Fast Bayesian parameter estimation for stochastic logistic growth models

The transition density of a stochastic, logistic population growth model with multiplicative intrinsic noise is analytically intractable. Inferring model parameter values by fitting such stochastic differential equation (SDE) models to data therefore requires relatively slow numerical simulation. Where such simulation is prohibitively slow, an alternative is to use model approximations which do have an analytically tractable transition density, enabling fast inference. We introduce two such approximations, with either multiplicative or additive intrinsic noise, each derived from the linear noise approximation of the logistic growth SDE. After Bayesian inference we find that our fast LNA models, using Kalman filter recursion for computation of marginal likelihoods, give similar posterior distributions to slow arbitrarily exact models. We also demonstrate that simulations from our LNA models better describe the characteristics of the stochastic logistic growth models than a related approach. Finally, we demonstrate that our LNA model with additive intrinsic noise and measurement error best describes an example set of longitudinal observations of microbial population size taken from a typical, genome-wide screening experiment.Comment: 24 pages, 5 figures and 2 table

HIV-related tuberculosis in South Africa - clinical features and outcome

No Abstract

Going with the floe

Julia Wilkinson and a Zooniverse citizen-science team examine Arctic auroral data, using observations from the ill-fated 19th-century Arctic exploration ship USS Jeannette

The Trypanosoma cruzi enzyme TcGPXI is a glycosomal peroxidase and can be linked to trypanothione reduction by glutathione or tryparedoxin.

Trypanosoma cruzi glutathione-dependent peroxidase I (TcGPXI) can reduce fatty acid, phospholipid, and short chain organic hydroperoxides utilizing a novel redox cycle in which enzyme activity is linked to the reduction of trypanothione, a parasite-specific thiol, by glutathione. Here we show that TcGPXI activity can also be linked to trypanothione reduction by an alternative pathway involving the thioredoxin-like protein tryparedoxin. The presence of this new pathway was first detected using dialyzed soluble fractions of parasite extract. Tryparedoxin was identified as the intermediate molecule following purification, sequence analysis, antibody studies, and reconstitution of the redox cycle in vitro. The system can be readily saturated by trypanothione, the rate-limiting step being the interaction of trypanothione with the tryparedoxin. Both tryparedoxin and TcGPXI operate by a ping-pong mechanism. Overexpression of TcGPXI in transfected parasites confers increased resistance to exogenous hydroperoxides. TcGPXI contains a carboxyl-terminal tripeptide (ARI) that could act as a targeting signal for the glycosome, a kinetoplastid-specific organelle. Using immunofluorescence, tagged fluorescent proteins, and biochemical fractionation, we have demonstrated that TcGPXI is localized to both the glycosome and the cytosol. The ability of TcGPXI to use alternative electron donors may reflect their availability at the corresponding subcellular sites

ADOPT: a tool for predicting adoption of agricultural innovations

A wealth of evidence exists about the adoption of new practices and technologies in agriculture but there does not appear to have been any attempt to simplify this vast body of research knowledge into a model to make quantitative predictions across a broad range of contexts. This is despite increasing demand from research, development and extension agencies for estimates of likely extent of adoption and the likely timeframes for project impacts. This paper reports on the reasoning underpinning the development of ADOPT (Adoption and Diffusion Outcome Prediction Tool). The tool has been designed to: 1) predict an innovation‘s likely peak extent of adoption and likely time for reaching that peak; 2) encourage users to consider the influence of a structured set of factors affecting adoption; and 3) engage R, D & E managers and practitioners by making adoptability knowledge and considerations more transparent and understandable. The tool is structured around four aspects of adoption: 1) characteristics of the innovation, 2) characteristics of the population, 3) actual advantage of using the innovation, and 4) learning of the actual advantage of the innovation. The conceptual framework used for developing ADOPT is described.Adoption, Diffusion, Prediction, Research and Development/Tech Change/Emerging Technologies,

A New Species of Skin-Feeding Caecilian and the First Report of Reproductive Mode in Microcaecilia (Amphibia: Gymnophiona: Siphonopidae)

A new species of siphonopid caecilian, Microcaecilia dermatophaga sp. nov., is described based on nine specimens from French Guiana. The new species is the first new caecilian to be described from French Guiana for more than 150 years. It differs from all other Microcaecilia in having fewer secondary annular grooves and/or in lacking a transverse groove on the dorsum of the first collar. Observations of oviparity and of extended parental care in M. dermatophaga are the first reproductive mode data for any species of the genus. Microcaecilia dermatophaga is the third species, and represents the third genus, for which there has been direct observation of young animals feeding on the skin of their attending mother. The species is named for this maternal dermatophagy, which is hypothesised to be characteristic of the Siphonopidae.Organismic and Evolutionary Biolog