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.

On the contemporary position of the Indigenous peoples of Australia

This paper highlights the contemporary disadvantaged position of Indigenous peoples of Australia.∗ It discusses a number of data quality issues on Indigenous data, before examining Indigenous disadvantage across five key areas: (1) education; (2) employment; (3) housing and living conditions; (4) health and wellbeing; and (5) crime and justice. Given the call for all governments to implement a framework to overcome Indigenous disadvantage, we recommend that future research begin with an investigation of non-Indigenous attitudes towards, and knowledge of, the position of Indigenous peoples in Australia. This is essential towards developing an understanding of the general public’s current perceptions of Indigenous peoples’ position in Australia, particularly where the development of policies pertaining to Indigenous peoples requires cooperative action and the support of the broader Australian population.

Issues and concerns of microscopic calibration process at different network levels : case study of pacific motorway

Calibration process in micro-simulation is an extremely complicated phenomenon. The difficulties are more prevalent if the process encompasses fitting aggregate and disaggregate parameters e.g. travel time and headway. The current practice in calibration is more at aggregate level, for example travel time comparison. Such practices are popular to assess network performance. Though these applications are significant there is another stream of micro-simulated calibration, at disaggregate level. This study will focus on such micro-calibration exercise-key to better comprehend motorway traffic risk level, management of variable speed limit (VSL) and ramp metering (RM) techniques. Selected section of Pacific Motorway in Brisbane will be used as a case study. The discussion will primarily incorporate the critical issues encountered during parameter adjustment exercise (e.g. vehicular, driving behaviour) with reference to key traffic performance indicators like speed, land distribution and headway; at specific motorway points. The endeavour is to highlight the utility and implications of such disaggregate level simulation for improved traffic prediction studies. The aspects of calibrating for points in comparison to that for whole of the network will also be briefly addressed to examine the critical issues such as the suitability of local calibration at global scale. The paper will be of interest to transport professionals in Australia/New Zealand where micro-simulation in particular at point level, is still comparatively a less explored territory in motorway management.

Judge George W Paul's Japanese house : a case study

In the late 1880s a pre-fabricated Japanese house was shipped from Kobe, Japan, to Brisbane, Australia, and erected in the up-market suburb of New Farm by Japanese tradesmen. This paper is developed from a broader project researching the life of G W Paul, the man who had the house built and subsequently lived in it for the remainder of his life. Paul’s motivation in importing the house represented a unique, but unfulfilled effort to develop a future, hybrid culture for Queensland. This effort took the form of a commercial venture to construct Japanese houses as desirable and climatically suitable dwellings. Against the backdrop of this ambition, this paper presents new research to elucidate and extend previous knowledge, assesses the reception of the house by its nineteenth century Brisbane audience, and considers possible reasons for the limited response which signalled the cancellation of the commercial venture.

Assessing performance capability in the work place

As universities worldwide begin to appreciate the value of authentic learning experiences, so they struggle with methods of assessing the outcomes from such experiences. This chapter describes the application of an assessment matrix developed by Queensland University of Technology(QUT) in Australia, to the assessment requirements and practices relating to work integrated learning at the University of Surrey in the UK. Despite the very different institutional contexts and independent way in which the assessment regimes have developed, it was found that the values and outcomes being assessed and the methods used to assess them were similar. The most important feature of assessing work integrated learning experiences is fitness for purpose, hence the learning objectives and assessment of outcomes for a WIL experience must be explicitly aligned to this objective.As universities worldwide begin to appreciate the value of authentic learning experiences, so they struggle with methods of assessing the outcomes from such experiences. This chapter describes the application of an assessment matrix developed by Queensland University of Technology (QUT) in Australia, to the assessment requirements and practices relating to work integrated learning at the University of Surrey in the UK. Despite the very different institutional contexts and independent way in which the assessment regimes have developed, it was found that the values and outcomes being assessed and the methods used to assess them were similar. The most important feature of assessing work integrated learning experiences is fitness for purpose, hence the learning objectives and assessment of outcomes for a WIL experience must be explicitly aligned to this objective.

Using strategic movement to calibrate a neural compass : a spiking network for tracking head direction in rats and robots

The head direction (HD) system in mammals contains neurons that fire to represent the direction the animal is facing in its environment. The ability of these cells to reliably track head direction even after the removal of external sensory cues implies that the HD system is calibrated to function effectively using just internal (proprioceptive and vestibular) inputs. Rat pups and other infant mammals display stereotypical warm-up movements prior to locomotion in novel environments, and similar warm-up movements are seen in adult mammals with certain brain lesion-induced motor impairments. In this study we propose that synaptic learning mechanisms, in conjunction with appropriate movement strategies based on warm-up movements, can calibrate the HD system so that it functions effectively even in darkness. To examine the link between physical embodiment and neural control, and to determine that the system is robust to real-world phenomena, we implemented the synaptic mechanisms in a spiking neural network and tested it on a mobile robot platform. Results show that the combination of the synaptic learning mechanisms and warm-up movements are able to reliably calibrate the HD system so that it accurately tracks real-world head direction, and that calibration breaks down in systematic ways if certain movements are omitted. This work confirms that targeted, embodied behaviour can be used to calibrate neural systems, demonstrates that ‘grounding’ of modeled biological processes in the real world can reveal underlying functional principles (supporting the importance of robotics to biology), and proposes a functional role for stereotypical behaviours seen in infant mammals and those animals with certain motor deficits. We conjecture that these calibration principles may extend to the calibration of other neural systems involved in motion tracking and the representation of space, such as grid cells in entorhinal cortex.

Proximity-to-goal as a constraint on patterns of behaviour in attacker–defender dyads in team games

The aim of this study was to determine whether spatiotemporal interactions between footballers and the ball in 1 vs. 1 sub-phases are influenced by their proximity to the goal area. Twelve participants (age 15.3 ± 0.5 years) performed as attackers and defenders in 1 vs. 1 dyads across three field positions: (a) attacking the goal, (b) in midfield, and (c) advancing away from the goal area. In each position, the dribbler was required to move beyond an immediate defender with the ball towards the opposition goal. Interactions of attacker-defender dyads were filmed with player and ball displacement trajectories digitized using manual tracking software. One-way repeated measures analysis of variance was used to examine differences in mean defender-to-ball distance after this value had stabilized. Maximum attacker-to-ball distance was also compared as a function of proximity-to-goal. Significant differences were observed for defender-to-ball distance between locations (a) and (c) at the moment when the defender-to-ball distance had stabilized (a: 1.69 ± 0.64 m; c: 1.15 ± 0.59 m; P < 0.05). Findings indicate that proximity-to-goal influenced the performance of players, particularly when attacking or advancing away from goal areas, providing implications for training design in football. In this study, the task constraints of football revealed subtly different player interactions than observed in previous studies of dyadic systems in basketball and rugby union.

Investigating pre-service teachers’ perceptions of their preparedness to teach

The experiences of transition to the teaching profession have a significant impact on a teachers’ potential length of career, feelings of professional efficacy and the quality of performance in the classroom (Gore & Thomas, 2003). While the transition to practice is characterized by much expectation and excitement, it also a time of stress and uncertainty for many beginning teachers. As such, it is important to investigate this period of transition for beginning teachers. This paper explores graduate teachers perceptions of their personal ‘preparedness to teach’. The group is graduating from one Australian university, and the data is captured at the end of their teacher preparation programs,before they take up positions in schools. These graduating pre-service teachers are from one year graduate entry programs that include individual programs of early years, middle years and senior years. The key findings indicate that this group of graduating pre-service teachers are already engaged in some level of reflective practice and are actively seeking further professional learning to improve the practical aspects of their classroom teaching.

Hierarchical robust design optimisation of shock control bump devices for airfoil drag reduction

The paper investigates a detailed Active Shock Control Bump Design Optimisation on a Natural Laminar Flow (NLF) aerofoil; RAE 5243 to reduce cruise drag at transonic flow conditions using Evolutionary Algorithms (EAs) coupled to a robust design approach. For the uncertainty design parameters, the positions of boundary layer transition (xtr) and the coefficient of lift (Cl) are considered (250 stochastic samples in total). In this paper, two robust design methods are considered; the first approach uses a standard robust design method, which evaluates one design model at 250 stochastic conditions for uncertainty. The second approach is the combination of a standard robust design method and the concept of hierarchical (multi-population) sampling (250, 50, 15) for uncertainty. Numerical results show that the evolutionary optimization method coupled to uncertainty design techniques produces useful and reliable Pareto optimal SCB shapes which have low sensitivity and high aerodynamic performance while having significant total drag reduction. In addition,it also shows the benefit of using hierarchical robust method for detailed uncertainty design optimization.

'The war of Canudos: a Euclidean interpretation.' [Guerra de Canudos: uma leitura euclidiana]

The publication of the book The interior, in 1902, would change the course of thinking about the War of Canudos, who for many years, had been known simply as' the history of Euclid. President Getulio Vargas became interested in the backwoods bloodbath after reading the book avenger-Euclidean. Liked the work he visited the place of occurrence of war promising enjoy the river poured-Barris with the construction of the weir Cocorobo. Euclides da Cunha lived and produced his work in a time of great change in thought, politics and technology. Despite having worked in the press throughout his life, was best known as an engineer, for having exercised the office during the reconstruction of the bridge, in Sao Jose do Rio Pardo. This article aims to illuminate the event of war in light of the Euclidean work. We will examine the trajectory of Euclides da Cunha in journalism. Your learning process to execute the office newsreader and war correspondent, the newspaper O Estado de S. Paul, as well as their reports and work-monument the hinterlands. Resumo: A publicação da obra Os sertões, em 1902, mudaria os rumos do pensamento sobre a Guerra de Canudos, que, por muitos anos, ficara conhecida, simplesmente, como ‘história de Euclides’. O presidente Getúlio Vargas interessou-se pela hecatombe sertaneja após ter lido o livro-vingador euclidiano. Gostou tanto da obra que visitou o lugar de acontecimento da guerra prometendo aproveitar as águas do rio Vaza-Barris com a construção do açude de Cocorobó. Euclides da Cunha viveu e produziu a sua obra em um momento de grandes transformações no pensamento, na política e na tecnologia. Apesar de ter atuado na imprensa ao longo de toda a sua vida, ficou mais conhecido como engenheiro, por ter exercido o ofício, durante a reconstrução da ponte, em São José do Rio Pardo. O presente artigo visa iluminar o acontecimento da guerra à luz da obra euclidiana. Examinaremos a trajetória de Euclides da Cunha no jornalismo. O seu processo de aprendizagem para exercer o ofício de noticiarista e correspondente de guerra, pelo jornal O Estado de S. Paulo, bem como, as suas reportagens e obra-monumento Os sertões.

Optimisation of process parameters for the removal of hydroxycinnamic acids in sugar solutions

Colour is one of the most important parameters in sugar quality and its presence in raw sugar plays a key role in the marketing strategy of sugar industries worldwide. This study investigated the degradation of a mixture of colour precursors using the Fenton oxidation process. These colour precursors are caffeic acid, p–coumaric acid and ferulic acid, which are present in cane juice. Results showed that with a Fe(II) to H2O2 molar ratio of 1:15 in an aqueous system at 25 °C, 77% of the total phenolic acid content was removed at pH 4.72. However, in a synthetic juice solution which contained 13 mass % sucrose (35 °C, pH 5.4), only 60% of the total phenolic acid content was removed.

Purine Nucleoside Phosphorylase mediated molecular chemotherapy and conventional chemotherapy: A tangible union against chemoresistant cancer

Background Late stage Ovarian Cancer is essentially incurable primarily due to late diagnosis and its inherent heterogeneity. Single agent treatments are inadequate and generally lead to severe side effects at therapeutic doses. It is crucial to develop clinically relevant novel combination regimens involving synergistic modalities that target a wider repertoire of cells and lead to lowered individual doses. Stemming from this premise, this is the first report of two- and three-way synergies between Adenovirus-mediated Purine Nucleoside Phosphorylase based gene directed enzyme prodrug therapy (PNP-GDEPT), docetaxel and/or carboplatin in multidrug-resistant ovarian cancer cells. Methods The effects of PNP-GDEPT on different cellular processes were determined using Shotgun Proteomics analyses. The in vitro cell growth inhibition in differentially treated drug resistant human ovarian cancer cell lines was established using a cell-viability assay. The extent of synergy, additivity, or antagonism between treatments was evaluated using CalcuSyn statistical analyses. The involvement of apoptosis and implicated proteins in effects of different treatments was established using flow cytometry based detection of M30 (an early marker of apoptosis), cell cycle analyses and finally western blot based analyses. Results Efficacy of the trimodal treatment was significantly greater than that achieved with bimodal- or individual treatments with potential for 10-50 fold dose reduction compared to that required for individual treatments. Of note was the marked enhancement in apoptosis that specifically accompanied the combinations that included PNP-GDEPT and accordingly correlated with a shift in the expression of anti- and pro-apoptotic proteins. PNP-GDEPT mediated enhancement of apoptosis was reinforced by cell cycle analyses. Proteomic analyses of PNP-GDEPT treated cells indicated a dowregulation of proteins involved in oncogenesis or cancer drug resistance in treated cells with accompanying upregulation of apoptotic- and tumour- suppressor proteins. Conclusion Inclusion of PNP-GDEPT in regular chemotherapy regimens can lead to significant enhancement of the cancer cell susceptibility to the combined treatment. Overall, these data will underpin the development of regimens that can benefit patients with late stage ovarian cancer leading to significantly improved efficacy and increased quality of life.

Novel molecular markers of Chlamydia pecorum genetic diversity in the koala (Phascolarctos cinereus)

Background Chlamydia pecorum is an obligate intracellular bacterium and the causative agent of reproductive and ocular disease in several animal hosts including koalas, sheep, cattle and goats. C. pecorum strains detected in koalas are genetically diverse, raising interesting questions about the origin and transmission of this species within koala hosts. While the ompA gene remains the most widely-used target in C. pecorum typing studies, it is generally recognised that surface protein encoding genes are not suited for phylogenetic analysis and it is becoming increasingly apparent that the ompA gene locus is not congruent with the phylogeny of the C. pecorum genome. Using the recently sequenced C. pecorum genome sequence (E58), we analysed 10 genes, including ompA, to evaluate the use of ompA as a molecular marker in the study of koala C. pecorum genetic diversity. Results Three genes (incA, ORF663, tarP) were found to contain sufficient nucleotide diversity and discriminatory power for detailed analysis and were used, with ompA, to genotype 24 C. pecorum PCR-positive koala samples from four populations. The most robust representation of the phylogeny of these samples was achieved through concatenation of all four gene sequences, enabling the recreation of a "true" phylogenetic signal. OmpA and incA were of limited value as fine-detailed genetic markers as they were unable to confer accurate phylogenetic distinctions between samples. On the other hand, the tarP and ORF663 genes were identified as useful "neutral" and "contingency" markers respectively, to represent the broad evolutionary history and intra-species genetic diversity of koala C. pecorum. Furthermore, the concatenation of ompA, incA and ORF663 sequences highlighted the monophyletic nature of koala C. pecorum infections by demonstrating a single evolutionary trajectory for koala hosts that is distinct from that seen in non-koala hosts. Conclusions While the continued use of ompA as a fine-detailed molecular marker for epidemiological analysis appears justified, the tarP and ORF663 genes also appear to be valuable markers of phylogenetic or biogeographic divisions at the C. pecorum intra-species level. This research has significant implications for future typing studies to understand the phylogeny, genetic diversity, and epidemiology of C. pecorum infections in the koala and other animal species.