Qualitative System Identification from Imperfect Data

Experience in the physical sciences suggests that the only realistic means of understanding complex systems is through the use of mathematical models. Typically, this has come to mean the identification of quantitative models expressed as differential equations. Quantitative modelling works best when the structure of the model (i.e., the form of the equations) is known; and the primary concern is one of estimating the values of the parameters in the model. For complex biological systems, the model-structure is rarely known and the modeler has to deal with both model-identification and parameter-estimation. In this paper we are concerned with providing automated assistance to the first of these problems. Specifically, we examine the identification by machine of the structural relationships between experimentally observed variables. These relationship will be expressed in the form of qualitative abstractions of a quantitative model. Such qualitative models may not only provide clues to the precise quantitative model, but also assist in understanding the essence of that model. Our position in this paper is that background knowledge incorporating system modelling principles can be used to constrain effectively the set of good qualitative models. Utilising the model-identification framework provided by Inductive Logic Programming (ILP) we present empirical support for this position using a series of increasingly complex artificial datasets. The results are obtained with qualitative and quantitative data subject to varying amounts of noise and different degrees of sparsity. The results also point to the presence of a set of qualitative states, which we term kernel subsets, that may be necessary for a qualitative model-learner to learn correct models. We demonstrate scalability of the method to biological system modelling by identification of the glycolysis metabolic pathway from data

Localities of Memory, Localities of Mobilisation: British Military Communities and the Great War, 1919-1939

PhDThis thesis examines the role of British localities in the production of military force during the 1920s and 1930s. I argue that, during an era so disenfranchising for the armed forces in national politics and culture, the ‘Local’ provided a haven for servicemen and military units. Rather than theorising mobilisation as a set of state centred economic or technocratic proscriptions, this research takes the social and cultural renewal of military units as a starting point. Drawing on a range of historical and anthropological methodologies, I have set out to uncover what were – to borrow Foucault’s phrase – ‘regimes of truth’: multiple ideological currents and social contexts that legitimised service identities during this period. Local spaces are not only useful arenas for dissecting these operations; local people and identities were crucial formative elements in these processes. Two case studies have provided the ground for this investigation: Newcastle and Glasgow. The thesis dissects the body of the British military machine at these entry points, viewing the configuration of military and naval power at ground level and the emergence of manpower from the collision between state directives and local society. It also examines the communities (soldiers, veterans) that arose through this. Focus moves from military to urban spaces, revealing the characters (pressmen, politicians) and practices (sociability, ritual, performance) that legitimised these communities. Much of this cultural work evoked the memory of the Great War and here the thesis intervenes in academic debates surrounding Commemoration after 1918. The final chapter unites these perspectives in a chronological elaboration of the period 1935-1939, detailing the ground level effort for national and civil defence. As well as enlivening our understanding of 20th century mobilisation, this research explores the depths of British local and national identities and the intricate ways in which the armed forces were framed within both.AHRC Queen Mary Central Research Fund and the Stretton Fund The Henkel Foundation Scholarship, awarded by the International Research Centre of the Historia de la Grande Guerre in 201

Genomic diversity in naturally transformable Streptococcus pneumoniae

Infections due to Streptococcus pneumoniae (the pneumococcus) remain a substantial source of morbidity and mortality in both developing and developed countries despite a century of research and the development of effective therapeutic interventions (such as antibiotic therapy and vaccination). The ability of the pneumococcus to evade multiple classes of antibiotic through several genetically determined resistance mechanisms and its evasion of capsular polysaccharide based vaccines through serotype replacement and capsular switching, all reflect the extensive diversity and plasticity of the genome of this naturally transformable organism which can readily alter its genome in response to its environment and the pressures placed upon it in order to survive. The purpose of this thesis is to investigate this diversity from a genome sequence perspective and to relate these observations to pneumococcal molecular epidemiology in a region of high biodiversity, the pathogenesis of certain disease manifestations and assess for a possible bacterial genetic basis for the pneumococcal phenotypes of, “carriage” and, “invasion.” In order to do this, microarray comparative genomic hybridization (CGH) has been utilized to compare DNA from a variety of pneumococcal isolates chosen from 10 diverse serotypes and Multilocus Sequence Types and from clinically relevant serotypes and sequence types (particularly serotypes 3, 4 and 14 and sequence types ST9, ST246 and ST180)) against a reference, sequenced pneumococcal genome from an extensively investigated serotype 4 isolate – TIGR4. Microarray comparison of the transcriptional profiles of several isolates has also been undertaken to compare gene expression from isolates of serotype 1 (ST227 and ST306) and serotype 3 (ST180) related to particular disease states and exposure of a multi-resistant pneumococcus to an antimicrobial (clarithromycin) commonly used to treat pneumococcal pneumonia

Preparation and characterization of a protein extract from date palm fruit (Phoenix dactylifera L.) : investigation of nutritional and functional properties

The world’s population will reach 9 billion by 2050, increasing the pressure to find alternative protein sources to animal protein. The high global demand for soy protein ingredients has resulted in tropical deforestation which is associated with adverse health impact, agronomic, environmental and climate damage and there is a need to find alternative plant protein sources to soy protein. The Kingdom of Saudi Arabia (KSA) is considered as the second largest producer of date palm fruit among the current date-producing countries, resulting also in significant quantities of dates going to waste. The aims of this study were to develop a process for extraction of protein from date fruit suitable to be implemented in the food industry, to characterise the protein’s electrophoretic profile by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), to identify the proteins by Liquid-Chromatography Coupled Tandem Mass Spectrometry (LC-MS/MS), to study the physicochemical and functional properties of date fruit protein extract (DFPE) and the effect of thermal treatment, to determine the chemical composition, nutritional value, anti-nutritional factors and anti-oxidant properties and to develop an infant cereal with reduced allergenicity. Proximate and mineral analysis, anti-oxidant, amino acid composition and digestibility analysis of DFPE, reported in Chapter 2 showed that the protein extract contains all essential amino acids, is a high source of iron and has excellent anti-oxidant properties matching that of ascorbic acid. The extract had a lower protein digestibility-corrected amino acid score (PDCAAS) value than soy protein isolate (SPI) and contained anti nutritional factors e.g. oxalate, tannin and phytate, yet at low quantities that is assumed not to be of anti-nutritional concern. Physicochemical and functional properties of the extract and the respective effect of thermal treatment are reported in Chapter 3. The concentration of free and total sulphydryl groups (FSH and TSH) were significantly less that for SPI, confirming the results of low cysteine in the amino acid analysis of DFPE. The effect of thermal treatment on the profile of sulphydryl (SH) groups indicates that DFPE is less thermally stable than SPI, whilst considering the fact that DFPE had been subjected to heat treatment during the extraction process. This physicochemical profile was mirrored by the corresponding decrease in functionality including decreases after longer heating times in solubility, foam capacity emulsion stability index and increased water separation in emulsions. Chapter 4 describes the development of a protein extract containing 25.8% protein per dry weight using a new extraction process, which is a 13-fold enrichment compared to the 2.8% in the initial sample. The extraction process resulted in 4.2% DFPE, 57.2% date syrup and 38.6% waste. DFPE contains 50% protein whereas the remainder was in the date syrup (26.7%) and in the waste (24.3%) which could also be lost due to protease activity. The electrophoretic profile was established. LC-MS/MS results indicated the two most abundant proteins to be sorbitol dehydrogenase-like with MW (kDa) 39, an energy-related protein and catalase isozyme 2 with MW (kDa) 57, a disease/defense-related protein. Chapter 5 describes the development of an infant cereal based on date fruit protein as a potential competitor to a commercial infant cereal (CERELAC) sold in the KSA. The date cereal product lacked certain amino acids and calcium and contained low levels of oxalate, phytate and tannin. A date-cereal porridge prepared with camel milk had a proximate and mineral composition matching that of a porridge made with CERELAC prepared with cow’s milk apart from lacking fat, calcium and selenium, resulting in a product with reduced allergenicity to gluten and cow’s milk. DFPE could add to the rising need to find replacement for soy protein because the expansion of soy bean production and consumption is associated with environmental threats, such as deforestation

Genomic diversity in naturally transformable Streptococcus pneumoniae

Infections due to Streptococcus pneumoniae (the pneumococcus) remain a substantial source of morbidity and mortality in both developing and developed countries despite a century of research and the development of effective therapeutic interventions (such as antibiotic therapy and vaccination). The ability of the pneumococcus to evade multiple classes of antibiotic through several genetically determined resistance mechanisms and its evasion of capsular polysaccharide based vaccines through serotype replacement and capsular switching, all reflect the extensive diversity and plasticity of the genome of this naturally transformable organism which can readily alter its genome in response to its environment and the pressures placed upon it in order to survive. The purpose of this thesis is to investigate this diversity from a genome sequence perspective and to relate these observations to pneumococcal molecular epidemiology in a region of high biodiversity, the pathogenesis of certain disease manifestations and assess for a possible bacterial genetic basis for the pneumococcal phenotypes of, “carriage” and, “invasion.” In order to do this, microarray comparative genomic hybridization (CGH) has been utilized to compare DNA from a variety of pneumococcal isolates chosen from 10 diverse serotypes and Multilocus Sequence Types and from clinically relevant serotypes and sequence types (particularly serotypes 3, 4 and 14 and sequence types ST9, ST246 and ST180)) against a reference, sequenced pneumococcal genome from an extensively investigated serotype 4 isolate – TIGR4. Microarray comparison of the transcriptional profiles of several isolates has also been undertaken to compare gene expression from isolates of serotype 1 (ST227 and ST306) and serotype 3 (ST180) related to particular disease states and exposure of a multi-resistant pneumococcus to an antimicrobial (clarithromycin) commonly used to treat pneumococcal pneumonia.EThOS - Electronic Theses Online ServiceGBUnited Kingdo