Sequence and organization of barley yellow dwarf virus genomic RNA

The nucleotide sequence of the genomic RNA of barley yellow dwarf virus, PAV serotype was determined except for the 5′-terminal base, and its genome organization deduced. The 5,677 nucleotide genome contains five large open reading frames (ORFs). The genes for the coat protein (1) and the putative viral RNA-dependent RNA polymerase were identified. The latter shows a striking degree of similarity to that of carnation mottle virus (CarMV). By comparison with corona- and retrovirus RNAs, it is proposed that a translational frameshift is involved in expression of the polymerase. An ORF encoding an Mr 49,797 protein (50K ORF) may be translated by in-frame readthrough of the coat protein stop codon. The coat protein, an overlapping 17K ORF, and a 3′ 6.7K ORF are likely to be expressed via subgenomic mRNAs. © 1988 IRL Press Limited.

Carrot mottle mimic virus (CMoMV): A second umbravirus associated with carrot motley dwarf disease recognised by nucleic acid hybridisation

Carrot mottle umbravirus (CMoV) has always been found co-infecting plants with carrot red leaf luteovirus (CRLV) and in carrot (Daucus carota) these co-infections are associated with carrot motley dwarf disease (CMD). CMD occurs wherever carrots are grown. Hence, CMoV was believed to have a corresponding global distribution. However, little or no hybridisation was detected between cDNA generated from the sequenced Australian isolate of CMoV (CMoV-A) and RNA from the much studied Scottish isolate of CMoV (CMoV-S). A weak hybridisation signal was obtained using cDNA to a conserved part of the RNA-dependent RNA polymerase gene of CMoV-A, but when cDNAs to other parts of the CMoV-A genome were used as probes there was no detectable hybridisation with CMoV-S RNA. This lack of hybridisation suggests that the two virus isolates have relatively divergent genomes and that they should be regarded as distinct virus species. Both viruses are transmitted by Cavariella aegopodii, but only with the help of CRLV, and they yield almost identical double-stranded RNA profiles. For these reasons, we propose that the CMoV isolate from Australia be renamed carrot mottle mimic umbravirus (CMoMV). cDNA to CMoMV RNA hybridised with RNA from an isolate from New Zealand, whereas cDNA to CMoV-S RNA hybridised with RNA from isolates from England and Morocco but not to RNA from the isolate from New Zealand. Although preliminary, these data suggest that CMoV and CMoMV may have different global distributions.

Complete genomic sequence of a Rubus yellow net virus isolate and detection of genome-wide pararetrovirus-derived small RNAs

Rubus yellow net virus (RYNV) was cloned and sequenced from a red raspberry (Rubus idaeus L.) plant exhibiting symptoms of mosaic and mottling in the leaves. Its genomic sequence indicates that it is a distinct member of the genus Badnavirus, with 7932. bp and seven ORFs, the first three corresponding in size and location to the ORFs found in the type member Commelina yellow mottle virus. Bioinformatic analysis of the genomic sequence detected several features including nucleic acid binding motifs, multiple zinc finger-like sequences and domains associated with cellular signaling. Subsequent sequencing of the small RNAs (sRNAs) from RYNV-infected R. idaeus leaf tissue was used to determine any RYNV sequences targeted by RNA silencing and identified abundant virus-derived small RNAs (vsRNAs). The majority of the vsRNAs were 22-nt in length. We observed a highly uneven genome-wide distribution of vsRNAs with strong clustering to small defined regions distributed over both strands of the RYNV genome. Together, our data show that sequences of the aphid-transmitted pararetrovirus RYNV are targeted in red raspberry by the interfering RNA pathway, a predominant antiviral defense mechanism in plants. © 2013.

Putative full-length clones of the genomic DNA segments of subterranean clover stunt virus and identification of the segment coding for the viral coat protein

Subterranean clover stunt disease is an economically important aphid-borne virus disease affecting certain pasture and grain legumes in Australia. The virus associated with the disease, subterranean clover stunt virus (SCSV), was previously found to be representative of a new type of single-stranded DNA virus. Analysis of the virion DNA and restriction mapping of double-stranded cDNA synthesized from virion DNA suggested that SCSV has a segmented genome composed of 3 or 4 different species of circular ssDNA each of about 850-880 nucleotides. To further investigate the complexity of the SCSV genome, we have isolated the replicative form DNA from infected pea and from it prepared putative full-length clones representing the SCSV genome segments. Analysis of these clones by restriction mapping indicated that clones representing at least 4 distinct genomic segments were obtained. This method is thus suitable for generating an extensive genomic library of novel ssDNA viruses containing multiple genome segments such as SCSV and banana bunchy top virus. The N-terminal amino acid sequence and amino acid composition of the coat protein of SCSV were determined. Comparison of the amino acid sequence with partial DNA sequence data, and the distinctly different restriction maps obtained for the full-length clones suggested that only one of these clones contained the coat protein gene. The results confirmed that SCSV has a functionally divided genome composed of several distinct ssDNA circles each of about 1 kb.

Nucleotide sequences of an Australian and a Canadian isolate of potato leafroll luteovirus and their relationships with two European isolates

The genomes of an Australian and a Canadian isolate of potato leafroll virus have been cloned and sequenced. The sequences of both isolates are similar (about 93%), but the Canadian isolate (PLRV-C) is more closely related (about 98% identity) to a Scottish (PLRV-S) and a Dutch isolate (PLRV-N) than to the Australian isolate (PLRV-A). The 5'-terminal 18 nucleotide residues of PLRV-C, PLRV-A, PLRV-N and beet western yellows virus have 17 residues in common. In contrast, PLRV-S shows no obvious similarity in this region. PLRV-A and PLRV-C genomic sequences have localized regions of marked diversity, in particular a 600 nucleotide residue sequence in the polymerase gene. These data provide a world-wide perspective on the molecular biology of PLRV strains and their comparison with other luteoviruses and related RNA plant viruses suggests that there are two major subgroups in the plant luteoviruses.

Process mining for clinical processes: A comparative analysis of four Australian hospitals

Business process analysis and process mining, particularly within the health care domain, remain under-utilised. Applied research that employs such techniques to routinely collected, health care data enables stakeholders to empirically investigate care as it is delivered by different health providers. However, cross-organisational mining and the comparative analysis of processes present a set of unique challenges in terms of ensuring population and activity comparability, visualising the mined models and interpreting the results. Without addressing these issues, health providers will find it difficult to use process mining insights, and the potential benefits of evidence-based process improvement within health will remain unrealised. In this paper, we present a brief introduction on the nature of health care processes; a review of the process mining in health literature; and a case study conducted to explore and learn how health care data, and cross-organisational comparisons with process mining techniques may be approached. The case study applies process mining techniques to administrative and clinical data for patients who present with chest pain symptoms at one of four public hospitals in South Australia. We demonstrate an approach that provides detailed insights into clinical (quality of patient health) and fiscal (hospital budget) pressures in health care practice. We conclude by discussing the key lessons learned from our experience in conducting business process analysis and process mining based on the data from four different hospitals.

Motivating domestic energy conservation through comparative feedback in mobile applications and social networking sites

The progress of technology has led to the increased adoption of energy monitors among household energy consumers. While the monitors available on the market deliver real-time energy usage feedback to the consumer, the form of this data is usually unengaging and mundane. Moreover, it fails to address consumers with different motivations and needs to save and compare energy. This master‟s thesis project presents a study that seeks to inform design guidelines for differently motivated energy consumers. The focus of the research is on comparative feedback supported by a community of energy consumers. In particular, the discussed comparative feedback types are explanatory comparison, temporal self-comparison, norm comparison, one-on-one comparison and ranking, whereby the last three support exploring the potential of socialising energy-related feedback in social networking sites, such as Facebook. These feedback types were integrated in EnergyWiz – a mobile application that enables users to compare with their past performance, neighbours, contacts from social networking sites and other EnergyWiz users. The application was developed through a theory-driven approach and evaluated in personal, semi-structured interviews which provided insights on how motivation-related comparative feedback should be designed. It was also employed in expert focus group discussions which resulted in defining opportunities and challenges before mobile, social energy monitors. The findings have unequivocally shown that users with different motivations to compare and to conserve energy have different preferences for comparative feedback types and design. It was established that one of the most influential factors determining design factors is the people users compare to. In addition, the research found that even simple communication strategies in Facebook, such as wall posts and groups can contribute to engagement with energy conservation practices. The concept of mobility of the application was evaluated as positive since it provides place and time-independent access to the energy consumption data.

Australian domestic violence protection order legislation : a comparative quantitative content analysis of victim safety provisions

In Australia, protection orders are a key legal response to domestic violence, and are often viewed as a way of providing for victim safety. For instance, recently the joint Australian and New South Wales Law Reform Commissions recommended that a common core purpose of all state and territory domestic violence legislation should be ‘to ensure or maximise the safety and protection of persons who fear or experience family violence’ (2010:Recommendation 7-4). Drawing and building upon prior research in Australia and the United States (‘US’), this paper uses comparative quantitative content analysis to assess the victim safety focus of domestic violence protection order legislation in each Australian state and territory. The findings of this analysis show that the Northern Territory, South Australia and Victoria ‘stand out’ from the other jurisdictions, having the highest victim safety focus in their legislation. However, there remains sizeable scope for improvement in all Australian jurisdictions, in terms of the victim safety focus of their legislative provisions and the considerations of legislative inconsistency between jurisdictions.

Cumulative and comparative social media analytics for crisis communication

This paper draws on comparative analyses of Twitter data sets – over time and across different kinds of natural disasters and different national contexts – to demonstrate the value of shared, cumulative approaches to social media analytics in the context of crisis communication.

Functional significance of male attractants of Bactrocera tryoni (Diptera: Tephritidae) and underlying mechanisms

This project elucidated functional role of phytochemicals used in the management of pest fruit flies. Comparative behavioural, physiological and genomic approaches revealed that phytochemicals are mediating reproductive fitness by changing pheromonal compound males release and by making them physiologically more active. The possible mechanistic functions are that the phytochemicals act as a pheromone booster and as an energy supplement.

A comparative analysis of risk stratification tools for emergency department patients with chest pain

Background: Appropriate disposition of emergency department (ED) patients with chest pain is dependent on clinical evaluation of risk. A number of chest pain risk stratification tools have been proposed. The aim of this study was to compare the predictive performance for major adverse cardiac events (MACE) using risk assessment tools from the National Heart Foundation of Australia (HFA), the Goldman risk score and the Thrombolysis in Myocardial Infarction risk score (TIMI RS). Methods: This prospective observational study evaluated ED patients aged ≥30 years with non-traumatic chest pain for which no definitive non-ischemic cause was found. Data collected included demographic and clinical information, investigation findings and occurrence of MACE by 30 days. The outcome of interest was the comparative predictive performance of the risk tools for MACE at 30 days, as analyzed by receiver operator curves (ROC). Results: Two hundred eighty-one patients were studied; the rate of MACE was 14.1%. Area under the curve (AUC) of the HFA, TIMI RS and Goldman tools for the endpoint of MACE was 0.54, 0.71 and 0.67, respectively, with the difference between the tools in predictive ability for MACE being highly significant [chi2 (3) = 67.21, N = 276, p < 0.0001]. Conclusion: The TIMI RS and Goldman tools performed better than the HFA in this undifferentiated ED chest pain population, but selection of cutoffs balancing sensitivity and specificity was problematic. There is an urgent need for validated risk stratification tools specific for the ED chest pain population.

A comparative study of the semi-elastic and fully-elastic MapReduce models

MapReduce is a computation model for processing large data sets in parallel on large clusters of machines, in a reliable, fault-tolerant manner. A MapReduce computation is broken down into a number of map tasks and reduce tasks, which are performed by so called mappers and reducers, respectively. The placement of the mappers and reducers on the machines directly affects the performance and cost of the MapReduce computation in cloud computing. From the computational point of view, the mappers/reducers placement problem is a generation of the classical bin packing problem, which is NP-complete. Thus, in this paper we propose a new heuristic algorithm for the mappers/reducers placement problem in cloud computing and evaluate it by comparing with other several heuristics on solution quality and computation time by solving a set of test problems with various characteristics. The computational results show that our heuristic algorithm is much more efficient than the other heuristics and it can obtain a better solution in a reasonable time. Furthermore, we verify the effectiveness of our heuristic algorithm by comparing the mapper/reducer placement for a benchmark problem generated by our heuristic algorithm with a conventional mapper/reducer placement which puts a fixed number of mapper/reducer on each machine. The comparison results show that the computation using our mapper/reducer placement is much cheaper than the computation using the conventional placement while still satisfying the computation deadline.

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.

Mapping journalism cultures across nations : a comparative study of 18 countries

This article reports key findings from a comparative survey of the role perceptions, epistemological orientations and ethical views of 1800 journalists from 18 countries. The results show that detachment, non-involvement, providing political information and monitoring the government are considered essential journalistic functions around the globe. Impartiality, the reliability and factualness of information, as well as adherence to universal ethical principles are also valued worldwide, though their perceived importance varies across countries. Various aspects of interventionism, objectivism and the importance of separating facts from opinion, on the other hand, seem to play out differently around the globe. Western journalists are generally less supportive of any active promotion of particular values, ideas and social change, and they adhere more to universal principles in their ethical decisions. Journalists from non-western contexts, on the other hand, tend to be more interventionist in their role perceptions and more flexible in their ethical views.