Estimation of parameters for macroparasite population evolution using approximate Bayesian computation

We estimate the parameters of a stochastic process model for a macroparasite population within a host using approximate Bayesian computation (ABC). The immunity of the host is an unobserved model variable and only mature macroparasites at sacrifice of the host are counted. With very limited data, process rates are inferred reasonably precisely. Modeling involves a three variable Markov process for which the observed data likelihood is computationally intractable. ABC methods are particularly useful when the likelihood is analytically or computationally intractable. The ABC algorithm we present is based on sequential Monte Carlo, is adaptive in nature, and overcomes some drawbacks of previous approaches to ABC. The algorithm is validated on a test example involving simulated data from an autologistic model before being used to infer parameters of the Markov process model for experimental data. The fitted model explains the observed extra-binomial variation in terms of a zero-one immunity variable, which has a short-lived presence in the host.

Corneal sensitivity as an ophthalmic marker of diabetic neuropathy

Purpose. The objective of this study was to explore the discriminative capacity of non-contact corneal esthesiometry (NCCE) when compared with the neuropathy disability score (NDS) score—a validated, standard method of diagnosing clinically significant diabetic neuropathy. Methods. Eighty-one participants with type 2 diabetes, no history of ocular disease, trauma, or surgery and no history of systemic disease that may affect the cornea were enrolled. Participants were ineligible if there was history of neuropathy due to non-diabetic cause or current diabetic foot ulcer or infection. Corneal sensitivity threshold was measured on the eye of dominant hand side at a distance of 10 mm from the center of the cornea using a stimulus duration of 0.9 s. The NDS was measured producing a score ranging from 0 to 10. To determine the optimal cutoff point of corneal sensitivity that identified the presence of neuropathy (diagnosed by NDS), the Youden index and “closest-to-(0,1)” criteria were used. Results. The receiver-operator characteristic curve for NCCE for the presence of neuropathy (NDS ≥3) had an area under the curve of 0.73 (p = 0.001) and, for the presence of moderate neuropathy (NDS ≥6), area of 0.71 (p = 0.003). By using the Youden index, for an NDS ≥3, the sensitivity of NCCE was 70% and specificity was 75%, and a corneal sensitivity threshold of 0.66 mbar or higher indicated the presence of neuropathy. When NDS ≥6 (indicating risk of foot ulceration) was applied, the sensitivity was 52% with a specificity of 85%. Conclusions. NCCE is a sensitive test for the diagnosis of minimal and more advanced diabetic neuropathy and may serve as a useful surrogate marker for diabetic and perhaps other neuropathies.

Randomised controlled trial of an automated, interactive telephone intervention to improve type 2 diabetes self-management (Telephone-Linked Care Diabetes Project) : study protocol

Background: An estimated 285 million people worldwide have diabetes and its prevalence is predicted to increase to 439 million by 2030. For the year 2010, it is estimated that 3.96 million excess deaths in the age group 20-79 years are attributable to diabetes around the world. Self-management is recognised as an integral part of diabetes care. This paper describes the protocol of a randomised controlled trial of an automated interactive telephone system aiming to improve the uptake and maintenance of essential diabetes self-management behaviours. ---------- Methods/Design: A total of 340 individuals with type 2 diabetes will be randomised, either to the routine care arm, or to the intervention arm in which participants receive the Telephone-Linked Care (TLC) Diabetes program in addition to their routine care. The intervention requires the participants to telephone the TLC Diabetes phone system weekly for 6 months. They receive the study handbook and a glucose meter linked to a data uploading device. The TLC system consists of a computer with software designed to provide monitoring, tailored feedback and education on key aspects of diabetes self-management, based on answers voiced or entered during the current or previous conversations. Data collection is conducted at baseline (Time 1), 6-month follow-up (Time 2), and 12-month follow-up (Time 3). The primary outcomes are glycaemic control (HbA1c) and quality of life (Short Form-36 Health Survey version 2). Secondary outcomes include anthropometric measures, blood pressure, blood lipid profile, psychosocial measures as well as measures of diet, physical activity, blood glucose monitoring, foot care and medication taking. Information on utilisation of healthcare services including hospital admissions, medication use and costs is collected. An economic evaluation is also planned.---------- Discussion: Outcomes will provide evidence concerning the efficacy of a telephone-linked care intervention for self-management of diabetes. Furthermore, the study will provide insight into the potential for more widespread uptake of automated telehealth interventions, globally.

The ecology of Bactrocera tryoni (Froggatt) (Diptera: Tephritdae) : what do we know to assist pest management?

The distribution, systematics and ecology of Bactrocera tryoni, the Queensland fruit fly are reviewed. Bactrocera tryoni is a member of the B. tryoni complex of species, which currently includes four named species, viz. B. tryoni s.s., B. neohumeralis, B. melas and B. aquilonis. The species status of B. melas and B. aquilonis are unclear (they may be junior synonyms of B. tryoni) and their validity, or otherwise, needs to be confirmed as a matter of urgency. While Queensland fruit fly is regarded as a tropical species, it cannot be assumed that its distribution will spread further south under climate change scenarios. Increasing aridity and hot dry summers, as well as more complex, indirect interactions resulting from elevated CO2, make predicting the future distribution and abundance of B. tryoni difficult. The ecology of B. tryoni is reviewed with respect to current control approaches (with the exception of Sterile Insect Technique which is covered in a companion paper). We conclude that there are major gaps in the knowledge required to implement most non-insecticide based management approaches. Priority areas for future research include host plant interactions, protein and cue-lure foraging and use, spatial dynamics, development of new monitoring tools, investigating the use of natural enemies and better integration of fruit flies into general horticultural IPM systems.

Preference among four Bactrocera species (Diptera: Tephritidae) by Diachasmimorpha kraussii (Fullaway) (Hymenoptera: Braconidae)

Diachasmimorpha kraussii is an endoparasitoid of larval dacine fruit flies. To date the only host preference study done on D. kraussii has used fruit flies from outside its native range (Australia, Papua New Guinea, Solomon Islands). In contrast, this paper investigates host preference for four fly species (Bactrocera cacuminata, B. cucumis, B. jarvisi and B. tryoni) which occur sympatrically with the wasp in the Australian component of the native range. Diachasmimorpha kraussii oviposition preference, host suitability (parasitism rate, number of progeny, sex ratio), and offspring performance measures (body length, hind tibial length, developmental time) were investigated with respect to the four fly species in the laboratory in both no-choice and choice situations. The parasitoid accepted all four fruit fly species for oviposition in both no-choice and choice tests; however, adult wasps only emerged from B. jarvisi and B. tryoni. Through dissection, it was demonstrated that parasitoid eggs were encapsulated in both B. cacuminata and B. cucumis. Between the two suitable hosts, measurements of oviposition preference, host suitability and offspring performance measurements either did not vary significantly, or varied in an inconsistent manner. Based on our results, and a related study by other authors, we conclude that D. krausii, at the point of oviposition, cannot discriminate between physiologically suitable and unsuitable hosts.

Host use and crop impacts of Oribius Marshall species (Coleoptera: Curculionidae) in Eastern Highlands Province, Papua New Guinea

Oribius species are small flightless weevils endemic to the island of New Guinea and far northern Cape York, Australia. The adults feed externally on leaves, developing fruit and green bark, but their impact as pests and general host use patterns are poorly known. Working in Eastern Highlands Province, Papua New Guinea, we carried out structured host use surveys, farmer surveys, shade-house growth trials, and on-farm and on-station impact trials to: (i) estimate the host range of the local Oribius species; (ii) understand adult daily activity patterns; (iii) elucidate feeding habits of the soil dwelling larvae; and (iv) quantify the impacts of adult feeding damage. Oribius inimicus and O. destructor accounted for nearly all the Oribius species encountered locally: of these two O. inimicus was the most abundant. Weevils were collected from 31 of 33 plants surveyed in the Aiyura Valley and a combination of farmer interviews and literature records provided evidence for the beetles being pestiferous on 43 crops currently or previously grown in the Highlands. Adult weevils had a distinct diurnal pattern of being in the upper plant canopy early in the morning and, to a lesser extent, again late in the afternoon. For the remainder of the day beetles resided within the canopy, or possibly off the plant. Movement of adults between plants appeared frequent. Pot trials confirmed the larvae are root feeders. Quantified impact studies showed that the weevils are damaging to a range of vegetable and orchard crops (broccoli, capsicum, celery, French bean, Irish potato, lettuce, orange and strawberry), causing average yield losses of around 30-40%, but up to 100% on citrus. Oribius weevils pose a significant and apparently growing problem for Highland’s agriculture.

The seasonal phenology of Bactrocera tryoni (Froggatt) (Diptera: Tephritidae) in Queensland

Bactrocera tryoni is a polyphagous fruit fly, originally endemic to tropical and subtropical coastal eastern Australia, but now also widely distributed in temperate eastern Australia. In temperate parts of its range, B. tryoni populations show distinct seasonal peaks driven by changing seasonal climates, especially changing temperature. In contrast to temperate areas, the seasonal phenology of B. tryoni in subtropical and tropical parts of its range is poorly documented and the role of climate unknown. Using a large, historical (1940s and 1950s) fruit fly trapping data set, we present the seasonal phenology of B. tryoni at nine sites across Queensland for multiple (two to seven) years per site. We correlate monthly trap data for each site with monthly weather averages (temperature, rainfall and relative humidity) to investigate climatic influences. We also correlate observed population data with predicted population data generated by an existing B. tryoni population model. Supporting predictions from climate driven models, B. tryoni did show year-round breeding at most Queensland sites. However, contrary to predictions, there was a common pattern of a significant population decline in autumn and winter, followed by a rapid population increase in August and then one or more distinct peaks of abundance in spring and summer. Mean monthly fly abundance was significantly different across sites, but was not correlated with altitudinal, latitudinal or longitudinal gradients. There were very few significant correlations between monthly fly population size and weather variables for eight of the nine sites. For the southern site of Gatton fly population abundance was correlated with temperature. Results suggest that while climate factors may be influencing B. tryoni populations in southern subtropical Queensland, they appear to be having only minor or no influence in northern sub-tropical and tropical Queensland. In the discussion we focus on the role of other factors, particularly larval host plant availability, as likely drivers of B. tryoni abundance in tropical and subtropical parts of its range.

Positive correlation of male and female Bactrocera tryoni (Froggatt) (Diptera: Tephritidae) catches in orange-ammonia traps

Populations of the Queensland fruit fly, Bactrocera tryoni, are routinely monitored using cue-lure, a male-only attractant. Such monitoring provides no information about females and there is little information available to show if male and female B. tryoni numbers are correlated in the field. Using a data set of 1 148 weekly clearances of orange-ammonia baited traps, which catch both males and females, the correlation between male and female numbers was tested for 48 weeks of the year (four weeks each month) and for the combined data set. Weekly male and female trap catches were almost entirely highly correlated, regardless of mean population size or time of year. For the whole year, the correlation between male and female numbers was r = 0.722, significant at p<0.001. Results suggest that changes in the number if male B. tryoni, as detected through cue-lure sampling, will reflect changes in numbers of female B. tryoni.

Is a mango just a mango? Testing within-fruit oviposition site choice and larval performance of a highly polyphagous fruit fly

For fruit flies, fully ripe fruit is preferred for adult oviposition and is superior for offspring performance over unripe or ripening fruit. Because not all parts of a single fruit ripen simultaneously, the opportunity exists for adult fruit flies to selectively choose riper parts of a fruit for oviposition and such selection, if it occurs, could positively influence offspring performance. Such fine scale host variation is rarely considered in fruit fly ecology, however, especially for polyphagous species which are, by definition, considered to be generalist host users. Here we study the adult oviposition preference/larval performance relationship of the Oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), a highly polyphagous pest species, at the “within-fruit” level to see if such a host use pattern occurs. We recorded the number of oviposition attempts that female flies made into three fruit portions (top, middle and bottom), and larval behavior and development within different fruit portions for ripening (color change) and fully-ripe mango, Mangifera indica L. (Anacardiaceae). Results indicate that female B. dorsalis do not oviposit uniformly across a mango fruit, but lay most often in the top (i.e., stalk end) of fruit and least in the bottom portion, regardless of ripening stage. There was no evidence of larval feeding site preference or performance (development time, pupal weight, percent pupation) being influenced by fruit portion, within or across the fruit ripening stages. There was, however, a very significant effect on adult emergence rate from pupae, with adult emergence rate from pupae from the bottom of ripening mango being approximately only 50% of the adult emergence rate from the top of ripening fruit, or from both the top and bottom of fully-ripe fruit. Differences in mechanical (firmness) and chemical (total soluble solids, titratable acidity, total non-structural carbohydrates) traits between different fruit portions were correlated with adult fruit utilisation. Our results support a positive adult preference/offspring performance relationship at within-fruit level for B. dorsalis. The fine level of host discrimination exhibited by B. dorsalis is at odds with the general perception that, as a polyphagous herbivore, the fly should show very little discrimination in its host use behavior.

Can hybridization cause local extinction : the case for demographic swamping of the Australian native, Senecio pinnatifolius, by the invasive, S. madagascariensis?

The outcome of interspecific hybridization between native and invasive species depends on the relative frequencies of parental taxa and viability of hybrid progeny. We investigated individual and population level consequences of hybridization between the Australian native, Senecio pinnatifolius, and the exotic S. madagascariensis, with AFLP markers and used this information to simulate the expected outcome of hybridization.A high frequency (range 8.3-75.6 %) of hybrids was detected in open pollinated seeds of both species, but mature hybrids were absent from sympatric populations indicating that sympatric populations represent tension zones. A hybridization advantage was observed for S. madagascariensis,where significantly more progeny than expected were sired based on proportional representation of the two species in sympatric populations. Simulations indicated S. pinnatifolius could be replaced in sympatric populations if hybridization was density dependent.For this native-exotic pair, prezygotic isolating barriers are weak, but low hybrid viability maintains a strong postzygotic barrier to introgression. Due to asymmetric hybridization, S. pinnatifolius appears under threat from demographic swamping, and local extinction is possible where it occurs in sympatry with S. madagascariensis.

Ecology and behavior of first instar larval Lepidoptera

Neonate Lepidoptera are confronted with the daunting task of establishing themselves on a food plant. The factors relevant to this process need to be considered at spatial and temporal scales relevant to the larva and not the investigator. Neonates have to cope with an array of plant surface characters as well as internal characters once the integument is ruptured. These characters, as well as microclimatic conditions, vary within and between plant modules and interact with larval feeding requirements, strongly affecting movement behavior, which may be extensive even for such small organisms. In addition to these factors, there is an array of predators, pathogens, and parasitoids with which first instars must contend. Not surprisingly, mortality in neonates is high but can vary widely. Experimental and manipulative studies, as well as detailed observations of the animal, are vital if the subtle interaction of factors responsible for this high and variable mortality are to be understood. These studies are essential for an understanding of theories linking female oviposition behavior with larval survival, plant defense theory, and population dynamics, as well as modern crop resistance breeding programs.

An interview with Professor David Held : exploring the concepts of cosmopolitanism and democracy

David Held is the Graham Wallace Chair in Political Science, and co-director of LSE Global Governance, at the London School of Economics. He is the author of many works, such as Cosmopolitanism: Ideals and Realities (2010); The Cosmopolitanism Reader (2010), with Garrett Brown; Globalisation/AntiGlobalisation (2007), Models of Democracy (2006), Global Covenant (2004) and Global Transformations: Politics, Economics and Culture (1999). Professor Held is also the co-founder, alongside Lord Professor Anthony Giddens, of Polity Press. Professor Held is widely known for his work concerning cosmopolitan theory, democracy, and social, political and economic global improvement. His Global Policy Journal endeavours to marry academic developments with practitioner realities, and contributes to the understanding and improvement of our governing systems.

Accumulation of recombinant cellobiohydrolase and endoglucanase in the leaves of mature transgenic sugar cane

A major strategic goal in making ethanol from lignocellulosic biomass a cost-competitive liquid transport fuel is to reduce the cost of production of cellulolytic enzymes that hydrolyse lignocellulosic substrates to fermentable sugars. Current production systems for these enzymes, namely microbes, are not economic. One way to substantially reduce production costs is to express cellulolytic enzymes in plants at levels that are high enough to hydrolyse lignocellulosic biomass. Sugar cane fibre (bagasse) is the most promising lignocellulosic feedstock for conversion to ethanol in the tropics and subtropics. Cellulolytic enzyme production in sugar cane will have a substantial impact on the economics of lignocellulosic ethanol production from bagasse. We therefore generated transgenic sugar cane accumulating three cellulolytic enzymes, fungal cellobiohydrolase I (CBH I), CBH II and bacterial endoglucanase (EG), in leaves using the maize PepC promoter as an alternative to maize Ubi1 for controlling transgene expression. Different subcellular targeting signals were shown to have a substantial impact on the accumulation of these enzymes; the CBHs and EG accumulated to higher levels when fused to a vacuolar-sorting determinant than to an endoplasmic reticulum-retention signal, while EG was produced in the largest amounts when fused to a chloroplast-targeting signal. These results are the first demonstration of the expression and accumulation of recombinant CBH I, CBH II and EG in sugar cane and represent a significant first step towards the optimization of cellulolytic enzyme expression in sugar cane for the economic production of lignocellulosic ethanol.

Multivariate Markov Process Models for the transmission of methicillin-resistant Staphylococcus Aureus in a hospital ward

Methicillin-resistant Staphylococcus Aureus (MRSA) is a pathogen that continues to be of major concern in hospitals. We develop models and computational schemes based on observed weekly incidence data to estimate MRSA transmission parameters. We extend the deterministic model of McBryde, Pettitt, and McElwain (2007, Journal of Theoretical Biology 245, 470–481) involving an underlying population of MRSA colonized patients and health-care workers that describes, among other processes, transmission between uncolonized patients and colonized health-care workers and vice versa. We develop new bivariate and trivariate Markov models to include incidence so that estimated transmission rates can be based directly on new colonizations rather than indirectly on prevalence. Imperfect sensitivity of pathogen detection is modeled using a hidden Markov process. The advantages of our approach include (i) a discrete valued assumption for the number of colonized health-care workers, (ii) two transmission parameters can be incorporated into the likelihood, (iii) the likelihood depends on the number of new cases to improve precision of inference, (iv) individual patient records are not required, and (v) the possibility of imperfect detection of colonization is incorporated. We compare our approach with that used by McBryde et al. (2007) based on an approximation that eliminates the health-care workers from the model, uses Markov chain Monte Carlo and individual patient data. We apply these models to MRSA colonization data collected in a small intensive care unit at the Princess Alexandra Hospital, Brisbane, Australia.

Approximate Bayesian computation using indirect inference

We present a novel approach for developing summary statistics for use in approximate Bayesian computation (ABC) algorithms by using indirect inference. ABC methods are useful for posterior inference in the presence of an intractable likelihood function. In the indirect inference approach to ABC the parameters of an auxiliary model fitted to the data become the summary statistics. Although applicable to any ABC technique, we embed this approach within a sequential Monte Carlo algorithm that is completely adaptive and requires very little tuning. This methodological development was motivated by an application involving data on macroparasite population evolution modelled by a trivariate stochastic process for which there is no tractable likelihood function. The auxiliary model here is based on a beta–binomial distribution. The main objective of the analysis is to determine which parameters of the stochastic model are estimable from the observed data on mature parasite worms.