SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

Narratives of complexity : an ethnographic exploration of resilience and wellbeing among single refugee women in Brisbane

This study aimed to explore resilience and wellbeing among a group of eight refugee women originating from several countries (mainly African) and living in Brisbane, most of whom were single mothers. To challenge mostly quantitative and gender-blind explorations of mental health concepts among refugee groups, the project sought an emic and contextual understanding of resilience and wellbeing. Established perspectives, while useful, tend to overlook the complexities of refugee mental health experiences and can neglect the dense nature of individual stories. The purpose of my study was to contest relatively simplistic narratives of mental health constructs that tend to dominate migrant and refugee studies and influence practice paradigms in the human services field. In this ethnographic exploration of mental health constructs conducted in 2008 and 2009, the use of in-depth interviews, participant observations, and visual ethnographic elements provided an opportunity for refugee women to tell their own stories. The participants’ unique narratives of pre- and post-migration experiences, shaped by specific gender, age, social, cultural and political aspects prevailing in their lives, yielded ‘thick’ ethnographic description (Geertz, 1973) of their social worlds. The findings explored in this study, namely language issues, the impact of community dynamics, and the single status of refugee women, clearly demonstrate that mental health constructs are fluid, multifaceted and complex in reality. In fact, language, community dynamics, and being a single mother, represented both opportunities and barriers in the lives of participants. In some contexts, these factors were conducive to resilience and wellbeing, while in other circumstances, these three elements acted as a hindrance to positive mental health outcomes. There are multiple dimensions to the findings, signifying that the social worlds of refugee women cannot be simplified using set definitions and neat notions of resilience and wellbeing. Instead, the intricacies and complexities embedded in the mundane of the everyday highlight novel conceptualisations of resilience and wellbeing. Based on the particular circumstances of single refugee mothers, whose experiences differ from that of married women, this thesis presents novel articulations of mental health constructs, as an alternative view to existing trends in the literature on refugee issues. Rich and multi-dimensional meanings associated with the socio-cultural determinants of mental health emerged in the process. This thesis’ findings highlight a significant gap in diasporic studies as well as simplistic assumptions about refugee women’s resettlement experiences. Single refugee women’s distinct issues are so complex and dense, that a contextual approach is critical to yield accurate depictions of their circumstances. It is therefore essential to understand refugee lived experiences within broader socio-political contexts to truly appreciate the depth of these narratives. In this manner, critical aspects salient to refugee journeys can inform different understandings of resilience, wellbeing and mental health, and shape contemporary policy and human service practice paradigms.

Aerial SLAM with a single camera using visual expectation

Micro aerial vehicles (MAVs) are a rapidly growing area of research and development in robotics. For autonomous robot operations, localization has typically been calculated using GPS, external camera arrays, or onboard range or vision sensing. In cluttered indoor or outdoor environments, onboard sensing is the only viable option. In this paper we present an appearance-based approach to visual SLAM on a flying MAV using only low quality vision. Our approach consists of a visual place recognition algorithm that operates on 1000 pixel images, a lightweight visual odometry algorithm, and a visual expectation algorithm that improves the recall of place sequences and the precision with which they are recalled as the robot flies along a similar path. Using data gathered from outdoor datasets, we show that the system is able to perform visual recognition with low quality, intermittent visual sensory data. By combining the visual algorithms with the RatSLAM system, we also demonstrate how the algorithms enable successful SLAM.

Surrogacy and IVF

While in the past surrogacy was illegal in Queensland, since June 2010 the Surrogacy Act 2010 (Qld) (“the Act”) has made altruistic surrogacy arrangements lawful in Queensland. In addition, it provides a mechanism for transfer of legal parentage from the surrogate to the person(s) wishing to have a child (the intended parent(s)). Commercial surrogacy – where a payment, reward or other material benefit of advantage (other than the reimbursement of the “birth mother’s surrogacy costs” (s11 of the Act) is made for entering into a surrogacy arrangement – remains unlawful. The paramount guiding principle underpinning the Act is that of the wellbeing and best interests of a child born as a result of surrogacy. The Surrogacy Act 2010 (Qld) allows a single person or a couple (heterosexual or same sex couples) to enter into an agreement with a woman, and her partner (if she has one), to become pregnant with the intention that the child will be relinquished to the intended parent(s). The Act also provides a mechanism for the intended parent(s) to be legally recognised as the parent(s) of the child. In order for the intended parent(s) to be legally recognised (via a parentage order, discussed below) it must be shown that the surrogacy arrangement was entered into when all the parties were over 25 years of age and the intended parent(s) are male or, in a heterosexual or lesbian couple the female(s) are not likely to conceive or give birth to a healthy child due to medical reasons. The arrangement must be entered into before the surrogate becomes pregnant and all parties must have obtained independent legal advice and counselling about the proposed arrangement, and evidence of this is required at the time a parentage order is applied for. For the purposes of the Act it does not matter how the surrogate conceives the child or if the child is genetically related to the parties. During the period of the pregnancy, the surrogate has the right to manage her pregnancy in the way she wishes. Although she cannot profit from acting as a surrogate, section 11 states that she is entitled to surrogacy costs. These include, for example, reasonable medical costs related to pregnancy and the birth of the child; counselling and legal costs associated with the surrogacy arrangement; actual lost earnings because of leave taken during pregnancy or following birth and any reasonable travel expenses incurred. The surrogacy arrangement itself is not legally enforceable; however, obligations to pay a surrogate’s surrogacy costs are enforceable unless she chooses not to relinquish the child to the intending parents. While the Act does not specifically deal with the situation where the surrogate decides she is unprepared to relinquish the child to the intended parents, there have been examples where parties have entered into these kinds of arrangements, and the arrangements have become difficult. For example, the Family Court case of Re Evelyn (1998) FLC 92–807 involved a child born to a surrogate mother who decided not to surrender her. The child was the genetic child of the surrogate mother and the husband of the couple who had contracted with the surrogate mother. Both sets of parents brought proceedings in the court, seeking that the child live with them. In hearing the application, the court applied the paramount principle of the ‘best interests of the child’. The court made clear that there is no presumption in favour of the birth mother, although in this case the court found that the child may be better placed with the surrogate mother’s family.

Single crystal Raman spectroscopy of selected arsenite, antimonite and hydroxyantimonate minerals

This thesis concentrates on the characterisation of selected arsenite, antimonite, and hydroxyantimonate minerals based on their vibrational spectra. A number of natural arsenite and antimonite minerals were studied by single crystal Raman spectroscopy in order to determine the contribution of bridging and terminal oxygen atoms to the vibrational spectra. A series of natural hydrated antimonate minerals was also compared and contrasted using single crystal Raman spectroscopy to determine the contribution of the isolated antimonate ion. The single crystal data allows each band in the spectrum to be assigned to a symmetry species. The contribution of bridging and terminal oxygen atoms in the case of the arsenite and antimonite minerals was determined by factor group analysis, the results of which are correlated with the observed symmetry species. In certain cases, synthetic analogues of a mineral and/or synthetic compounds isostructural or related to the mineral of interest were also prepared. These synthetic compounds are studied by non-oriented Raman spectroscopy to further aid band assignments of the minerals of interest. Other characterisation techniques include IR spectroscopy, SEM and XRD. From the single crystal data, it was found that good separation between different symmetry species is observed for the minerals studied.

Parental responsibility and Australian legislative attempts to curb truancy

Statistical and anecdotal evidence suggests that truancy is a significant problem for Australian schools. This paper considers the efficacy of legislative attempts to curb truancy, focussing in particular on the Queensland experience. Both Queensland legislation and the Commonwealth Improving School Enrolment and Attendance Through Welfare reform Measure (SEAM) pilot program are explained and evaluated. The paper considers in particular the utility of parental responsibility strategies as a response to truancy - under the Education (General Provisions) Act 12006 (Queensland) parents of persistent truants may be prosecuted and fined; under the SEAM initiative parents may have their social security payments suspended. Despite the availability of these seemingly draconian penalties, there is a reluctance, in practice, to hold parents accountable. The paper attempts to explain this reluctance and asks whether parental responsibility legislation can deliver a solution to truancy.

Which way from here? The spatiality of maps & navigation in first-person single-player video games

Player experience of spatiality in first-person, single-player games is informed by the maps and navigational aids provided by the game. This project uses textual analysis to examine the way these maps and navigational aids inform the experience of spatiality in Fallout 3, BioShock and BioShock 2. Spatiality is understood as trialectic, incorporating perceived, conceived and lived space, drawing on the work of Henri Lefebvre and Edward Soja. The most prominent elements of the games’ maps and navigational aids are analysed in terms of how they inform players’ experience of the games’ spaces. In particular this project examines the in-game maps these games incorporate, the waypoint navigation and fast-travel systems in Fallout 3, and the guide arrow and environmental cues in the BioShock games.

Human-specific E. coli single nucleotide polymorphism (SNP) genotypes detected in a South-East Queensland waterway, Australia

The World Health Organization recommends that the majority of water monitoring laboratories in the world should test for E. coli daily since thermotolerant coliforms and E. coli are key indicators for risk assessment of recreational waters. Recently, we developed a new SNP method for typing E. coli strains, by which human-specific genotypes were identified. Here, we report the presence of these previously described specific SNP profiles in environmental water, sourced from the Coomera River, located on South East Queensland, Australia, over a period of two years. This study tested for the presence of human-specific E. coli to ascertain whether hydrologic and anthropogenic activity plays a key role in the pollution of the investigated watershed or whether the pollution is from other sources. We found six human-specific SNP profiles and one animal-specific SNP profile consistently across sampling sites and times. We have demonstrated that our SNP genotyping method is able to rapidly identify and characterise human- and animal-specific E. coli isolates in water sources.

Punishing 'poor parents': 'Respect', 'responsibility' and parenting orders in Scotland

This article critiques the rise of parenting orders in Scotland within New Labour’s self-styled model of ‘respect’ and ‘responsibility’. It examines the emergence of parenting orders in Scotland, which became available in April 2005, and argues that Scottish local authorities are sceptical of an approach they perceive as an ideological and legislative mix premised on punitive notions of individual responsibility and justice.

Free software as a democratic principle

Software forms an important part of the interface between citizens and their government. An increasing amount of government functions are being performed, controlled, or delivered electronically. This software, like all language, is never value-neutral, but must, to some extent, reflect the values of the coder and proprietor. The move that many governments are making towards e-governance, and the increasing reliance that is being placed upon software in government, necessitates a rethinking of the relationships of power and control that are embodied in software.

Single crystal raman spectroscopy of natural finnemanite and comparison with the synthesised analogue

The single crystal Raman spectra of natural mineral finnemanite Pb5(AsO3)3Cl from the Långban locality, Filipstad district, Värmland province, Sweden are presented for the first time. It is a hexagonal mineral belonging to the ortho arsenite group, where the [AsO3]3- ion is isolated. The spectra of finnemanite are characterized by a strong band at 734 cm-1 overlying a shoulder at 726 cm-1, and broad overlapping bands in the lower wavenumber with the strongest band positioned at 174 cm-1. Band assignments were made based on band symmetry, experimental band positions from literature and DFT calculated Raman spectrum, and spectral comparison with other ortho arsenite minerals reinerite, cafarsite, and nealite and synthetic lead arsenite compounds Pb2(AsO2)3Cl, Pb2As2O5, and PbAs2O4 . The band at 734 cm-1 was assigned to υ1(AsO3), bands at 726 and 640 cm-1 assigned to υ3, 372 and 357 cm-1 to υ2, and 244, 239 and 207 cm-1 to υ4. The single crystal spectra of finnemanite showed good mode separation, allowing bands to be assigned a symmetry species of Ag, E1g, or E2g.