Martin S. Ridout's research while affiliated with University of Kent and other places
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Publications (100)
The speed of muscle contraction is related to body size; muscles in larger species contract at slower rates. Since contraction speed is a property of the myosin isoform expressed in a muscle, we investigated how sequence changes in a range of muscle myosin II isoforms enable this slower rate of muscle contraction. We considered 798 sequences from 1...
Background:
Accurate prognostication is essential in caring for palliative patients. Various prognostication tools have been validated in many settings in the past few years. Biomarkers of inflammation (albumin and C-reactive protein) are combined to calculate the modified Glasgow prognostic score (mGPS), which has been found to be a simple progno...
The speed of muscle contraction is related to body size; muscles in larger species contract at a slower rate. We investigated the evolution of twelve myosin II isoforms to identify any adapted to increasing body mass in mammals. We identified a correlation between body mass and sequence divergence for the motor domain of three adult myosin II isofo...
Heart rate and the maximum velocity of contraction of striated muscle are inversely related to species size. As mammals evolve to different sizes, adaptations are required such as slower contracting heart and skeletal muscles. Analysis of the motor domain of β-myosin from 67 mammals from two clades identifies 14 sites, out of 800, strongly associat...
Objectives
In palliative care settings, predicting prognosis is important for patients and clinicians. The Palliative Prognostic Index (PPI), a prognostic tool calculated using clinical indices alone has been validated within cancer population. This study was to further test the discriminatory ability of the PPI (ie, its ability to determine whethe...
Biodiversity conservation requires reliable species assessments and rigorously designed surveys. However, determining the survey effort required to reliably detect population change can be challenging for rare, cryptic and elusive species. We used a tropical bromeliad-dwelling frog as a model system to explore a cost-effective sampling design that...
Conservationists often complain that their study species are ignored by donors. However, marketing theory could help understand and increase the profile and fundraising potential of these neglected species. We used linear regression with multimodel inference to analyse data on online behaviour from the websites of the World Wildlife Fund-US (WWF-US...
Appropriate large-scale citizen-science data present important new opportunities for biodiversity modelling, due in part to the wide spatial coverage of information. Recently proposed occupancy modelling approaches naturally incorporate random effects in order to account for annual variation in the composition of sites surveyed. In turn this leads...
Supplementary tables and figures.
(PDF)
Comparing a parametric and non-parametric bootstrap approach.
(PDF)
The Convention on the International Trade in Endangered Species of Wild Flora and Fauna (CITES) regulates trade in over 35,000 species, over 70% of which are orchids. To investigate rule-breaking behavior among traders and buyers in a specific international wildlife trading community, we used direct questions (DQs) and the unmatched count technique...
We consider designs for f factors each at m levels, where f is small but m is large. Main effect designs with mf experimental points are presented. For two factors, two types of designs are investigated, termed sawtooth and dumbbell designs, based on a graphical representation. For three factors, cyclic sawtooth designs are considered. The paper se...
Background Predicting prognosis accurately would help patients and clinicians to make informed decisions about treatment and referral to appropriate services. But user-friendly tools are lacking in clinical practice. The Palliative Prognostic Index(PPI), based on simple clinical indicators, has shown promise in several studies.
Aims Following a pre...
The N-mixture model is widely used to estimate the abundance of a population in the presence of unknown detection probability from only a set of counts subject to spatial and temporal replication (Royle, 2004, Biometrics
60, 105–115). We explain and exploit the equivalence of N-mixture and multivariate Poisson and negative-binomial models, which pr...
A problem of interest for ecology and conservation is that of determining the best allocation of survey effort in studies aimed at estimating the proportion of sites occupied by a species. Many species are difficult to detect and often remain undetected during surveys at sites where they are present. Hence, for the estimator of species occupancy to...
The Palliative Prognostic Index (PPI) is a prognostication tool for palliative care patients based on clinical indices developed in Japan and further validated by one study in the UK. The aim of this study was to test its prediction accuracy in a large inpatient hospice sample. The admitting doctor in three inpatient hospices calculated the PPI sco...
Abstract People’s perceptions of the risk posed by wild animals to human lives and/or livelihoods can influence the rate at which people intentionally kill these species. Consequently,human–wildlife conflict (HWC) management strategies may benefit from the inclusion of actions which reduce risk perceptions. This study uses Participatory Risk Mappin...
Local vote decision fusion is a recently proposed method of target detection for a wireless sensor network in which individual sensors combine their decisions with those of their neighbors and report to a fusion center only if there is a majority in favor of presence. The fusion center reaches a final decision about presence or absence according to...
The proportion of sampling sites occupied by a species is a concept of interest in ecology and biodiversity conservation.
Occupancy surveys based on collecting detection data along transects have become increasingly popular to monitor some species.
To date, the analysis of such data has been carried out by discretizing the data, dividing the transe...
Little is known about interactions between the critically endangered Sumatran tiger Panthera tigris sumatrae and its prey because of the difficulties associated with detecting these species. In this study, we quantify temporal overlap between the Sumatran tiger and five of its presumed prey species from four study areas comprising disturbed lowland...
A population of [PSI(+)] Saccharomyces cerevisiae cells can be cured of the [PSI(+)] prion by the addition of guanidine hydrochloride (GdnHCl). In this paper we extend existing nucleated polymerisation simulation models to investigate the mechanisms that might underlie curing. Our results are consistent with the belief that prions are dispersed thr...
1. Models have been devised previously that allow the estimation of abundance from detection data of unmarked individuals while accounting for imperfect detection, but these are restricted to models for discrete sampling protocols, i.e. replicated detection/non-detection or count data. Furthermore, these models assume that the detections from each...
Summary1. The dominant eigenvalue of the population projection matrix provides the asymptotic growth rate of a population. Perturbation analysis examines how changes in vital rates and transitions affect this growth rate. The standard approach to evaluating the effect of a perturbation uses sensitivities and elasticities to provide a linear approxi...
1. Occupancy is an important concept in ecology. To obtain an unbiased estimator of occupancy it is necessary to address the issue of imperfect detection, which requires conducting replicate surveys at the sites being sampled. As the allocation of total effort can be done in different ways, occupancy studies should be designed carefully to ensure a...
This paper discusses simulation from an absolutely continuous distribution on the positive real line when the Laplace transform
of the distribution is known but its density and distribution functions may not be available. We advocate simulation by the
inversion method using a modified Newton-Raphson method, with values of the distribution and dens...
Data from camera traps that record the time of day at which photographs are taken are used widely to study daily activity
patterns of photographed species. It is often of interest to compare activity patterns, for example, between males and females
of a species or between a predator and a prey species. In this article we propose that the similarity...
Estimates of n0 for Models A, B and C.
(0.03 MB DOC)
Observed proportion of [PSI+] cells and fitted curve of p+(t).
(0.15 MB DOC)
![Figure 1. Simulation showing the proportion of [ PSI + ] cells](profile/Mick-Tuite/publication/24178599/figure/fig1/AS:310241301417998@1450978698873/Simulation-showing-the-proportion-of-PSI-cells_Q320.jpg)
![Table 2 . Cell reproduction data for the strains YJW512 [PSI + ] [PIN +...](profile/Mick-Tuite/publication/24178599/figure/tbl1/AS:670537546203168@1536880017638/Cell-reproduction-data-for-the-strains-YJW512-PSI-PIN-and-YJW679-PSI_Q320.jpg)
![Figure 3. Observed proportion of [ PSI + ] cells and fitted curve of p...](profile/Mick-Tuite/publication/24178599/figure/fig3/AS:310241301418000@1450978698959/Observed-proportion-of-PSI-cells-and-fitted-curve-of-p-t-One-set-of-data-for_Q320.jpg)
Yeast (Saccharomyces cerevisiae) prions are efficiently propagated and the on-going generation and transmission of prion seeds (propagons) to daughter cells during cell division ensures a high degree of mitotic stability. The reversible inhibition of the molecular chaperone Hsp104p by guanidine hydrochloride (GdnHCl) results in cell division-depend...
The complex-step method is a clever way of obtaining a numerical approximation to the first derivative of a function, avoiding the round-off error that plagues standard finite difference approximations. An extension of the method allows second derivatives to be calculated with reduced round-off error. This article provides an overview of the method...
We evaluate the performance of a new mixture model for heterogeneity in capture probability when estimating the size of a
closed population of wild animals. The new model expresses the capture probability as a mixture of a binomial distribution
and a beta-binomial distribution. For real data sets, it is shown how the new model can provide a suitabl...
The short-term behavioural effects of helicopter overflights on breeding king penguins Aptenodytes patagonicus at South Georgia were examined. Seventeen helicopter overflights were made at altitudes between 230 and 1,768m (750–5,800ft)
above ground level. Noise from the aircraft engines and helicopter blades increased sound levels in the colony fro...
We propose a mixture of binomial and beta-binomial distributions for estimating the size of closed populations. The new mixture model is applied to several real capture-recapture data sets and is shown to provide a convenient, objective framework for model selection. The new model is compared with three alternative models in a simulation study, and...
We show that the family of tempered stable distributions has considerable potential for modelling cell generation time data. Several real examples illustrate how these distributions can improve on currently assumed models, including the gamma and inverse Gaussian distributions which arise as special cases. Our applications concentrate on the genera...
If the chemical guanidine hydrochloride is added to a dividing culture of yeast cells in which some of the protein Sup35p is in its prion form, the proportion of cells that carry replicating units of the prion, termed propagons, decreases gradually over time. Stochastic models to describe this process of 'curing' have been developed in earlier work...
Continuous time Markov models were used to analyse data from two bioassays to investigate the influence of β-fraction, a by-product of hop processing, on the two-spotted spider mite. The models were fitted to aggregate counts of the numbers of live and dead mites on treated and untreated halves of discs cut from leaves of hop and French bean plants...
A deterministic formula is commonly used to approximate the expected generation number of a population of growing cells. However, this can give misleading results because it does not allow for natural variation in the times that individual cells take to reproduce. Here we present more accurate approximations for both symmetric and asymmetric cell d...
Fusarium head blight (FHB) is an important disease of wheat crops. The incidence of diseased spikelets in the population is most naturally estimated by sampling ears of wheat and counting the number of infected spikelets, X, and the total number of spikelets, Y, on each ear. However, there is usually much more variation from ear to ear in the numbe...
![Fig. 3. Analysis of [PSI ] and [psi ] CFUs in the [PSI ] strain 780-1D...](profile/Lee-Byrne-3/publication/6230677/figure/fig1/AS:339808296685574@1458028019571/Analysis-of-PSI-and-psi-CFUs-in-the-PSI-strain-780-1D-cultured-in-the-presence_Q320.jpg)
Guanidine hydrochloride (Gdn·HCl) blocks the propagation of yeast prions by inhibiting Hsp104, a molecular chaperone that is absolutely required for yeast prion propagation. We had previously proposed that ongoing cell division is required for Gdn·HCl-induced loss of the [PSI ⁺] prion. Subsequently, Wu et al.[Wu Y, Greene LE, Masison DC, Eisenberg...
The effects of several factors on the estimation of Verticillium dahliae in soil by the wet-sieving method were studied. The following factors were important for maximising recovery: the removal of soil particles of < 20 μm size from suspensions before plating; the medium used for plating; the amount of sieved soil inoculated to plates; the length...
If one uses the observed information matrix, rather than the expected information matrix in a score test, then it is possible to obtain a negative test statistic. A simple illustration of this is provided for a zero-inflated Poisson distribution.
Approximations to the Malthusian parameter of an age-dependent branching process are obtained in terms of the moments of the lifetime distribution, by exploiting a link with renewal theory. In several examples, the new approximations are more accurate than those currently in use, even when based on only the first two moments. The new approximations...
Herbage height was measured in ryegrass/white clover (Lolium perenne/Trifolium repens) swards grazed by cattle using the rising plate meter or the sward stick. Ordinary single normal and double normal distributions were fitted to the data obtained. After the first 6 weeks of continuous grazing the double normal distributions fitted data for the tal...
Four experiments were conducted to assess the performance of ranked set sampling relative to random sampling for the estimation of herbage mass and clover content in grazed swards. The expected theoretical efficiencies were not observed due to the method of selection of quadrats and the nature of the distribution of herbage mass. Nevertheless there...
Herbage heights were measured with a rising plate meter in mixed perennial ryegrass/white clover (Lolium perenne/Trifolium repens) swards maintained under five different systems of management. Double normal distributions fitted to the height frequencies were used to interpret changes over the grazing season in the mean heights of the shorter ‘frequ...
This paper describes the derivation of a series of equations for estimating mean grass production on cut swards under different fertilizer nitrogen, soil and climatic regimes. Using data from the National Grassland Manuring Trial GM20 for a late flowering perennial ryegrass, equations have been estimated for the individual cuts. On the basis of dat...
Many pesticide sprays that are used for crop protection are harmful to honey-bees. It can therefore be beneficial to add to the spray chemical compounds that are repellent to bees, to discourage them from feeding on recently sprayed crops. Experiments were conducted using an artificial feeding station to assess the repellent effects of various comp...
The flowers of strawberry plants grow on very variable branched structures called inflorescences, in which each branch gives
rise to 0, 1, or 2 offspring branches. We extend previous modeling of the number of strawberry flowers at each individual
level in the inflorescence structure conditional on the number of strawberry flowers at the previous le...
Algorithms for finding optimal designs for three-parameter binary dose–response models that incorporate control mortality are described. Locally and Bayesian optimal designs for models with a range of link functions are considered. Design criteria looked at include D-optimal, DA-optimal and V-optimal designs, together with Ds-optimal designs where...
It is known that a single-locus gametophytic self-incompatibility (GSI) system can persist with just two distinct alleles in an autotetraploid population, in contrast to diploid GSI systems, assuming "competitive interaction" in which heteroallelic pollen is universally compatible. The steady-state population structure of a GSI system in autotetrap...
Concentrations of microorganisms can be estimated from colony counts at different dilutions. However, complications can occur
because of colony overlap or inhibition of colony growth. We develop a model of inhibition in which colonies fail to develop
if spores are close to spores of other inhibitory species. The model has three parameters, but a li...
Chelates of the transition metals copper, cobalt, manganese and zinc, available as foliar feeds, were identified as the most suitable spray tracers for comparisons of deposits arising from up to four sequential applications to a single target. Their use minimised many of the disadvantages associated with other commonly used tracers such as visible...
Certain yeast cells contain proteins that behave like the mammalian prion PrP and are called yeast prions. The yeast prion protein Sup35p can exist in one of two stable forms, giving rise to phenotypes [PSI(+)] and [psi(-)]. If the chemical guanidine hydrochloride (GdnHCl) is added to a culture of growing [PSI(+)] cells, the proportion of [PSI(+)]...
The establishment and spread of autotetraploids from an original diploid population in a heterogeneous environment were studied using a stochastic simulation model. Specifically, we investigated the effects of heterogeneous habitats and nonrandom pollen/seed dispersal on the critical value (micro) of unreduced 2n gamete production necessary for the...
We present a novel distribution for modelling count data that are underdispersed relative to the Poisson distribution. The distribution is a form of weighted Poisson distributions and is shown to have advantages over other weighted Poisson distributions that have been proposed to model underdispersion. One key difference is that the weights in our...
Strawberry inflorescences have a variable branching structure. This paper demonstrates how the inflorescence structure can be modelled concisely using binomial logistic generalized linear mixed models. Many different procedures exist for estimating the parameters of generalized linear mixed models, including penalized likelihood, EM, Bayesian techn...
The cytoplasmic heritable determinant [PSI+] of the yeast Saccharomyces cerevisiae exhibits prion-like properties. The properties of yeast prions are studied in the hope that this will enhance the understanding of mammalian prions, which cause mad-cow, Creutzfeldt-Jakob, and related neurodegenerative diseases. When host cells divide, the yeast prio...
Optimal designs are investigated for bioassays involving two parallel dose–response relationships, where estimating relative potency is the main interest. Local and Bayesian D-optimal designs are considered, as well as Ds-optimal designs where the mean response of one substance (standard) is regarded as of no interest. A range of link functions rel...
We consider the selection of samples in ranked set sampling when several attributes of each sample are of interest. We describe approaches that have appeared previously in the literature and present a novel method that seeks to achieve samples that are nearly balanced with respect to the ranks of all attributes. This method is shown to result in ve...
The estimation of micro-organism concentrations from dilution plate data is discussed for situations where expected counts are not proportional to the amount of sample per plate. Aspects of design and analysis are investigated in relation to an alternative non-linear model in which the concentration is given by the slope at the origin. This exponen...
Summary1 The pattern of dispersion within plants of the two-spotted spider mite, Tetranychus urticae, and its predator, the phytoseiid Phytoseiulus persimilis, was studied on the dwarf hop variety First Gold from May to September in 1997 and 1998.2 Spider mite populations developed on the lower leaves initially but, by late July, as the numbers of...
This paper discusses the inference of parental genotype based on segregation data from selfed progeny of allopolyploids when there is incomplete information about genotypes and when alleles are codominant or null. The distinct alleles that are present in a genotype are assumed to be known, but not the frequency with which they occur. These assumpti...
Polylink runs under Microsoft Windows (95 or later). It performs various calculations that are useful for investigating two-point linkage analysis for autopolyploids, based on the random chromosome pairing model. These include calculation of offspring phenotypic probabilities as functions of the recombination fraction, calculation of theoretical st...
Abstract The pattern of colonisation of dwarf hops (Humulus lupulus) by damson-hop aphid (Phorodon humuli (Schrank)) migrating from Prunus spp. was investigated at six plant spacings and where some of the hops were replaced by oilseed rape (Brassica napus L.), a non-host of the aphid. The number of migrant aphids that accumulated on hop stems (bine...
The emergence of the blackcurrant gall mite, Cecidophyopsis ribis (Westwood), from galls on the blackcurrant cultivars Ben Lomond and Ben Tirran was monitored closely in 1995-1999 using miniature sticky traps. Emergence was preceded by swelling of the galls. First, 5% and 50% emergences varied from Julian day 74-112, 84-121 and 101-129 respectively...
A stochastic simulation model was used to study the effects of the strength of prevailing wind (W), the size/ shape (Q) of sampling quadrats and their orientation in relation to the prevailing wind direction (D) on spatial statistics describing plant diseases. Spore dispersal followed a half-Cauchy distribution with median distance mu, which depend...
Count data often show a higher incidence of zero counts than would be expected if the data were Poisson distributed. Zero-inflated Poisson regression models are a useful class of models for such data, but parameter estimates may be seriously biased if the nonzero counts are overdispersed in relation to the Poisson distribution. We therefore provide...
ABSTRACT The spatiotemporal spread of plant diseases was simulated using a stochastic model to study the effects of initial conditions (number of plants initially infected and their spatial pattern), spore dispersal gradient, and size and shape of sampling quadrats on statistics describing the spatiotemporal dynamics of epidemics. The spatial sprea...
ABSTRACT This article investigates the relationships between various statistical measures that are used to summarize spatial aspects of disease incidence data. The focus is on quadrat data in which each plant in a quadrat is classified as diseased or healthy. We show that spatial autocorrelation plays a central role via the mean intraclass correlat...
The spread of race-specific and -nonspecific fungal pathogens in cultivar mixtures over space and time was simulated using an individual-based, spatially explicit stochastic model. The spatial spread of disease was simulated using a half-Cauchy distribution. The effects of five simulation variables on the effectiveness of cultivar mixtures in reduc...
We consider the estimation of the proportion of triploids in populations of plants or animals in which diploid and triploid
individuals coexist, using data from electrophoretic analysis of isozyme or microsatellite markers. Individuals that have
three distinct alleles at a locus are unambiguously triploid. However, other individuals cannot be class...
Ranked set sampling is a modification of simple random sampling that is intended to give improved precision. The method involves selecting small sets of samples and ranking them, for example visually. A single sample from each set is then measured. The performance of the method in estimating spray deposits on the leaves of apple trees was assessed....
Jolliffe and Jolliffe (1997, Biometrics 53, 1136-1142) proposed various models for data from an experiment on memory in coal tits. This article describes an alternative model, which fits equally well and which may be simpler to interpret.
This paper reviews many different estimators of intraclass correlation that have been proposed for binary data and compares them in an extensive simulation study. Some of the estimators are very specific, while others result from general methods such as pseudo-likelihood and extended quasi-likelihood estimation. The simulation study identifies seve...
The branching structure of inflorescences of the cultivated strawberry (Fragaria×ananassa Duch.) is very variable. This paper demonstrates that some aspects of this variability are well described by a simple stochastic model of branching that has two adjustable parameters. The model is shown to provide a good fit to data from a set of almost 700 in...
ABSTRACT A stochastic model that simulates the spread of disease over space and time was developed to study the effects of initial epidemic conditions (number of initial inocula and their spatial pattern), sporulation rate, and spore dispersal gradient on the spatio-temporal dynamics of plant disease epidemics. The spatial spread of disease was sim...
Four experiments were conducted with potted trees of several apple cultivars to study the effects of several factors on the incidence of canker and the length of the incubation period following the inoculation of pruning cuts with conidia of Nectria galligena. These factors included wound age (the interval between pruning and inoculation), inoculum...
A FORTRAN77 program for finding optimal designs for binary dose—response experiments is described. It is an enhancement of the program of Chaloner & Larntz (1988). The program finds locally and Bayesian optimal designs for models with a wide range of link functions. For Bayesian designs the parameters may have uniform, beta or bivariate normal prio...
Four experiments were conducted with potted trees of several apple cultivars to study the effects of several factors on the incidence of canker and the length of the incubation period following the inoculation of pruning cuts with conidia of Nectria galligena. These factors included wound age (the interval between pruning and inoculation), inoculum...
We consider the problem of modelling count data with excess zeros and review some possible models. Aspects of model fitting and inference are considered. An example from horticultural research is used for illustration.
Six data sets recording fetal control mortality in mouse litters are presented. The data are clearly overdispersed, and a standard approach would be to describe the data by means of a beta-binomial model or to use quasi-likelihood methods. For five of the examples, we show that beta-binomial model provides a reasonable description but that the fit...
Retrospective studies of fecundability, in which women are asked how many cycles they required to become pregnant, are often affected by problems of digit preference. A probability model for such digit preference is proposed in which misreporting favours 6 or 12 (and possibly also 3) cycles. It is assumed that in the absence of misreporting the num...
A population of [PSI + ] Saccharomyces cerevisiae cells can be cured of the [PSI + ] prion either by the addition of guanidine hydrochloride (GdnHCl) or by the overexpression of the molecular chaperone Hsp104. In this paper we extend existing nucleated polymerisa-tion simulation models to investigate the mechanisms that might underlie both types of...
Mallows' φ -model (Mallows, 1957, Biometrika, 44, 114-130) is a simple one-parameter distribution for ranking data. Various generalisations of the model have appeared in the literature. Here we describe a different generalisation that is a mixture model. The new distribution is shown to be more successful than the basic φ -model in describing visua...
Citations
... This is partly achieved by the scaling of the Vmax of β-slow MyHC, the dominant ventricular myosin in large animals, to around (body mass) −0.18 and by shifting the expression of ventricular MyHC to the faster α-cardiac MyHC in small eutherians (Lompre et al. 1981;Kessler-Icekson et al. 1988) as well as small marsupials (Hoh et al. 2007a). The changes in kinetics of β-slow MyHC of animals over a wide range of body masses are accomplished by mutations confined principally to 12 sites in the amino acid sequence of β-slow MyHC (Johnson et al. 2021). ...
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... To address the differences due only to the myosin isoform, we next performed simulations of the human twitch for the 100% α-myosin isoform. Deacon et al. generated a set of crossbridge parameters for human α-myosin [38], which were used by Johnson et al. [51] to model the complete crossbridge cycle for human αand β-myosins. This work was consistent, with little change in the rate constants for crossbridge attachment (k +A ) to and detachment (k −A ) from the A.M.D.Pi state between αand β-myosin. ...
![[object Object]](https://i1.rgstatic.net/ii/profile.image/272732017393679-1442035788722_Q64/Daniel-Mulvihill-3.jpg)