Bayesian computational methods for spatial analysis of images

This thesis introduces a new way of using prior information in a spatial model and develops scalable algorithms for fitting this model to large imaging datasets. These methods are employed for image-guided radiation therapy and satellite based classification of land use and water quality. This study has utilized a pre-computation step to achieve a hundredfold improvement in the elapsed runtime for model fitting. This makes it much more feasible to apply these models to real-world problems, and enables full Bayesian inference for images with a million or more pixels.

Where is spatial information and science in your world?

Skills in spatial sciences are fundamental to understanding our world in context. Increasing digital presence and the availability of data with accurate spatial components has allowed almost everything researchers and students do to be represented in a spatial context. Representing outcomes and disseminating information has moved from 2D to 4D with time series animation. In the next 5 years industry will not only demand QUT graduates have spatial skills along with analytical skills, graduates will be required to present their findings in spatial visualizations that show spatial, spectral and temporal contexts. Domains such as engineering and science will no longer be the leaders in spatial skills as social sciences, health, arts and the business community gain momentum from place-based research including human interactions. A university that can offer students a pathway to advanced spatial investigation will be ahead of the game.

Open access spatial data and collaboration

On 19 June 2015, representatives from over 40 Australian research institutions gathered in Canberra to launch their Open Data Collections. The one day event, hosted by the Australian National Data Service (ANDS), showcased to government and a range of national stakeholders the rich variety of data collections that have been generated through the Major Open Data Collections (MODC) project. Colin Eustace attended the showcase for QUT Library and presented a poster that reflected the work that he and Jodie Vaughan generated through the project. QUT’s Blueprint 4, the University’s five-year institutional strategic plan, outlines the key priorities of developing a commitment to working in partnership with industry, as well as combining disciplinary strengths with interdisciplinary application. The Division of Technology, Information and Learning Support (TILS) has undertaken a number of Australian National Data Service (ANDS) funded projects since 2009 with the aim of developing improved research data management services within the University to support these strategic aims. By leveraging existing tools and systems developed during these projects, the Major Open Data Collection (MODC) project delivered support to multi-disciplinary collaborative research activities through partnership building between QUT researchers and Queensland government agencies, in order to add to and promote the discovery and reuse of a collection of spatially referenced datasets. The MODC project built upon existing Research Data Finder infrastructure (which uses VIVO open source software, developed by Cornell University) to develop a separate collection, Spatial Data Finder (https://researchdatafinder.qut.edu.au/spatial) as the interface to display the spatial data collection. During the course of the project, 62 dataset descriptions were added to Spatial Data Finder, 7 added to Research Data Finder and two added to Software Finder, another separate collection. The project team met with 116 individual researchers and attended 13 school and faculty meetings to promote the MODC project and raise awareness of the Library’s services and resources for research data management.

Low voltage EPMA: Experiments on a new frontier in microanalysis—analytical spatial resolution

Field emission (FE) electron gun sources provide new capabilities for high lateral resolution EPMA. The determination of analytical lateral resolution is not as straightforward as that for electron microscopy imaging. Results from two sets of experiments to determine the actual lateral resolution for accurate EPMA are presented for Kα X-ray lines of Si and Al and Lα of Fe at 5 and 7 keV in a silicate glass. These results are compared to theoretical predictions and Monte Carlo simulations of analytical lateral resolution. The experiments suggest little is gained in lateral resolution by dropping from 7 to 5 keV in EPMA of this silicate glass.

Brain activity during the encoding, retention, and retrieval of stimulus representations

Studies of delayed nonmatching-to-sample (DNMS) performance following lesions of the monkey cortex have revealed a critical circuit of brain regions involved in forming memories and retaining and retrieving stimulus representations. Using event-related functional magnetic resonance imaging (fMRI), we measured brain activity in 10 healthy human participants during performance of a trial-unique visual DNMS task using novel barcode stimuli. The event-related design enabled the identification of activity during the different phases of the task (encoding, retention, and retrieval). Several brain regions identified by monkey studies as being important for successful DNMS performance showed selective activity during the different phases, including the mediodorsal thalamic nucleus (encoding), ventrolateral prefrontal cortex (retention), and perirhinal cortex (retrieval). Regions showing sustained activity within trials included the ventromedial and dorsal prefrontal cortices and occipital cortex. The present study shows the utility of investigating performance on tasks derived from animal models to assist in the identification of brain regions involved in human recognition memory.

fMRI evidence of word frequency and strength effects during episodic memory encoding

Word frequency (WF) and strength effects are two important phenomena associated with episodic memory. The former refers to the superior hit-rate (HR) for low (LF) compared to high frequency (HF) words in recognition memory, while the latter describes the incremental effect(s) upon HRs associated with repeating an item at study. Using the "subsequent memory" method with event-related fMRI, we tested the attention-at-encoding (AE) [M. Glanzer, J.K. Adams, The mirror effect in recognition memory: data and theory, J. Exp. Psychol.: Learn Mem. Cogn. 16 (1990) 5-16] explanation of the WF effect. In addition to investigating encoding strength, we addressed if study involves accessing prior representations of repeated items via the same mechanism as that at test [J.L. McClelland, M. Chappell, Familiarity breeds differentiation: a subjective-likelihood approach to the effects of experience in recognition memory, Psychol. Rev. 105 (1998) 724-760], entailing recollection [K.J. Malmberg, J.E. Holden, R.M. Shiffrin, Modeling the effects of repetitions, similarity, and normative word frequency on judgments of frequency and recognition memory, J. Exp. Psychol.: Learn Mem. Cogn. 30 (2004) 319-331] and whether less processing effort is entailed for encoding each repetition [M. Cary, L.M. Reder, A dual-process account of the list-length and strength-based mirror effects in recognition, J. Mem. Lang. 49 (2003) 231-248]. The increased BOLD responses observed in the left inferior prefrontal cortex (LIPC) for the WF effect provide support for an AE account. Less effort does appear to be required for encoding each repetition of an item, as reduced BOLD responses were observed in the LIPC and left lateral temporal cortex; both regions demonstrated increased responses in the conventional subsequent memory analysis. At test, a left lateral parietal BOLD response was observed for studied versus unstudied items, while only medial parietal activity was observed for repeated items at study, indicating that accessing prior representations at encoding does not necessarily occur via the same mechanism as that at test, and is unlikely to involve a conscious recall-like process such as recollection. This information may prove useful for constraining cognitive theories of episodic memory.

Seasonal and spatial variations in rare earth elements to identify inter-aquifer linkages and recharge processes in an Australian catchment

With the aim of elucidating the seasonal behaviour of rare earth elements (REEs), surface and groundwaters were collected under dry and wet conditions in different hydrological units of the Teviot Brook catchment (Southeast Queensland, Australia). Sampled waters showed a large degree of variability in both REE abundance and normalised patterns. Overall REE abundance ranged over nearly three orders of magnitude, and was consistently lower in the sedimentary bedrock aquifer (18ppt<∑REE<477ppt) than in the other hydrological systems studied. Abundance was greater in springs draining rhyolitic rocks (∑REE=300 and 2054ppt) than in springs draining basalt ranges (∑REE=25 and 83ppt), yet was highly variable in the shallow alluvial groundwater (16ppt<∑REE<5294ppt) and, to a lesser extent, in streamwater (85ppt<∑REE<2198ppt). Generally, waters that interacted with different rock types had different REE patterns. In order to obtain an unbiased characterisation of REE patterns, the ratios between light and middle REEs (R(M/L)) and the ratios between middle and heavy REEs (R(H/M)) were calculated for each sample. The sedimentary bedrock aquifer waters had highly evolved patterns depleted in light REEs and enriched in middle and heavy REEs (0.17spatial variations. Samples collected from the alluvium exhibited an increasing influence of the sedimentary bedrock from upgradient to downgradient; typically they showed flat patterns in the upstream section of the alluvium (median R(M/L)=0.21 and median R(H/M)=-0.06) gradually evolving towards patterns depleted in light REEs and enriched in middle and heavy REEs downgradient (median R(M/L)=0.48 and median R(H/M)=0.38). To document the seasonal variations in REE patterns, the difference in ratios between dry and wet sampling campaigns was determined for each repeated sampling location. Contributions from the sedimentary bedrock water to the alluvium during the wet season were identified at two locations (increase from R(H/M)=0.03 and 0.35 to R(H/M)=0.62 and 0.89). The effect of recharge through fractured igneous rocks was also observed in two boreholes intercepting the sedimentary bedrock, where the freshly recharged waters likely contributed to the deeper groundwater flow during the wet season (decrease from R(M/L)=0.81 and 0.56 to R(M/L)=0.46 and 0.17). Results from this study suggest that REEs may be usefully applied as indicators of recharge processes and inter-aquifer mixing. They also underline the importance of conducting seasonal sampling campaigns to capture possible short-term variations in REE patterns and abundance, which is essential to enable a better understanding of hydrological and hydrochemical processes in complex geological settings

Mutations in the gene encoding IFT dynein complex component WDR34 cause jeune asphyxiating thoracic dystrophy

Bidirectional (anterograde and retrograde) motor-based intraflagellar transport (IFT) governs cargo transport and delivery processes that are essential for primary cilia growth and maintenance and for hedgehog signaling functions. The IFT dynein-2 motor complex that regulates ciliary retrograde protein transport contains a heavy chain dynein ATPase/motor subunit, DYNC2H1, along with other less well functionally defined subunits. Deficiency of IFT proteins, including DYNC2H1, underlies a spectrum of skeletal ciliopathies. Here, by using exome sequencing and a targeted next-generation sequencing panel, we identified a total of 11 mutations in WDR34 in 9 families with the clinical diagnosis of Jeune syndrome (asphyxiating thoracic dystrophy). WDR34 encodes a WD40 repeat-containing protein orthologous to Chlamydomonas FAP133, a dynein intermediate chain associated with the retrograde intraflagellar transport motor. Three-dimensional protein modeling suggests that the identified mutations all affect residues critical for WDR34 protein-protein interactions. We find that WDR34 concentrates around the centrioles and basal bodies in mammalian cells, also showing axonemal staining. WDR34 coimmunoprecipitates with the dynein-1 light chain DYNLL1 in vitro, and mining of proteomics data suggests that WDR34 could represent a previously unrecognized link between the cytoplasmic dynein-1 and IFT dynein-2 motors. Together, these data show that WDR34 is critical for ciliary functions essential to normal development and survival, most probably as a previously unrecognized component of the mammalian dynein-IFT machinery.

Evidence of genetic association between TNFRSF1A encoding the p55 tumour necrosis factor receptor, and ankylosing spondylitis in UK Caucasians

Objectives: To replicate the possible genetic association between ankylosing spondylitis (AS) and TNFRSF1A. Methods: TNFRSF1A was re-sequenced in 48 individuals with AS to identify novel polymorphisms. Nine single nucleotide polymorphisms (SNPs) in TNFRSF1A and 5 SNPs in the neighbouring gene SCNN1A were genotyped in 1604 UK Caucasian individuals with AS and 1019 matched controls. An extended study was implemented using additional genotype data on 8 of these SNPs from 1400 historical controls from the 1958 British Birth Cohort. A meta-analysis of previously published results was also undertaken. Results: One novel variant in intron 6 was identified but no new coding variants. No definite associations were seen in the initial study but in the extended study there were weak associations with rs4149576 (p=0.04) and rs4149577 (p=0.007). In the metaanalysis consistent, somewhat stronger associations were seen with rs4149577 (p=0.002) and rs4149578 (p=0.006). Conclusions: These studies confirm the weak genetic associations between AS and TNFRSF1A. In view of the previously reported associations of TNFRSF1A with AS, in Caucasians and Chinese, and the biological plausibility of this candidate gene, replication of this finding in well powered studies is clearly indicated.

Imagined Landscapes: Geovisualizing Australian Spatial Narratives

Imagined Landscapes teams geocritical analysis with digital visualization techniques to map and interrogate films, novels, and plays in which space and place figure prominently. Drawing upon A Cultural Atlas of Australia, a database-driven interactive digital map that can be used to identify patterns of representation in Australia’s cultural landscape, the book presents an integrated perspective on the translation of space across narrative forms and pioneers new ways of seeing and understanding landscape. It offers fresh insights on cultural topography and spatial history by examining the technical and conceptual challenges of georeferencing fictional and fictionalized places in narratives. Among the items discussed are Wake in Fright, a novel by Kenneth Cook, adapted iconically to the screen and recently onto the stage; the Australian North as a mythic space; spatial and temporal narrative shifts in retellings of the story of Alexander Pearce, a convict who gained notoriety for resorting to cannibalism after escaping from a remote Tasmanian penal colony; travel narratives and road movies set in Western Australia; and the challenges and spatial politics of mapping spaces for which there are no coordinates.

The role of environmental factors in the spatial distribution of Japanese encephalitis in mainland China

Japanese encephalitis (JE) is the most common cause of viral encephalitis and an important public health concern in the Asia-Pacific region, particularly in China where 50% of global cases are notified. To explore the association between environmental factors and human JE cases and identify the high risk areas for JE transmission in China, we used annual notified data on JE cases at the center of administrative township and environmental variables with a pixel resolution of 1 km×1 km from 2005 to 2011 to construct models using ecological niche modeling (ENM) approaches based on maximum entropy. These models were then validated by overlaying reported human JE case localities from 2006 to 2012 onto each prediction map. ENMs had good discriminatory ability with the area under the curve (AUC) of the receiver operating curve (ROC) of 0.82-0.91, and low extrinsic omission rate of 5.44-7.42%. Resulting maps showed JE being presented extensively throughout southwestern and central China, with local spatial variations in probability influenced by minimum temperatures, human population density, mean temperatures, and elevation, with contribution of 17.94%-38.37%, 15.47%-21.82%, 3.86%-21.22%, and 12.05%-16.02%, respectively. Approximately 60% of JE cases occurred in predicted high risk areas, which covered less than 6% of areas in mainland China. Our findings will help inform optimal geographical allocation of the limited resources available for JE prevention and control in China, find hidden high-risk areas, and increase the effectiveness of public health interventions against JE transmission.

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

Missing in space: An evaluation of imputation methods for missing data in spatial analysis of risk factors for type II diabetes

Background Spatial analysis is increasingly important for identifying modifiable geographic risk factors for disease. However, spatial health data from surveys are often incomplete, ranging from missing data for only a few variables, to missing data for many variables. For spatial analyses of health outcomes, selection of an appropriate imputation method is critical in order to produce the most accurate inferences. Methods We present a cross-validation approach to select between three imputation methods for health survey data with correlated lifestyle covariates, using as a case study, type II diabetes mellitus (DM II) risk across 71 Queensland Local Government Areas (LGAs). We compare the accuracy of mean imputation to imputation using multivariate normal and conditional autoregressive prior distributions. Results Choice of imputation method depends upon the application and is not necessarily the most complex method. Mean imputation was selected as the most accurate method in this application. Conclusions Selecting an appropriate imputation method for health survey data, after accounting for spatial correlation and correlation between covariates, allows more complete analysis of geographic risk factors for disease with more confidence in the results to inform public policy decision-making.

On robust face recognition via sparse coding: The good, the bad and the ugly

In the field of face recognition, sparse representation (SR) has received considerable attention during the past few years, with a focus on holistic descriptors in closed-set identification applications. The underlying assumption in such SR-based methods is that each class in the gallery has sufficient samples and the query lies on the subspace spanned by the gallery of the same class. Unfortunately, such an assumption is easily violated in the face verification scenario, where the task is to determine if two faces (where one or both have not been seen before) belong to the same person. In this study, the authors propose an alternative approach to SR-based face verification, where SR encoding is performed on local image patches rather than the entire face. The obtained sparse signals are pooled via averaging to form multiple region descriptors, which then form an overall face descriptor. Owing to the deliberate loss of spatial relations within each region (caused by averaging), the resulting descriptor is robust to misalignment and various image deformations. Within the proposed framework, they evaluate several SR encoding techniques: l1-minimisation, Sparse Autoencoder Neural Network (SANN) and an implicit probabilistic technique based on Gaussian mixture models. Thorough experiments on AR, FERET, exYaleB, BANCA and ChokePoint datasets show that the local SR approach obtains considerably better and more robust performance than several previous state-of-the-art holistic SR methods, on both the traditional closed-set identification task and the more applicable face verification task. The experiments also show that l1-minimisation-based encoding has a considerably higher computational cost when compared with SANN-based and probabilistic encoding, but leads to higher recognition rates.

Spatial distribution of selected persistent organic pollutants (POPs) in Australia's atmosphere

A nation-wide passive air sampling campaign recorded concentrations of persistent organic pollutants in Australia's atmosphere in 2012. XAD-based passive air samplers were deployed for one year at 15 sampling sites located in remote/background, agricultural and semi-urban and urban areas across the continent. Concentrations of 47 polychlorinated biphenyls ranged from 0.73 to 72 pg m-3 (median of 8.9 pg m-3) and were consistently higher at urban sites. The toxic equivalent concentration for the sum of 12 dioxin-like PCBs was low, ranging from below detection limits to 0.24 fg m-3 (median of 0.0086 fg m-3). Overall, the levels of polychlorinated biphenyls in Australia were among the lowest reported globally to date. Among the organochlorine pesticides, hexachlorobenzene had the highest (median of 41 pg m-3) and most uniform concentration (with a ratio between highest and lowest value [similar]5). Bushfires may be responsible for atmospheric hexachlorobenzene levels in Australia that exceeded Southern Hemispheric baseline levels by a factor of [similar]4. Organochlorine pesticide concentrations generally increased from remote/background and agricultural sites to urban sites, except for high concentrations of [small alpha]-endosulfan and DDTs at specific agricultural sites. Concentrations of heptachlor (0.47-210 pg m-3), dieldrin (ND-160 pg m-3) and trans- and cis-chlordanes (0.83-180 pg m-3, sum of) in Australian air were among the highest reported globally to date, whereas those of DDT and its metabolites (ND-160 pg m-3, sum of), [small alpha]-, [small beta]-, [gamma]- and [small delta]-hexachlorocyclohexane (ND-6.7 pg m-3, sum of) and [small alpha]-endosulfan (ND-27 pg m-3) were among the lowest.