Secondary structure element alignment kernel method for prediction of protein structural classes

In this paper, we aim at predicting protein structural classes for low-homology data sets based on predicted secondary structures. We propose a new and simple kernel method, named as SSEAKSVM, to predict protein structural classes. The secondary structures of all protein sequences are obtained by using the tool PSIPRED and then a linear kernel on the basis of secondary structure element alignment scores is constructed for training a support vector machine classifier without parameter adjusting. Our method SSEAKSVM was evaluated on two low-homology datasets 25PDB and 1189 with sequence homology being 25% and 40%, respectively. The jackknife test is used to test and compare our method with other existing methods. The overall accuracies on these two data sets are 86.3% and 84.5%, respectively, which are higher than those obtained by other existing methods. Especially, our method achieves higher accuracies (88.1% and 88.5%) for differentiating the α + β class and the α/β class compared to other methods. This suggests that our method is valuable to predict protein structural classes particularly for low-homology protein sequences. The source code of the method in this paper can be downloaded at http://math.xtu.edu.cn/myphp/math/research/source/SSEAK_source_code.rar.

Prediction of the fate of oxytetracycline and oxolinic acid in a fish pond using simulation model: A preliminary study

The fate of two popular antibiotics, oxytetracycline and oxolinic acid, in a fish pond were simulated using a computational model. The VDC model, which is designed based on a model for predicting pesticide fate and transport in paddy fields, was modified to take into account the differences between the pond and the paddies as well as those between the fish and the rice plant behaviors. The pond conditions were set following the typical practice in South East Asia aquaculture. The two antibiotics were administered to the animal in the pond through medicated feed during a period of 5 days as in actual practice. Concentrations of oxytetracycline in pond water were higher than those of oxolinic acid at the beginning of the simulation. Dissipation rate of oxytetracycline is also higher as it is more readily available for degradation in the water. For the long term, oxolinic acid was present at higher concentration than oxytetracycline in pond water as well as pond sediment. The simulated results were expected to be conservative and can be useful for the lower tier assessment of exposure risk of veterinary medicine in aquaculture industry but more data are needed for the complete validation of the model.

Ability of commonly used prediction equations to predict resting energy expenditure in children with inflammatory bowel disease

Background: Paediatric onset inflammatory bowel disease (IBD) may cause alterations in energy requirements and invalidate the use of standard prediction equations. Our aim was to evaluate four commonly used prediction equations for resting energy expenditure (REE) in children with IBD. Methods: Sixty-three children had repeated measurements of REE as part of a longitudinal research study yielding a total of 243 measurements. These were compared with predicted REE from Schofield, Oxford, FAO/WHO/UNU, and Harris-Benedict equations using the Bland-Altman method. Results: Mean (±SD) age of the patients was 14.2 (2.4) years. Mean measured REE was 1566 (336) kcal per day compared with 1491 (236), 1441 (255), 1481 (232), and 1435 (212) kcal per day calculated from Schofield, Oxford, FAO/WHO/UNU, and Harris-Benedict, respectively. While the Schofield equation demonstrated the least difference between measured and predicted REE, it, along with the other equations tested, did not perform uniformly across all subjects, indicating greater errors at either end of the spectrum of energy expenditure. Smaller differences were found for all prediction equations for Crohn's disease compared with ulcerative colitis. Conclusions: Of the commonly used equations, the equation of Schofield should be used in pediatric patients with IBD when measured values are not able to be obtained. (Inflamm Bowel Dis 2010;) Copyright © 2010 Crohn's & Colitis Foundation of America, Inc.

Assessment of body composition in Sri Lankan children: Validation of a bioelectrical impedance prediction equation

Objective: To develop bioelectrical impedance analysis (BIA) equations to predict total body water (TBW) and fat-free mass (FFM) of Sri Lankan children. Subjects/Methods: Data were collected from 5- to 15-year-old healthy children. They were randomly assigned to validation (M/F: 105/83) and cross-validation (M/F: 53/41) groups. Height, weight and BIA were measured. TBW was assessed using isotope dilution method (D2 O). Multiple regression analysis was used to develop preliminary equations and cross-validated on an independent group. Final prediction equation was constructed combining the two groups and validated by PRESS (prediction of sum of squares) statistics. Impedance index (height2/impedance; cm2/Ω), weight and sex code (male = 1; female = 0) were used as variables. Results: Independent variables of the final prediction equation for TBW were able to predict 86.3% of variance with root means-squared error (RMSE) of 2.1l. PRESS statistics was 2.1l with press residuals of 1.2l. Independent variables were able to predict 86.9% of variance of FFM with RMSE of 2.7 kg. PRESS statistics was 2.8 kg with press residuals of 1.4 kg. Bland Altman technique showed that the majority of the residuals were within mean bias±1.96 s.d. Conclusions: Results of this study provide BIA equation for the prediction of TBW and FFM in Sri Lankan children. To the best of our knowledge there are no published BIA prediction equations validated on South Asian populations. Results of this study need to be affirmed by more studies on other closely related populations by using multi-component body composition assessment.

A methodological survey of future mobility literature: Opportunities for design research

This research establishes that the study of mobility and transportation is multi-disciplinary and highly complex, involving the diverse interplay between infrastructural and psychological factors. Coincidently, a new paradigm in personal mobility is developing. A new generation of mobility solutions is becoming widely available in the form of car and ride sharing services. These services build on the assumption that customers no longer need ownership of a product in order to benefit from it. With the emergence of this new paradigm, this paper presents a methodological review of current practises used by the wider research community. Therefore, this research piece aims to explore methodological approaches involved in the study the effect of community on an individual’s attitudes, perceptions and behaviours of future mobility solutions. The results of this review indicate that the majority of published literature uses quantitative methods as opposed to qualitative and even fewer studies have sought to understand the human factors in these new mobility solutions. This gap in knowledge is a valuable opportunity for design. Inherently qualitative and human focused, design research can fill this gap in knowledge by applying distinctly user-centred methods such as persona design, narrative storytelling, and in-depth observations to discover deeper human insights.

Design-driven digital futures: The role of design-led innovation in the creation of online connected communities for new mobility solutions

Online communities have fundamentally changed how humans connected and are now so common they are fundamental to the human experience. As the Internet developed for Web 1.0 to Web 2.0, the functionality of these communities has far exceeded initial expectations. These communities have shifted from simply places to share information to ways to access products and services that bridge the online and offline worlds. This shift has led to the disruption of many industries with the transportation industry being one such sector. Both private transport providers and public transport systems face competition from online communities who are able to link services providers and customers more effectively and innovatively. These types of communities fall under what has been popularised as collaborative consumption or the sharing economy. The aim of this study is to explore the role of Design-led Innovation in the creation of digital futures, specifically online connected communities for successful new mobility solutions. To explore this proposition multiple data collection methods are proposed;Content Analysis, ii) A Comparative Qualitative Study consisting of Qualitative Interviews and Focus Groups / Design Workshops and iii) An Action Research Cycle of Embedded Practice. The multidisciplinary nature of this study grounds this research in a novel position contributing to new knowledge in both the field of design, and also a deeper understanding of the larger fast-growing online community phenomena.

Prediction of a large-gap quantum-spin-Hall insulator: Diamond-like GaBi bilayer

A quantum-spin-Hall (QSH) state was achieved experimentally, albeit at a low critical temperature because of the narrow band gap of the bulk material. Twodimensional topological insulators are critically important for realizing novel topological applications. Using density functional theory (DFT), we demonstrated that hydrogenated GaBi bilayers (HGaBi) form a stable topological insulator with a large nontrivial band gap of 0.320 eV, based on the state-of-the-art hybrid functional method, which is implementable for achieving QSH states at room temperature. The nontrivial topological property of the HGaBi lattice can also be confirmed from the appearance of gapless edge states in the nanoribbon structure. Our results provide a versatile platform for hosting nontrivial topological states usable for important nanoelectronic device applications.

Use of personal mobility devices for first-and-last mile travel: The Macquarie-Ryde trial

Electric-motored personal mobility devices (PMDs) are appearing on Australian roads. While legal to import and own, their use is typically illegal for adult riders within the road transport system. However, these devices could provide an answer to traffic congestion by getting people out of cars for short trips (“first-and-last mile” travel). City of Ryde council, Macquarie University, and Transport for NSW examined PMD use within the road transport system. Stage 1 of the project examined PMD use within a controlled pedestrian environment on the Macquarie University campus. Three PMD categories were used: one-wheelers (an electric unicycle, the Solowheel); two-wheelers (an electric scooter, the Egret); and three-wheelers (the Qugo). The two-wheeled PMD was most effective in terms of flexibility. In contrast, the three-wheeled PMD was most effective in terms of speed. One-wheeled PMD riders were very satisfied with their device, especially at speed, but significant training and practice was required. Two-wheeled PMD riders had less difficulty navigating through pedestrian precincts and favoured the manoeuvrability of the device as the relative narrowness of the two-wheeled PMD made it easier to use on a diversity of path widths. The usability of all PMDs was compromised by the weight of the devices, difficulties in ascending steeper gradients, portability, and parking. This was a limited trial, with a small number of participants and within a unique environment. However, agreement has been reached for a Stage 2 extension into the Macquarie Park business precinct for further real-world trials within a fully functional road transport system.

Pulse-echo ultrasound transit time spectroscopy: A comparison of experimental measurements and simulation prediction

Considering ultrasound propagation through complex composite media as an array of parallel sonic rays, a comparison of computer simulated prediction with experimental data has previously been reported for transmission mode (where one transducer serves as transmitter, the other as receiver) in a series of ten acrylic step-wedge samples, immersed in water, exhibiting varying degrees of transit time inhomogeneity. In this study, the same samples were used but in pulse-echo mode, where the same ultrasound transducer served as both transmitter and receiver, detecting both ‘primary’ (internal sample interface) and ‘secondary’ (external sample interface) echoes. A transit time spectrum (TTS) was derived, describing the proportion of sonic rays with a particular transit time. A computer simulation was performed to predict the transit time and amplitude of various echoes created, and compared with experimental data. Applying an amplitude-tolerance analysis, 91.7±3.7% of the simulated data was within ±1 standard deviation (STD) of the experimentally measured amplitude-time data. Correlation of predicted and experimental transit time spectra provided coefficients of determination (R2) ranging from 100.0% to 96.8% for the various samples tested. The results acquired from this study provide good evidence for the concept of parallel sonic rays. Further, deconvolution of experimental input and output signals has been shown to provide an effective method to identify echoes otherwise lost due to phase cancellation. Potential applications of pulse-echo ultrasound transit time spectroscopy (PE-UTTS) include improvement of ultrasound image fidelity by improving spatial resolution and reducing phase interference artefacts.

Sediment concentration prediction and statistical evaluation for annual load estimation

We consider the development of statistical models for prediction of constituent concentration of riverine pollutants, which is a key step in load estimation from frequent flow rate data and less frequently collected concentration data. We consider how to capture the impacts of past flow patterns via the average discounted flow (ADF) which discounts the past flux based on the time lapsed - more recent fluxes are given more weight. However, the effectiveness of ADF depends critically on the choice of the discount factor which reflects the unknown environmental cumulating process of the concentration compounds. We propose to choose the discount factor by maximizing the adjusted R-2 values or the Nash-Sutcliffe model efficiency coefficient. The R2 values are also adjusted to take account of the number of parameters in the model fit. The resulting optimal discount factor can be interpreted as a measure of constituent exhaustion rate during flood events. To evaluate the performance of the proposed regression estimators, we examine two different sampling scenarios by resampling fortnightly and opportunistically from two real daily datasets, which come from two United States Geological Survey (USGS) gaging stations located in Des Plaines River and Illinois River basin. The generalized rating-curve approach produces biased estimates of the total sediment loads by -30% to 83%, whereas the new approaches produce relatively much lower biases, ranging from -24% to 35%. This substantial improvement in the estimates of the total load is due to the fact that predictability of concentration is greatly improved by the additional predictors.

Association of hearing impairment and subsequent driving mobility in older adults

- Purpose of the study Hearing impairment (HI) is associated with driving safety (e.g., increased crashes and poor on-road driving performance). However, little is known about HI and driving mobility. This study examined the longitudinal association of audiometric hearing with older adults’ driving mobility over three years. - Design and Methods Secondary data analyses were conducted of 500 individuals (63-90 years) from the Staying Keen in Later Life (SKILL) study. Hearing (pure tone average of 0.5, 1, and 2 kHz) was assessed in the better hearing ear and categorized into normal hearing <25 dB HL; mild HI 26-40 dB HL; or moderate and greater HI>41 dB HL. The Useful Field of View Test (UFOV) was used to estimate the risk for adverse driving events. MANCOVA compared driving mobility between HI levels across time, adjusting for age, sex, race, hypertension, and stroke. Adjusting for these same covariates, Cox regression analyses examined incidence of driving cessation by HI across three years. - Results Individuals with moderate or greater HI performed poorly on the UFOV, indicating increased risk for adverse driving events (p<.001). No significant differences were found among older adults with varying levels of HI for driving mobility (ps>.05), including driving cessation rates (p=.38), across time. - Implications Although prior research indicates older adults with HI may be at higher risk for crashes, they may not modify driving over time. Further exploration of this issue is required to optimize efforts to improve driving safety and mobility among older adults.

An experimental analysis of information acquisition in prediction markets

We study which factors in terms of trading environment and trader characteristics determine individual information acquisition in experimental asset markets. Traders with larger endowments, existing inconclusive information, lower risk aversion, and less experience in financial markets tend to acquire more information. Overall, we find that traders overacquire information, so that informed traders on average obtain negative profits net of information costs. Information acquisition and the associated losses do not diminish over time. This overacquisition phenomenon is inconsistent with predictions of rational expectations equilibrium, and we argue it resembles the overdissipation results from the contest literature. We find that more acquired information in the market leads to smaller differences between fundamental asset values and prices. Thus, the overacquisition phenomenon is a novel explanation for the high forecasting accuracy of prediction markets.

Combining propensity and influence models for product adoption prediction

This paper studies the problem of selecting users in an online social network for targeted advertising so as to maximize the adoption of a given product. In previous work, two families of models have been considered to address this problem: direct targeting and network-based targeting. The former approach targets users with the highest propensity to adopt the product, while the latter approach targets users with the highest influence potential – that is users whose adoption is most likely to be followed by subsequent adoptions by peers. This paper proposes a hybrid approach that combines a notion of propensity and a notion of influence into a single utility function. We show that targeting a fixed number of high-utility users results in more adoptions than targeting either highly influential users or users with high propensity.

Shaping global teacher identity in a short-term mobility programme

This article explores the shaping of Australian and Malaysian pre-service teachers’ possible selves in a short-term mobility programme. With the theory of possible selves, individuals imagine who they will become based on their past and current selves. The focus of the research was on pre-service teachers’ possible selves as global and culturally responsive teachers. The experiential learning through participation in the programme allowed participants to consider their future possible selves as teachers with a deeper understanding of diverse learners’ needs and how they might strive to address these needs in their own classrooms. The scaffolding of reflections in the programme encouraged the pre-service teachers to take on multiple perspectives, to step outside their comfort zones and in many ways to see the world from different eyes. The research found that through experiential learning in the short-term mobility programme both the Australian and Malaysian pre-service teachers gained in positioning their cultural selves currently and as future teachers, suggesting that there is merit in utilising the theory of possible selves in future research in the area of shaping teacher identity.