Impacts of traditional husbandry practices on exploitable levels of genetic diversity in cultured 'Tra' catfish (Pangasianodon hypophthalmus) in the Mekong Delta, Vietnam

Sutchi catfish (Pangasianodon hypophthalmus) – known more universally by the Vietnamese name ‘Tra’ is an economically important freshwater fish in the Mekong Delta in Vietnam that constitutes an important food resource. Artificial propagation technology for Tra catfish has only recently been developed along the main branches of the Mekong River where more than 60% of the local human population participate in fishing or aquaculture. Extensive support for catfish culture in general, and that of Tra (P. hypophthalmus) in particular, has been provided by the Vietnamese government to increase both the scale of production and to develop international export markets. In 2006, total Vietnamese catfish exports reached approximately 286,602 metric tons (MT) and were valued at 736.87 $M with a number of large new export destinations being developed. Total value of production from catfish culture has been predicted to increase to approximately USD 1 billion by 2020. While freshwater catfish culture in Vietnam has a promising future, concerns have been raised about long-term quality of fry and the effectiveness of current brood stock management practices, issues that have been largely neglected to date. In this study, four DNA markers (microsatellite loci: CB4, CB7, CB12 and CB13) that were developed specifically for Tra (P. hypophthalmus) in an earlier study were applied to examine the genetic quality of artificially propagated Tra fry in the Mekong Delta in Vietnam. The goals of the study were to assess: (i) how well available levels of genetic variation in Tra brood stock used for artificial propagation in the Mekong Delta of Vietnam (breeders from three private hatcheries and Research Institute of Aquaculture No2 (RIA2) founders) has been conserved; and (ii) whether or not genetic diversity had declined significantly over time in a stock improvement program for Tra catfish at RIA2. A secondary issue addressed was how genetic markers could best be used to assist industry development. DNA was extracted from fins of catfish collected from the two main branches of the Mekong River inf Vietnam, three private hatcheries and samples from the Tra improvement program at RIA2. Study outcomes: i) Genetic diversity estimates for Tra brood stock samples were similar to, and slightly higher than, wild reference samples. In addition, the relative contribution by breeders to fry in commercial private hatcheries strongly suggest that the true Ne is likely to be significantly less than the breeder numbers used; ii) in a stock improvement program for Tra catfish at RIA2, no significant differences were detected in gene frequencies among generations (FST=0.021, P=0.036>0.002 after Bonferroni correction); and only small differences were observed in alleles frequencies among sample populations. To date, genetic markers have not been applied in the Tra catfish industry, but in the current project they were used to evaluate the levels of genetic variation in the Tra catfish selective breeding program at RIA2 and to undertake genetic correlations between genetic marker and trait variation. While no associations were detected using only four loci, they analysis provided training in the practical applications of the use of molecular markers in aquaculture in general, and in Tra culture, in particular.

Systematics of the Ustilago-Sporisorium-Macalpinomyces complex of smut fungi

Smut fungi are important pathogens of grasses, including the cultivated crops maize, sorghum and sugarcane. Typically, smut fungi infect the inflorescence of their host plants. Three genera of smut fungi (Ustilago, Sporisorium and Macalpinomyces) form a complex with overlapping morphological characters, making species placement problematic. For example, the newly described Macalpinomyces mackinlayi possesses a combination of morphological characters such that it cannot be unambiguously accommodated in any of the three genera. Previous attempts to define Ustilago, Sporisorium and Macalpinomyces using morphology and molecular phylogenetics have highlighted the polyphyletic nature of the genera, but have failed to produce a satisfactory taxonomic resolution. A detailed systematic study of 137 smut species in the Ustilago-Sporisorium- Macalpinomyces complex was completed in the current work. Morphological and DNA sequence data from five loci were assessed with maximum likelihood and Bayesian inference to reconstruct a phylogeny of the complex. The phylogenetic hypotheses generated were used to identify morphological synapomorphies, some of which had previously been dismissed as a useful way to delimit the complex. These synapomorphic characters are the basis for a revised taxonomic classification of the Ustilago-Sporisorium-Macalpinomyces complex, which takes into account their morphological diversity and coevolution with their grass hosts. The new classification is based on a redescription of the type genus Sporisorium, and the establishment of four genera, described from newly recognised monophyletic groups, to accommodate species expelled from Sporisorium. Over 150 taxonomic combinations have been proposed as an outcome of this investigation, which makes a rigorous and objective contribution to the fungal systematics of these important plant pathogens.

Comparison of Kenz Lifecorder EX and ActiGraph accelerometers in 10-yr-old children

A new accelerometer, the Kenz Lifecorder EX (LC; Suzuken Co. Ltd, Nagoya, Japan), offers promise as a feasible monitor alternative to the commonly used Actigraph (AG: Actigraph LLC, Fort Walton Beach, FL). Purpose: This study compared the LC and AG accelerometers and the Yamax SW-200 pedometer (DW) under free-living conditions with regard to children's steps taken and time in light-intensity physical activity (PA) and moderate to vigorous PA (MVPA). Methods: Participants (N = 31, age = 10.2 ± 0.4 yr) wore LC, AG, and DW monitors from arrival at school (7:45 a.m.) until they went to bed. Time in light and MVPA intensities were calculated using two separate intensity classifications for the LC (LC_4 and LC_5) and four classifications for the AG (AG_Treuth, AG_Puyau, AG_Trost, and AG_Freedson). Both accelerometers provided steps as outputs. DW steps were self-recorded. Repeated-measures ANOVA was used to assess overlapping monitor outputs. Results: There was no difference between DW and LC steps (Δ = 200 steps), but a nonsignificant trend was observed in the pairwise comparison between DW and AG steps (Δ = 1001 steps, P = 0.058). AG detected significantly greater steps than the LC (Δ = 801 steps, P = 0.001). Estimates of light-intensity activity minutes ranged from a low of 75.6 ± 18.4 min (LC_4) to a high of 309 ± 69.2 min (AG_Treuth). Estimates of MVPA minutes ranged from a low of 25.9 ± 9.4 min (LC_5) to a high of 112.2 ± 34.5 min (AG_Freedson). No significant differences in MVPA were seen between LC_5 and AG_Treuth (Δ = 4.9 min) or AG_Puyau (Δ = 1.7 min). Conclusion: The LC detected a comparable number of steps as the DW but significantly fewer steps than the AG in children. Current results indicate that the LC_5 and either AG_Treuth or AG_Puyau intensity derivations provide similar mean estimates of time in MVPA during-free living activity in 10-yr-old children.

Overview of the INEX 2009 Ad Hoc Track

This paper gives an overview of the INEX 2009 Ad Hoc Track. The main goals of the Ad Hoc Track were three-fold. The first goal was to investigate the impact of the collection scale and markup, by using a new collection that is again based on a the Wikipedia but is over 4 times larger, with longer articles and additional semantic annotations. For this reason the Ad Hoc track tasks stayed unchanged, and the Thorough Task of INEX 2002–2006 returns. The second goal was to study the impact of more verbose queries on retrieval effectiveness, by using the available markup as structural constraints—now using both the Wikipedia’s layout-based markup, as well as the enriched semantic markup—and by the use of phrases. The third goal was to compare different result granularities by allowing systems to retrieve XML elements, ranges of XML elements, or arbitrary passages of text. This investigates the value of the internal document structure (as provided by the XML mark-up) for retrieving relevant information. The INEX 2009 Ad Hoc Track featured four tasks: For the Thorough Task a ranked-list of results (elements or passages) by estimated relevance was needed. For the Focused Task a ranked-list of non-overlapping results (elements or passages) was needed. For the Relevant in Context Task non-overlapping results (elements or passages) were returned grouped by the article from which they came. For the Best in Context Task a single starting point (element start tag or passage start) for each article was needed. We discuss the setup of the track, and the results for the four tasks.

Melanoma cell invasiveness is regulated by miR-211 suppression of the BRN2 transcription factor

To identify microRNAs potentially involved in melanomagenesis, we compared microRNA expression profiles between melanoma cell lines and cultured melanocytes. The most differentially expressed microRNA between the normal and tumor cell lines was miR-211. We focused on this pigment-cell-enriched miRNA as it is derived from the microphthalmia-associated transcription factor (MITF)-regulated gene, TRPM1 (melastatin). We find that miR-211 expression is greatly decreased in melanoma cells and melanoblasts compared to melanocytes. Bioinformatic analysis identified a large number of potential targets of miR-211, including POU3F2 (BRN2). Inhibition of miR-211 in normal melanocytes resulted in increased BRN2 protein, indicating that endogenous miR-211 represses BRN2 in differentiated cells. Over-expression of miR-211 in melanoma cell lines changed the invasive potential of the cells in vitro through directly targeting BRN2 translation. We propose a model for the apparent non-overlapping expression levels of BRN2 and MITF in melanoma, mediated by miR-211 expression.

Atomistic exploration of deformation properties of copper nanowires with pre-existing defects

Based on the embedded atom method (EAM) and molecular dynamics (MD) method, in this paper, the tensile deformation properties of Cu nanowires (NWs) with different pre-existing defects, including single surface defects, surface bi-defects and single internal defects, are systematically studied. In-depth deformation mechanisms of NWs with pre-existing defects are also explored. It is found that Young's modulus is insensitive to different pre-existing defects, but yield strength shows an obvious decrease. Defects are observed influencing greatly on NWs' tensile deformation mechanisms, and playing a role of dislocation sources. Besides of the traditional deformation process dominated by the nucleation and propagation of partial dislocations, the generations of twins, grain boundaries, fivefold deformation twins, hexagonal close-packed (HCP) structure and phase transformation from face-centred cubic (FCC) structure to HCP structure have been triggered by pre-existing defects. It is found that surface defect intends to induce larger influence to yield strength than internal defect. Most importantly, the defect that lies on slip planes exerts larger influence than other defects. As expected, it is also found that the more or longer of the defect, the bigger influence will be induced.

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.

Connecting Diversity : Paradoxes of Multicultural Australia

Commissioned by SBS, and published in March 2006, Connecting Diversity: Paradoxes of Multicultural Australia is a follow-up study to SBS’s 2002 report, Living Diversity: Australia’s Multicultural Future. The attitudes of many younger Australians from culturally diverse backgrounds reveal paradoxes about Australian multiculturalism today. This report sheds light on their views, experiences and expectations and the role of media in their lives. Younger, culturally and linguistically diverse Australians are often the subject of mediafanned controversy about disaffection, ‘ethnic gangs’ and cultural isolation. While these controversies tend to be localised – Cronulla, Inala or Bankstown – Connecting Diversity tells a national and quite different story. This research builds upon the findings of the 2002 report, Living Diversity: Australia’s Multicultural Future, which challenged common assumptions about contemporary multicultural Australia. In an era of fragmenting media and assumed political apathy, Connecting Diversity further examines many of the findings of the earlier study, with a new focus on younger people, cultural identity and media use. Connecting Diversity reveals individual experiences and often contradictory ideas about media and diversity in Australia. Disjunctions appear to exist between an individual’s experience and their thoughts about Australia’s national identity. Multiculturalism is valued for broadening the appreciation of difference, yet this support can coexist with concerns about perceived segregation, usually ‘elsewhere’ in Australia. Younger people tend to be more comfortable with cultural difference than previous generations and cite their own diverse network of friends as one of the reasons for this. Even so, some describe experiences of racism that engender a feeling of exclusion from ‘mainstream’ society. In their everyday lives, social relationships are navigated through regular and familiar connections on the one hand, and experiences and expressions of disconnection on the other. Racism and tolerance may be expressed almost simultaneously. These disconnections are often managed through ‘practical tolerance',allowing them to negotiate these apparent contradictions. The connections can be based simultaneously on such things as work, family,religion, friendships or location. The result is a multilayered sense of personal belonging and community connection. A large number of respondents in these focus groups expressed frustration at the failings of media, especially news and current affairs coverage, yet spoke enthusiastically about the accessibility and range of media compared to what was available to previous generations. In their many forms, media remain a key ingredient of self-identification among younger Australians of culturally diverse backgrounds who are especially cynical about media and disillusioned by their perceived inability to influence issues that are important to them. These findings reveal that although they may be cynical about media messages, these younger Australians are looking for connection through media and are seeking ways to participate in meaningful ways. This raises questions about the possibilities for media to empower younger people to play a part in genuine cultural democracy. By capturing the attitudes of Australians of culturally diverse backgrounds under the age of 40, Connecting Diversity: Paradoxes of Multicultural Australia provides an insight into social trends and the generational and cultural changes that are now shaping Australia.

Fuzzy methods for analysis of microarrays and networks

Bioinformatics involves analyses of biological data such as DNA sequences, microarrays and protein-protein interaction (PPI) networks. Its two main objectives are the identification of genes or proteins and the prediction of their functions. Biological data often contain uncertain and imprecise information. Fuzzy theory provides useful tools to deal with this type of information, hence has played an important role in analyses of biological data. In this thesis, we aim to develop some new fuzzy techniques and apply them on DNA microarrays and PPI networks. We will focus on three problems: (1) clustering of microarrays; (2) identification of disease-associated genes in microarrays; and (3) identification of protein complexes in PPI networks. The first part of the thesis aims to detect, by the fuzzy C-means (FCM) method, clustering structures in DNA microarrays corrupted by noise. Because of the presence of noise, some clustering structures found in random data may not have any biological significance. In this part, we propose to combine the FCM with the empirical mode decomposition (EMD) for clustering microarray data. The purpose of EMD is to reduce, preferably to remove, the effect of noise, resulting in what is known as denoised data. We call this method the fuzzy C-means method with empirical mode decomposition (FCM-EMD). We applied this method on yeast and serum microarrays, and the silhouette values are used for assessment of the quality of clustering. The results indicate that the clustering structures of denoised data are more reasonable, implying that genes have tighter association with their clusters. Furthermore we found that the estimation of the fuzzy parameter m, which is a difficult step, can be avoided to some extent by analysing denoised microarray data. The second part aims to identify disease-associated genes from DNA microarray data which are generated under different conditions, e.g., patients and normal people. We developed a type-2 fuzzy membership (FM) function for identification of diseaseassociated genes. This approach is applied to diabetes and lung cancer data, and a comparison with the original FM test was carried out. Among the ten best-ranked genes of diabetes identified by the type-2 FM test, seven genes have been confirmed as diabetes-associated genes according to gene description information in Gene Bank and the published literature. An additional gene is further identified. Among the ten best-ranked genes identified in lung cancer data, seven are confirmed that they are associated with lung cancer or its treatment. The type-2 FM-d values are significantly different, which makes the identifications more convincing than the original FM test. The third part of the thesis aims to identify protein complexes in large interaction networks. Identification of protein complexes is crucial to understand the principles of cellular organisation and to predict protein functions. In this part, we proposed a novel method which combines the fuzzy clustering method and interaction probability to identify the overlapping and non-overlapping community structures in PPI networks, then to detect protein complexes in these sub-networks. Our method is based on both the fuzzy relation model and the graph model. We applied the method on several PPI networks and compared with a popular protein complex identification method, the clique percolation method. For the same data, we detected more protein complexes. We also applied our method on two social networks. The results showed our method works well for detecting sub-networks and give a reasonable understanding of these communities.

A deductive system for proving workflow models from operational procedures

Many modern business environments employ software to automate the delivery of workflows; whereas, workflow design and generation remains a laborious technical task for domain specialists. Several differ- ent approaches have been proposed for deriving workflow models. Some approaches rely on process data mining approaches, whereas others have proposed derivations of workflow models from operational struc- tures, domain specific knowledge or workflow model compositions from knowledge-bases. Many approaches draw on principles from automatic planning, but conceptual in context and lack mathematical justification. In this paper we present a mathematical framework for deducing tasks in workflow models from plans in mechanistic or strongly controlled work environments, with a focus around automatic plan generations. In addition, we prove an associative composition operator that permits crisp hierarchical task compositions for workflow models through a set of mathematical deduction rules. The result is a logical framework that can be used to prove tasks in workflow hierarchies from operational information about work processes and machine configurations in controlled or mechanistic work environments.

Scaffolding for integrated reflection

This paper presents some theoretical perspectives that might inform the design and development of information and communications technology (ICT) tools to support integrated (in-session) reflection and deep learning during e-learning. The role of why questioning provides the focus of discussion and is informed by the literature on critical thinking, sense-making, and reflective practice, as well as recent developments in knowledge management, computational linguistics and automated question generation. It is argued that there exists enormous scope for the development of ICT scaffolding targeted at supporting reflective practice during e-learning. The first generations of e-Portfolio tools provide some evidence for the significance of the benefits of integrating reflection into the design of ICT systems; however, following the review of a number of such systems, as well as a range of ICT applications and services designed to support e-learning, it is argued that the scope of implementation is limited.

Murray-Darling basin governance : the focus of the law

The legal arrangements for the management of the Murray-Darling Basin in Australia have changed significantly over the years. The Constitution of the Commonwealth has led to the legal arrangements for the management of the Murray-Darling Basin. The Water Act 2000 of Queensland aimed at advancing sustainable management and efficient use of water and other resources by establishing a system for the planning, allocation and use of water. The Water Management Act 2000 of New South Wales ensures the sustainable and integrated management of the water resources of the state benefiting the present and future generations. The Natural Resources Management Act 2004 of South Australia applies to water resources and to other natural resources. The Act aimed at assisting the achievement of ecologically sustainable development in the state.

Little Birung

The field of research was contemporary indigenous theatre practice. The aim of the project was to produce theatre that remained as close and true to its source as possible, in both form and content. Little Birung is the final part of a 6-year mentorship of young indigenous artist, Megan Samardin, conducted by renowned musician and composer, John Rodgers, producer Leah Cotterell and director Sean Mee. The culminating event of the mentorship was to develop to create an original music theatre piece, composed by John Rodgers and Megan Samardin, that featured both Megan’s prodigious talent as a singer and her family’s remarkable story. Creative development consisted of extensive interviews with family members, creative development workshops (supported by both State and Federal Government) and critique and input from leading indigenous creatives such as Wesley Enoch (artistic director, Queensland Theatre Company). The challenge was to keep faith with the family and their story whilst creating a work that would appeal to national/international producers and their audiences. The result is a song cycle of 12 original songs that presents an intensely personal exploration of 6 generations of Megan’s family down the maternal line, as told through Megan’s sometimes uneasy relationship with her great grandmother, Flora. Uniquely, each of the 12 songs presents the personal response of each of the women as they confronted the often-brutal consequences of institutionalised racism and government-imposed oppression. The work was produced in Cairns in 2011 as part of the Cairns Festival to substantial critical acclaim and was an official event of Cairns Indigenous Arts Fair. A revised version was successfully presented at the Judith Wright Centre, Brisbane in November 2011. As a result of the Brisbane season, Little Birung has been invited to make a presentation at the 2012 APAM (Australian Performing Arts Market) in Adelaide. Importantly, the family and the indigenous community have embraced the work and have continued their fervent support. It has strengthened them as a family and as a part of the indigenous people of Australia.

MRI study of the changes in crystalline lens shape with accommodation and ageing in humans

Magnetic Resonance Imaging was used to study changes in the crystalline lens and ciliary body with accommodation and aging. Monocular images were obtained in 15 young (19-29 years) and 15 older (60-70 years) emmetropes when viewing at far (6m) and at individual near points (14.5 to 20.9 cm) in the younger group. With accommodation, lens thickness increased (mean±95% CI: 0.33±0.06mm) by a similar magnitude to the decrease in anterior chamber depth (0.31±0.07mm) and equatorial diameter (0.32±0.04mm) with a decrease in the radius of curvature of the posterior lens surface (0.58±0.30mm). Anterior lens surface shape could not be determined due to the overlapping region with the iris. Ciliary ring diameter decreased (0.44±0.17mm) with no decrease in circumlental space or forward ciliary body movement. With aging, lens thickness increased (mean±95% CI: 0.97±0.24mm) similar in magnitude to the sum of the decrease in anterior chamber depth (0.45±0.21mm) and increase in anterior segment depth (0.52±0.23mm). Equatorial lens diameter increased (0.28±0.23mm) with no change in the posterior lens surface radius of curvature. Ciliary ring diameter decreased (0.57±0.41mm) with reduced circumlental space (0.43±0.15mm) and no forward ciliary body movement. Accommodative changes support the Helmholtz theory of accommodation including an increase in posterior lens surface curvature. Certain aspects of aging changes mimic accommodation.

Diagnosed artist : what is the understanding of 'artist' held by a person with a mental illness?

What is the understanding of ‘artist’ held by a person with a mental illness? Being diagnosed with a mental illness often results in social isolation. Art programs are often used to address this isolation, and to expedite positive mental health and wellbeing. In these programs the cultural value of art can be moderated and replaced with therapeutic meanings or used for purposes of community integration. Some individuals develop artistic identities within these programs. These artists personify representative tensions within the art world. Artists with mental illness are symbolically positioned within the history of art as holding special creative providence and, yet are also viewed as having a peripheral position outside the cultural framework of the art world. This research engaged with eight artists to determine the understanding of artist held by a person with a mental illness. Through shared activities around the curatorial aspects of an exhibition entitled "Artist Citizen" the impact of illness, culture and alterity were examined. Overlapping approaches of Community Cultural Development and Participatory Action Research have been used. A perspective of alterity is given which was apparent in transformative processes of the research. This thesis shows that alterity and difference are both important social resources as well as positions of isolation and discrimination. Finally, conclusions are presented that indicated that a more nuanced understanding of alterity offers potential to discussions of the complex experiences of a person with a mental illness to negotiate subjective constructions of an identity for participation in broader political, social, health and cultural contexts.