Incorporating spatial correlations into multispecies mean-field models

In biology, we frequently observe different species existing within the same environment. For example, there are many cell types in a tumour, or different animal species may occupy a given habitat. In modelling interactions between such species, we often make use of the mean field approximation, whereby spatial correlations between the locations of individuals are neglected. Whilst this approximation holds in certain situations, this is not always the case, and care must be taken to ensure the mean field approximation is only used in appropriate settings. In circumstances where the mean field approximation is unsuitable we need to include information on the spatial distributions of individuals, which is not a simple task. In this paper we provide a method that overcomes many of the failures of the mean field approximation for an on-lattice volume-excluding birth-death-movement process with multiple species. We explicitly take into account spatial information on the distribution of individuals by including partial differential equation descriptions of lattice site occupancy correlations. We demonstrate how to derive these equations for the multi-species case, and show results specific to a two-species problem. We compare averaged discrete results to both the mean field approximation and our improved method which incorporates spatial correlations. We note that the mean field approximation fails dramatically in some cases, predicting very different behaviour from that seen upon averaging multiple realisations of the discrete system. In contrast, our improved method provides excellent agreement with the averaged discrete behaviour in all cases, thus providing a more reliable modelling framework. Furthermore, our method is tractable as the resulting partial differential equations can be solved efficiently using standard numerical techniques.

Developing sustainable ‘liveable’ buildings, cities and communities for a sub-tropical context : residents’ perspectives

A key challenge for the 21st Century is to make our cities more liveable and foster economically sustainable, environmentally responsible, and socially inclusive communities. Design thinking, particularly a human-centred approach, offers a way to tackle this challenge. Findings from two recent Australian research projects highlight how facilitating sustainable, liveable communities in a humid sub-tropical environment requires an in-depth understanding of people’s perspectives, experiences and practices. Project 1 (‘Research House’) documents the reflections of a family who lived in a ‘test’ sustainable house for two years, outlining their experience and evaluations of universal design and sustainable technologies. The study family was very impressed with the natural lighting, natural ventilation, spaciousness and ease of access, which contributed significantly to their comfort and the liveability of their home. Project 2 (‘Inner-Urban High Density Living’) explored Brisbane residents’ opinions about high-density living, through a survey (n=636), interviews (n=24), site observations (over 300 hours) and environmental monitoring, assessing opinions on the liveability of their individual dwelling, the multi-unit host building and the surrounding neighbourhood. Nine areas, categorised into three general domains, were identified as essential for enhancing high density liveability. In terms of the dwelling, thermal comfort/ventilation, natural light, noise mitigation were important; shared space, good neighbour protocols, and support for environmentally sustainable behaviour were desired in the building/complex; and accessible/sustainable transport, amenities and services, sense of community were considered important in the surrounding neighbourhood. Combined, these findings emphasise the importance and complexity associated with designing liveable building, cities and communities, illustrating how adopting a design thinking, human-centred approach will help create sustainable communities that will meet the needs of current and future generations.

Locally weighted learning model predictive control for nonlinear and time varying dynamics

This paper proposes an online learning control system that uses the strategy of Model Predictive Control (MPC) in a model based locally weighted learning framework. The new approach, named Locally Weighted Learning Model Predictive Control (LWL-MPC), is proposed as a solution to learn to control robotic systems with nonlinear and time varying dynamics. This paper demonstrates the capability of LWL-MPC to perform online learning while controlling the joint trajectories of a low cost, three degree of freedom elastic joint robot. The learning performance is investigated in both an initial learning phase, and when the system dynamics change due to a heavy object added to the tool point. The experiment on the real elastic joint robot is presented and LWL-MPC is shown to successfully learn to control the system with and without the object. The results highlight the capability of the learning control system to accommodate the lack of mechanical consistency and linearity in a low cost robot arm.

Development of a computer based 1D-2D dynamic flood model. Case study of the Pagsangaan river basin in Leyte, the Philippines

Floods are among the most devastating events that affect primarily tropical, archipelagic countries such as the Philippines. With the current predictions of climate change set to include rising sea levels, intensification of typhoon strength and a general increase in the mean annual precipitation throughout the Philippines, it has become paramount to prepare for the future so that the increased risk of floods on the country does not translate into more economic and human loss. Field work and data gathering was done within the framework of an internship at the former German Technical Cooperation (GTZ) in cooperation with the Local Government Unit of Ormoc City, Leyte, The Philippines, in order to develop a dynamic computer based flood model for the basin of the Pagsangaan River. To this end, different geo-spatial analysis tools such as PCRaster and ArcGIS, hydrological analysis packages and basic engineering techniques were assessed and implemented. The aim was to develop a dynamic flood model and use the development process to determine the required data, availability and impact on the results as case study for flood early warning systems in the Philippines. The hope is that such projects can help to reduce flood risk by including the results of worst case scenario analyses and current climate change predictions into city planning for municipal development, monitoring strategies and early warning systems. The project was developed using a 1D-2D coupled model in SOBEK (Deltares Hydrological modelling software package) and was also used as a case study to analyze and understand the influence of different factors such as land use, schematization, time step size and tidal variation on the flood characteristics. Several sources of relevant satellite data were compared, such as Digital Elevation Models (DEMs) from ASTER and SRTM data, as well as satellite rainfall data from the GIOVANNI server (NASA) and field gauge data. Different methods were used in the attempt to partially calibrate and validate the model to finally simulate and study two Climate Change scenarios based on scenario A1B predictions. It was observed that large areas currently considered not prone to floods will become low flood risk (0.1-1 m water depth). Furthermore, larger sections of the floodplains upstream of the Lilo- an’s Bridge will become moderate flood risk areas (1 - 2 m water depth). The flood hazard maps created for the development of the present project will be presented to the LGU and the model will be used to create a larger set of possible flood prone areas related to rainfall intensity by GTZ’s Local Disaster Risk Management Department and to study possible improvements to the current early warning system and monitoring of the basin section belonging to Ormoc City; recommendations about further enhancement of the geo-hydro-meteorological data to improve the model’s accuracy mainly on areas of interest will also be presented at the LGU.

Play and heal : randomized controlled trial of Ditto intervention efficacy on improving re-epithelialization in pediatric burns

BACKGROUND: The relationships between pain, stress and anxiety, and their effect on burn wound re-epithelialization have not been well explored to-date. The aim of this study was to investigate the effect of the Ditto (a hand-held electronic medical device providing procedural preparation and distraction) intervention on re-epithelialization rates in acute pediatric burns. METHODS/DESIGN: From August 2011 to August 2012, children (4-12 years) with an acute burn presenting to the Royal Children's Hospital, Brisbane, Australia fulfilled the study requirements and were randomized to [1] Ditto intervention or [2] standard practice. Burn re-epithelialization, pain intensity, anxiety and stress measures were obtained at every dressing change until complete wound re-epithelialization. RESULTS: One hundred and seventeen children were randomized and 75 children were analyzed (n=40 standard group; n=35 Ditto group). Inability to predict wound management resulted in 42 participants no longer meeting the eligibility criteria. Wounds in the Ditto intervention group re-epithelialized faster than the standard practice group (-2.14 days (CI: -4.38 to 0.10), p-value=0.061), and significantly faster when analyses were adjusted for mean burn depth (-2.26 days (CI: -4.48 to -0.04), p-value=0.046). Following procedural preparation at the first change of dressing, the Ditto group reported lower pain intensity scores (-0.64 (CI: -1.28, 0.01) p=0.052) and lower anxiety ratings (-1.79 (CI: -3.59, 0.01) p=0.051). At the second and third dressing removals average pain (FPS-R and FLACC) and anxiety scores (VAS-A) were at least one point lower when Ditto intervention was received. CONCLUSIONS: The Ditto procedural preparation and distraction device is a useful tool alongside pharmacological intervention to improve the rate of burn re-epithelialization and manage pain and anxiety during burn wound care procedures.

Supplementary information : weighted tree kernels for sequence analysis

Genomic sequences are fundamentally text documents, admitting various representations according to need and tokenization. Gene expression depends crucially on binding of enzymes to the DNA sequence at small, poorly conserved binding sites, limiting the utility of standard pattern search. However, one may exploit the regular syntactic structure of the enzyme's component proteins and the corresponding binding sites, framing the problem as one of detecting grammatically correct genomic phrases. In this paper we propose new kernels based on weighted tree structures, traversing the paths within them to capture the features which underpin the task. Experimentally, we and that these kernels provide performance comparable with state of the art approaches for this problem, while offering significant computational advantages over earlier methods. The methods proposed may be applied to a broad range of sequence or tree-structured data in molecular biology and other domains.

Axial elongation associated with biomechanical factors during near work

Purpose: To investigate the changes occurring in the axial length, choroidal thickness and anterior biometrics of the eye during a 10 minute near task performed in downward gaze. Methods: Twenty young adult subjects (10 emmetropes and 10 myopes) participated in this study. To measure ocular biometrics in downward gaze, an optical biometer was inclined on a custom built, height and tilt adjustable table. Baseline measures were collected after each subject performed a distance primary gaze control task for 10 mins, to provide wash-out period for prior visual tasks before each of three different accommodation/gaze conditions. These other three conditions included a near task (2.5 D) in primary gaze, and a near (2.5 D) and a far (0 D) accommodative task in downward gaze (25°), all for 10 mins duration. Immediately after, and then 5 and 10 mins from the commencement of each trial, measurements of ocular biometrics (e.g. anterior biometrics, axial length, choroidal thickness and retinal thickness) were obtained. Results: Axial length increased with accommodation and was significantly greater for downward gaze with accommodation (mean change ± SD 23 ± 13 µm at 10 mins) compared to primary gaze with accommodation (mean change 8 ± 15 µm at 10 mins) (p < 0.05). A small amount of choroidal thinning was also found during accommodation that was statistically significant in downward gaze (13 ± 14 µm at 10 mins, p < 0.05). Accommodation in downward gaze also caused greater changes in anterior chamber depth and lens thickness compared to accommodation in primary gaze. Conclusion: Axial length, choroidal thickness and anterior eye biometrics change significantly during accommodation in downward gaze as a function of time. These changes appear to be due to the combined influence of biomechanical factors (i.e. extraocular muscle forces, ciliary muscle contraction) associated with near tasks in downward gaze.

A Bayesian regression approach to assess uncertainty in pollutant wash-off modelling

Due to knowledge gaps in relation to urban stormwater quality processes, an in-depth understanding of model uncertainty can enhance decision making. Uncertainty in stormwater quality models can originate from a range of sources such as the complexity of urban rainfall-runoff-stormwater pollutant processes and the paucity of observed data. Unfortunately, studies relating to epistemic uncertainty, which arises from the simplification of reality are limited and often deemed mostly unquantifiable. This paper presents a statistical modelling framework for ascertaining epistemic uncertainty associated with pollutant wash-off under a regression modelling paradigm using Ordinary Least Squares Regression (OLSR) and Weighted Least Squares Regression (WLSR) methods with a Bayesian/Gibbs sampling statistical approach. The study results confirmed that WLSR assuming probability distributed data provides more realistic uncertainty estimates of the observed and predicted wash-off values compared to OLSR modelling. It was also noted that the Bayesian/Gibbs sampling approach is superior compared to the most commonly adopted classical statistical and deterministic approaches commonly used in water quality modelling. The study outcomes confirmed that the predication error associated with wash-off replication is relatively higher due to limited data availability. The uncertainty analysis also highlighted the variability of the wash-off modelling coefficient k as a function of complex physical processes, which is primarily influenced by surface characteristics and rainfall intensity.

Noise levels in a general intensive care unit : a descriptive study.

The aim of this small-scale study was to measure, analyse and compare levels of acoustic noise, in a nine-bedded general intensive care unit (ICU). Measurements were undertaken using the Norsonic 116 sound level meter recording noise levels in the internationally agreed ‘A’ weighted scale. Noise level data were obtained and recorded at 5 min over 3 consecutive days. Results of noise level analysis indicated that mean noise levels within this clinical area was 56·42 dB(A), with acute spikes reaching 80 dB(A). The quietest noise level attained was that of 50 dB(A) during sporadic intervals throughout the 24-h period. Parametric testing using analysis of variance found a positive relationship (p ≤ 0·001) between the nursing shifts and the day of the week. However, Scheffe multiple range testing showed significant differences between the morning shift, and the afternoon and night shifts combined (p ≤ 0·05). There was no statistical difference between the afternoon and night shifts (p ≥ 0·05). While the results of this study may seem self-evident in many respects, what it has highlighted is that the problem of excessive noise exposure within the ICU continues to go unabated. More concerning is that the prolonged effects of excessive noise exposure on patients and staff alike can have deleterious effect on the health and well-being of these individuals.

Noise levels in a General Surgical Ward : a descriptive study

Aims and objectives.  This study was undertaken to measure and analyse levels of acoustic noise in a General Surgical Ward. Method.  Measurements were undertaken using the Norsonic 116 sound level meter (SLM) recording noise levels in the internationally agreed ‘A’ weighted scale. Noise level data and observational data as to the number of staff present were obtained and recorded at 5-min intervals over three consecutive days. Results.  Results of noise level analysis indicated that mean noise level within this clinical area was 42.28 dB with acute spikes reaching 70 dB(A). The lowest noise level attained was that of 36 dB(A) during the period midnight to 7 a.m. Non-parametric testing, using Spearman's Rho (two-tailed), found a positive relationship between the number of staff present and the level of noise recorded, indicating that the presence of hospital personnel strongly influences the level of noise within this area. Relevance to clinical practice.  Whilst the results of this may seem self-evident in many respects the problems of excessive noise production and the exposure to it for patients, hospital personnel and relatives alike continues unabated. What must be of concern is the psychophysiological effects excessive noise exposure has on individuals, for example, decreased wound healing, sleep deprivation and cardiovascular stimulation.

Back to the roots : mean-variance analysis of relevance estimations

Recently, mean-variance analysis has been proposed as a novel paradigm to model document ranking in Information Retrieval. The main merit of this approach is that it diversifies the ranking of retrieved documents. In its original formulation, the strategy considers both the mean of relevance estimates of retrieved documents and their variance. How- ever, when this strategy has been empirically instantiated, the concepts of mean and variance are discarded in favour of a point-wise estimation of relevance (to replace the mean) and of a parameter to be tuned or, alternatively, a quantity dependent upon the document length (to replace the variance). In this paper we revisit this ranking strategy by going back to its roots: mean and variance. For each retrieved document, we infer a relevance distribution from a series of point-wise relevance estimations provided by a number of different systems. This is used to compute the mean and the variance of document relevance estimates. On the TREC Clueweb collection, we show that this approach improves the retrieval performances. This development could lead to new strategies to address the fusion of relevance estimates provided by different systems.

Comparison of intensity-based cut-points for the RT3 accelerometer in youth

OBJECTIVES: To compare the classification accuracy of previously published RT3 accelerometer cut-points for youth using energy expenditure, measured via portable indirect calorimetry, as a criterion measure. DESIGN: Cross-sectional cross-validation study. METHODS: 100 children (mean age 11.2±2.8 years, 61% male) completed 12 standardized activities trials (3 sedentary, 5 lifestyle and 4 ambulatory) while wearing an RT3 accelerometer. V˙O2 was measured concurrently using the Oxycon Mobile portable calorimeter. Cut-points by Vanhelst (VH), Rowlands (RW), Chu (CH), Kavouras (KV) and the RT3 manufacturer (RT3M) were used to classify PA intensity as sedentary (SED), light (LPA), moderate (MPA) or vigorous (VPA). Classification accuracy was evaluated using the area under the Receiver Operating Characteristic curve (ROC-AUC) and weighted Kappa (κ). RESULTS: For moderate-to-vigorous PA (MVPA), VH, KV and RW exhibited excellent accuracy classification (ROC-AUC≥0.90), while the CH and RT3M exhibited good classification accuracy (ROC-AUC>0.80). Classification accuracy for LPA was fair to poor (ROC-AUC<0.76). For SED, VH exhibited excellent classification accuracy (ROC-AUC>0.90), while RW, CH, and RT3M exhibited good classification accuracy (ROC-AUC>0.80). Kappa statistics ranged from 0.67 (VH) to 0.55 (CH). CONCLUSIONS: All cut-points provided acceptable classification accuracy for SED and MVPA, but limited accuracy for LPA. On the basis of classification accuracy over all four levels of intensity, the use of the VH cut-points is recommended.

Effect of crack depth and specimen width on fracture toughness of a carbon steel in the ductile-brittle transition region

The effects of crack depth (a/W) and specimen width W on the fracture toughness and ductile±brittle transition have been investigated using three-point bend specimens. Finite element analysis is employed to obtain the stress-strain fields ahead of the crack tip. The results show that both normalized crack depth (a/W) and specimen width (W) affect the fracture toughness and ductile±brittle fracture transition. The measured crack tip opening displacement decreases and ductile±brittle transition occurs with increasing crack depth (a/W) from 0.1 to 0.2 and 0.3. At a fixed a/W (0.2 or 0.3), all specimens fail by cleavage prior to ductile tearing when specimen width W increases from 25 to 40 and 50 mm. The lower bound fracture toughness is not sensitive to crack depth and specimen width. Finite element analysis shows that the opening stress in the remaining ligament is elevated with increasing crack depth or specimen width due to the increase of in-plane constraint. The average local cleavage stress is dependent on both crack depth and specimen width but its lower bound value is not sensitive to constraint level. No fixed distance can be found from the cleavage initiation site to the crack tip and this distance increases gradually with decreasing inplane constraint.

Changes in ocular biometrics and refraction during near work in downward gaze over time

PURPOSE To investigate changes in the characteristics of the corneal optics, total optics, anterior biometrics and axial length of the eye during a near task, in downward gaze, over 10 min. METHODS Ten emmetropes (mean - 0.14 ± 0.24 DS) and 10 myopes (mean - 2.26 ± 1.42 DS) aged from 18 to 30 years were recruited. To measure ocular biometrics and corneal topography in downward gaze, an optical biometer (Lenstar LS900) and a rotating Scheimpflug camera (Pentacam HR) were inclined on a custom built, height and tilt adjustable table. The total optics of the eye were measured in downward gaze with binocular fixation using a modified Shack-Hartmann wavefront sensor. Initially, subjects performed a distance viewing task at primary gaze for 10 min to provide a "wash-out" period for prior visual tasks. A distance task (watching video at 6 m) in downward gaze (25°) and a near task (watching video on a portable LCD screen with 2.5 D accommodation demand) in primary gaze and 25°downward gaze were then carried out, each for 10 min in a randomized order. During measurements, in dichoptic view, a Maltese cross was fixated with the right (untested) eye and the instrument’s fixation target was fixated with the subject’s tested left eye. Immediately after (0 min), 5 and 10 min from the commencement of each trial, measurements of ocular parameters were acquired in downward gaze. RESULTS Axial length exhibited a significant increase with downward gaze and accommodation over time (p<0.05). The greatest axial elongation was observed in downward gaze with 2.5 D accommodation after 10 min (mean change from baseline 23±3 µm). Downward gaze also caused greater changes in anterior chamber depth (ACD) and lens thickness (LT) with accommodation (ACD mean change -163±12µm at 10 min; LT mean change 173±17 µm at 10 min) compared to primary gaze with accommodation (ACD mean change -138±12µm at 10 min; LT mean change 131±15 µm at 10 min). Both corneal power and total ocular power changed by a small but significant amount with downward gaze (p<0.05), resulting in a myopic shift (~0.10 D) in the spherical power of the eye compared with primary gaze. CONCLUSION The axial length, anterior biometrics and ocular refraction change significantly with accommodation in downward gaze as a function of time. These findings provide new insights into the optical and bio-mechanical changes of the eye during typical near tasks.

What does it mean to 'securitize' infectious diseases?

This paper seeks to explain how the selective securitization of infectious disease arose, and to analyze the policy successes from this move. It is argued that despite some success, such as the revised International Health Regulations (IHR) in 2005, there remain serious deficiencies in the political outputs from the securitization of infectious disease.