Development of novel vaccine strategies to prevent genital tract chlamydial infections

Chlamydia trachomatis is the most prevalent bacterial sexually transmitted infection in the developed world and the leading cause of preventable blindness worldwide. As reported by the World Health Organization in 2001, there are approximately 92 million new infections detected annually, costing health systems billions of dollars to treat not only the acute infection, but also to treat infection-associated sequelae. The majority of genital infections are asymptomatic, with 50-70% going undetected. Genital tract infections can be easily treated with antibiotics when detected. Lack of treatment can lead to the development of pelvic inflammatory disease, ectopic pregnancies and tubal factor infertility in women and epididymitis and prostatitis in men. With infection rates on the continual rise and the large number of infections going undetected, there is a need to develop an efficacious vaccine which prevents not only infection, but also the development of infection-associated pathology. Before a vaccine can be developed and administered, the pathogenesis of chlamydial infections needs to be fully understood. This includes the kinetics of ascending infection and the effects of inoculating dose on ascension and development of pathology. The first aim in this study was to examine these factors in a murine model. Female BALB/c mice were infected intravaginally with varying doses of C. muridarum, the mouse variant of human C. trachomatis, and the ascension of infection along the reproductive tract and the time-course of infection-associated pathology development, including inflammatory cell infiltration, pyosalpinx and hydrosalpinx, were determined. It was found that while the inoculating dose did affect the rate and degree of infection, it did not affect any of the pathological parameters examined. This highlighted that the sexual transmission dose may have minimal effect on the development of reproductive sequelae. The results of the first section enabled further studies presented here to use an optimal inoculating dose that would ascend the reproductive tract and cause pathology development, so that vaccine efficacy could be determined. There has been a large amount of research into the development of an efficacious vaccine against genital tract chlamydial infections, with little success. However, there have been no studies examining the effects of the timing of vaccination, including the effects of vaccination during an active genital infection, or after clearance of a previous infection. These are important factors that need to be examined, as it is not yet known whether immunization will enhance not only the individual's immune response, but also pathology development. It is also unknown whether any enhancement of the immune responses will cause the Chlamydia to enter a dormant, persistent state, and possibly further enhance any pathology development. The second section of this study aimed to determine if vaccination during an active genital tract infection, or after clearance of a primary infection, enhanced the murine immune responses and whether any enhanced or reduced pathology occurred. Naïve, actively infected, or previously infected animals were immunized intranasally or transcutaneously with the adjuvants cholera toxin and CpG-ODN in combination with either the major outer membrane protein (MOMP) of C. muridarum, or MOMP and ribonucleotide reductase small chain protein (NrdB) of C. muridarum. It was found that the systemic immune responses in actively or previously infected mice were altered in comparison to animals immunized naïve with the same combinations, however mucosal antibodies were not enhanced. It was also found that there was no difference in pathology development between any of the groups. This suggests that immunization of individuals who may have an asymptomatic infection, or may have been previously exposed to a genital infection, may not benefit from vaccination in terms of enhanced immune responses against re-exposure. The final section of this study aimed to determine if the vaccination regimes mentioned above caused in vivo persistence of C. muridarum in the upper reproductive tracts of mice. As there has been no characterization of C. muridarum persistence in vitro, either ultrastructurally or via transcriptome analysis, this was the first aim of this section. Once it had been shown that C. muridarum could be induced into a persistent state, the gene transcriptional profiles of the selected persistent marker genes were used to determine if persistent infections were indeed present in the upper reproductive tracts of the mice. We found that intranasal immunization during an active infection induced persistent infections in the oviducts, but not the uterine horns, and that intranasal immunization after clearance of infection, caused persistent infections in both the uterine horns and the oviducts of the mice. This is a significant finding, not only because it is the first time that C. muridarum persistence has been characterized in vitro, but also due to the fact that there is minimal characterization of in vivo persistence of any chlamydial species. It is possible that the induction of persistent infections in the reproductive tract might enhance the development of pathology and thereby enhance the risk of infertility, factors that need to be prevented by vaccination, not enhanced. Overall, this study has shown that the inoculating dose does not affect pathology development in the female reproductive tract of infected mice, but does alter the degree and rate of ascending infection. It has also been shown that intranasal immunization during an active genital infection, or after clearance of one, induces persistent infections in the uterine horns and oviducts of mice. This suggests that potential vaccine candidates will need to have these factors closely examined before progressing to clinical trials. This is significant, because if the same situation occurs in humans, a vaccine administered to an asymptomatic, or previously exposed individual may not afford any extra protection and may in fact enhance the risk of development of infection-associated sequelae. This suggests that a vaccine may serve the community better if administered before the commencement of sexual activity.

Analysis of acoustic emission data for accurate damage assessment for structural health monitoring applications

Structural health monitoring (SHM) refers to the procedure used to assess the condition of structures so that their performance can be monitored and any damage can be detected early. Early detection of damage and appropriate retrofitting will aid in preventing failure of the structure and save money spent on maintenance or replacement and ensure the structure operates safely and efficiently during its whole intended life. Though visual inspection and other techniques such as vibration based ones are available for SHM of structures such as bridges, the use of acoustic emission (AE) technique is an attractive option and is increasing in use. AE waves are high frequency stress waves generated by rapid release of energy from localised sources within a material, such as crack initiation and growth. AE technique involves recording these waves by means of sensors attached on the surface and then analysing the signals to extract information about the nature of the source. High sensitivity to crack growth, ability to locate source, passive nature (no need to supply energy from outside, but energy from damage source itself is utilised) and possibility to perform real time monitoring (detecting crack as it occurs or grows) are some of the attractive features of AE technique. In spite of these advantages, challenges still exist in using AE technique for monitoring applications, especially in the area of analysis of recorded AE data, as large volumes of data are usually generated during monitoring. The need for effective data analysis can be linked with three main aims of monitoring: (a) accurately locating the source of damage; (b) identifying and discriminating signals from different sources of acoustic emission and (c) quantifying the level of damage of AE source for severity assessment. In AE technique, the location of the emission source is usually calculated using the times of arrival and velocities of the AE signals recorded by a number of sensors. But complications arise as AE waves can travel in a structure in a number of different modes that have different velocities and frequencies. Hence, to accurately locate a source it is necessary to identify the modes recorded by the sensors. This study has proposed and tested the use of time-frequency analysis tools such as short time Fourier transform to identify the modes and the use of the velocities of these modes to achieve very accurate results. Further, this study has explored the possibility of reducing the number of sensors needed for data capture by using the velocities of modes captured by a single sensor for source localization. A major problem in practical use of AE technique is the presence of sources of AE other than crack related, such as rubbing and impacts between different components of a structure. These spurious AE signals often mask the signals from the crack activity; hence discrimination of signals to identify the sources is very important. This work developed a model that uses different signal processing tools such as cross-correlation, magnitude squared coherence and energy distribution in different frequency bands as well as modal analysis (comparing amplitudes of identified modes) for accurately differentiating signals from different simulated AE sources. Quantification tools to assess the severity of the damage sources are highly desirable in practical applications. Though different damage quantification methods have been proposed in AE technique, not all have achieved universal approval or have been approved as suitable for all situations. The b-value analysis, which involves the study of distribution of amplitudes of AE signals, and its modified form (known as improved b-value analysis), was investigated for suitability for damage quantification purposes in ductile materials such as steel. This was found to give encouraging results for analysis of data from laboratory, thereby extending the possibility of its use for real life structures. By addressing these primary issues, it is believed that this thesis has helped improve the effectiveness of AE technique for structural health monitoring of civil infrastructures such as bridges.

Global story-telling in a socially-networked world

Journalists work in an intensively time-pressured environment, researching and writing to daily, often 24 hour, deadlines and always aware of the competition with other news outlets to be first with the news. This results, as Karen Sanders has observed, in journalists having very little time for reflection. “If they do reflect, it’s usually after a decision has been made” (Sanders 2003, 168). Yet time for reflection upon professional practice is important, especially in an era of extremely rapid and seismic technological change in the global media. This paper will reflect upon how freelance journalists can use advances in social media and web-based connectedness to tell global stories via mainstream media outlets. In exploring this question, I will examine the techniques and communications technologies used by three reporters working in the UK and Australia to find, investigate and break a series of articles, published simultaneously on the front pages of The Australian and The Times (London) newspapers, was a result of a six month investigation. The series exposed a 50-year cover-up of the serial abuse of children by one of the Church of England's most senior clergy, Robert Waddington, in Australia and the UK. It unearthed the existence of a culture of physical and sexual abuse at St Barnabas boarding school in Queensland, the sudden closure of the school and disappearance of student files - as well as Waddington's subsequent offences against children while Dean of Manchester Cathedral. We produced more than 20 articles. The coverage sparked church-ordered investigations in both countries, and also prompted the Archbishop of Canterbury to order a commission of inquiry – headed by a sitting UK judge - as well as a nationwide child safety audit of dioceses in Britain. In Australia, the church referred the case and handed its files to the Royal Commission into Child Sexual Abuse. The coverage marked the first publishing collaboration between The Australian and The Times to break an exclusive story in Australia and Britain simultaneously, on May 10, 2013.

One tune, three dances : using a traumatic stress framework to understand trauma survivors as networked news sources

Newman and Nelson (2012) describe three ‘dances’ to explain the vacillating psychological states of trauma survivors: the dance of approach and avoidance; the dance of fragmentation and integration; and the dance of resilience and vulnerability. The first pair of seemingly opposite responses describes how survivors at times cope by ‘approaching’ the trauma, for example by gathering information about what happened; whilst at other times, the same person will cope by ‘avoiding’ the trauma by engaging in activities which distract them from the memory of the trauma or having to deal with the consequences of it. The ‘dance’ of fragmentation and integration describes the opposing individual or group experiences encountered after traumas or disasters. Individuals may experience fragmentation, or emotional disconnection, from the trauma as an adaptive means of survival. The ‘dance’ of resilience and vulnerability refers to an individual’s ability to ‘process’ trauma and return to a resilient state in which they re-learn to trust people and the world around them and ‘bounce back’ to a state of being resilient again. This paper will illustrate how an understanding of the three dances can be used to enable survivors of child sexual assault to engage with the media to tell their stories. I will give current examples from six months of journalism research, collaboration and writing of a series of news stories and features which broke an exclusive story simultaneously in The Australian and The Times in London during 2013.

Child sex scandal in two countries rocks Anglican church

A CHILD sex scandal involving victims in Australia and Britain has hit the top echelon of the Anglican Church, with allegations that some of its most senior clergymen failed to respond properly to complaints of horrific abuse. The former archbishop of York, now Lord (David) Hope of Thornes, yesterday expressed regret over failing to report to police allegations in 1999 and 2003 about a former Queensland Anglican school principal, who rose to become the head of education for the church in Britain. The late reverend Robert Waddington has been accused of beating and sexually abusing students during the 1960s at St Barnabas boarding school in Ravenshoe, north Queensland, and later, when he was in charge of the choir as dean of Manchester. A joint investigation by The Australian and The Times newspaper in London has revealed that church officials, including Lord Hope, failed to report the 1999 allegations of abuse made by a former Queensland student and similar claims made in 2003 by the family of a choirboy in Manchester. The alleged victims were never told of the existence of the other allegations.

Choirboy haunted by painful memories

IT was in the magnificent Manchester Cathedral that Eli Ward's pure soprano attracted the attention of the new dean, the Reverend Robert Waddington. When Waddington called for volunteers to help him polish the gold leaf on the altar railings, several choirboys came forward. Among them was Eli, a working-class 11-year-old from a council estate, who loved singing in the choir and was happy to help...

Former Archbishop of York ‘covered up’ sex abuse scandal

The former Archbishop of York stood accused last night of covering up allegations that a senior Church of England clergyman had abused choirboys and school pupils. Lord Hope of Thornes was made aware of the accusations against the Very Rev Robert Waddington, a former Dean of Manchester Cathedral and once the cleric in overall charge of Church schools, in 1999 and again in 2003. Waddington was stripped of his right to conduct church services but the archbishop did not report concerns about alleged past abuse or a potential continuing threat to children to police or child protection agencies. The extent of Waddington’s alleged history of abuse and the Church’s inaction has been revealed through a joint investigation by The Times and The Australian newspaper in Sydney.

Self-exciting hurdle models for terrorist activity

A predictive model of terrorist activity is developed by examining the daily number of terrorist attacks in Indonesia from 1994 through 2007. The dynamic model employs a shot noise process to explain the self-exciting nature of the terrorist activities. This estimates the probability of future attacks as a function of the times since the past attacks. In addition, the excess of nonattack days coupled with the presence of multiple coordinated attacks on the same day compelled the use of hurdle models to jointly model the probability of an attack day and corresponding number of attacks. A power law distribution with a shot noise driven parameter best modeled the number of attacks on an attack day. Interpretation of the model parameters is discussed and predictive performance of the models is evaluated.

Accused cleric built reputation at small school in Australia

The little Anglican boarding school of St Barnabas, in the mountain town of Ravenshoe, north Queensland, was where Robert Waddington built his reputation as an educationalist. He was headmaster there from 1961-70, but a growing number of former pupils are now coming forward to say they were subjected to sexual and physical abuse by him. Bim Atkinson, 58, said that his ordeal began after he was sent to the school and joined the choir. “I was absolutely petrified of the man,” Mr Atkinson recalls. “After I joined the choir, the abuse started. He would tell me to go to the sickbay, which had a connecting door to his bedroom and then I would end up in his room.”

Robert Waddington's cycle of abuse stretches beyond 50 years

THE Church of England banished serial pedophile priest Robert Waddington to Australia, where he abused children across a decade, after suspicions were raised about him molesting choirboys in his London parish. In an alleged church cover-up spanning almost 60 years, Waddington was suddenly and unexpectedly sent to a small school in regional Queensland in 1956 amid claims he was molesting the son of an English politician. Last month the Church of England ordered an independent inquiry into the handling of allegations against Waddington, after a joint investigation by The Australian and The Times of London. But it can now be revealed that Waddington - who died in 2007, facing allegations he abused students in Australia in the 1960s and English choirboys in the 80s and 90s - was molesting children as soon as he joined the church in 1953. The latest allegations have been made by Ray Munn, 70, who was recruited by Waddington, then a curate at St John's church in Bethnal Green, East London, to sing in the choir in 1953. He was almost immediately groomed by the Cambridge University-educated clergyman, who took him on holidays in the English countryside, before he began molesting the then 11-year-old.

Expressive cryptography : lattice perspectives

The invention of asymmetric encryption back in the seventies was a conceptual leap that vastly increased the expressive power of encryption of the times. For the first time, it allowed the sender of a message to designate the intended recipient in an cryptographic way, expressed as a “public key” that was related to but distinct from the “private key” that, alone, embodied the ability to decrypt. This made large-scale encryption a practical and scalable endeavour, and more than anything else—save the internet itself—led to the advent of electronic commerce as we know and practice it today.

Crime in rural Australia

As an academic who has spent a quarter of a century living, lecturing and researching in a rural community, I am often impressed by the discrepancies between the reality of rural life and its image in the public consciousness. At least two aspects of this are the most striking. First, there is often - especially, but not exclusively in English-speaking societies - the idea that rural communities represent the "real" or "true" aspects of a society's culture. For example, judging by the representations of rural Australia in the media, rural life is where we find the true Australian, the laconic, taciturn, but decent everyday man and woman, the "battlers", who are not corrupted by urban life. Such an attribution of genuineness to rurality is especially interesting given that the vast majority of contemporary Australians live in cities and that Australia is one of the most urbanised countries in the world. Second, and following from the first point, is the idea that rural areas remain somewhat behind the times, that somehow they are not quite part of the contemporary world. This is a mixed image as it combines both the negative idea of backwardness with the more positive one of a society that has not lost the virtues of stability and civility that we often feel is missing in the city. Both of these ideas combine in the popular image of rural communities as safe places in an increasingly dangerous world. In the popular mind it seems that there is an idea that whatever rural communities may lack in conveniences and sophistication, they remain places where you might walk down the street safely, leave your doors unlocked at night and raise your children confident that they will not be exposed to drugs, gangs and violence. Unfortunately, all of these ideas are fantasies. There is no reason to believe that the residents of rural communities are anymore the truer representations of Australian culture than the average suburbanite.

Left versus right hemisphere differences in brain connectivity: 4-Tesla HARDI tractography in 569 twins

Diffusion imaging can map anatomical connectivity in the living brain, offering new insights into fundamental questions such as how the left and right brain hemispheres differ. Anatomical brain asymmetries are related to speech and language abilities, but less is known about left/right hemisphere differences in brain wiring. To assess this, we scanned 457 young adults (age 23.4±2.0 SD years) and 112 adolescents (age 12-16) with 4-Tesla 105-gradient high-angular resolution diffusion imaging. We extracted fiber tracts throughout the brain with a Hough transform method. A 70×70 connectivity matrix was created, for each subject, based on the proportion of fibers intersecting 70 cortical regions. We identified significant differences in the proportions of fibers intersecting left and right hemisphere cortical regions. The degree of asymmetry in the connectivity matrices varied with age, as did the asymmetry in network topology measures such as the small-world effect.

Hierarchical topological network analysis of anatomical human brain connectivity and differences related to sex and kinship

Modern non-invasive brain imaging technologies, such as diffusion weighted magnetic resonance imaging (DWI), enable the mapping of neural fiber tracts in the white matter, providing a basis to reconstruct a detailed map of brain structural connectivity networks. Brain connectivity networks differ from random networks in their topology, which can be measured using small worldness, modularity, and high-degree nodes (hubs). Still, little is known about how individual differences in structural brain network properties relate to age, sex, or genetic differences. Recently, some groups have reported brain network biomarkers that enable differentiation among individuals, pairs of individuals, and groups of individuals. In addition to studying new topological features, here we provide a unifying general method to investigate topological brain networks and connectivity differences between individuals, pairs of individuals, and groups of individuals at several levels of the data hierarchy, while appropriately controlling false discovery rate (FDR) errors. We apply our new method to a large dataset of high quality brain connectivity networks obtained from High Angular Resolution Diffusion Imaging (HARDI) tractography in 303 young adult twins, siblings, and unrelated people. Our proposed approach can accurately classify brain connectivity networks based on sex (93% accuracy) and kinship (88.5% accuracy). We find statistically significant differences associated with sex and kinship both in the brain connectivity networks and in derived topological metrics, such as the clustering coefficient and the communicability matrix.

A revisit to Pope's cohort analysis

Gulland's [Gulland, J.A., 1965. Estimation of mortality rates. Annex to Arctic Fisheries Working Group Report (meeting in Hamburg, January 1965). ICES. C.M. 1965, Doc. No. 3 (mimeographed)] virtual population analysis (VPA) is commonly used for studying the dynamics of harvested fish populations. However, it necessitates the solving of a nonlinear equation for the instantaneous rate of fishing mortality of the fish in a population. Pope [Pope, J.G., 1972. An investigation of the accuracy of Virtual Population Analysis using cohort analysis. ICNAF Res. Bull. 9, 65-74. Also available in D.H. Cushing (ed.) (1983), Key Papers on Fish Populations, p. 291-301, IRL Press, Oxford, 405 p.] eliminated this necessity in his cohort analysis by approximating its underlying age- and time-dependent population model. His approximation has since become one of the most commonly used age- and time-dependent fish population models in fisheries science. However, some of its properties are not well understood. For example, many assert that it describes the dynamics of a fish population, from which the catch of fish is taken instantaneously in the middle of the year. Such an assertion has never been proven, nor has its implied instantaneous rate of fishing mortality of the fish of a particular age at a particular time been examined, nor has its implied catch equation been derived from a general catch equation. In this paper, we prove this assertion, examine its implied instantaneous rate of fishing mortality of the fish of a particular age at a particular time, derive its implied catch equation from a general catch equation, and comment on how to structure an age- and time-dependent population model to ensure its internal consistency. This work shows that Gulland's (1965) virtual population analysis and Pope's (1972) cohort analysis lie at the opposite end of a continuous spectrum as a general model for a seasonally occurring fishery; Pope's (1972) approximation implies an infinitely large instantaneous rate of fishing mortality of the fish of a particular age at a particular time in a fishing season of zero length; and its implied catch equation has an undefined instantaneous rate of fishing mortality of the fish in a population, but a well-defined cumulative instantaneous rate of fishing mortality of the fish in the population. This work also highlights a need for a more careful treatment of the times of start and end of a fishing season in fish population models.