A5090284787- COVID-19 epidemiological studies
- Neural dynamics and brain function
- Functional Brain Connectivity Studies
- EEG and Brain-Computer Interfaces
- Sleep and Wakefulness Research
- Viral Infections and Outbreaks Research
- Data-Driven Disease Surveillance
- COVID-19 Digital Contact Tracing
- SARS-CoV-2 and COVID-19 Research
- Influenza Virus Research Studies
- demographic modeling and climate adaptation
- Circadian rhythm and melatonin
- Vaccine Coverage and Hesitancy
- Infection Control and Ventilation
- Healthcare Systems and Reforms
- COVID-19 Pandemic Impacts
- Cervical Cancer and HPV Research
- Health Systems, Economic Evaluations, Quality of Life
- Advanced MRI Techniques and Applications
- Tuberculosis Research and Epidemiology
- COVID-19 and healthcare impacts
- Anomaly Detection Techniques and Applications
- Computational Physics and Python Applications
- Health Policy Implementation Science
- Time Series Analysis and Forecasting
Burnet Institute
2020-2025
Monash University
2019-2024
Gates Foundation
2023-2024
Institute for Disease Modeling
2023-2024
QIMR Berghofer Medical Research Institute
2023
Wellcome Centre for Integrative Neuroimaging
2017-2020
University of Oxford
2017-2020
University College London
2019
The University of Sydney
2010-2018
ARC Centre of Excellence for Integrative Brain Function
2015-2018
The COVID-19 pandemic has created an urgent need for models that can project epidemic trends, explore intervention scenarios, and estimate resource needs. Here we describe the methodology of Covasim (COVID-19 Agent-based Simulator), open-source model developed to help address these questions. includes country-specific demographic information on age structure population size; realistic transmission networks in different social layers, including households, schools, workplaces, long-term care...
Brain activity is a dynamic combination of the responses to sensory inputs and its own spontaneous processing. Consequently, such brain continuously changing whether or not one focusing on an externally imposed task. Previously, we have introduced analysis method that allows us, using Hidden Markov Models (HMM), model task rest as sequence distinct networks, overcoming many limitations posed by sliding window approaches. Here, present advance enables HMM handle very large amounts data,...
Abstract Traveling patterns of neuronal activity—brain waves—have been observed across a breadth recordings, states awareness, and species, but their emergence in the human brain lacks firm understanding. Here we analyze complex nonlinear dynamics that emerge from modeling large-scale spontaneous neural activity on whole-brain network derived tractography. We find rich array three-dimensional wave patterns, including traveling waves, spiral sources, sinks. These are metastable, such multiple...
Complex thought and behavior arise through dynamic recruitment of large-scale brain networks. The signatures this process may be observable in electrophysiological data; yet robust modeling rapidly changing functional network structure on rapid cognitive timescales remains a considerable challenge. Here, we present one potential solution using Hidden Markov Models (HMMs), which are able to identify states characterized by engaging distinct networks that reoccur over time. We show how the HMM...
Abstract The COVID-19 pandemic has created an urgent need for models that can project epidemic trends, explore intervention scenarios, and estimate resource needs. Here we describe the methodology of Covasim (COVID-19 Agent-based Simulator), open-source model developed to help address these questions. includes country-specific demographic information on age structure population size; realistic transmission networks in different social layers, including households, schools, workplaces,...
Abstract Initial COVID-19 containment in the United States focused on limiting mobility, including school and workplace closures. However, these interventions have had enormous societal economic costs. Here, we demonstrate feasibility of an alternative control strategy, test-trace-quarantine: routine testing primarily symptomatic individuals, tracing their known contacts, placing contacts quarantine. We perform this analysis using Covasim, open-source agent-based model, which has been...
Over long timescales, neuronal dynamics can be robust to quite large perturbations, such as changes in white matter connectivity and grey structure through processes including learning, aging, development certain disease processes. One possible explanation is that are facilitated by homeostatic mechanisms dynamically rebalance brain networks. In this study, we simulate a cortical network using the Wilson-Cowan neural mass model with conduction delays noise, use inhibitory synaptic plasticity...
A biophysical model of the key aspects melatonin synthesis and excretion has been developed, which is able to predict experimental dynamics in plasma saliva, its urinary metabolite 6-sulfatoxymelatonin (aMT6s). This new coupled an established arousal dynamics, predicts sleep circadian based on light exposure times wakefulness. The combined thus levels over sleep-wake/dark-light cycle enables prediction melatonin-based phase markers, such as dim onset (DLMO) aMT6s acrophase under conditions...
Objectives To assess the risks associated with relaxing coronavirus disease 2019 (COVID-19)-related physical distancing restrictions and lockdown policies during a period of low viral transmission. Design Network-based transmission in households, schools, workplaces, variety community spaces activities were simulated an agent-based model, Covasim. Setting The model was calibrated for baseline scenario reflecting epidemiological policy environment Victoria March–May 2020, Intervention Policy...
A user ready, portable, documented software package, NFTsim, is presented to facilitate numerical simulations of a wide range brain systems using continuum neural field modeling. NFTsim enables users simulate key aspects activity at multiple scales. At the microscopic scale, it incorporates characteristics local interactions between cells, neurotransmitter effects, synaptodendritic delays and feedbacks. mesoscopic information about medium large scale axonal ranges fibers, which are essential...
Vietnam has emerged as one of the world's leading success stories in responding to COVID-19. After a prolonged period little no transmission, there was an outbreak unknown source July, 2020, Da Nang region, but quickly suppressed. We aimed use epidemiological, behavioural, demographic, and policy data from COVID-19 calibrate agent-based model transmission for Vietnam, estimate risk future outbreaks associated with reopening international borders country.
In 2020, the WHO launched its first global strategy to accelerate elimination of cervical cancer, outlining an ambitious set targets for countries achieve over next decade. At same time, new tools, technologies, and strategies are in pipeline that may improve screening performance, expand reach prophylactic vaccines, prevent acquisition, persistence progression oncogenic HPV. Detailed mechanistic modelling can help identify combinations current future combat cancer. Open-source tools needed...
Background Immunisation is an effective tool for responding to disease outbreaks, but in low- and middle-income countries (LMICs) accessing vaccine stockpiles can be slowed by logistical challenges. The 7-1-7 outbreak timeliness targets propose that outbreaks detected within seven days; notification occur one day; responses started another days. For of measles, cholera, yellow fever, meningococcal meningitis, we aim estimate the impact initiating response immunisation (ORI) programs 15 days...
Mammalian sleep varies widely, ranging from frequent napping in rodents to consolidated blocks primates and unihemispheric cetaceans. In humans, rats, mice cats, patterns are orchestrated by homeostatic circadian drives the sleep–wake switch, but it is not known whether this system ubiquitous among mammals. Here, changes of just two parameters a recent quantitative model switch shown reproduce typical for 17 species across 7 orders. Furthermore, parameter variations found be consistent with...
Long-term control of SARS-CoV-2 outbreaks depends on the widespread coverage effective vaccines. In Australia, two-dose vaccination above 90% adult population was achieved. However, between August 2020 and 2021, hesitancy fluctuated dramatically. This raised question whether settings with low naturally derived immunity, such as Queensland where less than <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mn>0.005</mml:mn> <mml:mi mathvariant="normal">%</mml:mi> </mml:math> is...
The effects of permanent shift work on entrainment and sleepiness are examined using a mathematical model that combines sleep-wake switch in the brain with human circadian pacemaker entrained by light nonphotic inputs. is applied to 8-hour schedules understand basic mechanisms underlying changes sleepiness. Average shown increase during first days night evening schedules, is, start times between 0000 0700 h 1500 2200 h, respectively. After initial increase, decreases stabilizes via...
Abstract Initial COVID-19 containment in the United States focused on limiting mobility, including school and workplace closures. However, these interventions have had enormous societal economic costs. Here we demonstrate feasibility of an alternative control strategy, test-trace-quarantine: routine testing primarily symptomatic individuals, tracing their known contacts, placing contacts quarantine. We performed this analysis using Covasim, open-source agent-based model, which was calibrated...
In settings with zero community transmission, any new SARS-CoV-2 outbreaks are likely to be the result of random incursions. The level restrictions in place at time incursion is considerably affect possible outbreak trajectories, but probability that a large eventuates not known.We used an agent-based model investigate relationship between ongoing and behavioural factors, causing resulting growth rate. We applied our state Victoria, Australia, which has reached transmission as November...
Abstract Background Policy responses to COVID-19 in Victoria, Australia over 2020–2021 have been supported by evidence generated through mathematical modelling. This study describes the design, key findings, and process for policy translation of a series modelling studies conducted Victorian Department Health response team during this period. Methods An agent-based model, Covasim, was used simulate impact interventions on outbreaks epidemic waves. The model continually adapted enable...
The impact of outbreak response immunization (ORI) can be estimated by comparing observed outcomes to modelled counterfactual scenarios without ORI, but the most appropriate metrics depend on stakeholder needs and data availability. This study developed a framework for using mathematical models assess ORI vaccine-preventable diseases. Framework development involved (1) assessment based interviews literature reviews determining availability capacity capture as model outcomes; (2) mapping...