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)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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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.
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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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ItemCharge Has a Marked Influence on Hyperbranched Polymer Nanoparticle Association in Whole Human Blood(AMER CHEMICAL SOC, 2017-06)In this study, we synthesize charge-varied hyperbranched polymers (HBPs) and demonstrate surface charge as a key parameter directing their association with specific human blood cell types. Using fresh human blood, we investigate the association of 5 nm HBPs with six white blood cell populations in their natural milieu by flow cytometry. While most cell types associate with cationic HBPs at 4 °C, at 37 °C phagocytic cells display similar (monocyte, dendritic cell) or greater (granulocyte) association with anionic HBPs compared to cationic HBPs. Neutral HBPs display remarkable stealth properties. Notably, these charge-association patterns are not solely defined by the plasma protein corona and are material and/or size dependent. As HBPs progress toward clinical use as imaging and drug delivery agents, the ability to engineer HBPs with defined biological properties is increasingly important. This knowledge can be used in the rational design of HBPs for more effective delivery to desired cell targets.
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ItemErratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls.(NATURE PUBLISHING GROUP, 2018-01-23)This corrects the article DOI: 10.1038/sdata.2017.179.