Prediction of IBD based on population history for fine gene mapping

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBDL), among individuals without pedigree, given information on surrounding markers and population history. These IBDL probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD L are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.

Small business entity tax concessions : through the eyes of the practitioner

Australia’s small business sector has pursued often-competing imperatives of simplicity, equity and efficiency in the income tax regime (particularly focusing on the notion of simplicity) over the last decade. In 2001, there was an attempt to provide such simplification and reduce the compliance burden faced by Australian small businesses through the ‘simplified tax system’ (‘STS’). However, despite amendments over the years, the regime is much criticised. This article explores how the STS (now known as the ‘small business entity’ regime or ‘SBE’) is utilised from the perspective of tax practitioners, by analysing their recommendations to small business clients in respect of the regime. The results indicate that practitioners believe the regime did nothing to simplify the tax system for small businesses or reduce tax compliance costs. Indeed, the practitioners believed that the introduction of small business concessions had actually achieved the opposite result — it had increased tax compliance costs for their small business clients. However, tax practitioners still recommend the regime highly because it minimises their client’s tax liability.

Towards a right to sustainable energy

Energy represents the cornerstone of modern life. However, current patterns of energy production are unsustainable. This is true for both the developed and developing worlds. In this context, this paper considers how, from a conceptual perspective, the law can contribute to more sustainable patterns of energy production can be addressed. The approach that this paper adopts is to consider two of the most important concepts that are relevant to the governance of modern environmental and societal challenges: human dignity and sustainable development. It is within this context that this paper contends that the convergence of these concepts provides the platform for a novel approach to encourage the sustainable production of energy by way of a ‘right to sustainable energy’. With this in mind, this paper considers the forum in which a right to sustainable energy may be developed and outlines the content of the proposed right.

A quasi-maximum likelihood method for estimating the parameters of multivariate diffusions

A quasi-maximum likelihood procedure for estimating the parameters of multi-dimensional diffusions is developed in which the transitional density is a multivariate Gaussian density with first and second moments approximating the true moments of the unknown density. For affine drift and diffusion functions, the moments are exactly those of the true transitional density and for nonlinear drift and diffusion functions the approximation is extremely good and is as effective as alternative methods based on likelihood approximations. The estimation procedure generalises to models with latent factors. A conditioning procedure is developed that allows parameter estimation in the absence of proxies.

Achieving high reliability for ambiguity resolutions with multiple GNSS constellations

Global Navigation Satellite Systems (GNSS)-based observation systems can provide high precision positioning and navigation solutions in real time, in the order of subcentimetre if we make use of carrier phase measurements in the differential mode and deal with all the bias and noise terms well. However, these carrier phase measurements are ambiguous due to unknown, integer numbers of cycles. One key challenge in the differential carrier phase mode is to fix the integer ambiguities correctly. On the other hand, in the safety of life or liability-critical applications, such as for vehicle safety positioning and aviation, not only is high accuracy required, but also the reliability requirement is important. This PhD research studies to achieve high reliability for ambiguity resolution (AR) in a multi-GNSS environment. GNSS ambiguity estimation and validation problems are the focus of the research effort. Particularly, we study the case of multiple constellations that include initial to full operations of foreseeable Galileo, GLONASS and Compass and QZSS navigation systems from next few years to the end of the decade. Since real observation data is only available from GPS and GLONASS systems, the simulation method named Virtual Galileo Constellation (VGC) is applied to generate observational data from another constellation in the data analysis. In addition, both full ambiguity resolution (FAR) and partial ambiguity resolution (PAR) algorithms are used in processing single and dual constellation data. Firstly, a brief overview of related work on AR methods and reliability theory is given. Next, a modified inverse integer Cholesky decorrelation method and its performance on AR are presented. Subsequently, a new measure of decorrelation performance called orthogonality defect is introduced and compared with other measures. Furthermore, a new AR scheme considering the ambiguity validation requirement in the control of the search space size is proposed to improve the search efficiency. With respect to the reliability of AR, we also discuss the computation of the ambiguity success rate (ASR) and confirm that the success rate computed with the integer bootstrapping method is quite a sharp approximation to the actual integer least-squares (ILS) method success rate. The advantages of multi-GNSS constellations are examined in terms of the PAR technique involving the predefined ASR. Finally, a novel satellite selection algorithm for reliable ambiguity resolution called SARA is developed. In summary, the study demonstrats that when the ASR is close to one, the reliability of AR can be guaranteed and the ambiguity validation is effective. The work then focuses on new strategies to improve the ASR, including a partial ambiguity resolution procedure with a predefined success rate and a novel satellite selection strategy with a high success rate. The proposed strategies bring significant benefits of multi-GNSS signals to real-time high precision and high reliability positioning services.

Re-framing infrastructure investment decision-making processes : a preliminary scoping study for urban flood risk management in Jakarta, Indonesia

Jakarta, Indonesia’s chronic housing shortage poses multiple challenges for contemporary policy-makers. While it may be in the city’s interest to increase the availability of housing, there is limited land to do so. Market pressures, in tandem with government’s desire for housing availability, demand consideration of even marginal lands, such as those within floodplains, for development. Increasingly, planning for a flood resilient Jakarta is complicated by a number of factors, including: the city is highly urbanized and land use data is limited; flood management is technically complex, creating potential barriers to engagement for both decision-makers and the public; inherent uncertainty exists throughout modelling efforts, central to management; and risk and liability for infrastructure investments is unclear. These obstacles require localized watershed-level participatory planning to address risks of flooding where possible and reduce the likelihood that informal settlements occur in areas of extreme risk. This paper presents a preliminary scoping study for determination of an effective participatory planning method to encourage more resilient development. First, the scoping study provides background relevant to the challenges faced in planning for contemporary Jakarta. Second, the study examines the current use of decision-support tools, such as Geographic Information Systems (GIS), in planning for Jakarta. Existing capacity in the use of GIS allows for consideration of the use of an emerging method of community consultation - Multi-Criteria Decision-Making (MCDM) support systems infused with geospatial information - to aid in engagement with the public and improve decision-making outcomes. While these methods have been used in Australia to promote stakeholder engagement in urban intensification, the planned research will be an early introduction of the method to Indonesia. As a consequence of this intervention, it is expected that planning activities will result in a more resilient city, capable of engaging with disaster risk management in a more effective manner.

Wrongful birth : assessment of damages in 2013

More than 10 years have passed since the High Court of Australia confirmed the recoverability of damages for the cost of raising a child, in the well-known decision in Cattanach v Melchior. Yet a number of aspects of the assessment of such “wrongful birth” damages had not been the subject of a comprehensive court ruling. The recent decision in Waller v James was widely anticipated as potentially providing a comprehensive discussion of the principles relevant to the assessment of damages in wrongful birth cases. However, given a finding on causation adverse to the plaintiffs, the trial judge held that it was unnecessary to determine the quantum of damages. Justice Hislop did, however, make some comments in relation to the assessment of damages. This article focuses mostly on the argued damages issues relating to the costs of raising the child and the trial judge’s comments regarding the same. The Waller v James claim was issued before the enactment of the Health Care Liability Act 2001 (NSW) and the Civil Liability Act 2002 (NSW). Although the case was therefore decided according to the “common law”, as explained below, his Honour’s comments may be of relevance to more recent claims governed by the civil liability legislation in New South Wales, Queensland and South Australia.

Overstepping the fiduciary mark

The decision of Justice Boddice in The Public Trustee of Queensland (as Litigation Guardian for ADF) v Ban & Anor is the latest in a series of Supreme Court actions arising out of Ms Ban’s management of the affairs of her long-time elderly friend, ADF. Following on from an earlier decision in which it was determined that Ms Ban held her share of funds in a joint bank account with ADF on trust for him, this most recent case concerned a claim for an account of funds withdrawn from that account on the basis that as trustee Ms Ban owed fiduciary duties to ADF. The purpose of the accounting was to determine whether any withdrawals had been made in breach of trust, which would give rise to equitable remedies. The primary question for determination was therefore whether the withdrawals were applied for the benefit of ADF. Having regard to all the circumstances of the case, his Honour found that although some transactions were for ADF’s benefit, substantial withdrawals, (including a significant portion of a $700,000 transfer), were not applied for his benefit, and were therefore made in breach of fiduciary obligation, giving rise to equitable rights and remedies.

Pleading intention

This article considers the scope of the application of the civil liability legislation, an issue which is still being clarified by the courts, despite the passage of some ten years since the enactment of the non-uniform civil liability legislation across Australia. The introduction of the civil liability legislation has made more important the pleading of intention, in addition to negligence, so as to maximise damages awards. This involves pleading torts traditionally referred to as intentional torts – particularly trespass to the person. Such an approach is attractive for plaintiffs because, in several jurisdictions, tort claims which plead intention have been excluded from the operation of the legislative restrictions on the quantum of damages awards, and prohibitions on exemplary and aggravated damages. This approach reflects the policy that those who intend the harmful consequences of their actions should be held fully responsible.

Calligraphy and causation : two obstetric management cases - Hirst v Sydney South West Area Health and King v Western Sydney local health network

Two recent decisions of the Supreme Court of New South Wales in the context of obstetric management have highlighted firstly, the importance of keeping legible, accurate and detailed medical records; and secondly, the challenges faced by those seeking to establish causation, particularly where epidemiological evidence is relied upon...

Monocular vision based autonomous navigation for a cost-effective MAV in GPS-denied environments

In this paper, we present a monocular vision based autonomous navigation system for Micro Aerial Vehicles (MAVs) in GPS-denied environments. The major drawback of monocular systems is that the depth scale of the scene can not be determined without prior knowledge or other sensors. To address this problem, we minimize a cost function consisting of a drift-free altitude measurement and up-to-scale position estimate obtained using the visual sensor. We evaluate the scale estimator, state estimator and controller performance by comparing with ground truth data acquired using a motion capture system. All resources including source code, tutorial documentation and system models are available online.

The linking of plate tectonics and evolutionary divergence

It is exciting to be living at a time when the big questions in biology can be investigated using modern genetics and computing [1]. Bauzà-Ribot et al.[2] take on one of the fundamental drivers of biodiversity, the effect of continental drift in the formation of the world’s biota 3 and 4, employing next-generation sequencing of whole mitochondrial genomes and modern Bayesian relaxed molecular clock analysis. Bauzà-Ribot et al.[2] conclude that vicariance via plate tectonics best explains the genetic divergence between subterranean metacrangonyctid amphipods currently found on islands separated by the Atlantic Ocean. This finding is a big deal in biogeography, and science generally [3], as many other presumed biotic tectonic divergences have been explained as probably due to more recent transoceanic dispersal events [4]. However, molecular clocks can be problematic 5 and 6 and we have identified three issues with the analyses of Bauzà-Ribot et al.[2] that cast serious doubt on their results and conclusions. When we reanalyzed their mitochondrial data and attempted to account for problems with calibration 5 and 6, modeling rates across branches 5 and 7 and substitution saturation [5], we inferred a much younger date for their key node. This implies either a later trans-Atlantic dispersal of these crustaceans, or more likely a series of later invasions of freshwaters from a common marine ancestor, but either way probably not ancient tectonic plate movements.

What the plaintiff would have done in informed consent cases

Both at common law and under the various civil liability acts, in deciding liability for breach of duty, the plaintiff always bears the onus of proving, on the balance of probabilities, any fact relevant to the issue of causation. For plaintiffs in medical negligence claims founded on negligent failure to provide sufficient information (informed consent cases), this onus involves persuading the court to make a favourable determination as to what a particular patient would have done (from a subjective perspective) in the hypothetical situation of the defendant not being negligent (that is, in the event that the medical practitioner had provided sufficient information to the patient)

Fraud risk and the visibility of carbon

In recent years, carbon has been increasingly rendered ‘visible’ both discursively and through political processes that have imbued it with economic value. Greenhouse gas (GHG) emissions have been constructed as social and environmental costs and their reduction or avoidance as social and economic gain. The ‘marketisation’ of carbon, which has been facilitated through various compliance schemes such as the European Union Emissions Trading Scheme (EU ETS), the Kyoto Protocol, the proposed Australian Emissions Reduction Scheme and through the voluntary carbon credit market, have attempted to bring carbon into the ‘foreground’ as an economic liability and/or opportunity. Accompanying the increasing economic visibility of carbon are reports of frauds and scams – the ‘gaming of carbon markets’(Chan 2010). As Lohmann (2010: 21) points out, ‘what are conventionally classed as scams or frauds are an inevitable feature of carbon offset markets, not something that could be eliminated by regulation targeting the specific businesses or state agencies involved’. This paper critiques the disparate discourses of fraud risk in carbon markets and examines cases of fraud within emerging landscapes of green criminology.

Complete mitochondrial genome sequencing reveals novel haplotypes in a Polynesian population

The high risk of metabolic disease traits in Polynesians may be partly explained by elevated prevalence of genetic variants involved in energy metabolism. The genetics of Polynesian populations has been shaped by island hoping migration events which have possibly favoured thrifty genes. The aim of this study was to sequence the mitochondrial genome in a group of Maoris in an effort to characterise genome variation in this Polynesian population for use in future disease association studies. We sequenced the complete mitochondrial genomes of 20 non-admixed Maori subjects using Affymetrix technology. DNA diversity analyses showed the Maori group exhibited reduced mitochondrial genome diversity compared to other worldwide populations, which is consistent with historical bottleneck and founder effects. Global phylogenetic analysis positioned these Maori subjects specifically within mitochondrial haplogroup - B4a1a1. Interestingly, we identified several novel variants that collectively form new and unique Maori motifs – B4a1a1c, B4a1a1a3 and B4a1a1a5. Compared to ancestral populations we observed an increased frequency of non-synonymous coding variants of several mitochondrial genes in the Maori group, which may be a result of positive selection and/or genetic drift effects. In conclusion, this study reports the first complete mitochondrial genome sequence data for a Maori population. Overall, these new data reveal novel mitochondrial genome signatures in this Polynesian population and enhance the phylogenetic picture of maternal ancestry in Oceania. The increased frequency of several mitochondrial coding variants makes them good candidates for future studies aimed at assessment of metabolic disease risk in Polynesian populations.