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There is growing recognition in both the experimental and modelling literature of the importance of spatial structure to the dynamics of viral infections in tissues. Aided by the evolution of computing power and motivated by recent biological insights, there has been an explosion of new, spatially-explicit models for within-host viral dynamics in recent years. This development has only been accelerated in the wake of the COVID-19 pandemic. Spatially-structured models offer improved biological realism and can account for dynamics which cannot be well-described by conventional, mean-field approaches. However, despite their growing popularity, spatially-structured models of viral dynamics are underused in biological applications. One major obstacle to the wider application of such models is the huge variety in approaches taken, with little consensus as to which features should be included and how they should be implemented for a given biological context. Previous reviews of the field have focused on specific modelling frameworks or on models for particular viral species. Here, we instead apply a scoping review approach to the literature of spatially-structured viral dynamics models as a whole to provide an exhaustive update of the state of the field. Our analysis is structured along two axes, methodology and viral species, in order to examine the breadth of techniques used and the requirements of different biological applications. We then discuss the contributions of mathematical and computational modelling to our understanding of key spatially-structured aspects of viral dynamics, and suggest key themes for future model development to improve robustness and biological utility.

During the COVID-19 pandemic, case isolation emerged as a key non-pharmaceutical intervention in pandemic response. Its effectiveness hinges on the timing of isolation, which is often dictated by the onset of contagiousness. While minimizing isolation delays is crucial, the impact of evolving epidemic dynamics, such as changes in viral load distributions among cases, is less understood. These dynamics could inform more efficient isolation strategies. We developed a multi-scale agent-based model to assess isolation policies that consider viral loads. Our model compares the outcomes of universal isolation with strategies that exempt low viral load cases post-peak. We found that most low viral load cases identified after the peak are less contagious, raising the question of their need for isolation. Our analysis reveals that exempting these individuals slightly increases new infections and, unexpectedly, reduces efficiency, defined as infections averted per isolation. These results advise caution with adaptive isolation policies. Our flexible model can evaluate complex strategies, aiding future public health planning.

As standards of care advance, patients are living longer and once-fatal diseases are becoming manageable. Clinical trials increasingly focus on reducing disease burden, which can be quantified by the timing and occurrence of multiple non-fatal clinical events. Most existing methods for the analysis of multiple event-time data require stringent modeling assumptions that can be difficult to verify empirically, leading to treatment efficacy estimates that forego interpretability when the underlying assumptions are not met. Moreover, most existing methods do not appropriately account for informative terminal events, such as premature treatment discontinuation or death, which prevent the occurrence of subsequent events. To address these limitations, we derive and validate estimation and inference procedures for the area under the mean cumulative function (AUMCF), an extension of the restricted mean survival time to the multiple event-time setting. The AUMCF is nonparametric, clinically interpretable, and properly accounts for terminal competing risks. To enable covariate adjustment, we also develop an augmentation estimator that provides efficiency at least equaling, and often exceeding, the unadjusted estimator. The utility and interpretability of the AUMCF are illustrated with extensive simulation studies and through an analysis of multiple heart-failure-related endpoints using data from the Beta-Blocker Evaluation of Survival Trial (BEST) clinical trial. Our open-source R package MCC makes conducting AUMCF analyses straightforward and accessible.

From structural biology to epidemiology, predictions from machine learning (ML) models increasingly complement costly gold-standard data to enable faster, more affordable, and scalable scientific inquiry. In response, prediction-based (PB) inference has emerged to accommodate statistical analysis using a large volume of predictions together with a small amount of gold-standard data. The goals of PB inference are two-fold: (i) to mitigate bias from errors in predictions and (ii) to improve efficiency relative to traditional inference using only the gold-standard data. Motwani and Witten (2023) recently revisited two key PB inference approaches and found that only one method, Prediction-powered Inference (PPI) proposed by Angelopoulos et al. (2023), achieves (i). In this paper, we find that PPI does not achieve (ii). We revisit the double sampling literature and show that, with a simple modification, PPI can be adjusted to provide theoretically justified improvements in efficiency. We also contextualize PB inference with economics and statistics literature dating back to the 1960s to highlight the utility of classical methods in this contemporary problem. Our extensive theoretical analyses, along with an analysis of UK Biobank data, indicate that our proposal effectively mitigates bias and improves efficiency, making it preferable for use in practice.

Mediation analysis for survival outcomes is challenging. Most existing methods quantify the treatment effect using the hazard ratio (HR) and attempt to decompose the HR into the direct effect of treatment plus an indirect, or mediated, effect. However, the HR is not expressible as an expectation, which complicates this decomposition, both in terms of estimation and interpretation. Here, we present an alternative approach which leverages pseudo-values to simplify estimation and inference. Pseudo-values take censoring into account during their construction, and once derived, can be modeled in the same way as any continuous outcome. Thus, pseudo-values enable mediation analysis for a survival outcome to fit seamlessly into standard mediation software (e.g. CMAverse in R). Pseudo-values are easy to calculate via a leave-one-observation-out procedure (i.e. jackknifing) and the calculation can be accelerated when the influence function of the estimator is known. Mediation analysis for causal effects defined by survival probabilities, restricted mean survival time, and cumulative incidence functions - in the presence of competing risks - can all be performed within this framework. Extensive simulation studies demonstrate that the method is unbiased across 324 scenarios/estimands and controls the type-I error at the nominal level under the null of no mediation. We illustrate the approach using data from the PARADIGMS clinical trial for the treatment of pediatric multiple sclerosis using fingolimod. In particular, we evaluate whether an imaging biomarker lies on the causal path between treatment and time-to-relapse, which aids in justifying this biomarker as a surrogate outcome. Our approach greatly simplifies mediation analysis for survival data and provides a decomposition of the total effect that is both intuitive and interpretable., Comment: Mediation, Pseudo-Values, Time-to-event, Survival Analysis, Restricted Mean Survival Time, Competing Risks

Increasingly, experimentalists and modellers alike have come to recognise the important role of spatial structure in infection dynamics. Almost invariably, spatial computational models of viral infections - as with in vitro experimental systems - represent the tissue as wide and flat, which is often assumed to be representative of entire affected tissue within the host. However, this assumption fails to take into account the distinctive geometry of the respiratory tract in the context of viral infections. The respiratory tract is characterised by a tubular, branching structure, and moreover is spatially heterogeneous: deeper regions of the lung are composed of far narrower airways and are associated with more severe infection. Here, we extend a typical multicellular model of viral dynamics to account for two essential features of the geometry of the respiratory tract: the tubular structure of airways, and the branching process between airway generations. We show that, with this more realistic tissue geometry, the dynamics of infection are substantially changed compared to standard computational and experimental approaches, and that the resulting model is equipped to tackle important biological phenomena that do not arise in a flat host tissue, including viral lineage dynamics, and heterogeneity in immune responses to infection in different regions of the respiratory tree. Our findings suggest aspects of viral dynamics which current in vitro systems may be insufficient to describe, and point to several features of respiratory infections which can be experimentally assessed.

Ensuring that machine learning (ML) models are safe, effective, and equitable across all patient groups is essential for clinical decision-making and for preventing the reinforcement of existing health disparities. This review examines notions of fairness used in ML for health, including a review of why ML models can be unfair and how fairness has been quantified in a wide range of real-world examples. We provide an overview of commonly used fairness metrics and supplement our discussion with a case-study of an openly available electronic health record (EHR) dataset. We also discuss the outlook for future research, highlighting current challenges and opportunities in defining fairness in health.

Plasmodium vivax is the most geographically widespread malaria parasite due to its ability to remain dormant (as a hypnozoite) in the human liver and subsequently reactivate. Given the majority of P. vivax infections are due to hypnozoite reactivation, targeting the hypnozoite reservoir with a radical cure is crucial for achieving P. vivax elimination. Stochastic effects can strongly influence dynamics when disease prevalence is low or when the population size is small. Hence, it is important to account for this when modelling malaria elimination.cWe use a stochastic multiscale model of P. vivax transmission to study the impacts of multiple rounds of mass drug administration (MDA) with a radical cure, accounting for superinfection and hypnozoite dynamics. Our results indicate multiple rounds of MDA with a high-efficacy drug are needed to achieve a substantial probability of elimination. This work has the potential to help guide P. vivax elimination strategies by quantifying elimination probabilities for an MDA approach.

Quantum photonic integrated circuits, composed of linear-optical elements, offer an efficient way for encoding and processing quantum information on-chip. At their core, these circuits rely on reconfigurable phase shifters, typically constructed from classical components such as thermo- or electro-optical materials, while quantum solid-state emitters such as quantum dots are limited to acting as single-photon sources. Here, we demonstrate the potential of quantum dots as reconfigurable phase shifters. We use numerical models based on established literature parameters to show that circuits utilizing these emitters enable high-fidelity operation and are scalable. Despite the inherent imperfections associated with quantum dots, such as imperfect coupling, dephasing, or spectral diffusion, our optimization shows that these do not significantly impact the unitary infidelity. Specifically, they do not increase the infidelity by more than 0.001 in circuits with up to 10 modes, compared to those affected only by standard nanophotonic losses and routing errors. For example, we achieve fidelities of 0.9998 in quantum-dot-based circuits enacting controlled-phase and -not gates without any redundancies. These findings demonstrate the feasibility of quantum emitter-driven quantum information processing and pave the way for cryogenically-compatible, fast, and low-loss reconfigurable quantum photonic circuits., Comment: manuscript includes 10 pages, 4 figures followed by the supplement with 11 pages, 6 figures

The role of direct cell-to-cell spread in viral infections - where virions spread between host and susceptible cells without needing to be secreted into the extracellular environment - has come to be understood as essential to the dynamics of medically significant viruses like hepatitis C and influenza. Recent work in both the experimental and mathematical modelling literature has attempted to quantify the prevalence of cell-to-cell infection compared to the conventional free virus route using a variety of methods and experimental data. However, estimates are subject to significant uncertainty and moreover rely on data collected by inhibiting one mode of infection by either chemical or physical factors, which may influence the other mode of infection to an extent which is difficult to quantify. In this work, we conduct a simulation-estimation study to probe the practical identifiability of the proportion of cell-to-cell infection, using two standard mathematical models and synthetic data that would likely be realistic to obtain in the laboratory. We show that this quantity cannot be estimated using non-spatial data alone, and that the collection of a data which describes the spatial structure of the infection is necessary to infer the proportion of cell-to-cell infection. Our results provide guidance for the design of relevant experiments and mathematical tools for accurately inferring the prevalence of cell-to-cell infection in $\textit{in vitro}$ and $\textit{in vivo}$ contexts.

Causal mediation analysis, pleiotropy analysis, and replication analysis are three highly popular genetic study designs. Although these analyses address different scientific questions, the underlying inference problems all involve large-scale testing of composite null hypotheses. The goal is to determine whether all null hypotheses - as opposed to at least one - in a set of individual tests should simultaneously be rejected. Various recent methodology has been proposed for the aforementioned situations, and an appealing empirical Bayes strategy is to apply the popular two-group model, calculating local false discovery rates (lfdr) for each set of hypotheses. However, such a strategy is difficult due to the need for multivariate density estimation. Furthermore, the multiple testing rules for the empirical Bayes lfdr approach and conventional frequentist z-statistics can disagree, which is troubling for a field that ubiquitously utilizes summary statistics. This work proposes a framework to unify two-group testing in genetic association composite null settings, the conditionally symmetric multidimensional Gaussian mixture model (csmGmm). The csmGmm is shown to demonstrate more robust operating characteristics than recently-proposed alternatives. Crucially, the csmGmm also offers strong interpretability guarantees by harmonizing lfdr and z-statistic testing rules. We extend the base csmGmm to cover each of the mediation, pleiotropy, and replication settings, and we prove that the lfdr z-statistic agreement holds in each situation. We apply the model to a collection of translational lung cancer genetic association studies that motivated this work.

Plasmodium vivax is one of the most geographically widespread malaria parasites in the world due to its ability to remain dormant in the human liver as hypnozoites and subsequently reactivate after the initial infection (i.e. relapse infections). More than 80% of P. vivax infections are due to hypnozoite reactivation. Mathematical modelling approaches have been widely applied to understand P. vivax dynamics and predict the impact of intervention outcomes. In this article, we provide a scoping review of mathematical models that capture P. vivax transmission dynamics published between January 1988 and May 2023 to provide a comprehensive summary of the mathematical models and techniques used to model P. vivax dynamics. We aim to assist researchers working on P. vivax transmission and other aspects of P. vivax malaria by highlighting best practices in currently published models and highlighting where future model development is required. We provide an overview of the different strategies used to incorporate the parasite's biology, use of multiple scales (within-host and population-level), superinfection, immunity, and treatment interventions. In most of the published literature, the rationale for different modelling approaches was driven by the research question at hand. Some models focus on the parasites' complicated biology, while others incorporate simplified assumptions to avoid model complexity. Overall, the existing literature on mathematical models for P. vivax encompasses various aspects of the parasite's dynamics. We recommend that future research should focus on refining how key aspects of P. vivax dynamics are modelled, including spatial heterogeneity in exposure risk, the accumulation of hypnozoite variation, the interaction between P. falciparum and P. vivax, acquisition of immunity, and recovery under superinfection.

Malaria is a parasitic disease, transmitted by mosquito vectors. Plasmodium vivax presents particular challenges for disease control, in light of an undetectable reservoir of latent parasites (hypnozoites) within the host liver. Superinfection, which is driven by temporally proximate mosquito inoculation and/or hypnozoite activation events, is an important feature of P. vivax. Here, we present a model of hypnozoite accrual and superinfection for P. vivax. To couple host and vector dynamics, we construct a density-dependent Markov population process with countably many types, for which disease extinction is shown to occur almost surely. We also establish a functional law of large numbers, taking the form of an infinite-dimensional system of ordinary differential equations that can also be recovered under the hybrid approximation or a standard compartment modelling approach. Recognising that the subset of these equations that models the infection status of human hosts has precisely the same form as the Kolmogorov forward equations for a Markovian network of infinite server queues with an inhomogeneous batch arrival process, we use physical insight into the evolution of the latter to write down a time-dependent multivariate generating function for the solution. We use this characterisation to collapse the infinite-compartment model into a single integrodifferential equation (IDE) governing the intensity of mosquito-to-human transmission. Through a steady state analysis, we recover a threshold phenomenon for this IDE in terms of a bifurcation parameter $R_0$, with the disease-free equilibrium shown to be uniformly asymptotically stable if $R_0<1$ and an endemic equilibrium solution emerging if $R_0>1$. Our work provides a theoretical basis to explore the epidemiology of P. vivax, and introduces a general strategy for constructing tractable population-level models of malarial superinfection.

Meta-analysis aggregates information across related studies to provide more reliable statistical inference and has been a vital tool for assessing the safety and efficacy of many high profile pharmaceutical products. A key challenge in conducting a meta-analysis is that the number of related studies is typically small. Applying classical methods that are asymptotic in the number of studies can compromise the validity of inference, particularly when heterogeneity across studies is present. Moreover, serious adverse events are often rare and can result in one or more studies with no events in at least one study arm. Practitioners often apply arbitrary continuity corrections or remove zero-event studies to stabilize or define effect estimates in such settings, which can further invalidate subsequent inference. To address these significant practical issues, we introduce an exact inference method for comparing event rates in two treatment arms under a random effects framework, which we coin "XRRmeta". In contrast to existing methods, the coverage of the confidence interval from XRRmeta is guaranteed to be at or above the nominal level (up to Monte Carlo error) when the event rates, number of studies, and/or the within-study sample sizes are small. Extensive numerical studies indicate that XRRmeta does not yield overly conservative inference and we apply our proposed method to two real-data examples using our open source R package.

To support the ongoing management of viral respiratory diseases, many countries are moving towards an integrated model of surveillance for SARS-CoV-2, influenza, and other respiratory pathogens. While many surveillance approaches catalysed by the COVID-19 pandemic provide novel epidemiological insight, continuing them as implemented during the pandemic is unlikely to be feasible for non-emergency surveillance, and many have already been scaled back. Furthermore, given anticipated co-circulation of SARS-CoV-2 and influenza, surveillance activities in place prior to the pandemic require review and adjustment to ensure their ongoing value for public health. In this perspective, we highlight key challenges for the development of integrated models of surveillance. We discuss the relative strengths and limitations of different surveillance practices and studies, their contribution to epidemiological assessment, forecasting, and public health decision making.

Mathematical modelling has been used to support the response to the COVID-19 pandemic in countries around the world including Australia and New Zealand. Both these countries have followed similar pandemic response strategies, using a combination of strict border measures and community interventions to minimise infection rates until high vaccine coverage was achieved. This required a different set of modelling tools to those used in countries that experienced much higher levels of prevalence throughout the pandemic. In this article, we provide an overview of some of the mathematical modelling and data analytics work that has helped to inform the policy response to the pandemic in Australia and New Zealand. This is a reflection on our experiences working at the modelling-policy interface and the impact this has had on the pandemic response. We outline the various types of model outputs, from short-term forecasts to longer-term scenario models, that have been used in different contexts. We discuss issues relating to communication between mathematical modellers and stakeholders such as health officials and policymakers. We conclude with some future challenges and opportunities in this area.

\textit{Plasmodium vivax} is the most geographically widespread malaria-causing parasite resulting in significant associated global morbidity and mortality. One of the factors driving this widespread phenomenon is the ability of the parasites to remain dormant in the liver. Known as hypnozoites, they reside in the liver following an initial exposure, before activating later to cause further infections, referred to as relapses. As around 79-96$\%$ of infections are attributed to relapses, we expect it will be highly impactful to apply treatment to target the hypnozoite reservoir to eliminate \textit{P. vivax}. Treatment with a radical cure to target the hypnozoite reservoir is a potential tool to control or eliminate \textit{P. vivax}. We have developed a multiscale mathematical model as a system of integro-differential equations that captures the complex dynamics of \textit{P. vivax} hypnozoites and the effect of hypnozoite relapse on disease transmission. Here, we use our model to study the anticipated effect of radical cure treatment administered via a mass drug administration (MDA) program. We implement multiple rounds of MDA with a fixed interval between rounds, starting from different steady-state disease prevalences. We then construct an optimisation model to obtain the optimal MDA interval. We also incorporate mosquito seasonality in our model to study its effect on the optimal treatment regime. We find that the effect of MDA interventions is temporary and depends on the pre-intervention disease prevalence (and choice of model parameters) as well as the number of MDA rounds under consideration. We find radical cure alone may not be enough to lead to \textit{P. vivax} elimination under our mathematical model (and choice of model parameters) since the prevalence of infection eventually returns to pre-MDA levels., Comment: 39 pages, 14 figures

Malaria is a vector-borne disease that exacts a grave toll in the Global South. The epidemiology of Plasmodium vivax, the most geographically expansive agent of human malaria, is characterised by the accrual of a reservoir of dormant parasites known as hypnozoites. Relapses, arising from hypnozoite activation events, comprise the majority of the blood-stage infection burden, with implications for the acquisition of immunity and the distribution of superinfection. Here, we construct a hybrid transmission model for P. vivax that concurrently accounts for the accrual of the hypnozoite reservoir, (blood-stage) superinfection and the acquisition of immunity. We begin by analytically characterising within-host dynamics as a function of mosquito-to-human transmission intensity, extending our previous model (comprising an open network of infinite server queues) to capture a discretised immunity level. To model transmission-blocking and antidisease immunity, we allow for geometric decay in the respective probabilities of successful human-to-mosquito transmission and symptomatic blood-stage infection as a function of this immunity level. Under a hybrid approximation -- whereby probabilistic within-host distributions are cast as expected population-level proportions -- we couple host and vector dynamics to recover a deterministic compartmental model in line with Ross-Macdonald theory. We then perform a steady-state analysis for this compartmental model, informed by the (analytic) distributions derived at the within-host level. To characterise transient dynamics, we derive a reduced system of integrodifferential equations (IDEs), likewise informed by our within-host queueing network, allowing us to recover population-level distributions for various quantities of epidemiological interest. Our model provides insights into important, but poorly understood, epidemiological features of P. vivax.

There has been an increasing recognition of the utility of models of the spatial dynamics of viral spread within tissues. Multicellular models, where cells are represented as discrete regions of space coupled to a virus density surface, are a popular approach to capture these dynamics. Conventionally, such models are simulated by discretising the viral surface and depending on the rate of viral diffusion and other considerations, a finer or coarser discretisation may be used. The impact that this choice may have on the behaviour of the system has not been studied. Here we demonstrate that, if rates of viral diffusion are small, then the choice of spatial discretisation of the viral surface can have quantitative and even qualitative influence on model outputs. We investigate in detail the mechanisms driving these phenomena and discuss the constraints on the design and implementation of multicellular viral dynamics models for different parameter configurations., Comment: 28 pages, 11 figures

Plasmodium (P.) falciparum and P. vivax are the two most common causes of malaria. While the majority of deaths and severe morbidity are due to P. falciparum, P. vivax poses a greater challenge to eliminating malaria outside of Africa due to its ability to form latent liver stage parasites (hypnozoites), which can cause relapsing episodes within an individual patient. In areas where P. falciparum and P. vivax are co-endemic, individuals can carry parasites of both species simultaneously. These mixed infections complicate dynamics in several ways; treatment of mixed infections will simultaneously affect both species, P. falciparum can mask the detection of P. vivax, and it has been hypothesised that clearing P. falciparum may trigger a relapse of dormant P. vivax. When mixed infections are treated for only blood-stage parasites, patients are at risk of relapse infections due to P. vivax hypnozoites. We present a stochastic mathematical model that captures interactions between P. falciparum and P. vivax, and incorporates both standard schizontocidal treatment (which targets blood-stage parasites) and radical treatment (which additionally targets liver-stage parasites). We apply this model to assess the implications of different treatment coverage of radical cure for mixed and P. vivax infections and a so-called "unified radical cure" treatment strategy for P. falciparum, P. vivax and mixed infections. We find that a unified radical cure strategy, with G6PD screening, leads to a substantially lower incidence of malaria cases and deaths overall. We perform a one-way sensitivity analysis to highlight important model parameters.

In controlling transmission of COVID-19, the effectiveness of border quarantine strategies is a key concern for jurisdictions in which the local prevalence of disease and immunity is low. In settings like this such as China, Australia, and New Zealand, rare outbreak events can lead to escalating epidemics and trigger the imposition of large scale lockdown policies. Here, we examine to what degree vaccination status of incoming arrivals and the quarantine workforce can allow relaxation of quarantine requirements. To do so, we develop and apply a detailed model of COVID-19 disease progression and transmission taking into account nuanced timing factors. Key among these are disease incubation periods and the progression of infection detectability during incubation. Using the disease characteristics associated with the ancestral lineage of SARS-CoV-2 to benchmark the level of acceptable risk, we examine the performance of the border quarantine system for vaccinated arrivals. We examine disease transmission and vaccine efficacy parameters over a wide range, covering plausible values for the Delta variant currently circulating globally. Our results indicate a threshold in outbreak potential as a function of vaccine efficacy, with the time until an outbreak increasing by up to two orders of magnitude as vaccine efficacy against transmission increases from 70% to 90%. For parameters corresponding to the Delta variant, vaccination is able to maintain the capacity of quarantine systems to reduce case importation and outbreak risk, by counteracting the pathogen's increased infectiousness. To prevent outbreaks, heightened vaccination in border quarantine systems must be combined with mass vaccination. The ultimate success of these programs will depend sensitively on the efficacy of vaccines against viral transmission.

Malaria is a mosquito-borne disease with a devastating global impact. Plasmodium vivax is a major cause of human malaria beyond sub-Saharan Africa. Relapsing infections, driven by a reservoir of liver-stage parasites known as hypnozoites, present unique challenges for the control of P. vivax malaria. Following indeterminate dormancy periods, hypnozoites may activate to trigger relapses. Clearance of the hypnozoite reservoir through drug treatment (radical cure) has been proposed as a potential tool for the elimination of P. vivax malaria. Here, we introduce a stochastic, within-host model to jointly characterise hypnozoite and infection dynamics for an individual in a general transmission setting, allowing for radical cure. We begin by extending an existing activation-clearance model for a single hypnozoite, adapted to both short- and long-latency strains, to include drug treatment. We then embed this activation-clearance model in an epidemiological framework accounting for repeated mosquito inoculation and the administration of radical cure. By constructing an open network of infinite server queues, we derive analytic expressions for several quantities of epidemiological significance, including the size of the hypnozoite reservoir; the relative contribution of relapses to the infection burden; the distribution of multiple infections; the cumulative number of recurrences over time, and the time to first recurrence following drug treatment. By deriving, rather than assuming parameteric forms, we characterise the transient dynamics of the hypnozoite reservoir following radical cure more accurately than previous approaches. To yield population-level insights, our analytic within-host distributions can be embedded in multiscale models. Our work thus contributes to the epidemiological understanding of the effects of radical cure on P. vivax malaria.

Malaria is an infectious disease with an immense global health burden. Plasmodium vivax is the most geographically widespread species of malaria. Relapsing infections, caused by the activation of liver-stage parasites known as hypnozoites, are a critical feature of the epidemiology of Plasmodium vivax. Hypnozoites remain dormant in the liver for weeks or months after inoculation, but cause relapsing infections upon activation. Here, we introduce a dynamic probability model of the activation-clearance process governing both potential relapses and the size of the hypnozoite reservoir. We begin by modelling activation-clearance dynamics for a single hypnozoite using a continuous-time Markov chain. We then extend our analysis to consider activation-clearance dynamics for a single mosquito bite, which can simultaneously establish multiple hypnozoites, under the assumption of independent hypnozoite behaviour. We derive analytic expressions for the time to first relapse and the time to hypnozoite clearance for mosquito bites establishing variable numbers of hypnozoites, both of which are quantities of epidemiological significance. Our results extend those in the literature, which were limited due to an assumption of non-independence. Our within-host model can be embedded readily in multi-scale models and epidemiological frameworks, with analytic solutions increasing the tractability of statistical inference and analysis. Our work therefore provides a foundation for further work on immune development and epidemiological-scale analysis, both of which are important for achieving the goal of malaria elimination., Comment: This is a pre-copyedit version of an article published in Bulletin of Mathematical Biology. The final authenticated version is available online at: https://doi.org/10.1007/s11538-020-00706-1

Genome-wide association studies (GWAS) require accurate cohort phenotyping, but expert labeling can be costly, time-intensive, and variable. Here we develop a machine learning (ML) model to predict glaucomatous optic nerve head features from color fundus photographs. We used the model to predict vertical cup-to-disc ratio (VCDR), a diagnostic parameter and cardinal endophenotype for glaucoma, in 65,680 Europeans in the UK Biobank (UKB). A GWAS of ML-based VCDR identified 299 independent genome-wide significant (GWS; $P\leq5\times10^{-8}$) hits in 156 loci. The ML-based GWAS replicated 62 of 65 GWS loci from a recent VCDR GWAS in the UKB for which two ophthalmologists manually labeled images for 67,040 Europeans. The ML-based GWAS also identified 92 novel loci, significantly expanding our understanding of the genetic etiologies of glaucoma and VCDR. Pathway analyses support the biological significance of the novel hits to VCDR, with select loci near genes involved in neuronal and synaptic biology or known to cause severe Mendelian ophthalmic disease. Finally, the ML-based GWAS results significantly improve polygenic prediction of VCDR and primary open-angle glaucoma in the independent EPIC-Norfolk cohort., Comment: Includes Supplementary Information and Tables

Scientific knowledge and advances are a cornerstone of modern society. They improve our understanding of the world we live in and help us navigate global challenges including emerging infectious diseases, climate change and the biodiversity crisis. For any scientist, whether they work primarily in fundamental knowledge generation or in the applied sciences, it is important to understand how science fits into a decision-making framework. Decision science is a field that aims to pinpoint evidence-based management strategies. It provides a framework for scientists to directly impact decisions or to understand how their work will fit into a decision process. Decision science is more than undertaking targeted and relevant scientific research or providing tools to assist policy makers; it is an approach to problem formulation, bringing together mathematical modelling, stakeholder values and logistical constraints to support decision making. In this paper we describe decision science, its use in different contexts, and highlight current gaps in methodology and application. The COVID-19 pandemic has thrust mathematical models into the public spotlight, but it is one of innumerable examples in which modelling informs decision making. Other examples include models of storm systems (eg. cyclones, hurricanes) and climate change. Although the decision timescale in these examples differs enormously (from hours to decades), the underlying decision science approach is common across all problems. Bridging communication gaps between different groups is one of the greatest challenges for scientists. However, by better understanding and engaging with the decision-making processes, scientists will have greater impact and make stronger contributions to important societal problems.

Combinations of intense non-pharmaceutical interventions ('lockdowns') were introduced in countries worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement lockdown exit strategies that allow restrictions to be relaxed 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 diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, will 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. The roadmap requires a global collaborative effort from the scientific community and policy-makers, and is made up of three parts: i) improve estimation of key epidemiological parameters; ii) understand sources of heterogeneity in populations; 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.