Blast atlas: a virtual observatory for genomes

Following the completion of the draft Human Genome in 2001, genomic sequence data is becoming available at an accelerating rate, fueled by advances in sequencing and computational technology. Meanwhile, large collections of astronomical and geospatial data have allowed the creation of virtual observatories, accessible throughout the world and requiring only commodity hardware. Through a combination of advances in data management, data mining and visualization, this infrastructure enables the development of new scientific and educational applications as diverse as galaxy classification and real-time tracking of earthquakes and volcanic plumes. In the present paper, we describe steps taken along a similar path towards a virtual observatory for genomes – an immersive three-dimensional visual navigation and query system for comparative genomic data.

Informational city

Many cities worldwide face the prospect of major transformation as the world moves towards a global information order. In this new era, urban economies are being radically altered by dynamic processes of economic and spatial restructuring. The result is the creation of ‘informational cities’ or its new and more popular name, ‘knowledge cities’. For the last two centuries, social production had been primarily understood and shaped by neo-classical economic thought that recognized only three factors of production: land, labor and capital. Knowledge, education, and intellectual capacity were secondary, if not incidental, factors. Human capital was assumed to be either embedded in labor or just one of numerous categories of capital. In the last decades, it has become apparent that knowledge is sufficiently important to deserve recognition as a fourth factor of production. Knowledge and information and the social and technological settings for their production and communication are now seen as keys to development and economic prosperity. The rise of knowledge-based opportunity has, in many cases, been accompanied by a concomitant decline in traditional industrial activity. The replacement of physical commodity production by more abstract forms of production (e.g. information, ideas, and knowledge) has, however paradoxically, reinforced the importance of central places and led to the formation of knowledge cities. Knowledge is produced, marketed and exchanged mainly in cities. Therefore, knowledge cities aim to assist decision-makers in making their cities compatible with the knowledge economy and thus able to compete with other cities. Knowledge cities enable their citizens to foster knowledge creation, knowledge exchange and innovation. They also encourage the continuous creation, sharing, evaluation, renewal and update of knowledge. To compete nationally and internationally, cities need knowledge infrastructures (e.g. universities, research and development institutes); a concentration of well-educated people; technological, mainly electronic, infrastructure; and connections to the global economy (e.g. international companies and finance institutions for trade and investment). Moreover, they must possess the people and things necessary for the production of knowledge and, as importantly, function as breeding grounds for talent and innovation. The economy of a knowledge city creates high value-added products using research, technology, and brainpower. Private and the public sectors value knowledge, spend money on its discovery and dissemination and, ultimately, harness it to create goods and services. Although many cities call themselves knowledge cities, currently, only a few cities around the world (e.g., Barcelona, Delft, Dublin, Montreal, Munich, and Stockholm) have earned that label. Many other cities aspire to the status of knowledge city through urban development programs that target knowledge-based urban development. Examples include Copenhagen, Dubai, Manchester, Melbourne, Monterrey, Singapore, and Shanghai. Knowledge-Based Urban Development To date, the development of most knowledge cities has proceeded organically as a dependent and derivative effect of global market forces. Urban and regional planning has responded slowly, and sometimes not at all, to the challenges and the opportunities of the knowledge city. That is changing, however. Knowledge-based urban development potentially brings both economic prosperity and a sustainable socio-spatial order. Its goal is to produce and circulate abstract work. The globalization of the world in the last decades of the twentieth century was a dialectical process. On one hand, as the tyranny of distance was eroded, economic networks of production and consumption were constituted at a global scale. At the same time, spatial proximity remained as important as ever, if not more so, for knowledge-based urban development. Mediated by information and communication technology, personal contact, and the medium of tacit knowledge, organizational and institutional interactions are still closely associated with spatial proximity. The clustering of knowledge production is essential for fostering innovation and wealth creation. The social benefits of knowledge-based urban development extend beyond aggregate economic growth. On the one hand is the possibility of a particularly resilient form of urban development secured in a network of connections anchored at local, national, and global coordinates. On the other hand, quality of place and life, defined by the level of public service (e.g. health and education) and by the conservation and development of the cultural, aesthetic and ecological values give cities their character and attract or repel the creative class of knowledge workers, is a prerequisite for successful knowledge-based urban development. The goal is a secure economy in a human setting: in short, smart growth or sustainable urban development.

Spatiotemporal investigations of DNA damage repair using microbeams

Cellular response to radiation damage is made by a complex network of pathways and feedback loops whose spatiotemporal organisation is still unclear despite its decisive role in determining the fate of the damaged cell. Revealing the dynamic sequence of the repair proteins is therefore critical in understanding how the DNA repair mechanisms work. There are also still open questions regarding the possible movement of damaged chromatin domains and its role as trigger for lesion recognition and signalling in the DNA repair context. The single-cell approach and the high spatial resolution offered by microbeams provide the perfect tool to study and quantify the dynamic processes associated with the induction and repair of DNA damage. We have followed the development of radiation-induced foci for three DNA damage markers (i.e. γ-H2AX, 53BP1 and hSSB1) using normal fibroblasts (AG01522), human breast adenocarcinoma cells (MCF7) and human fibrosarcoma cells (HT1080) stably transfected with yellow fluorescent protein fusion proteins following irradiation with the QUB X-ray microbeam (carbon X-rays <2 µm spot). The size and intensity of the foci has been analysed as a function of dose and time post-irradiation to investigate the dynamics of the above-mentioned DNA repair processes and monitor the remodelling of chromatin structure that the cell undergoes to deal with DNA damage.

The influence of underreported crashes on hotspot identification

Hot spot identification (HSID) plays a significant role in improving the safety of transportation networks. Numerous HSID methods have been proposed, developed, and evaluated in the literature. The vast majority of HSID methods reported and evaluated in the literature assume that crash data are complete, reliable, and accurate. Crash under-reporting, however, has long been recognized as a threat to the accuracy and completeness of historical traffic crash records. As a natural continuation of prior studies, the paper evaluates the influence that under-reported crashes exert on HSID methods. To conduct the evaluation, five groups of data gathered from Arizona Department of Transportation (ADOT) over the course of three years are adjusted to account for fifteen different assumed levels of under-reporting. Three identification methods are evaluated: simple ranking (SR), empirical Bayes (EB) and full Bayes (FB). Various threshold levels for establishing hotspots are explored. Finally, two evaluation criteria are compared across HSID methods. The results illustrate that the identification bias—the ability to correctly identify at risk sites--under-reporting is influenced by the degree of under-reporting. Comparatively speaking, crash under-reporting has the largest influence on the FB method and the least influence on the SR method. Additionally, the impact is positively related to the percentage of the under-reported PDO crashes and inversely related to the percentage of the under-reported injury crashes. This finding is significant because it reveals that despite PDO crashes being least severe and costly, they have the most significant influence on the accuracy of HSID.

Of ivory towers and boundary spanners

We all live in a yellow submarine… When I go to work in the morning, in the office building that hosts our BPM research group, on the way up to our level I come by this big breakout room that hosts a number of computer scientists, working away at the next generation software algorithms and iPad applications (I assume). I have never actually been in that room, but every now and then the door is left ajar for a while and I can spot couches, lots (I mean, lots!) of monitors, the odd scientist, a number of Lara Croft posters, and the usual room equipment you’d probably expect from computer scientists (and, no, it’s not like that evil Dennis guy from the Jurassic Park movie, buried in chips, coke, and flickering code screens… It’s also not like the command room from the Nebuchadnezzar, Neo’s hovercraft in the Matrix movies, although I still strongly believe these green lines of code make a good screensaver).

A prototype augmented reality collaborative process modelling tool

Identifying, modelling and documenting business processes usually requires the collaboration of many stakeholders that may be spread across companies in inter-organizational business settings. While there are many process modelling tools available, the support they provide for remote collaboration is still limited. This demonstration showcases a novel prototype application that implements collaborative virtual environment and augmented reality technologies to improve remote collaborative process modelling, with an aim to assisting common collaboration tasks by providing an increased sense of immersion in an intuitive shared work and task space. Our tool is easily deployed using open source software, and commodity hardware, and is expected to assist with saving money on travel costs for large scale process modelling projects covering national and international centres within an enterprise.

Included by design : a case for regulation for accessible housing in Australia

Accessible housing is a scarce yet much needed commodity in Australia. A national agreement between industry and advocacy groups to a voluntary approach, called the Livable Design program, aims to provide access features in all new housing by 2020. Through a range of awareness raising initiatives, the program is anticipating increased supply by builders and increased demand by home-buyers. However the people who need accessible housing are the least likely and least able to buy it at the point of new sale and average homebuyers do not consider access features as a priority. This approach has not been successful overseas or in Australia in the past. Regulation with incentives supported by education and awareness has provided the best results, yet, regulation typically comes with controversy and resistance from the housing industry. A study is planned to identify how effective the Livable Design program is likely to be, what is likely to hinder it and why regulation is likely to be needed.

Diversification and value-at-risk

A pervasive and puzzling feature of banks’ Value-at-Risk (VaR) is its abnormally high level, which leads to excessive regulatory capital. A possible explanation for the tendency of commercial banks to overstate their VaR is that they incompletely account for the diversification effect among broad risk categories (e.g., equity, interest rate, commodity, credit spread, and foreign exchange). By underestimating the diversification effect, bank’s proprietary VaR models produce overly prudent market risk assessments. In this paper, we examine empirically the validity of this hypothesis using actual VaR data from major US commercial banks. In contrast to the VaR diversification hypothesis, we find that US banks show no sign of systematic underestimation of the diversification effect. In particular, diversification effects used by banks is very close to (and quite often larger than) our empirical diversification estimates. A direct implication of this finding is that individual VaRs for each broad risk category, just like aggregate VaRs, are biased risk assessments.

A sociolinguistic approach to applied epistemology : examining technocratic values in global 'Knowledge' policy

This special issue presents an excellent opportunity to study applied epistemology in public policy. This is an important task because the arena of public policy is the social domain in which macro conditions for ‘knowledge work’ and ‘knowledge industries’ are defined and created. We argue that knowledge-related public policy has become overly concerned with creating the politico-economic parameters for the commodification of knowledge. Our policy scope is broader than that of Fuller (1988), who emphasizes the need for a social epistemology of science policy. We extend our focus to a range of policy documents that include communications, science, education and innovation policy (collectively called knowledge-related public policy in acknowledgement of the fact that there is no defined policy silo called ‘knowledge policy’), all of which are central to policy concerned with the ‘knowledge economy’ (Rooney and Mandeville, 1998). However, what we will show here is that, as Fuller (1995) argues, ‘knowledge societies’ are not industrial societies permeated by knowledge, but that knowledge societies are permeated by industrial values. Our analysis is informed by an autopoietic perspective. Methodologically, we approach it from a sociolinguistic position that acknowledges the centrality of language to human societies (Graham, 2000). Here, what we call ‘knowledge’ is posited as a social and cognitive relationship between persons operating on and within multiple social and non-social (or, crudely, ‘physical’) environments. Moreover, knowing, we argue, is a sociolinguistically constituted process. Further, we emphasize that the evaluative dimension of language is most salient for analysing contemporary policy discourses about the commercialization of epistemology (Graham, in press). Finally, we provide a discourse analysis of a sample of exemplary texts drawn from a 1.3 million-word corpus of knowledge-related public policy documents that we compiled from local, state, national and supranational legislatures throughout the industrialized world. Our analysis exemplifies a propensity in policy for resorting to technocratic, instrumentalist and anti-intellectual views of knowledge in policy. We argue that what underpins these patterns is a commodity-based conceptualization of knowledge, which is underpinned by an axiology of narrowly economic imperatives at odds with the very nature of knowledge. The commodity view of knowledge, therefore, is flawed in its ignorance of the social systemic properties of knowing’.

Unbiased estimation of the half-life to price index convergence among U.S. cities

Estimates of the half-life to convergence of prices across a panel of cities are subject to bias from three potential sources: inappropriate cross-sectional aggregation of heterogeneous coefficients, presence of lagged dependent variables in a model with individual fixed effects, and time aggregation of commodity prices. This paper finds no evidence of heterogeneity bias in annual CPI data for 17 U.S. cities from 1918 to 2006, but correcting for the “Nickell bias” and time aggregation bias produces a half-life of 7.5 years, shorter than estimates from previous studies.

Proactive detection of high collision concentration locations on highways

In previous research (Chung et al., 2009), the potential of the continuous risk profile (CRP) to proactively detect the systematic deterioration of freeway safety levels was presented. In this paper, this potential is investigated further, and an algorithm is proposed for proactively detecting sites where the collision rate is not sufficiently high to be classified as a high collision concentration location but where a systematic deterioration of safety level is observed. The approach proposed compares the weighted CRP across different years and uses the cumulative sum (CUSUM) algorithm to detect the sites where changes in collision rate are observed. The CRPs of the detected sites are then compared for reproducibility. When high reproducibility is observed, a growth factor is used for sequential hypothesis testing to determine if the collision profiles are increasing over time. Findings from applying the proposed method using empirical data are documented in the paper together with a detailed description of the method.

The role of institutional rural property in diversified investment portfolios in NSW, Australia

The food and fuel crisis experienced in 2006 to 2008 has highlighted the importance of agricultural commodity production throughout developing and developed economies and has placed greater awareness and importance on rural property and rural property markets. These factors have led to an increased interest from major property investment institutions and property companies in the role of rural property in a mixed asset or mixed property investment portfolio. This paper will analyse rural property sales in New South Wales for the period 1990-2008, and will compare total return performance across a number of rural property sectors based on geographic location and land use type. These results show that the inclusion of rural property in an investment portfolio has benefits in relation to return and risk.

The global division of labour and the division in global labour

Since the 1980s the locus of manufacturing and some services have moved to countries of the Global South. Liberalization of trade and investment has added two billion people to world labour supply and brought workers everywhere into intense competition with each other. Under orthodox neoliberal and neoclassical approaches free trade and open investment should benefit all countries and lead to convergence. However considerable differences in wages and working hours exist between workers of the Global North and those of the Global South. The organising question for the thesis is why workers in different countries but the same industries get different wages. Empirical evidence reviewed in the thesis shows that productivity does not explain these wage differences and that workers in some parts of the South are more productive than workers in the North. Part of the thesis examines the usefulness of explanations drawn from Marxist, institutionalist and global commodity chain approaches. There is a long established argument in Marxist and neo-Marxist writings that differences between North and South result from imperialism and the exercise of power. This is the starting point to review ways of understanding divisions between workers as the outcome of a global class structure. In turn, a fault line is postulated between productive and unproductive labour that largely replicates the division between the Global North and the Global South. Workers and their organizations need shared actions if they are to resist global competition and wage disparities. Solidarity has been the clarion of progressive movements from the Internationals of the early C19th through to the current Global Unions and International Confederation of Trade Unions (ICTU). The thesis examines how nationalism and particular interests have undermined solidarity and reviews the major implications for current efforts to establish and advance a global labour position.

Urban food futures : ICTs and opportunities

Food is a vital foundation of all human life. It is essential to a myriad of political, socio-cultural, economic and environmental practices throughout history. However, those practices of food production, consumption, and distribution have the potential to now go through immensely transformative shifts as network technologies become increasingly embedded in every domain of contemporary life. Information and communication technologies (ICTs) are one of the key foundations of global functionality and sustenance today and undoubtedly will continue to present new challenges and opportunities for the future. As such, this Symposium will bring together leading scholars across disciplines to address challenges and opportunities at the intersection of food and ICTs in everyday urban environment. In particular, the discussion will revolve around the question: What are the key roles that network technologies play in re-shaping the food systems at micro- to macroscopic level? The symposium will contribute a unique perspective on urban food futures through the lens of network society paradigm where ICTs enable innovations in production, organisation, and communication within society. Some of the topics addressed will include encouraging transparency in food commodity chains; value of cultural understanding and communication in global food sustainability; and technologies to social inclusion; all of which evoke and examine the question surrounding networked individuals as changes catalysts for urban food futures. The event will provide an avenue for new discussions and speculations on key issues surrounding urban food futures in the network era, with a particular focus on bottom-up micro actions that challenge the existing food systems towards a broader sociocultural, political, technological, and environmental transformations. One central area of concern is that current systems of food production, distribution, and consumption do not ensure food security for the future, but rather seriously threaten it. With the recent unprecedented scale of urban growth and rise of middle-class, the problem continues to intensify. This situation requires extensive distribution networks to feed urban residents, and therefore poses significant infrastructural challenges to both the public and private sectors. The symposium will also address the transferability of citizen empowerment that network technologies enable as demonstrated in various significant global political transformations from the bottom-up, such as the recent Egyptian Youth Revolution. Another key theme of the discussion will be the role of ICTs (and the practices that they mediate) in fostering transparency in commodity chains. The symposium will ask what differences these technologies can make on the practices of food consumption and production. After discussions, we will initiate an international network of food-thinkers and actors that will function as a platform for knowledge sharing and collaborations. The participants will be invited to engage in planning for the on-going future development of the network.

From bust to boom : towards a strategic cognition perspective on Australian mining firms’ adaption

While the role of executives’ cognition in organisations’ responses to change is a central topic in strategic cognition research, changes in firms’ environment are typically not measured directly but described either as an event (for example, new industry legislation) or represented by a time period (e.g. when a new technology impacted an industry). The Australian mining sector has witnessed a historically significant change in demand for its products and we begin by developing measures of changes in supply and demand for key commodities during the period 1992-2008. We identify sub-groups of firms based on their activities and commodity sector and examine the relation of these variables to executives’ cognition and to firms’ CapEx. We find industry, firm and cognitive variables are related to both strategic cognition and firms’ CapEx.