Comparative analysis of panicum streak virus and maize streak virus diversity, recombination patterns and phylogeography

Background: Panicum streak virus (PanSV; Family Geminiviridae; Genus Mastrevirus) is a close relative of Maize streak virus (MSV), the most serious viral threat to maize production in Africa. PanSV and MSV have the same leafhopper vector species, largely overlapping natural host ranges and similar geographical distributions across Africa and its associated Indian Ocean Islands. Unlike MSV, however, PanSV has no known economic relevance. Results: Here we report on 16 new PanSV full genome sequences sampled throughout Africa and use these together with others in public databases to reveal that PanSV and MSV populations in general share very similar patterns of genetic exchange and geographically structured diversity. A potentially important difference between the species, however, is that the movement of MSV strains throughout Africa is apparently less constrained than that of PanSV strains. Interestingly the MSV-A strain which causes maize streak disease is apparently the most mobile of all the PanSV and MSV strains investigated. Conclusion: We therefore hypothesize that the generally increased mobility of MSV relative to other closely related species such as PanSV, may have been an important evolutionary step in the eventual emergence of MSV-A as a serious agricultural pathogen. The GenBank accession numbers for the sequences reported in this paper are GQ415386-GQ415401. © 2009 Varsani et al; licensee BioMed Central Ltd.

Analysis of environmental efficiency variation : a materials balance approach

Recent literature has argued that environmental efficiency (EE), which is built on the materials balance (MB) principle, is more suitable than other EE measures in situations where the law of mass conversation regulates production processes. In addition, the MB-based EE method is particularly useful in analysing possible trade-offs between cost and environmental performance. Identifying determinants of MB-based EE can provide useful information to decision makers but there are very few empirical investigations into this issue. This article proposes the use of data envelopment analysis and stochastic frontier analysis techniques to analyse variation in MB-based EE. Specifically, the article develops a stochastic nutrient frontier and nutrient inefficiency model to analyse determinants of MB-based EE. The empirical study applies both techniques to investigate MB-based EE of 96 rice farms in South Korea. The size of land, fertiliser consumption intensity, cost allocative efficiency, and the share of owned land out of total land are found to be correlated with MB-based EE. The results confirm the presence of a trade-off between MB-based EE and cost allocative efficiency and this finding, favouring policy interventions to help farms simultaneously achieve cost efficiency and MP-based EE.

Analysis of productive performance of crop production systems: an integrated analytical framework

Recent literature has argued that environmental efficiency (EE), which is built on the materials balance (MB) principle, is more suitable than other EE measures in situations where the law of mass conversation regulates production processes. In addition, the MB-based EE method is particularly useful in analysing possible trade-offs between cost and environmental performance. Identifying determinants of MB-based EE can provide useful information to decision makers but there are very few empirical investigations into this issue. This article proposes the use of data envelopment analysis and stochastic frontier analysis techniques to analyse variation in MB-based EE. Specifically, the article develops a stochastic nutrient frontier and nutrient inefficiency model to analyse determinants of MB-based EE. The empirical study applies both techniques to investigate MB-based EE of 96 rice farms in South Korea. The size of land, fertiliser consumption intensity, cost allocative efficiency, and the share of owned land out of total land are found to be correlated with MB-based EE. The results confirm the presence of a trade-off between MB-based EE and cost allocative efficiency and this finding, favouring policy interventions to help farms simultaneously achieve cost efficiency and MP-based EE.

Critical discourse analysis and political economy of communication : understanding the new corporate order

This article uses critical discourse analysis to analyse material shifts in the political economy of communications. It examines texts of major corporations to describe four key changes in political economy: (1) the separation of ownership from control; (2) the separation of business from industry; (3) the separation of accountability from responsibility; and (4) the subjugation of ‘going concerns’ by overriding concerns. The authors argue that this amounts to a political economic shift from traditional concepts of ‘capitalism’ to a new ‘corporatism’ in which the relationships between public and private, state and individual interests have become redefined and obscured through new discourse strategies. They conclude that the present financial and regulatory ‘crisis’ cannot be adequately resolved without a new analytic framework for examining the relationships between corporation, discourse and political economy.

Designing the information architecture of governmental one-stop portals : on the application and analysis of card sorting

The latest paradigm shift in government, termed Transformational Government, puts the citizen in the centre of attention. Including citizens in the design of online one-stop portals can help governmental organisations to become more customer focussed. This study describes the initial efforts of an Australian state government to develop an information architecture to structure the content of their future one-stop portal. Hereby, card sorting exercises have been conducted and analysed, utilising contemporary approaches found in academic and non-scientific literature. This paper describes the findings of the card sorting exercises in this particular case and discusses the suitability of the applied approaches in general. These are distinguished into non-statistical, statistical, and hybrid approaches. Thus, on the one hand, this paper contributes to academia by describing the application of different card sorting approaches and discussing their strengths and weaknesses. On the other hand, this paper contributes to practice by explaining the approach that has been taken by the authors’ research partner in order to develop a customer-focussed governmental one-stop portal. Thus, they provide decision support for practitioners with regard to different analysis methods that can be used to complement recent approaches in Transformational Government.

Retrieval of health advice on the web: AEHRC at ShARe/CLEF eHealth Evaluation Lab Task 3

This paper details the participation of the Australian e- Health Research Centre (AEHRC) in the ShARe/CLEF 2013 eHealth Evaluation Lab { Task 3. This task aims to evaluate the use of information retrieval (IR) systems to aid consumers (e.g. patients and their relatives) in seeking health advice on the Web. Our submissions to the ShARe/CLEF challenge are based on language models generated from the web corpus provided by the organisers. Our baseline system is a standard Dirichlet smoothed language model. We enhance the baseline by identifying and correcting spelling mistakes in queries, as well as expanding acronyms using AEHRC's Medtex medical text analysis platform. We then consider the readability and the authoritativeness of web pages to further enhance the quality of the document ranking. Measures of readability are integrated in the language models used for retrieval via prior probabilities. Prior probabilities are also used to encode authoritativeness information derived from a list of top-100 consumer health websites. Empirical results show that correcting spelling mistakes and expanding acronyms found in queries signi cantly improves the e ectiveness of the language model baseline. Readability priors seem to increase retrieval e ectiveness for graded relevance at early ranks (nDCG@5, but not precision), but no improvements are found at later ranks and when considering binary relevance. The authoritativeness prior does not appear to provide retrieval gains over the baseline: this is likely to be because of the small overlap between websites in the corpus and those in the top-100 consumer-health websites we acquired.

Identify disorders in health records using Conditional Random Fields and Metamap: AEHRC at ShARe/CLEF 2013 eHealth Evaluation Lab Task 1

The Australian e-Health Research Centre (AEHRC) recently participated in the ShARe/CLEF eHealth Evaluation Lab Task 1. The goal of this task is to individuate mentions of disorders in free-text electronic health records and map disorders to SNOMED CT concepts in the UMLS metathesaurus. This paper details our participation to this ShARe/CLEF task. Our approaches are based on using the clinical natural language processing tool Metamap and Conditional Random Fields (CRF) to individuate mentions of disorders and then to map those to SNOMED CT concepts. Empirical results obtained on the 2013 ShARe/CLEF task highlight that our instance of Metamap (after ltering irrelevant semantic types), although achieving a high level of precision, is only able to identify a small amount of disorders (about 21% to 28%) from free-text health records. On the other hand, the addition of the CRF models allows for a much higher recall (57% to 79%) of disorders from free-text, without sensible detriment in precision. When evaluating the accuracy of the mapping of disorders to SNOMED CT concepts in the UMLS, we observe that the mapping obtained by our ltered instance of Metamap delivers state-of-the-art e ectiveness if only spans individuated by our system are considered (`relaxed' accuracy).

Making the train : re-conceptualising accessibility for intra-urban rail travel

Australian authorities have set ambitious policy objectives to shift Australia’s current transport profile of heavy reliance on private motor cars to sustainable modes. Improving accessibility of public transport is a central component of that objective. Past studies on accessibility to public transport focus on walking time and/or waiting time. However, travellers’ perceptions of the interface leg journeys may depend not only on these direct and tangible factors but also on social and psychological factors. This paper extends previous research that identified five salient perspectives of rail access by means of a statement sorting activity and cluster analysis with a small sample of rail passengers in three Australian cities (Zuniga et al, 2013). This study collects a new data set including 144 responses from Brisbane and Melbourne to an online survey made up of a Likert-scaled statement sorting exercise and questionnaire. It employs factor analysis to examine the statement rankings and uncovers seven underlying factors in the exploratory manner, i.e., station, safety, access, transfer, service attitude, traveler’s physical activity levels, and environmental concern. Respondents from groups stratified by rail use frequency are compared in terms of their scores of those factors. Findings from this study indicate a need to re-conceptualize accessibility to intra-urban rail travel in agreement with current policy agenda, and to target behavioral intervention to multiple dimensions of accessibility influencing passengers’ travel choices. Arguments in this paper are not limited to intra-urban rail transit, but may also be relevant to public transport in general.

Analysis of nonlinear sequences and streamciphers

Streamciphers are common cryptographic algorithms used to protect the confidentiality of frame-based communications like mobile phone conversations and Internet traffic. Streamciphers are ideal cryptographic algorithms to encrypt these types of traffic as they have the potential to encrypt them quickly and securely, and have low error propagation. The main objective of this thesis is to determine whether structural features of keystream generators affect the security provided by stream ciphers.These structural features pertain to the state-update and output functions used in keystream generators. Using linear sequences as keystream to encrypt messages is known to be insecure. Modern keystream generators use nonlinear sequences as keystream.The nonlinearity can be introduced through a keystream generator's state-update function, output function, or both. The first contribution of this thesis relates to nonlinear sequences produced by the well-known Trivium stream cipher. Trivium is one of the stream ciphers selected in a final portfolio resulting from a multi-year project in Europe called the ecrypt project. Trivium's structural simplicity makes it a popular cipher to cryptanalyse, but to date, there are no attacks in the public literature which are faster than exhaustive keysearch. Algebraic analyses are performed on the Trivium stream cipher, which uses a nonlinear state-update and linear output function to produce keystream. Two algebraic investigations are performed: an examination of the sliding property in the initialisation process and algebraic analyses of Trivium-like streamciphers using a combination of the algebraic techniques previously applied separately by Berbain et al. and Raddum. For certain iterations of Trivium's state-update function, we examine the sets of slid pairs, looking particularly to form chains of slid pairs. No chains exist for a small number of iterations.This has implications for the period of keystreams produced by Trivium. Secondly, using our combination of the methods of Berbain et al. and Raddum, we analysed Trivium-like ciphers and improved on previous on previous analysis with regards to forming systems of equations on these ciphers. Using these new systems of equations, we were able to successfully recover the initial state of Bivium-A.The attack complexity for Bivium-B and Trivium were, however, worse than exhaustive keysearch. We also show that the selection of stages which are used as input to the output function and the size of registers which are used in the construction of the system of equations affect the success of the attack. The second contribution of this thesis is the examination of state convergence. State convergence is an undesirable characteristic in keystream generators for stream ciphers, as it implies that the effective session key size of the stream cipher is smaller than the designers intended. We identify methods which can be used to detect state convergence. As a case study, theMixer streamcipher, which uses nonlinear state-update and output functions to produce keystream, is analysed. Mixer is found to suffer from state convergence as the state-update function used in its initialisation process is not one-to-one. A discussion of several other streamciphers which are known to suffer from state convergence is given. From our analysis of these stream ciphers, three mechanisms which can cause state convergence are identified.The effect state convergence can have on stream cipher cryptanalysis is examined. We show that state convergence can have a positive effect if the goal of the attacker is to recover the initial state of the keystream generator. The third contribution of this thesis is the examination of the distributions of bit patterns in the sequences produced by nonlinear filter generators (NLFGs) and linearly filtered nonlinear feedback shift registers. We show that the selection of stages used as input to a keystream generator's output function can affect the distribution of bit patterns in sequences produced by these keystreamgenerators, and that the effect differs for nonlinear filter generators and linearly filtered nonlinear feedback shift registers. In the case of NLFGs, the keystream sequences produced when the output functions take inputs from consecutive register stages are less uniform than sequences produced by NLFGs whose output functions take inputs from unevenly spaced register stages. The opposite is true for keystream sequences produced by linearly filtered nonlinear feedback shift registers.

Security analysis of linearly filtered NLFSRs

Non-linear feedback shift register (NLFSR) ciphers are cryptographic tools of choice of the industry especially for mobile communication. Their attractive feature is a high efficiency when implemented in hardware or software. However, the main problem of NLFSR ciphers is that their security is still not well investigated. The paper makes a progress in the study of the security of NLFSR ciphers. In particular, we show a distinguishing attack on linearly filtered NLFSR (or LF-NLFSR) ciphers. We extend the attack to a linear combination of LF-NLFSRs. We investigate the security of a modified version of the Grain stream cipher and show its vulnerability to both key recovery and distinguishing attacks.

Internet-enabled tourism entrepreneurs. International entrepreneurial values elicited through repertory test and laddering analysis

Although the tourism industry has been dramatically altered due to the Internet, there has been limited research published about international entrepreneurial values and Internet use in tourism firms. The findings of this study point to a relationship between the values of Internet-enabled international entrepreneurs in small-sized to medium-sized enterprises and the inclination of the firm to develop and initiate international activity. The findings of this study suggest that Internet-enabled tourism entrepreneurs share similar construct values. Two effective but underutilized qualitative methods were used in this study. The first method, repertory test, is an efficient technique for exploring constructs in decision making; the second method, laddering analysis, facilitates understanding of the perceived consequences and personal values guiding behaviour.

Metabolomic analysis of siderophore cheater mutants reveals metabolic costs of expression in uropathogenic escherichia coli

Bacterial siderophores are a group of chemically diverse, virulence-associated secondary metabolites whose expression exerts metabolic costs. A combined bacterial genetic and metabolomic approach revealed differential metabolomic impacts associated with biosynthesis of different siderophore structural families. Despite myriad genetic differences, the metabolome of a cheater mutant lacking a single set of siderophore biosynthetic genes more closely approximate that of a nonpathogenic K12 strain than its isogenic, uropathogen parent strain. Siderophore types associated with greater metabolomic perturbations are less common among human isolates, suggesting that metabolic costs influence success in a human population. Although different siderophores share a common iron acquisition function, our analysis shows how a metabolomic approach can distinguish their relative metabolic impacts in E.coli.

Bike share's impact on car use : evidence from the United States, Great Britain, and Australia

There are currently more than 400 cities operating bike share programs. Purported benefits of bike share programs include flexible mobility, physical activity, reduced congestion, emissions and fuel use. Implicit or explicit in the calculation of program benefits are assumptions regarding the modes of travel replaced by bike share journeys. This paper examines the degree to which car trips are replaced by bike share, through an examination of survey and trip data from bike share programs in Melbourne, Brisbane, Washing, D.C., London, and Minneapolis/St. Paul. A secondary and unique component of this analysis examines motor vehicle support services required for bike share fleet rebalancing and maintenance. These two components are then combined to estimate bike share’s overall contribution to changes in vehicle kilometres traveled. The results indicate that the estimated mean reduction in car use due to bike share is at least twice the distance covered by operator support vehicles, with the exception of London, in which the relationship is reversed, largely due to a low car mode substitution rate. As bike share programs mature, evaluation of their effectiveness in reducing car use may become increasingly important. This paper reveals that by increasing the convenience of bike share relative to car use and by improving perceptions of safety, the capacity of bike share programs to reduce vehicle trips and yield overall net benefits will be enhanced. Researchers can adapt the analytical approach proposed in this paper to assist in the evaluation of current and future bike share programs.

Multifunctional agriculture in policy and practice? A comparative analysis of Norway and Australia

Ideals of productivist agriculture in the Western world have faded as the unintended consequences of intensive agriculture and pastoralism have contributed to rural decline and environmental problems. In Norway and Australia, there has been an increasing acceptance of the equal importance of social and environmental sustainability as well as economic sustainability. Alongside this shift is a belief that primary production needs to move away from an intensive, productivist-based agriculture to one that may be defined as post-productivist. In this paper, we argue that the dualism of productivism and post-productivism as concepts on agricultural policy regimes are too simplistic and discuss whether multifunctional agriculture is a better concept for a comparison of rural primary production at two extreme points of the scale, the market-oriented, liberalistic Australian agriculture and the market-protected small-scale Norwegian agriculture. We argue that multifunctionality in Australia rates relatively weakly as an ideology or policy and even less as a discourse or practice and hence is situated toward a ‘weak’ end of a continuum of a level of multifunctional agriculture. In Norwegian agriculture, multifunctional agriculture has thrived within a protectionist setting with the support of the public, the state and agricultural actors. In this sense it is very clearly a policy, practice and discourse that aims to preserve and conserve rural spaces, the cultural landscape, the farming way of life and food safety. Norway is as such situated toward a ‘strong’ end of a continuum of a level of multifunctional agriculture.

Representations of foreign places outside the news : an analysis of Australian newspaper travel sections

Despite continued growth over recent decades, travel journalism has so far gained little attention in journalism research, with scholars often ridiculing it and other forms of lifestyle journalism as not being real journalism. This paper aims to the shift the focus by arguing that non-news journalism is increasingly important as a site for research. It reports the results from a content analysis of Australian newspaper travel sections and examines the role they play in mediating foreign places. The results demonstrate that travel stories can be mostly classed as service stories in that they focus on destinations which are already popular with Australians. At the same time they report very little about local cultures at the destinations, demonstrating a focus on the tourist experience and a missed opportunity for improving inter-cultural understanding. A visual analysis of photographs shows stereotypical portrayals of destinations broadly in line with tourism promotion materials.