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.

Early intervention music therapy : reporting on a 3-year project to address needs with at-risk families

Sing & Grow is an early intervention music therapy project presented to families with additional needs, or those at risk of experiencing disadvantage due to social and/or economic circumstances that may impact on their parenting experiences. The aim of the project is to provide short term music therapy programs to families in communities where access to such services may be limited. The program is strengths-based and focuses on building upon a parent’s capacity to relate to and respond to their child’s emotional and developmental needs.

Sing & Grow : the co-existence of evaluation research and clinical practice in an early intervention music therapy project

Sing & Grow is a short term early intervention music therapy program for at risk families. Sing & Grow uses music to strengthen parent-child relationships by increasing positive parent-child interactions, assisting parents to bond with their children, and extending the repertoire of parents’ skills in relating to their child through interactive . Both the Australian and New Zealand governments are looking for evidence based research to highlight the effectiveness of funded programs in early childhood. As a government funded program, independent evaluation is a requirement of the delivery of the service. This paper explains the process involved in setting up and managing this large scale evaluation from engaging the evaluators and designing the project, to the data gathering stage. It describes the various challenges encountered and concludes that a highly collaborative and communicative partnership bet en researchers and clinicians is essential to ensure data can be gathered with minimal disturbance to clinical music therapy practice.

Reflections on music therapy with Indigenous families : cultural learning put into practice

This paper will describe the process of learning and development that occurred when the Sing & Grow prevention and early intervention project began to provide services to Indigenous families, a relatively new area or music therapy, particularly in Brisbane. The first attempt at establishing a weekly group music therapy program for Indigenous families was not as successful as anticipated; however through analysis of the contributing factors, guidelines were developed and implemented in the following program, which resulted in a positive learning experience for the families and therapists involved.

Analysis of the CDKN2A, CDKN2B and CDK4 genes in 48 Australian melanoma kindreds

Germline mutations within the cyclin-dependent kinase inhibitor 2A (CDKN2A) gene and one of its targets, the cyclin dependent kinase 4 (CDK4) gene, have been identified in a proportion of melanoma kindreds. In the case of CDK4, only one specific mutation, resulting in the substitution of a cysteine for an arginine at codon 24 (R24C), has been found to be associated with melanoma. We have previously reported the identification of germline CDKN2A mutations in 7/18 Australian melanoma kindreds and the absence of the R24C CDK4 mutation in 21 families lacking evidence of a CDKN2A mutation. The current study represents an expansion of these efforts and includes a total of 48 melanoma families from Australia. All of these families have now been screened for mutations within CDKN2A and CDK4, as well as for mutations within the CDKN2A homolog and 9p21 neighbor, the CDKN2B gene, and the alternative exon 1 (E1beta) of CDKN2A. Families lacking CDKN2A mutations, but positive for a polymorphism(s) within this gene, were further evaluated to determine if their disease was associated with transcriptional silencing of one CDKN2A allele. Overall, CDKN2A mutations were detected in 3/30 (10%) of the new kindreds. Two of these mutations have been observed previously: a 24 bp duplication at the 5' end of the gene and a G to C transversion in exon 2 resulting in an M531 substitution. A novel G to A transition in exon 2, resulting in a D108N substitution was also detected. Combined with our previous findings, we have now detected germline CDKN2A mutations in 10/48 (21%) of our melanoma kindreds. In none of the 'CDKN2A-negative' families was melanoma found to segregate with either an untranscribed CDKN2A allele, an R24C CDK4 mutation, a CDKN2B mutation, or an E1beta mutation. The last three observations suggest that these other cell cycle control genes (or alternative gene products) are either not involved at all, or to any great extent, in melanoma predisposition.

Haplotype analysis of two recurrent CDKN2A mutations in 10 melanoma families : evidence for common founders and independent mutations

Germ-line mutations in CDKN2A have been shown to predispose to cutaneous malignant melanoma. We have identified 2 new melanoma kindreds which carry a duplication of a 24bp repeat present in the 5' region of CDKN2A previously identified in melanoma families from Australia and the United States. This mutation has now been reported in 5 melanoma families from 3 continents: Europe, North America, and Australasia. The M53I mutation in exon 2 of CDKN2A has also been documented in 5 melanoma families from Australia and North America. The aim of this study was to determine whether the occurrence of the mutations in these families from geographically diverse populations represented mutation hotspots within CDKN2A or were due to common ancestors. Haplotypes of 11 microsatellite markers flanking CDKN2A were constructed in 5 families carrying the M53I mutation and 5 families carrying the 24bp duplication. There were some differences in the segregating haplotypes due primarily to recombinations and mutations within the short tandem-repeat markers; however, the data provide evidence to indicate that there were at least 3 independent 24bp duplication events and possibly only 1 original M53I mutation. This is the first study to date which indicates common founders in melanoma families from different continents.

Mutation analysis of the CDKN2A promoter in Australian melanoma families

Approximately 50% of all melanoma families worldwide show linkage to 9p21-22, but only about half of these have been shown to contain germ line CDKN2A mutations. It has been hypothesized that a proportion of these families carry mutations in the noncoding regions of CDKN2A. Several Canadian families have been reported to carry a mutation in the 5' UTR, at position -34 relative to the start site, which gives rise to a novel AUG translation initiation codon that markedly decreases translation from the wild-type AUG (Liu et al., 1999). Haplotype sharing in these Canadian families suggested that this mutation is of British origin. We sequenced 1,327 base pairs (bp) of CDKN2A, making up 1,116 bp of the 5' UTR and promoter, all of exon 1, and 61 bp of intron 1, in at least one melanoma case from 110 Australian families with three or more affected members known not to carry mutations within the p16 coding region. In addition, 431 bp upstream of the start codon was sequenced in an additional 253 affected probands from two-case melanoma families for which the CDKN2A mutation status was unknown. Several known polymorphisms at positions -33, -191, -493, and -735 were detected, in addition to four novel variants at positions 120, -252, -347, and -981 relative to the start codon. One of the probands from a two-case family was found to have the previously reported Q50R mutation. No family member was found to carry the mutation at position -34 or any other disease-associated mutation. For further investigation of noncoding CDKN2A mutations that may affect transcription, allele-specific expression analysis was carried out in 31 of the families with at least three affected members who showed either complete or "indeterminate" 9p haplotype sharing without CDKN2A exonic mutations. Reverse transcription polymerase chain reaction and automated sequencing showed expression of both CDKN2A alleles in all family members tested. The lack of CDKN2A promoter mutations and the absence of transcriptional silencing in the germ line of this cohort of families suggest that mutations in the promoter and 5' UTR play a very limited role in melanoma predisposition.

Teachers’ and parents’ perspectives of digital technology in the lives of young children

The pervasiveness of technology in the 21st Century has meant that adults and children live in a society where digital devices are integral to their everyday lives and participation in society. How we communicate, learn, work, entertain ourselves, and even shop is influenced by technology. Therefore, before children begin school they are potentially exposed to a range of learning opportunities mediated by digital devices. These devices include microwaves, mobile phones, computers, and console games such as Playstations® and iPods®. In Queensland preparatory classrooms and in the homes of these children, teachers and parents support and scaffold young children’s experiences, providing them with access to a range of tools that promote learning and provide entertainment. This paper examines teachers’ and parents’ perspectives and considers whether they are techno-optimists who advocate for and promote the inclusion of digital technology, or whether they are they techno-pessimists, who prefer to exclude digital devices from young children’s everyday experiences. An exploratory, single case study design was utilised to gather data from three teachers and ten parents of children in the preparatory year. Teacher data was collected through interviews and email correspondence. Parent data was collected from questionnaires and focus groups. All parents who responded to the research invitation were mothers. The results of data analysis identified a misalignment among adults’ perspectives. Teachers were identified as techno-optimists and parents were identified as techno-pessimists with further emergent themes particular to each category being established. This is concerning because both teachers and mothers influence young children’s experiences and numeracy knowledge, thus, a shared understanding and a common commitment to supporting young children’s use of technology would be beneficial. Further research must investigate fathers’ perspectives of digital devices and the beneficial and detrimental roles that a range of digital devices, tools, and entertainment gadgets play in 21st Century children’s lives.

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.

The development of an observation tool for use with parents with psychiatric disability and their preschool children

Community-based treatment and care of people with psychiatric disabilities has meant that they are now more likely to engage in the parenting role. This has led to the development of programs designed to enhance the parenting skills of people with psychiatric disabilities. Evaluation of these programs has been hampered by a paucity of evaluation tools. This study's aim was to develop and trial a tool that examined the parent-child interaction within a group setting, was functional and easy to use, required minimum training and equipment, and had acceptable levels of reliability and validity. The revised tool yielded a single scale with acceptable reliability. It had discriminative validity and concurrent validity with non-independent global ratings of parenting. Sensitivity to change was not investigated. The findings suggest that this method of evaluating parenting is likely to have both clinical and research utility and further investigation of the psychometric properties of the tool is warranted.

Impact of disability on families : Grandparents’ perspectives

Background Caring for a child with a disability can be a unique and challenging experience, with families often relying on informal networks for support. Often, grandparents are key support resources, yet little is known about their roles and experiences. Reporting on data collected in a larger Australian study, this article explores grandparents' experiences of caring for a child with a disability and the impact on their family relationships and quality of life. Method A qualitative purposive sampling design was utilised; semi-structured interviews were conducted with 22 grandparents (17 women, 5 men) of children with a disability. Grandparents ranged in age from 55 to 75 years old and lived within a 90-min drive of Brisbane, Australia. Interviews were transcribed and responses analysed using a thematic approach, identifying categories, themes and patterns. Findings Four key themes characterised grandparents' views about their role in the family: holding own emotions (decision to be positive), self-sacrifice (decision to put family needs first), maintaining family relationships (being the ‘go-between’) and quality of life for family in the future (concerns about the future). Conclusions Grandparents are central to family functioning and quality of life, but this contribution comes with a significant cost to their own personal well-being. Implications for policy, practice and research are discussed, particularly grandparents' fear that their family could not cope without their support.