Stochastic simulation for spatial modelling of dynamic process in a living cell

One of the fundamental motivations underlying computational cell biology is to gain insight into the complicated dynamical processes taking place, for example, on the plasma membrane or in the cytosol of a cell. These processes are often so complicated that purely temporal mathematical models cannot adequately capture the complex chemical kinetics and transport processes of, for example, proteins or vesicles. On the other hand, spatial models such as Monte Carlo approaches can have very large computational overheads. This chapter gives an overview of the state of the art in the development of stochastic simulation techniques for the spatial modelling of dynamic processes in a living cell.

Spatial modelling of population health screening : the role of accessibility in predicting expected patient flows

This paper describes a generalised linear mixed model (GLMM) approach for understanding spatial patterns of participation in population health screening, in the presence of multiple screening facilities. The models presented have dual focus, namely the prediction of expected patient flows from regions to services and relative rates of participation by region- service combination, with both outputs having meaningful implications for the monitoring of current service uptake and provision. The novelty of this paper lies with the former focus, and an approach for distributing expected participation by region based on proximity to services is proposed. The modelling of relative rates of participation is achieved through the combination of different random effects, as a means of assigning excess participation to different sources. The methodology is applied to participation data collected from a government-funded mammography program in Brisbane, Australia.

Copula-based spatial modelling of geometallurgical variables

The most important aspect of modelling a geological variable, such as metal grade, is the spatial correlation. Spatial correlation describes the relationship between realisations of a geological variable sampled at different locations. Any method for spatially modelling such a variable should be capable of accurately estimating the true spatial correlation. Conventional kriged models are the most commonly used in mining for estimating grade or other variables at unsampled locations, and these models use the variogram or covariance function to model the spatial correlations in the process of estimation. However, this usage assumes the relationships of the observations of the variable of interest at nearby locations are only influenced by the vector distance between the locations. This means that these models assume linear spatial correlation of grade. In reality, the relationship with an observation of grade at a nearby location may be influenced by both distance between the locations and the value of the observations (ie non-linear spatial correlation, such as may exist for variables of interest in geometallurgy). Hence this may lead to inaccurate estimation of the ore reserve if a kriged model is used for estimating grade of unsampled locations when nonlinear spatial correlation is present. Copula-based methods, which are widely used in financial and actuarial modelling to quantify the non-linear dependence structures, may offer a solution. This method was introduced by Bárdossy and Li (2008) to geostatistical modelling to quantify the non-linear spatial dependence structure in a groundwater quality measurement network. Their copula-based spatial modelling is applied in this research paper to estimate the grade of 3D blocks. Furthermore, real-world mining data is used to validate this model. These copula-based grade estimates are compared with the results of conventional ordinary and lognormal kriging to present the reliability of this method.

A spatial modelling framework for assessing climate change impacts on freshwater ecosystems: Response of brown trout (Salmo trutta L.) biomass to warming water temperature

Mountain regions worldwide are particularly sensitive to on-going climate change. Specifically in the Alps in Switzerland, the temperature has increased twice as fast than in the rest of the Northern hemisphere. Water temperature closely follows the annual air temperature cycle, severely impacting streams and freshwater ecosystems. In the last 20 years, brown trout (Salmo trutta L) catch has declined by approximately 40-50% in many rivers in Switzerland. Increasing water temperature has been suggested as one of the most likely cause of this decline. Temperature has a direct effect on trout population dynamics through developmental and disease control but can also indirectly impact dynamics via food-web interactions such as resource availability. We developed a spatially explicit modelling framework that allows spatial and temporal projections of trout biomass using the Aare river catchment as a model system, in order to assess the spatial and seasonal patterns of trout biomass variation. Given that biomass has a seasonal variation depending on trout life history stage, we developed seasonal biomass variation models for three periods of the year (Autumn-Winter, Spring and Summer). Because stream water temperature is a critical parameter for brown trout development, we first calibrated a model to predict water temperature as a function of air temperature to be able to further apply climate change scenarios. We then built a model of trout biomass variation by linking water temperature to trout biomass measurements collected by electro-fishing in 21 stations from 2009 to 2011. The different modelling components of our framework had overall a good predictive ability and we could show a seasonal effect of water temperature affecting trout biomass variation. Our statistical framework uses a minimum set of input variables that make it easily transferable to other study areas or fish species but could be improved by including effects of the biotic environment and the evolution of demographical parameters over time. However, our framework still remains informative to spatially highlight where potential changes of water temperature could affect trout biomass. (C) 2015 Elsevier B.V. All rights reserved.-

Landscape characteristics associated with species richness and occurrence of small native mammals inhabiting a coastal heathland: a spatial modelling approach

In the coastal region of south-western Victoria, Australia, populations of native small mammal species are restricted to patches of suitable habitat in a highly fragmented landscape. The size and spatial arrangement of these patches is likely to influence both the occupancy and richness of species at a location. Geographic Information System (GIS)-based habitat models of the species richness of native small mammals, and individual species  occurrences, were developed to produce maps displaying the spatial  configuration of suitable habitat. Models were generated using either generalised linear Poisson regression (for species richness) or logistic regression (for species occurrences) with species richness or  presence/absence as the dependent variable and landscape variables, extracted from both GIS data layers and multi-spectral digital imagery, as the predictor variables. A multi-model inference approach based on the Akaike Information Criterion was used and the resulting model was applied in a GIS framework to extrapolate predicted richness/likelihood of occurrence across the entire area of the study. A negative association between species  richness and elevation, habitat complexity and sun index indicated that richness within the study area decreases with increasing altitude, vertical vegetation structure and exposure to solar radiation. Landform  characteristics were important (to varying degrees) in determining habitat occupancy for all of the species examined, while the influence of habitat complexity was important for only one of the species. Performance of all but one of the models generated using presence/absence data was high, as indicated by the area under the curve of a receiver-operating characteristic plot. The effective conservation of the small mammal species in the area of concern is likely to depend on management actions that promote the protection of the critical habitats identified in the models.

Spatial modelling and prediction on river networks: up model, down model or hybrid?

Preservation of rivers and water resources is crucial in most environmental policies and many efforts are made to assess water quality. Environmental monitoring of large river networks are based on measurement stations. Compared to the total length of river networks, their number is often limited and there is a need to extend environmental variables that are measured locally to the whole river network. The objective of this paper is to propose several relevant geostatistical models for river modeling. These models use river distance and are based on two contrasting assumptions about dependency along a river network. Inference using maximum likelihood, model selection criterion and prediction by kriging are then developed. We illustrate our approach on two variables that differ by their distributional and spatial characteristics: summer water temperature and nitrate concentration. The data come from 141 to 187 monitoring stations in a network on a large river located in the Northeast of France that is more than 5000 km long and includes Meuse and Moselle basins. We first evaluated different spatial models and then gave prediction maps and error variance maps for the whole stream network.

BIVARIATE BINOMIAL SPATIAL MODELLING LOA loa PREVALENCE IN TROPICAL AFRICA

We present a state-of-the-art application of smoothing for dependent bivariate binomial spatial data to Loa loa prevalence mapping in West Africa. This application is special because it starts with the non-spatial calibration of survey instruments, continues with the spatial model building and assessment and ends with robust, tested software that will be used by the field scientists of the World Health Organization for online prevalence map updating. From a statistical perspective several important methodological issues were addressed: (a) building spatial models that are complex enough to capture the structure of the data but remain computationally usable; (b)reducing the computational burden in the handling of very large covariate data sets; (c) devising methods for comparing spatial prediction methods for a given exceedance policy threshold.

High-resolution spatial modelling of greenhouse gas emissions from land-use change to energy crops in the United Kingdom

Funded by Energy Technologies Institute EPSRC-Supergen. Grant Number: EP/M013200/1

SimuMap: a computational system for spatial modelling

The paper presents a computational system based upon formal principles to run spatial models for environmental processes. The simulator is named SimuMap because it is typically used to simulate spatial processes over a mapped representation of terrain. A model is formally represented in SimuMap as a set of coupled sub-models. The paper considers the situation where spatial processes operate at different time levels, but are still integrated. An example of such a situation commonly occurs in watershed hydrology where overland flow and stream channel flow have very different flow rates but are highly related as they are subject to the same terrain runoff processes. SimuMap is able to run a network of sub-models that express different time-space derivatives for water flow processes. Sub-models may be coded generically with a map algebra programming language that uses a surface data model. To address the problem of differing time levels in simulation, the paper: (i) reviews general approaches for numerical solvers, (ii) considers the constraints that need to be enforced to use more adaptive time steps in discrete time specified simulations, and (iii) scaling transfer rates in equations that use different time bases for time-space derivatives. A multistep scheme is proposed for SimuMap. This is presented along with a description of its visual programming interface, its modelling formalisms and future plans. (C) 2003 Elsevier Ltd. All rights reserved.

A way forward for land-use planning to achieve policy goals by using spatial modelling scenarios

This paper investigates how demographic (socioeconomic) and land-use (physical and environmental) data can be integrated within a decision support framework to formulate and evaluate land-use planning scenarios. A case-study approach is undertaken with land-use planning scenarios for a rapidly growing coastal area in Australia, the Shire of Hervey Bay. The town and surrounding area require careful planning of the future urban growth between competing land uses. Three potential urban growth scenarios are put forth to address this issue. Scenario A ('continued growth') is based on existing socioeconomic trends. Scenario B ('maximising rates base') is derived using optimisation modelling of land-valuation data. Scenario C ('sustainable development') is derived using a number of social, economic, and environmental factors and assigning weightings of importance to each factor using a multiple criteria analysis approach. The land-use planning scenarios are presented through the use of maps and tables within a geographical information system, which delineate future possible land-use allocations up until 2021. The planning scenarios are evaluated by using a goal-achievement matrix approach. The matrix is constructed with a number of criteria derived from key policy objectives outlined in the regional growth management framework and town planning schemes. The authors of this paper examine the final efficiency scores calculated for each of the three planning scenarios and discuss the advantages and disadvantages of the three land-use modelling approaches used to formulate the final scenarios.

Spatial modelling of cloud

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ELUM: a spatial modelling tool to predict soil greenhouse gas changes from land conversion to bioenergy in the UK

Acknowledgements This work is based on the Ecosystem Land Use Modelling & Soil Carbon GHG Flux Trial (ELUM) project, which was commissioned and funded by the Energy Technologies Institute (ETI). The authors are grateful to Niall McNamara (Centre for Ecology & Hydrology, Lancaster) for coordinating the project and to Dagmar Henner (University of Aberdeen) for project assistance. We are also grateful to staff at the ETI, particularly to Geraldine Newton-Cross, Geraint Evans and Hannah Evans for constructive advice and feedback, and to Jonathan Oxley for project support. The ELUM Software Package contains Ordnance Survey data © Crown copyright and database right 2012.

Spatial analysis of melioidosis distribution in a suburban area

Burkholderia pseudomallei, the causative agent of melioidosis is associated with soil. This study used a geographic information system (GIS) to determine the spatial distribution of clinical cases of melioidosis in the endemic suburban region of Townsville in Australia. A total of 65 cases over the period 1996–2008 were plotted using residential address. Two distinct groupings were found. One was around the base of a hill in the city centre and the other followed the old course of a major waterway in the region. Both groups (accounting for 43 of the 65 cases examined) are in areas expected to have particularly wet topsoils following intense rainfall, due to soil type or landscape position.

Predicting health programme participation: A gravity‐based, hierarchical modelling approach

Statistical analyses of health program participation seek to address a number of objectives compatible with the evaluation of demand for current resources. In this spirit, a spatial hierarchical model is developed for disentangling patterns in participation at the small area level, as a function of population-based demand and additional variation. For the former, a constrained gravity model is proposed to quantify factors associated with spatial choice and account for competition effects, for programs delivered by multiple clinics. The implications of gravity model misspecification within a mixed effects framework are also explored. The proposed model is applied to participation data from a no-fee mammography program in Brisbane, Australia. Attention is paid to the interpretation of various model outputs and their relevance for public health policy.