Conceptual Ecological Modelling of Sublittoral Rock Habitats to Inform Indicator Selection

The purpose of this study is to produce a series of Conceptual Ecological Models (CEMs) that represent sublittoral rock habitats in the UK. CEMs are diagrammatic representations of the influences and processes that occur within an ecosystem. They can be used to identify critical aspects of an ecosystem that may be studied further, or serve as the basis for the selection of indicators for environmental monitoring purposes. The models produced by this project are control diagrams, representing the unimpacted state of the environment free from anthropogenic pressures. It is intended that the models produced by this project will be used to guide indicator selection for the monitoring of this habitat in UK waters. CEMs may eventually be produced for a range of habitat types defined under the UK Marine Biodiversity Monitoring R&D Programme (UKMBMP), which, along with stressor models, are designed to show the interactions within impacted habitats, would form the basis of a robust method for indicator selection. This project builds on the work to develop CEMs for shallow sublittoral coarse sediment habitats (Alexander et al 2014). The project scope included those habitats defined as ‘sublittoral rock’. This definition includes those habitats that fall into the EUNIS Level 3 classifications A3.1 Atlantic and Mediterranean high energy infralittoral rock, A3.2 Atlantic and Mediterranean moderate energy infralittoral rock, A3.3 Atlantic and Mediterranean low energy infralittoral rock, A4.1 Atlantic and Mediterranean high energy circalittoral rock, A4.2 Atlantic and Mediterranean moderate energy circalittoral rock, and A4.3 Atlantic and Mediterranean low energy circalittoral rock as well as the constituent Level 4 and 5 biotopes that are relevant to UK waters. A species list of characterising fauna to be included within the scope of the models was identified using an iterative process to refine the full list of species found within the relevant Level 5 biotopes. A literature review was conducted using a pragmatic and iterative approach to gather evidence regarding species traits and information that would be used to inform the models and characterise the interactions that occur within the sublittoral rock habitat. All information gathered during the literature review was entered into a data logging pro-forma spreadsheet that accompanies this report. Wherever possible, attempts were made to collect information from UK-specific peer-reviewed studies, although other sources were used where necessary. All data gathered was subject to a detailed confidence assessment. Expert judgement by the project team was utilised to provide information for aspects of the models for which references could not be sourced within the project timeframe. A multivariate analysis approach was adopted to assess ecologically similar groups (based on ecological and life history traits) of fauna from the identified species to form the basis of the models. A model hierarchy was developed based on these ecological groups. One general control model was produced that indicated the high-level drivers, inputs, biological assemblages, ecosystem processes and outputs that occur in sublittoral rock habitats. In addition to this, seven detailed sub-models were produced, which each focussed on a particular ecological group of fauna within the habitat: ‘macroalgae’, ‘temporarily or permanently attached active filter feeders’, ‘temporarily or permanently attached passive filter feeders’, ‘bivalves, brachiopods and other encrusting filter feeders’, ‘tube building fauna’, ‘scavengers and predatory fauna’, and ‘non-predatory mobile fauna’. Each sub-model is accompanied by an associated confidence model that presents confidence in the links between each model component. The models are split into seven levels and take spatial and temporal scale into account through their design, as well as magnitude and direction of influence. The seven levels include regional to global drivers, water column processes, local inputs/processes at the seabed, habitat and biological assemblage, output processes, local ecosystem functions, and regional to global ecosystem functions. The models indicate that whilst the high level drivers that affect each ecological group are largely similar, the output processes performed by the biota and the resulting ecosystem functions vary both in number and importance between groups. Confidence within the models as a whole is generally high, reflecting the level of information gathered during the literature review. Physical drivers which influence the ecosystem were found to be of high importance for the sublittoral rock habitat, with factors such as wave exposure, water depth and water currents noted to be crucial in defining the biological assemblages. Other important factors such as recruitment/propagule supply, and those which affect primary production, such as suspended sediments, light attenuation and water chemistry and temperature, were also noted to be key and act to influence the food sources consumed by the biological assemblages of the habitat, and the biological assemblages themselves. Output processes performed by the biological assemblages are variable between ecological groups depending on the specific flora and fauna present and the role they perform within the ecosystem. Of particular importance are the outputs performed by the macroalgae group, which are diverse in nature and exert influence over other ecological groups in the habitat. Important output processes from the habitat as a whole include primary and secondary production, bioengineering, biodeposition (in mixed sediment habitats) and the supply of propagules; these in turn influence ecosystem functions at the local scale such as nutrient and biogeochemical cycling, supply of food resources, sediment stability (in mixed sediment habitats), habitat provision and population and algae control. The export of biodiversity and organic matter, biodiversity enhancement and biotope stability are the resulting ecosystem functions that occur at the regional to global scale. Features within the models that are most useful for monitoring habitat status and change due to natural variation have been identified, as have those that may be useful for monitoring to identify anthropogenic causes of change within the ecosystem. Biological, physical and chemical features of the ecosystem have been identified as potential indicators to monitor natural variation, whereas biological factors and those physical /chemical factors most likely to affect primary production have predominantly been identified as most likely to indicate change due to anthropogenic pressures.

Modelling of Unsteady Gas-Dynamic Flow in a Pipe and at its Exit Using CFD

Traditionally the simulation of the thermodynamic aspects of the internal combustion engine has been undertaken using one-dimensional gas-dynamic models to represent the intake and exhaust systems. CFD analysis of engines has been restricted to modelling of in-cylinder flow structures. With the increasing accessibility of CFD software it is now worth considering its use for complete gas-dynamic engine simulation. This paper appraises the accuracy of various CFD models in comparison to a 1D gas-dynamic simulation. All of the models are compared to experimental data acquired on an apparatus that generates a single gas-dynamic pressure wave. The progress of the wave along a constant area pipe and its subsequent reflection from the open pipe end are recorded with a number of high speed pressure transducers. It was found that there was little to choose between the accuracy of the 1D model and the best CFD model. The CFD model did not require experimentally derived loss coefficients to accurately represent the open pipe end; however, it took several hundred times longer to complete its analysis. The best congruency between the CFD models and the experimental data was achieved using the RNG k-e turbulence model. The open end of the pipe was most effectively represented by surrounding it with a relatively small volume of cells connected to the rest of the environment using a pressure boundary.

Economic modelling of antenatal screening and ultrasound scanning programmes for identification of fetal abnormalities

Objective Within the framework of a health technology assessment and using an economic model, to determine the most clinically and cost effective policy of scanning and screening for fetal abnormalities in early pregnancy. Design A discrete event simulation model of 50,000 singleton pregnancies. Setting Maternity services in Scotland. Population Women during the first 24 weeks of their pregnancy. Methods The mathematical model was populated with data on uptake of screening, prevalence, detection and false positive rates for eight fetal abnormalities and with costs for ultrasound scanning and serum screening. Inclusion of abnormalities was based on the relative prevalence and clinical importance of conditions and the availability of data. Six strategies for the identification of abnormalities prenatally including combinations of first and second trimester ultrasound scanning and first and second trimester screening for chromosomal abnormalities were compared. Main outcome measures The number of abnormalities detected and missed, the number of iatrogenic losses resulting from invasive tests, the total cost of strategies and the cost per abnormality detected were compared between strategies. Results First trimester screening for chromosomal abnormalities costs more than second trimester screening but results in fewer iatrogenic losses. Strategies which include a second trimester ultrasound scan result in more abnormalities being detected and have lower costs per anomaly detected. Conclusions The preferred strategy includes both first and second trimester ultrasound scans and a first trimester screening test for chromosomal abnormalities. It has been recommended that this policy is offered to all women in Scotland.

Linear quadratic and tumour control probability modelling in external beam radiotherapy

The standard linear-quadratic (LQ) survival model for external beam radiotherapy is reviewed with particular emphasis on studying how different schedules of radiation treatment planning may be affected by different tumour repopulation kinetics. The LQ model is further examined in the context of tumour control probability (TCP) models. The application of the Zaider and Minerbo non-Poissonian TCP model incorporating the effect of cellular repopulation is reviewed. In particular the recent development of a cell cycle model within the original Zaider and Minerbo TCP formalism is highlighted. Application of this TCP cell-cycle model in clinical treatment plans is explored and analysed.

Correction of dielectric losses in practical leaky-wave antenna designs

In this paper, the leaky-mode theory is applied to take into account for the dielectric losses in millimetre waveband inhomogeneous leaky-wave antennas. A practical dielectric-filled cosine-tapered periodic leaky-wave antenna working in the 45GHz band is studied, showing how the desired sidelobes level and directivity are spoilt due to the effect of the losses. An iterative procedure is used to correct the negative effects of the losses in the radiation patterns of the leaky-wave structure. It is also shown the practical limits of the proposed correction approach. The leaky-mode theory is applied for the first time to compensate the losses in a practical leaky-wave antenna in hybrid waveguide printed circuit technology. This leaky-mode theory is validated with full-wave three-dimensional finite element method simulations of the designed antenna.

Efficient modelling technique for fractal electromagnetic band-gap arrays

An efficient modelling technique is proposed for the analysis of a fractal-element electromagnetic band-gap array. The modelling is based on a method of moments modal analysis in conjunction with an interpolation scheme, which significantly accelerates the computations. The plane-wave and the surface-wave responses of the structure have been studied by means of transmission coefficients and dispersion diagrams. The multiband properties and the compactness of the proposed structure are presented. The technique is general and can be applied to arbitrary-shaped element geometries.

Developments in X-ray laser pumping with travelling wave at Vulcan

Saturated output has been observed for both Ne and Ni-like X-ray lasers when Pumped in the transient mode. As these 'normal' transitions display very high gain, attempts have been made to observe a 2p --> 2s inner shell transition in Ne-like ions, which scale well towards the water window. Modelling of the pump conditions for Ge lasing at 6.2 run is presented. As the predicted gain is low the experiment was set up for 18 mm targets. Shots were taken on Ti, Fe, Ni and Ge. A similar to1.5 ps travelling wave pulse is applied at various times after the peak of a long, preforming Pulse. Various pump conditions were attempted but no inner shell X-ray laser was detected.

Modelling the comet assay

The single-cell gel electrophoresis technique or comet assay is widely regarded as a quick and reliable method of analysing DNA damage in individual cells. It has a proven track record from the fields of biomonitoring to nutritional studies. The assay operates by subjecting cells that are fixed in agarose to high salt and detergent lysis, thus removing all the cellular content except the DNA. By relaxing the DNA in an alkaline buffer, strands containing breaks are released from supercoiling. Upon electrophoresis, these strands are pulled out into the agarose, forming a tail which, when stained with a fluorescent dye, can be analysed by fluorescence microscopy. The intensity of this tail reflects the amount of DNA damage sustained. Despite being such an established and widely used assay, there are still many aspects of the comet assay which are not fully understood. The present review looks at how the comet assay is being used, and highlights some of its limitations. The protocol itself varies among laboratories, so results from similar studies may vary. Given such discrepancies, it would be attractive to break the assay into components to generate a mathematical model to investigate specific parameters.

Formulation of Locally Reacting Surfaces in FDTD/K-DWM Modelling of Acoustic Spaces

In this paper, we present new methods for constructing and analysing formulations of locally reacting surfaces that can be used in finite difference time domain (FDTD) simulations of acoustic spaces. Novel FDTD formulations of frequency-independent and simple frequency-dependent impedance boundaries are proposed for 2D and 3D acoustic systems, including a full treatment of corners and boundary edges. The proposed boundary formulations are designed for virtual acoustics applications using the standard leapfrog scheme based on a rectilinear grid, and apply to FDTD as well as Kirchhoff variable digital waveguide mesh (K-DWM) methods. In addition, new analytic evaluation methods that accurately predict the reflectance of numerical boundary formulations are proposed. numerical experiments and numerical boundary analysis (NBA) are analysed in time and frequency domains in terms of the pressure wave reflectance for different angles of incidence and various impedances. The results show that the proposed boundary formulations structurally adhere well to the theoretical reflectance. In particular, both reflectance magnitude and phase are closely approximated even at high angles of incidence and low impedances. Furthermore, excellent agreement was found between the numerical boundary analysis and the experimental results, validating both as tools for researching FDTD boundary formulations.

Computational simulation methodologies for mechanobiological modelling: a cell-centred approach to neointima development in stents

The design of medical devices could be very much improved if robust tools were available for computational simulation of tissue response to the presence of the implant. Such tools require algorithms to simulate the response of tissues to mechanical and chemical stimuli. Available methodologies include those based on the principle of mechanical homeostasis, those which use continuum models to simulate biological constituents, and the cell-centred approach, which models cells as autonomous agents. In the latter approach, cell behaviour is governed by rules based on the state of the local environment around the cell; and informed by experiment. Tissue growth and differentiation requires simulating many of these cells together. In this paper, the methodology and applications of cell-centred techniques-with particular application to mechanobiology-are reviewed, and a cell-centred model of tissue formation in the lumen of an artery in response to the deployment of a stent is presented. The method is capable of capturing some of the most important aspects of restenosis, including nonlinear lesion growth with time. The approach taken in this paper provides a framework for simulating restenosis; the next step will be to couple it with more patient-specific geometries and quantitative parameter data.