Approximate Bayesian computation using indirect inference

We present a novel approach for developing summary statistics for use in approximate Bayesian computation (ABC) algorithms by using indirect inference. ABC methods are useful for posterior inference in the presence of an intractable likelihood function. In the indirect inference approach to ABC the parameters of an auxiliary model fitted to the data become the summary statistics. Although applicable to any ABC technique, we embed this approach within a sequential Monte Carlo algorithm that is completely adaptive and requires very little tuning. This methodological development was motivated by an application involving data on macroparasite population evolution modelled by a trivariate stochastic process for which there is no tractable likelihood function. The auxiliary model here is based on a beta–binomial distribution. The main objective of the analysis is to determine which parameters of the stochastic model are estimable from the observed data on mature parasite worms.

Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje

Two archaeal Holliday junction resolving enzymes, Holliday junction cleavage (Hjc) and Holliday junction endonuclease (Hje), have been characterized. Both are members of a nuclease superfamily that includes the type II restriction enzymes, although their DNA cleaving activity is highly specific for four-way junction structure and not nucleic acid sequence. Despite 28% sequence identity, Hje and Hjc cleave junctions with distinct cutting patterns—they cut different strands of a four-way junction, at different distances from the junction centre. We report the high-resolution crystal structure of Hje from Sulfolobus solfataricus. The structure provides a basis to explain the differences in substrate specificity of Hje and Hjc, which result from changes in dimer organization, and suggests a viral origin for the Hje gene. Structural and biochemical data support the modelling of an Hje:DNA junction complex, highlighting a flexible loop that interacts intimately with the junction centre. A highly conserved serine residue on this loop is shown to be essential for the enzyme's activity, suggesting a novel variation of the nuclease active site. The loop may act as a conformational switch, ensuring that the active site is completed only on binding a four-way junction, thus explaining the exquisite specificity of these enzymes.

hSSB1 interacts directly with the MRN complex stimulating its recruitment to DNA double-strand breaks and its endo-nuclease activity

hSSB1 is a recently discovered single-stranded DNA binding protein that is essential for efficient repair of DNA double-strand breaks (DSBs) by the homologous recombination pathway. hSSB1 is required for the efficient recruitment of the MRN complex to sites of DSBs and for the efficient initiation of ATM dependent signalling. Here we explore the interplay between hSSB1 and MRN. We demonstrate that hSSB1 binds directly to NBS1, a component of the MRN complex, in a DNA damage independent manner. Consistent with the direct interaction, we observe that hSSB1 greatly stimulates the endo-nuclease activity of the MRN complex, a process that requires the C-terminal tail of hSSB1. Interestingly, analysis of two point mutations in NBS1, associated with Nijmegen breakage syndrome, revealed weaker binding to hSSB1, suggesting a possible disease mechanism.

hSSB1 rapidly binds at the sites of DNA double-strand breaks and is required for the efficient recruitment of the MRN complex

hSSB1 is a newly discovered single-stranded DNA (ssDNA)-binding protein that is essential for efficient DNA double-strand break signalling through ATM. However, the mechanism by which hSSB1 functions to allow efficient signalling is unknown. Here, we show that hSSB1 is recruited rapidly to sites of double-strand DNA breaks (DSBs) in all interphase cells (G1, S and G2) independently of, CtIP, MDC1 and the MRN complex (Rad50, Mre11, NBS1). However expansion of hSSB1 from the DSB site requires the function of MRN. Strikingly, silencing of hSSB1 prevents foci formation as well as recruitment of MRN to sites of DSBs and leads to a subsequent defect in resection of DSBs as evident by defective RPA and ssDNA generation. Our data suggests that hSSB1 functions upstream of MRN to promote its recruitment at DSBs and is required for efficient resection of DSBs. These findings, together with previous work establish essential roles of hSSB1 in controlling ATM activation and activity, and subsequent DSB resection and homologous recombination (HR).

Detecting collusive fraud in enterprise resource planning systems

In today's technological age, fraud has become more complicated, and increasingly more difficult to detect, especially when it is collusive in nature. Different fraud surveys showed that the median loss from collusive fraud is much greater than fraud perpetrated by a single person. Despite its prevalence and potentially devastating effects, collusion is commonly overlooked as an organizational risk. Internal auditors often fail to proactively consider collusion in their fraud assessment and detection efforts. In this paper, we consider fraud scenarios with collusion. We present six potentially collusive fraudulent behaviors and show their detection process in an ERP system. We have enhanced our fraud detection framework to utilize aggregation of different sources of logs in order to detect communication and have further enhanced it to render it system-agnostic thus achieving portability and making it generally applicable to all ERP systems.

Single-stranded DNA-binding protein hSSB1 is critical for genomic stability

Single-strand DNA (ssDNA)-binding proteins (SSBs) are ubiquitous and essential for a wide variety of DNA metabolic processes, including DNA replication, recombination, DNA damage detection and repair1. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating nucleases, helicases and strand-exchange proteins, activating transcription and mediating protein–protein interactions. In eukaryotes, the major SSB, replication protein A (RPA), is a heterotrimer1. Here we describe a second human SSB (hSSB1), with a domain organization closer to the archaeal SSB than to RPA. Ataxia telangiectasia mutated (ATM) kinase phosphorylates hSSB1 in response to DNA double-strand breaks (DSBs). This phosphorylation event is required for DNA damage-induced stabilization of hSSB1. Upon induction of DNA damage, hSSB1 accumulates in the nucleus and forms distinct foci independent of cell-cycle phase. These foci co-localize with other known repair proteins. In contrast to RPA, hSSB1 does not localize to replication foci in S-phase cells and hSSB1 deficiency does not influence S-phase progression. Depletion of hSSB1 abrogates the cellular response to DSBs, including activation of ATM and phosphorylation of ATM targets after ionizing radiation. Cells deficient in hSSB1 exhibit increased radiosensitivity, defective checkpoint activation and enhanced genomic instability coupled with a diminished capacity for DNA repair. These findings establish that hSSB1 influences diverse endpoints in the cellular DNA damage response.

Conformational flexibility revealed by the crystal structure of a crenarchaeal RadA

Homologous recombinational repair is an essential mechanism for repair of double-strand breaks in DNA. Recombinases of the RecA-fold family play a crucial role in this process, forming filaments that utilize ATP to mediate their interactions with singleand double-stranded DNA. The recombinase molecules present in the archaea (RadA) and eukaryota (Rad51) are more closely related to each other than to their bacterial counterpart (RecA) and, as a result, RadA makes a suitable model for the eukaryotic system. The crystal structure of Sulfolobus solfataricus RadA has been solved to a resolution of 3.2 A° in the absence of nucleotide analogues or DNA, revealing a narrow filamentous assembly with three molecules per helical turn. As observed in other RecA-family recombinases, each RadA molecule in the filament is linked to its neighbour via interactions of a short b-strand with the neighbouring ATPase domain. However, despite apparent flexibility between domains, comparison with other structures indicates conservation of a number of key interactions that introduce rigidity to the system, allowing allosteric control of the filament by interaction with ATP. Additional analysis reveals that the interaction specificity of the five human Rad51 paralogues can be predicted using a simple model based on the RadA structure.

Bushfire sustainability : Strategies for reconciling bushfire and biodiversity with daily life

This exhibition and catalogue provides a visual record of student work exhibited at the Australian Institute of Architects offices in Brisbane from November 15 to 29, 2010. The exhibition features the final design outcomes of the inaugural Bushfire Sustainability unit conducted at QUT in semester two, 2010. The core objective of this unit was to develop our students’ skills in collaborative practice in design, research and presentation. The theme of ‘bushfire sustainability’ was chosen because living sustainably in bushfire prone landscapes presents a number of problems, the nature of which might only be resolved via multidisciplinary collaboration among the design disciplines. The students involved represent the disciplines of Interior Design, Landscape Architecture, Industrial Design, Architecture and Sustainability – all from within the School of Design at QUT. 55 students, mostly in their third year of study, worked in teams of five (one from each discipline) to design one of a number of homes in highly bushfire prone sites in either Western Australia or SE Queensland. This year level and the interdisciplinary mix are perhaps the best placed to resolve these problems: being unrestrained from the burdens of professional practice and technical overload they retain the potential for innovative, lateral thinking across the range of spatial scales and philosophical perspectives associated with inhabitation of bushfire prone landscapes. It is envisaged that, through the ‘vehicle’ of this design research, that the students’ work will contribute to understandings of how creative design disciplines might respond to this significant national problem, which hitherto has been attended to primarily by engineering and the sciences.

Minority activism : trends informing political participation across Australian communities

In the late 1990’s, intense and vigorous debate surrounded the impact of minority communities on Australia’s mainstream society. The rise of far-right populism took the stage with the introduction to the political landscape of Pauline Hanson and her One Nation party, whilst John Howard’s Liberal-National Coalition Government took the fore on debate over immigration issues corresponding with an influx of irregular arrivals. In 2001, following the September 11 terrorist attacks in the United States of America and subsequent attacks on western targets globally, many of these issues continued to be debated through the security posturing that followed. In recent years, much effort has been afforded to countering the threat of terrorism from home grown assailants. The Government has introduced stringent legislative responses whilst researchers have studied social movements and trends within Australian communities, particularly with respect to minorities. In 2008, the Scanlon Foundation, in association with Monash University and various government entities, released its findings into its survey approach to mapping social cohesion in Australia. It identified a number of spheres of exploration which it believed were essential to measuring cohesiveness of Australian communities generally including, economic, political and socio-cultural factors (Markus and Dharmalingam, 2008). This doctoral project report will explore the political sphere as identified in the Mapping Social Cohesion project and apply it to identified minority ethnic communities. The Scanlon Foundation project identified political participation as one of a number of true indicators of social cohesion. This project acknowledges that democracy in Australia is represented predominantly by two political entities representing a vast majority of constituents under a compulsory voting regime. This essay will identify the levels of political activism achieved by minority ethnic communities and access to democratic participation within the Australian political structure. It will define a ten year period from 1999 to 2009, identifying trends and issues within minority communities that have proactively and reactively promoted engagement in achieving a political voice, framed within a mainstream-dominated political system. It will research social movements and other influential factors over that period to enrich existing knowledge in relation to political participation rates across Australian communities.

The legal role of medical professionals in decisions to withhold or withdraw life-sustaining treatment : Part 1 (New South Wales)

This is the first article in a series of three that examines the legal role of medical professionals in decisions to withhold or withdraw life-sustaining treatment from adults who lack capacity. This article considers the position in New South Wales. A review of the law in this State reveals that medical professionals play significant legal roles in these decisions. However, the law is problematic in a number of respects and this is likely to impede medical professionals’ legal knowledge in this area. The article examines the level of training medical professionals receive on issues such as advance directives and substitute decision-making, and the available empirical evidence as to the state of medical professionals’ knowledge of the law at the end of life. It concludes that there are gaps in legal knowledge and that law reform is needed in New South Wales.

The legal role of medical professionals in decisions to withhold or withdraw life-sustaining treatment : Part 2 (Queensland)

This is the second article in a series of three that examines the legal role of medical professionals in decisions to withhold or withdraw life-sustaining treatment from adults who lack capacity. This article considers the position in Queensland, including the parens patriae jurisdiction of the Supreme Court. A review of the law in this State reveals that medical professionals play significant legal roles in these decisions. However, the law is problematic in a number of respects and this is likely to impede medical professionals’ legal knowledge in this area. The article examines the level of training medical professionals receive on issues such as advance health directives and substitute decision-making, and the available empirical evidence as to the state of medical professionals’ knowledge of the law at the end of life. It concludes that there are gaps in legal knowledge and that law reform is needed in Queensland.

Strategies for managing osteoarthritis

Background Although there are recommendations for the management of osteoarthritis (OA), little is known about how people with OA actually manage this chronic condition. Purpose The aims of this study were to identify the non-pharmacological and pharmacological therapies most commonly used for the management of hip or knee OA, in a community-based sample of adults, and to compare these with evidence-based recommendations. Methods A questionnaire was mailed to 2200 adult members of Arthritis Queensland living in Brisbane, Australia. It included questions about OA symptoms, management therapies and demographic characteristics. Results Of the 485 participants (192 men, 293 women) with hip or knee OA who completed the questionnaire, most had mild to moderate symptoms. Ninety-six percent of participants (aged 27–95 years) reported using at least one non-pharmacological therapy, and 78% reported using at least one pharmacological therapy. The most common currently used non-pharmacological strategy was range-of-motion exercises (men 52%, women 61%, p=0.05) and the most common frequently used pharmacological strategy was glucosamine/chondroitin (men 51%, women 60%, ns). For the most highly recommended strategies, 65% of men and 54% of women had never attended an information/education course (p=0.04), and fewer than half (46% of women and 42% of men, p=0.03) were frequent users of anti-inflammatory agents. Conclusion The findings suggest that many people with knee or hip OA do not follow the most highly endorsed of the OARSI (Osteoarthritis Research Society International) recommendations for management of OA. Health professionals should be encouraged to recommend evidence-based therapies to their patients.

The legal role of medical professionals in decisions to withhold or withdraw life-sustaining treatment : part 3 (Victoria)

This is the final article in a series of three that examines the legal role of medical professionals in decisions to withhold or withdraw life-sustaining treatment from adults who lack capacity. This article considers the position in Victoria. A review of the law in this State reveals that medical professionals play significant legal roles in these decisions. However, the law is problematic in a number of respects and this is likely to impede medical professionals’ legal knowledge in this area. The article examines the level of training that medical professionals receive on issues such as refusal of treatment certificates and substitute decision-making, and the available empirical evidence as to the state of medical professionals’ knowledge of the law at the end of life. It concludes that there are gaps in legal knowledge and that law reform is needed in Victoria. The article also draws together themes from the series as a whole, including conclusions about the need for more and better medical education and about law reform generally.

Transgression and the everyday : art and fashion in the 1970s

Former Sex Pistols manager Malcolm McLaren has said that punk fashion truly began in New York. In the 1970s, New York was home to the burgeoning punk scene, Fluxus artists and Andy Warhol’s ‘Factory’. Trace the connections between designers, artists and the musicians who became fashion icons such as Robert Mapplethorpe, Patti Smith, Malcolm McLaren, Richard Hell, Lou Reed, and Andy Warhol with Alice Payne (PhD candidate).

Rodent blood-stage Plasmodium survive in dendritic cells that infect naive mice.

Plasmodium spp. parasites cause malaria in 300 to 500 million individuals each year. Disease occurs during the blood-stage of the parasite’s life cycle, where the parasite is thought to replicate exclusively within erythrocytes. Infected individuals can also suffer relapses after several years, from Plasmodium vivax and Plasmodium ovale surviving in hepatocytes. Plasmodium falciparum and Plasmodium malariae can also persist after the original bout of infection has apparently cleared in the blood, suggesting that host cells other than erythrocytes (but not hepatocytes) may harbor these blood-stage parasites, thereby assisting their escape from host immunity. Using blood stage transgenic Plasmodium berghei-expressing GFP (PbGFP) to track parasites in host cells, we found that the parasite had a tropism for CD317+ dendritic cells. Other studies using confocal microscopy, in vitro cultures, and cell transfer studies showed that blood-stage parasites could infect, survive, and replicate within CD317+ dendritic cells, and that small numbers of these cells released parasites infectious for erythrocytes in vivo. These data have identified a unique survival strategy for blood-stage Plasmodium, which has significant implications for understanding the escape of Plasmodium spp. from immune-surveillance and for vaccine development.