Cross-scale biophysics modelling of F-actin cytoskeleton in cell

This thesis is a comparative study of the modelling of mechanical behaviours of F-actin cytoskeleton which is an important structural component in living cells. A new granular model was developed for F-actin cytoskeleton based on the concept of multiscale modelling. This framework overcomes difficulties encountered in physical modelling of cytoskeleton in conventional continuum mechanics modelling, and the computational challenges in all-atom molecular dynamics simulation. The thermostat algorithm was further modified to better predict the thermodynamic properties of F-actin cytoskeleton in modelling. This multiscale modelling framework was applied in explaining the physical mechanisms of cytoskeleton responses to external mechanical loads.

Development and validation of the Self-Gifting Consumer Behaviour scale

Self-gifting consumer behaviour (SGCB) is on the rise as consumers seek reward and therapeutic benefits from their shopping experiences. SGCB is defined as personally symbolic, self-communication through special indulgences, which tend to be premeditated and highly context bound. Prior research into the measurement of this growing behavioural phenomenon has been fragmented because of differences in conceptualisation. This research builds upon the prior literature and through a series of qualitative and quantitative studies, develops a valid, multidimensional measure of SGCB that will be useful for future quantitative inquiry into self-gifting consumption.

The validity of personal disturbance scale (DSSI/sAD) in people with diabetes mellitus, using longitudinal data

Despite being used since 1976, Delusions-Symptoms-States-Inventory/states of Anxiety and Depression (DSSI/sAD) has not yet been validated for use among people with diabetes. The aim of this study was to examine the validity of the personal disturbance scale (DSSI/sAD) among women with diabetes using Mater-University of Queensland Study of Pregnancy (MUSP) cohort data. The DSSI subscales were compared against DSM-IV disorders, the Mental Component Score of the Short Form 36 (SF-36 MCS), and Center for Epidemiologic Studies Depression Scale (CES-D). Factor analyses, odds ratios, receiver operating characteristic (ROC) analyses and diagnostic efficiency tests were used to report findings. Exploratory factor analysis and fit indices confirmed the hypothesized two-factor model of DSSI/sAD. We found significant variations in the DSSI/sAD domain scores that could be explained by CES-D (DSSI-Anxiety: 55%, DSSI-Depression: 46%) and SF-36 MCS (DSSI-Anxiety: 66%, DSSI-Depression: 56%). The DSSI subscales predicted DSM-IV diagnosed depression and anxiety disorders. The ROC analyses show that although the DSSI symptoms and DSM-IV disorders were measured concurrently the estimates of concordance remained only moderate. The findings demonstrate that the DSSI/sAD items have similar relationships to one another in both the diabetes and non-diabetes data sets which therefore suggest that they have similar interpretations.

Dynamic agent composition for large-scale agent-based models

PURPOSE: This paper describes dynamic agent composition, used to support the development of flexible and extensible large-scale agent-based models (ABMs). This approach was motivated by a need to extend and modify, with ease, an ABM with an underlying networked structure as more information becomes available. Flexibility was also sought after so that simulations are set up with ease, without the need to program. METHODS: The dynamic agent composition approach consists in having agents, whose implementation has been broken into atomic units, come together at runtime to form the complex system representation on which simulations are run. These components capture information at a fine level of detail and provide a vast range of combinations and options for a modeller to create ABMs. RESULTS: A description of the dynamic agent composition is given in this paper, as well as details about its implementation within MODAM (MODular Agent-based Model), a software framework which is applied to the planning of the electricity distribution network. Illustrations of the implementation of the dynamic agent composition are consequently given for that domain throughout the paper. It is however expected that this approach will be beneficial to other problem domains, especially those with a networked structure, such as water or gas networks. CONCLUSIONS: Dynamic agent composition has many advantages over the way agent-based models are traditionally built for the users, the developers, as well as for agent-based modelling as a scientific approach. Developers can extend the model without the need to access or modify previously written code; they can develop groups of entities independently and add them to those already defined to extend the model. Users can mix-and-match already implemented components to form large-scales ABMs, allowing them to quickly setup simulations and easily compare scenarios without the need to program. The dynamic agent composition provides a natural simulation space over which ABMs of networked structures are represented, facilitating their implementation; and verification and validation of models is facilitated by quickly setting up alternative simulations.

Building cross-scale models of epigenetic mechanisms

Epigenetic changes correspond to heritable modifications of the chromosome structure, which do not involve alteration of the DNA sequence but do affect gene expression. These mechanisms play an important role in normal cell differentiation, but aberration is associated also with several diseases, including cancer and neural disorders. In consequence, despite intensive studies in recent years, the contribution of modifications remains largely unquantified due to overall system complexity and insufficient data. Computational models can provide powerful auxiliary tools to experimentation, not least as scales from the sub-cellular through cell populations (or to networks of genes) can be spanned. In this paper, the challenges to development, of realistic cross-scale models, are discussed and illustrated with respect to current work.

Hearing parties' voices in Coordinated Family Dispute Resolution (CFDR) : An Australian pilot of a family mediation model designed for matters involving a history of domestic violence

This paper discusses the Coordinated Family Dispute Resolution (family mediation) process piloted in Australia in 2010–2012. This process was evaluated by the Australian Institute of Family Studies as being ‘at the cutting edge of family law practice’ because it involves the conscious application of mediation where there has been a history of family violence, in a clinically collaborative multidisciplinary and multi-agency setting. The Australian government’s failure to invest resources in the ongoing funding of this model jeopardises the safety and efficacy of family dispute resolution practice in family violence contexts, and compromises the hearing of the voices of family violence victims and their children.

Large-scale interlaboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens-to-hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma, and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and 7 control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to sub-nanogram/mL sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and inter-laboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy isotope labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an inter-laboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality c`ontrol measures, enables sensitive, specific, reproducible and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.

Load applied on a bone-anchored transfemoral prosthesis: characterisation of a prosthesis : a pilot study

The objectives of this study were (A) to record the inner prosthesis loading during activities of daily living (ADL), (B) to present a set of variables comparing loading data, and (C) to provide an example of characterisation of two prostheses. The load was measured at 200 Hz using a multi-axial transducer mounted between the residuum and the knee of an individual with unilateral transfemoral amputation fitted with a bone-anchored prosthesis. The load was measured while using two different prostheses including a mechanically (PRO1) and a microprocessor controlled (PRO2) knee during six ADL. The characterisation of prosthesis was achieved using a set of variables split into four categories, including temporal characteristics, maximum loading, loading slopes and impulse. Approximately 360 gait cycles were analysed for each prosthesis. PRO1 showed a cadence improved by 19% and 7%, a maximum force on the long axis reduced by 11% and 19%, as well as an impulse reduced by 32% and 15% during descent of incline and stairs compared to PRO2, respectively. This work confirmed that the proposed apparatus and characterisation can reveal how changes of prosthetic components are translated into inner loading.

Knowledge unlatched: A global library consortium model for funding open access scholarly books: Full report on the Proof of Concept Pilot 2014

This special issue of Cultural Science Journal is devoted to the report of a groundbreaking experiment in re-coordinating global markets for specialist scholarly books and enabling the knowledge commons: the Knowledge Unlatched proof-of-concept pilot. The pilot took place between January 2012 and September 2014. It involved libraries, publishers, authors, readers and research funders in the process of developing and testing a global library consortium model for supporting Open Access books. The experiment established that authors, librarians, publishers and research funding agencies can work together in powerful new ways to enable open access; that doing so is cost effective; and that a global library consortium model has the potential dramatically to widen access to the knowledge and ideas contained in book-length scholarly works.

Uptake of influenza vaccination in pregnancy amongst Australian Aboriginal and Torres Strait Islander women: A mixed-methods pilot study

Background Influenza infection during pregnancy is associated with significant morbidity and mortality. Immunisation against influenza is recommended during pregnancy in several countries but uptake of vaccine is poor. There are limited data on vaccine uptake, and the determinants of vaccination, in Australian Aboriginal and/or Torres Islander women during pregnancy. This study aimed to establish an appropriate methodology and collect pilot data on vaccine uptake and attitudes towards, and perceptions of, maternal influenza vaccination in that population in order to inform the development of larger studies. Methods A mixed-methods study comprised of a cross-sectional survey and yarning circles (focus groups) amongst Aboriginal and Torres Strait Islander women attending two primary health care services. The women were between 28 weeks gestation and less than 16 weeks post-birth. These data were supplemented by data collected in an ongoing national Australian study of maternal influenza vaccination. Aboriginal research officers collected community data and data from the yarning circles which were based on a narrative enquiry framework. Descriptive statistics were used to analyse quantitative data and thematic analyses were applied to qualitative data. Results Quantitative data were available for 53 women and seven of these women participated in the yarning circles. The proportion of women who reported receipt of an influenza vaccine during their pregnancy was 9/53. Less than half of the participants (21/53) reported they had been offered the vaccine in pregnancy. Forty-three percent reported they would get a vaccine if they became pregnant again. Qualitative data suggested perceived benefits to themselves and their infants were important factors in the decision to be vaccinated but there was insufficient information available to women to make that choice. Conclusions The rates of influenza immunisation may continue to remain low for Aboriginal and/or Torres Strait Islander women during pregnancy. Access to services and recommendations by a health care worker may be factors in the lower rates. Our findings support the need for larger studies directed at monitoring and understanding the determinants of maternal influenza vaccine uptake during pregnancy in Australian Aboriginal and Torres Strait Islander women. This research will best be achieved using methods that account for the social and cultural contexts of Aboriginal and Torres Strait Islander communities in Australia.

Feasibility and acceptability of wrist actigraph in assessing sleep quality and sleep quantity: A home-based pilot study in healthy volunteers

Purpose This study aimed to determine the feasibility and acceptability of actigraphy to monitor sleep quality and quantity in healthy self-rated good sleeper adults at home-based settings. Method Sixteen healthy volunteers (age > 18) were invited to participate. Each participant was provided with a wrist actigraph device to be worn for 24-hour/day for seven consecutive days to monitor their sleep-wake patterns. Actigraphy data were downloaded using-proprietary software to generate an individual-sleep report. Participants also completed a set of self-reported Health Related Quality of Life (HRQOL) using WHO (five) Well Being Index (WBI) questionnaires. Results Actigraphy was well accepted by all participants. Only 43.8% of the participants achieved normal total sleep time (TST) and 62.5% had a mean sleep efficiency value below the normal range. Despite a reduced quality of sleep among the participants, the self-reported HRQOL scores produced by the WHO-5 WBI showed a “fair” to “good” among the participants. Conclusions To maintain healthy well-being, it is vital to have efficient and quality sleep. Insufficient and poor sleep may contribute to various health problems and hazardous outcomes. People often believe they have normal and efficient sleep, not realising they may be developing poor sleep habits. This study found that actigraphy can be easily utilized to monitor sleep-wake patterns at home-based settings. We proposed that actigraphy could be adapted for use in the primary care settings (e.g. community pharmacy) to improve the sleep health management in the community.

Parallel streaming signature EM-tree: A clustering algorithm for web scale applications

The proliferation of the web presents an unsolved problem of automatically analyzing billions of pages of natural language. We introduce a scalable algorithm that clusters hundreds of millions of web pages into hundreds of thousands of clusters. It does this on a single mid-range machine using efficient algorithms and compressed document representations. It is applied to two web-scale crawls covering tens of terabytes. ClueWeb09 and ClueWeb12 contain 500 and 733 million web pages and were clustered into 500,000 to 700,000 clusters. To the best of our knowledge, such fine grained clustering has not been previously demonstrated. Previous approaches clustered a sample that limits the maximum number of discoverable clusters. The proposed EM-tree algorithm uses the entire collection in clustering and produces several orders of magnitude more clusters than the existing algorithms. Fine grained clustering is necessary for meaningful clustering in massive collections where the number of distinct topics grows linearly with collection size. These fine-grained clusters show an improved cluster quality when assessed with two novel evaluations using ad hoc search relevance judgments and spam classifications for external validation. These evaluations solve the problem of assessing the quality of clusters where categorical labeling is unavailable and unfeasible.

Increasing enjoyable activities to treat depression in nursing home residents with dementia: A pilot study

This pilot study aimed to assess the feasibility and acceptability of a Behavioral Activities intervention (BE-ACTIV) in Australian nursing homes. BE-ACTIV was developed by researchers at the University of Louisville, USA, to improve mood and quality of life (QOL) in nursing home residents with mild to moderate dementia. An 8-week trial was conducted and 10 residents with mild to moderate dementia received the BE-ACTIV intervention while 8 residents received a Walking and Talking intervention. Measures of depression (GDS–12R), and QOL (QOL-AD-NH) were administered prior to and following the interventions. Qualitative feedback indicated residents benefited from BE-ACTIV, evident by improved mood, although no statistically significant treatment effect was found. Moreover, the intervention was found to be feasible and acceptable to Australian nursing home staff and our findings highlight the importance of individualizing activities for people with dementia, of which 1:1 staff attention was a key component.

Validity of the geriatric depression scale and the collateral source version of the geriatric depression scale in nursing homes

Background Depression is a common psychiatric disorder in older people. The study aimed to examine the screening accuracy of the Geriatric Depression Scale (GDS) and the Collateral Source version of the Geriatric Depression Scale (CS-GDS) in the nursing home setting. Methods Eighty-eight residents from 14 nursing homes were assessed for depression using the GDS and the CS-GDS, and validated against clinician diagnosed depression using the Semi-structured Clinical Diagnostic Interview for DSM-IV-TR Axis I Disorders (SCID) for residents without dementia and the Provisional Diagnostic Criteria for Depression in Alzheimer Disease (PDCdAD) for those with dementia. The screening performances of five versions of the GDS (30-, 15-, 10-, 8-, and 4-item) and two versions of the CS-GDS (30- and 15-item) were analyzed using receiver operating characteristic (ROC) curves. Results Among residents without dementia, both the self-rated (AUC = 0.75–0.79) and proxy-rated (AUC = 0.67) GDS variations performed significantly better than chance in screening for depression. However, neither instrument adequately identified depression among residents with dementia (AUC between 0.57 and 0.70). Among the GDS variations, the 4- and 8-item scales had the highest AUC and the optimal cut-offs were >0 and >3, respectively. Conclusions The validity of the GDS in detecting depression requires a certain level of cognitive functioning. While the CS-GDS is designed to remedy this issue by using an informant, it did not have adequate validity in detecting depression among residents with dementia. Further research is needed on informant selection and other factors that can potentially influence the validity of proxy-based measures in the nursing home setting.

Cyclic Salinity Model for deposition of large-scale coal deposits

Existing field data for Rangal coals (Late Permian) of the Bowen Basin, Queensland, Australia, are inconsistent with the depositional model generally accepted in the current geological literature to explain coal deposition. Given the apparent unsuitability of the current depositional model to the Bowen Basin coal data, a new depositional model, here named the Cyclic Salinity Model, is proposed and tested in this study.