Chancellery Research - Research Publications
Now showing items 1-12 of 421
How Do Data Bolster Pandemic Preparedness and Response? How Do We Improve Data and Systems to Be Better Prepared?
How are data driving the response for the ongoing COVID-19 pandemic? How do data support preparedness toward epidemics and pandemics? How do data inform the potential severity and spread of an outbreak? Past infectious disease outbreaks have demonstrated several challenges associated with rapid aggregation, integration, and sharing of data to inform a response during an outbreak. The ongoing pandemic response has demonstrated the value of timely data collection and sharing and the usage of data for decision-making.
Designing Multi-Agent System Organisations for Flexible Runtime Behaviour
<jats:p>We address the challenge of multi-agent system (MAS) design for organisations of agents acting in dynamic and uncertain environments where runtime flexibility is required to enable improvisation through sharing knowledge and adapting behaviour. We identify behavioural features that correspond to runtime improvisation by agents in a MAS organisation and from this analysis describe the OJAzzIC meta-model and an associated design method. We present results from simulation scenarios, varying both problem complexity and the level of organisational support provided in the design, to show that increasing design time guidance in the organisation specification can enable runtime flexibility afforded to agents and improve performance. Hence the results demonstrate the usefulness of the constructs captured in the OJAzzIC meta-model.</jats:p>
Improving Personalized Structure to Function Mapping From Optic Nerve Head to Visual Field.
(Association for Research in Vision and Ophthalmology (ARVO), 2021-01)
Purpose: Maps are required to relate visual field locations to optic nerve head regions. We compare individualized structure-to-function mapping (CUSTOM-MAP) to a population-derived mapping schema (POP-MAP). Methods: Maps were compared for 118 eyes with glaucomatous field loss, circumpapillary retinal nerve fiber layer (cpRNFL) thickness measured using spectral domain optical coherence tomography (OCT), and two landmarks: the optic nerve head (ONH) position relative to the fovea and the temporal raphe angle. Locations with visual field damage (total deviation < -6 dB) were mapped to 30° ONH sectors centered on the angle given by each mapping schema. The concordance between damaged function and damaged structure was determined per location for various cpRNFL damage probability levels, with the number of concordant locations divided by the total number of damaged field locations providing a concordance ratio per eye. Results: For the strictest concordance criteria (minimum cpRNFL thickness < 1% of normal), CUSTOM-MAP had higher mean concordance ratio than POP-MAP (60.5% c.f. 57.0% paired Wilcoxon, P = 0.005), with CUSTOM-MAP having a higher ratio in 43 eyes and POP-MAP having a higher ratio in 21 eyes. For all cpRNFL probability levels <20% of normal, more locations concorded for CUSTOM-MAP than POP-MAP. Inspection of the spatial patterns of differences revealed that CUSTOM-MAP often performed better in the arcuate regions, whereas POP-MAP had benefits inferior to the macula. Conclusions: Anatomic parameters required for individualized structure-function mapping are readily measured with OCT and can provide improved concordance for some eyes. Translational Relevance: Personalizing structure-function mapping may improve concordance between these measures. We provide a web-based tool for creating customized maps.
Effects of Criterion Bias on Perimetric Sensitivity and Response Variability in Glaucoma
(ASSOC RESEARCH VISION OPHTHALMOLOGY INC, 2021-01-01)
Purpose: The purpose of this study was to isolate and quantify the effects of observer response criterion on perimetric sensitivity, response variability, and maximum response probability. Methods: Twelve people with glaucoma were tested at three locations in the visual field (age = 47-77 years, mean deviation = -0.61 to -14.54 dB, test location Humphrey field analyzer [HFA] sensitivities = 1 to 30 dB). Frequency of seeing (FoS) curves were measured using a method of constant stimuli with two response paradigms: a "yes-no" paradigm similar to static automated perimetry and a criterion-free two interval forced choice (2IFC) paradigm. Comparison measures of sensitivity, maximum response probability, and response variability were derived from the fitted FoS curves. Results: Sensitivity differences between the tasks varied widely (range = -11.3 dB to 21.6 dB) and did not correlate with visual field sensitivity nor whether the visual field location was in an area of steep sensitivity gradient within the visual field. Due to the wide variation in differences between the methods, there was no significant difference in mean sensitivity between the 2IFC task relative to the yes-no task, but a trend for higher sensitivity (mean = 1.9 dB, SD = 6.0 dB, P = 0.11). Response variability and maximum response probability did not differ between the tasks (P > 0.99 and 0.95, respectively). Conclusions: Perimetric sensitivity estimates are demonstrably altered by observer response criterion but the effect varies widely and unpredictably, even within a single test. Response bias should be considered a factor in perimetric test variability and when comparing sensitivities to nonperimetric data. Translational Relevance: The effect of response criterion on perimetric response variability varies widely and unpredictably, even within a single test.
Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine.
(Public Library of Science (PLoS), 2009)
Brachyspira hyodysenteriae is an anaerobic intestinal spirochete that colonizes the large intestine of pigs and causes swine dysentery, a disease of significant economic importance. The genome sequence of B. hyodysenteriae strain WA1 was determined, making it the first representative of the genus Brachyspira to be sequenced, and the seventeenth spirochete genome to be reported. The genome consisted of a circular 3,000,694 base pair (bp) chromosome, and a 35,940 bp circular plasmid that has not previously been described. The spirochete had 2,122 protein-coding sequences. Of the predicted proteins, more had similarities to proteins of the enteric Escherichia coli and Clostridium species than they did to proteins of other spirochetes. Many of these genes were associated with transport and metabolism, and they may have been gradually acquired through horizontal gene transfer in the environment of the large intestine. A reconstruction of central metabolic pathways identified a complete set of coding sequences for glycolysis, gluconeogenesis, a non-oxidative pentose phosphate pathway, nucleotide metabolism, lipooligosaccharide biosynthesis, and a respiratory electron transport chain. A notable finding was the presence on the plasmid of the genes involved in rhamnose biosynthesis. Potential virulence genes included those for 15 proteases and six hemolysins. Other adaptations to an enteric lifestyle included the presence of large numbers of genes associated with chemotaxis and motility. B. hyodysenteriae has diverged from other spirochetes in the process of accommodating to its habitat in the porcine large intestine.
Assessing the genetic diversity of Cu resistance in mine tailings through high-throughput recovery of full-length copA genes.
(Springer Science and Business Media LLC, 2015-08-19)
Characterizing the genetic diversity of microbial copper (Cu) resistance at the community level remains challenging, mainly due to the polymorphism of the core functional gene copA. In this study, a local BLASTN method using a copA database built in this study was developed to recover full-length putative copA sequences from an assembled tailings metagenome; these sequences were then screened for potentially functioning CopA using conserved metal-binding motifs, inferred by evolutionary trace analysis of CopA sequences from known Cu resistant microorganisms. In total, 99 putative copA sequences were recovered from the tailings metagenome, out of which 70 were found with high potential to be functioning in Cu resistance. Phylogenetic analysis of selected copA sequences detected in the tailings metagenome showed that topology of the copA phylogeny is largely congruent with that of the 16S-based phylogeny of the tailings microbial community obtained in our previous study, indicating that the development of copA diversity in the tailings might be mainly through vertical descent with few lateral gene transfer events. The method established here can be used to explore copA (and potentially other metal resistance genes) diversity in any metagenome and has the potential to exhaust the full-length gene sequences for downstream analyses.
SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction
BACKGROUND: A central goal of genomics is to predict phenotypic variation from genetic variation. Fitting predictive models to genome-wide and whole genome single nucleotide polymorphism (SNP) profiles allows us to estimate the predictive power of the SNPs and potentially develop diagnostic models for disease. However, many current datasets cannot be analysed with standard tools due to their large size. RESULTS: We introduce SparSNP, a tool for fitting lasso linear models for massive SNP datasets quickly and with very low memory requirements. In analysis on a large celiac disease case/control dataset, we show that SparSNP runs substantially faster than four other state-of-the-art tools for fitting large scale penalised models. SparSNP was one of only two tools that could successfully fit models to the entire celiac disease dataset, and it did so with superior performance. Compared with the other tools, the models generated by SparSNP had better than or equal to predictive performance in cross-validation. CONCLUSIONS: Genomic datasets are rapidly increasing in size, rendering existing approaches to model fitting impractical due to their prohibitive time or memory requirements. This study shows that SparSNP is an essential addition to the genomic analysis toolkit.SparSNP is available at http://www.genomics.csse.unimelb.edu.au/SparSNP.
Information Extraction from Legal Documents: A Study in the Context of Common Law Court Judgements
(Australasian Language Technology Association, 2021)
‘Common Law’ judicial systems follow the doctrine of precedent, which means the legal principles articulated in court judgements are binding in subsequent cases in lower courts. For this reason, lawyers must search prior judgements for the legal principles that are relevant to their case. The difficulty for those within the legal profession is that the information that they are looking for may be contained within a few paragraphs or sentences, but those few paragraphs may be buried within a hundred-page document. In this study, we create a schema based on the relevant information that legal professionals seek within judgements and perform text classification based on it, with the aim of not only assisting lawyers in researching cases, but eventually enabling large-scale analysis of legal judgements to find trends in court outcomes over time.
Regionally aggregated, stitched and de-drifted CMIP-climate data, processed with netCDF-SCM v2.0.0
(Wiley Open Access, 2021-01-01)
The world's most complex climate models are currently running a range of experiments as part of the Sixth Coupled Model Intercomparison Project (CMIP6). Added to the output from the Fifth Coupled Model Intercomparison Project (CMIP5), the total data volume will be in the order of 20PB. Here, we present a dataset of annual, monthly, global, hemispheric and land/ocean means derived from a selection of experiments of key interest to climate data analysts and reduced complexity climate modellers. The derived dataset is a key part of validating, calibrating and developing reduced complexity climate models against the behaviour of more physically complete models. In addition to its use for reduced complexity climate modellers, we aim to make our data accessible to other research communities. We facilitate this in a number of ways. Firstly, given the focus on annual, monthly, global, hemispheric and land/ocean mean quantities, our dataset is orders of magnitude smaller than the source data and hence does not require specialized ‘big data’ expertise. Secondly, again because of its smaller size, we are able to offer our dataset in a text-based format, greatly reducing the computational expertise required to work with CMIP output. Thirdly, we enable data provenance and integrity control by tracking all source metadata and providing tools which check whether a dataset has been retracted, that is identified as erroneous. The resulting dataset is updated as new CMIP6 results become available and we provide a stable access point to allow automated downloads. Along with our accompanying website (cmip6.science.unimelb.edu.au), we believe this dataset provides a unique community resource, as well as allowing non-specialists to access CMIP data in a new, user-friendly way.
A Review of Programs That Targeted Environmental Determinants of Aboriginal and Torres Strait Islander Health
(MDPI AG, 2013-08-01)
OBJECTIVE: Effective interventions to improve population and individual health require environmental change as well as strategies that target individual behaviours and clinical factors. This is the basis of implementing an ecological approach to health programs and health promotion. For Aboriginal People and Torres Strait Islanders, colonisation has made the physical and social environment particularly detrimental for health. METHODS AND RESULTS: We conducted a literature review to identify Aboriginal health interventions that targeted environmental determinants of health, identifying 21 different health programs. Program activities that targeted environmental determinants of health included: Caring for Country; changes to food supply and/or policy; infrastructure for physical activity; housing construction and maintenance; anti-smoking policies; increased workforce capacity; continuous quality improvement of clinical systems; petrol substitution; and income management. Targets were categorised according to Miller's Living Systems Theory. Researchers using an Indigenous community based perspective more often identified interpersonal and community-level targets than were identified using a Western academic perspective. CONCLUSIONS: Although there are relatively few papers describing interventions that target environmental determinants of health, many of these addressed such determinants at multiple levels, consistent to some degree with an ecological approach. Interpretation of program targets sometimes differed between academic and community-based perspectives, and was limited by the type of data reported in the journal articles, highlighting the need for local Indigenous knowledge for accurate program evaluation. IMPLICATIONS: While an ecological approach to Indigenous health is increasingly evident in the health research literature, the design and evaluation of such programs requires a wide breadth of expertise, including local Indigenous knowledge.