Development and validation of novel methods for microbial source tracking based on Escherichia coli as an indicator of water quality

Microbial pollution in water periodically affects human health in Australia, particularly in times of drought and flood. There is an increasing need for the control of waterborn microbial pathogens. Methods, allowing the determination of the origin of faecal contamination in water, are generally referred to as Microbial Source Tracking (MST). Various approaches have been evaluated as indicatorsof microbial pathogens in water samples, including detection of different microorganisms and various host-specific markers. However, until today there have been no universal MST methods that could reliably determine the source (human or animal) of faecal contamination. Therefore, the use of multiple approaches is frequently advised. MST is currently recognised as a research tool, rather than something to be included in routine practices. The main focus of this research was to develop novel and universally applicable methods to meet the demands for MST methods in routine testing of water samples. Escherichia coli was chosen initially as the object organism for our studies as, historically and globally, it is the standard indicator of microbial contamination in water. In this thesis, three approaches are described: single nucleotide polymorphism (SNP) genotyping, clustered regularly interspaced short palindromic repeats (CRISPR) screening using high resolution melt analysis (HRMA) methods and phage detection development based on CRISPR types. The advantage of the combination SNP genotyping and CRISPR genes has been discussed in this study. For the first time, a highly discriminatory single nucleotide polymorphism interrogation of E. coli population was applied to identify the host-specific cluster. Six human and one animal-specific SNP profile were revealed. SNP genotyping was successfully applied in the field investigations of the Coomera watershed, South-East Queensland, Australia. Four human profiles [11], [29], [32] and [45] and animal specific SNP profile [7] were detected in water. Two human-specific profiles [29] and [11] were found to be prevalent in the samples over a time period of years. The rainfall (24 and 72 hours), tide height and time, general land use (rural, suburban), seasons, distance from the river mouth and salinity show a lack of relashionship with the diversity of SNP profiles present in the Coomera watershed (p values > 0.05). Nevertheless, SNP genotyping method is able to identify and distinquish between human- and non-human specific E. coli isolates in water sources within one day. In some samples, only mixed profiles were detected. To further investigate host-specificity in these mixed profiles CRISPR screening protocol was developed, to be used on the set of E. coli, previously analysed for SNP profiles. CRISPR loci, which are the pattern of previous DNA coliphages attacks, were considered to be a promising tool for detecting host-specific markers in E. coli. Spacers in CRISPR loci could also reveal the dynamics of virulence in E. coli as well in other pathogens in water. Despite the fact that host-specificity was not observed in the set of E. coli analysed, CRISPR alleles were shown to be useful in detection of the geographical site of sources. HRMA allows determination of ‘different’ and ‘same’ CRISPR alleles and can be introduced in water monitoring as a cost-effective and rapid method. Overall, we show that the identified human specific SNP profiles [11], [29], [32] and [45] can be useful as marker genotypes globally for identification of human faecal contamination in water. Developed in the current study, the SNP typing approach can be used in water monitoring laboratories as an inexpensive, high-throughput and easy adapted protocol. The unique approach based on E. coli spacers for the search for unknown phage was developed to examine the host-specifity in phage sequences. Preliminary experiments on the recombinant plasmids showed the possibility of using this method for recovering phage sequences. Future studies will determine the host-specificity of DNA phage genotyping as soon as first reliable sequences can be acquired. No doubt, only implication of multiple approaches in MST will allow identification of the character of microbial contamination with higher confidence and readability.

A preliminary theory of dark network resilience

A crucial contemporary policy question for governments across the globe is how to cope with international crime and terrorist networks. Many such “dark” networks—that is, networks that operate covertly and illegally—display a remarkable level of resilience when faced with shocks and attacks. Based on an in-depth study of three cases (MK, the armed wing of the African National Congress in South Africa during apartheid; FARC, the Marxist guerrilla movement in Colombia; and the Liberation Tigers of Tamil Eelam, LTTE, in Sri Lanka), we present a set of propositions to outline how shocks impact dark network characteristics (resources and legitimacy) and networked capabilities (replacing actors, linkages, balancing integration and differentiation) and how these in turn affect a dark network's resilience over time. We discuss the implications of our findings for policymakers.

How to pick a fight : Visualisation and sharing in catastrophic times

In a post September 11 era “the fight”, as a cultural construct, could hardly be more pertinent. We are seemingly forever poised on the edge of controversial U.S. led attacks on wayward Middle Eastern states and unexamined oppositions between the concepts of ‘good’ and ‘evil’ are evoked as valid justifications for battle. Our leaders muster us into wars of vigilance and national cohesion against unseen, unknown and uncomprehended terrorists hiding where communists once lurked under our beds. The articles in this issue examine fights in terms of media strategies and cultural divides in a range of contexts.

Towards a provably secure DoS-Resilient key exchange protocol with perfect forward secrecy

Just Fast Keying (JFK) is a simple, efficient and secure key exchange protocol proposed by Aiello et al. (ACM TISSEC, 2004). JFK is well known for its novel design features, notably its resistance to denial-of-service (DoS) attacks. Using Meadows’ cost-based framework, we identify a new DoS vulnerability in JFK. The JFK protocol is claimed secure in the Canetti-Krawczyk model under the Decisional Diffie-Hellman (DDH) assumption. We show that security of the JFK protocol, when reusing ephemeral Diffie-Hellman keys, appears to require the Gap Diffie-Hellman (GDH) assumption in the random oracle model. We propose a new variant of JFK that avoids the identified DoS vulnerability and provides perfect forward secrecy even under the DDH assumption, achieving the full security promised by the JFK protocol.

State convergence and the effectiveness of time-memory-data tradeoffs

Various time-memory tradeoffs attacks for stream ciphers have been proposed over the years. However, the claimed success of these attacks assumes the initialisation process of the stream cipher is one-to-one. Some stream cipher proposals do not have a one-to-one initialisation process. In this paper, we examine the impact of this on the success of time-memory-data tradeoff attacks. Under the circumstances, some attacks are more successful than previously claimed while others are less. The conditions for both cases are established.

Teaching and Learning in Maritime Security: A Literature Review

With the rise in attacks and attempted attacks on marine‐based critical infrastructure, maritime security is an issue of increasing importance worldwide. However, there are three significant shortfalls in the efforts to overcome potential threats to maritime security: the need for greater understanding of whether current standards of best practice are truly successful in combating and reducing the risks of terrorism and other security issues, the absence of a collective maritime security best practice framework and the need for improved access to maritime security specific graduate and postgraduate (long) courses. This paper presents an overview of existing international, regional national standards of best practice and shows that literature concerning the measurement and/ or success of standards is virtually non‐existent. In addition, despite the importance of maritime workers to ensuring the safety of marine based critical infrastructure, a similar review of available Australian education courses shows a considerable lack of availability of maritime security‐specific courses other than short courses that cover only basic security matters. We argue that the absence of an Australian best practice framework informed by evaluation of current policy responses – particularly in the post 9/11 environment – leaves Australia vulnerable to maritime security threats. As this paper shows, the reality is that despite the security measures put in place post 9/11, there is still considerable work to be done to ensure Australia is equipped to overcome the threats posed to maritime security.

Efficient modular exponentiation-based puzzles for denial-of-service protection

Client puzzles are moderately-hard cryptographic problems neither easy nor impossible to solve that can be used as a counter-measure against denial of service attacks on network protocols. Puzzles based on modular exponentiation are attractive as they provide important properties such as non-parallelisability, deterministic solving time, and linear granularity. We propose an efficient client puzzle based on modular exponentiation. Our puzzle requires only a few modular multiplications for puzzle generation and verification. For a server under denial of service attack, this is a significant improvement as the best known non-parallelisable puzzle proposed by Karame and Capkun (ESORICS 2010) requires at least 2k-bit modular exponentiation, where k is a security parameter. We show that our puzzle satisfies the unforgeability and difficulty properties defined by Chen et al. (Asiacrypt 2009). We present experimental results which show that, for 1024-bit moduli, our proposed puzzle can be up to 30 times faster to verify than the Karame-Capkun puzzle and 99 times faster than the Rivest et al.'s time-lock puzzle.

Tracking the defining moments of crisis process and practice

Crisis holds the potential for profound change in organizations and industries. The past 50 years of crisis management highlight key shifts in crisis practice, creating opportunities for multiple theories and research tracks. Defining crises such as Tylenol, Exxon Valdez, and September 11 terrorist attacks have influenced or challenged the principles of best practice of crisis communication in public relations. This study traces the development of crisis process and practice by identifying shifts in crisis research and models and mapping these against key management theories and practices. The findings define three crisis domains: crisis planning, building and testing predictive models, and mapping and measuring external environmental influences. These crisis domains mirror but lag the evolution of management theory, suggesting challenges for researchers to reshape the research agenda to close the gap and lead the next stage of development in the field of crisis communication for effective organizational outcomes.

A different algebraic analysis of the ZUC stream cipher

Existing algebraic analyses of the ZUC cipher indicate that the cipher should be secure against algebraic attacks. In this paper, we present an alternative algebraic analysis method for the ZUC stream cipher, where a combiner is used to represent the nonlinear function and to derive equations representing the cipher. Using this approach, the initial states of ZUC can be recovered from 2^97 observed words of keystream, with a complexity of 2^282 operations. This method is more successful when applied to a modified version of ZUC, where the number of output words per clock is increased. If the cipher outputs 120 bits of keystream per clock, the attack can succeed with 219 observed keystream bits and 2^47 operations. Therefore, the security of ZUC against algebraic attack could be significantly reduced if its throughput was to be increased for efficiency.

Algebraic analysis of the SSS stream cipher

Both the SSS and SOBER-t32 stream cipher designs use a single word-based shift register and a nonlinear filter function to produce keystream. In this paper we show that the algebraic attack method previously applied to SOBER-t32 is prevented from succeeding on SSS by the use of the key dependent substitution box (SBox) in the nonlinear filter of SSS. Additional assumptions and modifications to the SSS cipher in an attempt to enable algebraic analysis result in other difficulties that also render the algebraic attack infeasible. Based on these results, we conclude that a well chosen key-dependent substitution box used in the nonlinear filter of the stream cipher provides resistance against such algebraic attacks.

Bollywood Extras

"Bollywood Extras" has been described as a bit like Vladimir Nabokov's "Lolita" (1955) meets Nathanael West's "Day of the Locust" (1939). Unlike those two classics, this new novel by Dr D. Bruno Starrs is set in 21st Century India's Hindi-language film industry epicenter known as 'Bollywood', Mumbai's answer to America's 'Hollywood'. And there is another major difference: the story (i.e. the narrative interaction between an American Extras Casting Agent, 'Dr Arden Pyle', an under-age wannabe Bollywood starlet, 'Chandy', and the despicable but wealthy Indian man who stalks her, 'Ishmail'), is all staged against a backdrop of rabid religious terrorism. Written with the unique black comedic and literary flair Dr D. Bruno Starrs is renown for, this, his 3rd full-length novel, boldly captures the feel of Mumbai and the small-time players in its big-time film industry, with style, humor and originality. Tom Flood, winner of the Miles Franklin Literary Award and founder of Flood Manuscripts, said this of the novel's second last draft: "What is best about 'Bollywood Extras' will likely be its albatross in the sliced bread world of mainstream publishing. Three strengths that make the work what it is - the length, the style, the intellectual capital - will be three strikes against it when it comes to the money. While I delight in rich language and agile invention, I've given you the reasons the trade ('legit') presses won't take 'Bollywood Extras'. Do I think you should you change it? No. I like it. Why ruin an interesting work for money?" As a professional assessor, Flood did, of course, offer many suggestions and these were duly implemented, although the author steadfastly adhered to the style he had already cemented, thus not changing in anyway what Flood refers to as its three strengths. Dr Starrs knew (having accessed Flood's professional services previously) that a 'Thumbs Up' from the best manuscript assessor in the country meant that Bollywood Extras was ready to be birthed. So, here it is: Dr Starrs has delivered his 3rd baby and 'christened' it "Bollywood Extras"!

Ennui and Anomie : from existential dilemma to meaning

This background paper to a panel discussion by four QUT staff members explores depression, mood disorders, suicide and meaning in life.

Introduction to special issue on what criminology can say about the war on terror

On 20 September 2001, the former US President, George W. Bush, declared what is now widely, and arguably infamously, known as a ‘war on terror’. In response to the fatal 9/11 attacks in New York and Washington, DC, President Bush identified the US military response as having far-reaching and long-lasting consequences. It was, he argued, ‘our war on terror’ that began ‘with al Qaeda, but … it will not end until every terrorist group of global reach has been found, stopped and defeated’ (CNN 2001). This was to be a war that would, in the words of former British Prime Minister, Tony Blair, seek to eliminate a threat that was ‘aimed at the whole democratic world’ (Blair 2001). Blair claimed that this threat is of such magnitude that unprecedented measures would need to be taken to uphold freedom and security. Blair would later admit that it was a war that ‘divided the country’ and was based on evidence ‘about Saddam having actual biological and chemical weapons, as opposed to the capability to develop them, has turned out to be wrong’ (Blair 2004). The failures of intelligence ushered in new political rhetoric in the form of ‘trust me’ because ‘instinct is no science’ (Blair 2004). The war on terror has been one of the most significant international events in the past three decades, alongside the collapse of the former Soviet Union, the end of apartheid in South Africa, the unification of Europe and the marketization of the People's Republic of China. Yet, unlike the other events, it will not be remembered for advancing democracy or sovereignty, but for the conviction politics of particular politicians who chose to dispense with international law and custom in pursuit of personal instincts that proved fatal. Since the invasions of Afghanistan in October 2001 and …

Improvisation in interactive music systems

This project investigates machine listening and improvisation in interactive music systems with the goal of improvising musically appropriate accompaniment to an audio stream in real-time. The input audio may be from a live musical ensemble, or playback of a recording for use by a DJ. I present a collection of robust techniques for machine listening in the context of Western popular dance music genres, and strategies of improvisation to allow for intuitive and musically salient interaction in live performance. The findings are embodied in a computational agent – the Jambot – capable of real-time musical improvisation in an ensemble setting. Conceptually the agent’s functionality is split into three domains: reception, analysis and generation. The project has resulted in novel techniques for addressing a range of issues in each of these domains. In the reception domain I present a novel suite of onset detection algorithms for real-time detection and classification of percussive onsets. This suite achieves reasonable discrimination between the kick, snare and hi-hat attacks of a standard drum-kit, with sufficiently low-latency to allow perceptually simultaneous triggering of accompaniment notes. The onset detection algorithms are designed to operate in the context of complex polyphonic audio. In the analysis domain I present novel beat-tracking and metre-induction algorithms that operate in real-time and are responsive to change in a live setting. I also present a novel analytic model of rhythm, based on musically salient features. This model informs the generation process, affording intuitive parametric control and allowing for the creation of a broad range of interesting rhythms. In the generation domain I present a novel improvisatory architecture drawing on theories of music perception, which provides a mechanism for the real-time generation of complementary accompaniment in an ensemble setting. All of these innovations have been combined into a computational agent – the Jambot, which is capable of producing improvised percussive musical accompaniment to an audio stream in real-time. I situate the architectural philosophy of the Jambot within contemporary debate regarding the nature of cognition and artificial intelligence, and argue for an approach to algorithmic improvisation that privileges the minimisation of cognitive dissonance in human-computer interaction. This thesis contains extensive written discussions of the Jambot and its component algorithms, along with some comparative analyses of aspects of its operation and aesthetic evaluations of its output. The accompanying CD contains the Jambot software, along with video documentation of experiments and performances conducted during the project.

A research framework for assessing the effects of heat stress on construction workers

Hong Kong in summer (June - October) is hot and humid. Construction workers have to undertake physically demanding activities and often in confined spaces. They are vulnerable to heat stress in summer hence health and safety measures associated to heat stress measured by scientific and clinical parameters are urgently needed. This paper provides an initial report of a research project funded by the Research Grants Council (RGC) of the HKSAR. The aim of this study is to develop a set of indices measured by clinical and scientific methods to detect impending attacks of heat stress. These indices would be of tremendous value in better safeguarding workers’ health and safety by reducing the occurrences of heat stress on site. This paper firstly reports on the statistics of construction incidents arising from heat stress. Qualitative and quantitative research methods applied in conducting the research are discussed. It is believed that the construction industry and the government would benefit a lot as a result of this study.