https://hdl.handle.net/2123/8969 2026-06-04T14:46:16Z https://hdl.handle.net/2123/34598 Demonstration of a photonic-lantern focal-plane wavefront sensor using fiber mode conversion and deep learning Norris, Barnaby; Wei, Jin; Betters, Christopher H.; Leon-Saval, Sergio G.; Xin, Yinzi; Lin, Jonathan; Kim, Yoo Jung; Sallum, Steph; Lozi, Julien; Vievard, Sebastian; Guyon, Olivier; Gatkine, Pradip; Jovanovic, Nemanja; Mawet, Dimitri; Fitzgerald, Michael P. A focal plane wavefront sensor offers major advantages to adaptive optics, including removal of non-commonpath error and providing sensitivity to blind modes (such as petalling). But simply using the observed point spread function (PSF) is not sufficient for wavefront correction, as only the intensity, not phase, is measured. Here we demonstrate the use of a multimode fiber mode converter (photonic lantern) to directly measure the wavefront phase and amplitude at the focal plane. Starlight is injected into a multimode fiber at the image plane, with the combination of modes excited within the fiber a function of the phase and amplitude of the incident wavefront. The fiber undergoes an adiabatic transition into a set of multiple, single-mode outputs, such that the distribution of intensities between them encodes the incident wavefront. The mapping (which may be strongly non-linear) between spatial modes in the PSF and the outputs is stable but must be learned. This is done by a deep neural network, trained by applying random combinations of spatial modes to the deformable mirror. Once trained, the neural network can instantaneously predict the incident wavefront for any set of output intensities. We demonstrate the successful reconstruction of wavefronts produced in the laboratory with low-wind-effect, and an on-sky demonstration of reconstruction of low-order modes consistent with those measured by the existing pyramid wavefront sensor, using SCExAO observations at the Subaru Telescope. 2022-01-01T00:00:00Z https://hdl.handle.net/2123/34596 The photonic lantern wavefront sensor and imager: focal plane wavefront sensing and optimal imaging at the diffraction limit and beyond Norris, Barnaby; Leon-Saval, Sergio G.; Wei, Jin; Betters, Christopher H.; Taras, Adam; Lin, Jonathan; Xin, Yinzi; Kim, Yoo Jung; Fitzgerald, Michael; Sallum, Steph; Sengupta, Aditya; Gatkine, Pradip; Jovanovic, Nemanja; Mawet, Dimitri; Lozi, Julien; Vievard, Sebastian; Deo, Vincent; Lallement, Manon; Levinstein, Daniel; Guyon, Olivier The use of a photonic lantern as focal plane wavefront sensor has seen recent widespread interest - it can remove non-common-path aberrations, accurately sense low-wind-effect and petal modes, and provide wavelength resolution. It encodes both the PSFs phase and amplitude into the intensities of its single-mode-fibre outputs, from which the wavefront is reconstructed (by neural network or other algorithm). It also offers exciting potential as an imager to resolve structure at and beyond the telescope diffraction limit, filling in a coronagraphs IWA blind spot. This can utilise interferometric techniques, or an oversampled photonic lantern, having sufficient measurement dimensions that the amplitude, phase and spatial coherence of the science field can be entirely constrained by the output fluxes, and so the wavefront-error-induced components can be disambiguated from the source spatial structure. Other applications such as fibre nulling, optimal single-mode fibre injection, spectroastrometry, and others are also in development. Here, a brief overview of the photonic lantern sensor and these various applications will be given, along with key references. 2024-01-01T00:00:00Z https://hdl.handle.net/2123/34489 Absence of Galilean invariance for pure-quartic solitons Widjaja, Justin; Kobakhidze, Erekle; Cartwright, Tiernan R; Lourdesamy, Joshua P.; Runge, Antoine F. J.; Alexander, Tristram J.; de Sterke, C. Martijn Optical temporal solitons, arising from self-phase modulation and negative quadratic ($\beta_2$) dispersion, are Galilean invariant, and therefore their properties do not depend on their group velocity. This is no longer true for pure-quartic soliton pulses arising from quartic ($\beta_4$) dispersion, for which a change in group velocity necessarily leads to nonzero quadratic and cubic ($\beta_3$) dispersion. Analyzing the generalized nonlinear Schrödinger equation for such dispersion relations analytically and numerically, we find that pure-quartic solitons are members of a larger family traveling at other speeds. These solitons, which appear to be stable, have a complex phase structure and have an asymmetric spectrum. Our results extend the understanding of solitons arising from high orders of dispersion. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/34488 Optimization of nonlinear enhancement through linear dispersion engineering Lourdesamy, Joshua P.; Widjaja, Justin; Hawi, Georgio; Kesarwani, Sharvil; Runge, Antoine F. J.; de Sterke, C. Martijn We consider nonlinear pulse propagation in media with a dispersion relation exhibiting $J$ periodically spaced identical maxima in a co-moving frame. The nonlinear interactions lead to $J$ pulses centered at each of these frequencies. These pulses propagate at the same group velocity and interfere, leading to a highly non-uniform signal in time. This results in the enhancement of effective nonlinear effects, as we recently demonstrated experimentally [Nat. Phys. {\bf 18}, 59 (2022)]. Here we present a detailed theoretical and numerical study of this nonlinear enhancement. We show that the amplitudes of the frequency components approximately follow a simple relation, which allows us to derive that the nonlinear enhancement factor increases as $0.687J$. Hence, enhancements of order $10$ can be achieved with $15$ frequency components. 2023-01-01T00:00:00Z https://hdl.handle.net/2123/34487 Theory of multicolor soliton microcombs Silvestri, Carlo; Widjaja, Justin; Lin, Austin; de Sterke, C. Martijn; Runge, Antoine F. J. We present a general theory of multicolor soliton microcombs. These frequency combs require engineered dispersion and have an optical spectrum consisting of multiple spectral windows, centered at distinct frequencies. Our theory is based on a multiple-scale approach applied to the Lugiato-Lefever equation, and provides a framework to investigate different pumping configurations. For multi-frequency pumping, we predict a decreasing pumping threshold as the number of spectral windows increases due to an enhanced effective nonlinear parameter. However, comb formation does not require multi-frequency pumping and can emerge even with a single driving field. Our theoretical predictions are in excellent agreement with numerical simulations. 2025-01-01T00:00:00Z https://hdl.handle.net/2123/34486 Pure high-order dispersion dissipative Kerr solitons in optical cavities Silvestri, Carlo; Qiang, Y. Long; Panda, Krupamaya; Widjaja, Justin; Coen, Stephane; de Sterke, C. Martijn; Runge, Antoine F. J. Through numerical simulations we demonstrate the existence of an infinite family of temporal cavity solitons which balance arbitrary negative pure, even-order dispersion $k$ and self-phase moduation, as well as loss and parametric gain. These correspond to frequency combs with increasingly flatter spectra as $k$ increases. We determine the analytic forms of these solitons in the limit of high pump power and detuning, and derive their scaling properties. In particular, we show that their energy is related to the pulse duration $\Delta\tau$ as $\Delta\tau^{-(k-1)}$. 2025-01-01T00:00:00Z https://hdl.handle.net/2123/34485 Phase-locked and -unlocked multicolor solitons in a fiber laser Widjaja, Justin; Hoang, Van Thuy; de Sterke, C. Martijn; Runge, Antoine F. J. Multicolor solitons are nonlinear pulses composed of two or more solitons centered at different frequencies, propagating with the same group velocity. In the time domain, multicolor solitons consist of an envelope multiplying a more rapidly varying fringe pattern that results from the interference of the frequency components. Here, we report the observation in a fiber laser of a novel type of dynamics in which the different frequency components still have the same group velocity but have different propagation constants. This causes the relative phases between the constituent spectral components to change upon propagation, corresponding to the fringes moving under the envelope. This leads to small periodic energy variations that we directly measure. Our experimental results are in good agreement with realistic numerical simulations based on an iterative cavity map. 2024-01-01T00:00:00Z https://hdl.handle.net/2123/34473 Linear pulse propagation with high-order dispersion Runge, Antoine F. J.; Qiang, Y. Long; Alexander, Tristram J.; de Sterke, C. Martijn We present an approximate, but intuitively appealing theoretical study of the linear propagation of optical pulses in media with high-order dispersion. Our analysis, which is fully consistent with numerical simulations, is based on the pulses' full-width at half maximum and shows that the effect of high-order dispersion differs significantly from that of the well-understood second order dispersion. For high dispersion orders m, the central part of the pulses, where the intensity is highest, evolve in the same way, independent of m, though at different rates, with a weak dependence on the initial pulse shape. We also find that all pulses, irrespective of initial pulse shape, eventually evolve to a sinc function. Our treatment allows us to find expressions for the characteristic dispersion lengths for high dispersion orders. 2022-01-01T00:00:00Z https://hdl.handle.net/2123/34400 Event classification datasets for the Cairns, Trevett, and Graham paper "Statistical Investigation of Langmuir Waves in Type III and II Sources" Cairns, Iver; Trevett, William; Graham, Daniel Stored here are files that describe the events studied in the paper. Both text and CSV formats are used.The files contain column headings and other headings that describe the contents, including variously the observing spacecraft, date and time of a STEREO Time Domain Sampler (TDS) waveform capture event, the analysed spectral and field statistical properties, and the various classifications of the event. 2025-10-16T00:00:00Z https://hdl.handle.net/2123/33528 Output dataset for radio emission produced by the code hybrid_3DNov.m for standard parameters Oppel, Patrick; Cairns, Iver This is an example output file of the code hybrid_3DNov.m for the "standard" case with 400km/s vsw and 60deg theta_bn (see input file init.m). This output is one of those presented in the Cairns and Oppel paper on images of Earth's foreshock radiation sources. 2025-01-14T00:00:00Z https://hdl.handle.net/2123/33527 Matlab software for the paper "First predictions for images of Earth's foreshock radiation sources" by Cairns and Oppel Oppel, Patrick; Cairns, Iver Examples of the Matlab software for the Cairns and Oppel paper on images for Earth's foreshock radiation sources. The file init.m gives the input parameters. The code hybrid_3DNov calculates the emissions for multiple planes from given input parameters. The code line_of_sight_new.m produces the view of the foreshock emissions from 9 locations. 2025-01-14T00:00:00Z https://hdl.handle.net/2123/32608 Outputs for the paper "Space Weather Effects on the Altitude of the CUAVA-1 2 CubeSat" by Cairns, Monger, and Arudselvan Cairns, Iver; Monger, Tony; Arudselvan, Vanathy This gzipped folder contains the output files for the work reported in the paper "Space Weather Effects on the Altitude of the CUAVA-1 CubeSat" by Cairns et al. submitted to the journal Space Weather. 2024-05-31T00:00:00Z https://hdl.handle.net/2123/32607 Dataset and software for the paper "Space Weather Effects on the Altitude of the CUAVA-1 2 CubeSat" by Cairns, Monger, and Arudselvan Cairns, Iver; Monger, Tony; Arudselvan, Vanathy This zipped folder contains the datsets and some python codes used to perform the analyses described in the paper "Space Weather Effects on the Altitude of the CUAVA-12 CubeSat" by Cairns et a. submitted to the AGU journal Space Weather in May 2024. 2024-05-31T00:00:00Z https://hdl.handle.net/2123/31951 SPIS simulations with and without the thruster from 0.067 AU to 1 AU Shinde, Tejaswi The file includes raw data extracted from the SPIS simulations for two cases a.) with SPT-100 thruster and b.) Without thruster. The plots in the manuscript are generated using this data. Additionally for full reproducibility of the simulation please find the .spis file, .geo and .msh file with and without the thruster at 1AU. Note that for any other location, the simulation files (.spis, .geo and .msh) can be modified using the right environmental parameters. 2023-12-08T00:00:00Z https://hdl.handle.net/2123/29502 Generalized dispersion Kerr solitons Tam, Kevin K. K.; Alexander, Tristram J.; Blanco Redondo, Andrea; de Sterke, C. Martijn We report a continuum of pulse-like soliton solutions to the generalized nonlinear Schr ̈odinger equation with both quadratic and quartic dispersion and a Kerr nonlinearity. We show that the well-known nonlinear Schr ̈odinger solitons, which occur in the presence of only negative (anomalous) quadratic dispersion, and pure-quartic solitons, which occur in the presence of only negative quartic dispersion, are members of a large superfamily, encompassing both. The members of this family, none of which are unstable, have exponentially decaying tails, which can exhibit oscillations. We find new analytic solutions for positive quadratic dispersion and negative quartic dispersion and investigate the soliton dynamics. We also find evidence that a combination of the quadratic and quartic dispersion, rather than exclusively quadratic dispersion, is likely to improve the performance of soliton lasers. 2020-01-01T00:00:00Z https://hdl.handle.net/2123/29501 Stationary and Dynamical Properties of Pure-Quartic Solitons Tam, Kevin K. K.; Alexander, Tristram J.; Blanco Redondo, Andrea; de Sterke, C. Martijn We numerically solve a generalized nonlinear Schrödinger equation and find a family of pure-quartic solitons, existing through a balance of positive Kerr nonlinearity and negative quartic dispersion. These solitons have oscillatory tails, which can be understood analytically from the properties of linear waves with quartic dispersion. By computing the linear eigenspectrum of the solitons, we show that they are stable, but that they possess a nontrivial internal mode close to the radiation continuum. We also demonstrate evolution into a pure-quartic soliton from Gaussian initial conditions. The energy-width scaling of pure-quartic solitons differs strongly from that for conventional solitons, opening possibilities for pure-quartic soliton lasers. 2019-01-01T00:00:00Z https://hdl.handle.net/2123/29499 Generalized self-similar propagation and amplification of optical pulses in nonlinear media with high-order normal dispersion Runge, Antoine F.J.; Alexander, Tristram J.; Talathi, Harsh P.; Hudson, Darren D.; Blanco Redondo, Andrea; de Sterke, C. Martijn We investigate theoretically and numerically the self-similar propagation of optical pulses in the presence of gain, positive Kerr nonlinearity and positive (i.e. normal) dispersion of even order m. Starting from a modified nonlinear Schr̈odinger equation, separating the evolution of amplitude and phase, we find that the resulting equations simplify considerably in the asymptotic limit. Exact solutions to the resulting equations indicate that the temporal intensity profile follows a 1−T^(m/(m−1)) function with an m-dependent scaling relation, with a T ^(1/(m−1)) chirp, where T is the pulse’s local time. These correspond to a triangle and a step function respectively, as m → ∞. These results are borne out by numerical simulations, though we do observe indications of non-asymptotic behaviour. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/29494 Self-similar propagation of optical pulses in fibers with positive quartic dispersion Runge, Antoine F.J.; Alexander, Tristram J.; Newton, Joseph; Alavandi, Pranav A.; Hudson, Darren D.; Blanco Redondo, Andrea; de Sterke, C. Martijn We study the propagation of ultrashort pulses in optical fiber with gain and positive (or normal) quartic dispersion by self-similarity analysis of the modified nonlinear Schrödinger equation. We find an exact asymptotic solution, corresponding to a triangle-like, T^4/3 intensity profile, with a T^1/3 chirp, which is confirmed by numerical simulations. This solution follows different amplitude and width scaling compared to the conventional case with quadratic dispersion. We also suggest, and numerically investigate, a fiber laser consisting of components with positive quartic dispersion which emits quartic self-similar pulses. 2020-01-01T00:00:00Z https://hdl.handle.net/2123/29092 Scenario modelling of biomass usage in the Australian electricity grid Li, M.; Middelhoff, E.; Ximenes, F.A.; Carney, C.; Madden, B.; Florin, N.; Malik, A.; Lenzen, M. Responding to the global crises - Covid19 and climate change - governments around the world are formulating green recovery plans to stimulate economic growth, boost clean energy technologies and cut emissions. Potential transition pathways for low carbon energy systems, however, remain as open questions. Generally, the simulation of biomass in the grid models is limited in their tempo-spatial resolution, transition pathways description, and/or biomass feedstock supply representation. This study aims to provide spatio-temporal highly resolved grid configurations featuring disaggregated biomass feedstocks, to assess Australia's potential energy transition pathways and 100% renewable electricity supply scenarios under various biomass bidding strategies and cost assumptions. We find that, as carbon prices increase, bioelectricity will prove to be a cost-effective flexible option compared to other low-carbon (such as CSP) and fossil-based flexible options (e.g. coal and gas), with its generation share reaching _9%-12% at higher carbon price scenarios. Biomass power plants can be well suited for operating in gap-filling mode to provide flexible power generation and to facilitate grid stability and load balancing. In light of the high biomass resource potential in Australia, keeping bioelectricity in the generation mix is beneficial for reducing system capacity and cost by 32% and 21%, respectively, under a future renewable-dominated Australian grid system. 2022-01-01T00:00:00Z https://hdl.handle.net/2123/28332 Simulating Transmission Scenarios of the Delta Variant of SARS-CoV-2 in Australia Chang, Sheryl L.; Cliff, Oliver M.; Zachreson, Cameron; Prokopenko, Mikhail An outbreak of the Delta (B.1.617.2) variant of SARS-CoV-2 that began around mid-June 2021 in Sydney, Australia, quickly developed into a nation-wide epidemic. The ongoing epidemic is of major concern as the Delta variant is more infectious than previous variants that circulated in Australia in 2020. Using a re-calibrated agent-based model, we explored a feasible range of non-pharmaceutical interventions, including case isolation, home quarantine, school closures, and stay-at-home restrictions (i.e., "social distancing.") Our modelling indicated that the levels of reduced interactions in workplaces and across communities attained in Sydney and other parts of the nation were inadequate for controlling the outbreak. A counter-factual analysis suggested that if 70% of the population followed tight stay-at-home restrictions, then at least 45 days would have been needed for new daily cases to fall from their peak to below ten per day. Our model predicted that, under a progressive vaccination rollout, if 40-50% of the Australian population follow stay-at-home restrictions, the incidence will peak by mid-October 2021: the peak in incidence across the nation was indeed observed in mid-October. We also quantified an expected burden on the healthcare system and potential fatalities across Australia. 2022-01-01T00:00:00Z https://hdl.handle.net/2123/28320 Modelling the impact of reopening schools in the UK in early 2021 in the presence of the alpha variant and with roll-out of vaccination against SARS-CoV-2 Panovska-Griffiths, J.; Stuart, R.M.; Kerr, C.C.; Rosenfield, K.; Mistry, D.; Waites, W.; Klein, D.J.; Bonell, C.; Viner, R.M. Following the resurgence of the COVID-19 epidemic in the UK in late 2020 and the emergence of the alpha (also known as B117) variant of the SARS-CoV-2 virus, a third national lockdown was imposed from January 4, 2021. Following the decline of COVID-19 cases over the remainder of January 2021, the question of when and how to reopen schools became an increasingly pressing one in early 2021. This study models the impact of a partial national lockdown with social distancing measures enacted in communities and workplaces under different strategies of reopening schools from March 8, 2021 and compares it to the impact of continual full national lockdown remaining until April 19, 2021. We used our previously published agent-based model, Covasim, to model the emergence of the alpha variant over September 1, 2020 to January 31, 2021 in presence of Test, Trace and Isolate (TTI) strategies. We extended the model to incorporate the impacts of the roll-out of a two-dose vaccine against COVID-19, with 200,000 daily vaccine doses prioritised by age starting with people 75 years or older, assuming vaccination offers a 95% reduction in disease acquisition risk and a 30% reduction in transmission risk. We used the model, calibrated until January 25, 2021, to simulate the impact of a full national lockdown (FNL) with schools closed until April 19, 2021 versus four different partial national lockdown (PNL) scenarios with different elements of schooling open: 1) staggered PNL with primary schools and exam-entry years (years 11 and 13) returning on March 8, 2021 and the rest of the schools years on March 15, 2020; 2) full-return PNL with both primary and secondary schools returning on March 8, 2021; 3) primary-only PNL with primary schools and exam critical years (years 11 and 13) going back only on March 8, 2021 with the rest of the secondary schools back on April 19, 2021 and 4) part-rota PNL with both primary and secondary schools returning on March 8, 2021 with primary schools remaining open continuously but secondary schools on a two-weekly rota-system with years alternating between a fortnight of face-to-face and remote learning until April 19, 2021. Across all scenarios, we projected the number of new daily cases, cumulative deaths and effective reproduction number R until April 30, 2021. Our calibration across different scenarios is consistent with alpha variant being around 60% more transmissible than the wild type. We find that strict social distancing measures, i.e. national lockdowns, were essential in containing the spread of the virus and controlling hospitalisations and deaths during January and February 2021. We estimated that a national lockdown over January and February 2021 would reduce the number of cases by early March to levels similar to those seen in October 2020, with R also falling and remaining below 1 over this period. We estimated that infections would start to increase when schools reopened, but found that if other parts of society remain closed, this resurgence would not be sufficient to bring R above 1. Reopening primary schools and exam critical years only or having primary schools open continuously with secondary schools on rotas was estimated to lead to lower increases in cases and R than if all schools opened. Without an increase in vaccination above the levels seen in January and February, we estimate that R could have increased above 1 following the reopening of society, simulated here from April 19, 2021. Our findings suggest that stringent measures were integral in mitigating the increase in cases and bringing R below 1 over January and February 2021. We found that it was plausible that a PNL with schools partially open from March 8, 2021 and the rest of the society remaining closed until April 19, 2021 would keep R below 1, with some increase evident in infections compared to continual FNL until April 19, 2021. Reopening society in mid-April, without an increase in vaccination levels, could push R above 1 and induce a surge in infections, but the effect of vaccination may be able to control this in future depending on the transmission blocking properties of the vaccines. 2022-01-01T00:00:00Z https://hdl.handle.net/2123/28298 Tourism, job vulnerability and income inequality during the COVID-19 pandemic Sun, Ya-Yen; Li, Mengyu; Lenzen, Manfred; Malik, Arunima; Pomponi, Francesco The COVID-19 pandemic demonstrated the vulnerability of tourism workers, but no detailed job loss figures are available that links tourism vulnerability with income inequality. This study evaluates how reduced international tourism consumption affects tourism employment and their income loss potential for 132 countries. This analysis shows that higher proportions of female (9.6%) and youth (10.1%) experienced unemployment whilst they were paid significantly less because they worked in tourism (_5%) and if they were women (_23%). Variations in policy support and pre-existing economic condition further created significant disparities on lost-income subsidies across countries. With the unequal financial burden across groups, income and regions, the collapse of international travel exacerbates short-term income inequality within and between countries. 2022-01-01T00:00:00Z https://hdl.handle.net/2123/28296 Preventing a cluster from becoming a new wave in settings with zero community COVID-19 cases Abeysuriya, Romesh G.; Delport, Dominic; Stuart, Robyn M.; Sacks-Davis, Rachel; Kerr, Cliff C.; Mistry, Dina; Klein, Daniel J.; Hellard, Margaret; Scott, Nick BackgroundIn settings with zero community transmission, any new SARS-CoV-2 outbreaks are likely to be the result of random incursions. The level of restrictions in place at the time of the incursion is likely to considerably affect possible outbreak trajectories, but the probability that a large outbreak eventuates is not known.MethodsWe used an agent-based model to investigate the relationship between ongoing restrictions and behavioural factors, and the probability of an incursion causing an outbreak and the resulting growth rate. We applied our model to the state of Victoria, Australia, which has reached zero community transmission as of November 2020.ResultsWe found that a future incursion has a 45% probability of causing an outbreak (defined as a 7-day average of>5 new cases per day within 60 days) if no restrictions were in place, decreasing to 23% with a mandatory masks policy, density restrictions on venues such as restaurants, and if employees worked from home where possible. A drop in community symptomatic testing rates was associated with up to a 10-percentage point increase in outbreak probability, highlighting the importance of maintaining high testing rates as part of a suppression strategy.ConclusionsBecause the chance of an incursion occurring is closely related to border controls, outbreak risk management strategies require an integrated approaching spanning border controls, ongoing restrictions, and plans for response. Each individual restriction or control strategy reduces the risk of an outbreak. They can be traded off against each other, but if too many are removed there is a danger of accumulating an unsafe level of risk. The outbreak probabilities estimated in this study are of particular relevance in assessing the downstream risks associated with increased international travel. 2022-01-01T00:00:00Z https://hdl.handle.net/2123/28288 Dynamical analysis of the infection status in diverse communities due to COVID-19 using a modified SIR model Cooper, Ian; Mondal, Argha; Antonopoulos, Chris G.; Mishra, Arindam In this article, we model and study the spread of COVID-19 in Germany, Japan, India and highly impacted states in India, i.e., in Delhi, Maharashtra, West Bengal, Kerala and Karnataka. We consider recorded data published in Worldometers and COVID-19 India websites from April 2020 to July 2021, including periods of interest where these countries and states were hit severely by the pandemic. Our methodology is based on the classic susceptible-infected-removed (SIR) model and can track the evolution of infections in communities, i.e., in countries, states or groups of individuals, where we (a) allow for the susceptible and infected populations to be reset at times where surges, outbreaks or secondary waves appear in the recorded data sets, (b) consider the parameters in the SIR model that represent the effective transmission and recovery rates to be functions of time and (c) estimate the number of deaths by combining the model solutions with the recorded data sets to approximate them between consecutive surges, outbreaks or secondary waves, providing a more accurate estimate. We report on the status of the current infections in these countries and states, and the infections and deaths in India and Japan. Our model can adapt to the recorded data and can be used to explain them and importantly, to forecast the number of infected, recovered, removed and dead individuals, as well as it can estimate the effective infection and recovery rates as functions of time, assuming an outbreak occurs at a given time. The latter information can be used to forecast the future basic reproduction number and together with the forecast on the number of infected and dead individuals, our approach can further be used to suggest the implementation of intervention strategies and mitigation policies to keep at bay the number of infected and dead individuals. This, in conjunction with the implementation of vaccination programs worldwide, can help reduce significantly the impact of the spread around the world and improve the wellbeing of people. 2022-01-01T00:00:00Z https://hdl.handle.net/2123/27375 Country interaction matrix for consumption footprints Irwin, Amanda This matrix provides information on the flow of extinction-risk footprint from each country’s consumption footprint (in the columns) to each other country’s territorial footprint (in the rows), expressed as a percentage of each consumption country’s total consumption footprint. Countries are depicted using their 3-digit ISO code. 2022-01-28T00:00:00Z https://hdl.handle.net/2123/27374 Country interaction matrix for territorial footprints Irwin, Amanda This matrix provides information on the flow of extinction-risk footprint from each country’s territorial footprint (in the rows) to each other country’s consumption footprint (in the columns), expressed as a percentage of each source country’s total territorial footprint. Countries are depicted using their 3-digit ISO code. 2022-01-28T00:00:00Z https://hdl.handle.net/2123/27373 Country specific extinction-risk footprint details Irwin, Amanda This dataset provides detailed information on the extinction-risk footprints for each country, to support the research presented in "Quantifying and categorizing national extinction-risk footprints" 2022-01-28T00:00:00Z https://hdl.handle.net/2123/27289 Thermally Drawn Polycaprolactone Fibres with Customised Cross Sections Farajikhah, Syamak; Rukhlenko, Ivan; Stefani, Alessio; Large, Maryanne; Chrzanowskic, Wojciech; Fleming, Simon There is growing demand for biodegradable polymer fibres in tissue engineering and nerve regeneration. We demonstrate a scalable and inexpensive fabrication technique to produce polycaproactone (PCL) fibres using fibredrawing technique. Here we report on the first successful drawing of hollow-core and solid-core PCL fibres of different cross sections. The demonstrated capacity to tailor the surface morphology of PCL fibres, together with their biodegradability and tissue compatibility, makes them a unique material base for tissue engineering and nerve regeneration applications. 2019-01-01T00:00:00Z https://hdl.handle.net/2123/27285 Measurement of weak low frequency pressure signal using stretchable polyurethane fiber sensor for application in wearables Kaysir, Rejvi; Stefani, Alessio; Lwin, Richard; Fleming, Simon The practical realization of low Young’s modulus Polyurethane (PU) based optical fibers offers new possibilities for sensing on bodies due to its bio-compatibility and high material sensitivity. Here, we experimentally demonstrate a PU fiber pressure sensor using the simplest possible structure (i.e. a capillary) to measure a weak low frequency signal comparable to respiration/heart rate. We characterized the fiber and measured the sensitivity of a PU capillary using a speaker connected to a function generator. The frequency of the modulated signal was recovered using Fourier Transform (FT). This bodes well for applying more sophisticated structures to wearable devices. 2017-01-01T00:00:00Z https://hdl.handle.net/2123/27284 Multimaterial and Flexible Devices Made by Fiber Drawing Stefani, Alessio; Kuhlmey, Boris; Large, Maryanne; Hayashi, Juliano; Farajikhah, Syamak; Rukhlenko, Ivan; Runge, Antione; Fleming, Simon The ability to co-process different materials at the same time in a thermal process opens up the possibility of scalable fabrication of volumetric multimaterial and multifunctional devices with operation spanning from the UV to the microwave. Combining optical, mechanical and electronic properties of dielectrics (such as glass and polymers) and metals enables a plethora of applications in radiation manipulation. In this presentation I will discuss the process and the challenges of fiber drawing novel materials and material combinations such as: elastic polymers, biocompatible polymers, arsenic free soft-glasses and combinations of metal-dielectric structures. After discussing the process behind the realization of the novel fibers, I will show some very diverse uses of these exotic materials. I will report on our latest results on flexible fibers in generation of orbital angular momentum, realization of tunable metamaterials and wearable sensors, and I will present some applications of fiber drawn metamaterials for THz radiation. 2020-01-01T00:00:00Z https://hdl.handle.net/2123/27281 OAM generation, tunable metamaterials and sensors with highly deformable fibers Stefani, Alessio; Lwin, Richard; Kuhlmey, Boris; Fleming, Simon A flexible fiber-drawn material, i.e. polyurethane, allows for novel applications from THz to the visible. We exploit its elastic properties to generate orbital angular momentum modes, to make pressure sensors and to realize tunable metamaterials. 2018-01-01T00:00:00Z https://hdl.handle.net/2123/27280 Wearable polyurethane optical fiber based sensor for breathing monitoring Runge, Antoine; Stefani, Alessio; Lwin, Richard; Fleming, Simon We experimentally demonstrate a wearable breathing monitoring sensor based on a polyurethane (PU) optical fiber. The mechanical flexibility of the PU fiber allows for the simple measurement of inhalation and exhalation motions through optical transmission variations of the fiber induced by bending and stretching. 2018-01-01T00:00:00Z https://hdl.handle.net/2123/27278 Pulse wave velocity measurement with soft-polymer optical fibers for wearable continuous blood pressure monitoring Stefani, Alessio; Rukhlenko, Ivan; Ward, Rebecca; Prinable, Joseph; Large, Maryanne; Fleming, Simon Soft-polymer fibers allow strong conformal contact with the skin and are extremely sensitive for deformation, despite high propagation loss. This enables pulse wave velocities measurements. Blood pressure can then be inferred using the Moens-Kortweg model. 2020-01-01T00:00:00Z https://hdl.handle.net/2123/27277 Tunable Metamaterials Fabricated by Fiber Drawing Fleming, Simon; Stefani, Alessio; Tang, Xiaoli; Argyros, Alexander; Kemsley, Daniel; Cordi, James; Lwin, Richard We demonstrate a practical scalable approach to the fabrication of tunable metamaterials. Designed for terahertz (THz) wavelengths, the metamaterial is comprised of polyurethane filled with an array of indium wires using the well-established fiber drawing technique. Modification of the dimensions of the metamaterial provides tunability; by compressing the metamaterial we demonstrated a 50% plasma frequency shift using THz time-domain spectroscopy. Releasing the compression allowed the metamaterial to return to its original dimensions and plasma frequency, demonstrating dynamic reversible tunability. 2017-01-01T00:00:00Z https://hdl.handle.net/2123/27271 Thermally Drawn Biodegradable Fibers with Tailored Topography for Biomedical Applications Farajikhah, Syamak; Runge, Antoine; Boumelhem, Badwi; Rukhlenko, Ivan; Stefani, Alessio; Sepidar, Sayyar; Innis, Peter; Fraser, Stuart; Fleming, Simon; Large, Maryanne There is a growing demand for polymer fiber scaffolds for biomedical applications and tissue engineering. Biodegradable polymers such as polycaprolactone have attracted particular attention due to their applicability to tissue engineering and optical neural interfacing. Here we report on a scalable and inexpensive fiber fabrication technique, which enables the drawing of PCL fibers in a single process without the use of auxiliary cladding. We demonstrate the possibility of drawing PCL fibers of different geometries and cross-sections, including solid-core, hollow-core, and grooved fibers. The solid-core fibers of different geometries are shown to support cell growth, through successful MCF-7 breast cancer cell attachment and proliferation. We also show that the hollow-core fibers exhibit a relatively stable optical propagation loss after submersion into a biological fluid for up to 21 days with potential to be used as waveguides in optical neural interfacing. The capacity to tailor the surface morphology of biodegradable PCL fibers and their non-cytotoxicity make the proposed approach an attractive platform for biomedical applications and tissue engineering. 2020-01-01T00:00:00Z https://hdl.handle.net/2123/27265 Highly deformable optical fibers made of polyurethane: OAM generation, tunable metamaterials and sensors Stefani, Alessio; Lwin, Richard; Fleming, Simon Polyurethane has a Young’s modulus three orders of magnitude lower than silica and can be stretched up to 600%. We report the fabrication of polyurethane optical fibers for applications from THz to the visible. We exploit its elastic properties to generate orbital angular momentum modes, to make pressure sensors and to realize tunable metamaterials by co-drawing polyurethane with poly(methyl methacrylate) and indium. 2017-01-01T00:00:00Z https://hdl.handle.net/2123/27261 Orbital angular momentum modes by twisting of a hollow core antiresonant fiber Stefani, Alessio; Kuhlmey, Boris; Fleming, Simon Generation and use of orbital angular momentum (OAM) of light is finding more and more interest in a wide variety of fields of photonics: communications, optical trapping, quantum optics, and many more [1]. In the investigation of such behavior, twisting of photonic crystal fibers shows interesting physical phenomena [2]. We previously reported the ability to create helical hollow fibers by mechanically twisting a tube lattice fiber made of polyurethane, the twist of which can be adjusted and reversed [3]. In this work we report how such deformation induces a mode transformation to an OAM mode, allowing a simple and tunable way to generate OAM modes. We take advantage of THz time domain spectroscopy to obtain information on both intensity and field components, and to be able to investigate how they change both in time and with frequency. The fiber here reported is 10 cm long, has a core diameter of 3 mm, it is twisted with twist rates between 0 and 62 rad/m and it is designed for frequencies 0.2 to 1.5 THz. A microscope image of the fiber is shown as inset of Fig. 1(a). The transmission spectrum of the fiber when straight and twisted was measured and is shown in Fig. 1(a). Above and below, the measured near-field images of the untwisted and twisted fiber output, respectively, are plotted for some selected frequencies in the different transmission bands. The twisted fiber in the transmission band centered at 750 GHz has a mode with a central minimum. The effect of twist on this fiber’s modes is investigated by finite-element (COMSOL) simulations by using a helical coordinate transformation [2] (Fig. 1(b)). A small amount of twist is not sufficient to perturb the guided mode. However, when sufficient twist is applied, the mode shows a singularity at its center. Increasing the twist further compromises guidance and the mode leaks into the cladding. Comparison between measurements and simulations for both mode intensity and x component of the electric field (Fig. 1(c)) confirms agreement between the two. Moreover, from the electric field it is possible to infer that the mode observed is radially polarized as the measured x-component of the output mode has a zero of electric field occurring along y. To ensure this mode possesses orbital angular momentum (which is expected because of the helicity of the fiber), the temporal evolution of the mode is examined: as the input is not a continuous wave, but a pulse, an OAM mode will have a temporal spiraling evolution. Snapshots of the temporal evolution of the mode are shown is Fig. 1(d). The mode starts from the lower-right corner and spirals to the top-left confirming the mode carries an orbital angular momentum. 2017-01-01T00:00:00Z https://hdl.handle.net/2123/27259 Flexible optical fiber sensor based on polyurethane Kaysir, Rejvi; Stefani, Alessio; Lwin, Richard; Fleming, Simon Polyurethane (PU) based hollow core fibers are investigated as optical sensors. The flexibility of PU fibers makes it suitable for sensing mechanical perturbations. We fabricated a PU fiber using the fiber drawing method, characterized the fiber and experimentally demonstrated a simple way to measure deformation, in the form of applied pressure. 2017-01-01T00:00:00Z https://hdl.handle.net/2123/27258 Deformable wire array: fiber drawn tunable metamaterials Fleming, Simon; Stefani, Alessio; Tang, Xiaoli; Argyros, Alexander; Kemsley, Daniel; Cordi, James; Lwin, Richard By fiber drawing we fabricate a wire array metamaterial, the structure of which can be actively modified. The plasma frequency can be tuned by 50% by compressing the metamaterial; recovers when released and the process can be repeated. 2017-01-01T00:00:00Z https://hdl.handle.net/2123/27070 Predicting the unpredictable: how dynamic COVID-19 policies and restrictions challenge model forecasts Houdroge, Farah; Palmer, Anna; Delport, Dominic; Walsh, Tom; Kelly, Sherrie L; Hainsworth, Samuel W; Abeysuriya, Romesh; Stuart, Robyn M; Kerr, Cliff C; Coplan, Paul; Wilson, David P; Scott, Nick Abstract Introduction To retrospectively assess the accuracy of a mathematical modelling study that projected the rate of COVID-19 diagnoses for 72 locations worldwide in 2021, and to identify predictors of model accuracy. Methods Between June and August 2020, an agent-based model was used to project rates of COVID-19 infection incidence and cases diagnosed as positive from 15 September to 31 October 2020 for 72 geographic settings. Five scenarios were modelled: a baseline scenario where no future changes were made to existing restrictions, and four scenarios representing small or moderate changes in restrictions at two intervals. Post hoc, upper and lower bounds for number of diagnosed Covid-19 cases were compared with actual data collected during the prediction window. A regression analysis with 17 covariates was performed to determine correlates of accurate projections. Results The actual data fell within the lower and upper bounds in 27 settings and out of bounds in 45 settings. The only statistically significant predictor of actual data within the predicted bounds was correct assumptions about future policy changes (OR = 15.04; 95%CI 2.20-208.70; p=0.016). Conclusions For this study, the accuracy of COVID-19 model projections was dependent on whether assumptions about future policies are correct. Frequent changes in restrictions implemented by governments, which the modelling team was not always able to predict, in part explains why the majority of model projections were inaccurate compared with actual outcomes and supports revision of projections when policies are changed as well as the importance of policy experts collaborating on modelling projects. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/26569 Linking the Galactic and Extragalactic -- A Virtual Meeting During a World-Wide Pandemic van de Sande, Jesse; Scott, Nicholas How do we bridge the gap between the Galactic and the extragalactic? By focusing on the topic of stellar dynamics and stellar populations of the Milky Way and its siblings this virtual meeting aimed at connecting both fields that each bring unique perspectives to understanding how disk galaxies form and evolve. As this meeting took place during a global pandemic, we also give our perspective on the challenges and best practises for running a virtual meeting. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/26254 Australian IOPC sectors to IUCN Threat Classification concordance Irwin, Amanda This concordance was used to connect IUCN Red List threat data to economic sectors in Australia, classified according to the Australian Bureau of Statistics' Product Classification 2021-09-27T00:00:00Z https://hdl.handle.net/2123/26105 Evolving ribonucleocapsid assembly/packaging signals in the genomes of the human and animal coronaviruses: targeting, transmission and evolution. Chechetkin, Vladimir R; Lobzin, Vasily V A world-wide COVID-19 pandemic intensified strongly the studies of molecular mechanisms related to the coronaviruses. The origin of coronaviruses and the risks of human-to-human, animal-to-human and human-to-animal transmission of coronaviral infections can be understood only on a broader evolutionary level by detailed comparative studies. In this paper, we studied ribonucleocapsid assembly-packaging signals (RNAPS) in the genomes of all seven known pathogenic human coronaviruses, SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-OC43, HCoV-HKU1, HCoV-229E and HCoV-NL63 and compared them with RNAPS in the genomes of the related animal coronaviruses including SARS-Bat-CoV, MERS-Camel-CoV, MHV, Bat-CoV MOP1, TGEV and one of camel alphacoronaviruses. RNAPS in the genomes of coronaviruses were evolved due to weakly specific interactions between genomic RNA and N proteins in helical nucleocapsids. Combining transitional genome mapping and Jaccard correlation coefficients allows us to perform the analysis directly in terms of underlying motifs distributed over the genome. In all coronaviruses, RNAPS were distributed quasi-periodically over the genome with the period about 54_nt biased to 57_nt and to 51_nt for the genomes longer and shorter than that of SARS-CoV, respectively. The comparison with the experimentally verified packaging signals for MERS-CoV, MHV and TGEV proved that the distribution of particular motifs is strongly correlated with the packaging signals. We also found that many motifs were highly conserved in both characters and positioning on the genomes throughout the lineages that make them promising therapeutic targets. The mechanisms of encapsidation can affect the recombination and co-infection as well.Communicated by Ramaswamy H. Sarma. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/25626 Professional practice changes in radiotherapy physics during the COVID-19 pandemic Bertholet, Jenny; Aznar, Marianne C.; Garibaldi, Cristina; Thwaites, David; Gershkevitsh, Eduard; Thorwarth, Daniela; Verellen, Dirk; Heijmen, Ben; Hurkmans, Coen; Muren, Ludvig; Redalen, Kathrine Røe; Siebert, Frank-André; Schwarz, Marco; Van Elmpt, Wouter; Georg, Dietmar; Jornet, Nuria; Clark, Catharine H. Background and purpose The COVID-19 pandemic has imposed changes in radiotherapy (RT) departments worldwide. Medical physicists (MPs) are key healthcare professionals in maintaining safe and effective RT. This study reports on MPs experience during the first pandemic peak and explores the consequences on their work. Methods A 39-question survey on changes in departmental and clinical practice and on the impact for the future was sent to the global MP community. A total of 433 responses were analysed by professional role and by country clustered on the daily infection numbers. Results The impact of COVID-19 was bigger in countries with high daily infection rate. The majority of MPs worked in alternation at home/on-site. Among practice changes, implementation and/or increased use of hypofractionation was the most common (47% of the respondents). Sixteen percent of respondents modified patient-specific quality assurance (QA), 21% reduced machine QA, and 25% moved machine QA to weekends/evenings. The perception of trust in leadership and team unity was reversed between management MPs (towards increased trust and unity) and clinical MPs (towards a decrease). Changes such as home-working and increased use of hypofractionation were welcomed. However, some MPs were concerned about pressure to keep negative changes (e.g. weekend work). Conclusion COVID-19 affected MPs through changes in practice and QA procedures but also in terms of trust in leadership and team unity. Some changes were welcomed but others caused worries for the future. This report forms the basis, from a medical physics perspective, to evaluate long-lasting changes within a multi-disciplinary setting. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/25365 Radiation oncology in the new virtual and digital era Aznar, M.C.; Bacchus, C.; Coppes, R.P.; Deutsch, E.; Georg, D.; Haustermans, K.; Hoskin, P.; Krause, M.; Lartigau, E.F.; L�ck, S.; Offersen, B.; Overgaard, J.; Thwaites, D.I.; van der Kogel, A.J.; van der Heide, U.A.; Valentini, V.; Baumann, M. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/25246 Mathematical modeling as a tool for policy decision making: Applications to the COVID-19 pandemic Panovska-Griffiths, J.; Kerr, C.C.; Waites, W.; Stuart, R.M. The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of mathematical modeling in advising scientific bodies and informing public policy making. Modeling allows a flexible theoretical framework to be developed in which different scenarios around spread of diseases and strategies to prevent it can be explored. This work brings together perspectives on mathematical modeling of infectious diseases, highlights the different modeling frameworks that have been used for modeling COVID-19 and illustrates some of the models that our groups have developed and applied specifically for COVID-19. We discuss three models for COVID-19 spread: the modified Susceptible-Exposed-Infected-Recovered model that incorporates contact tracing (SEIR-TTI model) and describes the spread of COVID-19 among these population cohorts, the more detailed agent-based model called Covasim describing transmission between individuals, and the Rule-Based Model (RBM) which can be thought of as a combination of both. We showcase the key methodologies of these approaches, their differences as well as the ways in which they are interlinked. We illustrate their applicability to answer pertinent questions associated with the COVID-19 pandemic such as quantifying and forecasting the impacts of different test-trace-isolate (TTI) strategies. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/25241 Predicting COVID-19 mortality with electronic medical records Estiri, Hossein; Strasser, Zachary H.; Klann, Jeffy G.; Naseri, Pourandokht; Wagholikar, Kavishwar B.; Murphy, Shawn N. This study aims to predict death after COVID-19 using only the past medical information routinely collected in electronic health records (EHRs) and to understand the differences in risk factors across age groups. Combining computational methods and clinical expertise, we curated clusters that represent 46 clinical conditions as potential risk factors for death after a COVID-19 infection. We trained age-stratified generalized linear models (GLMs) with component-wise gradient boosting to predict the probability of death based on what we know from the patients before they contracted the virus. Despite only relying on previously documented demographics and comorbidities, our models demonstrated similar performance to other prognostic models that require an assortment of symptoms, laboratory values, and images at the time of diagnosis or during the course of the illness. In general, we found age as the most important predictor of mortality in COVID-19 patients. A history of pneumonia, which is rarely asked in typical epidemiology studies, was one of the most important risk factors for predicting COVID-19 mortality. A history of diabetes with complications and cancer (breast and prostate) were notable risk factors for patients between the ages of 45 and 65 years. In patients aged 65–85 years, diseases that affect the pulmonary system, including interstitial lung disease, chronic obstructive pulmonary disease, lung cancer, and a smoking history, were important for predicting mortality. The ability to compute precise individual-level risk scores exclusively based on the EHR is crucial for effectively allocating and distributing resources, such as prioritizing vaccination among the general population. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/25237 Modelling the impact of reopening schools in early 2021 in the presence of the new SARS-CoV-2 variant and with roll-out of vaccination against COVID-19 Panovska-Griffiths, J.; Stuart, R.M.; Kerr, C.C.; Rosenfield, K.; Mistry, D.; Waites, W.; Klein, D.J.; Bonell, C.; Viner, R.M. Background Following the resurgence of the COVID-19 epidemic in the UK in late 2020 and the emergence of the new variant of the SARS-CoV-2 virus, B.1.1.7, a third national lockdown was imposed from January 5, 2021. Following the decline of COVID-19 cases over the remainder of January 2021, it is important to assess the conditions under which reopening schools from early March is likely to lead to resurgence of the epidemic. This study models the impact of a partial national lockdown with social distancing measures enacted in communities and workplaces under different strategies of reopening schools from March 8, 2021 and compares it to the impact of continual full national lockdown remaining until April 19, 2021. Methods We used our previously published model, Covasim, to model the emergence of B.1.1.7 over September 1, 2020 to January 31, 2021. We extended the model to incorporate the impacts of the roll-out of a two-dose vaccine against COVID-19, assuming 200,000 daily doses of the vaccine in people 75 years or older with vaccination that offers 95% reduction in disease acquisition and 10% reduction of transmission blocking. We used the model, calibrated until January 25, 2021, to simulate the impact of a full national lockdown (FNL) with schools closed until April 19, 2021 versus four different partial national lockdown (PNL) scenarios with different elements of schooling open: 1) staggered PNL with primary schools and exam-entry years (years 11 and 13) returning on March 8, 2021 and the rest of the schools years on March 15, 2020; 2) full-return PNL with both primary and secondary schools returning on March 8, 2021; 3) primary-only PNL with primary schools and exam critical years (Y11 and Y13) going back only on March 8, 2021 with the rest of the secondary schools back on April 19, 2021 and 4) part-Rota PNL with both primary and secondary schools returning on March 8, 2021 with primary schools remaining open continuously but secondary schools on a two-weekly rota-system with years alternating between a fortnight of face-to-face and remote learning until April 19, 2021. Across all scenarios, we projected the number of new daily cases, cumulative deaths and effective reproduction number R until April 30, 2020. Results Our calibration across different scenarios is consistent with the new variant B.1.1.7 being around 60% more transmissible. Strict social distancing measures, i.e. national lockdowns, are required to contain the spread of the virus and control the hospitalisations and deaths during January and February 2021. The national lockdown will reduce the number of cases by early March levels similar to those seen in October with R also falling and remaining below 1 during the lockdown. Infections start to increase when schools open but if other parts of society remain closed this resurgence is not sufficient to bring R above 1. Reopening primary schools and exam critical years only or having primary schools open continuously with secondary schools on rotas will lead to lower increases in cases and R than if all schools open. Under the current vaccination assumptions and across the set of scenarios considered, R would increase above 1 if society reopens simultaneously, simulated here from April 19, 2021. Findings Our findings suggest that stringent measures are necessary to mitigate the increase in cases and bring R below 1 over January and February 2021. It is plausible that a PNL with schools partially open from March 8, 2021 and the rest of the society remaining closed until April 19, 2021 may keep R below 1, with some increase evident in infections compared to continual FNL until April 19, 2021. Reopening society in mid-April, with the vaccination strategy we model, could push R above 1 and induce a surge in infections, but the effect of vaccination may be able to control this in future depending on the transmission blocking properties of the vaccines. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/25164 Estimating and mitigating the risk of COVID-19 epidemic rebound associated with reopening of international borders in Vietnam: a modelling study Pham, Quang D; Stuart, Robyn M; Nguyen, Thuong V; Luong, Quang C; Tran, Quang D; Pham, Thai Q; Phan, Lan T; Dang, Tan Q; Tran, Duong N; Do, Hung T; Mistry, Dina; Klein, Daniel J; Abeysuriya, Romesh G; Oron, Assaf P; Kerr, Cliff C BACKGROUND: Vietnam has emerged as one of the world's leading success stories in responding to COVID-19. After a prolonged period of little to no transmission, there was an outbreak of unknown source in July, 2020, in the Da Nang region, but the outbreak was quickly suppressed. We aimed to use epidemiological, behavioural, demographic, and policy data from the COVID-19 outbreak in Da Nang to calibrate an agent-based model of COVID-19 transmission for Vietnam, and to estimate the risk of future outbreaks associated with reopening of international borders in the country. METHODS: For this modelling study, we used comprehensive data from June 15 to Oct 15, 2020, on testing, COVID-19 cases, and quarantine breaches within an agent-based model of SARS-CoV-2 transmission to model a COVID-19 outbreak in Da Nang in July, 2020. We applied this model to quantify the risk of future outbreaks in Vietnam in the 3 months after the reopening of international borders, under different behavioural scenarios, policy responses (ie, closure of workplaces and schools), and ongoing testing. FINDINGS: We estimated that the outbreak in Da Nang between July and August, 2020, resulted in substantial community transmission, and that higher levels of symptomatic testing could have mitigated this transmission. We estimated that the outbreak peaked on Aug 2, 2020, with an estimated 1060 active infections (95% projection interval 890-1280). If the population of Vietnam remains highly compliant with mask-wearing policies, our projections indicate that the epidemic would remain under control even if a small but steady flow of imported infections escaped quarantine into the community. However, if complacency increases and testing rates are relatively low (10% of symptomatic individuals are tested), the epidemic could rebound again, resulting in an estimated 2100 infections (95% projected interval 1050-3610) in 3 months. These outcomes could be mitigated if the behaviour of the general population responds dynamically to increases in locally acquired cases that exceed specific thresholds, but only if testing of symptomatic individuals is also increased. INTERPRETATION: The successful response to COVID-19 in Vietnam could be improved even further with higher levels of symptomatic testing. If the previous approaches are used in response to new COVID-19 outbreaks, epidemic control is possible even in the presence of low levels of imported cases. FUNDING: Ministry of Science and Technology (Vietnam). TRANSLATION: For the Vietnamese translation of the abstract see Supplementary Materials section. 2021-01-01T00:00:00Z https://hdl.handle.net/2123/25147 Role of masks, testing and contact tracing in preventing COVID-19 resurgences: a case study from New South Wales, Australia Stuart, Robyn M; Abeysuriya, Romesh G; Kerr, Cliff C; Mistry, Dina; Klein, Dan J; Gray, Richard T; Hellard, Margaret; Scott, Nick OBJECTIVES: The early stages of the COVID-19 pandemic illustrated that SARS-CoV-2, the virus that causes the disease, has the potential to spread exponentially. Therefore, as long as a substantial proportion of the population remains susceptible to infection, the potential for new epidemic waves persists even in settings with low numbers of active COVID-19 infections, unless sufficient countermeasures are in place. We aim to quantify vulnerability to resurgences in COVID-19 transmission under variations in the levels of testing, tracing and mask usage. SETTING: The Australian state of New South Wales (NSW), a setting with prolonged low transmission, high mobility, non-universal mask usage and a well-functioning test-and-trace system. PARTICIPANTS: None (simulation study). RESULTS: We find that the relative impact of masks is greatest when testing and tracing rates are lower and vice versa. Scenarios with very high testing rates (90% of people with symptoms, plus 90% of people with a known history of contact with a confirmed case) were estimated to lead to a robustly controlled epidemic. However, across comparable levels of mask uptake and contact tracing, the number of infections over this period was projected to be 2-3 times higher if the testing rate was 80% instead of 90%, 8-12 times higher if the testing rate was 65% or 30-50 times higher with a 50% testing rate. In reality, NSW diagnosed 254 locally acquired cases over this period, an outcome that had a moderate probability in the model (10%-18%) assuming low mask uptake (0%-25%), even in the presence of extremely high testing (90%) and near-perfect community contact tracing (75%-100%), and a considerably higher probability if testing or tracing were at lower levels. CONCLUSIONS: Our work suggests that testing, tracing and masks can all be effective means of controlling transmission. A multifaceted strategy that combines all three, alongside continued hygiene and distancing protocols, is likely to be the most robust means of controlling transmission of SARS-CoV-2. 2021-01-01T00:00:00Z