Echology: Making sense of data - reflections on resilient ecologies of partnership [Abstract]

The Echology: Making Sense of Data initiative seeks to break new ground in arts practice by asking artists to innovate with respect to a) the possible forms of data representation in public art and b) the artist's role in engaging publics on environmental sustainability in new urban developments. Initiated by ANAT and Carbon Arts in 2011, Echology has seen three artists selected by National competition in 2012 for Lend Lease sites across Australia. In 2013 commissioning of one of these works, the Mussel Choir by Natalie Jeremijenko, began in Melbourne's Victoria Harbour development. This emerging practice of data - driven and environmentally engaged public artwork presents multiple challenges to established systems of public arts production and management, at the same time as offering up new avenues for artists to forge new modes of collaboration. The experience of Echology and in particular, the Mussel Choir is examined here to reveal opportunities for expansion of this practice through identification of the factors that lead to a resilient 'ecology of part nership' between stakeholders that include science and technology researchers, education providers, city administrators, and urban developers.

The potential for new understandings of normal and abnormal cognition by integration of neuroimaging and behavioral data : Not an exercise in carrying coals to Newcastle

Discovering the means to prevent and cure schizophrenia is a vision that motivates many scientists. But in order to achieve this goal, we need to understand its neurobiological basis. The emergent metadiscipline of cognitive neuroscience fields an impressive array of tools that can be marshaled towards achieving this goal, including powerful new methods of imaging the brain (both structural and functional) as well as assessments of perceptual and cognitive capacities based on psychophysical procedures, experimental tasks and models developed by cognitive science. We believe that the integration of data from this array of tools offers the greatest possibilities and potential for advancing understanding of the neural basis of not only normal cognition but also the cognitive impairments that are fundamental to schizophrenia. Since sufficient expertise in the application of these tools and methods rarely reside in a single individual, or even a single laboratory, collaboration is a key element in this endeavor. Here, we review some of the products of our integrative efforts in collaboration with our colleagues on the East Coast of Australia and Pacific Rim. This research focuses on the neural basis of executive function deficits and impairments in early auditory processing in patients using various combinations of performance indices (from perceptual and cognitive paradigms), ERPs, fMRI and sMRI. In each case, integration of two or more sources of information provides more information than any one source alone by revealing new insights into structure-function relationships. Furthermore, the addition of other imaging methodologies (such as DTI) and approaches (such as computational models of cognition) offers new horizons in human brain imaging research and in understanding human behavior.

Recruiting, Sampling and Data Collection with Difficult Populations: Clients of Male Sex Workers.

Although there are many potential new insights to be gained through advancing research on the clients of male sex workers, significant social, ethical and methodological challenges to accessing this population exist. This research project case explores our attempts to recruit a population that does not typically form a cohesive or coherent 'community' and often avoids self-identifying to mitigate the stigma attached to buying sex. We used an arms-length recruitment campaign that focussed on directing potential participants to our study website, which could in turn lead them to participate in an anonymous telephone interview. Barriers to reaching male sex-work clients, however, demanded the evolution of our recruitment strategy. New technologies are part of the solution to accessing a hard-to-reach population, but they only work if researchers engage responsively. We also show how we conducted an in-depth interview with a client and discuss the value of using secondary data.

An efficient tagging data interpretation and representation scheme for item recommendation

A tag-based item recommendation method generates an ordered list of items, likely interesting to a particular user, using the users past tagging behaviour. However, the users tagging behaviour varies in different tagging systems. A potential problem in generating quality recommendation is how to build user profiles, that interprets user behaviour to be effectively used, in recommendation models. Generally, the recommendation methods are made to work with specific types of user profiles, and may not work well with different datasets. In this paper, we investigate several tagging data interpretation and representation schemes that can lead to building an effective user profile. We discuss the various benefits a scheme brings to a recommendation method by highlighting the representative features of user tagging behaviours on a specific dataset. Empirical analysis shows that each interpretation scheme forms a distinct data representation which eventually affects the recommendation result. Results on various datasets show that an interpretation scheme should be selected based on the dominant usage in the tagging data (i.e. either higher amount of tags or higher amount of items present). The usage represents the characteristic of user tagging behaviour in the system. The results also demonstrate how the scheme is able to address the cold-start user problem.

Synonymization of key pest species within the Bactrocera dorsalis species complex (Diptera: Tephritidae): Taxonomic changes based on a review of 20 years of integrative morphological, molecular, cytogenetic, behavioural and chemoecological data

Bactrocera papayae Drew & Hancock, Bactrocera philippinensis Drew & Hancock, Bactrocera carambolae Drew & Hancock, and Bactrocera invadens Drew, Tsuruta & White are four horticultural pest tephritid fruit fly species that are highly similar, morphologically and genetically, to the destructive pest, the Oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae). This similarity has rendered the discovery of reliable diagnostic characters problematic, which, in view of the economic importance of these taxa and the international trade implications, has resulted in ongoing difficulties for many areas of plant protection and food security. Consequently, a major international collaborative and integrated multidisciplinary research effort was initiated in 2009 to build upon existing literature with the specific aim of resolving biological species limits among B. papayae, B. philippinensis, B. carambolae, B. invadens and B. dorsalis to overcome constraints to pest management and international trade. Bactrocera philippinensis has recently been synonymized with B. papayae as a result of this initiative and this review corroborates that finding; however, the other names remain in use. While consistent characters have been found to reliably distinguish B. carambolae from B. dorsalis, B. invadens and B. papayae, no such characters have been found to differentiate the latter three putative species. We conclude that B. carambolae is a valid species and that the remaining taxa, B. dorsalis, B. invadens and B. papayae, represent the same species. Thus, we consider B. dorsalis (Hendel) as the senior synonym of B. papayae Drew and Hancock syn.n. and B. invadens Drew, Tsuruta & White syn.n. A redescription of B. dorsalis is provided. Given the agricultural importance of B. dorsalis, this taxonomic decision will have significant global plant biosecurity implications, affecting pest management, quarantine, international trade, postharvest treatment and basic research. Throughout the paper, we emphasize the value of independent and multidisciplinary tools in delimiting species, particularly in complicated cases involving morphologically cryptic taxa.

Memory management and parallelization of data intensive all-to-all comparison in shared-memory systems

This thesis presents a novel program parallelization technique incorporating with dynamic and static scheduling. It utilizes a problem specific pattern developed from the prior knowledge of the targeted problem abstraction. Suitable for solving complex parallelization problems such as data intensive all-to-all comparison constrained by memory, the technique delivers more robust and faster task scheduling compared to the state-of-the art techniques. Good performance is achieved from the technique in data intensive bioinformatics applications.

Using qualitative mixed methods to study small health care organizations while maximising trustworthiness and authenticity

Background The primary health care sector delivers the majority of health care in western countries through small, community-based organizations. However, research into these healthcare organizations is limited by the time constraints and pressure facing them, and the concern by staff that research is peripheral to their work. We developed Q-RARA—Qualitative Rapid Appraisal, Rigorous Analysis—to study small, primary health care organizations in a way that is efficient, acceptable to participants and methodologically rigorous. Methods Q-RARA comprises a site visit, semi-structured interviews, structured and unstructured observations, photographs, floor plans, and social scanning data. Data were collected over the course of one day per site and the qualitative analysis was integrated and iterative. Results We found Q-RARA to be acceptable to participants and effective in collecting data on organizational function in multiple sites without disrupting the practice, while maintaining a balance between speed and trustworthiness. Conclusions The Q-RARA approach is capable of providing a richly textured, rigorous understanding of the processes of the primary care practice while also allowing researchers to develop an organizational perspective. For these reasons the approach is recommended for use in small-scale organizations both within and outside the primary health care sector.

AITSL pilot projects [Queensland University of Technology : The existing school-based practices and processes for the use of NAPLAN data] Final report

This pilot project investigated the existing practices and processes of Proficient, Highly Accomplished and Lead teachers in the interpretation, analysis and implementation of National Assessment Program – Literacy and Numeracy (NAPLAN) data. A qualitative case study approach was the chosen methodology, with nine teachers across a variety of school sectors interviewed. Themes and sub-themes were identified from the participants’ interview responses revealing the ways in which Queensland teachers work with NAPLAN data. The data illuminated that generally individual schools and teachers adopted their own ways of working with data, with approaches ranging from individual/ad hoc, to hierarchical or a whole school approach. Findings also revealed that data are the responsibility of various persons from within the school hierarchy; some working with the data electronically whilst others rely on manual manipulation. Manipulation of data is used for various purposes including tracking performance, value adding and targeting programmes for specific groups of students, for example the gifted and talented. Whilst all participants had knowledge of intervention programmes and how practice could be modified, there were large inconsistencies in knowledge and skills across schools. Some see the use of data as a mechanism for accountability, whilst others mention data with regards to changing the school culture and identifying best practice. Overall, the findings showed inconsistencies in approach to focus area 5.4. Recommendations therefore include a more national approach to the use of educational data.

In silico analyses reveal common cellular pathways affected by loss of heterozygosity (LOH) events in the lymphomagenesis of Non-Hodgkin’s lymphoma (NHL)

Background The analysis of cellular networks and pathways involved in oncogenesis has increased our knowledge about the pathogenic mechanisms that underlie tumour biology and has unmasked new molecular targets that may lead to the design of better anti-cancer therapies. Recently, using a high resolution loss of heterozygosity (LOH) analysis, we identified a number of potential tumour suppressor genes (TSGs) within common LOH regions across cases suffering from two of the most common forms of Non-Hodgkin’s lymphoma (NHL), Follicular Lymphoma (FL) and Diffuse Large B-cell Lymphoma (DLBCL). From these studies LOH of the protein tyrosine phosphatase receptor type J (PTPRJ) gene was identified as a common event in the lymphomagenesis of these B-cell lymphomas. The present study aimed to determine the cellular pathways affected by the inactivation of these TSGs including PTPRJ in FL and DLBCL tumourigenesis. Results Pathway analytical approaches identified that candidate TSGs located within common LOH regions participate within cellular pathways, which may play a crucial role in FL and DLBCL lymphomagenesis (i.e., metabolic pathways). These analyses also identified genes within the interactome of PTPRJ (i.e. PTPN11 and B2M) that when inactivated in NHL may play an important role in tumourigenesis. We also detected genes that are differentially expressed in cases with and without LOH of PTPRJ, such as NFATC3 (nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3). Moreover, upregulation of the VEGF, MAPK and ERBB signalling pathways was also observed in NHL cases with LOH of PTPRJ, indicating that LOH-driving events causing inactivation of PTPRJ, apart from possibly inducing a constitutive activation of these pathways by reduction or abrogation of its dephosphorylation activity, may also induce upregulation of these pathways when inactivated. This finding implicates these pathways in the lymphomagenesis and progression of FL and DLBCL. Conclusions The evidence obtained in this research supports findings suggesting that FL and DLBCL share common pathogenic mechanisms. Also, it indicates that PTPRJ can play a crucial role in the pathogenesis of these B-cell tumours and suggests that activation of PTPRJ might be an interesting novel chemotherapeutic target for the treatment of these B-cell tumours.

Easy data, hard data : the politics and pragmatics of Twitter research after the computational turn

In this chapter, we draw out the relevant themes from a range of critical scholarship from the small body of digital media and software studies work that has focused on the politics of Twitter data and the sociotechnical means by which access is regulated. We highlight in particular the contested relationships between social media research (in both academic and non-academic contexts) and the data wholesale, retail, and analytics industries that feed on them. In the second major section of the chapter we discuss in detail the pragmatic edge of these politics in terms of what kinds of scientific research is and is not possible in the current political economy of Twitter data access. Finally, at the end of the chapter we return to the much broader implications of these issues for the politics of knowledge, demonstrating how the apparently microscopic level of how the Twitter API mediates access to Twitter data actually inscribes and influences the macro level of the global political economy of science itself, through re-inscribing institutional and traditional disciplinary privilege We conclude with some speculations about future developments in data rights and data philanthropy that may at least mitigate some of these negative impacts.

Adverse breast cancer treatment effects: The economic case for making rehabilitative programs standard of care

Purpose: The purpose of this work was to evaluate the patient-borne financial cost of common, adverse breast cancer treatment-associated effects, comparing cost across women with or without these side-effects. Methods: 287 Australian women diagnosed with early-stage breast cancer were prospectively followed starting at six months post-surgery for 12 months, with three-monthly assessment of detailed treatment-related side effects and their direct and indirect patient costs attributable to breast cancer. Bootstrapping statistics were used to analyze cost data and adjusted logistic regression was used to evaluate the association between costs and adverse events from breast cancer. Costs were inflated and converted from 2002 Australian to 2014 US dollars. Results: More than 90% of women experienced at least one adverse effect (i.e. post-surgical issue, reaction to radiotherapy, upper-body symptoms or reduced function, lymphedema, fatigue or weight gain). On average, women paid $5,636 (95%CI: $4,694, $6,577) in total costs. Women with any one of the following symptoms (fatigue, reduced upper-body function, upper-body symptoms) or women who report ≥4 adverse treatment-related effects, have 1.5 to nearly 4 times the odds of having higher healthcare costs than women who do not report these complaints (p<0.05). Conclusions: Women face substantial economic burden due to a range of treatment-related health problems, which may persist beyond the treatment period. Improving breast cancer care by incorporating prospective surveillance of treatment-related side effects, and strategies for prevention and treatment of concerns (e.g., exercise) has real potential for reducing patient-borne costs.

Practical analysis of big acoustic sensor data for environmental monitoring

Monitoring the environment with acoustic sensors is an effective method for understanding changes in ecosystems. Through extensive monitoring, large-scale, ecologically relevant, datasets can be produced that can inform environmental policy. The collection of acoustic sensor data is a solved problem; the current challenge is the management and analysis of raw audio data to produce useful datasets for ecologists. This paper presents the applied research we use to analyze big acoustic datasets. Its core contribution is the presentation of practical large-scale acoustic data analysis methodologies. We describe details of the data workflows we use to provide both citizen scientists and researchers practical access to large volumes of ecoacoustic data. Finally, we propose a work in progress large-scale architecture for analysis driven by a hybrid cloud-and-local production-grade website.

Piecing the puzzle together : enhancing the quality of road trauma surveillance through linkage of police and health data

This program of research linked police and health data collections to investigate the potential benefits for road safety in terms of enhancing the quality of data. This research has important implications for road safety because, although police collected data has historically underpinned efforts in the area, it is known that many road crashes are not reported to police and that these data lack specific injury severity information. This research shows that data linkage provides a more accurate quantification of the severity and prevalence of road crash injuries which is essential for: prioritising funding; targeting interventions; and estimating the burden and cost of road trauma.

Circulating antibodies against Plasmodium falciparum histidine-rich proteins 2 interfere with antigen detection by rapid diagnostic tests

Background Rapid diagnostic tests (RDTs) for detection of Plasmodium falciparum infection that target P. falciparum histidine-rich protein 2 (PfHRP2), a protein that circulates in the blood of patients infected with this species of malaria, are widely used to guide case management. Understanding determinants of PfHRP2 availability in circulation is therefore essential to understanding the performance of PfHRP2-detecting RDTs. Methods The possibility that pre-formed host anti-PfHRP2 antibodies may block target antigen detection, thereby causing false negative test results was investigated in this study. Results Anti-PfHRP2 antibodies were detected in 19/75 (25%) of plasma samples collected from patients with acute malaria from Cambodia, Nigeria and the Philippines, as well as in 3/28 (10.7%) asymptomatic Solomon Islands residents. Pre-incubation of plasma samples from subjects with high-titre anti-PfHRP2 antibodies with soluble PfHRP2 blocked the detection of the target antigen on two of the three brands of RDTs tested, leading to false negative results. Pre-incubation of the plasma with intact parasitized erythrocytes resulted in a reduction of band intensity at the highest parasite density, and a reduction of lower detection threshold by ten-fold on all three brands of RDTs tested. Conclusions These observations indicate possible reduced sensitivity for diagnosis of P. falciparum malaria using PfHRP2-detecting RDTs among people with high levels of specific antibodies and low density infection, as well as possible interference with tests configured to detect soluble PfHRP2 in saliva or urine samples. Further investigations are required to assess the impact of pre-formed anti-PfHRP2 antibodies on RDT performance in different transmission settings.