Multipath Transmission

Contains reports on two research projects

Software testing in a scientific research group

Scientific software is more difficult to test than many other software products, but scientists are not usually trained in software engineering techniques. Considering how often software is used to produce scientific results, how can we be sure the predictions made from these results are correct? Software engineering techniques should be useful for computational scientists. The problem is they find it difficult to know how to apply domain-independent techniques to the specific problems they face in their work. Nevertheless, we have discovered scientists use their own intuition to reinvent techniques surprisingly similar to those in software engineering. This seems like a good place to start our training.This work was supported by the University of Cambridge/ Wellcome Trust Junior Interdisciplinary Fellowship “Making scientific software easier to understand, test and communicate through modern advances in software engineering”.This is the author accepted manuscript. The final version is available from the Association for Computing Machinery via http://dx.doi.org/10.1145/2851613.285178

A modelling framework to assess the likely effectiveness of facemasks in combination with 'lock-down' in managing the COVID-19 pandemic.

COVID-19 is characterized by an infectious pre-symptomatic period, when newly infected individuals can unwittingly infect others. We are interested in what benefits facemasks could offer as a non-pharmaceutical intervention, especially in the settings where high-technology interventions, such as contact tracing using mobile apps or rapid case detection via molecular tests, are not sustainable. Here, we report the results of two mathematical models and show that facemask use by the public could make a major contribution to reducing the impact of the COVID-19 pandemic. Our intention is to provide a simple modelling framework to examine the dynamics of COVID-19 epidemics when facemasks are worn by the public, with or without imposed 'lock-down' periods. Our results are illustrated for a number of plausible values for parameter ranges describing epidemiological processes and mechanistic properties of facemasks, in the absence of current measurements for these values. We show that, when facemasks are used by the public all the time (not just from when symptoms first appear), the effective reproduction number, Re , can be decreased below 1, leading to the mitigation of epidemic spread. Under certain conditions, when lock-down periods are implemented in combination with 100% facemask use, there is vastly less disease spread, secondary and tertiary waves are flattened and the epidemic is brought under control. The effect occurs even when it is assumed that facemasks are only 50% effective at capturing exhaled virus inoculum with an equal or lower efficiency on inhalation. Facemask use by the public has been suggested to be ineffective because wearers may touch their faces more often, thus increasing the probability of contracting COVID-19. For completeness, our models show that facemask adoption provides population-level benefits, even in circumstances where wearers are placed at increased risk. At the time of writing, facemask use by the public has not been recommended in many countries, but a recommendation for wearing face-coverings has just been announced for Scotland. Even if facemask use began after the start of the first lock-down period, our results show that benefits could still accrue by reducing the risk of the occurrence of further COVID-19 waves. We examine the effects of different rates of facemask adoption without lock-down periods and show that, even at lower levels of adoption, benefits accrue to the facemask wearers. These analyses may explain why some countries, where adoption of facemask use by the public is around 100%, have experienced significantly lower rates of COVID-19 spread and associated deaths. We conclude that facemask use by the public, when used in combination with physical distancing or periods of lock-down, may provide an acceptable way of managing the COVID-19 pandemic and re-opening economic activity. These results are relevant to the developed as well as the developing world, where large numbers of people are resource poor, but fabrication of home-made, effective facemasks is possible. A key message from our analyses to aid the widespread adoption of facemasks would be: 'my mask protects you, your mask protects me'

Computational models to improve surveillance for cassava brown streak disease and minimize yield loss.

Cassava brown streak disease (CBSD) is a rapidly spreading viral disease that affects a major food security crop in sub-Saharan Africa. Currently, there are several proposed management interventions to minimize loss in infected fields. Field-scale data comparing the effectiveness of these interventions individually and in combination are limited and expensive to collect. Using a stochastic epidemiological model for the spread and management of CBSD in individual fields, we simulate the effectiveness of a range of management interventions. Specifically we compare the removal of diseased plants by roguing, preferential selection of planting material, deployment of virus-free 'clean seed' and pesticide on crop yield and disease status of individual fields with varying levels of whitefly density crops under low and high disease pressure. We examine management interventions for sustainable production of planting material in clean seed systems and how to improve survey protocols to identify the presence of CBSD in a field or quantify the within-field prevalence of CBSD. We also propose guidelines for practical, actionable recommendations for the deployment of management strategies in regions of sub-Saharan Africa under different disease and whitefly pressure

Time-dependent infectivity and flexible latent and infectious periods in compartmental models of plant disease

Compartmental models have become the dominant theoretical paradigm in mechanistic modeling of plant disease and offer well-known advantages in terms of analytic tractability, ease of simulation, and extensibility. However, underlying assumptions of constant rates of infection and of exponentially distributed latent and infectious periods are difficult to justify. Although alternative approaches, including van der Plank's seminal discrete time model and models based on the integro-differential formulation of Kermack and McKendrick's model, have been suggested for plant disease and relax these unrealistic assumptions, they are challenging to implement and to analyze. Here, we propose an extension to the susceptible, exposed, infected, and removed (SEIR) compartmental model, splitting the latent and infection compartments and thereby allowing time-varying infection rates and more realistic distributions of latent and infectious periods to be represented. Although the model is, in fact, more general, we specifically target plant disease by demonstrating how it can represent both the van der Plank model and the most commonly used variant of the Kermack and McKendrick (K &amp; M) model (in which the infectivity response is delay Gamma distributed). We show how our reformulation retains the numeric and analytic tractability of SEIR models, and how it can be used to replicate earlier analyses of the van der Plank and K &amp; M models. Our reformulation has the advantage of using elementary mathematical techniques, making implementation easier for the nonspecialist. We show a practical implication of these results for disease control. By taking advantage of the easy extensibility characteristic of compartmental models, we also investigate the effects of including additional biological realism. As an example, we show how the more realistic infection responses we consider interact with host demography and lead to divergent invasion thresholds when compared with the “standard” SEIR model. An ever-increasing number of analyses purportedly extract more biologically realistic invasion thresholds by adding additional biological detail to the SEIR model framework; we contend that our results demonstrate that extending a model that has such a simplistic representation of the infection dynamics may not, in fact, lead to more accurate results. Therefore, we suggest that modelers should carefully consider the underlying assumptions of the simplest compartmental models in their future work. </jats:p

Bed bug deterrence

A recent study in BMC Biology has determined that the immature stage of the bed bug (the nymph) signals its reproductive status to adult males using pheromones and thus avoids the trauma associated with copulation in this species. The success of this nymphal strategy of deterrence is instructive. Against the background of increasing problems with bed bugs, this research raises the question whether pheromones might be used to control them

No Detectable Fertility Benefit from a Single Additional Mating in Wild Stalk-Eyed Flies

Background: Multiple mating by female insects is widespread, and the explanation(s) for repeated mating by females has been the subject of much discussion. Females may profit from mating multiply through direct material benefits that increase their own reproductive output, or indirect genetic benefits that increase offspring fitness. One particular direct benefit that has attracted significant attention is that of fertility assurance, as females often need to mate multiply to achieve high fertility. This hypothesis has never been tested in a wild insect population.Methodology/Principal Findings: Female Malaysian stalk-eyed flies (Teleopsis dalmanni) mate repeatedly during their lifetime, and have been shown to be sperm limited under both laboratory and field conditions. Here we ask whether receiving an additional mating alleviates sperm limitation in wild females. In our experiment one group of females received a single additional mating, while a control group received an interrupted, and therefore unsuccessful, mating. Females that received an additional mating did not lay more fertilised eggs in total, nor did they lay proportionately more fertilised eggs. Female fertility declined significantly through time, demonstrating that females were sperm limited. However, receipt of an additional mating did not significantly alter the rate of this decline.Conclusions/Significance: Our data suggest that the fertility consequences of a single additional mating were small. We discuss this effect (or lack thereof), and suggest that it is likely to be attributed to small ejaculate size, a high proportion of failed copulations, and the presence of X-linked meiotic drive in this species

Communications Research

Contains reports on six research projects

Communication Research

Contains reports on five research projects.Rand Corporatio

Communication Research

Contains reports on six research projects.Rand Corporatio