Thomas Finnie
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View article: A mathematical framework for human neutrophil state transitions inferred from single-cell RNA sequence data
A mathematical framework for human neutrophil state transitions inferred from single-cell RNA sequence data Open
Neutrophils, the most abundant immune cells in the human circulation, play a central role in the innate immune system. While neutrophil heterogeneity is a topic of increasing research interest, few efforts have been made to model the dynam…
View article: The case for using flexible healthcare capacity constraints to optimise pandemic control strategies
The case for using flexible healthcare capacity constraints to optimise pandemic control strategies Open
During the COVID-19 pandemic, a key challenge was designing control strategies that balance the benefits and costs of public health and social measures while preventing healthcare systems becoming overwhelmed. This was often implemented by…
View article: Mechanistic within-host mathematical model of inhalational anthrax
Mechanistic within-host mathematical model of inhalational anthrax Open
We present a mathematical model of the dynamics of Bacillus anthracis bacteria within the lymph nodes and blood of a host, following inhalation of an initial dose of spores. We also incorporate the dynamics of protective antigen, which is …
View article: The urban mycobiome of transport environments: Characterising the fungal composition of passive dust samples collected in railway stations in England
The urban mycobiome of transport environments: Characterising the fungal composition of passive dust samples collected in railway stations in England Open
Fungal bioaerosols, including spores and fragments, are significant components of urban air and are associated with infectious and allergic disease. Despite their importance, fungal bioaerosols are less well studied compared to bacteria an…
View article: A mathematical framework for human neutrophil state transitions inferred from single-cell RNA sequence data
A mathematical framework for human neutrophil state transitions inferred from single-cell RNA sequence data Open
Neutrophils, the most abundant immune cells in the human circulation, play a central role in the innate immune system. While neutrophil heterogeneity is a topic of increasing research interest, few efforts have been made to model the dynam…
View article: Introducing a framework for within-host dynamics and mutations modelling of H5N1 influenza infection in humans
Introducing a framework for within-host dynamics and mutations modelling of H5N1 influenza infection in humans Open
Avian influenza A(H5N1) poses a public health risk due to its pandemic potential should the virus mutate to become human-to-human transmissible. To date, reported influenza A(H5N1) human cases have typically occurred in the lower respirato…
View article: Healthy LLMs? Benchmarking LLM Knowledge of UK Government Public Health Information
Healthy LLMs? Benchmarking LLM Knowledge of UK Government Public Health Information Open
As Large Language Models (LLMs) become widely accessible, a detailed understanding of their knowledge within specific domains becomes necessary for successful real world use. This is particularly critical in public health, where failure to…
View article: Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases
Backtracking: Improved methods for identifying the source of a deliberate release of Bacillus anthracis from the temporal and spatial distribution of cases Open
Reverse epidemiology is a mathematical modelling tool used to ascertain information about the source of a pathogen, given the spatial and temporal distribution of cases, hospitalisations and deaths. In the context of a deliberately release…
View article: Introducing a framework for within-host dynamics and mutations modelling of H5N1 influenza infection in humans
Introducing a framework for within-host dynamics and mutations modelling of H5N1 influenza infection in humans Open
Avian influenza A(H5N1) poses a public health risk due to its pandemic potential should the virus mutate to become human-to-human transmissible. To date, reported influenza A(H5N1) human cases have typically occurred in the lower respirato…
View article: Real-time modelling of the SARS-CoV-2 pandemic in England 2020-2023: a challenging data integration
Real-time modelling of the SARS-CoV-2 pandemic in England 2020-2023: a challenging data integration Open
A central pillar of the UK's response to the SARS-CoV-2 pandemic was the provision of up-to-the moment nowcasts and short term projections to monitor current trends in transmission and associated healthcare burden. Here we present a detail…
View article: Estimating the household secondary attack rate and serial interval of COVID-19 using social media
Estimating the household secondary attack rate and serial interval of COVID-19 using social media Open
We propose a method to estimate the household secondary attack rate (hSAR) of COVID-19 in the United Kingdom based on activity on the social media platform X, formerly known as Twitter. Conventional methods of hSAR estimation are resource …
View article: Symptom propagation in respiratory pathogens of public health concern: a review of the evidence
Symptom propagation in respiratory pathogens of public health concern: a review of the evidence Open
Symptom propagation occurs when the symptom set an individual experiences is correlated with the symptom set of the individual who infected them. Symptom propagation may dramatically affect epidemiological outcomes, potentially causing clu…
View article: Evaluating Large Language Models for Public Health Classification and Extraction Tasks
Evaluating Large Language Models for Public Health Classification and Extraction Tasks Open
Advances in Large Language Models (LLMs) have led to significant interest in their potential to support human experts across a range of domains, including public health. In this work we present automated evaluations of LLMs for public heal…
View article: Combining models to generate consensus medium-term projections of hospital admissions, occupancy and deaths relating to COVID-19 in England
Combining models to generate consensus medium-term projections of hospital admissions, occupancy and deaths relating to COVID-19 in England Open
Mathematical modelling has played an important role in offering informed advice during the COVID-19 pandemic. In England, a cross government and academia collaboration generated medium-term projections (MTPs) of possible epidemic trajector…
View article: Symptom propagation in respiratory pathogens of public health concern: a review of the evidence
Symptom propagation in respiratory pathogens of public health concern: a review of the evidence Open
Symptom propagation occurs when the symptom set an individual experiences is correlated with the symptom set of the individual who infected them. Symptom propagation may dramatically affect epidemiological outcomes, potentially causing clu…
Combining models to generate a consensus effective reproduction number<i>R</i>for the COVID-19 epidemic status in England Open
The effective reproduction number $ R $ was widely accepted as a key indicator during the early stages of the COVID-19 pandemic. In the UK, the $ R $ value published on the UK Government Dashboard has been generated as a combined value fro…
View article: Using mixture density networks to emulate a stochastic within-host model of Francisella tularensis infection
Using mixture density networks to emulate a stochastic within-host model of Francisella tularensis infection Open
For stochastic models with large numbers of states, analytical techniques are often impractical, and simulations time-consuming and computationally demanding. This limitation can hinder the practical implementation of such models. In this …
View article: Combining models to generate consensus medium-term projections of hospital admissions, occupancy and deaths relating to COVID-19 in England
Combining models to generate consensus medium-term projections of hospital admissions, occupancy and deaths relating to COVID-19 in England Open
Mathematical modelling has played an important role in offering informed advice during the COVID-19 pandemic. In England, a cross government and academia collaboration generated Medium-Term Projections (MTPs) of possible epidemic trajector…
View article: Using mixture density networks to emulate a stochastic within-host model of<i>Francisella tularensis</i>infection
Using mixture density networks to emulate a stochastic within-host model of<i>Francisella tularensis</i>infection Open
For stochastic models with large numbers of states, analytical techniques are often impractical, and simulations time-consuming and computationally demanding. This limitation can hinder the practical implementation of such models. In this …
View article: Responsive modelling of the mpox epidemic in England as a cross-government and academia collaboration: the process, challenges, and lessons learned
Responsive modelling of the mpox epidemic in England as a cross-government and academia collaboration: the process, challenges, and lessons learned Open
On May 7, 2022, mpox (formerly known as monkeypox) was detected in a traveller returning to the UK from Nigeria. Before this outbreak, the UK had three mpox cases in September, 2018, with the index case also from Nigeria,1Petersen E Abubak…
View article: Combining models to generate a consensus effective reproduction number<i>R</i>for the COVID-19 epidemic status in England
Combining models to generate a consensus effective reproduction number<i>R</i>for the COVID-19 epidemic status in England Open
The effective reproduction number R was widely accepted as a key indicator during the early stages of the COVID-19 pandemic. In the UK, the R value published on the UK Government Dashboard has been generated as a combined value from an ens…
View article: Backtracking: Improved methods for identifying the source of a deliberate release of<i>Bacillus anthracis</i>from the temporal and spatial distribution of cases
Backtracking: Improved methods for identifying the source of a deliberate release of<i>Bacillus anthracis</i>from the temporal and spatial distribution of cases Open
Reverse epidemiology is a mathematical modelling tool used to ascertain information about the source of a pathogen, given the spatial and temporal distribution of cases, hospitalisations and deaths. In the context of a deliberately release…
View article: Risk of paediatric multisystem inflammatory syndrome (PIMS-TS) during the SARS-CoV-2 alpha and delta variant waves: National observational and modelling study, 2020–21, England
Risk of paediatric multisystem inflammatory syndrome (PIMS-TS) during the SARS-CoV-2 alpha and delta variant waves: National observational and modelling study, 2020–21, England Open
Objectives Paediatric Multisystem Inflammatory Syndrome (PIMS-TS) is a rare life-threatening complication that typically occurs several weeks after SARS-CoV-2 infection in children and young people (CYP). We used national and regional-leve…
View article: Understanding the immunological landscape of England during SARS-CoV2 Omicron variant wave
Understanding the immunological landscape of England during SARS-CoV2 Omicron variant wave Open
Understanding the scale of the threat posed by SARS-CoV2 B.1.1.529, or Omicron , variant formed a key problem in public health in the early part of 2022. Early evidence indicated that the variant was more transmissible and less severe than…
View article: Simplified Within Host and Dose-response models of SARS-CoV-2
Simplified Within Host and Dose-response models of SARS-CoV-2 Open
Understanding the mechanistic dynamics of transmission is key to designing more targeted and effective interventions to limit the spread of infectious diseases. A well-described within-host model allows explicit simulation of how infectiou…
View article: Check your assumptions: Further scrutiny of basic model frameworks of antimicrobial resistance
Check your assumptions: Further scrutiny of basic model frameworks of antimicrobial resistance Open
Since the mid-1990s, growing concerns over antimicrobial resistant (AMR) organisms has led to an increase in the use of mathematical models to explore the inter-host transmission of such infections. Previous work reviewing such models cate…
View article: A within-host model of SARS-CoV-2 infection
A within-host model of SARS-CoV-2 infection Open
Within-host models have been used to successfully describe the dynamics of multiple viral infections, however, the dynamics of SARS-CoV-2 virus infection remain poorly understood. A greater understanding of how the virus interacts with the…
View article: Estimating the risk of hospitalisation and death in England’s remaining unvaccinated population
Estimating the risk of hospitalisation and death in England’s remaining unvaccinated population Open
The roll-out of COVID-19 vaccines in the England has generally been very good – with over 80% of over 12s having received two doses of vaccine by the start of February 2022, and 67% having received a further booster dose. Despite this, the…
View article: Understanding the immunological landscape of England during SARS-CoV2 Omicron variant wave
Understanding the immunological landscape of England during SARS-CoV2 Omicron variant wave Open
Understanding the scale of the threat posed by SARS-CoV2 B.1.1.529, or Omicron , variant formed a key problem in public health in the early part of 2022. Early evidence indicated that the variant was more transmissible and less severe than…