Comparing multilevel and Bayesian spatial random effects survival models to assess geographical inequalities in colorectal cancer survival: a case study

Background Multilevel and spatial models are being increasingly used to obtain substantive information on area-level inequalities in cancer survival. Multilevel models assume independent geographical areas, whereas spatial models explicitly incorporate geographical correlation, often via a conditional autoregressive prior. However the relative merits of these methods for large population-based studies have not been explored. Using a case-study approach, we report on the implications of using multilevel and spatial survival models to study geographical inequalities in all-cause survival. Methods Multilevel discrete-time and Bayesian spatial survival models were used to study geographical inequalities in all-cause survival for a population-based colorectal cancer cohort of 22,727 cases aged 20–84 years diagnosed during 1997–2007 from Queensland, Australia. Results Both approaches were viable on this large dataset, and produced similar estimates of the fixed effects. After adding area-level covariates, the between-area variability in survival using multilevel discrete-time models was no longer significant. Spatial inequalities in survival were also markedly reduced after adjusting for aggregated area-level covariates. Only the multilevel approach however, provided an estimation of the contribution of geographical variation to the total variation in survival between individual patients. Conclusions With little difference observed between the two approaches in the estimation of fixed effects, multilevel models should be favored if there is a clear hierarchical data structure and measuring the independent impact of individual- and area-level effects on survival differences is of primary interest. Bayesian spatial analyses may be preferred if spatial correlation between areas is important and if the priority is to assess small-area variations in survival and map spatial patterns. Both approaches can be readily fitted to geographically enabled survival data from international settings

Muscle activation patterns in the Nordic hamstring exercise: Impact of prior strain injury

This study aimed to determine: 1) the spatial patterns of hamstring activation during the Nordic hamstring exercise (NHE); 2) whether previously injured hamstrings display activation deficits during the NHE, and; 3) whether previously injured hamstrings exhibit altered cross-sectional area. Ten healthy, recreationally active males with a history of unilateral hamstring strain injury underwent functional magnetic resonance imaging (fMRI) of their thighs before and after 6 sets of 10 repetitions of the NHE. Transverse (T2) relaxation times of all hamstring muscles (biceps femoris long head, (BFlh); biceps femoris short head (BFsh); semitendinosus (ST); semimembranosus (SM)), were measured at rest and immediately after the NHE and cross-sectional area (CSA) was measured at rest. For the uninjured limb, the ST’s percentage increase in T2 with exercise was 16.8, 15.8 and 20.2% greater than the increases exhibited by the BFlh, BFsh and SM, respectively (p<0.002 for all). Previously injured hamstring muscles (n=10) displayed significantly smaller increases in T2 post-exercise than the homonymous muscles in the uninjured contralateral limb (mean difference -7.2%, p=0.001). No muscles displayed significant between limb differences in CSA. During the NHE, the ST is preferentially activated and previously injured hamstring muscles display chronic activation deficits compared to uninjured contralateral muscles.

Are low CO2 emitters in rural areas also socially excluded? An empirical investigation of travel diary data from rural Northern Ireland

The reduction of CO2 emissions and social exclusion are two key elements of UK transport strategy. Despite intensive research on each theme, little effort has so far been made linking the relationship between emissions and social exclusion. In addition, current knowledge on each theme is limited to urban areas; little research is available on these themes for rural areas. This research contributes to this gap in the literature by analysing 157 weekly activity-travel diary data collected from three case study areas with differential levels of area accessibility and area mobility options, located in rural Northern Ireland. Individual weekly CO2 emission levels from personal travel diaries (both hot exhaust emission and cold-start emission) were calculated using average speed models for different modes of transport. The socio-spatial patterns associated with CO2 emissions were identified using a general linear model whereas binary logistic regression analyses were conducted to identify mode choice behaviour and activity patterns. This research found groups that emitted a significantly lower level of CO2 included individuals living in an area with a higher level of accessibility and mobility, non-car, non-working, and low-income older people. However, evidence in this research also shows that although certain groups (e.g. those working, and residing in an area with a lower level of accessibility) emitted higher levels of CO2, their rate of participation in activities was however found to be significantly lower compared to their counterparts. Based on the study findings, this research highlights the need for both soft (e.g. teleworking) and physical (e.g. accessibility planning) policy measures in rural areas in order to meet government’s stated CO2 reduction targets while at the same time enhancing social inclusion.

The HarmonyGrid : music, space and performance in grid music systems

This research explores music in space, as experienced through performing and music-making with interactive systems. It explores how musical parameters may be presented spatially and displayed visually with a view to their exploration by a musician during performance. Spatial arrangements of musical components, especially pitches and harmonies, have been widely studied in the literature, but the current capabilities of interactive systems allow the improvisational exploration of these musical spaces as part of a performance practice. This research focuses on quantised spatial organisation of musical parameters that can be categorised as grid music systems (GMSs), and interactive music systems based on them. The research explores and surveys existing and historical uses of GMSs, and develops and demonstrates the use of a novel grid music system designed for whole body interaction. Grid music systems provide plotting of spatialised input to construct patterned music on a two-dimensional grid layout. GMSs are navigated to construct a sequence of parametric steps, for example a series of pitches, rhythmic values, a chord sequence, or terraced dynamic steps. While they are conceptually simple when only controlling one musical dimension, grid systems may be layered to enable complex and satisfying musical results. These systems have proved a viable, effective, accessible and engaging means of music-making for the general user as well as the musician. GMSs have been widely used in electronic and digital music technologies, where they have generally been applied to small portable devices and software systems such as step sequencers and drum machines. This research shows that by scaling up a grid music system, music-making and musical improvisation are enhanced, gaining several advantages: (1) Full body location becomes the spatial input to the grid. The system becomes a partially immersive one in four related ways: spatially, graphically, sonically and musically. (2) Detection of body location by tracking enables hands-free operation, thereby allowing the playing of a musical instrument in addition to “playing” the grid system. (3) Visual information regarding musical parameters may be enhanced so that the performer may fully engage with existing spatial knowledge of musical materials. The result is that existing spatial knowledge is overlaid on, and combined with, music-space. Music-space is a new concept produced by the research, and is similar to notions of other musical spaces including soundscape, acoustic space, Smalley's “circumspace” and “immersive space” (2007, 48-52), and Lotis's “ambiophony” (2003), but is rather more textural and “alive”—and therefore very conducive to interaction. Music-space is that space occupied by music, set within normal space, which may be perceived by a person located within, or moving around in that space. Music-space has a perceivable “texture” made of tensions and relaxations, and contains spatial patterns of these formed by musical elements such as notes, harmonies, and sounds, changing over time. The music may be performed by live musicians, created electronically, or be prerecorded. Large-scale GMSs have the capability not only to interactively display musical information as music representative space, but to allow music-space to co-exist with it. Moving around the grid, the performer may interact in real time with musical materials in music-space, as they form over squares or move in paths. Additionally he/she may sense the textural matrix of the music-space while being immersed in surround sound covering the grid. The HarmonyGrid is a new computer-based interactive performance system developed during this research that provides a generative music-making system intended to accompany, or play along with, an improvising musician. This large-scale GMS employs full-body motion tracking over a projected grid. Playing with the system creates an enhanced performance employing live interactive music, along with graphical and spatial activity. Although one other experimental system provides certain aspects of immersive music-making, currently only the HarmonyGrid provides an environment to explore and experience music-space in a GMS.

A critical regionalist approach to housing design in Vietnam : socio-environmental organisation of living spaces in pre- and post-reform houses

Vietnam has a unique culture which is revealed in the way that people have built and designed their traditional housing. Vietnamese dwellings reflect occupants’ activities in their everyday lives, while adapting to tropical climatic conditions impacted by seasoning monsoons. It is said that these characteristics of Vietnamese dwellings have remained unchanged until the economic reform in 1986, when Vietnam experienced an accelerated development based on the market-oriented economy. New housing types, including modern shop-houses, detached houses, and apartments, have been designed in many places, especially satisfying dwellers’ new lifestyles in Vietnamese cities. The contemporary housing, which has been mostly designed by architects, has reflected rules of spatial organisation so that occupants’ social activities are carried out. However, contemporary housing spaces seem unsustainable in relation to socio-cultural values because they has been influenced by globalism that advocates the use of homogeneous spatial patterns, modern technologies, materials and construction methods. This study investigates the rules of spaces in Vietnamese houses that were built before and after the reform to define the socio-cultural implications in Vietnamese housing design. Firstly, it describes occupants’ views of their current dwellings in terms of indoor comfort conditions and social activities in spaces. Then, it examines the use of spaces in pre-reform Vietnamese housing through occupants’ activities and material applications. Finally, it discusses the organisation of spaces in both pre- and post-reform housing to understand how Vietnamese housing has been designed for occupants to live, act, work, and conduct traditional activities. Understanding spatial organisation is a way to identify characteristics of the lived spaces of the occupants created from the conceived space, which is designed by designers. The characteristics of the housing spaces will inform the designers the way to design future Vietnamese housing in response to cultural contexts. The study applied an abductive approach for the investigation of housing spaces. It used a conceptual framework in relation to Henri Lefebvre’s (1991) theory to understand space as the main factor constituting the language of design, and the principles of semiotics to examine spatial structure in housing as a language used in the everyday life. The study involved a door-knocking survey to 350 households in four regional cities of Vietnam for interpretation of occupancy conditions and levels of occupants’ comfort. A statistical analysis was applied to interpret the survey data. The study also required a process of data selection and collection of fourteen cases of housing in three main climatic regions of the country for analysing spatial organisation and housing characteristics. The study found that there has been a shift in the relationship of spaces from the pre- to post-reform Vietnamese housing. It also indentified that the space for guest welcoming and family activity has been the central space of the Vietnamese housing. Based on the relationships of the central space with the others, theoretical models were proposed for three types of contemporary Vietnamese housing. The models will be significant in adapting to Vietnamese conditions to achieve socioenvironmental characteristics for housing design because it was developed from the occupants’ requirements for their social activities. Another contribution of the study is the use of methodological concepts to understand the language of living spaces. Further work will be needed to test future Vietnamese housing designs from the applications of the models.

Distinguishing between mechanisms of cell aggregation using pair-correlation functions

Many cell types form clumps or aggregates when cultured in vitro through a variety of mechanisms including rapid cell proliferation, chemotaxis, or direct cell-to-cell contact. In this paper we develop an agent-based model to explore the formation of aggregates in cultures where cells are initially distributed uniformly, at random, on a two-dimensional substrate. Our model includes unbiased random cell motion, together with two mechanisms which can produce cell aggregates: (i) rapid cell proliferation, and (ii) a biased cell motility mechanism where cells can sense other cells within a finite range, and will tend to move towards areas with higher numbers of cells. We then introduce a pair-correlation function which allows us to quantify aspects of the spatial patterns produced by our agent-based model. In particular, these pair-correlation functions are able to detect differences between domains populated uniformly at random (i.e. at the exclusion complete spatial randomness (ECSR) state) and those where the proliferation and biased motion rules have been employed - even when such differences are not obvious to the naked eye. The pair-correlation function can also detect the emergence of a characteristic inter-aggregate distance which occurs when the biased motion mechanism is dominant, and is not observed when cell proliferation is the main mechanism of aggregate formation. This suggests that applying the pair-correlation function to experimental images of cell aggregates may provide information about the mechanism associated with observed aggregates. As a proof of concept, we perform such analysis for images of cancer cell aggregates, which are known to be associated with rapid proliferation. The results of our analysis are consistent with the predictions of the proliferation-based simulations, which supports the potential usefulness of pair correlation functions for providing insight into the mechanisms of aggregate formation.

Terrestrial invertebrates of dry river beds are not simply subsets of riparian assemblages

Dry river beds are common worldwide and are rapidly increasing in extent due to the effects of water management and prolonged drought periods due to climate change. While attention has been given to the responses of aquatic invertebrates to drying rivers, few studies exist on the terrestrial invertebrates colonizing dry river beds. Dry river beds are physically harsh and they often differ substantially in substrate, topography, microclimate and inundation frequency from adjacent riparian zones. Given these differences, we predicted that dry river beds provide a unique habitat for terrestrial invertebrates, and that their assemblage composition differs from that in adjacent riparian zones. Dry river beds and riparian zones in Australia and Italy were sampled for terrestrial invertebrates with pitfall traps. Sites differed in substrate type, climate and flow regime. Dry river beds contained diverse invertebrate assemblages and their composition was consistently different from adjacent riparian zones, irrespective of substrate, climate or hydrology. Although some taxa were shared between dry river beds and riparian zones, 66 of 320 taxa occurred only in dry river beds. Differences were due to species turnover, rather than shifts in abundance, indicating that dry river bed assemblages are not simply subsets of riparian assemblages. Some spatial patterns in invertebrate assemblages were associated with environmental variables (irrespective of habitat type), but these associations were statistically weak. We suggest that dry river beds are unique habitats in their own right. We discuss potential human stressors and management issues regarding dry river beds and provide recommendations for future research.

An urban design perspective to classify knowledge precincts : a typological analysis of global best practices

Purpose: The paper seeks to investigate emerging knowledge precincts under the urban design lens in order to identify recurrent spatial patterns of urban forms and functions to gather an understanding of physical aspects that contribute to the creation of place quality. Scope: This paper focuses on the physical design and layout of specific precincts. Although socio-economic and other factors come into play imparting the distinctiveness; this paper only focuses on the spatial dimensions. Method: The research first develops a design typology framework through the lead of literature, and then utilizes it to identify recurrent elements in knowledge precinct design in order to develop taxonomy of patterns and layouts. Results: The research reported in this paper provides preliminary insights into the various form and functional factors playing role in the design of knowledge precincts and evaluates the elements that contribute to the success of these urban interventions. Recommendations: The paper recommends the use of particular design-based solutions in order to enhance the place making in knowledge precincts. Conclusions: The study concludes that despite the locational, regulatory and other contextual differences, the underlying driving principle of providing place quality to people leads to the emergence of identifiable spatial patterns across the knowledge precincts.

Emerging methods in using GIS to analyse Barmah Forest virus disease in Queensland, Australia

Barmah Forest virus (BFV) disease is an emerging mosquito-borne disease in Australia. We aimed to outline some recent methods in using GIS for the analysis of BFV disease in Queensland, Australia. A large database of geocoded BFV cases has been established in conjunction with population data. The database has been used in recently published studies conducted by the authors to determine spatio-temporal BFV disease hotspots and spatial patterns using spatial autocorrelation and semi-variogram analysis in conjunction with the development of interpolated BFV disease standardised incidence maps. This paper briefly outlines spatial analysis methodologies using GIS tools used in those studies. This paper summarises methods and results from previous studies by the authors, and presents a GIS methodology to be used in future spatial analytical studies in attempt to enhance the understanding of BFV disease in Queensland. The methodology developed is useful in improving the analysis of BFV disease data and will enhance the understanding of the BFV disease distribution in Queensland, Australia.

Hydrochemical evolution and groundwater flow processes in the Galilee and Eromanga basins, Great Artesian Basin, Australia: A multivariate statistical approach

The Galilee and Eromanga basins are sub-basins of the Great Artesian Basin (GAB). In this study, a multivariate statistical approach (hierarchical cluster analysis, principal component analysis and factor analysis) is carried out to identify hydrochemical patterns and assess the processes that control hydrochemical evolution within key aquifers of the GAB in these basins. The results of the hydrochemical assessment are integrated into a 3D geological model (previously developed) to support the analysis of spatial patterns of hydrochemistry, and to identify the hydrochemical and hydrological processes that control hydrochemical variability. In this area of the GAB, the hydrochemical evolution of groundwater is dominated by evapotranspiration near the recharge area resulting in a dominance of the Na–Cl water types. This is shown conceptually using two selected cross-sections which represent discrete groundwater flow paths from the recharge areas to the deeper parts of the basins. With increasing distance from the recharge area, a shift towards a dominance of carbonate (e.g. Na–HCO3 water type) has been observed. The assessment of hydrochemical changes along groundwater flow paths highlights how aquifers are separated in some areas, and how mixing between groundwater from different aquifers occurs elsewhere controlled by geological structures, including between GAB aquifers and coal bearing strata of the Galilee Basin. The results of this study suggest that distinct hydrochemical differences can be observed within the previously defined Early Cretaceous–Jurassic aquifer sequence of the GAB. A revision of the two previously recognised hydrochemical sequences is being proposed, resulting in three hydrochemical sequences based on systematic differences in hydrochemistry, salinity and dominant hydrochemical processes. The integrated approach presented in this study which combines different complementary multivariate statistical techniques with a detailed assessment of the geological framework of these sedimentary basins, can be adopted in other complex multi-aquifer systems to assess hydrochemical evolution and its geological controls.

Trailing Touch

Trailing Touch (2014) is a twenty minute classically-based dance work set to music by composers Carter Burwell and Hildur Gudnadottir. It is an abstract work that explores images based on imperfect patterns and seeks to transmit the sensations felt when clusters form and disperse through the space or crisscross to create swirling wave-like reactions in the dancers’ tulle skirts. These simple references are inspired by the lyrical use of arms found in ballet, particular to the ballet aesthetic. Trailing Touch was created in collaboration with QUT’s third-year BFA (Dance Performance) students and performed as part of Dance14 at QUT’s Gardens Points Theatre from the 4th to 8th November 2014 and was performed in Singapore as part of Contact Contemporary Dance Festival on 30th November, 2014. Additionally, the creative process of Trailing Touch (2014) forms the initial project of Phase III of my PhD research, Writing the Dance Score in the Twenty-first Century: An approach for the Independent Choreographer. This PhD research will examine the potential of dance scores as a suite of choreographic strategies to map key aspects of the choreographic process. While a certain degree of ambiguity drives the creative process, the suite of choreographic strategies attempt to capture what is transmitted through the lived experience of dance. “[T]hese documents harbor a force of expression, a visual energy related to the body and the movement” (Louppe 1994, 7) that triggers movement responses, unforeseen intensities and enables personal interpretation. Consequently, Phase III will test and evaluate the relevance of Phase II research within the pressures of mainstream dance rehearsal and performance contexts. In Project One Trailing Touch this was demonstrated in the dance scores produced by the choreographer and interpreted by the dancers within the performance. By drawing from both the theoretical and practical, it is anticipated that this research will suggest a form of languaging movement that is not reliant on images or numbers, but generated in response to the intuitive and complex process underpinning choreographic practice. Rather than constructing a codified dance notation system, it will focus on strategies that reveal movement, its spatial patterns, qualities and intensities of expression and the procedures underlying key choreographic concepts. The outcome of this research project aims to support the independent choreographer in two major areas, by facilitating and enriching the choreographic process for both the performers and choreographer, and by strengthening artistic development and performance outcomes.

A neuronal topography of visual and acoustic fear conditioning within the amygdala

The lateral amygdala (LA) receives information from auditory and visual sensory modalities, and uses this information to encode lasting memories that predict threat. One unresolved question about the amygdala is how multiple memories, derived from different sensory modalities, are organized at the level of neuronal ensembles. We previously showed that fear conditioning using an auditory conditioned stimulus (CS) was spatially allocated to a stable topography of neurons within the dorsolateral amygdala (LAd) (Bergstrom et al, 2011). Here, we asked how fear conditioning using a visual CS is topographically organized within the amygdala. To induce a lasting fear memory trace we paired either an auditory (2 khz, 55 dB, 20 s) or visual (1 Hz, 0.5 s on/0.5 s off, 35 lux, 20 s) CS with a mild foot shock unconditioned stimulus (0.6 mA, 0.5 s). To detect learning-induced plasticity in amygdala neurons, we used immunohistochemistry with an antibody for phosphorylated mitogen-activated protein kinase (pMAPK). Using a principal components analysis-based approach to extract and visualize spatial patterns, we uncovered two unique spatial patterns of activated neurons in the LA that were associated with auditory and visual fear conditioning. The first spatial pattern was specific to auditory cued fear conditioning and consisted of activated neurons topographically organized throughout the LAd and ventrolateral nuclei (LAvl) of the LA. The second spatial pattern overlapped for auditory and visual fear conditioning and was comprised of activated neurons located mainly within the LAvl. Overall, the density of pMAPK labeled cells throughout the LA was greatest in the auditory CS group, even though freezing in response to the visual and auditory CS was equivalent. There were no differences detected in the number of pMAPK activated neurons within the basal amygdala nuclei. Together, these results provide the first basic knowledge about the organizational structure of two different fear engrams within the amygdala and suggest they are dissociable at the level of neuronal ensembles within the LA

Investigating the link between carbon dioxide emissions and transport-related social exclusion in rural Northern Ireland

Carbon dioxide (CO2) is considered the most harmful of the greenhouse gases. Despite policy efforts, transport is the only sector experiencing an increase in the level of CO2 emissions and thereby possesses a major threat to sustainable development. In contrast, a reduced level of mobility has been associated with an increasing risk of being socially excluded. However, despite being the two key elements in transport policy, little effort has so far been made to investigate the links between CO2 emissions and social exclusion. This research contributes to this gap by analysing data from 157 weekly activity-travel diaries collected in rural Northern Ireland. CO2 emission levels were calculated using average speed models for different modes of transport. Regression analyses were then conducted to identify the socio-spatial patterns associated with these CO2 emissions, mode choice behaviour, and patterns of participation in activities. This research found that despite emitting a higher level of carbon dioxide, groups in rural areas possess the risk of being socially excluded due to their higher levels of mobility.

Fractional diffusion models of cardiac electrical propagation: Role of structural heterogeneity in dispersion of repolarization

Impulse propagation in biological tissues is known to be modulated by structural heterogeneity. In cardiac muscle, improved understanding on how this heterogeneity influences electrical spread is key to advancing our interpretation of dispersion of repolarization. We propose fractional diffusion models as a novel mathematical description of structurally heterogeneous excitable media, as a means of representing the modulation of the total electric field by the secondary electrical sources associated with tissue inhomogeneities. Our results, analysed against in vivo human recordings and experimental data of different animal species, indicate that structural heterogeneity underlies relevant characteristics of cardiac electrical propagation at tissue level. These include conduction effects on action potential (AP) morphology, the shortening of AP duration along the activation pathway and the progressive modulation by premature beats of spatial patterns of dispersion of repolarization. The proposed approach may also have important implications in other research fields involving excitable complex media.

Spectral analysis of pair-correlation bandwidth: Application to cell biology images

Images from cell biology experiments often indicate the presence of cell clustering, which can provide insight into the mechanisms driving the collective cell behaviour. Pair-correlation functions provide quantitative information about the presence, or absence, of clustering in a spatial distribution of cells. This is because the pair-correlation function describes the ratio of the abundance of pairs of cells, separated by a particular distance, relative to a randomly distributed reference population. Pair-correlation functions are often presented as a kernel density estimate where the frequency of pairs of objects are grouped using a particular bandwidth (or bin width), Δ>0. The choice of bandwidth has a dramatic impact: choosing Δ too large produces a pair-correlation function that contains insufficient information, whereas choosing Δ too small produces a pair-correlation signal dominated by fluctuations. Presently, there is little guidance available regarding how to make an objective choice of Δ. We present a new technique to choose Δ by analysing the power spectrum of the discrete Fourier transform of the pair-correlation function. Using synthetic simulation data, we confirm that our approach allows us to objectively choose Δ such that the appropriately binned pair-correlation function captures known features in uniform and clustered synthetic images. We also apply our technique to images from two different cell biology assays. The first assay corresponds to an approximately uniform distribution of cells, while the second assay involves a time series of images of a cell population which forms aggregates over time. The appropriately binned pair-correlation function allows us to make quantitative inferences about the average aggregate size, as well as quantifying how the average aggregate size changes with time.