Extended Tree Augmented Naive Classifier

This work proposes an extended version of the well-known tree-augmented naive Bayes (TAN) classifier where the structure learning step is performed without requiring features to be connected to the class. Based on a modification of Edmonds’ algorithm, our structure learning procedure explores a superset of the structures that are considered by TAN, yet achieves global optimality of the learning score function in a very efficient way (quadratic in the number of features, the same complexity as learning TANs). A range of experiments show that we obtain models with better accuracy than TAN and comparable to the accuracy of the state-of-the-art classifier averaged one-dependence estimator.

The extended phenotype of Scots pine Pinus sylvestris structures the understorey assemblage

Heritable variation in plant secondary compounds in dominant species has been hypothesised to effect ecosystem function and the structure of associated assemblages of plants, microbes and animals. The functioning of this extended phenotype in relation to the understorey vegetation composition was tested within a boreal forest system dominated by Pinus sylvestris which contains a range of monoterpenes, the composition of which is largely under genetic control. A variance partitioning approach was adopted to identify the relative importance of tree chemistry, environment, spatial location and tree architecture in controlling the distribution of species in the ground flora under individual trees. The monoterpene composition of the pine needles appeared to contribute significantly to controlling understorey vegetation composition, but was less important than environmental factors, though similar to spatial factors. Thus there appears to be a link between variation in the chemical composition of the single, dominant tree species within this system and the pattern of occurrence and abundance in other species at the same trophic level.

A techno-economic evaluation of changing from conventional vehicles to range extended electric vehicles

Transportation accounts for 22% of greenhouse gas emissions in the UK, and increases to 25% in Northern Ireland. Surface transport carbon dioxide emissions, consisting of road and rail, are dominated by cars. Demand for mobility is rising rapidly and vehicle numbers are expected to more than double by 2050. Car manufacturers are working towards reducing their carbon footprint through improving fuel efficiency and controlling exhaust emissions. Fuel efficiency is now a key consideration of consumers purchasing a new vehicle. While measures have been taken to help to reduce pollutants, in the future, alternative technologies will have to be used in the transportation industry to achieve sustainability. There are currently many alternatives to the market leader, the internal combustion engine. These alternatives include hydrogen fuel cell vehicles and electric vehicles, a term which is widely used to cover battery electric vehicles, plug-in hybrid electric vehicles and extended-range electric vehicles. This study draws direct comparisons measuring the differing performance in terms of fuel consumption, carbon emissions and range of a typical family saloon car using different fuel types. These comparisons will then be analysed to see what effect switching from a conventionally fuelled vehicle to a range extended electric vehicle would have not only on the end user, but also the UK government.

Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes

Biofilms are communities of microbial cells that underpin diverse processes including sewage bioremediation, plant growth promotion, chronic infections and industrial biofouling. The cells resident in the biofilm are encased within a self-produced exopolymeric matrix that commonly comprises lipids, proteins that frequently exhibit amyloid-like properties, eDNA and exopolysaccharides. This matrix fulfils a variety of functions for the community, from providing structural rigidity and protection from the external environment to controlling gene regulation and nutrient adsorption. Critical to the development of novel strategies to control biofilm infections, or the capability to capitalize on the power of biofilm formation for industrial and biotechnological uses, is an in-depth knowledge of the biofilm matrix. This is with respect to the structure of the individual components, the nature of the interactions between the molecules and the three-dimensional spatial organization. We highlight recent advances in the understanding of the structural and functional role that carbohydrates and proteins play within the biofilm matrix to provide three-dimensional architectural integrity and functionality to the biofilm community. We highlight, where relevant, experimental techniques that are allowing the boundaries of our understanding of the biofilm matrix to be extended using Escherichia coli, Staphylococcus aureus, Vibrio cholerae, and Bacillus subtilis as exemplars.

Hui and Walter's latent-class model extended to estimate diagnostic test properties from surveillance data: a latent model for latent data

Diagnostic test sensitivity and specificity are probabilistic estimates with far reaching implications for disease control, management and genetic studies. In the absence of 'gold standard' tests, traditional Bayesian latent class models may be used to assess diagnostic test accuracies through the comparison of two or more tests performed on the same groups of individuals. The aim of this study was to extend such models to estimate diagnostic test parameters and true cohort-specific prevalence, using disease surveillance data. The traditional Hui-Walter latent class methodology was extended to allow for features seen in such data, including (i) unrecorded data (i.e. data for a second test available only on a subset of the sampled population) and (ii) cohort-specific sensitivities and specificities. The model was applied with and without the modelling of conditional dependence between tests. The utility of the extended model was demonstrated through application to bovine tuberculosis surveillance data from Northern and the Republic of Ireland. Simulation coupled with re-sampling techniques, demonstrated that the extended model has good predictive power to estimate the diagnostic parameters and true herd-level prevalence from surveillance data. Our methodology can aid in the interpretation of disease surveillance data, and the results can potentially refine disease control strategies.

The role of WNT singling activation and its blockage in the focal retinal lesion of Ccl2-/-/Cx3cr1-/- mice with and without rd8 background

Purpose: The canonical Wnt signaling is activated by retinal injury. Under disease conditions, the Wnt mediates inflammatory responses. Inflammation has been detected in age-related macular degeneration (AMD) retinas and Ccl2-/-/Cx3cr1-/- (DKO) mice with or without rd8 background, a model with progressive AMD-like lesions including focal photoreceptor/RPE degeneration and A2E accumulation. We evaluated the effects of Wnt-β-catenin activation and an antibody against LRP6, the co-receptor of Wnt on these two models.

Methods: anti-LRP6 antibody (2F1, 1 μl of 5 μg/μL) was intravitreally injected into the right eyes in 3 separate experiments (DKOrd8, N=35; DKO, N=10). The left eyes were injected with mouse IgG as controls. Fundoscopy was taken before injection and sequentially monthly after injection. Two months after injection, light-adapted ERG responses were recorded; then the eyes were harvested for histopathology, the determination of retinal A2E, and molecular analysis. The microarray of ocular mRNA of 92 Wnt genes was compared between the treated and the control eyes. The phosphorylated types of LRP6 and β-catenin and endogenous forms of the proteins were assayed by Western blotting.

Results: For DKOrd8 mice, the fundus showed a slower progression or alleviation of retinal lesions in the right eyes as compared to the left eyes. Among 35 pairs of eyes, 26 (74.3%) were improved, 7 (20%) stayed the same and 2 (5.7%) remained progressing. Histology confirmed the clinical observation. Light-adapted ERG of the treated eyes exhibited larger amplitudes compared to control eyes (n=6), with greater improvements under UV light stimulus. There was a significantly lower A2E in the treated eyes compared to controls. Microarray of 92 Wnt genes expression pattern was similar in both eyes. Western blotting indicated local administration of 2F1 antibody to suppress the activation of Wnt pathway in the retina. For DKO mice, the treatment improved ERG but less effect on RPE degeneration.

Conclusions: The canonical Wnt signaling plays a role in the focal retina lesion of both DKOrd8 and DKO mice; and intravitreal anti-LRP6 antibody might be neuroprotective via deactivation of canonical Wnt pathway.

A multi-proxy chronological reconstruction of palaeosalinity in the eastern Limfjord, Denmark

The Jutland peninsula in northern Denmark is home to the Limfjord, one of the largest estuarine bodies of water in the region. Human inhabitance of the Limfjord’s surrounding coastlines stretches back further than 7,800 cal BP, with anthropogenic influence on the landscape beginning approximately 6,000 cal BP. Understanding how the Limfjord as a system has changed throughout time is useful in comprehending subsistence patterns and anthropogenic influence. This research is part of a larger project aimed at discerning subsistence patterns and environmental change in the region. Following the Younger Dryas, as the Fennoscandian ice sheet began to melt, Denmark experienced isostatic rebound, which contributed to the complex sea level history in the region. Between ice melt and isostatic rebound, the Jutland peninsula experienced many transgression and regression events. Connections to surrounding seas have shifted throughout time, with most attention focused on the western connection of the Limfjord with the North Sea, which has experienced numerous closures and subsequent re-openings throughout the Holocene. Furthermore, the Limfjord-North Sea connection has been the focal point of research because of the west to east water flow in the system, and the present day higher salinity in the west compared to the east. Little to no consideration has been paid to the influence of the Kattegat and Baltic on the Limfjord until now. A 10m sediment core was taken from Sebbersund (near Nibe, Limfjord), along the connection between the Limfjord and the Kattegat in the east to understand how the eastern part of the system has changed and differed from changes observed in the west. The Sebbersund sequence spans a majority of the Holocene, from 9600 cal BP to 1030 cal BP, determined via radiocarbon dating of terrestrial macrofossils and bulk sediment. Over this time period palaeoenvironmental conditions were reconstructed through the use of geochemical analyses (13C, 15N, C:N), physical sediment analyses, dinoflagellate cyst abundances and molluscan analyses. apart from two instances of low salinity, one at the top and one at the bottom of the core, the sequence has a strong marine signal for a majority of the Holocene. Radiocarbon dating of bulk sediment samples showed the presence of old carbon in the system, creating an age offset between 1,300 ± 200 and 2,800 ± 200 calibrated 14C years compared to the age-depth curve based on the terrestrial macrofossils. This finding, along with the strong marine influence in the system, discerned through geochemical data, dinoflagellate cyst and mollusc counts, is important for obtaining accurate radiocarbon ages in the region and stresses the importance of understanding both the marine and freshwater reservoir effects. The marine dominance in the eastern Limfjord differs from the west, which is characterized by a number of freshwater events when the North Sea connection was closed off during the Holocene. The eastern connection was open to the Kattegat throughout a large portion of the Holocene, with influx of open ocean water entering the system during periods of higher sea level.

A Conventional Internal Combustion Engine Versus a Range Extended Electric Vehicle Under the Current Regulatory Regime in the United Kingdom

Transport accounts for 22% of greenhouse gas emissions in the United Kingdom and cars are expected tomore than double by 2050. Car manufacturers are continually aiming for a substantially reduced carbonfootprint through improved fuel efficiency and better powertrain performance due to the strict EuropeanUnion emissions standards. However, road tax, not just fuel efficiency, is a key consideration of consumerswhen purchasing a car. While measures have been taken to reduce emissions through stricter standards, infuture, alternative technologies will be used. Electric vehicles, hybrid vehicles and range extended electricvehicles have been identified as some of these future technologies. In this research a virtual test bed of aconventional internal combustion engine and a range extended electric vehicle family saloon car were builtin AVL’s vehicle and powertrain system level simulation tool, CRUISE, to simulate the New EuropeanDrive Cycle and the results were then soft-linked to a techno-economic model to compare the effectivenessof current support mechanisms over the full life cycle of both cars. The key finding indicates that althoughcarbon emissions are substantially reduced, switching is still not financially the best option for either theconsumer or the government in the long run.