Extreme learning machine for predicting HLA-peptide binding

Machine learning techniques have been recognized as powerful tools for learning from data. One of the most popular learning techniques, the Back-Propagation (BP) Artificial Neural Networks, can be used as a computer model to predict peptides binding to the Human Leukocyte Antigens (HLA). The major advantage of computational screening is that it reduces the number of wet-lab experiments that need to be performed, significantly reducing the cost and time. A recently developed method, Extreme Learning Machine (ELM), which has superior properties over BP has been investigated to accomplish such tasks. In our work, we found that the ELM is as good as, if not better than, the BP in term of time complexity, accuracy deviations across experiments, and most importantly - prevention from over-fitting for prediction of peptide binding to HLA.

Formal change impact analyses for emulated control software

Processor emulators are a software tool for allowing legacy computer programs to be executed on a modern processor. In the past emulators have been used in trivial applications such as maintenance of video games. Now, however, processor emulation is being applied to safety-critical control systems, including military avionics. These applications demand utmost guarantees of correctness, but no verification techniques exist for proving that an emulated system preserves the original system’s functional and timing properties. Here we show how this can be done by combining concepts previously used for reasoning about real-time program compilation, coupled with an understanding of the new and old software architectures. In particular, we show how both the old and new systems can be given a common semantics, thus allowing their behaviours to be compared directly.

Numerical modelling of unsteady mixed flows

This thesis concerns mixed flows (which are characterized by the simultaneous occurrence of free-surface and pressurized flow in sewers, tunnels, culverts or under bridges), and contributes to the improvement of the existing numerical tools for modelling these phenomena. The classic Preissmann slot approach is selected due to its simplicity and capability of predicting results comparable to those of a more recent and complex two-equation model, as shown here with reference to a laboratory test case. In order to enhance the computational efficiency, a local time stepping strategy is implemented in a shock-capturing Godunov-type finite volume numerical scheme for the integration of the de Saint-Venant equations. The results of different numerical tests show that local time stepping reduces run time significantly (between −29% and −85% CPU time for the test cases considered) compared to the conventional global time stepping, especially when only a small region of the flow field is surcharged, while solution accuracy and mass conservation are not impaired. The second part of this thesis is devoted to the modelling of the hydraulic effects of potentially pressurized structures, such as bridges and culverts, inserted in open channel domains. To this aim, a two-dimensional mixed flow model is developed first. The classic conservative formulation of the 2D shallow water equations for free-surface flow is adapted by assuming that two fictitious vertical slots, normally intersecting, are added on the ceiling of each integration element. Numerical results show that this schematization is suitable for the prediction of 2D flooding phenomena in which the pressurization of crossing structures can be expected. Given that the Preissmann model does not allow for the possibility of bridge overtopping, a one-dimensional model is also presented in this thesis to handle this particular condition. The flows below and above the deck are considered as parallel, and linked to the upstream and downstream reaches of the channel by introducing suitable internal boundary conditions. The comparison with experimental data and with the results of HEC-RAS simulations shows that the proposed model can be a useful and effective tool for predicting overtopping and backwater effects induced by the presence of bridges and culverts.

The Internet and other IT resources:tools for translators within a translation programme

Information technology has increased both the speed and medium of communication between nations. It has brought the world closer, but it has also created new challenges for translation — how we think about it, how we carry it out and how we teach it. Translation and Information Technology has brought together experts in computational linguistics, machine translation, translation education, and translation studies to discuss how these new technologies work, the effect of electronic tools, such as the internet, bilingual corpora, and computer software, on translator education and the practice of translation, as well as the conceptual gaps raised by the interface of human and machine.

"Well did you feel jealous?" Control and ideology in police interviews with rape complainants

The methods used by the UK Police to investigate complaints of rape have unsurprisingly come under much scrutiny in recent times, with a 2007 joint report on behalf of HM Crown Prosecution Service Inspectorate and HM Inspectorate of Constabulary concluding that there were many areas where improvements should be made. The research reported here forms part of a larger project which draws on various discourse analytical tools to identify the processes at work during police interviews with women reporting rape. Drawing on a corpus of video recorded police interviews with women reporting rape, this study applies a two pronged analysis to reveal the presence of these ideologies. Firstly, an analysis of the discourse markers ‘well’ and ‘so’ demonstrates the control exerted on the interaction by interviewing officers, as they attach importance to certain facts while omitting much of the information provided by the victim. Secondly, the interpretative repertoires relied upon by officers to ‘make sense’ of victim’s accounts are subject to scrutiny. As well as providing micro-level analyses which demonstrate processes of interactional control at the local level, the findings of these analyses can be shown to relate to a wider context – specifically prevailing ideologies about sexual violence in society as a whole.

Role of hexose transport in control of glycolytic flux in Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae predominantly ferments glucose to ethanol at high external glucose concentrations, irrespective of the presence of oxygen. In contrast, at low external glucose concentrations and in the presence of oxygen, as in a glucose-limited chemostat, no ethanol is produced. The importance of the external glucose concentration suggests a central role for the affinity and maximal transport rates of yeast's glucose transporters in the control of ethanol production. Here we present a series of strains producing functional chimeras between the hexose transporters Hxt1 and Hxt7, each of which lias distinct glucose transport characteristics. The strains display a range of decreasing glycolytic rates resulting in a proportional decrease in ethanol production. Using these strains, we show for the first time that at high glucose levels, the glucose uptake capacity of wild-type S. cerevisiae does not control glycolytic flux during exponential batch growth. In contrast, our chimeric Hxt transporters control the rate of glycolysis to a high degree. Strains whose glucose uptake is mediated by these chimeric transporters will undoubtedly provide a powerful tool with which to examine in detail the mechanism underlying the switch between fermentation and respiration in S. cerevisiae and will provide new tools for the control of industrial fermentations.

International technology transfer and collaborative new product development:evidence and a case from the machine tool industry

In recent years, it has become increasingly common for companies to improve their competitiveness and find new markets by extending their operations through international new product development collaborations involving technology transfer. Technology development, cost reduction and market penetration are seen as the foci in such collaborative operations with the aim being to improve the competitive position of both partners. In this paper, the case of technology transfer through collaborative new product development in the machine tool sector is used to provide a typical example of such partnerships. The paper outlines the links between the operational aspects of collaborations and their strategic objectives. It is based on empirical data collected from the machine tool industries in the UK and China. The evidence includes longitudinal case studies and questionnaire surveys of machine tool manufacturers in both countries. The specific case of BSA Tools Ltd and its Chinese partner the Changcheng Machine Tool Works is used to provide an in-depth example of the operational development of a successful collaboration. The paper concludes that a phased coordination of commercial, technical and strategic interactions between the two partners is essential for such collaborations to work.

Canonical solution groups of a homomorphism : manipulator kinematics, nonparametric regression and distributed object systems

The kinematic mapping of a rigid open-link manipulator is a homomorphism between Lie groups. The homomorphisrn has solution groups that act on an inverse kinematic solution element. A canonical representation of solution group operators that act on a solution element of three and seven degree-of-freedom (do!) dextrous manipulators is determined by geometric analysis. Seven canonical solution groups are determined for the seven do! Robotics Research K-1207 and Hollerbach arms. The solution element of a dextrous manipulator is a collection of trivial fibre bundles with solution fibres homotopic to the Torus. If fibre solutions are parameterised by a scalar, a direct inverse funct.ion that maps the scalar and Cartesian base space coordinates to solution element fibre coordinates may be defined. A direct inverse pararneterisation of a solution element may be approximated by a local linear map generated by an inverse augmented Jacobian correction of a linear interpolation. The action of canonical solution group operators on a local linear approximation of the solution element of inverse kinematics of dextrous manipulators generates cyclical solutions. The solution representation is proposed as a model of inverse kinematic transformations in primate nervous systems. Simultaneous calibration of a composition of stereo-camera and manipulator kinematic models is under-determined by equi-output parameter groups in the composition of stereo-camera and Denavit Hartenberg (DH) rnodels. An error measure for simultaneous calibration of a composition of models is derived and parameter subsets with no equi-output groups are determined by numerical experiments to simultaneously calibrate the composition of homogeneous or pan-tilt stereo-camera with DH models. For acceleration of exact Newton second-order re-calibration of DH parameters after a sequential calibration of stereo-camera and DH parameters, an optimal numerical evaluation of DH matrix first order and second order error derivatives with respect to a re-calibration error function is derived, implemented and tested. A distributed object environment for point and click image-based tele-command of manipulators and stereo-cameras is specified and implemented that supports rapid prototyping of numerical experiments in distributed system control. The environment is validated by a hierarchical k-fold cross validated calibration to Cartesian space of a radial basis function regression correction of an affine stereo model. Basic design and performance requirements are defined for scalable virtual micro-kernels that broker inter-Java-virtual-machine remote method invocations between components of secure manageable fault-tolerant open distributed agile Total Quality Managed ISO 9000+ conformant Just in Time manufacturing systems.

Numerical modelling of dispersion managed soliton transmission

This thesis presents the results of numerical modelling of the propagation of dispersion managed solitons. The theory of optical pulse propagation in single mode optical fibre is introduced specifically looking at the use of optical solitons for fibre communications. The numerical technique used to solve the nonlinear Schrödinger equation is also introduced. The recent developments in the use of dispersion managed solitons are reviewed before the numerical results are presented. The work in this thesis covers two main areas; (i) the use of a saturable absorber to control the propagation of dispersion managed solutions and (ii) the upgrade of the installed standard fibre network to higher data rates through the use of solitons and dispersion management. Saturable absorbe can be used to suppress the build up of noise and dispersive radiation in soliton transmission lines. The use of saturable absorbers in conjunction with dispersion management has been investigated both as a single pulse and for the transmission of a 10Gbit/s data pattern. It is found that this system supports a new regime of stable soliton pulses with significantly increased powers. The upgrade of the installed standard fibre network to higher data rates through the use of fibre amplifiers and dispersion management is of increasing interest. In this thesis the propagation of data at both 10Gbit/s and 40Gbit/s is studied. Propagation over transoceanic distances is shown to be possible for 10Gbit/s transmission and for more than 2000km at 40Gbit/s. The contribution of dispersion managed solitons in the future of optical communications is discussed in the thesis conclusions.

Modelling and control of a hybrid stepping motor

The integration of a microprocessor and a medium power stepper motor in one control system brings together two quite different disciplines. Various methods of interfacing are examined and the problems involved in both hardware and software manipulation are investigated. Microprocessor open-loop control of the stepper motor is considered. The possible advantages of microprocessor closed-loop control are examined and the development of a system is detailed. The system uses position feedback to initiate each motor step. Results of the dynamic response of the system are presented and its performance discussed. Applications of the static torque characteristic of the stepper motor are considered followed by a review of methods of predicting the characteristic. This shows that accurate results are possible only when the effects of magnetic saturation are avoided or when the machine is available for magnetic circuit tests to be carried out. A new method of predicting the static torque characteristic is explained in detail. The method described uses the machine geometry and the magnetic characteristics of the iron types used in the machine. From this information the permeance of each iron component of the machine is calculated and by using the equivalent magnetic circuit of the machine, the total torque produced is predicted. It is shown how this new method is implemented on a digital computer and how the model may be used to investigate further aspects of the stepper motor in addition to the static torque.

Digital control system programming from process control diagrams

A graphical process control language has been developed as a means of defining process control software. The user configures a block diagram describing the required control system, from a menu of functional blocks, using a graphics software system with graphics terminal. Additions may be made to the menu of functional blocks, to extend the system capability, and a group of blocks may be defined as a composite block. This latter feature provides for segmentation of the overall system diagram and the repeated use of the same group of blocks within the system. The completed diagram is analyzed by a graphics compiler which generates the programs and data structure to realise the run-time software. The run-time software has been designed as a data-driven system which allows for modifications at the run-time level in both parameters and system configuration. Data structures have been specified to ensure efficient execution and minimal storage requirements in the final control software. Machine independence has been accomodated as far as possible using CORAL 66 as the high level language throughout the entire system; the final run-time code being generated by a CORAL 66 compiler appropriate to the target processor.

Distributed control of computer communication systems

Flow control in Computer Communication systems is generally a multi-layered structure, consisting of several mechanisms operating independently at different levels. Evaluation of the performance of networks in which different flow control mechanisms act simultaneously is an important area of research, and is examined in depth in this thesis. This thesis presents the modelling of a finite resource computer communication network equipped with three levels of flow control, based on closed queueing network theory. The flow control mechanisms considered are: end-to-end control of virtual circuits, network access control of external messages at the entry nodes and the hop level control between nodes. The model is solved by a heuristic technique, based on an equivalent reduced network and the heuristic extensions to the mean value analysis algorithm. The method has significant computational advantages, and overcomes the limitations of the exact methods. It can be used to solve large network models with finite buffers and many virtual circuits. The model and its heuristic solution are validated by simulation. The interaction between the three levels of flow control are investigated. A queueing model is developed for the admission delay on virtual circuits with end-to-end control, in which messages arrive from independent Poisson sources. The selection of optimum window limit is considered. Several advanced network access schemes are postulated to improve the network performance as well as that of selected traffic streams, and numerical results are presented. A model for the dynamic control of input traffic is developed. Based on Markov decision theory, an optimal control policy is formulated. Numerical results are given and throughput-delay performance is shown to be better with dynamic control than with static control.