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.

Machine recognition of hand-drawn circuit diagrams

An application of image processing techniques to recognition of hand-drawn circuit diagrams is presented. The scanned image of a diagram is pre-processed to remove noise and converted to bilevel. Morphological operations are applied to obtain a clean, connected representation using thinned lines. The diagram comprises of nodes, connections and components. Nodes and components are segmented using appropriate thresholds on a spatially varying object pixel density. Connection paths are traced using a pixel-stack. Nodes are classified using syntactic analysis. Components are classified using a combination of invariant moments, scalar pixel-distribution features, and vector relationships between straight lines in polygonal representations. A node recognition accuracy of 82% and a component recognition accuracy of 86% was achieved on a database comprising 107 nodes and 449 components. This recogniser can be used for layout “beautification” or to generate input code for circuit analysis and simulation packages

Dynamic texture reconstruction from sparse codes for unusual event detection in crowded scenes

Unusual event detection in crowded scenes remains challenging because of the diversity of events and noise. In this paper, we present a novel approach for unusual event detection via sparse reconstruction of dynamic textures over an overcomplete basis set, with the dynamic texture described by local binary patterns from three orthogonal planes (LBPTOP). The overcomplete basis set is learnt from the training data where only the normal items observed. In the detection process, given a new observation, we compute the sparse coefficients using the Dantzig Selector algorithm which was proposed in the literature of compressed sensing. Then the reconstruction errors are computed, based on which we detect the abnormal items. Our application can be used to detect both local and global abnormal events. We evaluate our algorithm on UCSD Abnormality Datasets for local anomaly detection, which is shown to outperform current state-of-the-art approaches, and we also get promising results for rapid escape detection using the PETS2009 dataset.

Managing the project learning paradox : a set-theoretic approach toward project knowledge transfer

Managing project-based learning is becoming an increasingly important part of project management. This article presents a comparative case study of 12 cases of knowledge transfer between temporary inter-organizational projects and permanent parent organizations. Our set-theoretic analysis of these data yields two major findings. First, a high level of absorptive capacity of the project owner is a necessary condition for successful project knowledge transfer, which implies that the responsibility for knowledge transfer seems to in the first place lie with the project parent organization, not with the project manager. Second, none of the factors are sufficient by themselves. This implies that successful project knowledge transfer is a complex process always involving configurations of multiple factors. We link these implications with the view of projects as complex temporary organizational forms in which successful project managers need to cope with complexity by simultaneously paying attention to both relational and organizational processes.

Urban Informatics Research and Insights for Libraries, Cultural Industries and Innovation Systems

Over less than a decade, we have witnessed a seismic shift in the way knowledge is produced and exchanged. This is opening up new opportunities for civic and community engagement, entrepreneurial behaviour, sustainability initiatives and creative practices. It also has the potential to create fresh challenges in areas of privacy, cyber-security and misuse of data and personal information. The field of urban informatics focuses on the use and impacts of digital media technology in urban environments. Urban informatics is a dynamic and cross-disciplinary area of inquiry that encapsulates social media, ubiquitous computing, mobile applications and location-based services. Its insights suggest the emergence of a new economic force with the potential for driving innovation, wealth and prosperity through technological advances, digital media and online networks that affect patterns of both social and economic development. Urban informatics explores the intersections between people, place and technology, and their implications for creativity, innovation and engagement. This paper examines how the key learnings from this field can be used to position creative and cultural institutions such as galleries, libraries, archives and museums (GLAM) to take advantage of the opportunities presented by these changing social and technological developments. This paper introduces the underlying principles, concepts and research areas of urban informatics, against the backdrop of modern knowledge economies. Both theoretical ideas and empirical examples are covered in this paper. The first part discusses three challenges: a. People, and the challenge of creativity: The paper explores the opportunities and challenges of urban informatics that can lead to the design and development of new tools, methods and applications fostering participation, the democratisation of knowledge, and new creative practices. b. Technology, and the challenge of innovation: The paper examines how urban informatics can be applied to support user-led innovation with a view to promoting entrepreneurial ideas and creative industries. c. Place, and the challenge of engagement: The paper discusses the potential to establish place-based applications of urban informatics, using the example of library spaces designed to deliver community and civic engagement strategies. The discussion of these challenges is illustrated by a review of projects as examples drawn from diverse fields such as urban computing, locative media, community activism, and sustainability initiatives. The second part of the paper introduces an empirically grounded case study that responds to these three challenges: The Edge, the Queensland Government’s Digital Culture Centre which is an initiative of the State Library of Queensland to explore the nexus of technology and culture in an urban environment. The paper not only explores the new role of libraries in the knowledge economy, but also how the application of urban informatics in prototype engagement spaces such as The Edge can provide transferable insights that can inform the design and development of responsive and inclusive new library spaces elsewhere. To set the scene and background, the paper begins by drawing the bigger picture and outlining some key characteristics of the knowledge economy and the role that the creative and cultural industries play in it, grasping new opportunities that can contribute to the prosperity of Australia.

The undirected feedback vertex set problem has a Poly(k) Kernel

Resolving a noted open problem, we show that the Undirected Feedback Vertex Set problem, parameterized by the size of the solution set of vertices, is in the parameterized complexity class Poly(k), that is, polynomial-time pre-processing is sufficient to reduce an initial problem instance (G, k) to a decision-equivalent simplified instance (G', k') where k' � k, and the number of vertices of G' is bounded by a polynomial function of k. Our main result shows an O(k11) kernelization bound.

Development and validation of novel methods for microbial source tracking based on Escherichia coli as an indicator of water quality

Microbial pollution in water periodically affects human health in Australia, particularly in times of drought and flood. There is an increasing need for the control of waterborn microbial pathogens. Methods, allowing the determination of the origin of faecal contamination in water, are generally referred to as Microbial Source Tracking (MST). Various approaches have been evaluated as indicatorsof microbial pathogens in water samples, including detection of different microorganisms and various host-specific markers. However, until today there have been no universal MST methods that could reliably determine the source (human or animal) of faecal contamination. Therefore, the use of multiple approaches is frequently advised. MST is currently recognised as a research tool, rather than something to be included in routine practices. The main focus of this research was to develop novel and universally applicable methods to meet the demands for MST methods in routine testing of water samples. Escherichia coli was chosen initially as the object organism for our studies as, historically and globally, it is the standard indicator of microbial contamination in water. In this thesis, three approaches are described: single nucleotide polymorphism (SNP) genotyping, clustered regularly interspaced short palindromic repeats (CRISPR) screening using high resolution melt analysis (HRMA) methods and phage detection development based on CRISPR types. The advantage of the combination SNP genotyping and CRISPR genes has been discussed in this study. For the first time, a highly discriminatory single nucleotide polymorphism interrogation of E. coli population was applied to identify the host-specific cluster. Six human and one animal-specific SNP profile were revealed. SNP genotyping was successfully applied in the field investigations of the Coomera watershed, South-East Queensland, Australia. Four human profiles [11], [29], [32] and [45] and animal specific SNP profile [7] were detected in water. Two human-specific profiles [29] and [11] were found to be prevalent in the samples over a time period of years. The rainfall (24 and 72 hours), tide height and time, general land use (rural, suburban), seasons, distance from the river mouth and salinity show a lack of relashionship with the diversity of SNP profiles present in the Coomera watershed (p values > 0.05). Nevertheless, SNP genotyping method is able to identify and distinquish between human- and non-human specific E. coli isolates in water sources within one day. In some samples, only mixed profiles were detected. To further investigate host-specificity in these mixed profiles CRISPR screening protocol was developed, to be used on the set of E. coli, previously analysed for SNP profiles. CRISPR loci, which are the pattern of previous DNA coliphages attacks, were considered to be a promising tool for detecting host-specific markers in E. coli. Spacers in CRISPR loci could also reveal the dynamics of virulence in E. coli as well in other pathogens in water. Despite the fact that host-specificity was not observed in the set of E. coli analysed, CRISPR alleles were shown to be useful in detection of the geographical site of sources. HRMA allows determination of ‘different’ and ‘same’ CRISPR alleles and can be introduced in water monitoring as a cost-effective and rapid method. Overall, we show that the identified human specific SNP profiles [11], [29], [32] and [45] can be useful as marker genotypes globally for identification of human faecal contamination in water. Developed in the current study, the SNP typing approach can be used in water monitoring laboratories as an inexpensive, high-throughput and easy adapted protocol. The unique approach based on E. coli spacers for the search for unknown phage was developed to examine the host-specifity in phage sequences. Preliminary experiments on the recombinant plasmids showed the possibility of using this method for recovering phage sequences. Future studies will determine the host-specificity of DNA phage genotyping as soon as first reliable sequences can be acquired. No doubt, only implication of multiple approaches in MST will allow identification of the character of microbial contamination with higher confidence and readability.

School education as social and economic governance : responsibilising communities through industry-school engagement

This article examines shifts in educational and social governance taking place in Queensland, Australia, through Industry School Engagement Strategy of Education Queensland and its Gateway Schools program. This significant educational initiative is set within the context of the social investment agenda first articulated in the education policy framework, Queensland State Education-2010. The article traces the historic extension of this governmental strategy through establishment of the Gateway Schools concept that brokers industry-school partnerships with global players in the Queensland economy. Industry sectors forming the partnerships include Minerals and Energy, Aerospace, Wine Tourism, Agribusiness, Manufacturing and Engineering, Building and Construction and ICT. We argue that this ‘post-bureaucratic’ model of schooling represents a new social settlement of neoliberal governance, in which educational outcomes align with economic objectives, and frame the conditions for community self-governance.

Beyond MOF constraints : multiple constraint set metamodelling for lifecycle management

The management of models over time in many domains requires different constraints to apply to some parts of the model as it evolves. Using EMF and its meta-language Ecore, the development of model management code and tools usually relies on the meta- model having some constraints, such as attribute and reference cardinalities and changeability, set in the least constrained way that any model user will require. Stronger versions of these constraints can then be enforced in code, or by attaching additional constraint expressions, and their evaluations engines, to the generated model code. We propose a mechanism that allows for variations to the constraining meta-attributes of metamodels, to allow enforcement of different constraints at different lifecycle stages of a model. We then discuss the implementation choices within EMF to support the validation of a state-specific metamodel on model graphs when changing states, as well as the enforcement of state-specific constraints when executing model change operations.