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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ItemSource-Based Jamming for Physical-Layer Security on Untrusted Full-Duplex Relay(IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2019-05)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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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)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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ItemAnatomy of a seasonal influenza epidemic forecast(Department of Health, Australian Government, 2019-03-15)Bayesian methods have been used to predict the timing of infectious disease epidemics in various settings and for many infectious diseases, including seasonal influenza. But integrating these techniques into public health practice remains an ongoing challenge, and requires close collaboration between modellers, epidemiologists, and public health staff. During the 2016 and 2017 Australian influenza seasons, weekly seasonal influenza forecasts were produced for cities in the three states with the largest populations: Victoria, New South Wales and Queensland. Forecast results were presented to Health Department disease surveillance units in these jurisdictions, who provided feedback about the plausibility and public health utility of these predictions. In earlier studies we found that delays in reporting and processing of surveillance data substantially limited forecast performance, and that incorporating climatic effects on transmission improved forecast performance. In this study of the 2016 and 2017 seasons, we sought to refine the forecasting method to account for delays in receiving the data, and used meteorological data from past years to modulate the force of infection. We demonstrate how these refinements improved the forecast’s predictive capacity, and use the 2017 influenza season to highlight challenges in accounting for population and clinician behaviour changes in response to a severe season.
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ItemMap and model-moving from observation to prediction in toxicogenomics.(Oxford University Press (OUP), 2019-06-01)BACKGROUND: Chemicals induce compound-specific changes in the transcriptome of an organism (toxicogenomic fingerprints). This provides potential insights about the cellular or physiological responses to chemical exposure and adverse effects, which is needed in assessment of chemical-related hazards or environmental health. In this regard, comparison or connection of different experiments becomes important when interpreting toxicogenomic experiments. Owing to lack of capturing response dynamics, comparability is often limited. In this study, we aim to overcome these constraints. RESULTS: We developed an experimental design and bioinformatic analysis strategy to infer time- and concentration-resolved toxicogenomic fingerprints. We projected the fingerprints to a universal coordinate system (toxicogenomic universe) based on a self-organizing map of toxicogenomic data retrieved from public databases. Genes clustering together in regions of the map indicate functional relation due to co-expression under chemical exposure. To allow for quantitative description and extrapolation of the gene expression responses we developed a time- and concentration-dependent regression model. We applied the analysis strategy in a microarray case study exposing zebrafish embryos to 3 selected model compounds including 2 cyclooxygenase inhibitors. After identification of key responses in the transcriptome we could compare and characterize their association to developmental, toxicokinetic, and toxicodynamic processes using the parameter estimates for affected gene clusters. Furthermore, we discuss an association of toxicogenomic effects with measured internal concentrations. CONCLUSIONS: The design and analysis pipeline described here could serve as a blueprint for creating comparable toxicogenomic fingerprints of chemicals. It integrates, aggregates, and models time- and concentration-resolved toxicogenomic data.
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ItemFluctuations of the number of excursion sets of planar Gaussian fields( 2019-08-28)For a smooth, stationary, planar Gaussian field, we consider the number of connected components of its excursion set (or level set) contained in a large square of area R2. The mean number of components is known to be of order R2 for generic fields and all levels. We show that for certain fields with positive spectral density near the origin (including the Bargmann-Fock field), and for certain levels ℓ, these random variables have fluctuations of order at least R, and hence variance of order at least R2. In particular this holds for excursion sets when ℓ is in some neighbourhood of zero, and it holds for excursion/level sets when ℓ is sufficiently large. We prove stronger fluctuation lower bounds of order Rα, α ∈ [1, 2], in the case that the spectral density has a singularity at the origin. Finally we show that the number of excursion/level sets for the Random Plane Wave at certain levels has fluctuations of order at least R3/2, and hence variance of order at least R3. We expect that these bounds are of the correct order, at least for generic levels.
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ItemNo Preview AvailableMass measurement of graphene using quartz crystal microbalances(AMER INST PHYSICS, 2019-07-29)Current wafer-scale fabrication methods for graphene-based electronics and sensors involve the transfer of single-layer graphene by a support polymer. This often leaves some polymer residue on the graphene, which can strongly impact its electronic, thermal, and mechanical resonance properties. To assess the cleanliness of graphene fabrication methods, it is thus of considerable interest to quantify the amount of contamination on top of the graphene. Here, we present a methodology for the direct measurement of the mass of the graphene sheet using quartz crystal microbalances (QCMs). By monitoring the QCM resonance frequency during removal of graphene in an oxygen plasma, the total mass of the graphene and contamination is determined with sub-graphene-monolayer accuracy. Since the etch-rate of the contamination is higher than that of graphene, quantitative measurements of the mass of contaminants below, on top, and between graphene layers are obtained. We find that polymer-based dry transfer methods can increase the mass of a graphene sheet by a factor of 10. The presented mass measurement method is conceptually straightforward to interpret and can be used for standardized testing of graphene transfer procedures in order to improve the quality of graphene devices in future applications.
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ItemNo Preview AvailableEffect of morphology on the large-amplitude flapping dynamics of an inverted flag in a uniform flow(CAMBRIDGE UNIV PRESS, 2019-09-10)The stability of a cantilevered elastic sheet in a uniform flow has been studied extensively due to its importance in engineering and its prevalence in natural structures. Varying the flow speed can give rise to a range of dynamics including limit cycle behaviour and chaotic motion of the cantilevered sheet. Recently, the ‘inverted flag’ configuration – a cantilevered elastic sheet aligned with the flow impinging on its free edge – has been observed to produce large-amplitude flapping over a finite band of flow speeds. This flapping phenomenon has been found to be a vortex-induced vibration, and only occurs at sufficiently large Reynolds numbers. In all cases studied, the inverted flag has been formed from a cantilevered sheet of rectangular morphology, i.e. the planform of its elastic sheet is a rectangle. Here, we investigate the effect of the inverted flag’s morphology on its resulting stability and dynamics. We choose a trapezoidal planform which is explored using experiment and an analytical theory for the divergence instability of an inverted flag of arbitrary morphology. Strikingly, for this planform we observe that the flow speed range over which flapping occurs scales approximately with the flow speed at which the divergence instability occurs. This provides a means by which to predict and control flapping. In a biological setting, leaves in a wind can also align themselves in an inverted flag configuration. Motivated by this natural occurrence we also study the effect of adding an artificial ‘petiole’ (a thin elastic stalk that connects the sheet to the clamp) on the inverted flag’s dynamics. We find that the petiole serves to partially decouple fluid forces from elastic forces, for which an analytical theory is also derived, in addition to increasing the freedom by which the flapping dynamics can be tuned. These results highlight the intricacies of the flapping instability and account for some of the varied dynamics of leaves in nature.