Assessing the dynamics and impact of COVID-19 vaccination on disease spread: A data-driven approach.

The COVID-19 pandemic has significantly impacted global health, social, and economic situations since its emergence in December 2019. The primary focus of this study is to propose a distinct vaccination policy and assess its impact on controlling COVID-19 transmission in Malaysia using a Bayesian data-driven approach, concentrating on the year 2021. We employ a compartmental Susceptible-Exposed-Infected-Recovered-Vaccinated (SEIRV) model, incorporating a time-varying transmission rate and a data-driven method for its estimation through an Exploratory Data Analysis (EDA) approach. While no vaccine guarantees total immunity against the disease, and vaccine immunity wanes over time, it is critical to include and accurately estimate vaccine efficacy, as well as a constant vaccine immunity decay or wane factor, to better simulate the dynamics of vaccine-induced protection over time. Based on the distribution and effectiveness of vaccines, we integrated a data-driven estimation of vaccine efficacy, calculated at 75% for Malaysia, underscoring the model's realism and relevance to the specific context of the country. The Bayesian inference framework is used to assimilate various data sources and account for underlying uncertainties in model parameters. The model is fitted to real-world data from Malaysia to analyze disease spread trends and evaluate the effectiveness of our proposed vaccination policy. Our findings reveal that this distinct vaccination policy, which emphasizes an accelerated vaccination rate during the initial stages of the program, is highly effective in mitigating the spread of COVID-19 and substantially reducing the pandemic peak and new infections. The study found that vaccinating 57-66% of the population (as opposed to 76% in the real data) with a better vaccination policy such as proposed here is able to significantly reduce the number of new infections and ultimately reduce the costs associated with new infections. The study contributes to the development of a robust and informative representation of COVID-19 transmission and vaccination, offering valuable insights for policymakers on the potential benefits and limitations of different vaccination policies, particularly highlighting the importance of a well-planned and efficient vaccination rollout strategy. While the methodology used in this study is specifically applied to national data from Malaysia, its successful application to local regions within Malaysia, such as Selangor and Johor, indicates its adaptability and potential for broader application. This demonstrates the model's adaptability for policy assessment and improvement across various demographic and epidemiological landscapes, implying its usefulness for similar datasets from various geographical regions.

Socioeconomic disparities in cancer incidence and mortality in England and the impact of age-at-diagnosis on cancer mortality.

BACKGROUND: We identify socioeconomic disparities by region in cancer morbidity and mortality in England for all-cancer and type-specific cancers, and use incidence data to quantify the impact of cancer diagnosis delays on cancer deaths between 2001-2016. METHODS AND FINDINGS: We obtain population cancer morbidity and mortality rates at various age, year, gender, deprivation, and region levels based on a Bayesian approach. A significant increase in type-specific cancer deaths, which can also vary among regions, is shown as a result of delay in cancer diagnoses. Our analysis suggests increase of 7.75% (7.42% to 8.25%) in female lung cancer mortality in London, as an impact of 12-month delay in cancer diagnosis, and a 3.39% (3.29% to 3.48%) increase in male lung cancer mortality across all regions. The same delay can cause a 23.56% (23.09% to 24.30%) increase in male bowel cancer mortality. Furthermore, for all-cancer mortality, the highest increase in deprivation gap happened in the East Midlands, from 199 (186 to 212) in 2001, to 239 (224 to 252) in 2016 for males, and from 114 (107 to 121) to 163 (155 to 171) for females. Also, for female lung cancer, the deprivation gap has widened with the highest change in the North West, e.g. for incidence from 180 (172 to 188) to 272 (261 to 282), whereas it has narrowed for prostate cancer incidence with the biggest reduction in the South West from 165 (139 to 190) in 2001 to 95 (72 to 117) in 2016. CONCLUSIONS: The analysis reveals considerable disparities in all-cancer and some type-specific cancers with respect to socioeconomic status. Furthermore, a significant increase in cancer deaths is shown as a result of delays in cancer diagnoses which can be linked to concerns about the effect of delay in cancer screening and diagnosis during the COVID-19 pandemic. Public health interventions at regional and deprivation level can contribute to prevention of cancer deaths.

Is Environmental and Occupational Particulate Air Pollution Exposure Related to Type-2 Diabetes and Dementia? A Cross-Sectional Analysis of the UK Biobank.

Human exposure to particulate air pollution (e.g., PM2.5) can lead to adverse health effects, with compelling evidence that it can increase morbidity and mortality from respiratory and cardiovascular disease. More recently, there has also been evidence that long-term environmental exposure to particulate air pollution is associated with type-2 diabetes mellitus (T2DM) and dementia. There are many occupations that may expose workers to airborne particles and that some exposures in the workplace are very similar to environmental particulate pollution. We conducted a cross-sectional analysis of the UK Biobank cohort to verify the association between environmental particulate air pollution (PM2.5) exposure and T2DM and dementia, and to investigate if occupational exposure to particulates that are similar to those found in environmental air pollution could increase the odds of developing these diseases. The UK Biobank dataset comprises of over 500,000 participants from all over the UK. Environmental exposure variables were used from the UK Biobank. To estimate occupational exposure both the UK Biobank's data and information from a job exposure matrix, specifically developed for UK Biobank (Airborne Chemical Exposure-Job Exposure Matrix (ACE JEM)), were used. The outcome measures were participants with T2DM and dementia. In appropriately adjusted models, environmental exposure to PM2.5 was associated with an odds ratio (OR) of 1.02 (95% CI 1.00 to 1.03) per unit exposure for developing T2DM, while PM2.5 was associated with an odds ratio of 1.06 (95% CI 0.96 to 1.16) per unit exposure for developing dementia. These environmental results align with existing findings in the published literature. Five occupational exposures (dust, fumes, diesel, mineral, and biological dust in the most recent job estimated with the ACE JEM) were investigated and the risks for most exposures for T2DM and for all the exposures for dementia were not significantly increased in the adjusted models. This was confirmed in a subgroup of participants where a full occupational history was available allowed an estimate of workplace exposures. However, when not adjusting for gender, some of the associations become significant, which suggests that there might be a bias between the occupational assessments for men and women. The results of the present study do not provide clear evidence of an association between occupational exposure to particulate matter and T2DM or dementia.

Latent likelihood ratio tests for assessing spatial kernels in epidemic models.

One of the most important issues in the critical assessment of spatio-temporal stochastic models for epidemics is the selection of the transmission kernel used to represent the relationship between infectious challenge and spatial separation of infected and susceptible hosts. As the design of control strategies is often based on an assessment of the distance over which transmission can realistically occur and estimation of this distance is very sensitive to the choice of kernel function, it is important that models used to inform control strategies can be scrutinised in the light of observation in order to elicit possible evidence against the selected kernel function. While a range of approaches to model criticism is in existence, the field remains one in which the need for further research is recognised. In this paper, building on earlier contributions by the authors, we introduce a new approach to assessing the validity of spatial kernels-the latent likelihood ratio tests-which use likelihood-based discrepancy variables that can be used to compare the fit of competing models, and compare the capacity of this approach to detect model mis-specification with that of tests based on the use of infection-link residuals. We demonstrate that the new approach can be used to formulate tests with greater power than infection-link residuals to detect kernel mis-specification particularly when the degree of mis-specification is modest. This new tests avoid the use of a fully Bayesian approach which may introduce undesirable complications related to computational complexity and prior sensitivity.

Evaluation of the Suitability of an Existing Job-Exposure Matrix for the Assessment of Exposure of UK Biobank Participants to Dust, Fumes, and Diesel Exhaust Particulates.

Many epidemiological studies have shown an association between outdoor particulate air pollutants and increased morbidity and mortality. Inhalation of ambient aerosols can exacerbate or promote the development of cardiovascular and pulmonary diseases as well as other diseases, such as type 2 diabetes mellitus (T2DM) and neurodegenerative diseases. Occupational exposure to dust, fumes and diesel exhaust particulates can also cause adverse health outcomes and there are numerous occupations where workers are exposed to airborne particles that are similar to ambient air pollution. An individual's job title has normally been identified as a major determinant of workplace exposure in epidemiological studies. This has led to the development of Job-Exposure Matrices (JEMs) as a way of characterising specific workplace exposures. One JEM for airborne chemical exposures is the Airborne Chemical Exposure Job-Exposure Matrix (ACE JEM), developed specifically for the UK Biobank cohort. The objective of this paper is to evaluate the suitability of the ACE JEM in assessing occupational aerosol exposure of participants in the UK Biobank. We searched the scientific literature to identify exposure data linked to selected jobs in the ACE JEM and compared these data with the JEM assessments. Additionally, we carried out an independent expert-based assessment of exposure to compare with the JEM estimates. There is good published evidence to substantiate the high dust and biological dust assignments in the JEM and more limited evidence for diesel exhaust particulates. There is limited evidence in the published literature to substantiate moderate or low exposure assignments in the JEM. The independent expert-based assessment found good agreement at the two extremes of exposure in the JEM (high and no exposure), with uncertainty in all other classifications. The ACE JEM assignments are probably reliable for highly exposed jobs and for jobs assigned as unexposed. However, the assignments for medium and low exposures are less reliable. The ACE JEM is likely to be a good tool to examine associations between occupational exposures to particulates and chronic disease, although it should be used with caution. Further efforts should be made to improve the reliability of the ACE JEM.

Cancer morbidity trends and regional differences in England-A Bayesian analysis.

Reliable modelling of the dynamics of cancer morbidity risk is important, not least due to its significant impact on healthcare and related policies. We identify morbidity trends and regional differences in England for all-cancer and type-specific incidence between 1981 and 2016. We use Bayesian modelling to estimate cancer morbidity incidence at various age, year, gender, and region levels. Our analysis shows increasing trends in most rates and marked regional variations that also appear to intensify through time in most cases. All-cancer rates have increased significantly, with the highest increase in East, North West and North East. The absolute difference between the rates in the highest- and lowest-incidence region, per 100,000 people, has widened from 39 (95% CI 33-45) to 86 (78-94) for females, and from 94 (85-104) to 116 (105-127) for males. Lung cancer incidence for females has shown the highest increase in Yorkshire and the Humber, while for males it has declined in all regions with the highest decrease in London. The gap between the highest- and lowest-incidence region for females has widened from 47 (42-51) to 94 (88-100). Temporal change in in bowel cancer risk is less manifested, with regional heterogeneity also declining. Prostate cancer incidence has increased with the highest increase in London, and the regional gap has expanded from 33 (30-36) to 76 (69-83). For breast cancer incidence the highest increase has occurred in North East, while the regional variation shows a less discernible increase. The analysis reveals that there are important regional differences in the incidence of all-type and type-specific cancers, and that most of these regional differences become more pronounced over time. A significant increase in regional variation has been demonstrated for most types of cancer examined here, except for bowel cancer where differences have narrowed.

Exposure to Environmental and Occupational Particulate Air Pollution as a Potential Contributor to Neurodegeneration and Diabetes: A Systematic Review of Epidemiological Research.

It has been hypothesised that environmental air pollution, especially airborne particles, is a risk factor for type 2 diabetes mellitus (T2DM) and neurodegenerative conditions. However, epidemiological evidence is inconsistent and has not been previously evaluated as part of a systematic review. Our objectives were to carry out a systematic review of the epidemiological evidence on the association between long-term exposure to ambient air pollution and T2DM and neurodegenerative diseases in adults and to identify if workplace exposures to particles are associated with an increased risk of T2DM and neurodegenerative diseases. Assessment of the quality of the evidence was carried out using the GRADE system, which considers the quality of the studies, consistency, directness, effect size, and publication bias. Available evidence indicates a consistent positive association between ambient air pollution and both T2DM and neurodegeneration risk, such as dementia and a general decline in cognition. However, corresponding evidence for workplace exposures are lacking. Further research is required to identify the link and mechanisms associated with particulate exposure and disease pathogenesis and to investigate the risks in occupational populations. Additional steps are needed to reduce air pollution levels and possibly also in the workplace environment to decrease the incidence of T2DM and cognitive decline.

The Essential Elements of a Risk Governance Framework for Current and Future Nanotechnologies.

Societies worldwide are investing considerable resources into the safe development and use of nanomaterials. Although each of these protective efforts is crucial for governing the risks of nanomaterials, they are insufficient in isolation. What is missing is a more integrative governance approach that goes beyond legislation. Development of this approach must be evidence based and involve key stakeholders to ensure acceptance by end users. The challenge is to develop a framework that coordinates the variety of actors involved in nanotechnology and civil society to facilitate consideration of the complex issues that occur in this rapidly evolving research and development area. Here, we propose three sets of essential elements required to generate an effective risk governance framework for nanomaterials. (1) Advanced tools to facilitate risk-based decision making, including an assessment of the needs of users regarding risk assessment, mitigation, and transfer. (2) An integrated model of predicted human behavior and decision making concerning nanomaterial risks. (3) Legal and other (nano-specific and general) regulatory requirements to ensure compliance and to stimulate proactive approaches to safety. The implementation of such an approach should facilitate and motivate good practice for the various stakeholders to allow the safe and sustainable future development of nanotechnology.

Evidence-based controls for epidemics using spatio-temporal stochastic models in a Bayesian framework.

The control of highly infectious diseases of agricultural and plantation crops and livestock represents a key challenge in epidemiological and ecological modelling, with implemented control strategies often being controversial. Mathematical models, including the spatio-temporal stochastic models considered here, are playing an increasing role in the design of control as agencies seek to strengthen the evidence on which selected strategies are based. Here, we investigate a general approach to informing the choice of control strategies using spatio-temporal models within the Bayesian framework. We illustrate the approach for the case of strategies based on pre-emptive removal of individual hosts. For an exemplar model, using simulated data and historic data on an epidemic of Asiatic citrus canker in Florida, we assess a range of measures for prioritizing individuals for removal that take account of observations of an emerging epidemic. These measures are based on the potential infection hazard a host poses to susceptible individuals (hazard), the likelihood of infection of a host (risk) and a measure that combines both the hazard and risk (threat). We find that the threat measure typically leads to the most effective control strategies particularly for clustered epidemics when resources are scarce. The extension of the methods to a range of other settings is discussed. A key feature of the approach is the use of functional-model representations of the epidemic model to couple epidemic trajectories under different control strategies. This induces strong positive correlations between the epidemic outcomes under the respective controls, serving to reduce both the variance of the difference in outcomes and, consequently, the need for extensive simulation.

A mechanistic spatio-temporal framework for modelling individual-to-individual transmission-With an application to the 2014-2015 West Africa Ebola outbreak.

In recent years there has been growing availability of individual-level spatio-temporal disease data, particularly due to the use of modern communicating devices with GPS tracking functionality. These detailed data have been proven useful for inferring disease transmission to a more refined level than previously. However, there remains a lack of statistically sound frameworks to model the underlying transmission dynamic in a mechanistic manner. Such a development is particularly crucial for enabling a general epidemic predictive framework at the individual level. In this paper we propose a new statistical framework for mechanistically modelling individual-to-individual disease transmission in a landscape with heterogeneous population density. Our methodology is first tested using simulated datasets, validating our inferential machinery. The methodology is subsequently applied to data that describes a regional Ebola outbreak in Western Africa (2014-2015). Our results show that the methods are able to obtain estimates of key epidemiological parameters that are broadly consistent with the literature, while revealing a significantly shorter distance of transmission. More importantly, in contrast to existing approaches, we are able to perform a more general model prediction that takes into account the susceptible population. Finally, our results show that, given reasonable scenarios, the framework can be an effective surrogate for susceptible-explicit individual models which are often computationally challenging.

Estimation of under-reporting in epidemics using approximations.

Under-reporting in epidemics, when it is ignored, leads to under-estimation of the infection rate and therefore of the reproduction number. In the case of stochastic models with temporal data, a usual approach for dealing with such issues is to apply data augmentation techniques through Bayesian methodology. Departing from earlier literature approaches implemented using reversible jump Markov chain Monte Carlo (RJMCMC) techniques, we make use of approximations to obtain faster estimation with simple MCMC. Comparisons among the methods developed here, and with the RJMCMC approach, are carried out and highlight that approximation-based methodology offers useful alternative inference tools for large epidemics, with a good trade-off between time cost and accuracy.

A Systematic Bayesian Integration of Epidemiological and Genetic Data.

Genetic sequence data on pathogens have great potential to inform inference of their transmission dynamics ultimately leading to better disease control. Where genetic change and disease transmission occur on comparable timescales additional information can be inferred via the joint analysis of such genetic sequence data and epidemiological observations based on clinical symptoms and diagnostic tests. Although recently introduced approaches represent substantial progress, for computational reasons they approximate genuine joint inference of disease dynamics and genetic change in the pathogen population, capturing partially the joint epidemiological-evolutionary dynamics. Improved methods are needed to fully integrate such genetic data with epidemiological observations, for achieving a more robust inference of the transmission tree and other key epidemiological parameters such as latent periods. Here, building on current literature, a novel Bayesian framework is proposed that infers simultaneously and explicitly the transmission tree and unobserved transmitted pathogen sequences. Our framework facilitates the use of realistic likelihood functions and enables systematic and genuine joint inference of the epidemiological-evolutionary process from partially observed outbreaks. Using simulated data it is shown that this approach is able to infer accurately joint epidemiological-evolutionary dynamics, even when pathogen sequences and epidemiological data are incomplete, and when sequences are available for only a fraction of exposures. These results also characterise and quantify the value of incomplete and partial sequence data, which has important implications for sampling design, and demonstrate the abilities of the introduced method to identify multiple clusters within an outbreak. The framework is used to analyse an outbreak of foot-and-mouth disease in the UK, enhancing current understanding of its transmission dynamics and evolutionary process.

New model diagnostics for spatio-temporal systems in epidemiology and ecology.

A cardinal challenge in epidemiological and ecological modelling is to develop effective and easily deployed tools for model assessment. The availability of such methods would greatly improve understanding, prediction and management of disease and ecosystems. Conventional Bayesian model assessment tools such as Bayes factors and the deviance information criterion (DIC) are natural candidates but suffer from important limitations because of their sensitivity and complexity. Posterior predictive checks, which use summary statistics of the observed process simulated from competing models, can provide a measure of model fit but appropriate statistics can be difficult to identify. Here, we develop a novel approach for diagnosing mis-specifications of a general spatio-temporal transmission model by embedding classical ideas within a Bayesian analysis. Specifically, by proposing suitably designed non-centred parametrization schemes, we construct latent residuals whose sampling properties are known given the model specification and which can be used to measure overall fit and to elicit evidence of the nature of mis-specifications of spatial and temporal processes included in the model. This model assessment approach can readily be implemented as an addendum to standard estimation algorithms for sampling from the posterior distributions, for example Markov chain Monte Carlo. The proposed methodology is first tested using simulated data and subsequently applied to data describing the spread of Heracleum mantegazzianum (giant hogweed) across Great Britain over a 30-year period. The proposed methods are compared with alternative techniques including posterior predictive checking and the DIC. Results show that the proposed diagnostic tools are effective in assessing competing stochastic spatio-temporal transmission models and may offer improvements in power to detect model mis-specifications. Moreover, the latent-residual framework introduced here extends readily to a broad range of ecological and epidemiological models.

Modelling under-reporting in epidemics.

Under-reporting of infected cases is crucial for many diseases because of the bias it can introduce when making inference for the model parameters. The objective of this paper is to study the effect of under-reporting in epidemics by considering the stochastic Markovian SIR epidemic in which various reporting processes are incorporated. In particular, we first investigate the effect on the estimation process of ignoring under-reporting when it is present in an epidemic outbreak. We show that such an approach leads to under-estimation of the infection rate and the reproduction number. Secondly, by allowing for the fact that under-reporting is occurring, we develop suitable models for estimation of the epidemic parameters and explore how well the reporting rate and other model parameters can be estimated. We consider the case of a constant reporting probability and also more realistic assumptions which involve the reporting probability depending on time or the source of infection for each infected individual. Due to the incomplete nature of the data and reporting process, the Bayesian approach provides a natural modelling framework and we perform inference using data augmentation and reversible jump Markov chain Monte Carlo techniques.

Non-exponential tolerance to infection in epidemic systems--modeling, inference, and assessment.

The transmission dynamics of infectious diseases have been traditionally described through a time-inhomogeneous Poisson process, thus assuming exponentially distributed levels of disease tolerance following the Sellke construction. Here we focus on a generalization using Weibull individual tolerance thresholds under the susceptible-exposed-infectious-removed class of models which is widely employed in epidemics. Applications with experimental foot-and-mouth disease and historical smallpox data are discussed, and simulation results are presented. Inference is carried out using Markov chain Monte Carlo methods following a Bayesian approach. Model evaluation is performed, where the adequacy of the models is assessed using methodology based on the properties of Bayesian latent residuals, and comparison between 2 candidate models is also considered using a latent likelihood ratio-type test that avoids problems encountered with relevant methods based on Bayes factors.

Modeling the consistency of hypoglycemic symptoms: high variability in diabetes.

BACKGROUND: The aim of the present study was to examine symptoms of hypoglycemia, to develop a method to quantify individual differences in the consistency of symptom reporting, and to investigate which factors affect these differences. METHODS: Participants recorded their symptoms with every episode of hypoglycemia over a 9-12-month period. A novel logistic-type latent variable model was developed to quantify the consistency of each individual's symptom complex and was used to analyze data from 59 subjects (median age, 57.5 years [range, 22-74 years], 65% male, 77% type 1 diabetes) who had experienced 19 or more hypoglycemic episodes. The association between the calculated consistency parameter and age, sex, type and duration of diabetes, and C-peptide and serum angiotensin converting enzyme concentration was examined using a generalized linear model. Analyses were performed under a Bayesian framework, using Markov chain Monte-Carlo methodology. RESULTS: Individuals exhibited substantial differences in between-episode consistency of their symptom reports, with only a small number of individuals exhibiting high levels of consistency. Men were more consistent than women. No other factors affected consistency in patients with normal hypoglycemia awareness. CONCLUSIONS: By using a novel stochastic model as a quantitative tool to compare the consistency of hypoglycemic symptom reporting, much greater intra-individual variability in symptom reporting was identified than has been recognized previously. This is relevant when instructing patients on identification of hypoglycemic symptoms and in interpreting symptomatic responses during experimentally induced hypoglycemia.

Bayesian analysis of experimental epidemics of foot-and-mouth disease.

We investigate the transmission dynamics of a certain type of foot-and-mouth disease (FMD) virus under experimental conditions. Previous analyses of experimental data from FMD outbreaks in non-homogeneously mixing populations of sheep have suggested a decline in viraemic level through serial passage of the virus, but these do not take into account possible variation in the length of the chain of viral transmission for each animal, which is implicit in the non-observed transmission process. We consider a susceptible-exposed-infectious-removed non-Markovian compartmental model for partially observed epidemic processes, and we employ powerful methodology (Markov chain Monte Carlo) for statistical inference, to address epidemiological issues under a Bayesian framework that accounts for all available information and associated uncertainty in a coherent approach. The analysis allows us to investigate the posterior distribution of the hidden transmission history of the epidemic, and thus to determine the effect of the length of the infection chain on the recorded viraemic levels, based on the posterior distribution of a p-value. Parameter estimates of the epidemiological characteristics of the disease are also obtained. The results reveal a possible decline in viraemia in one of the two experimental outbreaks. Our model also suggests that individual infectivity is related to the level of viraemia.