Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. Conclusion A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

Effective attacking strategies in rugby union

Evasive change-of-direction manoeuvres (agility skills) are a fundamental ability in rugby union. In this study, we explored the attributes of agility skill execution as they relate to effective attacking strategies in rugby union. Seven Super 14 games were coded using variables that assessed team patterns and individual movement characteristics during attacking ball carries. The results indicated that tackle-breaks are a key determinant of try-scoring ability and team success in rugby union. The ability of the attacking ball carrier to receive the ball at high speed with at least two body lengths from the defence line against an isolated defender promoted tackle-breaks. Furthermore, the execution of a side-step evasive manoeuvre at a change of direction angle of 20–60° and a distance of one to two body lengths from the defence, and then straightening the running line following the initial direction change at an angle of 20–60°, was associated with tackle-breaks. This study provides critical insight regarding the attributes of agility skill execution that are associated with effective ball carries in rugby union.

Oxygen delivery through high-flow nasal cannulae increase end-expiratory lung volume and reduce respiratory rate in post-cardiac surgical patients

Background: High-flow nasal cannulae (HFNC) create positive oropharyngeal airway pressure but it is unclear how their use affects lung volume. Electrical impedance tomography (EIT) allows assessment of changes in lung volume by measuring changes in lung impedance. Primary objectives were to investigate the effects of HFNC on airway pressure (Paw) and end-expiratory lung volume (EELV), and to identify any correlation between the two. Secondary objectives were to investigate the effects of HFNC on respiratory rate (RR), dyspnoea, tidal volume and oxygenation; and the interaction between body mass index (BMI) and EELV. Methods: Twenty patients prescribed HFNC post-cardiac surgery were investigated. Impedance measures, Paw, PaO2/FiO2 ratio, RR and modified Borg scores were recorded first on low flow oxygen (nasal cannula or Hudson face mask) and then on HFNC. Results: A strong and significant correlation existed between Paw and end-expiratory lung impedance (EELI) (r=0.7, p<0.001). Compared with low flow oxygen, HFNC significantly increased EELI by 25.6% (95% CI 24.3, 26.9) and Paw by 3.0 cmH2O (95% CI 2.4, 3.7). RR reduced by 3.4 breaths per minute (95% CI 1.7, 5.2) with HFNC use, tidal impedance variation increased by 10.5% (95% CI 6.1, 18.3) and PaO2/FiO2 ratio improved by 30.6 mmHg (95% CI 17.9, 43.3). HFNC improved subjective dyspnoea scoring (p=0.023). Increases in EELI were significantly influenced by BMI, with larger increases associated with higher BMIs (p<0.001). Conclusions: This study suggests that HFNC improve dyspnoea and oxygenation by increasing both EELV and tidal volume, and are most beneficial in patients with higher BMIs.

Multifractal characterisation and analysis of complex networks

Complex networks have been studied extensively due to their relevance to many real-world systems such as the world-wide web, the internet, biological and social systems. During the past two decades, studies of such networks in different fields have produced many significant results concerning their structures, topological properties, and dynamics. Three well-known properties of complex networks are scale-free degree distribution, small-world effect and self-similarity. The search for additional meaningful properties and the relationships among these properties is an active area of current research. This thesis investigates a newer aspect of complex networks, namely their multifractality, which is an extension of the concept of selfsimilarity. The first part of the thesis aims to confirm that the study of properties of complex networks can be expanded to a wider field including more complex weighted networks. Those real networks that have been shown to possess the self-similarity property in the existing literature are all unweighted networks. We use the proteinprotein interaction (PPI) networks as a key example to show that their weighted networks inherit the self-similarity from the original unweighted networks. Firstly, we confirm that the random sequential box-covering algorithm is an effective tool to compute the fractal dimension of complex networks. This is demonstrated on the Homo sapiens and E. coli PPI networks as well as their skeletons. Our results verify that the fractal dimension of the skeleton is smaller than that of the original network due to the shortest distance between nodes is larger in the skeleton, hence for a fixed box-size more boxes will be needed to cover the skeleton. Then we adopt the iterative scoring method to generate weighted PPI networks of five species, namely Homo sapiens, E. coli, yeast, C. elegans and Arabidopsis Thaliana. By using the random sequential box-covering algorithm, we calculate the fractal dimensions for both the original unweighted PPI networks and the generated weighted networks. The results show that self-similarity is still present in generated weighted PPI networks. This implication will be useful for our treatment of the networks in the third part of the thesis. The second part of the thesis aims to explore the multifractal behavior of different complex networks. Fractals such as the Cantor set, the Koch curve and the Sierspinski gasket are homogeneous since these fractals consist of a geometrical figure which repeats on an ever-reduced scale. Fractal analysis is a useful method for their study. However, real-world fractals are not homogeneous; there is rarely an identical motif repeated on all scales. Their singularity may vary on different subsets; implying that these objects are multifractal. Multifractal analysis is a useful way to systematically characterize the spatial heterogeneity of both theoretical and experimental fractal patterns. However, the tools for multifractal analysis of objects in Euclidean space are not suitable for complex networks. In this thesis, we propose a new box covering algorithm for multifractal analysis of complex networks. This algorithm is demonstrated in the computation of the generalized fractal dimensions of some theoretical networks, namely scale-free networks, small-world networks, random networks, and a kind of real networks, namely PPI networks of different species. Our main finding is the existence of multifractality in scale-free networks and PPI networks, while the multifractal behaviour is not confirmed for small-world networks and random networks. As another application, we generate gene interactions networks for patients and healthy people using the correlation coefficients between microarrays of different genes. Our results confirm the existence of multifractality in gene interactions networks. This multifractal analysis then provides a potentially useful tool for gene clustering and identification. The third part of the thesis aims to investigate the topological properties of networks constructed from time series. Characterizing complicated dynamics from time series is a fundamental problem of continuing interest in a wide variety of fields. Recent works indicate that complex network theory can be a powerful tool to analyse time series. Many existing methods for transforming time series into complex networks share a common feature: they define the connectivity of a complex network by the mutual proximity of different parts (e.g., individual states, state vectors, or cycles) of a single trajectory. In this thesis, we propose a new method to construct networks of time series: we define nodes by vectors of a certain length in the time series, and weight of edges between any two nodes by the Euclidean distance between the corresponding two vectors. We apply this method to build networks for fractional Brownian motions, whose long-range dependence is characterised by their Hurst exponent. We verify the validity of this method by showing that time series with stronger correlation, hence larger Hurst exponent, tend to have smaller fractal dimension, hence smoother sample paths. We then construct networks via the technique of horizontal visibility graph (HVG), which has been widely used recently. We confirm a known linear relationship between the Hurst exponent of fractional Brownian motion and the fractal dimension of the corresponding HVG network. In the first application, we apply our newly developed box-covering algorithm to calculate the generalized fractal dimensions of the HVG networks of fractional Brownian motions as well as those for binomial cascades and five bacterial genomes. The results confirm the monoscaling of fractional Brownian motion and the multifractality of the rest. As an additional application, we discuss the resilience of networks constructed from time series via two different approaches: visibility graph and horizontal visibility graph. Our finding is that the degree distribution of VG networks of fractional Brownian motions is scale-free (i.e., having a power law) meaning that one needs to destroy a large percentage of nodes before the network collapses into isolated parts; while for HVG networks of fractional Brownian motions, the degree distribution has exponential tails, implying that HVG networks would not survive the same kind of attack.

Useful field of view predicts driving in the presence of distracters

Purpose. The Useful Field of View (UFOV(R)) test has been shown to be highly effective in predicting crash risk among older adults. An important question which we examined in this study is whether this association is due to the ability of the UFOV to predict difficulties in attention-demanding driving situations that involve either visual or auditory distracters. Methods. Participants included 92 community-living adults (mean age 73.6 +/- 5.4 years; range 65-88 years) who completed all three subtests of the UFOV involving assessment of visual processing speed (subtest 1), divided attention (subtest 2), and selective attention (subtest 3); driving safety risk was also classified using the UFOV scoring system. Driving performance was assessed separately on a closed-road circuit while driving under three conditions: no distracters, visual distracters, and auditory distracters. Driving outcome measures included road sign recognition, hazard detection, gap perception, time to complete the course, and performance on the distracter tasks. Results. Those rated as safe on the UFOV (safety rating categories 1 and 2), as well as those responding faster than the recommended cut-off on the selective attention subtest (350 msec), performed significantly better in terms of overall driving performance and also experienced less interference from distracters. Of the three UFOV subtests, the selective attention subtest best predicted overall driving performance in the presence of distracters. Conclusions. Older adults who were rated as higher risk on the UFOV, particularly on the selective attention subtest, demonstrated poorest driving performance in the presence of distracters. This finding suggests that the selective attention subtest of the UFOV may be differentially more effective in predicting driving difficulties in situations of divided attention which are commonly associated with crashes.

A 2-h diagnostic protocol to assess patients with chest pain symptoms in the Asia-Pacific region (ASPECT): a prospective observational validation study

Background: Patients with chest pain contribute substantially to emergency department attendances, lengthy hospital stay, and inpatient admissions. A reliable, reproducible, and fast process to identify patients presenting with chest pain who have a low short-term risk of a major adverse cardiac event is needed to facilitate early discharge. We aimed to prospectively validate the safety of a predefined 2-h accelerated diagnostic protocol (ADP) to assess patients presenting to the emergency department with chest pain symptoms suggestive of acute coronary syndrome. Methods: This observational study was undertaken in 14 emergency departments in nine countries in the Asia-Pacific region, in patients aged 18 years and older with at least 5 min of chest pain. The ADP included use of a structured pre-test probability scoring method (Thrombolysis in Myocardial Infarction [TIMI] score), electrocardiograph, and point-of-care biomarker panel of troponin, creatine kinase MB, and myoglobin. The primary endpoint was major adverse cardiac events within 30 days after initial presentation (including initial hospital attendance). This trial is registered with the Australia-New Zealand Clinical Trials Registry, number ACTRN12609000283279. Findings: 3582 consecutive patients were recruited and completed 30-day follow-up. 421 (11•8%) patients had a major adverse cardiac event. The ADP classified 352 (9•8%) patients as low risk and potentially suitable for early discharge. A major adverse cardiac event occurred in three (0•9%) of these patients, giving the ADP a sensitivity of 99•3% (95% CI 97•9–99•8), a negative predictive value of 99•1% (97•3–99•8), and a specificity of 11•0% (10•0–12•2). Interpretation: This novel ADP identifies patients at very low risk of a short-term major adverse cardiac event who might be suitable for early discharge. Such an approach could be used to decrease the overall observation periods and admissions for chest pain. The components needed for the implementation of this strategy are widely available. The ADP has the potential to affect health-service delivery worldwide.

Non-destructive evaluation of articular cartilage defects using near-infrared (NIR) spectroscopy in osteoarthritic rat models and its direct relation to Mankin Score

Objective The aim of this study was to demonstrate the potential of near-infrared (NIR) spectroscopy for categorizing cartilage degeneration induced in animal models. Method Three models of osteoarthritic degeneration were induced in laboratory rats via one of the following methods: (i) menisectomy (MSX); (ii) anterior cruciate ligament transaction (ACLT); and (iii) intra-articular injection of mono-ido-acetete (1 mg) (MIA), in the right knee joint, with 12 rats per model group. After 8 weeks, the animals were sacrificed and tibial knee joints were collected. A custom-made nearinfrared (NIR) probe of diameter 5 mm was placed on the cartilage surface and spectral data were acquired from each specimen in the wavenumber range 4 000 – 12 500 cm−1. Following spectral data acquisition, the specimens were fixed and Safranin–O staining was performed to assess disease severity based on the Mankin scoring system. Using multivariate statistical analysis based on principal component analysis and partial least squares regression, the spectral data were then related to the Mankinscores of the samples tested. Results Mild to severe degenerative cartilage changes were observed in the subject animals. The ACLT models showed mild cartilage degeneration, MSX models moderate, and MIA severe cartilage degenerative changes both morphologically and histologically. Our result demonstrate that NIR spectroscopic information is capable of separating the cartilage samples into different groups relative to the severity of degeneration, with NIR correlating significantly with their Mankinscore (R2 = 88.85%). Conclusion We conclude that NIR is a viable tool for evaluating articularcartilage health and physical properties such as change in thickness with degeneration.

Interactive conference voting

We describe and analyze opinion polling results from interactive voting procedures undertaken before and after presentations during the Outcome Measures in Rheumatoid Arthritis Clinical Trials Conference (OMERACT II) in Ottawa, Canada, June 30-July 2, 1994. The scoring procedure was a matched voting design; when a participant used the same keypad at the beginning and end of voting, change within a participant could be estimated. Participants, experienced in the rheumatic diseases included clinicians, researchers, methodologists, regulators, and representatives of the pharmaceutical industry. Patients under consideration were those with any rheumatic diseases. Questions were constructed to evaluate the change in voting behavior expected from the content of the presentation. Statistically significant and substantively important changes were evident in most questions.

Characterizing multi-agent team behavior from partial team tracings : evidence from the English Premier League

Real-world AI systems have been recently deployed which can automatically analyze the plan and tactics of tennis players. As the game-state is updated regularly at short intervals (i.e. point-level), a library of successful and unsuccessful plans of a player can be learnt over time. Given the relative strengths and weaknesses of a player’s plans, a set of proven plans or tactics from the library that characterize a player can be identified. For low-scoring, continuous team sports like soccer, such analysis for multi-agent teams does not exist as the game is not segmented into “discretized” plays (i.e. plans), making it difficult to obtain a library that characterizes a team’s behavior. Additionally, as player tracking data is costly and difficult to obtain, we only have partial team tracings in the form of ball actions which makes this problem even more difficult. In this paper, we propose a method to overcome these issues by representing team behavior via play-segments, which are spatio-temporal descriptions of ball movement over fixed windows of time. Using these representations we can characterize team behavior from entropy maps, which give a measure of predictability of team behaviors across the field. We show the efficacy and applicability of our method on the 2010-2011 English Premier League soccer data.

Development of clinical competencies for emergency nurse practitioners : a pilot study

Background: Nurse practitioner education and practice has been guided by generic competency standards in Australia since 2006. Development of specialist competencies has been less structured and there are no formal standards to guide education and continuing professional development for specialty fields. There is limited international research and no Australian research into development of specialist nurse practitioner competencies. This pilot study aimed to test data collection methods, tools and processes in preparation for a larger national study to investigate specialist competency standards for emergency nurse practitioners. Research into specialist emergency nurse practitioner competencies has not been conducted in Australia. Methods: Mixed methods research was conducted with a sample of experienced emergency nurse practitioners. Deductive analysis of data from a focus group workshop informed development of a draft specialty competency framework. The framework was subsequently subjected to systematic scrutiny for consensus validation through a two round Delphi Study. Results: The Delphi study first round had a 100% response rate; the second round 75% response rate. The scoring for all items in both rounds was above the 80% cut off mark with the lowest mean score being 4.1 (82%) from the first round. Conclusion: The authors collaborated with emergency nurse practitioners to produce preliminary data on the formation of specialty competencies as a first step in developing an Australian framework.

I-vector based speaker recognition using advanced channel compensation techniques

This paper investigates advanced channel compensation techniques for the purpose of improving i-vector speaker verification performance in the presence of high intersession variability using the NIST 2008 and 2010 SRE corpora. The performance of four channel compensation techniques: (a) weighted maximum margin criterion (WMMC), (b) source-normalized WMMC (SN-WMMC), (c) weighted linear discriminant analysis (WLDA), and; (d) source-normalized WLDA (SN-WLDA) have been investigated. We show that, by extracting the discriminatory information between pairs of speakers as well as capturing the source variation information in the development i-vector space, the SN-WLDA based cosine similarity scoring (CSS) i-vector system is shown to provide over 20% improvement in EER for NIST 2008 interview and microphone verification and over 10% improvement in EER for NIST 2008 telephone verification, when compared to SN-LDA based CSS i-vector system. Further, score-level fusion techniques are analyzed to combine the best channel compensation approaches, to provide over 8% improvement in DCF over the best single approach, (SN-WLDA), for NIST 2008 interview/ telephone enrolment-verification condition. Finally, we demonstrate that the improvements found in the context of CSS also generalize to state-of-the-art GPLDA with up to 14% relative improvement in EER for NIST SRE 2010 interview and microphone verification and over 7% relative improvement in EER for NIST SRE 2010 telephone verification.

Calculation of dose kernels for radiotherapy applications using the GEANT 4 Monte Carlo toolkit

Dose kernels may be used to calculate dose distributions in radiotherapy (as described by Ahnesjo et al., 1999). Their calculation requires use of Monte Carlo methods, usually by forcing interactions to occur at a point. The Geant4 Monte Carlo toolkit provides a capability to force interactions to occur in a particular volume. We have modified this capability and created a Geant4 application to calculate dose kernels in cartesian, cylindrical, and spherical scoring systems. The simulation considers monoenergetic photons incident at the origin of a 3 m x 3 x 9 3 m water volume. Photons interact via compton, photo-electric, pair production, and rayleigh scattering. By default, Geant4 models photon interactions by sampling a physical interaction length (PIL) for each process. The process returning the smallest PIL is then considered to occur. In order to force the interaction to occur within a given length, L_FIL, we scale each PIL according to the formula: PIL_forced = L_FIL 9 (1 - exp(-PIL/PILo)) where PILo is a constant. This ensures that the process occurs within L_FIL, whilst correctly modelling the relative probability of each process. Dose kernels were produced for an incident photon energy of 0.1, 1.0, and 10.0 MeV. In order to benchmark the code, dose kernels were also calculated using the EGSnrc Edknrc user code. Identical scoring systems were used; namely, the collapsed cone approach of the Edknrc code. Relative dose difference images were then produced. Preliminary results demonstrate the ability of the Geant4 application to reproduce the shape of the dose kernels; median relative dose differences of 12.6, 5.75, and 12.6 % were found for an incident photon energy of 0.1, 1.0, and 10.0 MeV respectively.

Reducing the Risk of Alcohol and Other Drugs in Construction : An Australian Assessment

There is increasing concern about the impact of employees’ alcohol and other drug (AOD) consumption on workplace safety, particularly within the construction industry. No known study has scientifically evaluated the relationship between the use of drugs and alcohol and safety impacts in construction, and there has been only limited adoption of nationally coordinated strategies, supported by employers and employees to render it socially unacceptable to arrive at a construction workplace with impaired judgment from AODs. This research aims to scientifically evaluate the use of AODs within the Australian construction industry in order to reduce the potential resulting safety and performance impacts and engender a cultural change in the workforce. Using the Alcohol Use Disorders Identification Test (AUDIT), the study will adopt both quantitative and qualitative methods to evaluate the extent of general AOD use in the industry. Results indicate that a proportion of the construction sector may be at risk of hazardous alcohol consumption. A total of 286 respondents (58%) scored above the cut-off score for risky alcohol use with 43 respondents (15%) scoring in the significantly ‘at risk’ category. Other drug use was also identified as a major issue that must be addressed. Results support the need for evidence-based, preventative educational initiatives that are tailored specifically to the construction industry.

A pattern based two-stage text classifier

In a classification problem typically we face two challenging issues, the diverse characteristic of negative documents and sometimes a lot of negative documents that are closed to positive documents. Therefore, it is hard for a single classifier to clearly classify incoming documents into classes. This paper proposes a novel gradual problem solving to create a two-stage classifier. The first stage identifies reliable negatives (negative documents with weak positive characteristics). It concentrates on minimizing the number of false negative documents (recall-oriented). We use Rocchio, an existing recall based classifier, for this stage. The second stage is a precision-oriented “fine tuning”, concentrates on minimizing the number of false positive documents by applying pattern (a statistical phrase) mining techniques. In this stage a pattern-based scoring is followed by threshold setting (thresholding). Experiment shows that our statistical phrase based two-stage classifier is promising.

Soundage : a practice-led approach to Gertrude Stein, sound, and generative language

In this practice-led research project I work to show how a re-reading and a particular form of listening to the sound-riddled nature of Gertrude Stein's work, Two: Gertrude Stein and her Brother, presents us with a contemporary theory of sound in language. This theory, though in its infancy, is a particular enjambment of sounded language that presents itself as an event, engaged with meaning, with its own inherent voice. It displays a propensity through engagement with the 'other' to erupt into love. In this thesis these qualities are reverberated further through the work of Seth Kim-Cohen's notion of the non-cochlear, Simon Jarvis's notion of musical thinking, Jean-Jacques Lecercle's notion of délire or nonsense, Luce Irigaray's notion of jouissant love and the Bracha Ettinger's notion of the generative matrixial border space. This reading then is simultaneously paired with my own work of scoring and creating a digital opera from Stein's work, thereby testing and performing Stein's theory. In this I show how a re-reading and relistening to Stein's work can be significant to feminist ethical language frames, contemporary philosophy, sonic art theory and digital language frames. Further significance of this study is that when the reverberation of Stein's engagements with language through sound can be listened to, a pattern emerges, one that encouragingly problematizes subjectivity and interweaves genres/methods and means, creating a new frame for sound in language, one with its own voice that I call soundage.