ORCID Profile
0000-0002-9918-8167
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Stochastic Analysis and Modelling | Statistics | Epidemiology | Invasive Species Ecology | Wildlife and Habitat Management | Epidemiology | Genetics | Global Change Biology | Stochastic Analysis And Modelling | Developmental Genetics (incl. Sex Determination) | Biological Mathematics | Biostatistics | Other Biological Sciences | Conservation and Biodiversity | Conservation And Biodiversity |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Mathematical Sciences | Border Biosecurity (incl. Quarantine and Inspection) | Control of Animal Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments | Ecosystem Assessment and Management at Regional or Larger Scales | Biological sciences | Expanding Knowledge in the Medical and Health Sciences | Mathematical sciences | Pre-Border Biosecurity | Zoonoses | Expanding Knowledge in the Environmental Sciences | Disease distribution and transmission | Flora, Fauna and Biodiversity at Regional or Larger Scales | Disease Distribution and Transmission (incl. Surveillance and Response) | Infectious Diseases | Health Protection and/or Disaster Response
Related Links
Publications
Inference of epidemiological parameters from household stratified data
Publisher: Public Library of Science (PLoS)
Date: 18-10-2017
Dataset of seized wildlife and their intended uses
Publisher: Elsevier BV
Date: 12-2021
On the efficient determination of optimal Bayesian experimental designs using ABC: A case study in optimal observation of epidemics
Publisher: Elsevier BV
Date: 05-2016
A Y-chromosome shredding gene drive for controlling pest vertebrate populations
Publisher: eLife Sciences Publications, Ltd
Date: 15-02-2019
DOI: 10.7554/ELIFE.41873
Abstract: Self-replicating gene drives that modify sex ratios or infer a fitness cost could be used to control populations of invasive alien species. The targeted deletion of Y sex chromosomes using CRISPR technology offers a new approach for sex bias that could be incorporated within gene-drive designs. We introduce a novel gene-drive strategy termed Y-CHromosome deletion using Orthogonal Programmable Endonucleases (Y-CHOPE), incorporating a programmable endonuclease that ‘shreds’ the Y chromosome, thereby converting XY males into fertile XO females. Firstly, we demonstrate that the CRISPR/Cas12a system can eliminate the Y chromosome in embryonic stem cells with high efficiency (c. 90%). Next, using stochastic, in idual-based models of a pest mouse population, we show that a Y-shredding drive that progressively depletes the pool of XY males could effect population eradication through mate limitation. Our molecular and modeling data suggest that a Y-CHOPE gene drive could be a viable tool for vertebrate pest control.
Correction to ‘Dodging silver bullets: good CRISPR gene-drive design is critical for eradicating exotic vertebrates’
Publisher: The Royal Society
Date: 10-10-2018
Predicting the Risk of Biological Invasions Using Environmental Similarity and Transport Network Connectedness
Publisher: Wiley
Date: 10-08-2019
DOI: 10.1111/RISA.12870
Abstract: Understanding the risk of biological invasions associated with particular transport pathways and source regions is critical for implementing effective biosecurity management. This may require both a model for physical connectedness between regions, and a measure of environmental similarity, so as to quantify the potential for a species to be transported from a given region and to survive at a destination region. We present an analysis of integrated biosecurity risk into Australia, based on flights and shipping data from each global geopolitical region, and an adaptation of the "range bagging" method to determine environmental matching between regions. Here, we describe global patterns of environmental matching and highlight those regions with many physical connections. We classify patterns of global invasion risk (high to low) into Australian states and territories. We validate our analysis by comparison with global presence data for 844 phytophagous insect pest species, and produce a list of high-risk species not previously known to be present in Australia. We determined that, of the insect pest species used for validation, the species most likely to be present in Australia were those also present in geopolitical regions with high transport connectivity to Australia, and those regions that were geographically close, and had similar environments.
Characterising seasonal influenza epidemiology using primary care surveillance data
Publisher: Public Library of Science (PLoS)
Date: 16-08-2018
A comparison of models for predicting population persistence
Publisher: Elsevier BV
Date: 02-2007
Probing the Diameter Limit of Single Walled Carbon Nanotubes in SWCNT: Fullerene Solar Cells
Publisher: Wiley
Date: 02-08-2016
Interpreting scratch assays using pair density dynamics and approximate Bayesian computation
Publisher: The Royal Society
Date: 09-2014
DOI: 10.1098/RSOB.140097
Abstract: Quantifying the impact of biochemical compounds on collective cell spreading is an essential element of drug design, with various applications including developing treatments for chronic wounds and cancer. Scratch assays are a technically simple and inexpensive method used to study collective cell spreading however, most previous interpretations of scratch assays are qualitative and do not provide estimates of the cell diffusivity, D , or the cell proliferation rate, λ . Estimating D and λ is important for investigating the efficacy of a potential treatment and provides insight into the mechanism through which the potential treatment acts. While a few methods for estimating D and λ have been proposed, these previous methods lead to point estimates of D and λ , and provide no insight into the uncertainty in these estimates. Here, we compare various types of information that can be extracted from images of a scratch assay, and quantify D and λ using discrete computational simulations and approximate Bayesian computation. We show that it is possible to robustly recover estimates of D and λ from synthetic data, as well as a new set of experimental data. For the first time, our approach also provides a method to estimate the uncertainty in our estimates of D and λ . We anticipate that our approach can be generalized to deal with more realistic experimental scenarios in which we are interested in estimating D and λ , as well as additional relevant parameters such as the strength of cell-to-cell adhesion or the strength of cell-to-substrate adhesion.
Estimating the basic reproductive number during the early stages of an emerging epidemic
Publisher: Elsevier BV
Date: 02-2018
DOI: 10.1016/J.TPB.2017.10.004
Abstract: A novel outbreak will generally not be detected until such a time that it has become established. When such an outbreak is detected, public health officials must determine the potential of the outbreak, for which the basic reproductive numberR
The dark web trades wildlife, but mostly for use as drugs
Publisher: Wiley
Date: 03-05-2023
DOI: 10.1002/PAN3.10469
Abstract: Contemporary wildlife trade is massively facilitated by the Internet. By design, the dark web is one layer of the Internet that is difficult to monitor and continues to lack thorough investigation. Here, we accessed a comprehensive database of dark web marketplaces to search across c . 2 million dark web advertisements over 5 years using c . 7 k wildlife trade‐related search terms. We found 153 species traded in 3332 advertisements ( c . 600 advertisements per year). We characterized a highly specialized wildlife trade market, where c . 90% of dark‐web wildlife advertisements were for recreational drugs. We verified that 68 species contained chemicals with drug properties. Species advertised as drugs mostly comprised of plant species, however, fungi and animals were also traded as drugs. Most species with drug properties were psychedelics (45 species), including one genera of fungi, Psilocybe , with 19 species traded on the dark web. The native distribution of plants with drug properties were clustered in Central and South America. A smaller proportion of trade was for purported medicinal properties of wildlife, clothing, decoration, and as pets. Synthesis and applications . Our results greatly expand on what wildlife species are currently traded on the dark web and provide a baseline to track future changes. Given the low number of advertisements, we assume current conservation and biosecurity risks of the dark web are low. While wildlife trade is r ant on other layers of the Internet, particularly on e‐commerce and social media sites, trade on the dark web may still increase if these popular platforms are rendered less accessible to traders (e.g., via an increase in enforcement). We recommend focussing on surveillance of e‐commerce and social media sites, but we encourage continued monitoring of the dark web periodically to evaluate potential shifts in wildlife trade across this more occluded layer of the Internet. Read the free Plain Language Summary for this article on the Journal blog.
Identification of the relative timing of infectiousness and symptom onset for outbreak control
Publisher: Elsevier BV
Date: 02-2020
An induced natural selection heuristic for finding optimal Bayesian experimental designs
Publisher: Elsevier BV
Date: 10-2018
The Impact of Antimalarial Use on the Emergence and Transmission of Plasmodium falciparum Resistance: A Scoping Review of Mathematical Models
Publisher: MDPI AG
Date: 15-10-2017
Low detectability of alien reptiles can lead to biosecurity management failure: a case study from Christmas Island (Australia)
Publisher: Pensoft Publishers
Date: 07-05-2019
DOI: 10.3897/NEOBIOTA.45.31009
Abstract: When we assume that contemporary management actions will be effective against the global rise of emerging alien species, we can develop management complacency, which leads to potentially disastrous outcomes for native bio ersity. Here, we propose the use of the probability of detection as a metric to assess the feasibility of management actions for alien species. We explore how detectability can influence the management of alien reptiles, a group of emergent alien vertebrates globally. We use a Rapid Biological Assessment method (time-limited transects) to estimate the probability of detection for alien reptiles present on Christmas Island (Australia). Across the five species studied, we found low probabilities of detection and poor explanatory capacity of the in idual covariates included in our models. These findings indicate that management options to deal with alien reptiles are limited due to the potential high cost and low efficacy associated with low probabilities of detection. Strict preventive strategies, firmly espousing the principles of adaptiveness and precautionary policies, combined with early detection and biosecurity response activities are needed to address the emergence of alien reptiles. Our research was focussed on alien reptiles on islands, but the rise of new pools of alien species from all taxonomic realms across the world suggests that our conclusions may be applicable more generally. Further research is called for to explore the applicability of our conclusions and recommendations to other taxonomic groups and regions of the world.
Bayesian model discrimination for partially-observed epidemic models
Publisher: Elsevier BV
Date: 11-2019
DOI: 10.1016/J.MBS.2019.108266
Abstract: An efficient method for Bayesian model selection is presented for a broad class of continuous-time Markov chain models and is subsequently applied to two important problems in epidemiology. The first problem is to identify the shape of the infectious period distribution the second problem is to determine whether in iduals display symptoms before, at the same time, or after they become infectious. In both cases we show that the correct model can be identified, in the majority of cases, from symptom onset data generated from multiple outbreaks in small populations. The method works by evaluating the likelihood using a particle filter that incorporates a novel importance s ling algorithm designed for partially-observed continuous-time Markov chains. This is combined with another importance s ling method to unbiasedly estimate the model evidence. These come with estimates of precision, which allow for stopping criterion to be employed. Our method is general and can be applied to a wide range of model selection problems in biological and epidemiological systems with intractable likelihood functions.
Managing the risk of wildlife disease introduction: pathway-level biosecurity for preventing the introduction of alien ranaviruses
Publisher: Wiley
Date: 09-08-2017
The probability of epidemic fade-out is non-monotonic in transmission rate for the Markovian SIR model with demography
Publisher: Elsevier BV
Date: 03-2016
DOI: 10.1016/J.JTBI.2016.01.012
Abstract: Epidemic fade-out refers to infection elimination in the trough between the first and second waves of an outbreak. The number of infectious in iduals drops to a relatively low level between these waves of infection, and if elimination does not occur at this stage, then the disease is likely to become endemic. For this reason, it appears to be an ideal target for control efforts. Despite this obvious public health importance, the probability of epidemic fade-out is not well understood. Here we present new algorithms for approximating the probability of epidemic fade-out for the Markovian SIR model with demography. These algorithms are more accurate than previously published formulae, and one of them scales well to large population sizes. This method allows us to investigate the probability of epidemic fade-out as a function of the effective transmission rate, recovery rate, population turnover rate, and population size. We identify an interesting feature: the probability of epidemic fade-out is very often greatest when the basic reproduction number, R0, is approximately 2 (restricting consideration to cases where a major outbreak is possible, i.e., R0>1). The public health implication is that there may be instances where a non-lethal infection should be allowed to spread, or antiviral usage should be moderated, to maximise the chance of the infection being eliminated before it becomes endemic.
Identification of the relative timing of infectiousness and symptom onset for outbreak control
Publisher: Cold Spring Harbor Laboratory
Date: 08-03-2019
DOI: 10.1101/571547
Abstract: In an outbreak of an emerging disease the epidemiological characteristics of the pathogen may be largely unknown. A key determinant of ability to control the outbreak is the relative timing of infectiousness and symptom onset. We provide a method for identifying this relationship with high accuracy based on data from household-stratified symptom-onset data. Further, this can be achieved with observations taken on only a few specific days, chosen optimally, within each household. This constitutes an important tool for outbreak response. An accurate and computationally-efficient heuristic for determining the optimal surveillance scheme is introduced. This heuristic provides a novel approach to optimal design for Bayesian model discrimination.
Ant interceptions reveal roles of transport and commodity in identifying biosecurity risk pathways into Australia
Publisher: Pensoft Publishers
Date: 22-11-2019
DOI: 10.3897/NEOBIOTA.53.39463
Abstract: We obtained 14,140 interception records of ants arriving in Australia between 1986 and 2010 to examine taxonomic and biogeographic patterns of invasion. We also evaluated how trade and transport data influenced interception rates, the identity of species being transported, the commerce most associated with the transport of ants, and which countries are the primary sources for ants arriving in Australia. The majority of ant interceptions, accounting for 48% of interceptions, were from Asia and Oceania. The top commodities associated with ant interceptions were: (1) Live trees, plants, cut flowers (2) Wood and wood products (3) Edible vegetables and (4) Edible fruit and nuts. The best fitting model for predicting ant interceptions included volumes for these four commodities, as well as total trade value, transport volume, and geographic distance (with increased distance decreasing predicted ant interceptions). Intercepted ants identified to species consisted of a combination of species native to Australia, introduced species already established in Australia, and species not yet known to be established. 82% of interceptions identified to species level were of species already known to be established in Australia with Paratrechina longicornis having the most records. These data provide key biogeographic insight into the overlooked transport stage of the invasion process. Given the difficult nature of eradication, once an ant species is firmly established, focusing on early detection and quarantine is key for reducing the establishment of new invasions.
On parameter estimation in population models II: Multi-dimensional processes and transient dynamics
Publisher: Elsevier BV
Date: 03-2009
DOI: 10.1016/J.TPB.2008.12.002
Abstract: Recently, a computationally-efficient method was presented for calibrating a wide-class of Markov processes from discrete-s led abundance data. The method was illustrated with respect to one-dimensional processes and required the assumption of stationarity. Here we demonstrate that the approach may be directly extended to multi-dimensional processes, and two analogous computationally-efficient methods for non-stationary processes are developed. These methods are illustrated with respect to disease and population models, including application to infectious count data from an outbreak of "Russian influenza" (A/USSR/1977 H1N1) in an educational institution. The methodology is also shown to provide an efficient, simple and yet rigorous approach to calibrating disease processes with gamma-distributed infectious period.
Optimal use of GPS transmitter for estimating species migration rate
Publisher: Elsevier BV
Date: 2013
Fisher Information for a partially observable simple birth process
Publisher: Informa UK Limited
Date: 02-02-2016
Pest demography critically determines the viability of synthetic gene drives for population control
Publisher: Elsevier BV
Date: 11-2018
DOI: 10.1016/J.MBS.2018.09.005
Abstract: Synthetic gene drives offer a novel solution for the control of invasive alien species. CRISPR-based gene drives can positively bias their own inheritance, and comprise a DNA sequence that is replicated by homologous recombination. Since gene drives can be positioned to silence fertility or developmental genes, they could be used for population suppression. However, the production of resistant alleles following self-replication errors threatens the technology's viability for pest eradication in real-world applications. Further, a robust assessment of how pest demography impacts the expected progression of gene drives through populations is currently lacking. We used a deterministic, two-sex, birth-death model to investigate how demographic assumptions affect the efficiency of suppression drives for controlling invasive rodents on islands, for two different gene-drive strategies. We show that mass-action reproduction results in overly optimistic eradication outcomes when compared to the more realistic assumption of polygynous breeding. When polygyny was assumed, both gene-strategies failed due to the evolution of resistance unless a reproductive Allee effect (reduced reproductive rates at low population density) was also included although model outcomes were highly sensitive to the strength of this effect. Increasing the size of the initial gene-drive introduction (up to 10% of carrying capacity) had little impact on population outcomes. Understanding the demography of a population targeted for eradication is critical before the viability of gene-drive suppression can be adequately assessed.
Influencing public health policy with data-informed mathematical models of infectious diseases: Recent developments and new challenges
Publisher: Elsevier BV
Date: 09-2020
Author response: A Y-chromosome shredding gene drive for controlling pest vertebrate populations
Publisher: eLife Sciences Publications, Ltd
Date: 25-01-2019
Where did all the pangolins go? International CITES trade in pangolin species
Publisher: Elsevier BV
Date: 10-2016
Choice of Antiviral Allocation Scheme for Pandemic Influenza Depends on Strain Transmissibility, Delivery Delay and Stockpile Size
Publisher: Springer Science and Business Media LLC
Date: 02-2016
DOI: 10.1007/S11538-016-0144-6
Abstract: Recently, pandemic response has involved the use of antivirals. These antivirals are often allocated to households dynamically throughout the pandemic with the aim being to retard the spread of infection. A drawback of this is that there is a delay until infection is confirmed and antivirals are delivered. Here an alternative allocation scheme is considered, where antivirals are instead preallocated to households at the start of a pandemic, thus reducing this delay. To compare these two schemes, a deterministic approximation to a novel stochastic household model is derived, which allows efficient computation of key quantities such as the expected epidemic final size, expected early growth rate, expected peak size and expected peak time of the epidemic. It is found that the theoretical best choice of allocation scheme depends on strain transmissibility, the delay in delivering antivirals under a dynamic allocation scheme and the stockpile size. A broad summary is that for realistic stockpile sizes, a dynamic allocation scheme is superior with the important exception of the epidemic final size under a severe pandemic scenario. Our results, viewed in conjunction with the practical considerations of implementing a preallocation scheme, support a focus on attempting to reduce the delay in delivering antivirals under a dynamic allocation scheme during a future pandemic.
Elucidating user behaviours in a digital health surveillance system to correct prevalence estimates
Publisher: Elsevier BV
Date: 12-2020
Leveraging a natural murine meiotic drive to suppress invasive populations
Publisher: Proceedings of the National Academy of Sciences
Date: 08-11-2022
Abstract: Invasive rodents are a major cause of environmental damage and bio ersity loss, particularly on islands. Unlike insects, genetic biocontrol strategies including population-suppressing gene drives with biased inheritance have not been developed in mice. Here, we demonstrate a gene drive strategy ( t CRISPR ) that leverages super-Mendelian transmission of the t haplotype to spread inactivating mutations in a haplosufficient female fertility gene ( Prl ). Using spatially explicit in idual-based in silico modeling, we show that t CRISPR can eradicate island populations under a range of realistic field-based parameter values. We also engineer transgenic t CRISPR mice that, crucially, exhibit biased transmission of the modified t haplotype and Prl mutations at levels our modeling predicts would be sufficient for eradication. This is an ex le of a feasible gene drive system for invasive alien rodent population control.
Statistical description of wetland hydrological connectivity to the River Murray in South Australia under both natural and regulated conditions
Publisher: Elsevier BV
Date: 12-2015
Characterising pandemic severity and transmissibility from data collected during first few hundred studies
Publisher: Elsevier BV
Date: 06-2017
DOI: 10.1016/J.EPIDEM.2017.01.004
Abstract: Early estimation of the probable impact of a pandemic influenza outbreak can assist public health authorities to ensure that response measures are proportionate to the scale of the threat. Recently, frameworks based on transmissibility and severity have been proposed for initial characterization of pandemic impact. Data requirements to inform this assessment may be provided by "First Few Hundred" (FF100) studies, which involve surveillance-possibly in person, or via telephone-of household members of confirmed cases. This process of enhanced case finding enables detection of cases across the full spectrum of clinical severity, including the date of symptom onset. Such surveillance is continued until data for a few hundred cases, or satisfactory characterization of the pandemic strain, has been achieved. We present a method for analysing these data, at the household level, to provide a posterior distribution for the parameters of a model that can be interpreted in terms of severity and transmissibility of a pandemic strain. We account for imperfect case detection, where in iduals are only observed with some probability that can increase after a first case is detected. Furthermore, we test this methodology using simulated data generated by an independent model, developed for a different purpose and incorporating more complex disease and social dynamics. Our method recovers transmissibility and severity parameters to a high degree of accuracy and provides a computationally efficient approach to estimating the impact of an outbreak in its early stages.
Understanding the biological invasion risk posed by the global wildlife trade: Propagule pressure drives the introduction and establishment of Nearctic turtles
Publisher: Wiley
Date: 23-12-2015
DOI: 10.1111/GCB.12790
Abstract: Biological invasions are a key component of human‐induced global change. The continuing increase in global wildlife trade has raised concerns about the parallel increase in the number of new invasive species. However, the factors that link the wildlife trade to the biological invasion process are still poorly understood. Moreover, there are analytical challenges in researching the role of global wildlife trade in biological invasions, particularly issues related to the under‐reporting of introduced and established populations in areas with reduced s ling effort. In this work, we use high‐quality data on the international trade in Nearctic turtles (1999–2009) coupled with a statistical modelling framework, which explicitly accounts for detection, to investigate the factors that influence the introduction (release, or escape into the wild) of globally traded Nearctic turtles and the establishment success (self‐sustaining exotic populations) of slider turtles ( Trachemys scripta ), the most frequently traded turtle species. We found that the introduction of a species was influenced by the total number of turtles exported to a jurisdiction and the age at maturity of the species, while the establishment success of slider turtles was best associated with the propagule number (number of release events), and the number of native turtles in the jurisdiction of introduction. These results indicate both a direct and indirect association between the wildlife trade and the introduction of turtles and establishment success of slider turtles, respectively. Our results highlight the existence of gaps in the number of globally recorded introduction events and established populations of slider turtles, although the expected bias is low. We emphasize the importance of researching independently the factors that affect the different stages of the invasion pathway. Critically, we observe that the number of traded in iduals might not always be an adequate proxy for propagule pressure and establishment success.
Assessment of the Risk of Ebola Importation to Australia
Publisher: Public Library of Science (PLoS)
Date: 2014
DOI: 10.1371/CURRENTS.OUTBREAKS.AA0375FD48A92C7C9422AA543A88711F
Connecting surveillance and population-level influenza incidence
Publisher: Cold Spring Harbor Laboratory
Date: 28-09-2018
DOI: 10.1101/427708
Abstract: There is substantial interest in estimating and forecasting influenza incidence. Surveillance of influenza is challenging as one needs to demarcate influenza from other respiratory viruses, and due to asymptomatic infections. To circumvent these challenges, surveillance data often targets influenza-like-illness, or uses context-specific normalisations such as test positivity or per-consultation rates. Specifically, influenza incidence itself is not reported. We propose a framework to estimate population-level influenza incidence, and its associated uncertainty, using surveillance data and hierarchical observation processes. This new framework, and forecasting and forecast assessment methods, are demonstrated for three Australian states over 2016 and 2017. The framework allows for comparison within and between seasons in which surveillance effort has varied. Implementing this framework would improve influenza surveillance and forecasting globally, and could be applied to other diseases for which surveillance is difficult.
Australia's wish list of exotic pets: Biosecurity and conservation implications of desired alien and illegal pet species
Publisher: Pensoft Publishers
Date: 18-08-2020
DOI: 10.3897/NEOBIOTA.60.51431
Abstract: Globalisation of the live pet trade facilitates major pathways for the transport and introduction of invasive alien species across longer distances and at higher frequencies than previously possible. Moreover, the unsustainable trade of species is a major driver for the over-exploitation of wild populations. Australia minimises the biosecurity and conservation risk of the international pet trade by implementing highly stringent regulations on the live import and keeping of alien pets beyond its international CITES obligations. However, the public desire to possess prohibited alien pets has never been quantified and represents a number of species that could be acquired illegally or legally under different future legislative conditions. As such, highly desirable species represent an ongoing conservation threat and biosecurity risk via the pet-release invasion pathway. We aimed to characterise the Australian desire for illegal alien pets and investigate potential sources of external information that can be utilised to predict future desire. Using public live import enquiry records from the Australian Commonwealth Department of Agriculture, Water and the Environment as a proxy for alien pet desire, we tested for differences in the proportion of species with threatened listings and records of invasions, after accounting for taxonomy. Additionally, we used a United States of America (U.S.) live imports dataset to infer pet demand in another Western market with less stringent regulations and determined whether species highly desired in Australia had higher U.S. trade demand than would be expected by chance. The Australian public desire for alien pets is heavily and significantly biased towards species threatened with extinction, species popular in the U.S. trade and species with a history of successful invasions. Not only does this indicate the potential impacts of pet desire on invasion risk and the conservation of threatened species, but we also highlight the potential role of the U.S. trade as an effective predictor for Australian desire. Our research emphasises the value of novel datasets in building predictive capacity for improved biosecurity awareness.
Integrative Analysis of the Physical Transport Network into Australia
Publisher: Public Library of Science (PLoS)
Date: 16-02-2016
Designing group dose-response studies in the presence of transmission
Publisher: Elsevier BV
Date: 10-2018
DOI: 10.1016/J.MBS.2018.07.007
Abstract: Dose-response studies are used throughout pharmacology, toxicology and in clinical research to determine safe, effective, or hazardous doses of a substance. When involving animals, the subjects are often housed in groups this is in fact mandatory in many countries for social animals, on ethical grounds. An issue that may consequently arise is that of unregulated between-subject dosing (transmission), where a subject may transmit the substance to another subject. Transmission will obviously impact the assessment of the dose-response relationship, and will lead to biases if not properly modelled. Here we present a method for determining the optimal design - pertaining to the size of groups, the doses, and the killing times - for such group dose-response experiments, in a Bayesian framework. Our results are of importance to minimising the number of animals required in order to accurately determine dose-response relationships. Furthermore, we additionally consider scenarios in which the estimation of the amount of transmission is also of interest. A particular motivating ex le is that of C ylobacter jejuni in chickens. Code is provided so that practitioners may determine the optimal design for their own studies.
A data-driven model for influenza transmission incorporating media effects
Publisher: The Royal Society
Date: 10-2016
DOI: 10.1098/RSOS.160481
Abstract: Numerous studies have attempted to model the effect of mass media on the transmission of diseases such as influenza however, quantitative data on media engagement has until recently been difficult to obtain. With the recent explosion of ‘big data’ coming from online social media and the like, large volumes of data on a population’s engagement with mass media during an epidemic are becoming available to researchers. In this study, we combine an online dataset comprising millions of shared messages relating to influenza with traditional surveillance data on flu activity to suggest a functional form for the relationship between the two. Using this data, we present a simple deterministic model for influenza dynamics incorporating media effects, and show that such a model helps explain the dynamics of historical influenza outbreaks. Furthermore, through model selection we show that the proposed media function fits historical data better than other media functions proposed in earlier studies.
A hybrid model for studying spatial aspects of infectious diseases
Publisher: Cambridge University Press (CUP)
Date: 10-2012
DOI: 10.1017/S1446181112000296
Abstract: We consider a hybrid model, created by coupling a continuum and an agent-based model of infectious disease. The framework of the hybrid model provides a mechanism to study the spread of infection at both the in idual and population levels. This approach captures the stochastic spatial heterogeneity at the in idual level, which is directly related to deterministic population level properties. This facilitates the study of spatial aspects of the epidemic process. A spatial analysis, involving counting the number of infectious agents in equally sized bins, reveals when the spatial domain is nonhomogeneous.
The distribution of the time taken for an epidemic to spread between two communities
Publisher: Elsevier BV
Date: 09-2018
DOI: 10.1016/J.MBS.2018.07.004
Abstract: Assessing the risk of disease spread between communities is important in our highly connected modern world. However, the impact of disease- and population-specific factors on the time taken for an epidemic to spread between communities, as well as the impact of stochastic disease dynamics on this spreading time, are not well understood. In this study, we model the spread of an acute infection between two communities ('patches') using a susceptible-infectious-removed (SIR) metapopulation model. We develop approximations to efficiently evaluate the probability of a major outbreak in a second patch given disease introduction in a source patch, and the distribution of the time taken for this to occur. We use these approximations to assess how interventions, which either control disease spread within a patch or decrease the travel rate between patches, change the spreading probability and median spreading time. We find that decreasing the basic reproduction number in the source patch is the most effective way of both decreasing the spreading probability, and delaying epidemic spread to the second patch should this occur. Moreover, we show that the qualitative effects of interventions are the same regardless of the approximations used to evaluate the spreading time distribution, but for some regions in parameter space, quantitative findings depend upon the approximations used. Importantly, if we neglect the possibility that an intervention prevents a large outbreak in the source patch altogether, then intervention effectiveness is not estimated accurately.
The Illegal Wildlife Trade Is a Likely Source of Alien Species
Publisher: Wiley
Date: 27-10-2016
DOI: 10.1111/CONL.12301
Catastrophe management and inter-reserve distance for marine reserve networks
Publisher: Elsevier BV
Date: 02-2007
Key questions for modelling COVID-19 exit strategies
Publisher: The Royal Society
Date: 12-08-2020
Abstract: Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute ‘Models for an exit strategy’ workshop (11–15 May 2020). A erse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters (ii) understand sources of heterogeneity in populations and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.
Hybrid Markov chain models of S–I–R disease dynamics
Publisher: Springer Science and Business Media LLC
Date: 24-12-2016
DOI: 10.1007/S00285-016-1085-2
Abstract: Deterministic epidemic models are attractive due to their compact nature, allowing substantial complexity with computational efficiency. This partly explains their dominance in epidemic modelling. However, the small numbers of infectious in iduals at early and late stages of an epidemic, in combination with the stochastic nature of transmission and recovery events, are critically important to understanding disease dynamics. This motivates the use of a stochastic model, with continuous-time Markov chains being a popular choice. Unfortunately, even the simplest Markovian S-I-R model-the so-called general stochastic epidemic-has a state space of order [Formula: see text], where N is the number of in iduals in the population, and hence computational limits are quickly reached. Here we introduce a hybrid Markov chain epidemic model, which maintains the stochastic and discrete dynamics of the Markov chain in regions of the state space where they are of most importance, and uses an approximate model-namely a deterministic or a diffusion model-in the remainder of the state space. We discuss the evaluation, efficiency and accuracy of this hybrid model when approximating the distribution of the duration of the epidemic and the distribution of the final size of the epidemic. We demonstrate that the computational complexity is [Formula: see text] and that under suitable conditions our approximations are highly accurate.
Locally Fixed Alleles: A method to localize gene drive to island populations
Publisher: Springer Science and Business Media LLC
Date: 11-2019
DOI: 10.1038/S41598-019-51994-0
Abstract: Invasive species pose a major threat to bio ersity on islands. While successes have been achieved using traditional removal methods, such as toxicants aimed at rodents, these approaches have limitations and various off-target effects on island ecosystems. Gene drive technologies designed to eliminate a population provide an alternative approach, but the potential for drive-bearing in iduals to escape from the target release area and impact populations elsewhere is a major concern. Here we propose the “Locally Fixed Alleles” approach as a novel means for localizing elimination by a drive to an island population that exhibits significant genetic isolation from neighboring populations. Our approach is based on the assumption that in small island populations of rodents, genetic drift will lead to alleles at multiple genomic loci becoming fixed. In contrast, multiple alleles are likely to be maintained in larger populations on mainlands. Utilizing the high degree of genetic specificity achievable using homing drives, for ex le based on the CRISPR/Cas9 system, our approach aims at employing one or more locally fixed alleles as the target for a gene drive on a particular island. Using mathematical modeling, we explore the feasibility of this approach and the degree of localization that can be achieved. We show that across a wide range of parameter values, escape of the drive to a neighboring population in which the target allele is not fixed will at most lead to modest transient suppression of the non-target population. While the main focus of this paper is on elimination of a rodent pest from an island, we also discuss the utility of the locally fixed allele approach for the goals of population suppression or population replacement. Our analysis also provides a threshold condition for the ability of a gene drive to invade a partially resistant population.
Infectious disease pandemic planning and response: Incorporating decision analysis
Publisher: Public Library of Science (PLoS)
Date: 09-01-2020
Development of an influenza pandemic decision support tool linking situational analytics to national response policy
Publisher: Elsevier BV
Date: 09-2021
Dodging silver bullets: good CRISPR gene-drive design is critical for eradicating exotic vertebrates
Publisher: The Royal Society
Date: 09-08-2017
Abstract: Self-replicating gene drives that can spread deleterious alleles through animal populations have been promoted as a much needed but controversial ‘silver bullet’ for controlling invasive alien species. Homing-based drives comprise an endonuclease and a guide RNA (gRNA) that are replicated during meiosis via homologous recombination. However, their efficacy for controlling wild populations is threatened by inherent polymorphic resistance and the creation of resistance alleles via non-homologous end-joining (NHEJ)-mediated DNA repair. We used stochastic in idual-based models to identify realistic gene-drive strategies capable of eradicating vertebrate pest populations (mice, rats and rabbits) on islands. One popular strategy, a sex-reversing drive that converts heterozygous females into sterile males, failed to spread and required the ongoing deployment of gene-drive carriers to achieve eradication. Under alternative strategies, multiplexed gRNAs could overcome inherent polymorphic resistance and were required for eradication success even when the probability of NHEJ was low. Strategies causing homozygotic embryonic non-viability or homozygotic female sterility produced high probabilities of eradication and were robust to NHEJ-mediated deletion of the DNA sequence between multiplexed endonuclease recognition sites. The latter two strategies also purged the gene drive when eradication failed, therefore posing lower long-term risk should animals escape beyond target islands. Multiplexing gRNAs will be necessary if this technology is to be useful for insular extirpation attempts however, precise knowledge of homing rates will be required to design low-risk gene drives with high probabilities of eradication success.
Temporal modelling of ballast water discharge and ship-mediated invasion risk to Australia
Publisher: The Royal Society
Date: 04-2015
DOI: 10.1098/RSOS.150039
Abstract: Biological invasions have the potential to cause extensive ecological and economic damage. Maritime trade facilitates biological invasions by transferring species in ballast water, and on ships' hulls. With volumes of maritime trade increasing globally, efforts to prevent these biological invasions are of significant importance. Both the International Maritime Organization and the Australian government have developed policy seeking to reduce the risk of these invasions. In this study, we constructed models for the transfer of ballast water into Australian waters, based on historic ballast survey data. We used these models to hindcast ballast water discharge over all vessels that arrived in Australian waters between 1999 and 2012. We used models for propagule survival to compare the risk of ballast-mediated propagule transport between ecoregions. We found that total annual ballast discharge volume into Australia more than doubled over the study period, with the vast majority of ballast water discharge and propagule pressure associated with bulk carrier traffic. As such, the ecoregions suffering the greatest risk are those associated with the export of mining commodities. As global marine trade continues to increase, effective monitoring and biosecurity policy will remain necessary to combat the risk of future marine invasion events.
On the derivation of approximations to cellular automata models and the assumption of independence
Publisher: Elsevier BV
Date: 07-2014
DOI: 10.1016/J.MBS.2014.04.004
Abstract: Cellular automata are discrete agent-based models, generally used in cell-based applications. There is much interest in obtaining continuum models that describe the mean behaviour of the agents in these models. Previously, continuum models have been derived for agents undergoing motility and proliferation processes, however, these models only hold under restricted conditions. In order to narrow down the reason for these restrictions, we explore three possible sources of error in deriving the model. These sources are the choice of limiting arguments, the use of a discrete-time model as opposed to a continuous-time model and the assumption of independence between the state of sites. We present a rigorous analysis in order to gain a greater understanding of the significance of these three issues. By finding a limiting regime that accurately approximates the conservation equation for the cellular automata, we are able to conclude that the inaccuracy between our approximation and the cellular automata is completely based on the assumption of independence.
Metapopulation persistence in a dynamic landscape: More habitat or better stewardship?
Publisher: Wiley
Date: 04-2008
DOI: 10.1890/07-1094.1
Abstract: Habitat loss and fragmentation has created metapopulations where there were once continuous populations. Ecologists and conservation biologists have become interested in the optimal way to manage and conserve such metapopulations. Several authors have considered the effect of patch disturbance and recovery on metapopulation persistence, but almost all such studies assume that every patch is equally susceptible to disturbance. We investigated the influence of protecting patches from disturbance on metapopulation persistence, and used a stochastic metapopulation model to answer the question: How can we optimally trade off returns from protection of patches vs. creation of patches? We considered the problem of finding, under budgetary constraints, the optimal combination of increasing the number of patches in the metapopulation network vs. increasing the number of protected patches in the network. We discovered that the optimal trade-off is dependent upon all of the properties of the system: the species dynamics, the dynamics of the landscape, and the relative costs of each action. A stochastic model and accompanying methodology are provided allowing a manager to determine the optimal policy for small metapopulations. We also provide two approximations, including a rule of thumb, for determining the optimal policy for larger metapopulations. The method is illustrated with an ex le inspired by information for the greater bilby, Macrotis lagotis, inhabiting southwestern Queensland, Australia. We found that given realistic costs for each action, protection of patches should be prioritized over patch creation for improving the persistence of the greater bilby during the next 20 years.
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