Inferring phylogenies of evolving sequences without multiple sequence alignment

Alignment-free methods, in which shared properties of sub-sequences (e.g. identity or match length) are extracted and used to compute a distance matrix, have recently been explored for phylogenetic inference. However, the scalability and robustness of these methods to key evolutionary processes remain to be investigated. Here, using simulated sequence sets of various sizes in both nucleotides and amino acids, we systematically assess the accuracy of phylogenetic inference using an alignment-free approach, based on D2 statistics, under different evolutionary scenarios. We find that compared to a multiple sequence alignment approach, D2 methods are more robust against among-site rate heterogeneity, compositional biases, genetic rearrangements and insertions/deletions, but are more sensitive to recent sequence divergence and sequence truncation. Across diverse empirical datasets, the alignment-free methods perform well for sequences sharing low divergence, at greater computation speed. Our findings provide strong evidence for the scalability and the potential use of alignment-free methods in large-scale phylogenomics.

Learning the learning rate for prediction with expert advice

Most standard algorithms for prediction with expert advice depend on a parameter called the learning rate. This learning rate needs to be large enough to fit the data well, but small enough to prevent overfitting. For the exponential weights algorithm, a sequence of prior work has established theoretical guarantees for higher and higher data-dependent tunings of the learning rate, which allow for increasingly aggressive learning. But in practice such theoretical tunings often still perform worse (as measured by their regret) than ad hoc tuning with an even higher learning rate. To close the gap between theory and practice we introduce an approach to learn the learning rate. Up to a factor that is at most (poly)logarithmic in the number of experts and the inverse of the learning rate, our method performs as well as if we would know the empirically best learning rate from a large range that includes both conservative small values and values that are much higher than those for which formal guarantees were previously available. Our method employs a grid of learning rates, yet runs in linear time regardless of the size of the grid.

Using viewer’s facial expression and heart rate for sports video highlights detection

Viewer interests, evoked by video content, can potentially identify the highlights of the video. This paper explores the use of facial expressions (FE) and heart rate (HR) of viewers captured using camera and non-strapped sensor for identifying interesting video segments. The data from ten subjects with three videos showed that these signals are viewer dependent and not synchronized with the video contents. To address this issue, new algorithms are proposed to effectively combine FE and HR signals for identifying the time when viewer interest is potentially high. The results show that, compared with subjective annotation and match report highlights, ‘non-neutral’ FE and ‘relatively higher and faster’ HR is able to capture 60%-80% of goal, foul, and shot-on-goal soccer video events. FE is found to be more indicative than HR of viewer’s interests, but the fusion of these two modalities outperforms each of them.

Experimental and numerical investigation of strain-rate dependent mechanical properties of single living cells

The objective of this project is to investigate the strain-rate dependent mechanical behaviour of single living cells using both experimental and numerical techniques. The results revealed that living cells behave as porohyperlastic materials and that both solid and fluid phases within the cells play important roles in their mechanical responses. The research reported in this thesis provides a better understanding of the mechanisms underlying the cellular responses to external mechanical loadings and of the process of mechanical signal transduction in living cells. It would help us to enhance knowledge of and insight into the role of mechanical forces in supporting tissue regeneration or degeneration.

Negotiating indeterminacy in studio teaching: Using the zones of material and immaterial play to shape pedagogies and practices in art

The processes of studio-based teaching in visual art are often still tied to traditional models of discrete disciplines and largely immersed in skill-based learning. These approaches to training artists are also tied to an individual model of art practice that is clearly defined by the boundaries of those disciplines. This paper will explain how the open studio program at QUT can be broadly understood as an action research model of learning that ‘plays’ with the post-medium, post-studio genealogies and zones of contemporary art. This emphasises developing conceptual, contextual and formal skills as essential for engaging with and practicing in the often-indeterminate spatio-temporal sites of studio teaching. It will explore how this approach looks to Sutton-Smith’s observations on the role of play and Vygotsky’s zone of proximal development in early childhood learning as a way to develop strategies for promoting creative learning environments that are collaborative and self sustainable. Social, cultural, political and philosophical dialogues are examined as they relate to art practice with the aim of forming the shared interests, aims, and ambitions of graduating students into self initiated collectives or ARIs.

Estimates of lost material stock of buildings and roads due to the great east Japan earthquake and tsunami

This article describes research conducted for the Japanese government in the wake of the magnitude 9.0 earthquake and tsunami that struck eastern Japan on March 11, 2011. In this study, material stock analysis (MSA) is used to examine the losses of building and infrastructure materials after this disaster. Estimates of the magnitude of material stock that has lost its social function as a result of a disaster can indicate the quantities required for reconstruction, help garner a better understanding of the volumes of waste flows generated by that disaster, and also help in the course of policy deliberations in the recovery of disaster-stricken areas. Calculations of the lost building and road materials in the five prefectures most affected were undertaken. Analysis in this study is based on the use of geographical information systems (GIS) databases and statistics; it aims to (1) describe in spatial terms what construction materials were lost, (2) estimate the amount of infrastructure material needed to rehabilitate disaster areas, and (3) indicate the amount of lost material stock that should be taken into consideration during government policy deliberations. Our analysis concludes that the material stock losses of buildings and road infrastructure are 31.8 and 2.1 million tonnes, respectively. This research approach and the use of spatial MSA can be useful for urban planners and may also convey more appropriate information about disposal based on the work of municipalities in disaster-afflicted areas.

How does Australian diabetic foot screening rate on an international Stage?

Background From the conservative estimates of registrants with the National Diabetes Supply Scheme, we will be soon passing 1.1 Million Australians affected by all types of diabetes. The diabetes complications of foot ulceration and amputation are costly to all. These costs can be reduced with appropriate prevention strategies, starting with identifying people at risk through primary care diabetic foot screening. However, levels of diabetic foot screening in Australia are difficult to quantify. Methods This presentation reports on foot screening rates as recorded in the academic literature, national health surveys and national database reports. The focus is on type 1 and type 2 diabetes in adults, and not gestational diabetes or children. Literature searches included diabetic foot screening that occurred in the primary care setting for populations over 2000 people from 2002 to 2014. Searches were performed using Medline and CINAHL as well as internet searches of OECD health databases. The primary outcome measure was foot -screening rates as a percentage of adult diabetic population. Results The lack of a national diabetes database and register hampers efforts to analyse diabetic foot screening levels. The most recent and accurate level for Australian population review was in the AUSDIAB (Australian Diabetes and lifestyle survey) from 2004. This survey reported screening in primary care to be as low as 50%. Countries such as the United Kingdom and United States of America report much higher rates of foot screening (67-88%) using national databases and web based initiatives that involve patients and clinicians. Conclusions Australian rates of diabetic foot screening in primary care centres is ambiguous. Uptake of national registers, incentives and web based systems improve levels of diabetic foot assessment which are the first steps to a healthier diabetic population.

Fuzzy-logic based frequency controller for wind farms augmented with energy storage systems

Displacement of conventional synchronous generators by non-inertial units such as wind or solar generators will result in reduced-system inertia affecting under-frequency response. Frequency control is important to avoid equipment damage, load shedding, and possible blackouts. Wind generators along with energy storage systems can be used to improve the frequency response of low-inertia power system. This paper proposes a fuzzy-logic based frequency controller (FFC) for wind farms augmented with energy storage systems (wind-storage system) to improve the primary frequency response in future low-inertia hybrid power system. The proposed controller provides bidirectional real power injection using system frequency deviations and rate of change of frequency (RoCoF). Moreover, FFC ensures optimal use of energy from wind farms and storage units by eliminating the inflexible de-loading of wind energy and minimizing the required storage capacity. The efficacy of the proposed FFC is verified on the low-inertia hybrid power system.

Are there generalizable trends in the release of airborne synthetic clay nanoparticles from a jet milling process?

Despite recent efforts to assess the release of nanoparticles to the workplace during different nanotechnology activities, the existence of a generalizable trend in the particle release has yet to be identified. This study aimed to characterize the release of synthetic clay nanoparticles from a laboratory-based jet milling process by quantifying the variations arising from primary particle size and surface treatment of the material used, as well as the feed rate of the machine. A broad range of materials were used in this study, and the emitted particles mass (PM2.5) and number concentrations (PNC) were measured at the release source. Analysis of variance, followed by linear mixed-effects modeling, was applied to quantify the variations in PM2.5 and PNC of the released particles caused by the abovementioned factors. The results confirmed that using materials of different primary size and surface treatment affects the release of the particles from the same process by causing statistically-significant variations in PM2.5 and PNC. The interaction of these two factors should also be taken into account as it resulted in variations in the measured particles release properties. Furthermore, the feed rate of the milling machine was confirmed to be another influencing parameter. Although this research does not identify a specific pattern in the release of synthetic clay nanoparticles from the jet milling process generalizable to other similar settings, it emphasizes that each tested case should be handled individually in terms of exposure considerations.

Effect of constitutive material models on seismic response of two-story reinforced concrete frame

This paper focuses on the finite element (FE) response sensitivity and reliability analyses considering smooth constitutive material models. A reinforced concrete frame is modeled for FE sensitivity analysis followed by direct differentiation method under both static and dynamic load cases. Later, the reliability analysis is performed to predict the seismic behavior of the frame. Displacement sensitivity discontinuities are observed along the pseudo-time axis using non-smooth concrete and reinforcing steel model under quasi-static loading. However, the smooth materials show continuity in response sensitivity at elastic to plastic transition points. The normalized sensitivity results are also used to measure the relative importance of the material parameters on the structural responses. In FE reliability analysis, the influence of smoothness behavior of reinforcing steel is carefully noticed. More efficient and reasonable reliability estimation can be achieved by using smooth material model compare with bilinear material constitutive model.

Prediction of shrinkage and porosity during drying: Considering both material properties and process conditions

Drying of food materials offers a significant increase in the shelf life of food materials, along with the modification of quality attributes due to simultaneous heat and mass transfer. Shrinkage and variations in porosity are the common micro and microstructural changes that take place during the drying of mostly the food materials. Although extensive research has been carried out on the prediction of shrinkage and porosity over the time of drying, no single model exists which consider both material properties and process condition in the same model. In this study, an attempt has been made to develop and validate shrinkage and porosity models of food materials during drying considering both process parameters and sample properties. The stored energy within the sample, elastic potential energy, glass transition temperature and physical properties of the sample such as initial porosity, particle density, bulk density and moisture content have been taken into consideration. Physical properties and validation have been made by using a universal testing machine ( Instron 2kN), a profilometer (Nanovea) and a pycnometer. Apart from these, COMSOL Multiphysics 4.4 has been used to solve heat and mass transfer physics. Results obtained from models of shrinkage and porosity is quite consistent with the experimental data. Successful implementation of these models would ensure the use of optimum energy in the course of drying and better quality retention of dried foods.

A summary of the 'Engineering Education for Sustainable Development:Toolkit of Information & Teaching Material'

This paper reflects on the critical need for an urgent transformation of higher education curriculum globally, to equip society with professionals who can address our 21st Century sustainable living challenges. Specifically it discusses a toolkit called the ‘Engineering Sustainable Solutions Program’, which is a freely available, rigorously reviewed and robust content resource for higher education institutions to access content on innovations and opportunities in the process of evolving the curriculum...

Response of laminated glass panels to near field blast events

This thesis develops and applies an analytical method to treat the blast response of glass façades and studies the influence of controlling parameters such as all component materials and geometric properties, support conditions and energy absorption, and hence establishes a framework for their design for a credible blast event.

Minimising the failure of rail joints through managing the localised condition of track

To effectively address the high rate of failure of Insulated Rail Joints (IRJs) in the heavy haul lines, a research plan was designed and implemented with particular attention to understand their mechanical behaviour and deterioration process. In this paper, part of this ongoing research is described. During the past decades many studies have tried to improve the service life of IRJs by introducing a new structural design or material for IRJ components. This paper looks into this problem from a different perspective highlighting the significance of localised condition of track to the loads and responses of the IRJs. Results from a series of field measurements conducted in a rail track within the Australian Rail Track Corporation (ARTC) network are discussed. The interactive effects of IRJ responses and localised track condition are further investigated using the results obtained from numerical simulations. The field measurements and the simulation results provide valuable insight on the influence of track condition to the behaviour of IRJs.

Identifying rate-limiting nodes in large-scale cortical networks for visuospatial processing: An illustration using fMRI

With the advent of functional neuroimaging techniques, in particular functional magnetic resonance imaging (fMRI), we have gained greater insight into the neural correlates of visuospatial function. However, it may not always be easy to identify the cerebral regions most specifically associated with performance on a given task. One approach is to examine the quantitative relationships between regional activation and behavioral performance measures. In the present study, we investigated the functional neuroanatomy of two different visuospatial processing tasks, judgement of line orientation and mental rotation. Twenty-four normal participants were scanned with fMRI using blocked periodic designs for experimental task presentation. Accuracy and reaction time (RT) to each trial of both activation and baseline conditions in each experiment was recorded. Both experiments activated dorsal and ventral visual cortical areas as well as dorsolateral prefrontal cortex. More regionally specific associations with task performance were identified by estimating the association between (sinusoidal) power of functional response and mean RT to the activation condition; a permutation test based on spatial statistics was used for inference. There was significant behavioral-physiological association in right ventral extrastriate cortex for the line orientation task and in bilateral (predominantly right) superior parietal lobule for the mental rotation task. Comparable associations were not found between power of response and RT to the baseline conditions of the tasks. These data suggest that one region in a neurocognitive network may be most strongly associated with behavioral performance and this may be regarded as the computationally least efficient or rate-limiting node of the network.