Marker gene elimination from transgenic barley, using co-transformation with adjacent 'twin T-DNAs' on a standard Agrobacterium transformation vector

We have tested a methodology for the elimination of the selectable marker gene after Agrobacterium-mediated transformation of barley. This involves segregation of the selectable marker gene away from the gene of interest following co-transformation using a plasmid carrying two T-DNAs, which were located adjacent to each other with no intervening region. A standard binary transformation vector was modified by insertion of a small section composed of an additional left and right T-DNA border, so that the selectable marker gene and the site for insertion of the gene of interest (GOI) were each flanked by a left and right border. Using this vector three different GOIs were transformed into barley. Analysis of transgene inheritance was facilitated by a novel and rapid assay utilizing PCR amplification from macerated leaf tissue. Co-insertion was observed in two thirds of transformants, and among these approximately one quarter had transgene inserts which segregated in the next generation to yield selectable marker-free transgenic plants. Insertion of non-T-DNA plasmid sequences was observed in only one of fourteen SMF lines tested. This technique thus provides a workable system for generating transgenic barley free from selectable marker genes, thereby obviating public concerns regarding proliferation of these genes.

Co-creating knowledge online : approaches for community artists

Forming peer alliances to share and build knowledge is an important aspect of community arts practice, and these co-creation processes are increasingly being mediated by the internet. This paper offers guidance for practitioners who are interested in better utilising the internet to connect, share, and make new knowledge. It argues that new approaches are required to foster the organising activities that underpin online co-creation, building from the premise that people have become increasingly networked as individuals rather than in groups (Rainie and Wellman 2012: 6), and that these new ways of connecting enable new modes of peer-to-peer production and exchange. This position advocates that practitioners move beyond situating the internet as a platform for dissemination and a tool for co-creating media, to embrace its knowledge collaboration potential. Drawing on a design experiment I developed to promote online knowledge co-creation, this paper suggests three development phases – developing connections, developing ideas, and developing agility – to ground six methods. They are: switching and routing, engaging in small trades of ideas with networked individuals; organising, co-ordinating networked individuals and their data; beta-release, offering ‘beta’ artifacts as knowledge trades; beta-testing, trialing and modifying other peoples ‘beta’ ideas; adapting, responding to technological disruption; and, reconfiguring, embracing opportunities offered by technological disruption. These approaches position knowledge co-creation as another capability of the community artist, along with co-creating art and media.

Back to basics: Informing the public of co-morbid physical health problems in those with mental illness

Abstract OBJECTIVE: Those with mental illness are at increased risk of physical health problems. The current study aimed to examine the information available online to the Australian public about the increased risk and consequences of physical illness in those with mental health problems and the services available to address these co-morbidities. METHODS: A structured online search was conducted with the search engine Google Australia (www.google.com.au) using generic search terms 'mental health information Australia', 'mental illness information Australia', 'depression', 'anxiety', and 'psychosis'. The direct content of websites was examined for information on the physical co-morbidities of mental illness. All external links on high-profile websites [the first five websites retrieved under each search term (n = 25)] were examined for information pertaining to physical health. RESULTS: Only 4.2% of websites informing the public about mental health contained direct content information about the increased risk of physical co-morbidities. The Australian Government's Department of Health and Ageing site did not contain any information. Of the high-profile websites, 62% had external links to resources about physical health and 55% had recommendations or resources for physical health. Most recommendations were generic. CONCLUSIONS: Relative to the seriousness of this problem, there is a paucity of information available to the public about the increased physical health risks associated with mental illness. Improved public awareness is the starting point of addressing this health inequity.

Networked identity work as project development among co-creative communities

Networked identity work is the conscious negotiation or co-creation of identity, enacted by speaking and listening across differences among multiple publics, including those real and imagined, familiar and unknown, on and offline, present and future. It is a concept I explore extensively in research with queer Digital Storytellers who share their personal stories in public places to catalyse social change (Vivienne 2013). In this article I consider distinctions between ‘story’ and ‘identity’; ‘networking’ and ‘networked identity work’ and argue that the two concepts may be usefully employed in development of co-creative community projects. Finally I consider how variable definitions of co-creativity influence project development.

Secretome and degradome profiling shows that Kallikrein-related peptidases 4, 5, 6, and 7 induce TGFβ-1 signaling in ovarian cancer cells

Kallikrein-related peptidases, in particular KLK4, 5, 6 and 7 (4-7), often have elevated expression levels in ovarian cancer. In OV-MZ-6 ovarian cancer cells, combined expression of KLK4-7 reduces cell adhesion and increases cell invasion and resistance to paclitaxel. The present work investigates how KLK4-7 shape the secreted proteome ("secretome") and proteolytic profile ("degradome") of ovarian cancer cells. The secretome comparison consistently identified >900 proteins in three replicate analyses. Expression of KLK4-7 predominantly affected the abundance of proteins involved in cell-cell communication. Among others, this includes increased levels of transforming growth factor β-1 (TGFβ-1). KLK4-7 co-transfected OV-MZ-6 cells share prominent features of elevated TGFβ-1 signaling, including increased abundance of neural cell adhesion molecule L1 (L1CAM). Augmented levels of TGFβ-1 and L1CAM upon expression of KLK4-7 were corroborated in vivo by an ovarian cancer xenograft model. The degradomic analysis showed that KLK4-7 expression mostly affected cleavage sites C-terminal to arginine, corresponding to the preference of kallikreins 4, 5 and 6. Putative kallikrein substrates include chemokines, such as growth differentiation factor 15 (GDF 15) and macrophage migration inhibitory factor (MIF). Proteolytic maturation of TGFβ-1 was also elevated. KLK4-7 have a pronounced, yet non-degrading impact on the secreted proteome, with a strong association between these proteases and TGFβ-1 signaling in tumor biology. © 2013 Federation of European Biochemical Societies.

Neutrophil oxidative burst is primed by supernatant from stored red cells : implications for Transfusion-Related Acute Lung Injury (TRALI)

Aim/Background: Transfusion-related acute lung injury (TRALI) is a potentially fatal adverse transfusion reaction. It is hypothesised to occur via a two-insult mechanism: the recipient’s underlying co-morbidity in addition to the transfusion of blood products activate neutrophils in the lung resulting in damaged endothelium and capillary leakage. Neutrophil activation may occur by antibody or non-antibody related mechanisms, with the length of storage of cellular blood products implicated in the latter. This study investigated non-antibody mediated priming and/or activation of neutrophil oxidative burst. Methods: A cytochrome C reduction assay was used to assess priming and activation of neutrophil oxidative burst by pooled supernatant (SN) from day 1 (D1; n=75) and day 42 (D42; n=113) packed red blood cells (PRBC). Pooled PRBC-SN were assessed in parallel with PAF (priming), fMLP (activating), PAF + fMLP (priming + activating) and buffer only (negative) controls. Cytochrome C reduction was measured over 30min at 37oC (inclusive of 10min priming). Neutrophil activation by PRBC-SN was assessed cf. buffer only and neutrophil priming by PRBC-SN was assessed by co-incubation with fMLP cf. fMLP alone. One-way ANOVA; Newman-Keuls post-test; p<0.05; n=10 independent assays. Results: Neither D1- nor D42- PRBC-SN alone activated neutrophil oxidative burst. In addition, D1-PRBC-SN did not prime fMLP-activated neutrophil oxidative burst. D42-PRBC-SN did, however, prime neutrophils for subsequent activation of oxidative burst by fMLP, the magnitude of response being similar to PAF (a known neutrophil priming agonist). Conclusion: These findings are consistent with the two-insult mechanism of TRALI. Factors released into the SN during PRBC storage contributed to neutrophil priming synergistically with other neutrophil stimulating agonists. This implicates PRBC storage duration as a key factor contributing to non-immune neutrophil activation in the development of TRALI in patients with pre-disposing inflammatory conditions.

The art of co-creative media : an Australian survey

This article describes how - in the processes of responding to participatory storytelling practices - community, public service, and to a lesser extent, commercial media institutions are themselves negotiated and changed. Although there are significant variations in the conditions, durability, extent, motivations and quality of these developments and their impacts, they nonetheless increase the possibilities and pathways of participatory media culture. This description first frames digital storytelling as a ‘co-creative’ media practice. It then discusses the role of community arts and cultural development (CACD) practitioners and networks as co-creative media intermediaries, and then considers their influence in Australian broadcast and Internet media. It looks at how participatory storytelling methods are evolving in the Australian context and explores some of the implications for cultural inclusion arising from a shared interest in ‘co-creative’ media methods and approaches.

Validation of an instrument to measure governance and performance on collaborative infrastructure projects

Collaborative infrastructure projects use hybrid formal and informal governance structures to manage transactions. Based on previous desk-top research, the authors identified the key mechanisms underlying project governance, and posited the performance implications of the governance (Chen et al. 2012). The current paper extends that qualitative research by testing the veracity of those findings using data from 320 Australian construction organisations. The results provide, for the first time, reliable and valid scales to measure governance and performance of collaborative projects, and the relationship between them. The results confirm seven of seven hypothesised governance mechanisms; 30 of 43 hypothesised underlying actions; eight of eight hypothesised key performance indicators; and the dual importance of formal and informal governance. A startling finding of the study was that the implementation intensity of informal mechanisms (non-contractual conditions) is a greater predictor of project performance variance than that of formal mechanisms (contractual conditions). Further, contractual conditions do not directly impact project performance; instead their impact is mediated by the non-contractual features of a project. Obligations established under the contract are not sufficient to optimise project performance.

Slicing big data - Twitter, gambling and time sensitive information

Big Data presents many challenges related to volume, whether one is interested in studying past datasets or, even more problematically, attempting to work with live streams of data. The most obvious challenge, in a ‘noisy’ environment such as contemporary social media, is to collect the pertinent information; be that information for a specific study, tweets which can inform emergency services or other responders to an ongoing crisis, or give an advantage to those involved in prediction markets. Often, such a process is iterative, with keywords and hashtags changing with the passage of time, and both collection and analytic methodologies need to be continually adapted to respond to this changing information. While many of the data sets collected and analyzed are preformed, that is they are built around a particular keyword, hashtag, or set of authors, they still contain a large volume of information, much of which is unnecessary for the current purpose and/or potentially useful for future projects. Accordingly, this panel considers methods for separating and combining data to optimize big data research and report findings to stakeholders. The first paper considers possible coding mechanisms for incoming tweets during a crisis, taking a large stream of incoming tweets and selecting which of those need to be immediately placed in front of responders, for manual filtering and possible action. The paper suggests two solutions for this, content analysis and user profiling. In the former case, aspects of the tweet are assigned a score to assess its likely relationship to the topic at hand, and the urgency of the information, whilst the latter attempts to identify those users who are either serving as amplifiers of information or are known as an authoritative source. Through these techniques, the information contained in a large dataset could be filtered down to match the expected capacity of emergency responders, and knowledge as to the core keywords or hashtags relating to the current event is constantly refined for future data collection. The second paper is also concerned with identifying significant tweets, but in this case tweets relevant to particular prediction market; tennis betting. As increasing numbers of professional sports men and women create Twitter accounts to communicate with their fans, information is being shared regarding injuries, form and emotions which have the potential to impact on future results. As has already been demonstrated with leading US sports, such information is extremely valuable. Tennis, as with American Football (NFL) and Baseball (MLB) has paid subscription services which manually filter incoming news sources, including tweets, for information valuable to gamblers, gambling operators, and fantasy sports players. However, whilst such services are still niche operations, much of the value of information is lost by the time it reaches one of these services. The paper thus considers how information could be filtered from twitter user lists and hash tag or keyword monitoring, assessing the value of the source, information, and the prediction markets to which it may relate. The third paper examines methods for collecting Twitter data and following changes in an ongoing, dynamic social movement, such as the Occupy Wall Street movement. It involves the development of technical infrastructure to collect and make the tweets available for exploration and analysis. A strategy to respond to changes in the social movement is also required or the resulting tweets will only reflect the discussions and strategies the movement used at the time the keyword list is created — in a way, keyword creation is part strategy and part art. In this paper we describe strategies for the creation of a social media archive, specifically tweets related to the Occupy Wall Street movement, and methods for continuing to adapt data collection strategies as the movement’s presence in Twitter changes over time. We also discuss the opportunities and methods to extract data smaller slices of data from an archive of social media data to support a multitude of research projects in multiple fields of study. The common theme amongst these papers is that of constructing a data set, filtering it for a specific purpose, and then using the resulting information to aid in future data collection. The intention is that through the papers presented, and subsequent discussion, the panel will inform the wider research community not only on the objectives and limitations of data collection, live analytics, and filtering, but also on current and in-development methodologies that could be adopted by those working with such datasets, and how such approaches could be customized depending on the project stakeholders.

ADCS reaches adulthood : an analysis of the conference and its community over the last eighteen years

How influential is the Australian Document Computing Symposium (ADCS)? What do ADCS articles speak about and who cites them? Who is the ADCS community and how has it evolved? This paper considers eighteen years of ADCS, investigating both the conference and its community. A content analysis of the proceedings uncovers the diversity of topics covered in ADCS and how these have changed over the years. Citation analysis reveals the impact of the papers. The number of authors and where they originate from reveal who has contributed to the conference. Finally, we generate co-author networks which reveal the collaborations within the community. These networks show how clusters of researchers form, the effect geographic location has on collaboration, and how these have evolved over time.

Methodologies for measuring research impact for a new interdisciplinary institute

Interdisciplinary research is often funded by national government initiatives or large corporate sponsorship, and as such, demands periodic reporting on the use of those funds. For reasons of accountability, governance and communication to the tax payer, knowledge of the outcomes of the research need to be measured and understood. The interdisciplinary approach to research raises many challenges for impact reporting. This presentation will consider what are the best practice workflow models and methodologies.Novel methodologies that can be added to the usual metrics of academic publications include analysis of percentage share of total publications in a subject or keyword field, calculating most cited publication in a key phrase category, analysis of who has cited or reviewed the work, and benchmarking of this data against others in that same category. At QUT, interest in how collaborative networking is trending in a research theme has led to the creation of some useful co-authorship graphs that demonstrate the network positions of authors and the strength of their scientific collaborations within a group. The scale of international collaborations is also worth including in the assessment. However, despite all of the tools and techniques available, the most useful way a researcher can help themselves and the process is to set up and maintain their researcher identifier and profile.

Cyclic mechanical strain guides capillary-like morphology in vitro

Introduction Stretching of tissue stimulates angiogenesis but increased motion at a fracture site hinders revascularisation. In vitro studies have indicated that mechanical stimuli promote angiogenic responses in endothelial cells, but can either inhibit or enhance responses when applied directly to angiogenesis assays. We anticipated that cyclic tension applied during endothelial network assembly would increase vascular structure formation up to a certain threshold. Methods Fibroblast/HUVEC co-cultures were subjected to cyclic equibiaxial strain (1 Hz; 6 h/day; 7 days) using the FlexerCell FX-4000T system and limiting rings for simultaneous application of multiple strain magnitudes (0–13%). Cells were labelled using anti-PECAM-1, and image analysis provided measures of endothelial network length and numbers of junctions. Results Cyclic stretching had no significant effect on the total length of endothelial networks (P > 0.2) but resulted in a strain-dependent decrease in branching and localised alignments of endothelial structures, which were in turn aligned with the supporting fibroblastic construct. Conclusion The organisation of endothelial networks under cyclic strain is dominated by structural adaptation to the supporting construct. It may be that, in fracture healing, the formation and integrity of the granulation tissue and callus is ultimately critical in revascularisation and its failure under severe strain conditions.

Incidental treatment effects of CBT on suicidal ideation and hopelessness

Background: Depression and alcohol misuse are among the most prevalent diagnoses in suicide fatalities. The risk posed by these disorders is exacerbated when they co-occur. Limited research has evaluated the effectiveness of common depression and alcohol treatments for the reduction of suicide vulnerability in individuals experiencing comorbidity. Methods: Participants with depressive symptoms and hazardous alcohol use were selected from two randomised controlled trials. They had received either a brief (1 session) intervention, or depression-focused cognitive behaviour therapy (CBT), alcohol-focused CBT, therapist-delivered integrated CBT, computer-delivered integrated CBT or person-centred therapy (PCT) over a 10-week period. Suicidal ideation, hopelessness, depression severity and alcohol consumption were assessed at baseline and 12-month follow-up. Results: Three hundred three participants were assessed at baseline and 12 months. Both suicidal ideation and hopelessness were associated with higher severity of depressive symptoms, but not with alcohol consumption. Suicidal ideation did not improve significantly at follow-up, with no differences between treatment conditions. Improvements in hopelessness differed between treatment conditions; hopelessness improved more in the CBT conditions compared to PCT and in single-focused CBT compared to integrated CBT. Limitations: Low retention rates may have impacted on the reliability of our findings. Combining data from two studies may have resulted in heterogeneity of samples between conditions. Conclusions: CBT appears to be associated with reductions in hopelessness in people with co-occurring depression and alcohol misuse, even when it is not the focus of treatment. Less consistent results were observed for suicidal ideation. Establishing specific procedures or therapeutic content for clinicians to monitor these outcomes may result in better management of individuals with higher vulnerability for suicide.

Randomized controlled trial of MICBT for co-existing alcohol misuse and depression : outcomes to 36-months

Integrated psychological treatment addressing co-existing alcohol misuse and depression has not been compared with single-focused treatment. This trial evaluates changes over 36 months following randomization of 284 outpatients to one of four motivational interviewing and cognitive-behavior therapy (MICBT) based interventions: (1) brief integrated intervention (BI); or BI plus 9 further sessions with (2) an integrated-, (3) alcohol-, or (4) depression-focus. Outcome measures included changes in alcohol consumption, depression (BDI-II: Beck Depression Inventory) and functioning (GAF: Global Assessment of Functioning), with average improvements from baseline of 21.8 drinks per week, 12.6 BDI-II units and 8.2 GAF units. Longer interventions tended to be more effective in reducing depression and improving functioning in the long-term, and in improving alcohol consumption in the short-term. Integrated treatment was at least as good as single-focused MICBT. Alcohol-focused treatment was as effective as depression-focused treatment at reducing depression and more effective in reducing alcohol misuse. The best approach seems to be an initial focus on both conditions followed by additional integrated- or alcohol-focused sessions.

Visual metrics for the evaluation of sensor data quality in outdoor perception

This paper proposes an experimental study of quality metrics that can be applied to visual and infrared images acquired from cameras onboard an unmanned ground vehicle (UGV). The relevance of existing metrics in this context is discussed and a novel metric is introduced. Selected metrics are evaluated on data collected by a UGV in clear and challenging environmental conditions, represented in this paper by the presence of airborne dust or smoke. An example of application is given with monocular SLAM estimating the pose of the UGV while smoke is present in the environment. It is shown that the proposed novel quality metric can be used to anticipate situations where the quality of the pose estimate will be significantly degraded due to the input image data. This leads to decisions of advantageously switching between data sources (e.g. using infrared images instead of visual images).