Cerian Webb

University of Cambridge | Cam · Department of Plant Sciences

The ‘One Hundred Important Questions Facing Plant Science Research’ project aimed to capture a global snapshot of the current issues and future questions facing plant science. This revisiting builds on the original 2011 paper. Over 600 questions were collected from anyone interested in plants, which were reduced to a final list of 100 by four teams...

• The expansion of oak processionary moth (OPM) in South-East England continues despite ongoing efforts to control the pest since its introduction in 2006. • Using locations of OPM larval nests, supplied by the Forestry Commission and recorded as part of ongoing surveillance and control measures from 2006 onwards, we show that the expansion of the...

The COVID-19 pandemic has seen infectious disease modelling at the forefront of government decision-making. Models have been widely used throughout the pandemic to estimate pathogen spread and explore the potential impact of different intervention strategies. Infectious disease modellers and policymakers have worked effectively together, but there...

Societal Impact Statement Emerald ash borer (EAB) is thought to have arrived in North America and European Russia at least 10 years prior to detection. Despite heightened awareness that EAB could invade Great Britain (GB), detection in the early stages of establishment is difficult, and initial symptoms might be mistaken for Chalara ash dieback. Ou...

Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but th...

Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but th...

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 r...

This chapter introduces methods for importing data into the MATLAB® workspace and for exporting data for use in other applications. You will learn how to import data using the MATLAB interactive Import Tool and how to import data using built-in functions in script files. The chapter introduces the different formats that imported data can be stored...

In this chapter you will learn how to write separate function files which can be used to group together a set of commands. One of the major advantages of MATLAB® is the vast number of built-in functions; nevertheless the MATLAB library of functions cannot cover every possible scenario. Anonymous functions fill some of these gaps; however, separate...

In this chapter, you will learn the basics of MATLAB® using the command line. The notation for basic mathematical operators is introduced and the role of different types of parentheses summarized. MATLAB records your command history, and we will show you how to access this so that you can repeat commands without having to retype them and how to add...

MATLAB® provides a flexible environment for creating publication standard plots which can be easily modified to meet journal requirements and replicated for alternative data sets.

MATLAB® provides an enormous library of built-in functions; however, there will be times when you cannot find a suitable function. There are two approaches to developing your own functions: anonymous functions and separate function files. Anonymous functions are one-line functions which can be incorporated into a script file and used within that sc...

MATLAB® is a structured programming language – this means that you do not have to code everything from scratch. This makes it easier and quicker to develop sophisticated code. The program contains a large library of built-in functions, many of which are included in the core package available to all users. In this chapter, you will learn how to inte...

As you begin to develop and adapt code for your own projects, it is inevitable that you will come across questions which we have not answered in this book. The options for refining MATLAB® code and graphics are so vast that MATLAB no longer produce printed copies of manuals. Instead the manuals have been replaced with comprehensive documentation fi...

In this chapter, you will learn how to create and work with arrays, vectors and matrices. The chapter introduces the subscript and index methods of accessing data from an array and explores methods to create sequences of values. The built-in functions for creating standard matrices are introduced, and you will explore methods to concatenate and aug...

While MATLAB® can be used as an elaborate calculator and plotting program, to get the most of MATLAB, you will need to be able to do some basic programming. There are five key programming concepts which will enable you to write efficient scripts which automate repetitive tasks: relational operators, logical operators, conditional statements, for lo...

The name MATLAB® is an acronym for Matrix Laboratory and highlights its origins as a package of routines for matrix algebra. The first commercial version of MATLAB was released in 1984 with the MATLAB desktop version released in 2000. MATLAB is continuously evolving to reach a wider audience, and in 2016 a Live Editor interface was released enablin...

The MATLAB® command line is suitable for checking simple calculations and exploring how individual functions work. However, for most tasks it is more efficient to write your code in script files. In this chapter you will learn how to create, edit and save script files, add descriptive text that automatically generates a documentation file for your...

A neglected disease with a nearly forgotten name is making a comeback following a global control programme that almost eradicated it more than forty years ago. Until the 1970s the prevalence of non-venereal treponematosis, including yaws, was greatly reduced after worldwide mass treatment. In 2005, cases were again reported in the Democratic Republ...

Animals can act as a reservoir and source for the emergence of novel meticillin-resistant Staphylococcus aureus (MRSA) clones in human beings. Here, we report the discovery of a strain of S aureus (LGA251) isolated from bulk milk that was phenotypically resistant to meticillin but tested negative for the mecA gene and a preliminary investigation of...

A postal survey of all registered cattle and sheep farmers in East Anglia was carried out from July 2008 to determine bluetongue virus serotype 8 (BTV-8) vaccine uptake in the region. The vaccine was available to farmers in this region from May 2008. The survey was repeated in Cumbria and Northumberland at the beginning of 2009. In these regions, t...

The introduction of a centralized system for recording cattle movements in the UK has provided a framework for network-based models for disease spread. However, there are many types of non-reportable contacts between farms which may play a role in disease spread. The lack of real pathogen data with which to test network models makes it difficult to...

The detailed analysis of an outbreak database has been undertaken to examine the role of contact tracing in controlling an outbreak of possible avian influenza in humans. The outbreak, initiating from the purchase of infected domestic poultry, occurred in North Wales during May and June 2007. During this outbreak, extensive contact tracing was carr...

The British Cattle Movement Service (BCMS) database contains an unprecedented quantity of data on the movement of cattle within the UK. These data may be used to construct models of the contact structure of the UK cattle herd, for epidemiological purposes. There are two significant potential sources of inaccuracy within such models: movements that...

SIR, — The phased release of the blue-tongue vaccine Bovilis btv8 (Intervet) into the bluetongue protection zone since May 2008 has been supported by the Joint Campaign Against Bluetongue (jab). jab was launched to maximise vaccine uptake, with a targeted coverage of at least 80 per cent; it has

The implementation of national systems for recording the movements of cattle between agricultural holdings in the UK has enabled the development and parameterisation of network-based models for disease spread. These data can be used to form a network in which each cattle-holding location is represented by a single node and links between nodes are f...

The rate at which infectious diseases spread through farm animal populations depends both on individual disease characteristics and the opportunity for transmission via close contact. Data on the relationships affecting the contact structure of farm animal populations are, therefore, required to improve mathematical models for the spatial spread of...

Because of the risk to public health posed by the potential presence of bovine spongiform encephalopathy (BSE) in sheep, there are plans to eradicate transmissible spongiform encephalopathies (TSEs) from the British sheep population. We used a mathematical model for the spread of scrapie between sheep flocks to assess the efficacy of five control s...

The spatial and temporal dynamics of many farm animal diseases depend both on disease specific parameters and on the underlying contact structure between farms. Whilst many models for farm animal diseases focus on obtaining and estimating disease transmission parameters, relatively little attention has been given to modelling the underlying network...

Salmonella enterica causes severe systemic diseases in humans and animals and grows intracellularly within discrete tissue foci that become pathological lesions. Because of its lifestyle Salmonella is a superb model for studying the in vivo dynamics of bacterial distribution. Using multicolour fluorescence microscopy in the mouse typhoid model we h...

An accurate estimate of the prevalence of scrapie infection in the Great Britain (GB) sheep flock is essential when assessing any potential risk to human health through exposure to sheep transmissible spongiform encephalopathies (TSEs). One method for assessing the prevalence is to sample sheep intended for human consumption using a diagnostic test...

Our aim was to compare the efficiency of different surveillance strategies for detecting scrapie-infected sheep flocks in the Norwegian population using simulation modelling. The dynamic Monte Carlo simulation model has the flock as the unit. The input parameters include properties of the sheep population (number of flocks, flock size, age distribu...

Susceptibility to clinical scrapie is associated with polymorphisms in the PrP gene. The 'ARR' allele of this gene reduces susceptibility to clinical disease caused by all known strains of the transmissible spongiform encephalopathy (TSE) agent. The British government proposes to use a ram-genotyping scheme to breed genetic resistance to clinical s...

In 1997/1998, an abattoir survey was conducted to determine the likely exposure of the human population to transmissible spongiform encephalopathy (TSE) infection in sheep submitted for slaughter in Great Britain. The survey examined brain material from 2809 sheep processed through British abattoirs. Sampling was targeted by age: 45% of animals tes...

Polymyxa betae is the fungal vector of beet necrotic yellow vein virus (BNYVV), which is the causal agent of the sugar beet disease rhizomania. The within-season dynamics of the fungus are a crucial factor in the occurrence and severity of rhizomania. Late infection of the host by viruliferous fungi enables host resistance to the virus to develop a...

A randomised sample of 2,809 apparently healthy sheep, 55 per cent of them less than 15 months of age, which were slaughtered for human consumption at abattoirs in Great Britain in 1997/98, was taken to establish the prevalence of scrapie infection. The medulla oblongata of each sheep was examined histopathologically at the level of the obex, and f...

Models of particular epidemiological systems can rapidly become complicated by biological detail which can obscure their essential features and behaviour. In general, we wish to retain only those components and processes that contribute to the dynamics of the system. In this paper, we apply asymptotic techniques to an SEI-type model with primary an...

For many biological systems, the behavior of interest is contained in the evolution of transients rather than in the stability of equilibria. These include systems in which perturbations and interruptions occur on a time scale much shorter than the equilibration time, and those in which any final equilibrium is sensitive to initial conditions. In t...

Many models have been constructed to describe the growth of the sugar beet crop up to harvesting. In general, these models have a complex physiological basis, requiring a large number of parameters yet relying on empirical functions with no mechanistic basis to partition assimilates within the crop. An important factor in considering the growth of...