intranasal immunisation with CTA1-DD and chlamydial Major Outer Membrane Protein (MOMP) results in the induction of neutralising systemic and mucosal antibodies, and reduces the level of chlamydial shedding following intravaginal challenge with Chlamydia muridarum. Thus, CTA1-DD is an effective adjuvant for vaccine development against Chlamydia trachomatis, and possibly also a range of other genital pathogens.

Near real-time prediction of Zenith Tropospheric Delays for position estimation over long-baseline CORS network

This paper presents the preliminary results in establishing a strategy for predicting Zenith Tropospheric Delay (ZTD) and relative ZTD (rZTD) between Continuous Operating Reference Stations (CORS) in near real-time. It is anticipated that the predicted ZTD or rZTD can assist the network-based Real-Time Kinematic (RTK) performance over long inter-station distances, ultimately, enabling a cost effective method of delivering precise positioning services to sparsely populated regional areas, such as Queensland. This research firstly investigates two ZTD solutions: 1) the post-processed IGS ZTD solution and 2) the near Real-Time ZTD solution. The near Real-Time solution is obtained through the GNSS processing software package (Bernese) that has been deployed for this project. The predictability of the near Real-Time Bernese solution is analyzed and compared to the post-processed IGS solution where it acts as the benchmark solution. The predictability analyses were conducted with various prediction time of 15, 30, 45, and 60 minutes to determine the error with respect to timeliness. The predictability of ZTD and relative ZTD is determined (or characterized) by using the previously estimated ZTD as the predicted ZTD of current epoch. This research has shown that both the ZTD and relative ZTD predicted errors are random in nature; the STD grows from a few millimeters to sub-centimeters while the predicted delay interval ranges from 15 to 60 minutes. Additionally, the RZTD predictability shows very little dependency on the length of tested baselines of up to 1000 kilometers. Finally, the comparison of near Real-Time Bernese solution with IGS solution has shown a slight degradation in the prediction accuracy. The less accurate NRT solution has an STD error of 1cm within the delay of 50 minutes. However, some larger errors of up to 10cm are observed.

Visual impairment, postural stability and falls among older adults with glaucoma

Purpose: To investigate the impact of glaucomatous visual impairment on postural sway and falls among older adults.Methods: The sample comprised 72 community-dwelling older adults with open-angle glaucoma, aged 74.0 5.8 years (range 62 to 90 years). Measures of visual function included binocular visual acuity (high-contrast), binocular contrast sensitivity (Pelli- Robson) and binocular visual fields (merged monocular HFA 24-2 SITA-Std). Postural stability was assessed under four conditions: eyes open and closed, on a firm and on a foam surface. Falls were monitored for six months with prospective falls diaries. Regression models, adjusting for age and gender, examined the association between vision measures and postural stability (linear regression) and the number of falls (negative binomial regression). Results: Greater visual field loss was significantly associated with poorer postural stability with eyes open, both on firm (r = 0.34, p < 0.01) and foam (r = 0.45, p < 0.001) surfaces. Eighteen (25 per cent) participants experienced at least one fall: 12 (17 per cent) participants fell only once and six (eight per cent) participants fell two or more times (up to five falls). Visual field loss was significantly associated with falling; the rate of falls doubled for every 10 dB reduction in field sensitivity (rate ratio = 1.08, 95% CI = 1.02–1.13). Importantly, in a model comprising upper and lower field sensitivity, only lower field loss was significantly associated with the number of falls (rate ratio = 1.17, 95% CI = 1.04–1.33). Conclusions: Binocular visual field loss was significantly associated with postural instability and falls among older adults with glaucoma. These findings provide valuable directions for developing falls risk assessment and falls prevention strategies for this population.

Optimising figure of merit for phonetic spoken term detection

This paper introduces a novel technique to directly optimise the Figure of Merit (FOM) for phonetic spoken term detection. The FOM is a popular measure of sTD accuracy, making it an ideal candiate for use as an objective function. A simple linear model is introduced to transform the phone log-posterior probabilities output by a phe classifier to produce enhanced log-posterior features that are more suitable for the STD task. Direct optimisation of the FOM is then performed by training the parameters of this model using a non-linear gradient descent algorithm. Substantial FOM improvements of 11% relative are achieved on held-out evaluation data, demonstrating the generalisability of the approach.

Restarting trains under moving block signalling : an expert system approach

A high peak power demand at substations will result under Moving Block Signalling (MBS) when a dense queue of trains begins to start from a complete stop at the same time in an electrified railway system. This may cause the power supply interruption and in turn affect the train service substantially. In a recent study, measures of Starting Time Delay (STD) and Acceleration Rate Limit (ARL) are the possible approaches to reduce the peak power demand on the supply system under MBS. Nevertheless, there is no well-defined relationship between the two measures and peak power demand reduction (PDR). In order to attain a lower peak demand at substations on different traffic conditions and system requirements, an expert system is one of the possible approaches to procure the appropriate use of peak demand reduction measures. The main objective of this paper is to study the effect of the train re-starting strategies on the power demand at substations and the time delay suffered by the trains with the aid of computer simulation. An expert system is a useful tool to select various adoptions of STD and ARL under different operational conditions and system requirements.

Fast and accurate phonetic spoken term detection

For the first time in human history, large volumes of spoken audio are being broadcast, made available on the internet, archived, and monitored for surveillance every day. New technologies are urgently required to unlock these vast and powerful stores of information. Spoken Term Detection (STD) systems provide access to speech collections by detecting individual occurrences of specified search terms. The aim of this work is to develop improved STD solutions based on phonetic indexing. In particular, this work aims to develop phonetic STD systems for applications that require open-vocabulary search, fast indexing and search speeds, and accurate term detection. Within this scope, novel contributions are made within two research themes, that is, accommodating phone recognition errors and, secondly, modelling uncertainty with probabilistic scores. A state-of-the-art Dynamic Match Lattice Spotting (DMLS) system is used to address the problem of accommodating phone recognition errors with approximate phone sequence matching. Extensive experimentation on the use of DMLS is carried out and a number of novel enhancements are developed that provide for faster indexing, faster search, and improved accuracy. Firstly, a novel comparison of methods for deriving a phone error cost model is presented to improve STD accuracy, resulting in up to a 33% improvement in the Figure of Merit. A method is also presented for drastically increasing the speed of DMLS search by at least an order of magnitude with no loss in search accuracy. An investigation is then presented of the effects of increasing indexing speed for DMLS, by using simpler modelling during phone decoding, with results highlighting the trade-off between indexing speed, search speed and search accuracy. The Figure of Merit is further improved by up to 25% using a novel proposal to utilise word-level language modelling during DMLS indexing. Analysis shows that this use of language modelling can, however, be unhelpful or even disadvantageous for terms with a very low language model probability. The DMLS approach to STD involves generating an index of phone sequences using phone recognition. An alternative approach to phonetic STD is also investigated that instead indexes probabilistic acoustic scores in the form of a posterior-feature matrix. A state-of-the-art system is described and its use for STD is explored through several experiments on spontaneous conversational telephone speech. A novel technique and framework is proposed for discriminatively training such a system to directly maximise the Figure of Merit. This results in a 13% improvement in the Figure of Merit on held-out data. The framework is also found to be particularly useful for index compression in conjunction with the proposed optimisation technique, providing for a substantial index compression factor in addition to an overall gain in the Figure of Merit. These contributions significantly advance the state-of-the-art in phonetic STD, by improving the utility of such systems in a wide range of applications.

Use of IEEE 1588-2008 for a sampled value process bus in transmission substations

IEC Technical Committee 57 (TC57) published a series of standards and technical reports for “Communication networks and systems for power utility automation” as the IEC 61850 series. Sampled value (SV) process buses allow for the removal of potentially lethal voltages and damaging currents inside substation control rooms and marshalling kiosks, reduce the amount of cabling required in substations, and facilitate the adoption of non-conventional instrument transformers. IEC 61850-9-2 provides an inter-operable solution to support multi-vendor process bus solutions. A time synchronisation system is required for a SV process bus, however the details are not defined in IEC 61850-9-2. IEEE Std 1588-2008, Precision Time Protocol version 2 (PTPv2), provides the greatest accuracy of network based time transfer systems, with timing errors of less than 100 ns achievable. PTPv2 is proposed by the IEC Smart Grid Strategy Group to synchronise IEC 61850 based substation automation systems. IEC 61850-9-2, PTPv2 and Ethernet are three complementary protocols that together define the future of sampled value digital process connections in substations. The suitability of PTPv2 for use with SV is evaluated, with preliminary results indicating that steady state performance is acceptable (jitter < 300 ns), and that extremely stable grandmaster oscillators are required to ensure SV timing requirements are met when recovering from loss of external synchronisation (such as GPS).

Discriminative optimisation of the figure of merit for phonetic spoken term detection

This work proposes to improve spoken term detection (STD) accuracy by optimising the Figure of Merit (FOM). In this article, the index takes the form of phonetic posterior-feature matrix. Accuracy is improved by formulating STD as a discriminative training problem and directly optimising the FOM, through its use as an objective function to train a transformation of the index. The outcome of indexing is then a matrix of enhanced posterior-features that are directly tailored for the STD task. The technique is shown to improve the FOM by up to 13% on held-out data. Additional analysis explores the effect of the technique on phone recognition accuracy, examines the actual values of the learned transform, and demonstrates that using an extended training data set results in further improvement in the FOM.

Test and evaluation system for multi-protocol sampled value protection schemes

Proposed transmission smart grids will use a digital platform for the automation of substations operating at voltage levels of 110 kV and above. The IEC 61850 series of standards, released in parts over the last ten years, provide a specification for substation communications networks and systems. These standards, along with IEEE Std 1588-2008 Precision Time Protocol version 2 (PTPv2) for precision timing, are recommended by the both IEC Smart Grid Strategy Group and the NIST Framework and Roadmap for Smart Grid Interoperability Standards for substation automation. IEC 61850-8-1 and IEC 61850-9-2 provide an inter-operable solution to support multi-vendor digital process bus solutions, allowing for the removal of potentially lethal voltages and damaging currents from substation control rooms, a reduction in the amount of cabling required in substations, and facilitates the adoption of non-conventional instrument transformers (NCITs). IEC 61850, PTPv2 and Ethernet are three complementary protocol families that together define the future of sampled value digital process connections for smart substation automation. This paper describes a specific test and evaluation system that uses real time simulation, protection relays, PTPv2 time clocks and artificial network impairment that is being used to investigate technical impediments to the adoption of SV process bus systems by transmission utilities. Knowing the limits of a digital process bus, especially when sampled values and NCITs are included, will enable utilities to make informed decisions regarding the adoption of this technology.

Prediction model of the buildup of volatile organic compounds on urban roads

A model to predict the buildup of mainly traffic-generated volatile organic compounds or VOCs (toluene, ethylbenzene, ortho-xylene, meta-xylene, and para-xylene) on urban road surfaces is presented. The model required three traffic parameters, namely average daily traffic (ADT), volume to capacity ratio (V/C), and surface texture depth (STD), and two chemical parameters, namely total suspended solid (TSS) and total organic carbon (TOC), as predictor variables. Principal component analysis and two phase factor analysis were performed to characterize the model calibration parameters. Traffic congestion was found to be the underlying cause of traffic-related VOC buildup on urban roads. The model calibration was optimized using orthogonal experimental design. Partial least squares regression was used for model prediction. It was found that a better optimized orthogonal design could be achieved by including the latent factors of the data matrix into the design. The model performed fairly accurately for three different land uses as well as five different particle size fractions. The relative prediction errors were 10–40% for the different size fractions and 28–40% for the different land uses while the coefficients of variation of the predicted intersite VOC concentrations were in the range of 25–45% for the different size fractions. Considering the sizes of the data matrices, these coefficients of variation were within the acceptable interlaboratory range for analytes at ppb concentration levels.

Multicast traffic filtering for sampled value process bus networks

Ethernet is a key component of the standards used for digital process buses in transmission substations, namely IEC 61850 and IEEE Std 1588-2008 (PTPv2). These standards use multicast Ethernet frames that can be processed by more than one device. This presents some significant engineering challenges when implementing a sampled value process bus due to the large amount of network traffic. A system of network traffic segregation using a combination of Virtual LAN (VLAN) and multicast address filtering using managed Ethernet switches is presented. This includes VLAN prioritisation of traffic classes such as the IEC 61850 protocols GOOSE, MMS and sampled values (SV), and other protocols like PTPv2. Multicast address filtering is used to limit SV/GOOSE traffic to defined subsets of subscribers. A method to map substation plant reference designations to multicast address ranges is proposed that enables engineers to determine the type of traffic and location of the source by inspecting the destination address. This method and the proposed filtering strategy simplifies future changes to the prioritisation of network traffic, and is applicable to both process bus and station bus applications.

Use of precision time protocol to synchronize sampled value process buses

Transmission smart grids will use a digital platform for the automation of high voltage substations. The IEC 61850 series of standards, released in parts over the last ten years, provide a specification for substation communications networks and systems. These standards, along with IEEE Std 1588-2008 Precision Time Protocol version 2 (PTPv2) for precision timing, are recommended by the both IEC Smart Grid Strategy Group and the NIST Framework and Roadmap for Smart Grid Interoperability Standards for substation automation. IEC 61850, PTPv2 and Ethernet are three complementary protocol families that together define the future of sampled value digital process connections for smart substation automation. A time synchronisation system is required for a sampled value process bus, however the details are not defined in IEC 61850-9-2. PTPv2 provides the greatest accuracy of network based time transfer systems, with timing errors of less than 100 ns achievable. The suitability of PTPv2 to synchronise sampling in a digital process bus is evaluated, with preliminary results indicating that steady state performance of low cost clocks is an acceptable ±300 ns, but that corrections issued by grandmaster clocks can introduce significant transients. Extremely stable grandmaster oscillators are required to ensure any corrections are sufficiently small that time synchronising performance is not degraded.