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.

Role of kilometer-scale weak circular heterogeneities on upper crustal deformation patterns: Evidence from scaled analogue modeling and the Sudbury Basin, Canada

The Sudbury Basin is a non-cylindrical fold basin occupying the central portion of the Sudbury Impact Structure. The impact structure lends itself excellently to explore the structural evolution of continental crust containing a circular region of long-term weakness. In a series of scaled analogue experiments various model crustal configurations were shortened horizontally at a constant rate. In mechanically weakened crust, model basins formed that mimic several first-order structural characteristics of the Sudbury Basin: (1) asymmetric, non-cylindrical folding of the Basin, (2) structures indicating concentric shortening around lateral basin termini and (3) the presence of a zone of strain concentration near the hinge zones of model basins. Geometrically and kinematically this zone corresponds to the South Range Shear Zone of the Sudbury Basin. According to our experiments, this shear zone is a direct mechanical consequence of basin formation, rather than the result of thrusting following folding. Overall, the models highlight the structurally anomalous character of the Sudbury Basin within the Paleoproterozoic Eastern Penokean Orogen. In particular, our models suggest that the Basin formed by pure shear thickening of crust, whereas transpressive deformation prevailed elsewhere in the orogen. The model basin is deformed by thickening and non-cylindrical synformal buckling, while conjugate transpressive shear zones propagated away from its lateral tips. This is consistent with pure shear deformation of a weak circular inclusion in a strong matrix. The models suggest that the Sudbury Basin formed as a consequence of long-term weakening of the upper crust by meteorite impact.

The causes of sinuous crustal-scale deformation patterns in hot orogens: Evidence from scaled analogue experiments and the southern Central Andes

The cause of upper-crustal segmentation into rhomb-shaped, shear zone-bound domains associated with contractional sedimentary basins in hot, wide orogens is not well understood. Here we use scaled multilayered analogue experiments to investigate the role of an orogen-parallel crustal-strength gradient on the formation of such structures. We show that the aspect ratio and size of domains, the sinuous character and abundance of transpressional shear zones vary with the integrated mechanical strength of crust. Upper-crustal deformation patterns and the degree of strain localization in the experiments are controlled by the ratio between the brittle and ductile strength in the model crust as well as gradients in tectonic and buoyancy forces. The experimental results match the first-order kinematic and structural characteristics of the southern Central Andes and provide insight on the dynamics of underlying deformation patterns in hot, wide orogens.

Economic growth and inequality patterns in the presence of costly technology adoption and uncertainty

We develop a stochastic endogenous growth model to explain the diversity in growth and inequality patterns and the non-convergence of incomes in transitional economies where an underdeveloped financial sector imposes an implicit, fixed cost on the diversification of idiosyncratic risk. In the model endogenous growth occurs through physical and human capital deepening, with the latter being the more dominant element. We interpret the fixed cost as a ‘learning by doing’ cost for entrepreneurs who undertake risk in the absence of well developed financial markets and institutions that help diversify such risk. As such, this cost may be interpreted as the implicit returns foregone due to the lack of diversification opportunities that would otherwise have been available, had such institutions been present. The analytical and numerical results of the model suggest three growth outcomes depending on the productivity differences between the projects and the fixed cost associated with the more productive project. We label these outcomes as poverty trap, dual economy and balanced growth. Further analysis of these three outcomes highlights the existence of a diversity within diversity. Specifically, within the ‘poverty trap’ and ‘dual economy’ scenarios growth and inequality patterns differ, depending on the initial conditions. This additional diversity allows the model to capture a richer range of outcomes that are consistent with the empirical experience of several transitional economies.

Quantitative approaches to comparing communication patterns on Twitter

To date, the available literature mainly discusses Twitter activity patterns in the context of individual case studies, while comparative research on a large number of communicative events and their dynamics and patterns is missing. By conducting a comparative study of more than 40 different cases (covering topics such as elections, natural disasters, corporate crises, and televised events) we identify a number of distinct types of discussion that can be observed on Twitter. Drawing on a range of communicative metrics, we show that thematic and contextual factors influence the usage of different communicative tools available to Twitter users, such as original tweets, @replies, retweets, and URLs. Based on this first analysis of the overall metrics of Twitter discussions, we also demonstrate stable patterns in the use of Twitter in the context of major topics and events.

The process and patterns of combining the use of traditional Chinese medicine and Western medicine in Taiwanese people with cancer

Objective: The nature of contemporary cancer therapy means that patients are faced with difficult treatment decisions about surgery, chemotherapy and radiotherapy. For some, this process may also involve consideration of therapies that sit outside the biomedical approach to cancer treatment, in our research, traditional Chinese medicine (TCM). Thus, it is important to explore how cancer patients in Taiwan incorporate TCM into their cancer treatment journey. This paper aims to explore of the patterns of combining the use of TCM and Western medicine into cancer treatment journey in Taiwanese people with cancer. Methods: The sampling was purposive and the data collected through in-depth interviews. Data collection occurred over an eleven month. The research was grounded in the premises of symbolic interactionism and adopted the methods of grounded theory. Twenty four participants who were patients receiving cancer treatment were recruited from two health care settings in Taiwan. Results: The study findings suggest that perceptions of health and illness are mediated through ongoing interactions with different forms of therapy. The participants in this study had a clear focus on “process and patterns of using TCM and Western medicine”. Further, ‘different importance in Western medicine and TCM’, ‘taken for granted to use TCM’, ‘each has specialized skills in Western medicine and TCM’ and ‘different symptoms use different approaches (Western medicine or TCM)’ may explicit how the participants in this study see CAM and Western medicine. Conclusions/Implications for practice: The descriptive frame of the study suggests that TCM and Western medicine occupy quite distinct domains in terms of decision making over their use. People used TCM based on interpretations of the present and against a background of an enduring cultural legacy grounded in Chinese philosophical beliefs about health and healthcare. The increasingly popular term of 'integrative medicine' obscures the complex contexts of the patterns of use of both therapeutic modalities. It is this latter point that is worthy of further exploration.

Referral patterns and proximity to palliative care inpatient services by level of socio-economic disadvantage : a national study using spatial analysis

Background: A range of health outcomes at a population level are related to differences in levels of social disadvantage. Understanding the impact of any such differences in palliative care is important. The aim of this study was to assess, by level of socio-economic disadvantage, referral patterns to specialist palliative care and proximity to inpatient services. Methods: All inpatient and community palliative care services nationally were geocoded (using postcode) to one nationally standardised measure of socio-economic deprivation – Socio-Economic Index for Areas (SEIFA; 2006 census data). Referral to palliative care services and characteristics of referrals were described through data collected routinely at clinical encounters. Inpatient location was measured from each person’s home postcode, and stratified by socio-economic disadvantage. Results: This study covered July – December 2009 with data from 10,064 patients. People from the highest SEIFA group (least disadvantaged) were significantly less likely to be referred to a specialist palliative care service, likely to be referred closer to death and to have more episodes of inpatient care for longer time. Physical proximity of a person’s home to inpatient care showed a gradient with increasing distance by decreasing levels of socio-economic advantage. Conclusion: These data suggest that a simple relationship of low socioeconomic status and poor access to a referral-based specialty such as palliative care does not exist. Different patterns of referral and hence different patterns of care emerge.

Using patterns co-occurrence matrix for cleaning closed sequential patterns for text mining

With the overwhelming increase in the amount of texts on the web, it is almost impossible for people to keep abreast of up-to-date information. Text mining is a process by which interesting information is derived from text through the discovery of patterns and trends. Text mining algorithms are used to guarantee the quality of extracted knowledge. However, the extracted patterns using text or data mining algorithms or methods leads to noisy patterns and inconsistency. Thus, different challenges arise, such as the question of how to understand these patterns, whether the model that has been used is suitable, and if all the patterns that have been extracted are relevant. Furthermore, the research raises the question of how to give a correct weight to the extracted knowledge. To address these issues, this paper presents a text post-processing method, which uses a pattern co-occurrence matrix to find the relation between extracted patterns in order to reduce noisy patterns. The main objective of this paper is not only reducing the number of closed sequential patterns, but also improving the performance of pattern mining as well. The experimental results on Reuters Corpus Volume 1 data collection and TREC filtering topics show that the proposed method is promising.

Semantic labelling for document feature patterns using ontological subjects

Finding and labelling semantic features patterns of documents in a large, spatial corpus is a challenging problem. Text documents have characteristics that make semantic labelling difficult; the rapidly increasing volume of online documents makes a bottleneck in finding meaningful textual patterns. Aiming to deal with these issues, we propose an unsupervised documnent labelling approach based on semantic content and feature patterns. A world ontology with extensive topic coverage is exploited to supply controlled, structured subjects for labelling. An algorithm is also introduced to reduce dimensionality based on the study of ontological structure. The proposed approach was promisingly evaluated by compared with typical machine learning methods including SVMs, Rocchio, and kNN.

Spatial and temporal foraging patterns of Queensland fruit fly, Bactrocera tryoni(Froggatt) (Diptera: Tephritidae), for protein and implications for management

Fruit flies require protein for reproductive development and actively feed upon protein sources in the field. Liquid protein baits mixed with insecticide are used routinely to manage pest fruit flies, such as Bactrocera tryoni (Froggatt). However, there are still some gaps in the underpinning science required to improve the efficacy of bait spray technology. The spatial and temporal foraging behaviour of B. tryoni in response to protein was investigated in the field. A series of linked trials using either wild flies in the open field or laboratory-reared flies in field cages and a netted orchard were undertaken using nectarines and guavas. Key questions investigated were the fly's response to protein relative to: height of protein within the canopy, fruiting status of the tree, time of day, season and size of the experimental arena. Canopy height had a significant response on B. tryoni foraging, with more flies foraging on protein in the mid to upper canopy. Fruiting status also had a significant effect on foraging, with most flies responding to protein when applied to fruiting hosts. B. tryoni demonstrated a repeatable diurnal response pattern to protein, with the peak response being between 12:00–16:00 h. Season showed significant but unpredictable effects on fruit fly response to protein in the subtropical environment where the work was undertaken. Relative humidity, but not temperature or rainfall, was positively correlated with protein response. The number of B. tryoni responding to protein decreased dramatically as the spatial scale increased from field cage through to the open field. Based on these results, it is recommend that, to be most effective, protein bait sprays should be applied to the mid to upper canopies of fruiting hosts. Overall, the results show that the protein used, an industry standard, has very low attractancy to B. tryoni and that further work is urgently needed to develop more volatile protein baits.

Trends in cycling patterns and interactions with pedestrians in the city centre

All levels of government continue to advocate increasing the number of people cycling for recreation and transport. However, governments and the general public still have concerns about the implications for the safety of cyclists and other road users. While there is concern about injury for bicycle-pedestrian collisions, for 2008-09 in Australia only 40 pedestrians were hospitalised as a result of a collision with a cyclist (and 33 cyclists from collisions with pedestrians). There is little research that observes changes over time in actual cyclist behaviours and interactions with other road users. This paper presents the results of an observational study of cycling in the Brisbane Central Business District based on data collected using the same methodology in October 2010 and 2012.

Evaluation of strain energy based damage indices for flexural crack detection of RC beams

Vibration Based Damage Identification Techniques which use modal data or their functions, have received significant research interest in recent years due to their ability to detect damage in structures and hence contribute towards the safety of the structures. In this context, Strain Energy Based Damage Indices (SEDIs), based on modal strain energy, have been successful in localising damage in structuers made of homogeneous materials such as steel. However, their application to reinforced concrete (RC) structures needs further investigation due to the significant difference in the prominent damage type, the flexural crack. The work reported in this paper is an integral part of a comprehensive research program to develop and apply effective strain energy based damage indices to assess damage in reinforced concrete flexural members. This research program established (i) a suitable flexural crack simulation technique, (ii) four improved SEDI's and (iii) programmable sequentional steps to minimise effects of noise. This paper evaluates and ranks the four newly developed SEDIs and existing seven SEDIs for their ability to detect and localise flexural cracks in RC beams. Based on the results of the evaluations, it recommends the SEDIs for use with single and multiple vibration modes.

A cross-sectional analysis of patterns of obesity in a cohort of working nurses and midwives in Australia, New Zealand, and the United Kingdom

Objective The aim of this study was to examine the prevalence of overweight and obesity and the association with demographic, reproductive work variables in a representative cohort of working nurses and midwives. Design A cross sectional study of self reported survey data. Settings Australia, New Zealand and the United Kingdom. Methods Measurement outcomes included BMI categories, demographic (age, gender, marital status, ethnicity), reproductive (parity, number of births, mother's age at first birth, birth type and menopausal status) and workforce (registration council, employment type and principal specialty) variables. Participants 4996 respondents to the Nurses and Midwives e-Cohort study who were currently registered and working in nursing or midwifery in Australia (n=3144), New Zealand (n=778) or the United Kingdom (n=1074). Results Amongst the sample 61.87% were outside the healthy weight range and across all three jurisdictions the prevalence of obesity in nurses and midwives exceeded rates in the source populations by 1.73% up to 3.74%. Being overweight or obese was significantly associated with increasing age (35–44 yrs aOR 1.71, 95% CI 1.41–2.08; 45–55 yrs aOR 1.90, 95%CI 1.56–2.31; 55–64 aOR 2.22, 95% CI 1.71–2.88), and male gender (aOR 1.46, 95% CI 1.15–1.87). Primiparous nurses and midwives were more likely to be overweight or obese (aOR 1.37, 95% CI 1.06–1.76) as were those who had reached menopause (aOR 1.37, 95% CI 1.11–1.69). Nurses and midwives in part-time or casual employment had significantly reduced risk of being overweight or obese, (aOR 0.81, 95% CI 0.70–0.94 and aOR 0.75, 95% CI 0.59–0.96 respectively), whilst working in aged carried increased risk (aOR 1.37, 95% CI 1.04–1.80). Conclusion Nurses and midwives in this study have higher prevalence of obesity and overweight than the general population and those who are older, male, or female primiparous and menopausal have significantly higher risk of overweight or obesity as do those working fulltime, or in aged care. The consequences of overweight and obesity in this occupational group may impact on their workforce participation, their management of overweight and obese patients in their care as well as influencing their individual health behaviours and risks of occupational injury and chronic disease.

Image-based flow visualisation (IBFV) to enhance interpretation of complex flow patterns within a shallow tidal barrier estuary

We applied a texture-based flow visualisation technique to a numerical hydrodynamic model of the Pumicestone Passage in southeast Queensland, Australia. The quality of the visualisations using our flow visualisation tool, are compared with animations generated using more traditional drogue release plot and velocity contour and vector techniques. The texture-based method is found to be far more effective in visualising advective flow within the model domain. In some instances, it also makes it easier for the researcher to identify specific hydrodynamic features within the complex flow regimes of this shallow tidal barrier estuary as compared with the direct and geometric based methods.