The analysis of large scale data taken from the world groundnut (Arachis hypogaea L.) germplasm collection I. Two-way quantitative data

Data associated with germplasm collections are typically large and multivariate with a considerable number of descriptors measured on each of many accessions. Pattern analysis methods of clustering and ordination have been identified as techniques for statistically evaluating the available diversity in germplasm data. While used in many studies, the approaches have not dealt explicitly with the computational consequences of large data sets (i.e. greater than 5000 accessions). To consider the application of these techniques to germplasm evaluation data, 11328 accessions of groundnut (Arachis hypogaea L) from the International Research Institute for the Semi-Arid Tropics, Andhra Pradesh, India were examined. Data for nine quantitative descriptors measured in the rainy and post-rainy growing seasons were used. The ordination technique of principal component analysis was used to reduce the dimensionality of the germplasm data. The identification of phenotypically similar groups of accessions within large scale data via the computationally intensive hierarchical clustering techniques was not feasible and non-hierarchical techniques had to be used. Finite mixture models that maximise the likelihood of an accession belonging to a cluster were used to cluster the accessions in this collection. The patterns of response for the different growing seasons were found to be highly correlated. However, in relating the results to passport and other characterisation and evaluation descriptors, the observed patterns did not appear to be related to taxonomy or any other well known characteristics of groundnut.

The analysis of large scale data taken from the world groundnut (Arachis hypogaea L.) germplasm collection. II. Two-way data with mixed data types

As a sequel to a paper that dealt with the analysis of two-way quantitative data in large germplasm collections, this paper presents analytical methods appropriate for two-way data matrices consisting of mixed data types, namely, ordered multicategory and quantitative data types. While various pattern analysis techniques have been identified as suitable for analysis of the mixed data types which occur in germplasm collections, the clustering and ordination methods used often can not deal explicitly with the computational consequences of large data sets (i.e. greater than 5000 accessions) with incomplete information. However, it is shown that the ordination technique of principal component analysis and the mixture maximum likelihood method of clustering can be employed to achieve such analyses. Germplasm evaluation data for 11436 accessions of groundnut (Arachis hypogaea L.) from the International Research Institute of the Semi-Arid Tropics, Andhra Pradesh, India were examined. Data for nine quantitative descriptors measured in the post-rainy season and five ordered multicategory descriptors were used. Pattern analysis results generally indicated that the accessions could be distinguished into four regions along the continuum of growth habit (or plant erectness). Interpretation of accession membership in these regions was found to be consistent with taxonomic information, such as subspecies. Each growth habit region contained accessions from three of the most common groundnut botanical varieties. This implies that within each of the habit types there is the full range of expression for the other descriptors used in the analysis. Using these types of insights, the patterns of variability in germplasm collections can provide scientists with valuable information for their plant improvement programs.

Predictors of mental health in midlife and older women : results from the Australian Healthy Aging of Women Study

Purpose: To examine the extent to which socio-demographic characteristics, modifiable lifestyle factors and health status influence the mental health of midlife and older Australian women from the Australian Healthy Aging of Women (HOW) study. Methods: Data on health status, chronic disease and modifiable lifestyle factors were collected from a random sample of 340 women aged 40-65 years, residing in Queensland, Australia in 2011. Structural equation modelling (SEM) was used to measure the effect of a range of socio-demographic characteristics (marital status, age, income), modifiable lifestyle factors (caffeine intake, alcohol consumption, exercise, physical activity, sleep), and health markers (self-reported physical health, history of chronic illness) on the latent construct, mental health. Mental health was evaluated using the Medical Outcomes Study Short Form 12 (SF-12®) and the Center for Epidemiologic Studies Depression Scale (CES-D). Results: The model was a good fit for the data (χ2 = 40.166, df =312, p 0.125, CFI = 0.976, TLI = 0.950, RMSEA = 0.030, 90% CI = 0.000-0.053); the model suggested mental health was negatively influenced by sleep disturbance (β = -0.628), sedentary lifestyle (β = -0.137), having been diagnosed with one or more chronic illnesses (β = -0.203), and poor self-reported physical health (β = - 0.161). While mental health was associated with sleep, it was not correlated with many other lifestyle factors (BMI (β = -0.050), alcohol consumption (β = 0.079), or cigarette smoking (β = 0.008)) or background socio-demographic characteristics (age (β = 0.078), or income (β = -0.039)). Conclusion: While research suggests that it is important to engage in a range health promoting behaviours to preserve good health, we found that only sleep disturbance, physical health, chronic illness and level of physical activity predicted current mental health. However, while socio-demographic characteristics and modifiable lifestyle factors seemed to have little direct impact on mental health, they probably had an indirect effect.

Promoting law student well-being through the curriculum

The Australian tertiary sector is becoming increasingly concerned about the psychological well-being of its students.Empirical research in Australia indicates that more than one-third of law students suffer from psychological distress, and the competitive, isolated, adversarial learning environment at law school has been suggested as partly responsible (Brain and Mind Research Institute, 2009). This fellowship program has mobilised strategic change to improve the psychological health of law students. It has lead and stimulated advancement in the legal curriculum, its pedagogy, and assessment practice to better engage, motivate and support student learning of law, focussing on the potential of non-adversarial legal practice. A new conceptual framework for legal education has been developed, demonstrating the pursuit of excellence in the teaching of law, and raising the profile of learning and teaching in Australian law schools. In addition the fellowship has created a national community of practice around this issue through the Wellness Network for Law, and made significant contributions to research and scholarship in the field.

PTRF/cavin-1 neutralizes non-caveolar caveolin-1 microdomains in prostate cancer

Caveolin-1 has a complex role in prostate cancer and has been suggested to be a potential biomarker and therapeutic target. As mature caveolin-1 resides in caveolae, invaginated lipid raft domains at the plasma membrane, caveolae have been suggested as a tumor-promoting signaling platform in prostate cancer. However, caveola formation requires both caveolin-1 and cavin-1 (also known as PTRF; polymerase I and transcript release factor). Here, we examined the expression of cavin-1 in prostate epithelia and stroma using tissue microarray including normal, non-malignant and malignant prostate tissues. We found that caveolin-1 was induced without the presence of cavin-1 in advanced prostate carcinoma, an expression pattern mirrored in the PC-3 cell line. In contrast, normal prostate epithelia expressed neither caveolin-1 nor cavin-1, while prostate stroma highly expressed both caveolin-1 and cavin-1. Utilizing PC-3 cells as a suitable model for caveolin-1-positive advanced prostate cancer, we found that cavin-1 expression in PC-3 cells inhibits anchorage-independent growth, and reduces in vivo tumor growth and metastasis in an orthotopic prostate cancer xenograft mouse model. The expression of α-smooth muscle actin in stroma along with interleukin-6 (IL-6) in cancer cells was also decreased in tumors of mice bearing PC-3-cavin-1 tumor cells. To determine whether cavin-1 acts by neutralizing caveolin-1, we expressed cavin-1 in caveolin-1-negative prostate cancer LNCaP and 22Rv1 cells. Caveolin-1 but not cavin-1 expression increased anchorage-independent growth in LNCaP and 22Rv1 cells. Cavin-1 co-expression reversed caveolin-1 effects in caveolin-1-positive LNCaP cells. Taken together, these results suggest that caveolin-1 in advanced prostate cancer is present outside of caveolae, because of the lack of cavin-1 expression. Cavin-1 expression attenuates the effects of non-caveolar caveolin-1 microdomains partly via reduced IL-6 microenvironmental function. With circulating caveolin-1 as a potential biomarker for advanced prostate cancer, identification of the molecular pathways affected by cavin-1 could provide novel therapeutic targets.

Process of conducting qualitative research

In 2007 some of us were fortunate enough to be in Dundee for the Royal College of Nursing’s Annual International Nursing Research Conference. A highlight of that conference was an enactment of the process and context debate. The chair asked for volunteers and various members of the audience came forward giving the impression that they were nurses and that it was a chance selection. The audience accepted these individuals as their representatives and once they had gathered on stage we all expected the debate to begin. But the large number of researchers in the audience gave little thought to the selection and recruitment process they had just witnessed. Then the selected representatives stood up and sang A cappella. Suddenly the context was different and we questioned the process. The point was made: process or context, or both?

Orexin/hypocretin role in reward: implications for opioid and other addictions

Addiction is a devastating disorder that affects 15.3 million people worldwide. While prevalent, few effective treatments exist. Orexin receptors have been proposed as a potential target for anti-craving medications. Orexins, also known as hypocretins, are neuropeptides produced in neurons of the lateral and dorsomedial hypothalamus and perifornical area, which project widely throughout the brain. The absence of orexins in rodents and humans leads to narcolepsy. However, orexins also have an established role in reward seeking. This review will discuss some of the original studies describing the roles of the orexins in reward seeking as well as specific works that were presented at the 2013 International Narcotics Research Conference. Orexin signalling can promote drug-induced plasticity of glutamatergic synapses onto dopamine neurons of the ventral tegmental area (VTA), a brain region implicated in motivated behaviour. Additional evidence suggests that orexin signalling can also promote drug seeking by initiating an endocannabinoid-mediated synaptic depression of GABAergic inputs to the VTA, and thereby disinhibiting dopaminergic neurons. Orexin neurons co-express the inhibitory opioid peptide dynorphin. It has been proposed that orexin in the VTA may not mediate reward per se, but rather occludes the ‘anti-reward’ effects of dynorphin. Finally, orexin signalling in the prefrontal cortex and the central amygdala is implicated in reinstatement of reward seeking. This review will highlight recent work describing the role of orexin signalling in cellular processes underlying addiction-related behaviours and propose novel hypotheses for the mechanisms by which orexin signalling may impart drug seeking.

Editorial

The 2nd International Digital Human Modeling (DHM) Symposium was held at the renowned University of Michigan Transportation Research Institute (UMTRI) in Ann Arbor, Michigan in June 11–13, 2013. The symposium was co-organised by the UMTRI and Penn State University, and endorsed by the IEA Technical Committee on Human Simulation and Virtual Environments. The conference built on the very successful inaugural event DHM2011 held in Lyon two years before; and a decade of digital human modelling conferences held under the auspices of SAE International. Practitioners and scientists from 13 countries gathered to present their state-of-the-art developments and applied research, besides discussing the most recent advances in human modelling and directions for future work in DHM...

Determination of the levels of Polybrominated Diphenylethers (PBDEs) in pooled blood sera obtained from Australians aged 31-45 years

Polybrominated diphenylethers (PBDEs) are widely used as flame retardants in polymer materials, textiles, electronic boards and various other materials. Technical PBDE preparations are produced as mixtures of mainly penta-, octa- or decabrombiphenyl ethers1,2. PBDEs are structurally similar to other environmental pollutants like dioxins and PCBs, they are lipophilic and persistent compounds and are widespread in the environment. To date, no information is available on the levels of PBDEs in human serum in Australia. In 2003, more than 9000 blood samples were collected in Australia as part of the National Dioxins Program. The aim of this study was to evaluate PBDE concentrations in these samples, focusing on one age group.

Proceedings of the 3rd International Subtropical Cities Conference 2011 Subtropical Cities: Subtropical Urbanism -Beyond Climate Change

Climate has been, throughout modern history, a primary attribute for attracting residents to the “Sunshine States” of Florida (USA) and Queensland (Australia). The first major group of settlers capitalized on the winter growing season to support a year-­‐round agricultural economy. As these economies developed, the climate attracted tourism and retirement industries. Yet as Florida and Queensland have blossomed under beneficial climates, the stresses acting on the natural environment are exacting a toll. Southeast Florida and eastern Queensland are among the most vulnerable coastal metropolitan areas in the world. In these places the certainty of sea level rise is measurable with impacts, empirically observable, that will continue to increase regardless of any climate change mitigation.1 The cities of the subtropics share a series of paradoxes relating to climate, resources, environment, and culture. As the subtropical climate entices new residents and visitors there are increasing costs associated with urban infrastructure and the ravages of violent weather. The carefree lifestyle of subtropical cities is increasingly dependent on scarce water and energy resources and the flow of tangible goods that support a trade economy. The natural environment is no longer exploitable as the survival of the human environment is contingent upon the ability of natural ecosystems to absorb the impact of human actions. The quality of subtropical living is challenged by the mounting pressures of population growth and rapid urbanization yet urban form and contemporary building design fail to take advantage of the subtropical zone’s natural attributes of abundant sunshine, cooling breezes and warm temperatures. Yet, by building a global network of local knowledge, subtropical cities like Brisbane, the City of Gold Coast and Fort Lauderdale, are confidently leading the way with innovative and inventive solutions for building resiliency and adaptation to climate change. The Centre for Subtropical Design at Queensland University of Technology organized the first international Subtropical Cities conference in Brisbane, Australia, where the “fault-­‐lines” of subtropical cities at breaking points were revealed. The second conference, held in 2008, shed a more optimistic light with the theme "From fault-­‐lines to sight-­‐lines -­‐ subtropical urbanism in 20-­‐20" highlighting the leadership exemplified in the vitality of small and large works from around the subtropical world. Yet beyond these isolated local actions the need for more cooperation and collaboration was identified as the key to moving beyond the problems of the present and foreseeable future. The spirit of leadership and collaboration has taken on new force, as two institutions from opposite sides of the globe joined together to host the 3rd international conference Subtropical Cities 2011 -­‐ Subtropical Urbanism: Beyond Climate Change. The collaboration between Florida Atlantic University and the Queensland University of Technology to host this conference, for the first time in the United States, forges a new direction in international cooperative research to address urban design solutions that support sustainable behaviours, resiliency and adaptation to sea level rise, green house gas (GHG) reduction, and climate change research in the areas of architecture and urban design, planning, and public policy. With southeast Queensland and southern Florida as contributors to this global effort among subtropical urban regions that share similar challenges, opportunities, and vulnerabilities our mutual aim is to advance the development and application of local knowledge to the global problems we share. The conference attracted over 150 participants from four continents. Presentations by authors were organized into three sub-­‐themes: Cultural/Place Identity, Environment and Ecology, and Social Economics. Each of the 22 papers presented underwent a double-­‐blind peer review by a panel of international experts among the disciplines and research areas represented. The Centre for Subtropical Design at the Queensland University of Technology is leading Australia in innovative environmental design with a multi-­‐disciplinary focus on creating places that are ‘at home’ in the warm humid subtropics. The Broward Community Design Collaborative at Florida Atlantic University's College for Design and Social Inquiry has built an interdisciplinary collaboration that is unique in the United States among the units of Architecture, Urban and Regional Planning, Social Work, Public Administration, together with the College of Engineering and Computer Science, the College of Science, and the Center for Environmental Studies, to engage in funded action research through design inquiry to solve the problems of development for urban resiliency and environmental sustainment. As we move beyond debates about climate change -­‐ now acting upon us -­‐ the subtropical urban regions of the world will continue to convene to demonstrate the power of local knowledge against global forces, thereby inspiring us as we work toward everyday engagement and action that can make our cities more livable, equitable, and green.

Microscopy for the detection, identification and quantification of malaria parasites on stained thick and thin blood films in research settings

Summary This manual was developed to guide a move towards common standards for undertaking and reporting research microscopy for malaria parasite detection, identification and quantification. It contains procedures based on agreed quality assurance standards for research malaria microscopy defined at a consultation of: TDR, the Special Programme for Research and Training in Tropical Diseases; the Worldwide Antimalarial Resistance Network (WWARN), United Kingdom; the Foundation for Innovative New Diagnostics (FIND), Switzerland; the Centers for Disease Control and Prevention (CDC), USA; the Kenya Medical Research Institute (KEMRI) and later expanded to include Amref Health Africa (Kenya); the Eijkman-Oxford Clinical Research Unit (EOCRU), Indonesia; Institut Pasteur du Cambodge (IPC); Institut de recherche pour le Développement (IRD), Senegal; the Global Good and Intellectual Ventures Laboratory (GG-IVL), USA; the Mahidol-Oxford Tropical Medicine Research Unit (MORU), Thailand; Queensland University of Technology (QUT), Australia, and the Shoklo Malaria Research Unit (SMRU), Thailand. These collaborating institutions commit to adhering to these standards in published research studies. It is hoped that they will form a solid basis for the wider adoption of standardized reference microscopy protocols for malaria research.

Differential interaction between the C2B domain of synaptotagmin-I and the Drosophila stonedA and stonedB proteins

The stoned locus in Drosophila encodes two proteins StonedA (STNA) and StonedB (STNB), both of which have been suggested to act as adaptins in mediating synaptic vesicle recycling. A combination of immunological, genetic and biochemical studies have shown an interaction of STNA and STNB with the C2B domain of Synaptotagmin-I (SYT-1), an integral synaptic vesicle protein that mediates Ca2+-dependent exocytosis, as well as endocytosis. The C2B domain of SYT-1 contains an AP-2 binding site that controls the size of recycled vesicles, and a C-terminal tryptophan-containing motif that acts as an internalization signal. Investigation of SYT-1 mutations in Drosophila has shown that altering the Ca2+ binding region of the C2B domain, results in a reduction in the rate of vesicle recycling, implicating this region in SYT-I endocytosis. In this poster, we report the molecular dissection of the interactions between the STNA and STNB proteins and the C2B domain of SYT-1. Deletion of the AP-2 binding site decreased the binding of both STNA and STNB. However, C-terminal deletions of the C2B domain significantly increased STNB binding. In contrast, the same C-terminal deletions reduced the affinity of the C2B domain for STNA. The possible interactions of both STNB and STNA with the Ca2+ binding region of SYT-1 will be also investigated.

From Kafka to KAFTA: Intellectual property, and the Korea-Australia free trade agreement

This paper provides a critical examination of the intellectual property sections of the Korea-Australia Free Trade Agreement 2014. Chapter 13 of the Korea-Australia Free Trade Agreement 2014 deals with the subject of intellectual property law. The Chapter covers such topics as the purposes and objectives of intellectual property law; copyright law; trade mark law; patent law; and intellectual property enforcement. The Joint Standing Committee on Treaties in the Australian Parliament highlighted the controversy surrounding this chapter of the agreement: The intellectual property rights chapter of KAFTA has drawn considerable attention from academics and stakeholders regarding the proposed need for changes to Australian intellectual property law and the inclusion of intellectual property in the definition of investment with regard to the investor-state dispute mechanism. Other concerns raised with the Committee include the prescriptive nature of the chapter, the lack of recognition of the broader public interests of intellectual property rights, and possible changes to fair use provisions. Article 13.1.1 of the Korea-Australia Free Trade Agreement 2014 provides that: ‘Each Party recognises the importance of adequate and effective protection of intellectual property rights, while ensuring that measures to enforce those rights do not themselves become barriers to legitimate trade.’ This is an unsatisfactory description of the objectives and purposes of intellectual property law in both Australia and Korea. There is a failure to properly consider the range of public purposes served by intellectual property law – such as providing for access to knowledge, promoting competition and innovation, protecting consumer rights, and allowing for the protection of public health, food security, and the environment. Such a statement of principles and objectives detracts from the declaration in the TRIPS Agreement 1994 of the public interest objectives to be served by intellectual property. Chapter 11 of the Korea-Australia Free Trade Agreement 2014 is an investment chapter, with an investor-state dispute settlement regime. This chapter is highly controversial – given the international debate over investor-state dispute settlement; the Australian context for the debate; and the text of the Korea-Australia Free Trade Agreement 2014. In April 2014, the United Nations Conference on Trade and Development (UNCTAD) released a report on Recent Developments in Investor-State Dispute Settlement. The overall figures are staggering. UNCTAD reports a significant growth in investment-state dispute settlement, across a wide array of different fields of public regulation. Given the broad definition of investment, intellectual property owners will be able to use the investor-state dispute settlement regime in the Korea-Australia Free Trade Agreement 2014. This will have significant implications for all the various disciplines of intellectual property – including copyright law, trade mark law, and patent law.

Complex Symbolic Sequence Encodings for Predictive Monitoring of Business Processes

This paper addresses the problem of predicting the outcome of an ongoing case of a business process based on event logs. In this setting, the outcome of a case may refer for example to the achievement of a performance objective or the fulfillment of a compliance rule upon completion of the case. Given a log consisting of traces of completed cases, given a trace of an ongoing case, and given two or more possible out- comes (e.g., a positive and a negative outcome), the paper addresses the problem of determining the most likely outcome for the case in question. Previous approaches to this problem are largely based on simple symbolic sequence classification, meaning that they extract features from traces seen as sequences of event labels, and use these features to construct a classifier for runtime prediction. In doing so, these approaches ignore the data payload associated to each event. This paper approaches the problem from a different angle by treating traces as complex symbolic sequences, that is, sequences of events each carrying a data payload. In this context, the paper outlines different feature encodings of complex symbolic sequences and compares their predictive accuracy on real-life business process event logs.

Talking green: From Oz to Oz

This paper is an extension of Talking Green in Red States: Stories from the Great Plains (Gibson et al., 2014) that examined the communication strategies of planners involved in sustainability planning initiatives in the U.S. Great Plains. We expand these narratives beyond the Great Plains to Queensland, Australia by interviewing planners about their experiences when communicating and deliberating about issues of sustainability. Using a semi-formal structure, interviews are conducted as casual “coffee talks” (Maynard-Moody & Musheno, 2003). Together, these collected stories help us to understand how planners are “talking green” in conservative political atmospheres, across vastly differing geographies using an international comparative framework described by Reimer et al. (2014). The paper presents comparisons between the collected narratives, concerning similarities and differences in regard to the nuances of sustainability planning dialog. We relate the lessons learned about communication strategies of planners working in sustainability in Kansas and Queensland to the broader discourse of planning and politics, communicative planning and planning as storytelling, as they relate to sustainability planning in challenging situations. From this paper, the audience will better understand how: 1) to discuss environmental and sustainable planning in communities that have varying levels of distrust and suspicion towards these concepts; 2) to develop strategies to work around these planning communication issues, and; 3) international context affects these communication challenges.