Digital Commons Network^™

Occupational Respiratory Health Surveillance At Minara Resources, Murrin Murrin Mine Site [Journal Article], Martyn Cross, Jacques Oosthuizen

Research outputs 2013

A respiratory health study of fly-in-fly-out workers potentially exposed to airborne contaminants, and a control group, was conducted at the Murrin Murrin mine site in Western Australia. Lung function was measured in terms of validated protocols (American Thoracic Society, 1995; Miller et al, 2005). The effect of length of service, as well as work area/department on lung function was established. Repeat lung function tests were conducted after approximately two years, in order to measure decrements over time. Furthermore, testing was conducted on a cohort of refinery workers prior to commencement and upon completion of their work period on-site (swing), in …

How Mean Is The Mean?, Craig P. Speelman, Marek Mcgann

Research outputs 2013

In this paper we voice concerns about the uncritical manner in which the mean is often used as a summary statistic in psychological research. We identify a number of implicit assumptions underlying the use of the mean and argue that the fragility of these assumptions should be more carefully considered. We examine some of the ways in which the potential violation of these assumptions can lead us into significant theoretical and methodological error. Illustrations of alternative models of research already extant within Psychology are used to explore methods of research less mean-dependent and suggest that a critical assessment of the …

Toward A Phen(Omen)Ology Of The Seasons: The Emergence Of The Indigenous Weather Knowledge Project (Iwkp), John Charles Ryan

Research outputs 2013

Since European settlement, the Western calendar has insufficiently accounted for the seasonal nuances and multiple temporalities of Australia. Beginning with Tim Entwistle’s recent proposal to revise the four-season Australian norm, this article traces the emergence of the Western calendar in Europe and its institutionalization ‘Down Under.’ With its emphasis on land-based calendars, the Indigenous Weather Knowledge Project (IWKP) is a partnership between Aboriginal communities and the Bureau of Meteorology aimed at preserving and promoting knowledge of the endemic seasons of Australian regions. As the most recent addition to the IWKP, the six-season Nyoongar calendar of the South-West of Western Australia …

Protected Species: Perspectives On Organisational Life, Maryam Omari, Megan Paull, Julie A. Crews

Research outputs 2013

Analogies can be drawn between a modern organisation and a complex ecosystem. In both, the players compete for scarce resources; survival often depends on how effectively an individual, organism or group capitalises on what is available to them. In natural settings, the laws of nature provide a backdrop to relationships, including where each individual or group is positioned in the hierarchy. In such settings, unusual and complex interrelationships can be formed where groups either assist or manipulate each other to survive. In organisational settings, the laws and boundaries are less clear, context specific and subject to organisational cultures and norms, …

Multi-Component Adsorption Of Benzene, Toluene, Ethylbenzene, And Xylene From Aqueous Solutions By Montmorillonite Modified With Tetradecyl Trimethyl Ammonium Bromide, Heshmatola Nourmoradi, Mehdi Khiadani, Mahnaz Nikaeen

Research outputs 2013

Multicomponent adsorption of benzene, toluene, ethylbenzene, and xylene (BTEX) was assessed in aqueous solutions by montmorillonite modified with tetradecyl trimethyl ammonium bromide (TTAB-Mt). Batch experiments were conducted to determine the influences of parameters including loading rates of surfactant, contact time, pH, adsorbate concentration, and temperature on the adsorption efficiency. Scanning electron microscope (SEM) and X-ray diffractometer (XRD) were used to determine the adsorbent properties. Results showed that the modification of the adsorbent via the surfactant causes structural changes of the adsorbent. It was found that the optimum adsorption condition achieves with the surfactant loading rate of 200 of the cation …

Indirect Measures Of Learning Transfer Between Real And Virtual Environments, Michael J. Garrett, Mark T. Mcmahon

Research outputs 2013

This paper reports on research undertaken to determine the effectiveness of a 3D simulation environment used to train mining personnel in emergency evacuation procedures, designated the Fires in Underground Mines Evacuation Simulator (FUMES). Owing to the operational constraints of the mining facility, methods for measuring learning transfer were employed which did not require real world performance evaluation. Transfer measures that examined simulator performance relative to real world experience, fidelity assessment, and appraisal of the training value of the platform were utilised. Triangulation of results across all three measures indicated the presence of learning transfer, suggesting the viability of indirect measures …

Review Of Kidney Disease Among Indigenous People, Sasha A. Stumpers, Neil J. Thomson

Research outputs 2013

Kidney disease is a significant health problem for all Australians, but severe kidney disease is more common among Indigenous people than among non- Indigenous people. In particular, the prevalence of chronic kidney disease (CKD) and the overall levels of end-stage kidney disease (ESKD) among Aboriginal and Torres Strait Islander peoples are consistently reported as significantly higher than among other Australians. Information on CKD among Indigenous Australians is available from self-reported survey data, as well as from community-based studies and screening programs [10-20] but the main focus in the literature has been on ESKD. The incidence of ESKD is especially high …

Optical Magnetometer Employing Adaptive Noise Cancellation For Unshielded Magnetocardiography, Valentina Tiporlini, Kamal Alameh

Research outputs 2013

This paper demonstrates the concept of an optical magnetometer for magnetocardiography. The magnetometer employs a standard Least-Mean-Squares (LMS) algorithm for heart magnetic field measurement within unshielded environment. Experimental results show that the algorithm can extract a weak heart signal from a much-stronger magnetic noise and detect the P, QRS, and T heart features and completely suppress the common power line noise component at 50 Hz.

A Sense Of Home: A Cultural Geography Of The Leschenault Estuary District: Report, Sandra Wooltorton

Research outputs 2013

Executive Summary

In 2012, a project was implemented to determine the place-based social values of the people of the Leschenault Estuary district. The project included a historical study, a literature review, a survey with quantitative and qualitative questions, targeted community engagement (five focus groups, six individual interviews) and a photo-elicitation study with a group of high school children.

Research Question

What is history of the relationship between people and place in the Leschenault Estuary District, and what is the relationship in 2012? What were, and what are the place-based social values of the population?

"The Worst Female Character": Criminal Underclass Women In Perth And Fremantle, 1900-1939, Leigh S. Straw

Research outputs 2013

Women charged with offences against good order in Perth and Fremantle from 1900 to 1939 faced institutionalised sexism through the courts, police, and legislation. While men were also criminalised for good order offences, women suffered a double punishment. Charged with drunkenness, being idle and disorderly, and vagrancy, female offenders were further outcast by a public discourse stereotyping them as "bad" women. The extent to which they were able to negotiate and contest this stereotyping was limited, but a subtle negotiation of female identities was possible. This article suggests that female criminal lives offer alternative ways in which to understand women …

Release Of Dissolved Organic Carbon From Seagrass Wrack And Its Implications For Trophic Connectivity, Paul S. Lavery, Kathryn M. Mcmahon, Julia Weyers, Mary C. Boyce, Carolyn Elizabeth Oldham

Research outputs 2013

The export of old leaves and stems (wrack) from seagrass meadows provides a mechanism for trophic connectivity among coastal ecosystems. As little of this wrack is consumed by mesograzers, leached dissolved organic carbon (DOC) may determine the importance of wrack as a trophic subsidy. However, few studies have examined the effect of seagrass type or age on the release of DOC or its bioavailability. We examined the amount and composition of DOC released from different wrack: Posidonia sinuosa, Amphibolis antarctica and the alga Laurencia sp. We then examined the effect of age on DOC leaching from P. sinuosa wrack. The …

Resilience In Same-Sex-Parented Families: The Lived Experience Of Adults With Gay, Lesbian, Or Bisexual Parents, Angharad E. Titlestad, Julie Ann Pooley

Research outputs 2013

Gay, lesbian, and bisexual parents experience stress, as heterocentricism and/or homonegativity permeate the Australian context. Despite challenges faced by these parents and their families, research consistently shows children raised by same-sex parents to be as psychologically healthy, and as socially and academically well-adjusted, as their peers raised in traditional heterosexual-parented families. The ability of these children to flourish despite the challenges they face highlights the resilience of this minority group. Contrary to comparative research, the current study is framed by a phenomenological approach, and utilized narrative methodology to qualitatively explore the lived experiences of the adult children of same-sex parents. …

The Psychological Benefits Of Participating In Group Singing For Members Of The General Public, Marianne D. Judd, Julie Ann Pooley

Research outputs 2013

The last decade has produced a growing number of studies examining the potential psychological benefits of singing in a choir. Studies have tended to focus on the benefits for groups that might be described as marginalized or criminal. In contrast, the current study focused on members of the general public who regularly participate in choral singing. An in-depth qualitative design was utilized to explore the meaning and importance of group singing for 10 participants. Thematic analysis based on an interpretive approach was utilized to analyse the data. Psychological benefits emerged as two themes: individual and group. A third theme, mediating …

Masculinity, Mass Consumerism And Subversive Sex: A Case Study Of Second Life's 'Zeus' Gay Club, Judith A. Elund

Research outputs 2013

This article is a case study of a Second Life region in reference to the prevailing attitudes of sexual conservatism and the growing acceptance of homosexual coupling. The site of Zeus is a contested site of legitimacy in view of tensions regarding masculinity as it applies to sex, sexuality, gender conformity and consumption practices. Furthermore, it is representative of the tensions between an acceptable, albeit conservative gay male identity, and the subversive hyper-sexual and hyper-masculine subject of desire.

Changes To Land Tenure And Pastoral Lease Ownership In Western Australia's Central Rangelands: Implications For Co-Operative, Landscape-Scale Management, Eddie J. Van Etten

Research outputs 2013

The majority of arid and semiarid land in the Western Australian pastoral zone has a long history of livestock grazing within an extensive network of predominantly family-held pastoral leases. A variety of different groups have purchased pastoral leases in the last five decades and, for many, making a profit from pastoralism is no longer a priority. For the central rangelands of Western Australia, these groups have included: government agencies, who have purchased some 9% of pastoral leases by area; private conservation organisations (<1% purchased); aboriginal communities and groups (∼7%); and mining companies (∼13%). The purchases of pastoral leases by government agencies was designed to improve the conservation status of arid-zone ecosystems, and is the first step in a process of changing land tenure to a conservation reserve. This paper summarises the extent and other characteristics of these changes in land tenure and ownership of pastoral leases, and explores the implications for land management and conservation, stemming from these changes. It demonstrates that large areas of contiguous land with no or reduced domestic stocking can now be found in many parts of these rangelands, particularly in the Coolgardie, Yalgoo and Pilbara bio-regions, with some leaseholders actively managing land for the conservation of biodiversity and restoring sites degraded through past over-grazing. In some bio-regions, such land covers considerable proportions of sub-catchments, suggesting that broad-scale conservation management and restoration objectives may be realised. It is argued that to fully realise these objectives requires effective communication and co-ordination between land managers, including sharing of ideas, view-points and resources. In particular, mining companies, now major holders of pastoral leases in Western Australia, can play an important role in contributing to and even facilitating such objectives.

Monitoring Training Loads, Stress, Immune-Endocrine Responses And Performance In Tennis Players, R.V. Gomes, A. Moreira, L. Lodo, Kazunori Nosaka, A.J. Coutts, M.S. Aoki

Research outputs 2013

The study aim was to investigate the effect of a periodised pre-season training plan on internal training load and subsequent stress tolerance, immune-endocrine responses and physical performance in tennis players. Well-trained young tennis players (n = 10) were monitored across the pre-season period, which was divided into 4 weeks of progressive overloading training and a 1-week tapering period. Weekly measures of internal training load, training monotony and stress tolerance (sources and symptoms of stress) were taken, along with salivary testosterone, cortisol and immunoglobulin A. One repetition maximum strength, running endurance, jump height and agility were assessed before and after training. …

Millennial Scale Impact On The Marine Biogeochemical Cycle Of Mercury From Early Mining On The Iberian Peninsula, Oscar Serrano Gras, A. Martinez-Cortizas, M. A. Mateo, H. Biester, R. Bindler

Research outputs 2013

The high-resolution mercury record of a Posidonia oceanica mat in the northwest Mediterranean provides an unprecedented testimony of changes in environmental mercury (Hg) loading to the coastal marine environment over the past 4315 yr BP. The period reconstructed made it possible to establish tentative preanthropogenic background Hg levels for the area (6.8!1.5 ng g–1 in bulk sediments). A small, but significant, anthropogenic Hg increase was identifiable by ~2500 yr BP, in agreement with the beginning of intense mining in Spain. Changes in the record suggest four major periods of anthropogenic Hg pollution inputs to the Mediterranean: first, during the Roman …

Using Digital Representations Of Practical Production Work For Summative Assessment, C. Paul Newhouse

Research outputs 2013

This paper presents the findings of the first phase of a three-year study investigating the efficacy of the digitisation of creative practical work as digital portfolios for the purposes of high-stakes summative assessment. At the same time the paired comparisons method of scoring was tried as an alternative to analytical rubric-based marking because we believed that it was likely that a more holistic approach to scoring would be more appropriate. Researchers created digital representations of the practical submissions of 75 Visual Arts and 82 Design students graduating from secondary school in Western Australia. These digital portfolios were scored using the …

Meta-Analysis Reveals Complex Marine Biological Responses To The Interactive Effects Of Ocean Acidification And Warming, Ben P. Harvey, Dylan Gwynn-Jones, Philippa J. Moore

Research outputs 2013

Ocean acidification and warming are considered two of the greatest threats to marine biodiversity, yet the combined effect of these stressors on marine organisms remains largely unclear. Using a meta-analytical approach, we assessed the biological responses of marine organisms to the effects of ocean acidification and warming in isolation and combination. As expected biological responses varied across taxonomic groups, life-history stages, and trophic levels, but importantly, combining stressors generally exhibited a stronger biological (either positive or negative) effect. Using a subset of orthogonal studies, we show that four of five of the biological responses measured (calcification, photosynthesis, reproduction, and survival, …

Threats And Knowledge Gaps For Ecosystem Services Provided By Kelp Forests: A Northeast Atlantic Perspective, Dan A. Smale, Michael T. Burrows, Philippa J. Moore, Nessa O'Connor, Stephen J. Hawkins

Research outputs 2013

Kelp forests along temperate and polar coastlines represent some of most diverse and productive habitats on the Earth. Here, we synthesize information from >60 years of research on the structure and functioning of kelp forest habitats in European waters, with particular emphasis on the coasts of UK and Ireland, which represents an important biogeographic transition zone that is subjected to multiple threats and stressors. We collated existing data on kelp distribution and abundance and reanalyzed these data to describe the structure of kelp forests along a spatial gradient spanning more than 10° of latitude. We then examined ecological goods and …

A Necrotic Stimulus Is Required To Maximize Matrix-Mediated Myogenesis In Mice, Drew Kuraitis, Maria Grazia Berardinelli, Erik J. Suuronen, Antonio Musaro

Research outputs 2013

Biomaterials that are similar to skeletal muscle extracellular matrix have been shown to augment regeneration in ischemic muscle. In this study, treatment with a collagen-based matrix stimulated molecular myogenesis in an mdx murine model of necrosis. Matrix-treated animals ran ≥ 40% further, demonstrating functional regeneration, and expressed increased levels of myogenic transcripts. By contrast, matrix treatment was unable to induce transcriptional or functional changes in an MLC/SOD1G93A atrophic mouse model. In vitro, satellite cells were cultured under standard conditions, on matrix, in the presence of myocyte debris (to simulate a necrotic-like environment) or with both matrix and necrotic stimuli. Exposure …

The Genetic Contribution Of Cidea Polymorphisms, Haplotypes And Loci Interaction To Obesity In A Han Chinese Population, Jingjing Wu, Ling Zhang, Jie Zhang, Ying Dai, Lili Bian, Manshu Song, Alyce C. Russell, Wei Wang

Research outputs 2013

To investigate the association of tag-SNPs and haplotype structures of the CIDEA gene with obesity in a Han Chinese population. Five single nucleotide polymorphisms (SNPs) (rs1154588/V115F, rs4796955/SNP1, rs8092502/SNP2, rs12962340/SNP3 and rs7230480/SNP4) in the CIDEA gene were genotyped in a case-control study. Genotyping was performed using the sequenom matrixassisted laser desorption/ionization time-of-flight mass spectrometry iPLEX platform. There were significant differences between the obese and control groups in genotype distributions of V115F (P>0.001), SNP1 (P = 0.006) and SNP2 (P = 0.005). Carriers of V115F-TT, SNP1-GG and SNP2-CC genotypes had a 2.84-fold (95 % CI 1.73-4.66), 2.19-fold (95 % CI 1.09-4.38) …

The 6th Computational Structural Bioinformatics Workshop Introduction, Jing He, Amarda Shehu, Nurit Haspel, Brian Chen

Computer Science Faculty Publications

No abstract provided.

Estimating Loop Length From Cryoem Images At Medium Resolutions, Andrew Mcknight, Dong Si, Kamal Al Nasr, Andrey Chemikov, Nikos Chrisochoides, Jing He

Computer Science Faculty Publications

Background: De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein.

Results: We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was …

Image-Level And Group-Level Models For Drosophila Gene Expression Pattern Annotation, Quian Sun, Sherin Muckatira, Lei Yuan, Shuiwang Ji, Stuart Newfeld, Sudhir Kumar, Jieping Ye

Computer Science Faculty Publications

Background: Drosophila melanogaster has been established as a model organism for investigating the developmental gene interactions. The spatio-temporal gene expression patterns of Drosophila melanogaster can be visualized by in situ hybridization and documented as digital images. Automated and efficient tools for analyzing these expression images will provide biological insights into the gene functions, interactions, and networks. To facilitate pattern recognition and comparison, many web-based resources have been created to conduct comparative analysis based on the body part keywords and the associated images. With the fast accumulation of images from high-throughput techniques, manual inspection of images will impose a serious impediment …

Computational Genetic Neuroanatomy Of The Developing Mouse Brain: Dimensionality Reduction, Visualization, And Clustering, Shuiwang Ji

Computer Science Faculty Publications

Background: The structured organization of cells in the brain plays a key role in its functional efficiency. This delicate organization is the consequence of unique molecular identity of each cell gradually established by precise spatiotemporal gene expression control during development. Currently, studies on the molecular-structural association are beginning to reveal how the spatiotemporal gene expression patterns are related to cellular differentiation and structural development.

Results: In this article, we aim at a global, data-driven study of the relationship between gene expressions and neuroanatomy in the developing mouse brain. To enable visual explorations of the high-dimensional data, we map the in …

Dinosolve: A Protein Disulfide Bonding Prediction Server Using Context-Based Features To Enhance Prediction Accuracy, Ashraf Yaseen, Yaohang Li

Computer Science Faculty Publications

Background: Disulfide bonds play an important role in protein folding and structure stability. Accurately predicting disulfide bonds from protein sequences is important for modeling the structural and functional characteristics of many proteins.

Methods: In this work, we introduce an approach of enhancing disulfide bonding prediction accuracy by taking advantage of context-based features. We firstly derive the first-order and second-order mean-force potentials according to the amino acid environment around the cysteine residues from large number of cysteine samples. The mean-force potentials are integrated as context-based scores to estimate the favorability of a cysteine residue in disulfide bonding state as well as …

A Mesh Generation And Machine Learning Framework For Drosophila Gene Expression Pattern Image Analysis, Wenlu Zhang, Daming Feng, Rongjian Li, Andrey Chernikov, Nikos Chrisochoides, Christopher Osgood, Charlotte Konikoff, Stuart Newfeld, Sudhir Kumar, Shuiwang Ji

Computer Science Faculty Publications

Background: Multicellular organisms consist of cells of many different types that are established during development. Each type of cell is characterized by the unique combination of expressed gene products as a result of spatiotemporal gene regulation. Currently, a fundamental challenge in regulatory biology is to elucidate the gene expression controls that generate the complex body plans during development. Recent advances in high-throughput biotechnologies have generated spatiotemporal expression patterns for thousands of genes in the model organism fruit fly Drosophila melanogaster. Existing qualitative methods enhanced by a quantitative analysis based on computational tools we present in this paper would provide …

Conformational Sampling In Template Free Protein Loop Structure Modeling: An Overview, Yaohang Li

Computer Science Faculty Publications

Accurately modeling protein loops is an important step to predict three-dimensional structures as well as to understand functions of many proteins. Because of their high flexibility, modeling the three-dimensional structures of loops is difficult and is usually treated as a "mini protein folding problem" under geometric constraints. In the past decade, there has been remarkable progress in template-free loop structure modeling due to advances of computational methods as well as stably increasing number of known structures available in PDB. This mini review provides an overview on the recent computational approaches for loop structure modeling. In particular, we focus on the …

Intensity-Based Skeletonization Of Cryoem Gray-Scale Images Using A True Segmentation-Free Algorithm, Kamal Al Nasr, Chunmei Liu, Mugizi Rwebangira, Legand Burge, Jing He

Computer Science Faculty Publications

Cryo-electron microscopy is an experimental technique that is able to produce 3D gray-scale images of protein molecules. In contrast to other experimental techniques, cryo-electron microscopy is capable of visualizing large molecular complexes such as viruses and ribosomes. At medium resolution, the positions of the atoms are not visible and the process cannot proceed. The medium-resolution images produced by cryo-electron microscopy are used to derive the atomic structure of the proteins in de novo modeling. The skeletons of the 3D gray-scale images are used to interpret important information that is helpful in de novo modeling. Unfortunately, not all features of the …