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.

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.

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.

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.

Single crystal raman spectroscopy of natural paulmooreite Pb2As2O5 and in comparison with the synthesised analogue

The single crystal Raman spectra of natural mineral paulmooreite Pb2As2O5 from the Långban locality, Filipstad district, Värmland province, Sweden are presented for the first time. It is a monoclinic mineral containing an isolated [As2O5]4-. Depolarised and single crystal spectra of the natural and synthetic sample compare favorably and are characterized by strong bands around 186 and 140 cm-1 and three medium bands at 800 – 700 cm-1. Band assignments were made based on band symmetry and spectral comparison between experimental band positions and those resulting from Hartree-Fock calculation of an isolated [As2O5]4- ion. Spectral comparison was also made with lead arsenites such as synthetic PbAs2O4 and Pb2(AsO2)3Cl and natural finnemanite in order to determine the contribution of the terminal and bridging O in paulmooreite. Bands at 760 – 733 cm-1 were assigned to terminal As-O vibrations, whereas stretches of the bridging O occur at 562 and 503 cm-1. The single crystal spectra showed good mode separation, allowing bands to be assigned a symmetry species of Ag or Bg.

Strategic project evaluation for open pit mining ventures using real options and allied econometric techniques

Open pit mine operations are complex businesses that demand a constant assessment of risk. This is because the value of a mine project is typically influenced by many underlying economic and physical uncertainties, such as metal prices, metal grades, costs, schedules, quantities, and environmental issues, among others, which are not known with much certainty at the beginning of the project. Hence, mining projects present a considerable challenge to those involved in associated investment decisions, such as the owners of the mine and other stakeholders. In general terms, when an option exists to acquire a new or operating mining project, , the owners and stock holders of the mine project need to know the value of the mining project, which is the fundamental criterion for making final decisions about going ahead with the venture capital. However, obtaining the mine project’s value is not an easy task. The reason for this is that sophisticated valuation and mine optimisation techniques, which combine advanced theories in geostatistics, statistics, engineering, economics and finance, among others, need to be used by the mine analyst or mine planner in order to assess and quantify the existing uncertainty and, consequently, the risk involved in the project investment. Furthermore, current valuation and mine optimisation techniques do not complement each other. That is valuation techniques based on real options (RO) analysis assume an expected (constant) metal grade and ore tonnage during a specified period, while mine optimisation (MO) techniques assume expected (constant) metal prices and mining costs. These assumptions are not totally correct since both sources of uncertainty—that of the orebody (metal grade and reserves of mineral), and that about the future behaviour of metal prices and mining costs—are the ones that have great impact on the value of any mining project. Consequently, the key objective of this thesis is twofold. The first objective consists of analysing and understanding the main sources of uncertainty in an open pit mining project, such as the orebody (in situ metal grade), mining costs and metal price uncertainties, and their effect on the final project value. The second objective consists of breaking down the wall of isolation between economic valuation and mine optimisation techniques in order to generate a novel open pit mine evaluation framework called the ―Integrated Valuation / Optimisation Framework (IVOF)‖. One important characteristic of this new framework is that it incorporates the RO and MO valuation techniques into a single integrated process that quantifies and describes uncertainty and risk in a mine project evaluation process, giving a more realistic estimate of the project’s value. To achieve this, novel and advanced engineering and econometric methods are used to integrate financial and geological uncertainty into dynamic risk forecasting measures. The proposed mine valuation/optimisation technique is then applied to a real gold disseminated open pit mine deposit to estimate its value in the face of orebody, mining costs and metal price uncertainties.

Estimation of energy saving of commercial building by living wall and green facade in sub-tropical climate of Australia

This paper investigates energy saving potential of commercial building by living wall and green façade system using Envelope Thermal Transfer Value (ETTV) equation in Sub-tropical climate of Australia. Energy saving of four commercial buildings was quantified by applying living wall and green façade system to the west facing wall. A field experimental facility, from which temperature data of living wall system was collected, was used to quantify wall temperatures and heat gain under controlled conditions. The experimental parameters were accumulated with extensive data of existing commercial building to quantify energy saving. Based on temperature data of living wall system comprised of Australian native plants, equivalent temperature of living wall system has been computed. Then, shading coefficient of plants in green façade system has been included in mathematical equation and in graphical analysis. To minimize the air-conditioned load of commercial building, therefore to minimize the heat gain of commercial building, an analysis of building heat gain reduction by living wall and green façade system has been performed. Overall, cooling energy performance of commercial building before and after living wall and green façade system application has been examined. The quantified energy saving showed that only living wall system on opaque part of west facing wall can save 8-13 % of cooling energy consumption where as only green façade system on opaque part of west facing wall can save 9.5-18% cooling energy consumption of commercial building. Again, green façade system on fenestration system on west facing wall can save 28-35 % of cooling energy consumption where as combination of both living wall on opaque part of west facing wall and green façade on fenestration system on west facing wall can save 35-40% cooling energy consumption of commercial building in sub-tropical climate of Australia.

Hydrothermal synthesis of single crystallin strontium titanate nanocubes

Strontium titanate nanocubes with an average edge length of 150mm have been successfully synthesized from a simple hydrothermal system. Characterization techniques such as X-ray powder diffraction analysis, scanning electron microscopy and energy-dispersive analysis of X-rays were used to investigate the products. The results showed that as-prepared powders are pure SrTiO3 with cubic shape, which consists with the growth habit of its intrinsic crystal structure. These uniform nanocubes with high crystallinity will exhibit superior physical properties in the practical applications. Furthermore, during the experimental process, it has been found that the dilute acid washing process is very important to obtain high pure SrTiO3.

Investigation of cooling energy performance of commercial building in sub-tropical climate through the application of green roof and living wall

This paper investigates cooling energy performance of commercial building before and after green roof and living wall application based on integrated building heat gain model developed from Overall Thermal Transfer Value (OTTV) of building wall and steady state heat transfer process of roof in sub-tropical climate. Using the modelled equation and eQUEST energy simulation tool, commercial building envelope parameters and relevant heat gain parameters have been accumulated to analyse the heat gain and cooling energy consumption of commercial building. Real life commercial building envelope and air-conditioned load data for the sub-tropical climate zone have been collected and compared with the modelled analysis. Relevant temperature data required for living wall and green roof analysis have been collected from experimental setup comprised of both green roof and west facing living wall. Then, Commercial building heat flux and cooling energy performance before and after green roof and living wall application have been scrutinized.

Muro de las Lagrimas (wall of tears): Living with dementia; family experience of loss and grief

This brief paper will introduce a new theoretical framework or model which may be useful for putting a structure around the theme of ageing and its accompanying grief and loss. It is especially appropriate in the context of counselling families living with dementia, including those individuals with a diagnosis of alzheimers disease. The paper describes the origin of the Spanish expressions of the `wall of tears’ and `house of tears’ and involves an historical narrative of the first author as context to the framework.