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.

Benefit cost analysis applied to behavioral and engineering safety countermeasures in San Francisco, California

The state of the practice in safety has advanced rapidly in recent years with the emergence of new tools and processes for improving selection of the most cost-effective safety countermeasures. However, many challenges prevent fair and objective comparisons of countermeasures applied across safety disciplines (e.g. engineering, emergency services, and behavioral measures). These countermeasures operate at different spatial scales, are funded often by different financial sources and agencies, and have associated costs and benefits that are difficult to estimate. This research proposes a methodology by which both behavioral and engineering safety investments are considered and compared in a specific local context. The methodology involves a multi-stage process that enables the analyst to select countermeasures that yield high benefits to costs, are targeted for a particular project, and that may involve costs and benefits that accrue over varying spatial and temporal scales. The methodology is illustrated using a case study from the Geary Boulevard Corridor in San Francisco, California. The case study illustrates that: 1) The methodology enables the identification and assessment of a wide range of safety investment types at the project level; 2) The nature of crash histories lend themselves to the selection of both behavioral and engineering investments, requiring cooperation across agencies; and 3) The results of the cost-benefit analysis are highly sensitive to cost and benefit assumptions, and thus listing and justification of all assumptions is required. It is recommended that a sensitivity analyses be conducted when there is large uncertainty surrounding cost and benefit assumptions.

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.

Analysis of multilateral service conversations in global business networks

The rapid growth of services available on the Internet and exploited through ever globalizing business networks poses new challenges for service interoperability. New services, from consumer “apps”, enterprise suites, platform and infrastructure resources, are vying for demand with quickly evolving and overlapping capabilities, and shorter cycles of extending service access from user interfaces to software interfaces. Services, drawn from a wider global setting, are subject to greater change and heterogeneity, demanding new requirements for structural and behavioral interface adaptation. In this paper, we analyze service interoperability scenarios in global business networks, and propose new patterns for service interactions, above those proposed over the last 10 years through the development of Web service standards and process choreography languages. By contrast, we reduce assumptions of design-time knowledge required to adapt services, giving way to run-time mismatch resolutions, extend the focus from bilateral to multilateral messaging interactions, and propose declarative ways in which services and interactions take part in long-running conversations via the explicit use of state.

Identity theft, computers and behavioral biometrics

The increase of online services, such as eBanks, WebMails, in which users are verified by a username and password, is increasingly exploited by Identity Theft procedures. Identity Theft is a fraud, in which someone pretends to be someone else is order to steal money or get other benefits. To overcome the problem of Identity Theft an additional security layer is required. Within the last decades the option of verifying users based on their keystroke dynamics was proposed during login verification. Thus, the imposter has to be able to type in a similar way to the real user in addition to having the username and password. However, verifying users upon login is not enough, since a logged station/mobile is vulnerable for imposters when the user leaves her machine. Thus, verifying users continuously based on their activities is required. Within the last decade there is a growing interest and use of biometrics tools, however, these are often costly and require additional hardware. Behavioral biometrics, in which users are verified, based on their keyboard and mouse activities, present potentially a good solution. In this paper we discuss the problem of Identity Theft and propose behavioral biometrics as a solution. We survey existing studies and list the challenges and propose solutions.

A generic framework and runtime environment for development and evaluation of behavioral biometrics solutions

Increasing use of computerized systems in our daily lives creates new adversarial opportunities for which complex mechanisms are exploited to mend the rapid development of new attacks. Behavioral Biometrics appear as one of the promising response to these attacks. But it is a relatively new research area, specific frameworks for evaluation and development of behavioral biometrics solutions could not be found yet. In this paper we present a conception of a generic framework and runtime environment which will enable researchers to develop, evaluate and compare their behavioral biometrics solutions with repeatable experiments under the same conditions with the same data.

Behavioral biometrics for persistent single sign-on

Driven by the rapid development of ubiquitous and pervasive computing, personalized services and applications are deployed to support our lives. Accordingly, the number of interfaces and devices (smartphone, tablet computer, etc.) provided to access and consume these services is growing continuously. To simplify the complexity of managing many accounts with different credentials, Single Sign-On (SSO) solutions have been introduced. However, a single password for many accounts represents a single-point-of-failure. Furthermore, once initiated SSO session is a high potential risk when the working station is left unlocked and unattended. In this paper, we present a conception of a Persistent Single Sign-On (PSSO) for ubiquitous home environments by involving the capabilities of Behavioral Biometrics to check the identity of the user continuously in an unobtrusive manner.

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.