Chancellery Research - Research Publications

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    A macro-element model for predicting the combined load behaviour of spudcan foundations in clay overlying sand
    Wang, Y ; Cassidy, MJ ; Bienen, B (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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    Metaphor-A workflow for streamlined assembly and binning of metagenomes.
    Salazar, VW ; Shaban, B ; Quiroga, MDM ; Turnbull, R ; Tescari, E ; Rossetto Marcelino, V ; Verbruggen, H ; Lê Cao, K-A (Oxford University Press (OUP), 2022-12-28)
    Recent advances in bioinformatics and high-throughput sequencing have enabled the large-scale recovery of genomes from metagenomes. This has the potential to bring important insights as researchers can bypass cultivation and analyze genomes sourced directly from environmental samples. There are, however, technical challenges associated with this process, most notably the complexity of computational workflows required to process metagenomic data, which include dozens of bioinformatics software tools, each with their own set of customizable parameters that affect the final output of the workflow. At the core of these workflows are the processes of assembly-combining the short-input reads into longer, contiguous fragments (contigs)-and binning, clustering these contigs into individual genome bins. The limitations of assembly and binning algorithms also pose different challenges depending on the selected strategy to execute them. Both of these processes can be done for each sample separately or by pooling together multiple samples to leverage information from a combination of samples. Here we present Metaphor, a fully automated workflow for genome-resolved metagenomics (GRM). Metaphor differs from existing GRM workflows by offering flexible approaches for the assembly and binning of the input data and by combining multiple binning algorithms with a bin refinement step to achieve high-quality genome bins. Moreover, Metaphor generates reports to evaluate the performance of the workflow. We showcase the functionality of Metaphor on different synthetic datasets and the impact of available assembly and binning strategies on the final results.
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    Encountering a Pedagogy of the World in a University Setting
    Healy, S ; Coleman, K ; Sallis, RJ ; Belton, A ; Riddle, S ; Heffernan, A ; Bright, D (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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    Scicurious as method: Learning from GLAM young people living in a pandemic about cultivating digital co-research-creation spaces that ignite curiosity and creativity
    Coleman, K ; Healy, S ; Wouters, N ; Martin, J ; Campbell, L ; Peck, S ; Belton, A ; Hiscock, R ; Kara, H ; Khoo, S-M (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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    Cognition in healthy older women is a predictor of 14‐year falls risk
    Faux, NG ; Bird, S ; Michalewicz, A ; Pasco, JA ; Sales, MPR ; Russo‐Batterham, D ; Vogrin, S ; Williams, LJ ; Duque, G ; Szoeke, C (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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    The establishment of a cytomegalovirus -specific CD8+ T-cell threshold by kinetic modeling for the prediction of post-hemopoietic stem cell transplant reactivation
    Zhang, J ; Cao, J ; Zheng, R ; Yu, M ; Lin, Z ; Wang, C ; McCluskey, J ; Yang, J ; Chen, Z ; Corbett, AJ ; Cao, P ; Mo, W ; Wang, Z (CELL PRESS, 2022-11-18)
    The dynamic interaction between the CMV virus and host immune response remains obscure, thus hindering the diagnosis and therapeutic management of patients with HSCT. The current diagnosis of CMV viremia depends on viral load estimation. Medical intervention based on viral load, can be unnecessary or poorly timed for many patients. Here we examined the clinical features and blood samples of patients with HSCT and assessed the CMV reactivation kinetics and corresponding CMV antigen-specific T-cell response in individual patients based on a peptide pool stimulation T-cell assay, which showed that CMV-specific CD8+ T cells were more suitable to be a diagnosis indicator for suppressing CMV reactivation. Using ROC analysis, we defined and verified a CMV-specific CD8+ T-cell counts threshold (925 cells/106 PBMCs) as an indicator of CMV reactivation post-HSCT, and suggested that use of this threshold would provide more accurate guidance for prompt medication and better management of CMV infection post-HSCT.
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    Dual TCR-α Expression on Mucosal-Associated Invariant T Cells as a Potential Confounder of TCR Interpretation
    Suliman, S ; Kjer-Nielsen, L ; Iwany, SK ; Tamara, KL ; Loh, L ; Grzelak, L ; Kedzierska, K ; Ocampo, TA ; Corbett, AJ ; McCluskey, J ; Rossjohn, J ; Leon, SR ; Calderon, R ; Lecca-Garcia, L ; Murray, MB ; Moody, DB ; Van Rhijn, I (AMER ASSOC IMMUNOLOGISTS, 2022-03-15)
    Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant TCRα-chain that uses T cell receptor α-variable 1-2 (TRAV1-2) joined to TRAJ33/20/12 and recognizes metabolites from bacterial riboflavin synthesis bound to the Ag-presenting molecule MHC class I related (MR1). Our attempts to identify alternative MR1-presented Ags led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered Ag specificity likely alters affinity for the most potent known Ag, 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil (5-OP-RU), we performed bulk TCRα- and TCRβ-chain sequencing and single-cell-based paired TCR sequencing on T cells that bound the MR1-5-OP-RU tetramer with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramerlow cells. Although we initially interpreted these as diverse MR1-restricted TCRs, single-cell TCR sequencing revealed that cells expressing atypical TCRα-chains also coexpressed an invariant MAIT TCRα-chain. Transfection of each non-TRAV1-2 TCRα-chain with the TCRβ-chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRα-chain expression in human T cells and competition for the endogenous β-chain explains the existence of some MR1-5-OP-RU tetramerlow T cells. The discovery of simultaneous expression of canonical and noncanonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of Ag specificity.
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    Differential antigen requirements by diverse MR1-restricted T cells (vol 100, pg 112, 2022)
    Seneviratna, R ; Redmond, SJ ; McWilliam, HEG ; Reantragoon, R ; Villadangos, JA ; McCluskey, J ; Godfrey, D ; Gherardin, NA (WILEY, 2022-03)
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    Collaborative Development of Polymer-Based Collection Survey Methodology and Relational Data Model
    Bell, J ; Thompson, KM ; Palmer, K ; McCarthy, G ; Barrett, M ; Burrows, E ; Nel, P (ROUTLEDGE JOURNALS, TAYLOR & FRANCIS LTD, 2022-08-10)
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    Investigation of green solvents for the extraction of phenol and natural alkaloids: Solvent and extractant selection
    Wu, Y ; Li, W ; Vovers, J ; Lu, HT ; Stevens, GW ; Mumford, KA (ELSEVIER SCIENCE SA, 2022-08-15)