Dual-orthogonal radial basis function networks for nonlinear time series prediction

A new structure of Radial Basis Function (RBF) neural network called the Dual-orthogonal RBF Network (DRBF) is introduced for nonlinear time series prediction. The hidden nodes of a conventional RBF network compare the Euclidean distance between the network input vector and the centres, and the node responses are radially symmetrical. But in time series prediction where the system input vectors are lagged system outputs, which are usually highly correlated, the Euclidean distance measure may not be appropriate. The DRBF network modifies the distance metric by introducing a classification function which is based on the estimation data set. Training the DRBF networks consists of two stages. Learning the classification related basis functions and the important input nodes, followed by selecting the regressors and learning the weights of the hidden nodes. In both cases, a forward Orthogonal Least Squares (OLS) selection procedure is applied, initially to select the important input nodes and then to select the important centres. Simulation results of single-step and multi-step ahead predictions over a test data set are included to demonstrate the effectiveness of the new approach.

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution.

Ornamental Mediterranean plants in the UK: root adaptations to hypoxia and anoxia

Mediterranean species are popular landscape plants in the UK and well suited to the predicted climate change scenarios of hotter, drier summers. What is less clear is how these species will respond to the more unpredictable rainfall patterns also anticipated, where soil water-logging may become more prevalent, especially in urban environments where soil sealing can restrict drainage. Pot experiments on flooding of four Mediterranean species (Cistus × hybridus, Lavandula angustifolia ‘Munstead’, Salvia officinalis and Stachys byzantina) showed that the effects of waterlogging were only severe when the temperature was high and flooding prolonged. All plants survived the flooding in winter, but during the summer a 17-day flood resulted in the death of 30-40% of the Salvia officinalis and Cistus × hybridus. To examine the response of roots to oxygen deprivation over a range of conditions from total absence of oxygen (anoxia), low oxygen (hypoxia) and full aeration, rooted cuttings of Salvia officinalis were grown in a hydroponic-based system and mixtures of oxygen and nitrogen gases bubbled through the media. Anoxia was found to reduce root development dramatically. When the plants were subjected to a period of hypoxia they responded by increasing the production of lateral roots close to the surface thus enabling them to acclimate to subsequent anoxia. This greatly increased their chances of survival.

Resolving the spatial variability of soil N using fractions of soil organic matter

The spatial variability of soil nitrogen (N) mineralisation has not been extensively studied, which limits our capacity to make N fertiliser recommendations. Even less attention has been paid to the scale-dependence of the variation. The objective of this research was to investigate the scale-dependence of variation of mineral N (MinN, N–NO3− plus N–NH4+) at within-field scales. The study was based on the spatial dependence of the labile fractions of SOM, the key fractions for N mineralisation. Soils were sampled in an unbalanced nested design in a 4-ha arable field to examine the distribution of the variation of SOM at 30, 10, 1, and 0.12 m. Organic matter in free and intra-aggregate light fractions (FLF and IALF) was extracted by physical fractionation. The variation occurred entirely within 0.12 m for FLF and at 10 m for IALF. A subsequent sampling on a 5-m grid was undertaken to link the status of the SOM fractions to MinN, which showed uncorrelated spatial dependence. A uniform application of N fertiliser would be suitable in this case. The failure of SOM fractions to identify any spatial dependence of MinN suggests that other soil variables, or crop indicators, should be tested to see if they can identify different N supply areas within the field for a more efficient and environmentally friendly N management.

Canonical Wnt signalling induces satellite-cell proliferation during adult skeletal muscle regeneration

Satellite cells represent the stem cell population of adult skeletal muscle. The molecular mechanisms that control the proliferation of satellite cells are not well understood. In this study, we show that in response to injury, myofibres activate Wnt ligand transcription and activate a reporter cell line that is sensitive to the canonical Wnt-signalling pathway. Activated satellite cells on isolated cultured myofibres show robust expression of activated-β-catenin (Act-β-Cat), a key downstream transcriptional coactivator of canonical Wnt signalling. We provide evidence that the Wnt family of secreted glycoproteins act on satellite cells in a ligand-specific manner. Overexpression of Wnt1, Wnt3a or Wnt5a protein causes a dramatic increase in satellite-cell proliferation. By contrast, exposure of satellite cells to Wnt4 or Wnt6 diminishes this process. Moreover, we show that the prolonged satellite-cell quiescence induced by inhibitory Wnt is reversible and exposing inhibited satellite cells to stimulatory Wnt signalling restores their proliferation rate. Stimulatory Wnt proteins induce premature satellite cell BrdU incorporation as well as nuclear translocation of Act-β-Cat. Finally, we provide evidence that the Act-β-Cat translocation observed in single fibres during in vitro culture also occurs in cases of acute and chronic skeletal muscle regeneration in rodents and humans. We propose that Wnt proteins may be key factors that regulate the rate of satellite-cell proliferation on adult muscle fibres during the wound-healing response.