Predicting residue-wise contact orders in proteins by support vector regression

Background The residue-wise contact order (RWCO) describes the sequence separations between the residues of interest and its contacting residues in a protein sequence. It is a new kind of one-dimensional protein structure that represents the extent of long-range contacts and is considered as a generalization of contact order. Together with secondary structure, accessible surface area, the B factor, and contact number, RWCO provides comprehensive and indispensable important information to reconstructing the protein three-dimensional structure from a set of one-dimensional structural properties. Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships. Results We developed a novel approach to predict residue-wise contact order values in proteins based on support vector regression (SVR), starting from primary amino acid sequences. We explored seven different sequence encoding schemes to examine their effects on the prediction performance, including local sequence in the form of PSI-BLAST profiles, local sequence plus amino acid composition, local sequence plus molecular weight, local sequence plus secondary structure predicted by PSIPRED, local sequence plus molecular weight and amino acid composition, local sequence plus molecular weight and predicted secondary structure, and local sequence plus molecular weight, amino acid composition and predicted secondary structure. When using local sequences with multiple sequence alignments in the form of PSI-BLAST profiles, we could predict the RWCO distribution with a Pearson correlation coefficient (CC) between the predicted and observed RWCO values of 0.55, and root mean square error (RMSE) of 0.82, based on a well-defined dataset with 680 protein sequences. Moreover, by incorporating global features such as molecular weight and amino acid composition we could further improve the prediction performance with the CC to 0.57 and an RMSE of 0.79. In addition, combining the predicted secondary structure by PSIPRED was found to significantly improve the prediction performance and could yield the best prediction accuracy with a CC of 0.60 and RMSE of 0.78, which provided at least comparable performance compared with the other existing methods. Conclusion The SVR method shows a prediction performance competitive with or at least comparable to the previously developed linear regression-based methods for predicting RWCO values. In contrast to support vector classification (SVC), SVR is very good at estimating the raw value profiles of the samples. The successful application of the SVR approach in this study reinforces the fact that support vector regression is a powerful tool in extracting the protein sequence-structure relationship and in estimating the protein structural profiles from amino acid sequences.

Using multi-label classification for acoustic pattern detection and assisting bird species surveys

Acoustics is a rich source of environmental information that can reflect the ecological dynamics. To deal with the escalating acoustic data, a variety of automated classification techniques have been used for acoustic patterns or scene recognition, including urban soundscapes such as streets and restaurants; and natural soundscapes such as raining and thundering. It is common to classify acoustic patterns under the assumption that a single type of soundscapes present in an audio clip. This assumption is reasonable for some carefully selected audios. However, only few experiments have been focused on classifying simultaneous acoustic patterns in long-duration recordings. This paper proposes a binary relevance based multi-label classification approach to recognise simultaneous acoustic patterns in one-minute audio clips. By utilising acoustic indices as global features and multilayer perceptron as a base classifier, we achieve good classification performance on in-the-field data. Compared with single-label classification, multi-label classification approach provides more detailed information about the distributions of various acoustic patterns in long-duration recordings. These results will merit further biodiversity investigations, such as bird species surveys.

Multicultural education, global studies and studies of Asia

Like other nations, Australia has experienced significant change in the past few decades as its society has become increasingly diverse. The new cultures and traditions that result from ethnic and religious diversity have both enriched Australian society and presented it with some challenges. Other challenges have resulted from increased globalisation. For example, the economic fallout from the recent global financial crisis indicates that global issues can impact across a range of levels, from multinational corporations and nation-states to local sites and individual livelihoods. Some suggest that Australia fared better than other nations during this economic crisis because of its export trade with China. Although this is disputed by economists, it highlights another facet of change that is impacting on Australian society and this relates to Australia’s growing engagement with the nations of Asia. There is increasing awareness in education systems that if young people are to achieve their potential as future citizens they need to be able to negotiate the cultural, social, political and economic ties that connect them to the global and regional community through work, leisure and citizenship. Multicultural education, global studies and studies of Asia play a particular part in helping young people to: • appreciate cultural diversity within and beyond their own nation • imagine with some accuracy how others view their world • participate in shaping a better future. This chapter explores the origins, distinctions and common features of each approach.

Local and global : cultural globalization, consumerism, and children's fiction

According to Zygmunt Bauman in Liquid Modernity (2000), the formerly solid and stable institutions of social life that characterised earlier stages of modernity have become fluid. He sees this as an outcome of the modernist project of progress itself, which in seeking to dismantle oppressive structures failed to reconstruct new roles for society, community and the individual. The un-tethering of social life from tradition in the latter stages of the twentieth century has produced unprecedented freedoms and unparalleled uncertainties, at least in the West. Although Bauman’s elaboration of some of the features and drivers of liquid modernity – increased mobility, rapid communications technologies, individualism – suggests it to be a neologism for globalisation, it is arguably also the context which has allowed this phenomenon to flourish. The qualities of fluidity, leakage, and flow that distinguish uncontained liquids also characterise globalisation, which encompasses a range of global trends and processes no longer confined to, or controlled by, the ‘container’ of the nation or state. The concept of liquid modernity helps to explain the conditions under which globalisation discourses have found a purchase and, by extension, the world in which contemporary children’s literature, media, and culture are produced. Perhaps more significantly, it points to the fluid conceptions of self and other that inform the ‘liquid’ worldview of the current generation of consumers of texts for children and young adults. This generation is growing up under the phase of globalisation we describe in this chapter.

Global civil society and adult education for social change : a postcolonial perspective

Adult education plays an important role in global economic development and features prominently in debates about changing requirements of post-industrial knowledge societies. This dominant technical-instrumental understanding of adult education in public discourse masks the transformative function of certain types of adult education - that is, the possibilities of adult education to improve social justice issues such as workers’ rights, human rights, civic participation in governance and socially just development. Given the increasing social stratification between and within the North and South in the global era, the potential of adult education to effect social change has been rediscovered by organisations within global civil society, namely international non-governmental organisations (INGOs). The broad objective of this research was to carry out an in-depth qualitative case study of a human rights advocacy program provided by a Northern INGO predominantly operating within the global South. The study analyses how participants see this program in terms of its potential to contribute to progressive social change in their home communities across the Asia-Pacific region. The following questions guided the study: 1. To what extent does this adult education program challenge existing systems of domination and marginalisation? 2. How did completion of the program affect participants’ views of their abilities to facilitate social action within their communities? Data sources for this research were interviews with 19 participants and staff and questionnaires from 28 participants of the program from a variety of countries in the Asia-pacific region. The gap in the literature that this study addressed is that existing empirical research sidelines the analysis of the globalisation, adult education, and social change nexus from a perspective that takes the marginalised other seriously, tending instead to mirror the material subjugation of the South in discursive practices. Social change is highly context-specific and strategies to advance it depend on the way in which people understand their reality and are affected by adverse social conditions. The present study employed a postcolonial framework that provided a holistic approach to analysing adult education for social change inclusive of material, political, and social conditions and the interplay between these from the local to the global level. The program convincingly exemplified an example of adult education for counter-hegemonic resistance against the dominant neoliberal discourse. It achieved this by enabling participants, based on Freirian pedagogical principles, to locate the problem of social change and frame their strategies to address it within mutually constitutive local and global developments and the discourses that describe them. It provided the underpinning knowledge and skills for effective advocacy and created opportunities to build networks between various stakeholders. At minimum, most advocates accord their participation in the program a supporting role in enhancing their ability to examine causes for social injustices and ways to address these. Some advocates even regarded their program participation as fundamental in understanding these issues. Almost all participants reported an increased skill-set that enabled them to become more effective advocates.

Matching relevance features with ontological concepts

In order to comprehend user information needs by concepts, this paper introduces a novel method to match relevance features with ontological concepts. The method first discovers relevance features from user local instances. Then, a concept matching approach is developed for matching these features to accurate concepts in a global knowledge base. This approach is significant for the transition of informative descriptor and conceptional descriptor. The proposed method is elaborately evaluated by comparing against three information gathering baseline models. The experimental results shows the matching approach is successful and achieves a series of remarkable improvements on search effectiveness.

Global Human Trafficking : Critical Issues and Contexts

Human trafficking has moved from relative obscurity to a major area of research, policy and teaching over the past ten years. Research has sprung from criminology, public policy, women’s and gender studies, sociology, anthropology, and law, but has been somewhat hindered by the failure of scholars to engage beyond their own disciplines and favoured methodologies. Recent research has begun to improve efforts to understand the causes of the problem, the experiences of victims, policy efforts, and their consequences in specific cultural and historical contexts. Global Human Trafficking: Critical issues and contexts foregrounds recent empirical work on human trafficking from an interdisciplinary, critical perspective. The collection includes classroom-friendly features, such as introductory chapters that provide essential background for understanding the trafficking literature, textboxes explaining key concepts, discussion questions for each chapter, and lists of additional resources, including films, websites, and additional readings for each chapter. The authors include both eminent and emerging scholars from around the world, drawn from law, anthropology, criminology, sociology, cultural studies, and political science and the book will be useful for undergraduate and graduate courses in these areas, as well as for scholars interested in trafficking.

An analysis of the timeliness and nature of profit warnings in the aftermath of the Global Financial Crisis

The global financial crisis (GFC) has severely impacted the financial position and performance of many companies internationally. Because of its severity and associated increase in uncertainty it challenges the effectiveness of existing disclosure regulation. Australia provides a unique environment in which to test the effects of the GFC on corporate disclosure because statutory rules mandate the timely disclosure of ‘price-sensitive’ information (ASX Rule 3.1) by listed entities. Exploiting this institutional setting we investigate the determinants and timeliness of profit warnings issued by the top 500 ASX-listed firms with profit declines in the 2009 fiscal year. Our findings show that firms behave differently with regard to the issuance of profit warnings: larger and more indebted firms are more likely to issue a profit warning and tend to be timelier; surprisingly, poorer performing firms tend to release the news more quickly and this might be attributed to an increasing threat of litigation. Our analysis of profit warning determinants shows interesting results with the presence of asset impairments hindering the early disclosure of profit warnings. Our findings are novel for two main reasons: first, we provide insights into the impact of global financial crisis on profit warning behaviour; second, we are the first to examine the differential impact of alternative features of profit warnings on disclosure timeliness. The findings have implications for regulators in determining compliance with continuous disclosure rules and more broadly, for market participants in interpreting profit warnings.

Histogram matching and global initialization for laser-only SLAM in large unstructured environments

This paper presents an enhanced algorithm for matching laser scan maps using histogram correlations. The histogram representation effectively summarizes a map's salient features such that pairs of maps can be matched efficiently without any prior guess as to their alignment. The histogram matching algorithm has been enhanced in order to work well in outdoor unstructured environments by using entropy metrics, weighted histograms and proper thresholding of quality metrics. Thus our large-scale scan-matching SLAM implementation has a vastly improved ability to close large loops in real-time even when odometry is not available. Our experimental results have demonstrated a successful mapping of the largest area ever mapped to date using only a single laser scanner. We also demonstrate our ability to solve the lost robot problem by localizing a robot to a previously built map without any prior initialization.

Global journalism investigations in the digital age: Connections and collaborations

Investigative journalists who join what theorist Manuel Castells describes as the ‘network society’ can locate potential news sources using various social media platforms and interview them using Web-based communication technologies. The potential for journalistic investigations involving multi-directional conversations with news sources across the globe is beginning to be explored. Potential news sources who are part of the network society have unprecedented access to specialist investigative reporters irrespective of their location and can speak to them more cost effectively than in the past. This paper explores how new journalism technologies are allowing journalists to call powerful individuals and institutions to account, irrespective of national borders; and how previously silenced individuals are being given a voice. To read an example of international investigative journalism facilitated by a combination of social media, Web-based communications, reporter collaboration and news outlet collaborations see http://www.theaustralian.com.au/news/features/churchs-wall-of-silence-on-sexual-abuse/story-e6frg6z6-1226639077238.

Enhancing information about sustainability features for sustainable housing delivery

Sustainability practices in government regulations and within the society influence the delivery of sustainable housing. The actual delivery rate of Australian sustain-able housing is not as high as other countries. There is an absence of engagement by stakeholders in adopting sustainable housing practices. This may be due, in the current Australian property market, to confusion as to what sustainability features should be considered, given the large range of environmental, economic and social sustainability options possible. One of the main problems appears to be that information demanders, especially real estate agents, valuers, insurance agents and mortgage lenders do not include sustainability perspectives in their advice or in their decision processes. Information distribution in the Australian property market is flawed, resulting in a lack of return-on-investment value of ‘green’ features implemented by some stakeholders. This paper reviewed the global sustainable development concept and Australian sustainable assessment methods. This review identified the possibility of a research project which aimed at identifying and integrating different perceptions and priority needs of the information demanders, for developing a model for the potential implementation of sustainability features distribution in the property industry. This research will reduce confusion on the sustainability-related information which can influence the decision making of stakeholders in the supply and demand of sustainable housing.

A global perspective on psycho-educational assessment

For psychologists in less developed countries, psycho-educational assessment is often challenging due to a lack of specialist training and a scarcity of appropriate, psychometrically robust instruments. This paper focuses on school psychology and psycho-educational assessment in three countries: Bangladesh, China and Iran. Despite differences in demographic and cultural features, these countries share similar issues that restrict the practice of psycho-educational assessment. We conclude that it is important for psychologists in western countries to support professional training and testing practices in less developed countries.