Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model

Background The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny. Due to the problems caused by the uncertainty in alignment, existing tools for phylogenetic analysis based on multiple alignment could not be directly applied to the whole-genome comparison and phylogenomic studies of viruses. There has been a growing interest in alignment-free methods for phylogenetic analysis using complete genome data. Among the alignment-free methods, a dynamical language (DL) method proposed by our group has successfully been applied to the phylogenetic analysis of bacteria and chloroplast genomes. Results In this paper, the DL method is used to analyze the whole-proteome phylogeny of 124 large dsDNA viruses and 30 parvoviruses, two data sets with large difference in genome size. The trees from our analyses are in good agreement to the latest classification of large dsDNA viruses and parvoviruses by the International Committee on Taxonomy of Viruses (ICTV). Conclusions The present method provides a new way for recovering the phylogeny of large dsDNA viruses and parvoviruses, and also some insights on the affiliation of a number of unclassified viruses. In comparison, some alignment-free methods such as the CV Tree method can be used for recovering the phylogeny of large dsDNA viruses, but they are not suitable for resolving the phylogeny of parvoviruses with a much smaller genome size.

Cardiac health diagnosis using higher order spectra and support vector machine

The Electrocardiogram (ECG) is an important bio-signal representing the sum total of millions of cardiac cell depolarization potentials. It contains important insight into the state of health and nature of the disease afflicting the heart. Heart rate variability (HRV) refers to the regulation of the sinoatrial node, the natural pacemaker of the heart by the sympathetic and parasympathetic branches of the autonomic nervous system. The HRV signal can be used as a base signal to observe the heart's functioning. These signals are non-linear and non-stationary in nature. So, higher order spectral (HOS) analysis, which is more suitable for non-linear systems and is robust to noise, was used. An automated intelligent system for the identification of cardiac health is very useful in healthcare technology. In this work, we have extracted seven features from the heart rate signals using HOS and fed them to a support vector machine (SVM) for classification. Our performance evaluation protocol uses 330 subjects consisting of five different kinds of cardiac disease conditions. We demonstrate a sensitivity of 90% for the classifier with a specificity of 87.93%. Our system is ready to run on larger data sets.

Managing Wetlands Sustainably as Ecosystems: The Contribution of the Law (Part 2)

In this Part 2 attention is turned towards the legal arrangements in nation states for managing wetlands. These national arrangements have effect within the international arrangements already mentioned and any regional arrangements that are relevant. However, each national system is a reflection of its own historical, cultural, political and constitutional background. It is the purpose of this Part 2 to review and assess the national approaches to wetlands management. This involves an analysis of a range of instruments. These are: constitutional rules; strategic rules; regulatory rules; and management rules. Each of these sets of rules performs different functions, assumes different forms and is differentially capable of enforcement.

Spectroscopic and structural characterization of pascoite

Pascoite mineral having yellow-orange colour of Colorado, USA origin has been characterized by EPR, optical and NIR spectroscopy. The colour dark red-orange to yellow-orange colour of the pascoite indicates that the mineral contain mixed valency of vanadium. The optical spectrum exhibits a number of electronic bands due to presence of VO(II) ions in the mineral. From EPR studies, the parameters of g, A are evaluated and the data confirm that the ion is in distorted octahedron. Optical absorption studies reveal that two sets of VO(II) is in distorted octahedron. The bands in NIR spectra are due to the overtones and combinations of water molecules.

Beware of geeks bearing gifts? Online latent and untapped outlets for farmers' markets in South East Wales

This chapter sets out to identify related issues surrounding the use of Information and Computer Technology (ICT) in developing relationships between local food producers and consumers (both individuals and businesses). Three surveys were conducted in South- East Wales to consider the overlapping issues. The first concerned the role of ICT in relationships between farmers’ market (FMs) vendors and their traditional customers. The second survey examined potential new markets for farmers in the propensity of restaurants and hotels to buy locally, the types and sources of purchases made and the modes of advertising of these businesses. The final survey focused on the potential to expand local web- based selling of farmers’ produce in the future, by examining the potential market of high ICT- use small hotels. Despite the development of tailored ICT facilities, farmers’ market vendors and current individual customers are antipathetic to them. In addition, whilst there is a desire for more local produce particularly amongst independent local restaurants and hotels, this has not been capitalised upon and there is much work to be done even amongst high ICT-use small hotels, to expand the range and scope of farmers’ markets. This raises the need for creation and utilisation of enhanced logistics, payment and marketing management capacity available through a web- based presence, linked to promotion of FMs in business- to- business (B2B) links with local restaurants and hotels. This linked quantitative research highlights the potential value in substantial development of both web portals and supporting logistics to exploit this potential in the future.

Optimising collection of footprint evidence from crime scenes and suspects

Analysis of either footprints or footwear impressions which have been recovered from a crime scene is a well known and well accepted part of forensic investigation. When this evidence is obtained by investigating officers, comparative analysis to a suspect’s evidence may be undertaken. This can be done either by the detectives or in some cases, podiatrists with experience in forensic analysis. Frequently asked questions of a podiatrist include; “What additional information should be collected from a suspect (for the purposes of comparison), and how should it be collected?” This paper explores the answers to these and related questions based on 20 years of practical experience in the field of crime scene analysis as it relates to podiatry and forensics. Elements of normal and abnormal foot function are explored and used to explain the high degree of variability in wear patterns produced by the interaction of the foot and footwear. Based on this understanding the potential for identifying unique features of the user and correlating this to footwear evidence becomes apparent. Standard protocols adopted by podiatrists allow for more precise, reliable, and valid results to be obtained from their analysis. Complex data sets are now being obtained by investigating officers and, in collaboration with the podiatrist; higher quality conclusions are being achieved. This presentation details the results of investigations which have used standard protocols to collect and analyse footwear and suspects of recent major crimes.

Controlling chaos? The value and the challenges of applying complexity theory to project management

The literature abounds with descriptions of failures in high-profile projects and a range of initiatives has been generated to enhance project management practice (e.g., Morris, 2006). Estimating from our own research, there are scores of other project failures that are unrecorded. Many of these failures can be explained using existing project management theory; poor risk management, inaccurate estimating, cultures of optimism dominating decision making, stakeholder mismanagement, inadequate timeframes, and so on. Nevertheless, in spite of extensive discussion and analysis of failures and attention to the presumed causes of failure, projects continue to fail in unexpected ways. In the 1990s, three U.S. state departments of motor vehicles (DMV) cancelled major projects due to time and cost overruns and inability to meet project goals (IT-Cortex, 2010). The California DMV failed to revitalize their drivers’ license and registration application process after spending $45 million. The Oregon DMV cancelled their five year, $50 million project to automate their manual, paper-based operation after three years when the estimates grew to $123 million; its duration stretched to eight years or more and the prototype was a complete failure. In 1997, the Washington state DMV cancelled their license application mitigation project because it would have been too big and obsolete by the time it was estimated to be finished. There are countless similar examples of projects that have been abandoned or that have not delivered the requirements.

Gender equity policies in higher education in Japan

In a similar fashion to many western countries, the political context of Japan has been transformed since the 1975 UN World Conference on Women, which eventually led to the establishment of the Basic Law for a Gender-equal Society in Japan in 1999. The Basic Law sets out a series of general guidelines across every field of society, including education. This trajectory policy research study targets gender issues in Japanese higher education and follows the development of the Basic Law and, in particular, how it has been interpreted by bureaucrats and implemented within the field of higher education. This feminist policy research study examines Japanese power relationships within the field of gender and identifies gender discourses embedded within Japanese gender equity policy documents. The study documents the experiences of, and strategies used by, Japanese feminists in relation to gender equity policies in education. Drawing on critical feminist theory and feminist critical discourse theory, the study explores the relationship between gender discourses and social practices and analyses how unequal gender relations have been sustained through the implementation of Japanese gender equity policy. Feminist critical policy analysis and feminist critical discourse analysis have been used to examine data collected through interviews with key players, including policy makers and policy administrators from the national government and higher education institutions offering teacher education courses. The study also scrutinises the minutes of government meetings, and other relevant policy documents. The study highlights the struggles between policy makers in the government and bureaucracy, and feminist educators working for change. Following an anti-feminist backlash, feminist discourses in the original policy documents were weakened or marginalised in revisions, ultimately weakening the impact of the Basic Law in the higher education institutions. The following four key findings are presented within the research: 1) tracking of the original feminist teachers’ movement that existed just prior to the development of the Basic Law in 1999; 2) the formation of the Basic Law, and how the policy resulted in a weakening of the main tenets of women’s policy from a feminist perspective; 3) the problematic manner in which the Basic Law was interpreted at the bureaucratic level; and 4) the limited impact of the Basic Law on higher education and the strategies and struggles of feminist scholars in reaction to this law.

Consumers’ intentions to adopt 3G in regional cities in China : a comparative study

Rapid mobile technological evolution and the large economic stake in commercial development of mobile technological innovation make it necessary to understand consumers' motivations towards the latest advanced and updated technologies and services. 3G (the third generation of mobile communication technology) recently started its commercial development in the world‘s largest mobile communication market, China, after being delayed for a few years. Although China fell behind in commercially developing 3G, it is difficult to ignore studying this area, given the size of the market and promising future developments. This market deserves focused research attention, especially in terms of consumer behaviour towards the adoption of mobile technological innovation. Thus, the program of research in this thesis was designed to investigate how Chinese consumers respond to the use of this newly launched mobile technological innovation, with a focus on what factors affect their 3G adoption intentions. It aimed to yield important insights into Chinese consumers‘ innovation adoption behaviours and to contribute to marketing and innovation adoption research. Furthermore, it has been documented that Chinese consumers vary widely between regions in dialect, lifestyle, culture, purchasing power and consumption attitudes. Based on economic development and local culture, China can be divided geographically into distinctive regional consumer markets. Consequently, the results of consumer behaviour research in one region may not necessarily be extrapolated to other regions. In order to better understand Chinese consumers, the disparities between regions should not be overlooked. Therefore, another objective of this program of research was to examine regional variances in consumers' innovation adoption, specifically to identify the similarities and differences in factors influencing 3G adoption, contributing to intra-cultural studies. An extensive literature review identified two gaps: current China-based innovation adoption research studies are limited in providing adequate prediction and explanation of Chinese consumers' intentions to adopt 3G; and there was limited knowledge about the differences between regional Chinese consumers in innovation adoption. Two research questions therefore were developed to address these gaps: 1) What factors influence Chinese consumers' intentions to adopt 3G? 2) How do Chinese consumers differ between regional markets in the relative influence of the factors in determining their intentions to adopt 3G? In accordance with postpositivist research philosophy, two studies were designed to answer the research questions, using mixed methods. To meet the research objectives, the two studies were both conducted in three regional cities, namely Beijing, Shanghai and Wuhan, centred in the three regions of North China, East China and Central China respectively, with sufficient cultural and economical regional variances. Study One was an exploratory study with qualitative research methods. It involved 45 in-depth interviews in the three research cities to gain rich insights into the research context from natural settings. Eight important concepts related to 3G adoption were generated from analysis of the interview data, namely utilitarian expectation, hedonic expectation, status gains, status loss avoidance, normative influence, external influence, cost and quality concern. The concepts of social loss avoidance and quality concern were two unique findings, whereas the other concepts were similar to the findings in Western innovation adoption studies. Moreover, variances in 3G adoption between three groups of regional consumers were also identified, focusing on the perceptions of two concepts, namely status gains and normative influence. The conceptual research model was then developed incorporating the eight concepts plus the dependent variable of adoption intention. The hypothesized relationships between the nine constructs and hypotheses about the differences between regional consumers in 3G adoption were informed by the findings of Study One and the literature reviewed. Study Two was a quantitative study involving a web-based survey and statistical analysis procedure. The web-based survey attracted 800 residents from the three research cities, 270 from Beijing, 265 from Shanghai and 265 from Wuhan. They comprised three research samples for this study and consequently three sets of data were obtained. The data was analysed by Structural Equation Modelling together with Multi-group Analysis. The analysis confirmed that the concepts generated in Study One were influential factors affecting Chinese consumers' 3G adoption intention, with the exception of the concept external influence. Differences were found between the samples in the three research cities in the effect of hedonic expectation, status gains, status loss avoidance and normative influence on 3G adoption intention. The two Studies undertaken in this thesis contributed a better understanding of Chinese consumers' intentions to adopt advanced mobile technological innovation, namely 3G, in three regional markets. This knowledge contributes to innovation adoption and intra-cultural research, as well as consumer behaviour theory. It is also able to inform international and domestic telecommunication companies to develop and deliver more effective marketing strategies across Chinese regional markets. Limitations in the research were identified in terms of the sampling techniques used and the design of the two Studies. Future research was suggested in other Chinese regional markets and into consumer adoption of other types of mobile technological innovations.

Minimum labour standards enforcement in Australia : caught in the crossfire?

The complex transition from convict to free labour influenced state intervention in the employment relationship, and initiated the first minimum labour standards in Australia in 1828. Since then, two principal sets of tensions have affected the enforcement of such standards: tensions between government and employers, and tensions between the major political parties over industrial and economic issues. This article argues that these tensions have resulted in a sustained legacy affecting minimum labour standards’ enforcement in Australia. The article outlines broad historical developments and contexts of minimum labour standards’ enforcement in Australia since 1828, with more contemporary exploration focusing specifically on enforcement practices and policies in the Australian federal industrial relations jurisdiction. Current enforcement practices are an outcome of this volatile history, and past influences remain strong.

Marxism Today [Review]

The briefly resurrected Marxism Today (1998), edited by Martin Jacques, sets out to deal with perceived failures of the 'Blair project' (Jacques, 1998: 2). Jacques opens the issue by reaffirming that Blair, which is to say New Labour, is the successful creation of the 'New Left' projects, the first of which began in the late-fifties and early sixties in both Britain and the US, and which were vigorously revived in the late 1980s. However, the most comprehensive debate is fairly much contained in the first three articles, written by Hobsbawm, Hall, and Mulgan, insofar as the broadest defining parameters of Third Way 'values' are addressed by these writers.

Exponentiated gradient algorithms for conditional random fields and max-margin Markov Networks

Log-linear and maximum-margin models are two commonly-used methods in supervised machine learning, and are frequently used in structured prediction problems. Efficient learning of parameters in these models is therefore an important problem, and becomes a key factor when learning from very large data sets. This paper describes exponentiated gradient (EG) algorithms for training such models, where EG updates are applied to the convex dual of either the log-linear or max-margin objective function; the dual in both the log-linear and max-margin cases corresponds to minimizing a convex function with simplex constraints. We study both batch and online variants of the algorithm, and provide rates of convergence for both cases. In the max-margin case, O(1/ε) EG updates are required to reach a given accuracy ε in the dual; in contrast, for log-linear models only O(log(1/ε)) updates are required. For both the max-margin and log-linear cases, our bounds suggest that the online EG algorithm requires a factor of n less computation to reach a desired accuracy than the batch EG algorithm, where n is the number of training examples. Our experiments confirm that the online algorithms are much faster than the batch algorithms in practice. We describe how the EG updates factor in a convenient way for structured prediction problems, allowing the algorithms to be efficiently applied to problems such as sequence learning or natural language parsing. We perform extensive evaluation of the algorithms, comparing them to L-BFGS and stochastic gradient descent for log-linear models, and to SVM-Struct for max-margin models. The algorithms are applied to a multi-class problem as well as to a more complex large-scale parsing task. In all these settings, the EG algorithms presented here outperform the other methods.

Implicit online learning

Online learning algorithms have recently risen to prominence due to their strong theoretical guarantees and an increasing number of practical applications for large-scale data analysis problems. In this paper, we analyze a class of online learning algorithms based on fixed potentials and nonlinearized losses, which yields algorithms with implicit update rules. We show how to efficiently compute these updates, and we prove regret bounds for the algorithms. We apply our formulation to several special cases where our approach has benefits over existing online learning methods. In particular, we provide improved algorithms and bounds for the online metric learning problem, and show improved robustness for online linear prediction problems. Results over a variety of data sets demonstrate the advantages of our framework.

Relative entropy rate based design for linear hybrid system models

Hybrid system representations have been applied to many challenging modeling situations. In these hybrid system representations, a mixture of continuous and discrete states is used to capture the dominating behavioural features of a nonlinear, possible uncertain, model under approximation. Unfortunately, the problem of how to best design a suitable hybrid system model has not yet been fully addressed. This paper proposes a new joint state measurement relative entropy rate based approach for this design purpose. Design examples and simulation studies are presented which highlight the benefits of our proposed design approaches.

Evaluating the benefits of public bicycle schemes needs to be undertaken carefully

A letter in response to an article by David Rojas-Rueda, Audrey de Nazelle, Marko Tainio, Mark J Nieuwenhuijsen, The health risks and benefits of cycling in urban environments compared with car use: health impact assessment study. BMJ 2011;343:doi:10.1136/bmj.d4521 (Published 4 August 2011) This paper sets out to compare the health benefits of the Bicing scheme (Barcelona's public bicycle share scheme) with possible risks associated with increased bicycle riding. The key variables used by the researchers include physical activity, exposure to air pollution and road traffic injury. The authors rightly identify that although traffic congestion is often a major motivator behind the establishment of public bicycle share schemes (PBSS), the health benefits may well be the largest single benefit of such schemes. Certainly PBSS appear to be one of the most effective methods of increasing the number of bicycle trips across a population, providing additional transport options and improving awareness of the possibilities bicycles offer urban transport systems. Overall, the paper is a useful addition to the literature, in that it has attempted to assess the health benefits of a large scale PBSS and weighed these against potential risks related to cyclists exposure to air pollution and road traffic injuries. Unfortunately a fundamentally flawed assumption related to the proportion of Bicing trips replacing car journeys invalidates the results of this paper. A future paper with up to date data would create a significant contribution to this emerging area within the field of sustainable transport.