Vaccine adjuvant systems: enhancing the efficacy of sub-unit protein antigens

Vaccination remains a key tool in the protection and eradication of diseases. However, the development of new safe and effective vaccines is not easy. Various live organism based vaccines currently licensed, exhibit high efficacy; however, this benefit is associated with risk, due to the adverse reactions found with these vaccines. Therefore, in the development of vaccines, the associated risk-benefit issues need to be addressed. Sub-unit proteins offer a much safer alternative; however, their efficacy is low. The use of adjuvanted systems have proven to enhance the immunogenicity of these sub-unit vaccines through protection (i.e. preventing degradation of the antigen in vivo) and enhanced targeting of these antigens to professional antigen-presenting cells. Understanding of the immunological implications of the related disease will enable validation for the design and development of potential adjuvant systems. Novel adjuvant research involves the combination of both pharmaceutical analysis accompanied by detailed immunological investigations, whereby, pharmaceutically designed adjuvants are driven by an increased understanding of mechanisms of adjuvant activity, largely facilitated by description of highly specific innate immune recognition of components usually associated with the presence of invading bacteria or virus. The majority of pharmaceutical based adjuvants currently being investigated are particulate based delivery systems, such as liposome formulations. As an adjuvant, liposomes have been shown to enhance immunity against the associated disease particularly when a cationic lipid is used within the formulation. In addition, the inclusion of components such as immunomodulators, further enhance immunity. Within this review, the use and application of effective adjuvants is investigated, with particular emphasis on liposomal-based systems. The mechanisms of adjuvant activity, analysis of complex immunological characteristics and formulation and delivery of these vaccines are considered.

Analysis of computer communication systems by use of digital signal processing methods

Queueing theory is an effective tool in the analysis of canputer camrunication systems. Many results in queueing analysis have teen derived in the form of Laplace and z-transform expressions. Accurate inversion of these transforms is very important in the study of computer systems, but the inversion is very often difficult. In this thesis, methods for solving some of these queueing problems, by use of digital signal processing techniques, are presented. The z-transform of the queue length distribution for the Mj GY jl system is derived. Two numerical methods for the inversion of the transfom, together with the standard numerical technique for solving transforms with multiple queue-state dependence, are presented. Bilinear and Poisson transform sequences are presented as useful ways of representing continuous-time functions in numerical computations.

A structural method for the design of fault tolerant distributed control systems

Distributed digital control systems provide alternatives to conventional, centralised digital control systems. Typically, a modern distributed control system will comprise a multi-processor or network of processors, a communications network, an associated set of sensors and actuators, and the systems and applications software. This thesis addresses the problem of how to design robust decentralised control systems, such as those used to control event-driven, real-time processes in time-critical environments. Emphasis is placed on studying the dynamical behaviour of a system and identifying ways of partitioning the system so that it may be controlled in a distributed manner. A structural partitioning technique is adopted which makes use of natural physical sub-processes in the system, which are then mapped into the software processes to control the system. However, communications are required between the processes because of the disjoint nature of the distributed (i.e. partitioned) state of the physical system. The structural partitioning technique, and recent developments in the theory of potential controllability and observability of a system, are the basis for the design of controllers. In particular, the method is used to derive a decentralised estimate of the state vector for a continuous-time system. The work is also extended to derive a distributed estimate for a discrete-time system. Emphasis is also given to the role of communications in the distributed control of processes and to the partitioning technique necessary to design distributed and decentralised systems with resilient structures. A method is presented for the systematic identification of necessary communications for distributed control. It is also shwon that the structural partitions can be used directly in the design of software fault tolerant concurrent controllers. In particular, the structural partition can be used to identify the boundary of the conversation which can be used to protect a specific part of the system. In addition, for certain classes of system, the partitions can be used to identify processes which may be dynamically reconfigured in the event of a fault. These methods should be of use in the design of robust distributed systems.

Development of real-time process control systems using formal techniques

A major application of computers has been to control physical processes in which the computer is embedded within some large physical process and is required to control concurrent physical processes. The main difficulty with these systems is their event-driven characteristics, which complicate their modelling and analysis. Although a number of researchers in the process system community have approached the problems of modelling and analysis of such systems, there is still a lack of standardised software development formalisms for the system (controller) development, particular at early stage of the system design cycle. This research forms part of a larger research programme which is concerned with the development of real-time process-control systems in which software is used to control concurrent physical processes. The general objective of the research in this thesis is to investigate the use of formal techniques in the analysis of such systems at their early stages of development, with a particular bias towards an application to high speed machinery. Specifically, the research aims to generate a standardised software development formalism for real-time process-control systems, particularly for software controller synthesis. In this research, a graphical modelling formalism called Sequential Function Chart (SFC), a variant of Grafcet, is examined. SFC, which is defined in the international standard IEC1131 as a graphical description language, has been used widely in industry and has achieved an acceptable level of maturity and acceptance. A comparative study between SFC and Petri nets is presented in this thesis. To overcome identified inaccuracies in the SFC, a formal definition of the firing rules for SFC is given. To provide a framework in which SFC models can be analysed formally, an extended time-related Petri net model for SFC is proposed and the transformation method is defined. The SFC notation lacks a systematic way of synthesising system models from the real world systems. Thus a standardised approach to the development of real-time process control systems is required such that the system (software) functional requirements can be identified, captured, analysed. A rule-based approach and a method called system behaviour driven method (SBDM) are proposed as a development formalism for real-time process-control systems.

CADS*: Computer-Aided Development of self-* systems

We present the prototype tool CADS* for the computer-aided development of an important class of self-* systems, namely systems whose components can be modelled as Markov chains. Given a Markov chain representation of the IT components to be included into a self-* system, CADS* automates or aids (a) the development of the artifacts necessary to build the self-* system; and (b) their integration into a fully-operational self-* solution. This is achieved through a combination of formal software development techniques including model transformation, model-driven code generation and dynamic software reconfiguration.

The use of driven equilibrium conditions in the measurement of NMR relaxation times

The further development of the use of NMR relaxation times in chemical, biological and medical research has perhaps been curtailed by the length of time these measurements often take. The DESPOT (Driven Equilibrium Single Pulse Observation of T1) method has been developed, which reduces the time required to make a T1 measurement by a factor of up to 100. The technique has been studied extensively herein and the thesis contains recommendations for its successful experimental application. Modified DESPOT type equations for use when T2 relaxation is incomplete or where off-resonance effects are thought to be significant are also presented. A recently reported application of the DESPOT technique to MR imaging gave good initial results but suffered from the fact that the images were derived from spin systems that were not driven to equilibrium. An approach which allows equilibrium to be obtained with only one non-acquisition sequence is presented herein and should prove invaluable in variable contrast imaging. A DESPOT type approach has also been successfully applied to the measurement of T1. T_1's can be measured, using this approach significantly faster than by the use of the classical method. The new method also provides a value for T1 simultaneously and therefore the technique should prove valuable in intermediate energy barrier chemical exchange studies. The method also gives rise to the possibility of obtaining simultaneous T1 and T1 MR images. The DESPOT technique depends on rapid multipulsing at nutation angles, normally less than 90^o. Work in this area has highlighted the possible time saving for spectral acquisition over the classical technique (90^o-5T_1)_n. A new method based on these principles has been developed which permits the rapid multipulsing of samples to give T_1 and M_0 ratio information. The time needed, however, is only slightly longer than would be required to determine the M_0 ratio alone using the classical technique. In ^1H decoupled ^13C spectroscopy the method also gives nOe ratio information for the individual absorptions in the spectrum.

Approximating differentiable relationships between delay embedded dynamical systems with radical basis functions

This thesis is about the study of relationships between experimental dynamical systems. The basic approach is to fit radial basis function maps between time delay embeddings of manifolds. We have shown that under certain conditions these maps are generically diffeomorphisms, and can be analysed to determine whether or not the manifolds in question are diffeomorphically related to each other. If not, a study of the distribution of errors may provide information about the lack of equivalence between the two. The method has applications wherever two or more sensors are used to measure a single system, or where a single sensor can respond on more than one time scale: their respective time series can be tested to determine whether or not they are coupled, and to what degree. One application which we have explored is the determination of a minimum embedding dimension for dynamical system reconstruction. In this special case the diffeomorphism in question is closely related to the predictor for the time series itself. Linear transformations of delay embedded manifolds can also be shown to have nonlinear inverses under the right conditions, and we have used radial basis functions to approximate these inverse maps in a variety of contexts. This method is particularly useful when the linear transformation corresponds to the delay embedding of a finite impulse response filtered time series. One application of fitting an inverse to this linear map is the detection of periodic orbits in chaotic attractors, using suitably tuned filters. This method has also been used to separate signals with known bandwidths from deterministic noise, by tuning a filter to stop the signal and then recovering the chaos with the nonlinear inverse. The method may have applications to the cancellation of noise generated by mechanical or electrical systems. In the course of this research a sophisticated piece of software has been developed. The program allows the construction of a hierarchy of delay embeddings from scalar and multi-valued time series. The embedded objects can be analysed graphically, and radial basis function maps can be fitted between them asynchronously, in parallel, on a multi-processor machine. In addition to a graphical user interface, the program can be driven by a batch mode command language, incorporating the concept of parallel and sequential instruction groups and enabling complex sequences of experiments to be performed in parallel in a resource-efficient manner.

The design of a support department simulator for use in the design of manufacturing systems

Manufacturing firms are driven by competitive pressures to continually improve the effectiveness and efficiency of their organisations. For this reason, manufacturing engineers often implement changes to existing processes, or design new production facilities, with the expectation of making further gains in manufacturing system performance. This thesis relates to how the likely outcome of this type of decision should be predicted prior to its implementation. The thesis argues that since manufacturing systems must also interact with many other parts of an organisation, the expected performance improvements can often be significantly hampered by constraints that arise elsewhere in the business. As a result, decision-makers should attempt to predict just how well a proposed design will perform when these other factors, or 'support departments', are taken into consideration. However, the thesis also demonstrates that, in practice, where quantitative analysis is used to evaluate design decisions, the analysis model invariably ignores the potential impact of support functions on a system's overall performance. A more comprehensive modelling approach is therefore required. A study of how various business functions interact establishes that to properly represent the kind of delays that give rise to support department constraints, a model should actually portray the dynamic and stochastic behaviour of entities in both the manufacturing and non-manufacturing aspects of a business. This implies that computer simulation be used to model design decisions but current simulation software does not provide a sufficient range of functionality to enable the behaviour of all of these entities to be represented in this way. The main objective of the research has therefore been the development of a new simulator that will overcome limitations of existing software and so enable decision-makers to conduct a more holistic evaluation of design decisions. It is argued that the application of object-oriented techniques offers a potentially better way of fulfilling both the functional and ease-of-use issues relating to development of the new simulator. An object-oriented analysis and design of the system, called WBS/Office, are therefore presented that extends to modelling a firm's administrative and other support activities in the context of the manufacturing system design process. A particularly novel feature of the design is the ability for decision-makers to model how a firm's specific information and document processing requirements might hamper shop-floor performance. The simulator is primarily intended for modelling make-to-order batch manufacturing systems and the thesis presents example models created using a working version of WBS/Office that demonstrate the feasibility of using the system to analyse manufacturing system designs in this way.

An approach to the development of expert systems within production planning and control

The thesis presents an account of an attempt to utilize expert systems within the domain of production planning and control. The use of expert systems was proposed due to the problematical nature of a particular function within British Steel Strip Products' Operations Department: the function of Order Allocation, allocating customer orders to a production week and site. Approaches to tackling problems within production planning and control are reviewed, as are the general capabilities of expert systems. The conclusions drawn are that the domain of production planning and control contains both `soft' and `hard' problems, and that while expert systems appear to be a useful technology for this domain, this usefulness has by no means yet been demonstrated. Also, it is argued that the main stream methodology for developing expert systems is unsuited for the domain. A problem-driven approach is developed and used to tackle the Order Allocation function. The resulting system, UAAMS, contained two expert components. One of these, the scheduling procedure was not fully implemented due to inadequate software. The second expert component, the product routing procedure, was untroubled by such difficulties, though it was unusable on its own; thus a second system was developed. This system, MICRO-X10, duplicated the function of X10, a complex database query routine used daily by Order Allocation. A prototype version of MICRO-X10 proved too slow to be useful but allowed implementation and maintenance issues to be analysed. In conclusion, the usefulness of the problem-driven approach to expert systems development within production planning and control is demonstrated but restrictions imposed by current expert system software are highlighted in that the abilities of such software to cope with `hard' scheduling constructs and also the slow processing speeds of such software can restrict the current usefulness of expert systems within production planning and control.

Comparison of vesicle based antigen delivery systems for delivery of hepatitis B surface antigen

There is a clinical need for a more effective vaccine against hepatitis B, and in particular vaccines that may be suitable for therapeutic administration. This study assesses the potential of cationic surfactant vesicle based formulations using two agents; the cationic amine containing [N-(N′,N′-dimethylaminoethane)-carbamoyl] cholesterol (DC-Chol) or dimethyl dioctadecylammonium bromide (DDA) with hepatitis B surface antigen (HBsAg). Synthetic mycobacterial cord factor, trehalose 6,6′-dibehenate (TDB) has been used as an adjuvant and the addition of 1-monopalmitoyl glycerol (C16:0) (MP) and cholesterol (Chol) to DDA-TDB is assessed for its potential to facilitate formation of dehydration-rehydration vesicles (DRV) at room temperature, and the effect of this on immune responses. A DRV formulation is directly compared to an adsorbed formulation of the same composition and preparation protocol (MP:dioleoyl phosphoethanolamine (DOPE):Chol:DC-Chol) and the direct substitution of MP with phosphatidylcholine (PC) is also compared in DRV antigen-entrapped formulations. MP and Chol were shown to facilitate the use of DDA-TDB in DRV formulations prepared at room temperature, whilst there was marginal alteration of immunogenicity (a reduction in HBsAg-specific IL-2). The HBsAg adsorbed DRV formulation was not significantly different from the HBsAg entrapped DRV formulation. Overall, DDA formulations incorporating TDB showed markedly increased antigen specific splenocyte proliferation and elicited cytokine production concomitant with a strong T cell driven response, delineating formulations that may be useful for further evaluation of their clinical potential. © 2007 Elsevier B.V. All rights reserved.

Effect of aspect ratio on thermal convection in open and closed systems

Internally heated fluids are found across the nuclear fuel cycle. In certain situations the motion of the fluid is driven by the decay heat (i.e. corium melt pools in severe accidents, the shutdown of liquid metal reactors, molten salt and the passive control of light water reactors) as well as normal operation (i.e. intermediate waste storage and generation IV reactor designs). This can in the long-term affect reactor vessel integrity or lead to localized hot spots and accumulation of solid wastes that may prompt local increases in activity. Two approaches to the modeling of internally heated convection are presented here. These are based on numerical analysis using codes developed in-house and simulations using widely available computational fluid dynamics solvers. Open and closed fluid layers at around the transition between conduction and convection of various aspect ratios are considered. We determine optimum domain aspect ratio (1:7:7 up to 1:24:24 for open systems and 5:5:1, 1:10:10 and 1:20:20 for closed systems), mesh resolutions and turbulence models required to accurately and efficiently capture the convection structures that evolve when perturbing the conductive state of the fluid layer. Note that the open and closed fluid layers we study here are bounded by a conducting surface over an insulating surface. Conclusions will be drawn on the influence of the periodic boundary conditions on the flow patterns observed. We have also examined the stability of the nonlinear solutions that we found with the aim of identifying the bifurcation sequence of these solutions en route to turbulence.

An aspect-oriented and model-driven approach for managing dynamic variability

Constructing and executing distributed systems that can adapt to their operating context in order to sustain provided services and the service qualities are complex tasks. Managing adaptation of multiple, interacting services is particularly difficult since these services tend to be distributed across the system, interdependent and sometimes tangled with other services. Furthermore, the exponential growth of the number of potential system configurations derived from the variabilities of each service need to be handled. Current practices of writing low-level reconfiguration scripts as part of the system code to handle run time adaptation are both error prone and time consuming and make adaptive systems difficult to validate and evolve. In this paper, we propose to combine model driven and aspect oriented techniques to better cope with the complexities of adaptive systems construction and execution, and to handle the problem of exponential growth of the number of possible configurations. Combining these techniques allows us to use high level domain abstractions, simplify the representation of variants and limit the problem pertaining to the combinatorial explosion of possible configurations. In our approach we also use models at runtime to generate the adaptation logic by comparing the current configuration of the system to a composed model representing the configuration we want to reach. © 2008 Springer-Verlag Berlin Heidelberg.

Model-driven software adaptation:report on the workshop M-ADAPT at ECOOP 2007

This first edition of the workshop Model-driven Software Adaptation (M-ADAPT'07) took place in the Technische Universität Berlin with the International Conference ECOOP'07 in the beautiful and buzzing city of Berlin, on the 30th of July, 2007. The workshop was organized by Gordon Blair, Nelly Bencomo, and Robert France. Participants explored how to develop appropriate model-driven approaches to model, analyze, and validate the volatile properties of the behaviour of adaptive systems and its environments. This report gives an overview of the presentations as well as an account of the fruitful discussions that took place at M-ADAPT'07. © 2008 Springer-Verlag Berlin Heidelberg.

Using architecture models to support the generation and operation of component-based adaptive systems

Modelling architectural information is particularly important because of the acknowledged crucial role of software architecture in raising the level of abstraction during development. In the MDE area, the level of abstraction of models has frequently been related to low-level design concepts. However, model-driven techniques can be further exploited to model software artefacts that take into account the architecture of the system and its changes according to variations of the environment. In this paper, we propose model-driven techniques and dynamic variability as concepts useful for modelling the dynamic fluctuation of the environment and its impact on the architecture. Using the mappings from the models to implementation, generative techniques allow the (semi) automatic generation of artefacts making the process more efficient and promoting software reuse. The automatic generation of configurations and reconfigurations from models provides the basis for safer execution. The architectural perspective offered by the models shift focus away from implementation details to the whole view of the system and its runtime change promoting high-level analysis. © 2009 Springer Berlin Heidelberg.

Mitigating the obsolescence of quality specifications models in service-based systems

Requirements-aware systems address the need to reason about uncertainty at runtime to support adaptation decisions, by representing quality of services (QoS) requirements for service-based systems (SBS) with precise values in run-time queryable model specification. However, current approaches do not support updating of the specification to reflect changes in the service market, like newly available services or improved QoS of existing ones. Thus, even if the specification models reflect design-time acceptable requirements they may become obsolete and miss opportunities for system improvement by self-adaptation. This articles proposes to distinguish "abstract" and "concrete" specification models: the former consists of linguistic variables (e.g. "fast") agreed upon at design time, and the latter consists of precise numeric values (e.g. "2ms") that are dynamically calculated at run-time, thus incorporating up-to-date QoS information. If and when freshly calculated concrete specifications are not satisfied anymore by the current service configuration, an adaptation is triggered. The approach was validated using four simulated SBS that use services from a previously published, real-world dataset; in all cases, the system was able to detect unsatisfied requirements at run-time and trigger suitable adaptations. Ongoing work focuses on policies to determine recalculation of specifications. This approach will allow engineers to build SBS that can be protected against market-caused obsolescence of their requirements specifications. © 2012 IEEE.