Modelling the Somantic Electrical Response of Hippocampal Pyramidal Neurons

A modeling study of hippocampal pyramidal neurons is described. This study is based on simulations using HIPPO, a program which simulates the somatic electrical activity of these cells. HIPPO is based on a) descriptions of eleven non-linear conductances that have been either reported for this class of cell in the literature or postulated in the present study, and b) an approximation of the electrotonic structure of the cell that is derived in this thesis, based on data for the linear properties of these cells. HIPPO is used a) to integrate empirical data from a variety of sources on the electrical characteristics of this type of cell, b) to investigate the functional significance of the various elements that underly the electrical behavior, and c) to provide a tool for the electrophysiologist to supplement direct observation of these cells and provide a method of testing speculations regarding parameters that are not accessible.

An Interval Intelligent-based Approach for Fault Detection and Modelling

Not considered in the analytical model of the plant, uncertainties always dramatically decrease the performance of the fault detection task in the practice. To cope better with this prevalent problem, in this paper we develop a methodology using Modal Interval Analysis which takes into account those uncertainties in the plant model. A fault detection method is developed based on this model which is quite robust to uncertainty and results in no false alarm. As soon as a fault is detected, an ANFIS model is trained in online to capture the major behavior of the occurred fault which can be used for fault accommodation. The simulation results understandably demonstrate the capability of the proposed method for accomplishing both tasks appropriately

Systems Design: Activity and Sequence modelling using Visual Paradigm

This lab follows the lectures 'System Design: http://www.edshare.soton.ac.uk/9653/ and http://www.edshare.soton.ac.uk/6280/ . Students use Visual Paradigm for UML to build Activity and Sequence models through project examples: Library, Plant Nursery and a Health Spa

Functional studies of the deubiquitinating enzymes USP19, USP4 and UCH-L1

El marcaje de proteínas con ubiquitina, conocido como ubiquitinación, cumple diferentes funciones que incluyen la regulación de varios procesos celulares, tales como: la degradación de proteínas por medio del proteosoma, la reparación del ADN, la señalización mediada por receptores de membrana, y la endocitosis, entre otras (1). Las moléculas de ubiquitina pueden ser removidas de sus sustratos gracias a la acción de un gran grupo de proteasas, llamadas enzimas deubiquitinizantes (DUBs) (2). Las DUBs son esenciales para la manutención de la homeostasis de la ubiquitina y para la regulación del estado de ubiquitinación de diferentes sustratos. El gran número y la diversidad de DUBs descritas refleja tanto su especificidad como su utilización para regular un amplio espectro de sustratos y vías celulares. Aunque muchas DUBs han sido estudiadas a profundidad, actualmente se desconocen los sustratos y las funciones biológicas de la mayoría de ellas. En este trabajo se investigaron las funciones de las DUBs: USP19, USP4 y UCH-L1. Utilizando varias técnicas de biología molecular y celular se encontró que: i) USP19 es regulada por las ubiquitin ligasas SIAH1 y SIAH2 ii) USP19 es importante para regular HIF-1α, un factor de transcripción clave en la respuesta celular a hipoxia, iii) USP4 interactúa con el proteosoma, iv) La quimera mCherry-UCH-L1 reproduce parcialmente los fenotipos que nuestro grupo ha descrito previamente al usar otros constructos de la misma enzima, y v) UCH-L1 promueve la internalización de la bacteria Yersinia pseudotuberculosis.

Exploring chromium (VI) dioxodihalides chemistry: is density functional theory the most suitable tool?

A comparative systematic study of the CrO2F2 compound has been performed using different conventional ab initio methodologies and density functional procedures. Two points have been analyzed: first, the accuracy of results yielded by each method under study, and second, the computational cost required to reach such results. Weighing up both aspects, density functional theory has been found to be more appropriate than the Hartree-Fock (HF) and the analyzed post-HF methods. Hence, the structural characterization and spectroscopic elucidation of the full CrO2X2 series (X=F,Cl,Br,I) has been done at this level of theory. Emphasis has been given to the unknown CrO2I2 species, and specially to the UV/visible spectra of all four compounds. Furthermore, a topological analysis in terms of charge density distributions has revealed why the valence shell electron pair repulsion model fails in predicting the molecular shape of such CrO2X2 complexes

Knowledge-based modelling and simulation of operational problems of microbiological origin in wastewater treatment plants

The activated sludge and anaerobic digestion processes have been modelled in widely accepted models. Nevertheless, these models still have limitations when describing operational problems of microbiological origin. The aim of this thesis is to develop a knowledge-based model to simulate risk of plant-wide operational problems of microbiological origin.For the risk model heuristic knowledge from experts and literature was implemented in a rule-based system. Using fuzzy logic, the system can infer a risk index for the main operational problems of microbiological origin (i.e. filamentous bulking, biological foaming, rising sludge and deflocculation). To show the results of the risk model, it was implemented in the Benchmark Simulation Models. This allowed to study the risk model's response in different scenarios and control strategies. The risk model has shown to be really useful providing a third criterion to evaluate control strategies apart from the economical and environmental criteria.

Comparison of stochastic parameterisation approaches in a single-column model

We discuss and test the potential usefulness of single-column models (SCMs) for the testing of stochastic physics schemes that have been proposed for use in general circulation models (GCMs). We argue that although single column tests cannot be definitive in exposing the full behaviour of a stochastic method in the full GCM, and although there are differences between SCM testing of deterministic and stochastic methods, SCM testing remains a useful tool. It is necessary to consider an ensemble of SCM runs produced by the stochastic method. These can be usefully compared to deterministic ensembles describing initial condition uncertainty and also to combinations of these (with structural model changes) into poor man's ensembles. The proposed methodology is demonstrated using an SCM experiment recently developed by the GCSS (GEWEX Cloud System Study) community, simulating transitions between active and suppressed periods of tropical convection.

Modelling nitrogen fluxes from the land surface to the coastal zone in European systems: the perspective of the INCA project

This paper describes the results and conclusions of the INCA (Integrated Nitrogen Model for European CAtchments) project and sets the findings in the context of the ELOISE (European Land-Ocean Interaction Studies) programme. The INCA project was concerned with the development of a generic model of the major factors and processes controlling nitrogen dynamics in European river systems, thereby providing a tool (a) to aid the scientific understanding of nitrogen transport and retention in catchments and (b) for river-basin management and policy-making. The findings of the study highlight the heterogeneity of the factors and processes controlling nitrogen dynamics in freshwater systems. Nonetheless, the INCA model was able to simulate the in-stream nitrogen concentrations and fluxes observed at annual and seasonal timescales in Arctic, Continental and Maritime-Temperate regimes. This result suggests that the data requirements and structural complexity of the INCA model are appropriate to simulate nitrogen fluxes across a wide range of European freshwater environments. This is a major requirement for the production of coupled fiver-estuary-coastal shelf models for the management of our aquatic environment. With regard to river-basin management, to achieve an efficient reduction in nutrient fluxes from the land to the estuarine and coastal zone, the model simulations suggest that management options must be adaptable to the prevailing environmental and socio-economic factors in individual catchments: 'Blanket approaches' to environmental policy appear too simple. (c) 2004 Elsevier B.V. All rights reserved.

Modelling the inorganic nitrogen behaviour in a small Mediterranean forested catchment, Fuirosos (Catalonia)

The aim of this work was to couple a nitrogen (N) sub-model to already existent hydrological lumped (LU4-N) and semi-distributed (LU4-R-N and SD4-R-N) conceptual models, to improve our understanding of the factors and processes controlling nitrogen cycling and losses in Mediterranean catchments. The N model adopted provides a simplified conceptualization of the soil nitrogen cycle considering mineralization, nitrification, immobilization, denitrification, plant uptake, and ammonium adsorption/desorption. It also includes nitrification and denitrification in the shallow perched aquifer. We included a soil moisture threshold for all the considered soil biological processes. The results suggested that all the nitrogen processes were highly influenced by the rain episodes and that soil microbial processes occurred in pulses stimulated by soil moisture increasing after rain. Our simulation highlighted the riparian zone as a possible source of nitrate, especially after the summer drought period, but it can also act as an important sink of nitrate due to denitrification, in particular during the wettest period of the year. The riparian zone was a key element to simulate the catchment nitrate behaviour. The lumped LU4-N model (which does not include the riparian zone) could not be validated, while both the semi-distributed LU4-R-N and SD4-R-N model (which include the riparian zone) gave satisfactory results for the calibration process and acceptable results for the temporal validation process.

Adjoint goal-based error norms for adaptive mesh ocean modelling

Flow in the world's oceans occurs at a wide range of spatial scales, from a fraction of a metre up to many thousands of kilometers. In particular, regions of intense flow are often highly localised, for example, western boundary currents, equatorial jets, overflows and convective plumes. Conventional numerical ocean models generally use static meshes. The use of dynamically-adaptive meshes has many potential advantages but needs to be guided by an error measure reflecting the underlying physics. A method of defining an error measure to guide an adaptive meshing algorithm for unstructured tetrahedral finite elements, utilizing an adjoint or goal-based method, is described here. This method is based upon a functional, encompassing important features of the flow structure. The sensitivity of this functional, with respect to the solution variables, is used as the basis from which an error measure is derived. This error measure acts to predict those areas of the domain where resolution should be changed. A barotropic wind driven gyre problem is used to demonstrate the capabilities of the method. The overall objective of this work is to develop robust error measures for use in an oceanographic context which will ensure areas of fine mesh resolution are used only where and when they are required. (c) 2006 Elsevier Ltd. All rights reserved.

Global hydrology modelling and uncertainty: running multiple ensembles with a campus grid.

Uncertainties associated with the representation of various physical processes in global climate models (GCMs) mean that, when projections from GCMs are used in climate change impact studies, the uncertainty propagates through to the impact estimates. A complete treatment of this ‘climate model structural uncertainty’ is necessary so that decision-makers are presented with an uncertainty range around the impact estimates. This uncertainty is often underexplored owing to the human and computer processing time required to perform the numerous simulations. Here, we present a 189-member ensemble of global river runoff and water resource stress simulations that adequately address this uncertainty. Following several adaptations and modifications, the ensemble creation time has been reduced from 750 h on a typical single-processor personal computer to 9 h of high-throughput computing on the University of Reading Campus Grid. Here, we outline the changes that had to be made to the hydrological impacts model and to the Campus Grid, and present the main results. We show that, although there is considerable uncertainty in both the magnitude and the sign of regional runoff changes across different GCMs with climate change, there is much less uncertainty in runoff changes for regions that experience large runoff increases (e.g. the high northern latitudes and Central Asia) and large runoff decreases (e.g. the Mediterranean). Furthermore, there is consensus that the percentage of the global population at risk to water resource stress will increase with climate change.

Phytoestrogen consumption and association with breast, prostate and colorectal cancer in EPIC Norfolk

Phytoestrogens are polyphenolic secondary plant metabolites that have structural and functional similarities to 17β-oestradiol and have been associated with a protective effect against hormone-related cancers. Most foods in the UK only contain small amounts of phytoestrogens (median content 21 μg/100 g) and the highest content is found in soya and soya-containing foods. The highest phytoestrogen content in commonly consumed foods is found in breads (average content 450 μg/100 g), the main source of isoflavones in the UK diet. The phytoestrogen consumption in cases and controls was considerably lower than in Asian countries. No significant associations between phytoestrogen intake and breast cancer risk in a nested case-control study in EPIC Norfolk were found. Conversely, colorectal cancer risk was inversely associated with enterolignan intake in women but not in men. Prostate cancer risk was positively associated with enterolignan intake, however this association became non-significant when adjusting for dairy intake, suggesting that enterolignans can act as a surrogate marker for dairy or calcium intake.

Phyto-activity of biocides used to manipulate herbivory: tests of three pesticides on fourteen plant species

1. We tested three pesticides used for field manipulations of herbivory for direct phytoactive effects on the germination and growth of 14 herbaceous plant species selected to provide a range of life-history strategies and functional groups. 2. We report three companion experiments: (A) Two insecticides, chlorpyrifos (granular soil insecticide) and dimethoate (foliar spray), were applied in fully-factorial combination to pot-germinated individuals of 12 species. (B) The same fully-factorial design was used to test for direct effects on the germination of four herbaceous legumes. (C) The molluscicide, metaldehyde, was tested for direct effects on the germination and growth of six plant species. 3. The insecticides had few significant effects on growth and germination. Dimethoate acted only on growth stimulating Anisantha sterilis, Sonchus asper and Stellaria graminea. In contrast, chlorpyrifos acted on germination increasing the germination of Trifolium dubium and Trifolium pratense. There was also a significant interactive effect of chlorpyrifos and dimethoate on the germination of T pratense. However, all. effects were relatively small in magnitude and explanatory power. The molluscicide had no significant effect on plant germination or growth. 4. The small number and size of direct effects of the pesticides on plant performance is encouraging for the use of these pesticides in manipulative experiments on herbivory, especially for the molluscicide. However, a smatt number of direct (positive) effects of the insecticides on some plant species need to be taken into account when interpreting field manipulations of herbivory with these compounds, and emphasises the importance of conducting tests for direct phyto-active effects. (C) 2004 Elsevier GmbH. All rights reserved.

Changing precipitation patterns alter plant community dynamics and succession in an ex-arable grassland

1. Changes in the frequency of extreme events, such as droughts, may be one of the most significant impacts of climate change for ecosystems. Models predict more frequent summer droughts in much of England: this paper investigates the impact on different types of plants in an ex-arable grassland community. 2. A long-term experiment simulated increased and decreased summer precipitation. Substantial interannual variation allowed the effects of summer drought to be tested in combination with wet and dry weather in other seasons. This is important, as climate models predict increased winter precipitation. 3. Total cover abundance in early summer increased with increasing water supply in the previous summer; there was no effect of winter precipitation. Productivity is therefore likely to decrease with more frequent summer droughts, with no mitigating effect of wetter winters. 4. The percentage cover of perennial grasses declined during a natural drought in 1995-97; this was exacerbated by the experimental drought treatment and reduced by supplemented rainfall. Simultaneously, short-lived ruderal species increased; this was greatest in drought treatments and least with supplemented rainfall. 4. These trends were subsequently reversed during several years of unusually wet weather, with perennial grasses increasing and short-lived forbs decreasing. This occurred even in experimentally droughted plots, and we propose that it resulted from rapid coverage of gaps during wet autumns and winters. 6. Deep-rooted species generally proved to be more drought resistant, but there were exceptions. 7. We conclude that increased frequency of summer droughts could have serious implications for the establishment and successional development of ex-arable grasslands. Increased winter precipitation would moderate the impact on species composition, but not on productivity.

Modelling the partitioning of evapotranspiration in a maize-sunflower intercrop

The primary purpose of this study was to model the partitioning of evapotranspiration in a maize-sunflower intercrop at various canopy covers. The Shuttleworth-Wallace (SW) model was extended for intercropping systems to include both crop transpiration and soil evaporation and allowing interaction between the two. To test the accuracy of the extended SW model, two field experiments of maize-sunflower intercrop were conducted in 1998 and 1999. Plant transpiration and soil evaporation were measured using sap flow gauges and lysimeters, respectively. The mean prediction error (simulated minus measured values) for transpiration was zero (which indicated no overall bias in estimation error), and its accuracy was not affected by the plant growth stages, but simulated transpiration during high measured transpiration rates tended to be slightly underestimated. Overall, the predictions for daily soil evaporation were also accurate. Model estimation errors were probably due to the simplified modelling of soil water content, stomatal resistances and soil heat flux as well as due to the uncertainties in characterising the 2 micrometeorological conditions. The SW’s prediction of transpiration was most sensitive to parameters most directly related to the canopy characteristics such as the partitioning of captured solar radiation, canopy resistance, and bulk boundary layer resistance.