A hybrid model for studying spatial aspects of infectious diseases

We consider a hybrid model, created by coupling a continuum and an agent-based model of infectious disease. The framework of the hybrid model provides a mechanism to study the spread of infection at both the individual and population levels. This approach captures the stochastic spatial heterogeneity at the individual level, which is directly related to deterministic population level properties. This facilitates the study of spatial aspects of the epidemic process. A spatial analysis, involving counting the number of infectious agents in equally sized bins, reveals when the spatial domain is nonhomogeneous.

Pore structure characterization of North American shale gas reservoirs using USANS/SANS, gas adsorption, and mercury intrusion

Small-angle and ultra-small-angle neutron scattering (SANS and USANS), low-pressure adsorption (N2 and CO2), and high-pressure mercury intrusion measurements were performed on a suite of North American shale reservoir samples providing the first ever comparison of all these techniques for characterizing the complex pore structure of shales. The techniques were used to gain insight into the nature of the pore structure including pore geometry, pore size distribution and accessible versus inaccessible porosity. Reservoir samples for analysis were taken from currently-active shale gas plays including the Barnett, Marcellus, Haynesville, Eagle Ford, Woodford, Muskwa, and Duvernay shales. Low-pressure adsorption revealed strong differences in BET surface area and pore volumes for the sample suite, consistent with variability in composition of the samples. The combination of CO2 and N2 adsorption data allowed pore size distributions to be created for micro–meso–macroporosity up to a limit of �1000 Å. Pore size distributions are either uni- or multi-modal. The adsorption-derived pore size distributions for some samples are inconsistent with mercury intrusion data, likely owing to a combination of grain compression during high-pressure intrusion, and the fact that mercury intrusion yields information about pore throat rather than pore body distributions. SANS/USANS scattering data indicate a fractal geometry (power-law scattering) for a wide range of pore sizes and provide evidence that nanometer-scale spatial ordering occurs in lower mesopore–micropore range for some samples, which may be associated with inter-layer spacing in clay minerals. SANS/USANS pore radius distributions were converted to pore volume distributions for direct comparison with adsorption data. For the overlap region between the two methods, the agreement is quite good. Accessible porosity in the pore size (radius) range 5 nm–10 lm was determined for a Barnett shale sample using the contrast matching method with pressurized deuterated methane fluid. The results demonstrate that accessible porosity is pore-size dependent.

The impact of spatial scales and spatial smoothing on the outcome of Bayesian spatial model

Discretization of a geographical region is quite common in spatial analysis. There have been few studies into the impact of different geographical scales on the outcome of spatial models for different spatial patterns. This study aims to investigate the impact of spatial scales and spatial smoothing on the outcomes of modelling spatial point-based data. Given a spatial point-based dataset (such as occurrence of a disease), we study the geographical variation of residual disease risk using regular grid cells. The individual disease risk is modelled using a logistic model with the inclusion of spatially unstructured and/or spatially structured random effects. Three spatial smoothness priors for the spatially structured component are employed in modelling, namely an intrinsic Gaussian Markov random field, a second-order random walk on a lattice, and a Gaussian field with Matern correlation function. We investigate how changes in grid cell size affect model outcomes under different spatial structures and different smoothness priors for the spatial component. A realistic example (the Humberside data) is analyzed and a simulation study is described. Bayesian computation is carried out using an integrated nested Laplace approximation. The results suggest that the performance and predictive capacity of the spatial models improve as the grid cell size decreases for certain spatial structures. It also appears that different spatial smoothness priors should be applied for different patterns of point data.

Towards bio-inspired place recognition over multiple spatial scales

This paper presents a new multi-scale place recognition system inspired by the recent discovery of overlapping, multi-scale spatial maps stored in the rodent brain. By training a set of Support Vector Machines to recognize places at varying levels of spatial specificity, we are able to validate spatially specific place recognition hypotheses against broader place recognition hypotheses without sacrificing localization accuracy. We evaluate the system in a range of experiments using cameras mounted on a motorbike and a human in two different environments. At 100% precision, the multiscale approach results in a 56% average improvement in recall rate across both datasets. We analyse the results and then discuss future work that may lead to improvements in both robotic mapping and our understanding of sensory processing and encoding in the mammalian brain.

Geographical distribution of human Schistosoma japonicum infection in the Philippines : tools to support disease control and further elimination

S. japonicum infection is believed to be endemic in 28 of the 80 provinces of the Philippines and the most recent data on schistosomiasis prevalence have shown considerable variability between provinces. In order to increase the efficient allocation of parasitic disease control resources in the country, we aimed to describe the small scale spatial variation in S. japonicum prevalence across the Philippines, quantify the role of the physical environment in driving the spatial variation of S. japonicum, and develop a predictive risk map of S. japonicum infection. Data on S. japonicum infection from 35,754 individuals across the country were geo-located at the barangay level and included in the analysis. The analysis was then stratified geographically for Luzon, the Visayas and Mindanao. Zero-inflated binomial Bayesian geostatistical models of S. japonicum prevalence were developed and diagnostic uncertainty was incorporated. Results of the analysis show that in the three regions, males and individuals aged ≥ 20 years had significantly higher prevalence of S. japonicum compared with females and children <5 years. The role of the environmental variables differed between regions of the Philippines. S. japonicum infection was widespread in the Visayas whereas it was much more focal in Luzon and Mindanao. This analysis revealed significant spatial variation in prevalence of S. japonicum infection in the Philippines. This suggests that a spatially targeted approach to schistosomiasis interventions, including mass drug administration, is warranted. When financially possible, additional schistosomiasis surveys should be prioritized to areas identified to be at high risk, but which were underrepresented in our dataset.

Barriers to bikesharing : an analysis from Melbourne and Brisbane

This study quantifies the motivators and barriers to bikeshare program usage in Australia. An online survey was administered to a sample of annual members of Australia’s two bikeshare programs based in Brisbane and Melbourne, to assess motivations for joining the schemes. Non-members of the programs were also sampled in order to identify current barriers to joining bikeshare. Spatial analysis from Brisbane revealed residential and work locations of non-members were more geographically dispersed than for bikeshare members. An analysis of bikeshare usage in Melbourne showed a strong relationship between docking stations in areas with relatively less accessible public transit opportunities. The most influential barriers to bikeshare use related to motorized travel being too convenient and docking stations not being sufficiently close to home, work and other frequented destinations. The findings suggest that bikeshare programs may attract increased membership by ensuring travel times are competitive with motorized travel, for example through efficient bicycle routing and priority progression and, by expanding docking station locations, and by increasing the level of convenience associated with scheme use. Convenience considerations may include strategic location of docking stations, ease of signing up and integration with public transport.

‘Healthy mobile check-ins’ study: using GIS in smartphones to track use of urban environment by survivors of endometrial cancer

Aims/Objectives Our study aims to test the capacity of a newly developed smartphone innovation to obtain data on social, structural, and spatial determinants of the daily health-related behaviours of women living in urban Brisbane neighbourhoods who have survived endometrial cancer. Methods The women used a mobile web app designed specifically for the project to record GIS/location data on every destination they visited within their local urban neighbourhoods over a two-week period. Additionally, we gathered textual data on the social context/reasons for travel, as well as mode of transport to reach these destinations. The data was transported to SPSS and Google Earth for statistical and spatial analysis. We then met with the women to discuss lifestyle interventions to maximise their use of their local neighbourhoods in ways that could increase their physical activity levels and improve their overall health and well-being. These interventions will be evaluated and translated into a large-scale national study if effective. Results Initial findings about patterns in the group’s use of the local urban environment will be displayed, including daily distances travelled, types of locations visited, walking levels, use of public transport, use of green spaces and use of health-related resources. Any socio-demograpahic differences found between the women will be reported. Qualitative, quantitative, and spatial/mapping data will be displayed Conclusion The benefits and limitations of the mobile website designed to collect a range of data types about human-neighbourhood interactions with implications for intervention design will be discussed.

Spatiotemporal analysis of indigenous and imported dengue fever cases in Guangdong province, China

Background Dengue fever has been a major public health concern in China since it re-emerged in Guangdong province in 1978. This study aimed to explore spatiotemporal characteristics of dengue fever cases for both indigenous and imported cases during recent years in Guangdong province, so as to identify high-risk areas of the province and thereby help plan resource allocation for dengue interventions. Methods Notifiable cases of dengue fever were collected from all 123 counties of Guangdong province from 2005 to 2010. Descriptive temporal and spatial analysis were conducted, including plotting of seasonal distribution of cases, and creating choropleth maps of cumulative incidence by county. The space-time scan statistic was used to determine space-time clusters of dengue fever cases at the county level, and a geographical information system was used to visualize the location of the clusters. Analysis were stratified by imported and indigenous origin. Results 1658 dengue fever cases were recorded in Guangdong province during the study period, including 94 imported cases and 1564 indigenous cases. Both imported and indigenous cases occurred more frequently in autumn. The areas affected by the indigenous and imported cases presented a geographically expanding trend over the study period. The results showed that the most likely cluster of imported cases (relative risk = 7.52, p < 0.001) and indigenous cases (relative risk = 153.56, p < 0.001) occurred in the Pearl River Delta Area; while a secondary cluster of indigenous cases occurred in one district of the Chao Shan Area (relative risk = 471.25, p < 0.001). Conclusions This study demonstrated that the geographic range of imported and indigenous dengue fever cases has expanded over recent years, and cases were significantly clustered in two heavily urbanised areas of Guangdong province. This provides the foundation for further investigation of risk factors and interventions in these high-risk areas.

Spatial incidence of dengue infections in Queensland, Australia - reply

This study aimed to investigate the spatial clustering and dynamic dispersion of dengue incidence in Queensland, Australia. We used Moran's I statistic to assess the spatial autocorrelation of reported dengue cases. Spatial empirical Bayes smoothing estimates were used to display the spatial distribution of dengue in postal areas throughout Queensland. Local indicators of spatial association (LISA) maps and logistic regression models were used to identify spatial clusters and examine the spatio-temporal patterns of the spread of dengue. The results indicate that the spatial distribution of dengue was clustered during each of the three periods of 1993–1996, 1997–2000 and 2001–2004. The high-incidence clusters of dengue were primarily concentrated in the north of Queensland and low-incidence clusters occurred in the south-east of Queensland. The study concludes that the geographical range of notified dengue cases has significantly expanded in Queensland over recent years.

Utility of temporal artery biopsy samples for genome-wide analysis of giant cell arteritis

Giant Cell Arteritis (GCA) is the most common vasculitis affecting the elderly. Archived formalin-fixed paraffin-embedded (FFPE) temporal artery biopsy (TAB) specimens potentially represent a valuable resource for large-scale genetic analysis of this disease. FFPE TAB samples were obtained from 12 patients with GCA. Extracted TAB DNA was assessed by real time PCR before restoration using the Illumina HD FFPE Restore Kit. Paired FFPE-blood samples were genotyped on the Illumina OmniExpress FFPE microarray. The FFPE samples that passed stringent quality control measures had a mean genotyping success of >97%. When compared with their matching peripheral blood DNA, the mean discordant heterozygote and homozygote single nucleotide polymorphisms calls were 0.0028 and 0.0003, respectively, which is within the accepted tolerance of reproducibility. This work demonstrates that it is possible to successfully obtain high-quality microarray-based genotypes FFPE TAB samples and that this data is similar to that obtained from peripheral blood.

Research Monograph : Sustainable Australia : Containing travel in master planned estates

Low density suburban development and excessive use of automobiles are associated with serious urban and environmental problems. These problems include traffic congestion, longer commuting times, high automobile dependency, air and water pollution, and increased depletion of natural resources. Master planned development suggests itself as a possible palliative for the ills of low density and high travel. The following study examines the patterns and dynamics of movement in a selection of master planned estates in Australia. The study develops new approaches for assessing the containment of travel within planned development. Its key aim is to clarify and map the relationships between trip generation and urban form and structure. The initial conceptual framework of the report is developed in a review of literature related to urban form and travel behaviour. These concepts are tested empirically in a pilot study of suburban travel activity in master planned estates. A geographical information systems (GIS) methodology is used to determine regional journey-to-work patterns and travel containment rates. Factors that influence self-containment patterns are estimated with a regression model. The key research findings of the pilot study are: - There is a strong relation between urban structural form and patterns of trip generation; - The travel self-containment of Australian master planned estates is lower than the scholarly literature implies would occur if appropriate planning principles to achieve sustainable urban travel were followed; - Proximity to the central business district, income level and education status are positively correlated with travel containment; - Master planned estates depend more on local and regional centres for employment than on the central business district; - The service sector is the major employer in and around master planned estates. It tends to provide part-time and casual employment rather than full-time employment; - Travel self-containment is negative correlated with car dependency. Master planned estates with less car dependent residents, and with good access to public transport, appear to be more self-contained and, consequently, more sustainable than the norm. This research is a useful preliminary examination of travel self-containment in Australian master planned estates. It by no means exhausts the subject. In future research we hope to further assess sustainable travel patterns with more detailed spatial analysis.

Fatal motorcycle crashes in north Queensland : characteristics and potential interventions

Aims: The Rural and Remote Road Safety Study (RRRSS) addresses a recognised need for greater research on road trauma in rural and remote Australia, the costs of which are disproportionately high compared with urban areas. The 5-year multi-phase study with whole-of-government support concluded in June 2008. Drawing on RRRSS data, we analysed fatal motorcycle crashes which occurred over 39 months to provide a description of crash characteristics, contributing factors and people involved. The descriptive analysis and discussion may inform development of tailored motorcycle safety interventions. Methods: RRRSS criteria sought vehicle crashes resulting in death or hospitalisation for 24 hours minimum of at least 1 person aged 16 years or over, in the study area defined roughly as the Queensland area north from Bowen in the east and Boulia in the west (excluding Townsville and Cairns urban areas). Fatal motorcycle crashes were selected from the RRRSS dataset. Analysis considered medical data covering injury types and severity, evidence of alcohol, drugs and prior medical conditions, as well as crash descriptions supplied by police to Queensland Transport on contributing circumstances, vehicle types, environmental conditions and people involved. Crash data were plotted in a geographic information system (MapInfo) for spatial analysis. Results: There were 23 deaths from 22 motorcycle crashes on public roads meeting RRRSS criteria. Of these, half were single vehicle crashes and half involved 2 or more vehicles. In contrast to general patterns for driver/rider age distribution in crashes, riders below 25 years of age were represented proportionally within the population. Riders in their thirties comprised 41% of fatalities, with a further 36% accounted for by riders in their fifties. 18 crashes occurred in the Far North Statistical Division (SD), with 2 crashes in both the Northern and North West SDs. Behavioural factors comprised the vast majority of contributing circumstances cited by police, with adverse environmental conditions noted in only 4 cases. Conclusions: Fatal motorcycle crashes were more likely to involve another vehicle and less likely to involve a young rider than non-fatal crashes recorded by the RRRSS. Rider behaviour contributed to the majority of crashes and should be a major focus of research, education and policy development, while other road users’ behaviour and awareness also remains important. With 68% of crashes occurring on major and secondary roads within a 130km radius of Cairns, efforts should focus on this geographic area.

Trojan Horse or Rorschach Blot? Creative industries discourse around the world

One of the most wide-ranging and sophisticated critiques of creative industries policy argues that it is a kind of Trojan horse, secreting the intellectual heritage of the information society and its technocratic baggage into the realm of cultural practice, suborning the latter's proper claims on the public purse and self-understanding, and aligning it with inappropriate bedfellows such as business services, telecommunications and calls for increases in generic creativity. Reviewing the broad adoption of the concept in policy discourse around the world, this paper suggests that rather than a Trojan horse, it might be better thought of as a Rorschach blot, being invested in for varying reasons and with varying emphases and outcomes. Based on spatial analysis, then, the critique may need modification. Temporally as well, the critique may have been overtaken by later developments taking policy emphases 'beyond' the creative industries.

Use of Bayesian geostatistical prediction to estimate local variations in Schistosoma haematobium infection in western Africa

Objective We aimed to predict sub-national spatial variation in numbers of people infected with Schistosoma haematobium, and associated uncertainties, in Burkina Faso, Mali and Niger, prior to implementation of national control programmes. Methods We used national field survey datasets covering a contiguous area 2,750 × 850 km, from 26,790 school-aged children (5–14 years) in 418 schools. Bayesian geostatistical models were used to predict prevalence of high and low intensity infections and associated 95% credible intervals (CrI). Numbers infected were determined by multiplying predicted prevalence by numbers of school-aged children in 1 km2 pixels covering the study area. Findings Numbers of school-aged children with low-intensity infections were: 433,268 in Burkina Faso, 872,328 in Mali and 580,286 in Niger. Numbers with high-intensity infections were: 416,009 in Burkina Faso, 511,845 in Mali and 254,150 in Niger. 95% CrIs (indicative of uncertainty) were wide; e.g. the mean number of boys aged 10–14 years infected in Mali was 140,200 (95% CrI 6200, 512,100). Conclusion National aggregate estimates for numbers infected mask important local variation, e.g. most S. haematobium infections in Niger occur in the Niger River valley. Prevalence of high-intensity infections was strongly clustered in foci in western and central Mali, north-eastern and northwestern Burkina Faso and the Niger River valley in Niger. Populations in these foci are likely to carry the bulk of the urinary schistosomiasis burden and should receive priority for schistosomiasis control. Uncertainties in predicted prevalence and numbers infected should be acknowledged and taken into consideration by control programme planners.