SwarmPS: Rapid, semi-automated single particle selection software

Single particle analysis (SPA) coupled with high-resolution electron cryo-microscopy is emerging as a powerful technique for the structure determination of membrane protein complexes and soluble macromolecular assemblies. Current estimates suggest that ∼104–105 particle projections are required to attain a 3 Å resolution 3D reconstruction (symmetry dependent). Selecting this number of molecular projections differing in size, shape and symmetry is a rate-limiting step for the automation of 3D image reconstruction. Here, we present SwarmPS, a feature rich GUI based software package to manage large scale, semi-automated particle picking projects. The software provides cross-correlation and edge-detection algorithms. Algorithm-specific parameters are transparently and automatically determined through user interaction with the image, rather than by trial and error. Other features include multiple image handling (∼102), local and global particle selection options, interactive image freezing, automatic particle centering, and full manual override to correct false positives and negatives. SwarmPS is user friendly, flexible, extensible, fast, and capable of exporting boxed out projection images, or particle coordinates, compatible with downstream image processing suites.

The promise of computational journalism

Computational journalism involves the application of software and technologies to the activities of journalism, and it draws from the fields of computer science, the social sciences, and media and communications. New technologies may enhance the traditional aims of journalism, or may initiate greater interaction between journalists and information and communication technology (ICT) specialists. The enhanced use of computing in news production is related in particular to three factors: larger government data sets becoming more widely available; the increasingly sophisticated and ubiquitous nature of software; and the developing digital economy. Drawing upon international examples, this paper argues that computational journalism techniques may provide new foundations for original investigative journalism and increase the scope for new forms of interaction with readers. Computer journalism provides a major opportunity to enhance the delivery of original investigative journalism, and to attract and retain readers online.

Neo-planning: Location-based social media to engage Australia’s new digital locals

Community engagement with time poor and seemingly apathetic citizens continues to challenge local governments. Capturing the attention of a digitally literate community who are technology and socially savvy adds a new quality to this challenge. Community engagement is resource and time intensive, yet local governments have to manage on continually tightened budgets. The benefits of assisting citizens in taking ownership in making their community and city a better place to live in collaboration with planners and local governments are well established. This study investigates a new collaborative form of civic participation and engagement for urban planning that employs in-place digital augmentation. It enhances people’s experience of physical spaces with digital technologies that are directly accessible within that space, in particular through interaction with mobile phones and public displays. The study developed and deployed a system called Discussions in Space (DIS) in conjunction with a major urban planning project in Brisbane. Planners used the system to ask local residents planning-related questions via a public screen, and passers-by sent responses via SMS or Twitter onto the screen for others to read and reflect, hence encouraging in-situ, real-time, civic discourse. The low barrier of entry proved to be successful in engaging a wide range of residents who are generally not heard due to their lack of time or interest. The system also reflected positively on the local government for reaching out in this way. Challenges and implications of the short-texted and ephemeral nature of this medium were evaluated in two focus groups with urban planners. The paper concludes with an analysis of the planners’ feedback evaluating the merits of the data generated by the system to better engage with Australia’s new digital locals.

Food(ing): between human-computer and human-food-experience

This workshop is a continuation and extension to the successful past workshops exploring the intersection of food, technology, place, and people, namely 2009 OZCHI workshop, Hungry 24/7? HCI Design for Sustainable Food Culture and Sustainable Interaction with Food, Technology, and the City [1] and 2010 CHI panel Making Food, Producing Sustainability [3]. The workshop aims to bring together experts from diverse backgrounds including academia, government, industry, and non-for-profit organisations. It specifically aims to create a space for discussion and design of innovative approaches to understanding and cultivating sustainable food practices via human-computer-interaction (HCI) as well as addressing the wider opportunities for the HCI community to engage with food as a key issue for sustainability The workshop addresses environmental, health, and social domains of sustainability in particular, by looking at various conceptual and design approaches in orchestrating sustainable interaction of people and food in and through dynamic techno-social networks.

Identity management : strengthening one-time password authentication through usability

Usability in HCI (Human-Computer Interaction) is normally understood as the simplicity and clarity with which the interaction with a computer program or a web site is designed. Identity management systems need to provide adequate usability and should have a simple and intuitive interface. The system should not only be designed to satisfy service provider requirements but it has to consider user requirements, otherwise it will lead to inconvenience and poor usability for users when managing their identities. With poor usability and a poor user interface with regard to security, it is highly likely that the system will have poor security. The rapid growth in the number of online services leads to an increasing number of different digital identities each user needs to manage. As a result, many people feel overloaded with credentials, which in turn negatively impacts their ability to manage them securely. Passwords are perhaps the most common type of credential used today. To avoid the tedious task of remembering difficult passwords, users often behave less securely by using low entropy and weak passwords. Weak passwords and bad password habits represent security threats to online services. Some solutions have been developed to eliminate the need for users to create and manage passwords. A typical solution is based on generating one-time passwords, i.e. passwords for single session or transaction usage. Unfortunately, most of these solutions do not satisfy scalability and/or usability requirements, or they are simply insecure. In this thesis, the security and usability aspects of contemporary methods for authentication based on one-time passwords (OTP) are examined and analyzed. In addition, more scalable solutions that provide a good user experience while at the same time preserving strong security are proposed.

Exploratory investigation of atmospheric total suspended particulate matter and heavy metals in urban air

Atmospheric concentration of total suspended particulate matter (TSP) and associated heavy metals are a great concern due to their adverse health impacts and contribution to stormwater pollution. This paper discusses the outcomes of a study which investigated the variation of atmospheric TSP and heavy metal concentrations with traffic and land use characteristics during weekdays and weekends. Data for this study was gathered from fifteen sites at the Gold Coast, Australia using a high volume air sampler. The study detected consistently high TSP concentrations during weekdays compared to weekends. This confirms the significant influence of traffic related sources on TSP loads during weekdays. Both traffic and land use related sources equally contribute to TSP during weekends. Almost all the measured heavy metals showed high concentration on weekdays compared to weekends indicating significant contributions from traffic related emissions. Among the heavy metals, Zn concentration was the highest followed by Pb. It is postulated that re-suspension of previously deposited reserves was the main Pb source. Soil related sources were the main contributors of Mn.

Support for energy-oriented design in the Australian context

There is a need for decision support tools that integrate energy simulation into early design in the context of Australian practice. Despite the proliferation of simulation programs in the last decade, there are no ready-to-use applications that cater specifically for the Australian climate and regulations. Furthermore, the majority of existing tools focus on achieving interaction with the design domain through model-based interoperability, and largely overlook the issue of process integration. This paper proposes an energy-oriented design environment that both accommodates the Australian context and provides interactive and iterative information exchanges that facilitate feedback between domains. It then presents the structure for DEEPA, an openly customisable system that couples parametric modelling and energy simulation software as a means of developing a decision support tool to allow designers to rapidly and flexibly assess the performance of early design alternatives. Finally, it discusses the benefits of developing a dynamic and concurrent performance evaluation process that parallels the characteristics and relationships of the design process.

Big, bigger, best? The impact of reforms on the not-for-profit sector in Queensland

Organisations within the not-for-profit sector provide services to individuals and groups that government and for-profit organisations cannot or will not consider. The not-for-profit sector has come to be a vibrant and rich agglomeration of services and programs that operate under a myriad of philosophical stances, service orientation, client groupings and operational capacities. In Australia these organisations and services are providing social support and service assistance to many people in the community; often targeting their assistance to the most difficult of clients. Initially, in undertaking this role, the not-for-profit sector received limited sponsorship from government. Over time governments assumed greater responsibility in the form of service grants to particular groups: ‘the worthy poor’. More recently, they have entered into contractual service agreements with the not-for-profit sector, which specify the nature of the outcomes to be achieved and, to a degree, the way in which the services will be provided. A consequence of this growing shift to a more marketised model of service contracting, often offered-up under the label of enhanced collaborative practice, has been increased competitiveness between agencies that had previously worked well together (Keast and Brown, 2006). Another trend emerging from the market approach is the entrance of for-profit providers. These larger organisations have higher levels of organisational capacity with considerable organisational slack to allow them to adopt new service roles. Shaped almost as ‘shadow governments’ they appear to be a strong preference for governments looking for greater accountability of outcomes and an easier way to control the interaction with the conventional not-for-profit sector. The question is will governments’ apparent preference for larger organisational arrangements lead to the demise of the vibrancy of the not-for-profit sector and impact on service provision to those people who fall outside of the remit of the new service providers? To address this issue, this paper uses information gleaned from a state-wide survey of not-for-profit organisations in Queensland, Australia which included organisational size, operational scope, funding arrangements and governance/management approaches. Supplementing this information is qualitative data derived from 17 focus groups and 120 interviews conducted over ten years of study of this sector. The findings contribute to greater understanding of the practice and theory of the future provision of social services.

Impact of a data warehouse model for improved decision-making process in healthcare

The health system is one sector dealing with a deluge of complex data. Many healthcare organisations struggle to utilise these volumes of health data effectively and efficiently. Also, there are many healthcare organisations, which still have stand-alone systems, not integrated for management of information and decision-making. This shows, there is a need for an effective system to capture, collate and distribute this health data. Therefore, implementing the data warehouse concept in healthcare is potentially one of the solutions to integrate health data. Data warehousing has been used to support business intelligence and decision-making in many other sectors such as the engineering, defence and retail sectors. The research problem that is going to be addressed is, "how can data warehousing assist the decision-making process in healthcare". To address this problem the researcher has narrowed an investigation focusing on a cardiac surgery unit. This research used the cardiac surgery unit at the Prince Charles Hospital (TPCH) as the case study. The cardiac surgery unit at TPCH uses a stand-alone database of patient clinical data, which supports clinical audit, service management and research functions. However, much of the time, the interaction between the cardiac surgery unit information system with other units is minimal. There is a limited and basic two-way interaction with other clinical and administrative databases at TPCH which support decision-making processes. The aims of this research are to investigate what decision-making issues are faced by the healthcare professionals with the current information systems and how decision-making might be improved within this healthcare setting by implementing an aligned data warehouse model or models. As a part of the research the researcher will propose and develop a suitable data warehouse prototype based on the cardiac surgery unit needs and integrating the Intensive Care Unit database, Clinical Costing unit database (Transition II) and Quality and Safety unit database [electronic discharge summary (e-DS)]. The goal is to improve the current decision-making processes. The main objectives of this research are to improve access to integrated clinical and financial data, providing potentially better information for decision-making for both improved from the questionnaire and by referring to the literature, the results indicate a centralised data warehouse model for the cardiac surgery unit at this stage. A centralised data warehouse model addresses current needs and can also be upgraded to an enterprise wide warehouse model or federated data warehouse model as discussed in the many consulted publications. The data warehouse prototype was able to be developed using SAS enterprise data integration studio 4.2 and the data was analysed using SAS enterprise edition 4.3. In the final stage, the data warehouse prototype was evaluated by collecting feedback from the end users. This was achieved by using output created from the data warehouse prototype as examples of the data desired and possible in a data warehouse environment. According to the feedback collected from the end users, implementation of a data warehouse was seen to be a useful tool to inform management options, provide a more complete representation of factors related to a decision scenario and potentially reduce information product development time. However, there are many constraints exist in this research. For example the technical issues such as data incompatibilities, integration of the cardiac surgery database and e-DS database servers and also, Queensland Health information restrictions (Queensland Health information related policies, patient data confidentiality and ethics requirements), limited availability of support from IT technical staff and time restrictions. These factors have influenced the process for the warehouse model development, necessitating an incremental approach. This highlights the presence of many practical barriers to data warehousing and integration at the clinical service level. Limitations included the use of a small convenience sample of survey respondents, and a single site case report study design. As mentioned previously, the proposed data warehouse is a prototype and was developed using only four database repositories. Despite this constraint, the research demonstrates that by implementing a data warehouse at the service level, decision-making is supported and data quality issues related to access and availability can be reduced, providing many benefits. Output reports produced from the data warehouse prototype demonstrated usefulness for the improvement of decision-making in the management of clinical services, and quality and safety monitoring for better clinical care. However, in the future, the centralised model selected can be upgraded to an enterprise wide architecture by integrating with additional hospital units’ databases.

Inward internationalization of services : Exploring satisfaction and dissatisfaction of overseas students in Australia

Most research has assessed the outward internationalization process of service firms and less is known in the literature about the inward internationalization of services, or companies that provide the service to overseas customers in the domestic market (i.e., tourism, education, healthcare). Specifically, there is scant research looking at the overseas customer perspective. This study attempts to identify the main drivers of satisfaction and dissatisfaction for overseas customers. The critical incident technique (CIT) method was used to collect and analyse the data. A total of 107 critical incidents regarding drivers of satisfaction and dissatisfaction for overseas customers in a higher educational service context were collected. Findings of this study show that drivers of service satisfaction and dissatisfaction for overseas customers derive from elements of the core service and peripheral service. However, the findings show that elements of the peripheral service (living environment, socialization and interaction with others, and personal performance) are more important for international students.

Legal issues in carbon farming : biosequestration, carbon pricing, and carbon rights

This paper critically analyses the proposed Australian regulatory approach to the crediting of biological sequestration activities (biosequestration) under the Australian Carbon Farming Initiative and its interaction with State-based carbon rights, the national carbon-pricing mechanism, and the international Kyoto Protocol and carbon-trading markets. Norms and principles have been established by the Kyoto Protocol to guide the creation of additional, verifiable, and permanent credits from biosequestration activities. This paper examines the proposed arrangements under the Australian Carbon Farming Initiative and Carbon Pricing Mechanism to determine whether they are consistent with those international norms and standards. This paper identifies a number of anomalies associated with the legal treatment of additionality and permanence and issuance of carbon credits within the Australian schemes. In light of this, the paper considers the possible legal implications for the national and international transfer, surrender and use of these offset credits.

Application of operations research techniques to improve efficiency in the emergency department

The main aim of this thesis is to analyse and optimise a public hospital Emergency Department. The Emergency Department (ED) is a complex system with limited resources and a high demand for these resources. Adding to the complexity is the stochastic nature of almost every element and characteristic in the ED. The interaction with other functional areas also complicates the system as these areas have a huge impact on the ED and the ED is powerless to change them. Therefore it is imperative that OR be applied to the ED to improve the performance within the constraints of the system. The main characteristics of the system to optimise included tardiness, adherence to waiting time targets, access block and length of stay. A validated and verified simulation model was built to model the real life system. This enabled detailed analysis of resources and flow without disruption to the actual ED. A wide range of different policies for the ED and a variety of resources were able to be investigated. Of particular interest was the number and type of beds in the ED and also the shift times of physicians. One point worth noting was that neither of these resources work in isolation and for optimisation of the system both resources need to be investigated in tandem. The ED was likened to a flow shop scheduling problem with the patients and beds being synonymous with the jobs and machines typically found in manufacturing problems. This enabled an analytic scheduling approach. Constructive heuristics were developed to reactively schedule the system in real time and these were able to improve the performance of the system. Metaheuristics that optimised the system were also developed and analysed. An innovative hybrid Simulated Annealing and Tabu Search algorithm was developed that out-performed both simulated annealing and tabu search algorithms by combining some of their features. The new algorithm achieves a more optimal solution and does so in a shorter time.

Polymer self assembly on carbon nanotubes

This chapter analyses the poly(3-hexylthiophene) self-assembly on carbon nanotubes and the interaction between the two materials forming a new hybrid nanostructure. The chapter starts with a review of the several studies investigating polymers and biomolecules self-assembled on nanotubes. Then conducting polymers and polythiophenes are briefly introduced. Accordingly, carbon nanotube structure and properties are reported in Sect. 3. The experimental section starts with the bulk characterisation of polymer thin films with the inclusion of uniformly distributed carbon nanotubes. By using volume film analysis techniques (AFM, TEM, UV–Vis and Raman), we show how the polymer’s higher degree of order is a direct consequence of interaction with carbon nanotubes. Nevertheless, it is through the use of nanoscale analysis and molecular dynamic simulations that the self-assembly of the polymer on the nanotube surface can be clearly evidenced and characterised. In Sect. 6, the effect of the carbon templating structure on the P3HT organisation on the surface is investigated, showing the chirality-driven polymer assembly on the carbon nanotube surface. The interaction between P3HT and CNTs brings also to charge transfer, with the modification of physical properties for both species. In particular, the alteration of the polymer electronic properties and the modification of the nanotube mechanical structure are a direct consequence of the P3HT p-p stacking on the nanotube surface. Finally, some considerations based on molecular dynamics studies are reported in order to confirm and support the experimental results discussed.

Mobile applications of focused link discovery

Interaction with a mobile device remains difficult due to inherent physical limitations. This dif-ficulty is particularly evident for search, which re-quires typing. We extend the One-Search-Only search paradigm by adding a novel link-browsing scheme built on top of automatic link discovery. A prototype was built for iPhone and tested with 12 subjects. A post-use interview survey suggests that the extended paradigm improves the mobile information seeking experience.

Developing tools to facilitate integrated reflection

Much has been said and documented about the key role that reflection can play in the ongoing development of e-portfolios, particularly e-portfolios utilised for teaching and learning. A review of e-portfolio platforms reveals that a designated space for documenting and collating personal reflections is a typical design feature of both open source and commercial off-the-shelf software. Further investigation of tools within e-portfolio systems for facilitating reflection reveals that, apart from enabling personal journalism through blogs or other writing, scaffolding tools that encourage the actual process of reflection are under-developed. Investigation of a number of prominent e-portfolio projects also reveals that reflection, while presented as critically important, is often viewed as an activity that takes place after a learning activity or experience and not intrinsic to it. This paper assumes an alternative, richer conception of reflection: a process integral to a wide range of activities associated with learning, such as inquiry, communication, editing, analysis and evaluation. Such a conception is consistent with the literature associated with ‘communities of practice’, which is replete with insight into ‘learning through doing’, and with a ‘whole minded’ approach to inquiry. Thus, graduates who are ‘reflective practitioners’ who integrate reflection into their learning will have more to offer a prospective employer than graduates who have adopted an episodic approach to reflection. So, what kinds of tools might facilitate integrated reflection? This paper outlines a number of possibilities for consideration and development. Such tools do not have to be embedded within e-portfolio systems, although there are benefits in doing so. In order to inform future design of e-portfolio systems this paper presents a faceted model of knowledge creation that depicts an ‘ecology of knowing’ in which interaction with, and the production of, learning content is deepened through the construction of well-formed questions of that content. In particular, questions that are initiated by ‘why’ are explored because they are distinguished from the other ‘journalist’ questions (who, what, when, where, and where) in that answers to them demand explanative, as opposed to descriptive, content. They require a rationale. Although why questions do not belong to any one genre and are not simple to classify — responses can contain motivational, conditional, causal, and/or existential content — they do make a difference in the acquisition of understanding. The development of scaffolding that builds on why-questioning to enrich learning is the motivation behind the research that has informed this paper.