Chancellery Research - Research Publications
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Itemplyranges: a grammar of genomic data transformation(BMC, 2019-01-04)Bioconductor is a widely used R-based platform for genomics, but its host of complex genomic data structures places a cognitive burden on the user. For most tasks, the GRanges object would suffice, but there are gaps in the API that prevent its general use. By recognizing that the GRanges class follows "tidy" data principles, we create a grammar of genomic data transformation, defining verbs for performing actions on and between genomic interval data and providing a way of performing common data analysis tasks through a coherent interface to existing Bioconductor infrastructure. We implement this grammar as a Bioconductor/R package called plyranges.
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ItemA preliminary investigation into the influence of archaeological material on the yellowing of polyethylene storage bags(Routledge, 2021)Concerns around the degradation of plastics have been part of conservation discourse for decades. The spotlight is usually on art and objects, and conservation and display materials, however it could be argued that a significant volume of the plastics in museums is associated with storage bags. This study asked whether the condition of plastic storage bags might be influenced by what is stored inside them. If specific materials can be identified as more likely to affect plastic degradation, museums may have a lead-indicator for efficiently monitoring storage risks. This case study developed a methodology for applying multivariate analysis to collected data to answer this question. A subset of polyethylene self-seal bags used to pack archaeological material from the ‘Casselden Place’ assemblage at Museums Victoria was evaluated. Objective data were combined with subjective assessment of bag degradation features gathered during a collection survey and interrogated using multivariate statistical analysis. Results indicate (1) different levels of yellowing are associated with particular plastic bag stocks and (2) ceramic, slate and tile finds are more likely than other materials to be contained within yellower bags. The research points to future enquiry and demonstrates this methodology shows promise for extension to other large cultural datasets.
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ItemNo Preview AvailableThe Women’s Healthy Ageing Project: A pattern of cognitive decline after brain injury(Wiley, 2021-12)Abstract Background It is well recognised that damage sustained by traumatic brain injury (TBI) initiate injury mechanisms that continue to develop long after insult. Increasing evidence suggests TBI may lead to chronic cognitive decline and the development of dementia later in life. However, due to the low rate of TBI in the general community, there is a paucity of data on the impact of cognitive decline in community TBI. We examined longitudinal cognitive changes over a 12‐year period to determine if there was any relationship with community reported TBI. Method The Women’s Healthy Aging Project is an ongoing longitudinal cohort study of community‐dwelling Australian women. Assessments included an extensive range of measures, including neuropsychological testing of multiple cognitive domains and questions relating to head injury. In total, 110 women had complete neuropsychological testing at all three time points; from 2002, 2012 and 2014. Of these women, nine (aged 56‐65 in 2002) had a history of moderate to severe TBI. Composite cognitive scores were compared to 18 healthy controls randomly selected from the complete dataset individually matched for age, education, and APO4‐genotype. Analyses were conducted in five datasets drawn from the complete dataset and results were averaged. Result Median scores for executive function were similar for both the TBI group and healthy controls in 2002, lower in the TBI group by 2012 and this difference increased further in 2014. Median scores for verbal episodic memory were slightly lower in the TBI group than controls in 2002 and 2012, and this difference increased in 2014. Although this initial pilot study with small samples in mid‐aged healthy women did not show statistically significant results, the observed relationships were constant over the five datasets, warranting further exploration. Conclusion In our small pilot study, we observed greater rate of decline of both executive function and verbal episodic memory in women with a history of TBI. Findings warrant a need for larger studies to explore this relationship as it indicates that community‐based reported TBI may impact cognitive performance even in early ageing. Further work will continue to explore cognitive trajectories in women with a mean age 80 at next follow‐up.
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ItemNo Preview AvailableA macro-element model for predicting the combined load behaviour of spudcan foundations in clay overlying sand(Thomas Telford Ltd., 2021-10-26)A macro-element model for predicting the load–displacement behaviour of a spudcan foundation in clay overlying sand when subjected to combined vertical, horizontal and moment loading is introduced. Observations from detailed drum centrifuge tests that measured the effect of the underlying sand layer on the foundation behaviour are combined with finite-element results and theoretical developments to derive the components of the model. The yield surface defined by the centrifuge test results suggests that as the spudcan nears the underlying sand layer, the absolute horizontal capacity remains relatively constant, while the vertical and moment capacities increase at approximately the same normalised rate. The model is demonstrated to accurately predict foundation behaviour by retrospectively simulating the experimental results. This macro-element model has the advantage that it can be integrated into the structural analyses of jack-up platforms required for site-specific assessments.
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ItemEncountering a Pedagogy of the World in a University Setting(Taylor & Francis, 2021)Taking up Biesta’s (2019) notion of a pedagogy of the world, we ask: How might participating in an arts-based educational program with/in a university enable young people from schools with low Index of Community Socio-Educational Advantage (ICSEA) values to encounter the world of higher education differently and become different in that encounter? This chapter comes from our engagement with empirical material generated during a (post)qualitative inquiry into the pedagogy of The Art of Engagement-a multi-arts studio program involving relational pedagogy and a/r/tography as curriculum located in SPACE, 1 whereby secondary school students from schools in less socio-educationally advantaged communities came together with undergraduate university students for a five-day intensive within a University of Melbourne breadth subject. The program’s rationale was to connect with secondary school arts students completing their schooling in lower ICSEA value schools 2 through the design of authentic university encounters with/in site, practices and communities. It welcomed the secondary school students into the world of our university and enhanced their capacity to “be at home” in this world, creating the conditions for considering and potentially living different post-school futures.
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ItemScicurious as method: Learning from GLAM young people living in a pandemic about cultivating digital co-research-creation spaces that ignite curiosity and creativity(Bristol University Press, 2020-10-23)Could COVID-19, this unexpected crisis, act as a comma in a co-research-creation project to become a breathing space and not a full stop? Maybe this pause is a colon: the two different periods of the project (and life in general) on either side of the pandemic, equally important and dependent on each other for full meaning. In this chapter, we tell the story of how a co-research-creation event (the Sci Curious Project) unfolded before and during the COVID-19 pandemic; the lead-up to its irruption (St. Pierre, 1997) and then what came after. ‘Scicurious as method’ emerged out of the unexpected pause and recalibration of the project; a method that emphasizes the creation of research spaces that activate scicuriosity in situated practice. We understand scicuriosity as emerging from collaborative research-creation events that ignite curiosity and creativity. Scicurious as method is presented through an encounter with speculative fiction and scicurious zine travels. Scicurious as method has significant ethical implications, these reify the potential of co-designed speculative inquiries with creativity and curiosity at their heart. This is, in part, due to its contingency on cultivating digital co-research-creation spaces that enfold rather than eschew the analogue and highlight the joyous potential of a deeply situated, co-designed speculative inquiry; an inquiry with galleries, libraries, archives and museums (GLAM) young people living in a pandemic.
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ItemNo Preview AvailableCognition in healthy older women is a predictor of 14‐year falls risk(Wiley, 2021-12)Background: Falls are a significant cause of injuries, loss of confidence, increased morbidity, and institutionalisation in all older people, with women at 50% greater risk than men. The relationship between dementia and falls is well established and 2/3 of all dementia occurs in women. In this study we explored risk factors associated with a 14 year falls risk in a community-based cohort of women, which included validated measures across a wide range of clinical domains including neuropsychological, mood, quality of life and biomarkers (including hormonal). Method: The Australian Women’s Healthy Aging Project is an longitudinal observation study, assessments every year (1991 –1999), followed by assessments in 2002, 2004, 2012 and 2014. The assessments included cognitive (as of 2002), blood, and cardiovascular disease risk assessment, and questions related to falls. After data cleaning, the remaining cohort consisted of 180 participants (Table 1). Missing data were imputed using mice random forest. To identify key risk factors associated with a 14 year falls risk, random survival (time to event) forest (RSF) machine learning was used. Result: The RSF model, using all 290+ possible predictive variables, performed well with an Out Of Bag (OOB, withheld data) prediction error (C-index) of 32.8%. The most predictive variables in the model were identified using the variable importance measure (VIM). The initial model was refined by taking the top 30 predictive variables and retraining the RSF. This refined model resulted in an improved OOB C-index of 5.8% (27%). The top 20 predictive variables, Figure 1, include those associated with cardiovascular disease risk, cognitive performance, and hormone levels (e.g., family history of heart attack, digit symbol coding, and estradiol levels). Conclusion: Ninety percent of the top 20 predictive risk variables for the 14 year fall risk in women, were from three key domains, cognition (40%), cardiovascular (25%) and hormone-related measurements (25%). Our data suggest that for long term prevention of falls these domains may be important reducing risk of falls in the senior female population.
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ItemSimulated in vivo Electrophysiology Experiments Provide Previously Inaccessible Insights into Visual Physiology.( 2016)Lecture content and practical laboratory classes are ideally complementary. However, the types of experiments that have led to our detailed understanding of sensory neuroscience are often not amenable to classroom experimentation as they require expensive equipment, time-consuming surgeries, specialized experimental techniques, and the use of animals. While sometimes feasible in small group teaching, these experiments are not suitable for large cohorts of students. Previous attempts to expose students to sensory neuroscience experiments include: the use of electrophysiology preparations in invertebrates, data-driven simulations that do not replicate the experience of conducting an experiment, or simply observing an experiment in a research laboratory. We developed an online simulation of a visual neuroscience experiment in which extracellular recordings are made from a motion sensitive neuron. Students have control over stimulation parameters (direction and contrast) and can see and hear the action potential responses to stimuli as they are presented. The simulation provides an intuitive way for students to gain insight into neurophysiology, including experimental design, data collection and data analysis. Our simulation allows large cohorts of students to cost-effectively "experience" the results of animal research without ethical concerns, to be exposed to realistic data variability, and to develop their understanding of how sensory neuroscience experiments are conducted.
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ItemIL-23 costimulates antigen-specific MAIT cell activation and enables vaccination against bacterial infection(AMER ASSOC ADVANCEMENT SCIENCE, 2019-11-01)Mucosal-associated invariant T (MAIT) cells are activated in a TCR-dependent manner by antigens derived from the riboflavin synthesis pathway, including 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), bound to MHC-related protein-1 (MR1). However, MAIT cell activation in vivo has not been studied in detail. Here, we have found and characterized additional molecular signals required for optimal activation and expansion of MAIT cells after pulmonary Legionella or Salmonella infection in mice. We show that either bone marrow–derived APCs or non–bone marrow–derived cells can activate MAIT cells in vivo, depending on the pathogen. Optimal MAIT cell activation in vivo requires signaling through the inducible T cell costimulator (ICOS), which is highly expressed on MAIT cells. Subsequent expansion and maintenance of MAIT-17/1-type responses are dependent on IL-23. Vaccination with IL-23 plus 5-OP-RU augments MAIT cell–mediated control of pulmonary Legionella infection. These findings reveal cellular and molecular targets for manipulating MAIT cell function under physiological conditions.
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ItemOcular and Systemic Factors Affecting Laser Speckle Flowgraphy Measurements in the Optic Nerve Head(ASSOC RESEARCH VISION OPHTHALMOLOGY INC, 2021-01)PURPOSE: To investigate the ocular and systemic factors related to glaucoma and to be adjusted for interindividual comparison of ocular blood flow measurement results by laser speckle flowgraphy (LSFG) obtained from the optic nerve head (ONH) in normal Japanese individuals. METHODS: A multicenter, prospective cross-sectional study was conducted. The ONH tissue-area and vessel-area mean blur rate (MT and MV) were evaluated using LSFG and ONH structural parameters using planimetric methods. Multivariate linear mixed-effects modeled regression analysis was used to identify the contributing factors to the MT and MV. The explanatory variables were age; gender; smoking history; body mass index; mean arterial pressure (MAP); heart rate; intraocular pressure; axial length (AL); disc, rim, cup, and β-peripapillary atrophy (β-PPA) areas; and central retinal artery and vein equivalents. RESULTS: In total, 195 eyes of 126 healthy individuals with an average age of 48.1 years were included. Multivariate analysis showed that MAP and disc area had a negative (P < 0.001) correlation, whereas β-PPA area had a positive correlation with MT (P = 0.010). Age and AL had a negative correlation (P = 0.001 and P = 0.011, respectively), whereas cup area had a positive correlation (P = 0.012) with MV. CONCLUSIONS: Interindividual comparison of MT or MV must be adjusted for both systemic factors (blood pressure or age) and local ocular factors (AL and disc, cup, or β-PPA area). TRANSLATIONAL RELEVANCE: Our results provided reference data on the LSFG measurement and are important in comparing ocular blood flow between individuals using LSFG.