Discriminating antigen and non-antigen using proteome dissimilarity III:tumour and parasite antigens

Computational genome analysis enables systematic identification of potential immunogenic proteins within a pathogen. Immunogenicity is a system property that arises through the interaction of host and pathogen as mediated through the medium of a immunogenic protein. The overt dissimilarity of pathogenic proteins when compared to the host proteome is conjectured by some to be the determining principal of immunogenicity. Previously, we explored this idea in the context of Bacterial, Viral, and Fungal antigen. In this paper, we broaden and extend our analysis to include complex antigens of eukaryotic origin, arising from tumours and from parasite pathogens. For both types of antigen, known antigenic and non-antigenic protein sequences were compared to human and mouse proteomes. In contrast to our previous results, both visual inspection and statistical evaluation indicate a much wider range of homologues and a significant level of discrimination; but, as before, we could not determine a viable threshold capable of properly separating non-antigen from antigen. In concert with our previous work, we conclude that global proteome dissimilarity is not a useful metric for immunogenicity for presently available antigens arising from Bacteria, viruses, fungi, parasites, and tumours. While we see some signal for certain antigen types, using dissimilarity is not a useful approach to identifying antigenic molecules within pathogen genomes.

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity:in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide−MHC binding affinity. The ISC−PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide−MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms - q2, SEP, and NC - ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).

Noisy fitness evaluation in genetic algorithms and the dynamics of learning

A theoretical model is presented which describes selection in a genetic algorithm (GA) under a stochastic fitness measure and correctly accounts for finite population effects. Although this model describes a number of selection schemes, we only consider Boltzmann selection in detail here as results for this form of selection are particularly transparent when fitness is corrupted by additive Gaussian noise. Finite population effects are shown to be of fundamental importance in this case, as the noise has no effect in the infinite population limit. In the limit of weak selection we show how the effects of any Gaussian noise can be removed by increasing the population size appropriately. The theory is tested on two closely related problems: the one-max problem corrupted by Gaussian noise and generalization in a perceptron with binary weights. The averaged dynamics can be accurately modelled for both problems using a formalism which describes the dynamics of the GA using methods from statistical mechanics. The second problem is a simple example of a learning problem and by considering this problem we show how the accurate characterization of noise in the fitness evaluation may be relevant in machine learning. The training error (negative fitness) is the number of misclassified training examples in a batch and can be considered as a noisy version of the generalization error if an independent batch is used for each evaluation. The noise is due to the finite batch size and in the limit of large problem size and weak selection we show how the effect of this noise can be removed by increasing the population size. This allows the optimal batch size to be determined, which minimizes computation time as well as the total number of training examples required.

CDMA multiuser detection, neural networks, and statistical mechanics

A novel approach, based on statistical mechanics, to analyze typical performance of optimum code-division multiple-access (CDMA) multiuser detectors is reviewed. A `black-box' view ot the basic CDMA channel is introduced, based on which the CDMA multiuser detection problem is regarded as a `learning-from-examples' problem of the `binary linear perceptron' in the neural network literature. Adopting Bayes framework, analysis of the performance of the optimum CDMA multiuser detectors is reduced to evaluation of the average of the cumulant generating function of a relevant posterior distribution. The evaluation of the average cumulant generating function is done, based on formal analogy with a similar calculation appearing in the spin glass theory in statistical mechanics, by making use of the replica method, a method developed in the spin glass theory.

Development and evaluation of a non-destructive adhesion test

The object of this work was to further develop the idea introduced by Muaddi et al (1981) which enables some of the disadvantages of earlier destructive adhesion test methods to be overcome. The test is non-destructive in nature but it does need to be calibrated against a destructive method. Adhesion is determined by measuring the effect of plating on internal friction. This is achieved by determining the damping of vibrations of a resonating specimen before and after plating. The level of adhesion was considered by the above authors to influence the degree of damping. In the major portion of the research work the electrodeposited metal was Watt's nickel, which is ductile in nature and is therefore suitable for peel adhesion testing. The base metals chosen were aluminium alloys S1C and HE9 as it is relatively easy to produce varying levels of adhesion between the substrate and electrodeposited coating by choosing the appropriate process sequence. S1C alloy is the commercially pure aluminium and was used to produce good adhesion. HE9 aluminium alloy is a more difficult to plate alloy and was chosen to produce poorer adhesion. The "Modal Testing" method used for studying vibrations was investigated as a possible means of evaluating adhesion but was not successful and so research was concentrated on the "Q" meter. The method based on the use of a "Q" meter involves the principle of exciting vibrations in a sample, interrupting the driving signal and counting the number of oscillations of the freely decaying vibrations between two known preselected amplitudes of oscillations. It was not possible to reconstruct a working instrument using Muaddi's thesis (1982) as it had either a serious error or the information was incomplete. Hence a modified "Q" meter had to be designed and constructed but it was then difficult to resonate non-magnetic materials, such as aluminium, therefore, a comparison before and after plating could not be made. A new "Q" meter was then developed based on an Impulse Technique. A regulated miniature hammer was used to excite the test piece at the fundamental mode instead of an electronic hammer and test pieces were supported at the two predetermined nodal points using nylon threads. This instrument developed was not very successful at detecting changes due to good and poor pretreatments given before plating, however, it was more sensitive to changes at the surface such as room temperature oxidation. Statistical analysis of test results from untreated aluminium alloys show that the instrument is not always consistent, the variation was even bigger when readings were taken on different days. Although aluminium is said to form protective oxides at room temperature there was evidence that the aluminium surface changes continuously due to film formation, growth and breakdown. Nickel plated and zinc alloy immersion coated samples also showed variation in Q with time. In order to prove that the variations in Q were mainly due to surface oxidation, aluminium samples were lacquered and anodised Such treatments enveloped the active surfaces reacting with the environment and the Q variation with time was almost eliminated especially after hard anodising. This instrument detected major differences between different untreated aluminium substrates.Also Q values decreased progressively as coating thicknesses were increased. This instrument was also able to detect changes in Q due to heat-treatment of aluminium alloys.

Consumer brand equity : a model for the measurement, analysis and evaluation of consumer perceived value

The topic of my research is consumer brand equity (CBE). My thesis is that the success or otherwise of a brand is better viewed from the consumers’ perspective. I specifically focus on consumers as a unique group of stakeholders whose involvement with brands is crucial to the overall success of branding strategy. To this end, this research examines the constellation of ideas on brand equity that have hitherto been offered by various scholars. Through a systematic integration of the concepts and practices identified but these scholars (concepts and practices such as: competitiveness, consumer searching, consumer behaviour, brand image, brand relevance, consumer perceived value, etc.), this research identifies CBE as a construct that is shaped, directed and made valuable by the beliefs, attitudes and the subjective preferences of consumers. This is done by examining the criteria on the basis of which the consumers evaluate brands and make brand purchase decisions. Understanding the criteria by which consumers evaluate brands is crucial for several reasons. First, as the basis upon which consumers select brands changes with consumption norms and technology, understanding the consumer choice process will help in formulating branding strategy. Secondly, an understanding of these criteria will help in formulating a creative and innovative agenda for ‘new brand’ propositions. Thirdly, it will also influence firms’ ability to simulate and mould the plasticity of demand for existing brands. In examining these three issues, this thesis presents a comprehensive account of CBE. This is because the first issue raised in the preceding paragraph deals with the content of CBE. The second issue addresses the problem of how to develop a reliable and valid measuring instrument for CBE. The third issue examines the structural and statistical relationships between the factors of CBE and the consequences of CBE on consumer perceived value (CPV). Using LISREL-SIMPLIS 8.30, the study finds direct and significant influential links between consumer brand equity and consumer value perception.

Priority evaluation in transportation policies and programmes

This work is concerned with the development of techniques for the evaluation of large-scale highway schemes with particular reference to the assessment of their costs and benefits in the context of the current transport planning (T.P.P.) process. It has been carried out in close cooperation with West Midlands County Council, although its application and results are applicable elsewhere. The background to highway evaluation and its development in recent years has been described and the emergence of a number of deficiencies in current planning practise noted. One deficiency in particular stood out, that stemming from inadequate methods of scheme generation and the research has concentrated upon improving this stage of appraisal, to ensure that subsequent stages of design, assessment and implementation are based upon a consistent and responsive foundation. Deficiencies of scheme evaluation were found to stem from inadequate development of appraisal methodologies suffering from difficulties of valuation, measurement and aggregation of the disparate variables that characterise highway evaluation. A failure to respond to local policy priorities was also noted. A 'problem' rather than 'goals' based approach to scheme generation was taken, as it represented the current and foreseeable resource allocation context more realistically. A review of techniques with potential for highway problem based scheme generation, which would work within a series of practical and theoretical constraints were assessed and that of multivariate analysis, and classical factor analysis in particular, was selected, because it offerred considerable application to the difficulties of valuation, measurement and aggregation that existed. Computer programs were written to adapt classical factor analysis to the requirements of T.P.P. highway evaluation, using it to derive a limited number of factors which described the extensive quantity of highway problem data. From this, a series of composite problem scores for 1979 were derived for a case study area of south Birmingham, based upon the factorial solutions, and used to assess highway sites in terms of local policy issues. The methodology was assessed in the light of its ability to describe highway problems in both aggregate and disaggregate terms, to guide scheme design, coordinate with current scheme evaluation methods, and in general to improve upon current appraisal. Analysis of the results was both in subjective, 'common-sense' terms and using statistical methods to assess the changes in problem definition, distribution and priorities that emerged. Overall, the technique was found to improve upon current scheme generation methods in all respects and in particular in overcoming the problems of valuation, measurement and aggregation without recourse to unsubstantiated and questionable assumptions. A number of deficiencies which remained have been outlined and a series of research priorities described which need to be reviewed in the light of current and future evaluation needs.

Model evaluation and case series data

We discuss aggregation of data from neuropsychological patients and the process of evaluating models using data from a series of patients. We argue that aggregation can be misleading but not aggregating can also result in information loss. The basis for combining data needs to be theoretically defined, and the particular method of aggregation depends on the theoretical question and characteristics of the data. We present examples, often drawn from our own research, to illustrate these points. We also argue that statistical models and formal methods of model selection are a useful way to test theoretical accounts using data from several patients in multiple-case studies or case series. Statistical models can often measure fit in a way that explicitly captures what a theory allows; the parameter values that result from model fitting often measure theoretically important dimensions and can lead to more constrained theories or new predictions; and model selection allows the strength of evidence for models to be quantified without forcing this into the artificial binary choice that characterizes hypothesis testing methods. Methods that aggregate and then formally model patient data, however, are not automatically preferred to other methods. Which method is preferred depends on the question to be addressed, characteristics of the data, and practical issues like availability of suitable patients, but case series, multiple-case studies, single-case studies, statistical models, and process models should be complementary methods when guided by theory development.

Evaluation of hemifield sector analysis protocol in multifocal visual evoked potential (MFVEP) objective perimetry for the diagnosis and early detection of glaucomatous field defects

Visual field assessment is a core component of glaucoma diagnosis and monitoring, and the Standard Automated Perimetry (SAP) test is considered up until this moment, the gold standard of visual field assessment. Although SAP is a subjective assessment and has many pitfalls, it is being constantly used in the diagnosis of visual field loss in glaucoma. Multifocal visual evoked potential (mfVEP) is a newly introduced method used for visual field assessment objectively. Several analysis protocols have been tested to identify early visual field losses in glaucoma patients using the mfVEP technique, some were successful in detection of field defects, which were comparable to the standard SAP visual field assessment, and others were not very informative and needed more adjustment and research work. In this study, we implemented a novel analysis approach and evaluated its validity and whether it could be used effectively for early detection of visual field defects in glaucoma. OBJECTIVES: The purpose of this study is to examine the effectiveness of a new analysis method in the Multi-Focal Visual Evoked Potential (mfVEP) when it is used for the objective assessment of the visual field in glaucoma patients, compared to the gold standard technique. METHODS: 3 groups were tested in this study; normal controls (38 eyes), glaucoma patients (36 eyes) and glaucoma suspect patients (38 eyes). All subjects had a two standard Humphrey visual field HFA test 24-2 and a single mfVEP test undertaken in one session. Analysis of the mfVEP results was done using the new analysis protocol; the Hemifield Sector Analysis HSA protocol. Analysis of the HFA was done using the standard grading system. RESULTS: Analysis of mfVEP results showed that there was a statistically significant difference between the 3 groups in the mean signal to noise ratio SNR (ANOVA p<0.001 with a 95% CI). The difference between superior and inferior hemispheres in all subjects were all statistically significant in the glaucoma patient group 11/11 sectors (t-test p<0.001), partially significant 5/11 (t-test p<0.01) and no statistical difference between most sectors in normal group (only 1/11 was significant) (t-test p<0.9). sensitivity and specificity of the HAS protocol in detecting glaucoma was 97% and 86% respectively, while for glaucoma suspect were 89% and 79%. DISCUSSION: The results showed that the new analysis protocol was able to confirm already existing field defects detected by standard HFA, was able to differentiate between the 3 study groups with a clear distinction between normal and patients with suspected glaucoma; however the distinction between normal and glaucoma patients was especially clear and significant. CONCLUSION: The new HSA protocol used in the mfVEP testing can be used to detect glaucomatous visual field defects in both glaucoma and glaucoma suspect patient. Using this protocol can provide information about focal visual field differences across the horizontal midline, which can be utilized to differentiate between glaucoma and normal subjects. Sensitivity and specificity of the mfVEP test showed very promising results and correlated with other anatomical changes in glaucoma field loss.

Neurophysiological evaluation of convergent afferents innervating the human esophagus and area of referred pain on the anterior chest wall

Noxious stimuli in the esophagus cause pain that is referred to the anterior chest wall because of convergence of visceral and somatic afferents within the spinal cord. We sought to characterize the neurophysiological responses of these convergent spinal pain pathways in humans by studying 12 healthy subjects over three visits (V1, V2, and V3). Esophageal pain thresholds (Eso-PT) were assessed by electrical stimulation and anterior chest wall pain thresholds (ACW-PT) by use of a contact heat thermode. Esophageal evoked potentials (EEP) were recorded from the vertex following 200 electrical stimuli, and anterior chest wall evoked potentials (ACWEP) were recorded following 40 heat pulses. The fear of pain questionnaire (FPQ) was administered on V1. Statistical data are shown as point estimates of difference +/- 95% confidence interval. Pain thresholds increased between V1 and V3 [Eso-PT: V1-V3 = -17.9 mA (-27.9, -7.9) P < 0.001; ACW-PT: V1-V3 = -3.38 degrees C (-5.33, -1.42) P = 0.001]. The morphology of cortical responses from both sites was consistent and equivalent [P1, N1, P2, N2 complex, where P1 and P2 are is the first and second positive (downward) components of the CEP waveform, respectively, and N1 and N2 are the first and second negative (upward) components, respectively], indicating activation of similar cortical networks. For EEP, N1 and P2 latencies decreased between V1 and V3 [N1: V1-V3 = 13.7 (1.8, 25.4) P = 0.02; P2: V1-V3 = 32.5 (11.7, 53.2) P = 0.003], whereas amplitudes did not differ. For ACWEP, P2 latency increased between V1 and V3 [-35.9 (-60, -11.8) P = 0.005] and amplitudes decreased [P1-N1: V1-V3 = 5.4 (2.4, 8.4) P = 0.01; P2-N2: 6.8 (3.4, 10.3) P < 0.001]. The mean P1 latency of EEP over three visits was 126.6 ms and that of ACWEP was 101.6 ms, reflecting afferent transmission via Adelta fibers. There was a significant negative correlation between FPQ scores and Eso-PT on V1 (r = -0.57, P = 0.05). These data provide the first neurophysiological evidence of convergent esophageal and somatic pain pathways in humans.

Strategic supplier performance evaluation:a case-based action research of a UK manufacturing organisation

The main aim of this research is to demonstrate strategic supplier performance evaluation of a UK-based manufacturing organisation using an integrated analytical framework. Developing long term relationship with strategic suppliers is common in today's industry. However, monitoring suppliers' performance all through the contractual period is important in order to ensure overall supply chain performance. Therefore, client organisations need to measure suppliers' performance dynamically and inform them on improvement measures. Although there are many studies introducing innovative supplier performance evaluation frameworks and empirical researches on identifying criteria for supplier evaluation, little has been reported on detailed application of strategic supplier performance evaluation and its implication on overall performance of organisation. Additionally, majority of the prior studies emphasise on lagging factors (quality, delivery schedule and value/cost) for supplier selection and evaluation. This research proposes both leading (organisational practices, risk management, environmental and social practices) and lagging factors for supplier evaluation and demonstrates a systematic method for identifying those factors with the involvement of relevant stakeholders and process mapping. The contribution of this article is a real-life case-based action research utilising an integrated analytical model that combines quality function deployment and the analytic hierarchy process method for suppliers' performance evaluation. The effectiveness of the method has been demonstrated through number of validations (e.g. focus group, business results, and statistical analysis). Additionally, the study reveals that enhanced supplier performance results positive impact on operational and business performance of client organisation.

Evaluation of hemifield sector analysis protocol in multifocal visual evoked potential objective perimetry for the diagnosis and early detection of glaucomatous field defects

CONCLUSIONS: The new HSA protocol used in the mfVEP testing can be applied to detect glaucomatous visual field defects in both glaucoma and glaucoma suspect patients. Using this protocol can provide information about focal visual field differences across the horizontal midline, which can be utilized to differentiate between glaucoma and normal subjects. Sensitivity and specificity of the mfVEP test showed very promising results and correlated with other anatomical changes in glaucoma field loss. PURPOSE: Multifocal visual evoked potential (mfVEP) is a newly introduced method used for objective visual field assessment. Several analysis protocols have been tested to identify early visual field losses in glaucoma patients using the mfVEP technique, some were successful in detection of field defects, which were comparable to the standard automated perimetry (SAP) visual field assessment, and others were not very informative and needed more adjustment and research work. In this study we implemented a novel analysis approach and evaluated its validity and whether it could be used effectively for early detection of visual field defects in glaucoma. METHODS: Three groups were tested in this study; normal controls (38 eyes), glaucoma patients (36 eyes) and glaucoma suspect patients (38 eyes). All subjects had a two standard Humphrey field analyzer (HFA) test 24-2 and a single mfVEP test undertaken in one session. Analysis of the mfVEP results was done using the new analysis protocol; the hemifield sector analysis (HSA) protocol. Analysis of the HFA was done using the standard grading system. RESULTS: Analysis of mfVEP results showed that there was a statistically significant difference between the three groups in the mean signal to noise ratio (ANOVA test, p < 0.001 with a 95% confidence interval). The difference between superior and inferior hemispheres in all subjects were statistically significant in the glaucoma patient group in all 11 sectors (t-test, p < 0.001), partially significant in 5 / 11 (t-test, p < 0.01), and no statistical difference in most sectors of the normal group (1 / 11 sectors was significant, t-test, p < 0.9). Sensitivity and specificity of the HSA protocol in detecting glaucoma was 97% and 86%, respectively, and for glaucoma suspect patients the values were 89% and 79%, respectively.