Paul Tupper
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View article: Linear and Sublinear Diversities
Linear and Sublinear Diversities Open
Diversities are an extension of the concept of a metric space, where a non-negative value is assigned to every finite set of points, rather than just pairs. A general theory of diversities has been developed which exhibits many deep analog…
View article: Measuring genetic diversity across populations
Measuring genetic diversity across populations Open
Diversity plays an important role in various domains, including conservation, whether it describes diversity within a population or diversity over a set of species. While various strategies for measuring among-species diversity have emerge…
View article: Optimal Dosing Schedules for Substances Inducing Tolerance
Optimal Dosing Schedules for Substances Inducing Tolerance Open
Many drugs used therapeutically or recreationally induce tolerance: the effect of the substance decreases with repeated use. This phenomenon may reduce the efficacy of the substance unless dosage is increased beyond what is healthy for the…
View article: A method to estimate the serial interval distribution under partially-sampled data
A method to estimate the serial interval distribution under partially-sampled data Open
The serial interval of an infectious disease is an important variable in epidemiology. It is defined as the period of time between the symptom onset times of the infector and infectee in a direct transmission pair. Under partially sampled …
View article: A modeling link between cognitive and biological homeostasis
A modeling link between cognitive and biological homeostasis Open
The problem of stability has long been a limiting factor in developing neural networks that can grow in size and complexity. Outside of particular, narrow parameter ranges, changes in activity can easily result in total loss of control. Hu…
View article: Epidemiological cluster identification using multiple data sources: an approach using logistic regression
Epidemiological cluster identification using multiple data sources: an approach using logistic regression Open
In the management of infectious disease outbreaks, grouping cases into clusters and understanding their underlying epidemiology are fundamental tasks. In genomic epidemiology, clusters are typically identified either using pathogen sequenc…
View article: Game Theoretic Models of Clear versus Plain Speech
Game Theoretic Models of Clear versus Plain Speech Open
Clear speech is a vocal style used when a speaker wishes to improve comprehension, usually due to the presence of external noise, less-than-optimal listening conditions, or when they are simply instructed to speak clearly. Clear speech has…
View article: COVID-19 cluster size and transmission rates in schools from crowdsourced case reports
COVID-19 cluster size and transmission rates in schools from crowdsourced case reports Open
The role of schools in the spread of SARS-CoV-2 is controversial, with some claiming they are an important driver of the pandemic and others arguing that transmission in schools is negligible. School cluster reports that have been collecte…
View article: Author response: COVID-19 cluster size and transmission rates in schools from crowdsourced case reports
Author response: COVID-19 cluster size and transmission rates in schools from crowdsourced case reports Open
Article Figures and data Abstract Editor's evaluation eLife digest Introduction Materials and methods Results Discussion Appendix 1 Data availability References Decision letter Author response Article and author information Metrics Abstrac…
View article: LAG-1: A dynamic, integrative model of learning, attention, and gaze
LAG-1: A dynamic, integrative model of learning, attention, and gaze Open
It is clear that learning and attention interact, but it is an ongoing challenge to integrate their psychological and neurophysiological descriptions. Here we introduce LAG-1, a dynamic neural field model of learning, attention and gaze, t…
View article: Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19
Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19 Open
Estimating key aspects of transmission is crucial in infectious disease control. Serial intervals – the time between symptom onset in an infector and infectee – are fundamental, and help to define rates of transmission, estimates of reprod…
View article: COVID-19 endgame: from pandemic to endemic? Vaccination, reopening and evolution in a well-vaccinated population
COVID-19 endgame: from pandemic to endemic? Vaccination, reopening and evolution in a well-vaccinated population Open
COVID-19 remains a major public health concern, with large resurgences even where there has been widespread uptake of vaccines. Waning immunity and the emergence of new variants will shape the long-term burden and dynamics of COVID-19. We …
View article: COVID-19 cluster size and transmission rates in schools from crowdsourced case reports
COVID-19 cluster size and transmission rates in schools from crowdsourced case reports Open
The role of schools in the spread of the COVID-19 pandemic is controversial, with some claiming they are an important driver of the pandemic and others arguing that transmission in schools is negligible. School cluster reports that have be…
View article: Diversities and the Generalized Circumradius
Diversities and the Generalized Circumradius Open
The generalized circumradius of a set of points $A \subseteq \mathbb{R}^d$ with respect to a convex body $K$ equals the minimum value of $λ\geq 0$ such that $A$ is contained in a translate of $λK$. Each choice of $K$ gives a different func…
View article: Vaccine rollout strategies: The case for vaccinating essential workers early
Vaccine rollout strategies: The case for vaccinating essential workers early Open
In vaccination campaigns against COVID-19, many jurisdictions are using age-based rollout strategies, reflecting the much higher risk of severe outcomes of infection in older groups. In the wake of growing evidence that approved vaccines a…
View article: FRAÏSSÉ LIMITS FOR RELATIONAL METRIC STRUCTURES
FRAÏSSÉ LIMITS FOR RELATIONAL METRIC STRUCTURES Open
The general theory developed by Ben Yaacov for metric structures provides Fraïssé limits which are approximately ultrahomogeneous. We show here that this result can be strengthened in the case of relational metric structures. We give an ex…
View article: COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission
COVID-19 in schools: Mitigating classroom clusters in the context of variable transmission Open
Widespread school closures occurred during the COVID-19 pandemic. Because closures are costly and damaging, many jurisdictions have since reopened schools with control measures in place. Early evidence indicated that schools were low risk …
View article: The Effects of Thermonuclear Reaction‐Rate Variations on Nova Nucleosynthesis: A Sensitivity Study
The Effects of Thermonuclear Reaction‐Rate Variations on Nova Nucleosynthesis: A Sensitivity Study Open
We investigate the effects of thermonuclear reaction-rate uncertainties on nova nucleosynthesis. One-zone nucleosynthesis calculations have been performed by adopting temperature-density-time profiles of the hottest hydrogen-burning zone (…
View article: Vaccine Rollout Strategies: The Case for Vaccinating Essential Workers Early
Vaccine Rollout Strategies: The Case for Vaccinating Essential Workers Early Open
In planning for upcoming mass vaccinations against COVID-19, many jurisdictions have proposed using primarily age-based rollout strategies, where the oldest are vaccinated first and the youngest last. In the wake of growing evidence that a…
View article: Fundamental limitations of contact tracing for COVID-19
Fundamental limitations of contact tracing for COVID-19 Open
Contact tracing has played a central role in COVID-19 control in many jurisdictions and is often used in conjunction with other measures such as travel restrictions and social distancing mandates. Contact tracing is made ineffective, howev…
View article: Fundamental Limitations of Contact Tracing for COVID-19
Fundamental Limitations of Contact Tracing for COVID-19 Open
Contact tracing has played a central role in COVID-19 control in many jurisdictions and is often used in conjunction with other measures such as travel restrictions and social distancing mandates. Contact tracing is made ineffective, howev…
View article: Event-specific interventions to minimize COVID-19 transmission
Event-specific interventions to minimize COVID-19 transmission Open
Significance We provide a simple model of COVID-19 transmission at workplaces, events, and other settings. We use data from reported single-event, short-duration outbreaks to estimate the transmission rate, number of contacts, and turnover…
View article: Lattice Diversities
Lattice Diversities Open
Diversities are a generalization of metric spaces, where instead of the non-negative function being defined on pairs of points, it is defined on arbitrary finite sets of points. Diversities have a well-developed theory. This includes the c…
View article: COVID-19’s unfortunate events in schools: mitigating classroom clusters in the context of variable transmission
COVID-19’s unfortunate events in schools: mitigating classroom clusters in the context of variable transmission Open
Widespread school closures occurred during the COVID-19 pandemic. Because closures are costly and damaging, many jurisdictions have since reopened schools with control measures in place. Early evidence indicated that schools were low risk …
View article: Event-specific interventions to minimize COVID-19 transmission
Event-specific interventions to minimize COVID-19 transmission Open
Coronavirus disease 2019 (COVID-19) is a global pandemic with over 11 million cases worldwide. Currently there is no treatment and no vaccine. Interventions such as hand washing, masks, social distancing, and “social bubbles” are used to l…