Chancellery Research - Research Publications

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    A preliminary investigation into the influence of archaeological material on the yellowing of polyethylene storage bags
    Thompson, K ; Nel, P (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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    The Women’s Healthy Ageing Project: A pattern of cognitive decline after brain injury
    Bird, S ; Faux, NG ; Szoeke, C (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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    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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    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)