School of Mathematics and Statistics - Research Publications
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ItemOuter limits of subdifferentials for min–max type functions(Taylor and Francis Group, 2019-07-03)We generalise the outer subdifferential construction suggested by Cánovas, Henrion, L_opez and Parra for max type functions to pointwise minima of regular Lipschitz functions. We also answer an open question about the relation between the outer subdifferential of the support of a regular function and the end set of its subdifferential posed by Li, Meng and Yang.
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ItemNo Preview AvailableOn the Conjecture by Demyanov–Ryabova in Converting Finite Exhausters(Springer, 2017-09)The Demyanov–Ryabova conjecture is a geometric problem originating from duality relations between nonconvex objects. Given a finite collection of polytopes, one obtains its dual collection as convex hulls of the maximal facet of sets in the original collection, for each direction in the space (thus constructing upper convex representations of positively homogeneous functions from lower ones and, vice versa, via Minkowski duality). It is conjectured that an iterative application of this conversion procedure to finite families of polytopes results in a cycle of length at most two. We prove a special case of the conjecture assuming an affine independence condition on the vertices of polytopes in the collection. We also obtain a purely combinatorial reformulation of the conjecture.
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ItemSource-Based Jamming for Physical-Layer Security on Untrusted Full-Duplex Relay(IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2019-05-01)We address the problem of secure wireless communications over an untrusted full-duplex (FD) relay based on the source jamming scheme. The optimal power allocation between the confidential signal and the jamming signal is derived to maximize the secrecy rate. Then, the corresponding secrecy outage probability (SOP) and the average secrecy rate (ASR) are analyzed. A tight approximation and an asymptotic result are further obtained for the single-antenna destination case both in simple forms. The large-antenna destination case is also analyzed rigorously. Further discussion reveals that transmit-power dependent self-interference has significant negative impact on the secrecy performance.
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ItemNo Preview AvailablePhysical-Layer Security in Full-Duplex Multi-Hop Multi-User Wireless Network With Relay Selection(IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2019-02)This paper investigates the relay selection (RS) problem for multi-hop full-duplex relay networks where multiple source-destination (SD) pairs compete for the same pool of relays, under the attack of multiple eavesdroppers. To enhance the physical-layer security, within a given coherence time, our objective is to jointly assign the available relays at each hop to different SD pairs to maximize the minimum secrecy rate among all pairs. Two RS schemes, optimal RS and suboptimal RS (SRS), are proposed for two-hop networks based on global channel state information (CSI) and only SD pairs CSI, respectively. Since all users can communicate within the same coherence time, our joint RS schemes are important for the user-fairness and ultra-reliable low-latency communications. To evaluate the performance, the exact secrecy outage probability of the SRS scheme is derived under two residual self-interference models. The asymptotic analysis shows that the SRS scheme achieves full diversity. A relay-based jamming scheme is also proposed by using unassigned relays for user communications. Finally, the two-hop RS schemes and the analysis are extended to the general multi-hop network with multiple eavesdroppers. The numerical results reveal interesting fundamental trends where the proposed schemes can significantly enhance the secrecy performance.
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ItemPregnant women maintain body temperatures within safe limits during moderate-intensity aqua-aerobic classes conducted in pools heated up to 33 degrees Celsius: an observational study(AUSTRALIAN PHYSIOTHERAPY ASSOC, 2015-10-01)QUESTION: What is the body temperature response of healthy pregnant women exercising at moderate intensity in an aqua-aerobics class where the water temperature is in the range of 28 to 33 degrees Celsius, as typically found in community swimming pools? DESIGN: An observational study. PARTICIPANTS: One hundred and nine women in the second and third trimester of pregnancy who were enrolled in a standardised aqua-aerobics class. OUTCOME MEASURES: Tympanic temperature was measured at rest pre-immersion (T1), after 35minutes of moderate-intensity aqua-aerobic exercise (T2), after a further 10minutes of light exercise while still in the water (T3) and finally on departure from the facility (T4). The range of water temperatures in seven indoor community pools was 28.8 to 33.4 degrees Celsius. RESULTS: Body temperature increased by a mean of 0.16 degrees Celsius (SD 0.35, p<0.001) at T2, was maintained at this level at T3 and had returned to pre-immersion resting values at T4. Regression analysis demonstrated that the temperature response was not related to the water temperature (T2 r = -0.01, p = 0.9; T3 r = -0.02, p=0.9; T4 r=0.03, p=0.8). Analysis of variance demonstrated no difference in body temperature response between participants when grouped in the cooler, medium and warmer water temperatures (T2 F=0.94, p=0.40; T3 F=0.93, p=0.40; T4 F=0.70, p=0.50). CONCLUSIONS: Healthy pregnant women maintain body temperatures within safe limits during moderate-intensity aqua-aerobic exercise conducted in pools heated up to 33 degrees Celsius. The study provides evidence to inform guidelines for safe water temperatures for aqua-aerobic exercise during pregnancy.
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ItemA Bayesian method for comparing and combining binary classifiers in the absence of a gold standard.(Springer Science and Business Media LLC, 2012-07-27)BACKGROUND: Many problems in bioinformatics involve classification based on features such as sequence, structure or morphology. Given multiple classifiers, two crucial questions arise: how does their performance compare, and how can they best be combined to produce a better classifier? A classifier can be evaluated in terms of sensitivity and specificity using benchmark, or gold standard, data, that is, data for which the true classification is known. However, a gold standard is not always available. Here we demonstrate that a Bayesian model for comparing medical diagnostics without a gold standard can be successfully applied in the bioinformatics domain, to genomic scale data sets. We present a new implementation, which unlike previous implementations is applicable to any number of classifiers. We apply this model, for the first time, to the problem of finding the globally optimal logical combination of classifiers. RESULTS: We compared three classifiers of protein subcellular localisation, and evaluated our estimates of sensitivity and specificity against estimates obtained using a gold standard. The method overestimated sensitivity and specificity with only a small discrepancy, and correctly ranked the classifiers. Diagnostic tests for swine flu were then compared on a small data set. Lastly, classifiers for a genome-wide association study of macular degeneration with 541094 SNPs were analysed. In all cases, run times were feasible, and results precise. The optimal logical combination of classifiers was also determined for all three data sets. Code and data are available from http://bioinformatics.monash.edu.au/downloads/. CONCLUSIONS: The examples demonstrate the methods are suitable for both small and large data sets, applicable to the wide range of bioinformatics classification problems, and robust to dependence between classifiers. In all three test cases, the globally optimal logical combination of the classifiers was found to be their union, according to three out of four ranking criteria. We propose as a general rule of thumb that the union of classifiers will be close to optimal.
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ItemPsychosocial Well-Being and Functional Outcomes in Youth With Type 1 Diabetes 12 years After Disease Onset(AMER DIABETES ASSOC, 2010-07)OBJECTIVE: Type 1 diabetes in youth and community controls were compared on functional outcomes. Relationships were examined between psychosocial variables at diagnosis and functional outcome 12 years later. RESEARCH DESIGN AND METHODS: Participants were subjects with type 1 diabetes (n = 110, mean age 20.7 years, SD 4.3) and control subjects (n = 76, mean age 20.8 years, SD 4.0). The measures used included the Youth Self-Report and Young Adult Self-Report and a semi-structured interview of functional outcomes. Type 1 diabetes participants also provided information about current diabetes care and metabolic control from diagnosis. RESULTS: Type 1 diabetes participants and control subjects reported similar levels of current well-being but for the youth with type 1 diabetes, the mental health referral rates over the previous 12 years were higher by 19% and school completion rates were lower by 17%. Over one-third of clinical participants were not currently receiving specialist care and this group had higher mental health service usage in the past (61 vs. 33%) and lower current psychosocial well- being. Within the type 1 diabetes group, behavior problems, high activity, and low family cohesion at diagnosis predicted lower current well-being, but were not associated with metabolic control history. Poorer metabolic control was associated with higher mental health service usage. CONCLUSIONS: Type 1 diabetes participants report similar levels of current psychosocial well-being compared with control subjects, but higher levels of psychiatric morbidity since diagnosis and lower school completion rates. Psychiatric morbidity was associated with poor metabolic control and failure to transition to tertiary adult diabetes care.
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ItemExperimental and analytical evaluation of Incremental Sheet Hydro-Forming strategies to produce high forming angle sheets.(Elsevier BV, 2019-06)Incremental Sheet Hydro-Forming (ISHF) is a hybrid process of Incremental Sheet Forming (ISF) and Sheet Hydro-Forming (SHF). In the ISHF process, a single ball tool moves over one side of the surface of the sheet and hydraulic support is provided in another by using the pressurized hydraulic fluid. In the current research, an attempt has been made to achieve high forming angles using ISHF. The forming strategy, multi-stage & multi-step (MSMS), has been proposed to improve the formability in ISHF. The MSMS has resulted in the improvement in the formability and forming angle achieved is 78.75 o . The primary issue, identified in MSMS forming strategy, is the failure of the product due to thinning of the sheet. To address the failure of the sheet due to thinning, a modified version of MSMS was proposed. This modified version of MSMS has shown tremendous improvement in the formability of the ISHF. The forming angle upto 90 o has been successfully achieved using the modified version of MSMS. Analytical models have been developed for MSMS forming strategy and for the modified version of MSMS forming strategy. The experimental results are closely the same as predicted by analytical models.
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ItemEvaluating stably expressed genes in single cells(OXFORD UNIV PRESS, 2019-09-01)BACKGROUND: Single-cell RNA-seq (scRNA-seq) profiling has revealed remarkable variation in transcription, suggesting that expression of many genes at the single-cell level is intrinsically stochastic and noisy. Yet, on the cell population level, a subset of genes traditionally referred to as housekeeping genes (HKGs) are found to be stably expressed in different cell and tissue types. It is therefore critical to question whether stably expressed genes (SEGs) can be identified on the single-cell level, and if so, how can their expression stability be assessed? We have previously proposed a computational framework for ranking expression stability of genes in single cells for scRNA-seq data normalization and integration. In this study, we perform detailed evaluation and characterization of SEGs derived from this framework. RESULTS: Here, we show that gene expression stability indices derived from the early human and mouse development scRNA-seq datasets and the "Mouse Atlas" dataset are reproducible and conserved across species. We demonstrate that SEGs identified from single cells based on their stability indices are considerably more stable than HKGs defined previously from cell populations across diverse biological systems. Our analyses indicate that SEGs are inherently more stable at the single-cell level and their characteristics reminiscent of HKGs, suggesting their potential role in sustaining essential functions in individual cells. CONCLUSIONS: SEGs identified in this study have immediate utility both for understanding variation and stability of single-cell transcriptomes and for practical applications such as scRNA-seq data normalization. Our framework for calculating gene stability index, "scSEGIndex," is incorporated into the scMerge Bioconductor R package (https://sydneybiox.github.io/scMerge/reference/scSEGIndex.html) and can be used for identifying genes with stable expression in scRNA-seq datasets.
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ItemAccurate RNA Sequencing From Formalin-Fixed Cancer Tissue to Represent High-Quality Transcriptome From Frozen Tissue(AMER SOC CLINICAL ONCOLOGY, 2018-01-26)PURPOSE: Accurate transcriptional sequencing (RNA-seq) from formalin-fixation and paraffin-embedding (FFPE) tumor samples presents an important challenge for translational research and diagnostic development. In addition, there are now several different protocols to prepare a sequencing library from total RNA. We evaluated the accuracy of RNA-seq data generated from FFPE samples in terms of expression profiling. METHODS: We designed a biospecimen study to directly compare gene expression results from different protocols to prepare libraries for RNA-seq from human breast cancer tissues, with randomization to fresh-frozen (FF) or FFPE conditions. The protocols were compared using multiple computational methods to assess alignment of reads to reference genome, and the uniformity and continuity of coverage; as well as the variance and correlation, of overall gene expression and patterns of measuring coding sequence, phenotypic patterns of gene expression, and measurements from representative multigene signatures. RESULTS: The principal determinant of variance in gene expression was use of exon capture probes, followed by the conditions of preservation (FF versus FFPE), and phenotypic differences between breast cancers. One protocol, with RNase H-based rRNA depletion, exhibited least variability of gene expression measurements, strongest correlation between FF and FFPE samples, and was generally representative of the transcriptome from standard FF RNA-seq protocols. CONCLUSION: Method of RNA-seq library preparation from FFPE samples had marked effect on the accuracy of gene expression measurement compared to matched FF samples. Nevertheless, some protocols produced highly concordant expression data from FFPE RNA-seq data, compared to RNA-seq results from matched frozen samples.