A Kuhnian crisis in neo-Darwinism

Policy issues which receive large inputs of scientific and technical information are frequently marred by acrimonious controversies between contributing experts. There are few if any examples of a public policy decision being based on a firm consensus of scientific and technical experts. Such a consensus is taken for granted by the `Rational' model of decision making and its derivatives. Comparing the dynamics of conflict in policy-relevant issues with those of conflict in `pure' science, one is struck by their great similarity. In both cases we witness examples of rhetorical statements about incompetence, conflicting interpretations of data, and interdisciplinary communication problems. Noting this similarity, this thesis attempts to answer the question, `Is there a similarity of cause: do the same causes lie at the roots of conflict in policy-relevant and policy-irrelevant science?' In answering this question this thesis examines recent controversies in a generally policy-irrelevant science - evolutionary biology. Three episodes of conflict are studied: the `Neutral Allele Theory', `Punctuated Equilibrium', and `Structuralist versus Functionalist approaches to evolution'. These controversies are analysed in terms of both Kuhn's account of scientific `crises' and Collingridge and Reeve's (1986) `Overcritical Model'. Comparing its findings with those of Collingridge and Reeve, this thesis concludes that, (a) there is a Kuhnian crisis in contemporary evolution theory and, (b) that common causes do lie at the roots of conflict in policy-relevant and policy-irrelevant science. Science has an inherent tendency to degenerate into acrimonious conflict but at the same time has mechanisms which eventually resolve such conflicts. Unfortunately, when science is incorporated into the policy arena these mechanisms are prevented from operating. This thesis reinforces Collingridge and Reeve's conclusion that science is of little use to policy.

A converter compensator for power factor control in 3-phase induction machines

The advent of the harmonic neutralised shunt Converter Compensator as a practical means of reactive power compensation in power transmission systems has cleared ground for wider application of this type of equipment. An experimental 24-pulse voltage sourced convector has been successfully applied in controlling the terminal power factor of a 1.5kW, 240V three phase cage rotor induction motor, whose winding has been used in place of the usual phase shifting transformers. To achieve this, modifications have been made to the conventional stator winding of the induction machine. These include an unconventional phase spread and facilitation of compensator connections to selected tapping points between stator coils to give a three phase winding with a twelve phase connection to the twenty four pulse converter. Theoretical and experimental assessments of the impact of these modifications and attachment of the compensator have shown that there is a slight reduction in the torque developed at a given slip and in the combined system efficiency. There is also an increase in the noise level, also a consequence of the harmonics. The stator leakage inductance gave inadequate coupling reactance between the converter and the effective voltage source, necessitating the use of external inductors in each of the twelve phases. The terminal power factor is fully controllable when the induction machine is used either as a motor or as a generator.

30 years of retail change:where (and how) do you shop?

Purpose – The purpose of this paper is to investigate the extent of retail change in the UK grocery sector over the last 30 years. Design/methodology/approach – In 1980, a press article by Richard Milner and Patience Wheatcroft attempted to anticipate retail change by 1984. Taking that as a template, the paper examines how retail did, in fact, change over a much longer timescale: with some unanticipated innovations in place even by 1984. Reference is made to academic research on grocery retailing in progress at the time and which has recently been revisited. Findings – Although Milner and Wheatcroft tackled the modest task of looking ahead just four years, the content of their article is intriguingly reflective of the retail structure and systems of the UK at the time. Whilst some innovations were not anticipated, the broad themes of superstore power and market regulation still command attention 30 years on. Originality/value – Through reconsidering 30 years of retail change, the paper highlights that with time how do you shop has come to pose at least as interesting a question as where do you shop.

Modelling in the evaluation of a manufacturing strategy

This thesis describes research that has developed the principles of a modelling tool for the analytical evaluation of a manufacturing strategy. The appropriate process of manufacturing strategy formulation is based on mental synthesis with formal planning processes supporting this role. Inherent to such processes is a stage where the effects of alternative strategies on the performance of a manufacturing system must be evaluated so that a choice of preferred strategy can be made. Invariably this evaluation is carried out by practitioners applying mechanisms of judgement, bargaining and analysis. Ibis thesis makes a significant and original contribution to the provision of analytical support for practitioners in this role. The research programme commences by defining the requirements of analytical strategy evaluation from the perspective of practitioners. A broad taxonomy of models has been used to identify a set of potentially suitable techniques for the strategy evaluation task. Then, where possible, unsuitable modelling techniques have been identified on the basis of evidence in the literature and discarded from this set. The remaining modelling techniques have been critically appraised by testing representative contemporary modelling tools in an industrially based experimentation programme. The results show that individual modelling techniques exhibit various limitations in the strategy evaluation role, though some combinations do appear to provide the necessary functionality. On the basis of this comprehensive and in-depth knowledge a modelling tool ' has been specifically designed for this task. Further experimental testing has then been conducted to verify the principles of this modelling tool. Ibis research has bridged the fields of manufacturing strategy formulation and manufacturing systems modelling and makes two contributions to knowledge. Firstly, a comprehensive and in-depth platform of knowledge has been established about modelling techniques in manufacturing strategy evaluation. Secondly, the principles of a tool that supports this role have been formed and verified.

Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models

Background - The binding between peptide epitopes and major histocompatibility complex proteins (MHCs) is an important event in the cellular immune response. Accurate prediction of the binding between short peptides and the MHC molecules has long been a principal challenge for immunoinformatics. Recently, the modeling of MHC-peptide binding has come to emphasize quantitative predictions: instead of categorizing peptides as "binders" or "non-binders" or as "strong binders" and "weak binders", recent methods seek to make predictions about precise binding affinities. Results - We developed a quantitative support vector machine regression (SVR) approach, called SVRMHC, to model peptide-MHC binding affinities. As a non-linear method, SVRMHC was able to generate models that out-performed existing linear models, such as the "additive method". By adopting a new "11-factor encoding" scheme, SVRMHC takes into account similarities in the physicochemical properties of the amino acids constituting the input peptides. When applied to MHC-peptide binding data for three mouse class I MHC alleles, the SVRMHC models produced more accurate predictions than those produced previously. Furthermore, comparisons based on Receiver Operating Characteristic (ROC) analysis indicated that SVRMHC was able to out-perform several prominent methods in identifying strongly binding peptides. Conclusion - As a method with demonstrated performance in the quantitative modeling of MHC-peptide binding and in identifying strong binders, SVRMHC is a promising immunoinformatics tool with not inconsiderable future potential.

Modelling in the evaluation of a manufacturing strategy

This thesis describes research that has developed the principles of a modelling tool for the analytical evaluation of a manufacturing strategy. The appropriate process of manufacturing strategy formulation is based on mental synthesis with formal planning processes supporting this role. Inherent to such processes is a stage where the effects of alternative strategies on the performance of a manufacturing system must be evaluated so that a choice of preferred strategy can be made. Invariably this evaluation is carried out by practitioners applying mechanisms of judgement, bargaining and analysis. Ibis thesis makes a significant and original contribution to the provision of analytical support for practitioners in this role. The research programme commences by defining the requirements of analytical strategy evaluation from the perspective of practitioners. A broad taxonomy of models has been used to identify a set of potentially suitable techniques for the strategy evaluation task. Then, where possible, unsuitable modelling techniques have been identified on the basis of evidence in the literature and discarded from this set. The remaining modelling techniques have been critically appraised by testing representative contemporary modelling tools in an industrially based experimentation programme. The results show that individual modelling techniques exhibit various limitations in the strategy evaluation role, though some combinations do appear to provide the necessary functionality. On the basis of this comprehensive and in-depth knowledge a modelling tool ' has been specifically designed for this task. Further experimental testing has then been conducted to verify the principles of this modelling tool. Ibis research has bridged the fields of manufacturing strategy formulation and manufacturing systems modelling and makes two contributions to knowledge. Firstly, a comprehensive and in-depth platform of knowledge has been established about modelling techniques in manufacturing strategy evaluation. Secondly, the principles of a tool that supports this role have been formed and verified.

Modelling in the evaluation of a manufacturing strategy

This thesis describes research that has developed the principles of a modelling tool for the analytical evaluation of a manufacturing strategy. The appropriate process of manufacturing strategy formulation is based on mental synthesis with formal planning processes supporting this role. Inherent to such processes is a stage where the effects of alternative strategies on the performance of a manufacturing system must be evaluated so that a choice of preferred strategy can be made. Invariably this evaluation is carried out by practitioners applying mechanisms of judgement, bargaining and analysis. Ibis thesis makes a significant and original contribution to the provision of analytical support for practitioners in this role. The research programme commences by defining the requirements of analytical strategy evaluation from the perspective of practitioners. A broad taxonomy of models has been used to identify a set of potentially suitable techniques for the strategy evaluation task. Then, where possible, unsuitable modelling techniques have been identified on the basis of evidence in the literature and discarded from this set. The remaining modelling techniques have been critically appraised by testing representative contemporary modelling tools in an industrially based experimentation programme. The results show that individual modelling techniques exhibit various limitations in the strategy evaluation role, though some combinations do appear to provide the necessary functionality. On the basis of this comprehensive and in-depth knowledge a modelling tool ' has been specifically designed for this task. Further experimental testing has then been conducted to verify the principles of this modelling tool. Ibis research has bridged the fields of manufacturing strategy formulation and manufacturing systems modelling and makes two contributions to knowledge. Firstly, a comprehensive and in-depth platform of knowledge has been established about modelling techniques in manufacturing strategy evaluation. Secondly, the principles of a tool that supports this role have been formed and verified.

The Kim Dynasty and North-East Asian security:breaking the cycle of crises?

Purpose—This article considers North Korea and the notion of crisis, by linking historical development over the Korean peninsula to the conflict resolution literature, and investigates why despite a large number of destabilizing events, a war involving Pyongyang has yet to erupt. Design/methodology—This article uses historical data and a framework developed by Aggarwal et al., in order to highlight patterns of interaction between states such as the United States, North Korea and South Korea, organizations such as the United Nations, as well as processes such as the Six- Party Talks and the Agreed Framework. The article then develops a crisis framework based on conflict resolution and negotiation literature, and applies it to three North Korean administrations. Findings—Findings suggest that an open- ended understanding of time (for all parties involved on the peninsula) leads to an impossibility to reach a threshold where full- scale war would be triggered, thus leaving parties in a stable state of crisis for which escalating moves and de- escalating techniques might become irrelevant. Practical implications—It is hoped that this article will help further endeavors linking conflict resolution theoretical frameworks to the Korean peninsula security situation. In the case of the Korean peninsula, time has been understood as open-ended, leading parties to a lingering state of heightened hostilities that oscillates toward war, but that is controlled enough not to reach it. In-depth analysis of particular security sectors such as nuclear energy, food security, or missile testing would prove particularly useful in understanding the complexity of the Korean peninsula situation to a greater extent. It is hoped that this paper will help further endeavours linking conflict resolution theoretical frameworks to the Korean peninsula security situation. Originality/value—This research suggests that regarding the Korean peninsula, time has been understood as open- ended, leading parties to a lingering state of heightened.

A question of complexity:measuring the maturity of online enquiry communities

Online enquiry communities such as Question Answering (Q&A) websites allow people to seek answers to all kind of questions. With the growing popularity of such platforms, it is important for community managers to constantly monitor the performance of their communities. Although different metrics have been proposed for tracking the evolution of such communities, maturity, the process in which communities become more topic proficient over time, has been largely ignored despite its potential to help in identifying robust communities. In this paper, we interpret community maturity as the proportion of complex questions in a community at a given time. We use the Server Fault (SF) community, a Question Answering (Q&A) community of system administrators, as our case study and perform analysis on question complexity, the level of expertise required to answer a question. We show that question complexity depends on both the length of involvement and the level of contributions of the users who post questions within their community. We extract features relating to askers, answerers, questions and answers, and analyse which features are strongly correlated with question complexity. Although our findings highlight the difficulty of automatically identifying question complexity, we found that complexity is more influenced by both the topical focus and the length of community involvement of askers. Following the identification of question complexity, we define a measure of maturity and analyse the evolution of different topical communities. Our results show that different topical communities show different maturity patterns. Some communities show a high maturity at the beginning while others exhibit slow maturity rate. Copyright 2013 ACM.

Peptide binding to HLA-DP proteins at pH 5.0 and pH 7.0:a quantitative molecular docking study

Background: HLA-DPs are class II MHC proteins mediating immune responses to many diseases. Peptides bind MHC class II proteins in the acidic environment within endosomes. Acidic pH markedly elevates association rate constants but dissociation rates are almost unchanged in the pH range 5.0 - 7.0. This pH-driven effect can be explained by the protonation/deprotonation states of Histidine, whose imidazole has a pKa of 6.0. At pH 5.0, imidazole ring is protonated, making Histidine positively charged and very hydrophilic, while at pH 7.0 imidazole is unprotonated, making Histidine less hydrophilic. We develop here a method to predict peptide binding to the four most frequent HLA-DP proteins: DP1, DP41, DP42 and DP5, using a molecular docking protocol. Dockings to virtual combinatorial peptide libraries were performed at pH 5.0 and pH 7.0. Results: The X-ray structure of the peptide - HLA-DP2 protein complex was used as a starting template to model by homology the structure of the four DP proteins. The resulting models were used to produce virtual combinatorial peptide libraries constructed using the single amino acid substitution (SAAS) principle. Peptides were docked into the DP binding site using AutoDock at pH 5.0 and pH 7.0. The resulting scores were normalized and used to generate Docking Score-based Quantitative Matrices (DS-QMs). The predictive ability of these QMs was tested using an external test set of 484 known DP binders. They were also compared to existing servers for DP binding prediction. The models derived at pH 5.0 predict better than those derived at pH 7.0 and showed significantly improved predictions for three of the four DP proteins, when compared to the existing servers. They are able to recognize 50% of the known binders in the top 5% of predicted peptides. Conclusions: The higher predictive ability of DS-QMs derived at pH 5.0 may be rationalised by the additional hydrogen bond formed between the backbone carbonyl oxygen belonging to the peptide position before p1 (p-1) and the protonated ε-nitrogen of His 79β. Additionally, protonated His residues are well accepted at most of the peptide binding core positions which is in a good agreement with the overall negatively charged peptide binding site of most MHC proteins. © 2012 Patronov et al.; licensee BioMed Central Ltd.

BRACHYURY confers cancer stem cell characteristics on colorectal cancer cells

Cancer stem cells (CSCs) are initiating cells in colorectal cancer (CRC). Colorectal tumours undergo epithelial to mesenchymal transition (EMT)-like processes at the invasive front, enabling invasion and metastasis, and recent studies have linked this process to the acquisition of stem cell-like properties. It is of fundamental importance to understand the molecular events leading to the establishment of cancer initiating cells and how these mechanisms relate to cellular transitions during tumourigenesis. We use an in vitro system to recapitulate changes in CRC cells at the invasive front (mesenchymal-like cells) and central mass (epithelial-like cells) of tumours. We show that the mesoderm inducer BRACHYURY is expressed in a subpopulation of CRC cells that resemble invasive front mesenchymal-like cells, where it acts to impose characteristics of CSCs in a fully reversible manner, suggesting reversible formation and modulation of such cells. BRACHYURY, itself regulated by the oncogene β-catenin, influences NANOG and other 'stemness' markers including a panel of markers defining CRC-CSC whose presence has been linked to poor patient prognosis. Similar regulation of NANOG through BRACHYURY was observed in other cells lines, suggesting this might be a pathway common to cancer cells undergoing mesenchymal transition. We suggest that BRACHYURY may regulate NANOG in mesenchymal-like CRC cells to impose a 'plastic-state', allowing competence of cells to respond to signals prompting invasion or metastasis. Copyright © 2011 UICC.

Consistency of the decision-maker in pair-wise comparisons

Most authors assume that the natural behaviour of the decision-maker is being inconsistent. This paper investigates the main sources of inconsistency and analyses methods for reducing or eliminating inconsistency. Decision support systems can contain interactive modules for that purpose. In a system with consistency control, there are three stages. First, consistency should be checked: a consistency measure is needed. Secondly, approval or rejection has to be decided: a threshold value of inconsistency measure is needed. Finally, if inconsistency is ‘high’, corrections have to be made: an inconsistency reducing method is needed. This paper reviews the difficulties in all stages. An entirely different approach is to elaborate a decision support system in order to force the decision-maker to give consistent values in each step of answering pair-wise comparison questions. An interactive questioning procedure resulting in consistent (sub) matrices has been demonstrated.

Post-Crisis Lessons for Open Economies

In a systemic perspective, what are the primary transmitters of global competitiveness with the proper coordination mechanism? What are the systemic impacts of the U.S. economy on world markets? Will the United States stay the main engine of world economic growth for quite some time to come, or at least in the current decade? Will and should the United States, as the single largest open economy of the world, be in some way responsible for the provision of global economic stability as a valuable public good? Was the recent crisis predictable? These are the main questions addressed, all of which are answered in a new global context, and the responses are based on some known principles of international economics and economic history.

A comprehensive study of bankruptcy prediction: Accounting ratios, market variables, and microstructure

Bankruptcy prediction has been a fruitful area of research. Univariate analysis and discriminant analysis were the first methodologies used. While they perform relatively well at correctly classifying bankrupt and nonbankrupt firms, their predictive ability has come into question over time. Univariate analysis lacks the big picture that financial distress entails. Multivariate discriminant analysis requires stringent assumptions that are violated when dealing with accounting ratios and market variables. This has led to the use of more complex models such as neural networks. While the accuracy of the predictions has improved with the use of more technical models, there is still an important point missing. Accounting ratios are the usual discriminating variables used in bankruptcy prediction. However, accounting ratios are backward-looking variables. At best, they are a current snapshot of the firm. Market variables are forward-looking variables. They are determined by discounting future outcomes. Microstructure variables, such as the bid-ask spread, also contain important information. Insiders are privy to more information that the retail investor, so if any financial distress is looming, the insiders should know before the general public. Therefore, any model in bankruptcy prediction should include market and microstructure variables. That is the focus of this dissertation. The traditional models and the newer, more technical models were tested and compared to the previous literature by employing accounting ratios, market variables, and microstructure variables. Our findings suggest that the more technical models are preferable, and that a mix of accounting and market variables are best at correctly classifying and predicting bankrupt firms. Multi-layer perceptron appears to be the most accurate model following the results. The set of best discriminating variables includes price, standard deviation of price, the bid-ask spread, net income to sale, working capital to total assets, and current liabilities to total assets.

The inclusion of differentially assessed lands in urban growth model calibration: a comparison of two approaches using SLEUTH

This research sought to understand the role that differentially assessed lands (lands in the United States given tax breaks in return for their guarantee to remain in agriculture) play in influencing urban growth. Our method was to calibrate the SLEUTH urban growth model under two different conditions. The first used an excluded layer that ignored such lands, effectively rendering them available for development. The second treated those lands as totally excluded from development. Our hypothesis was that excluding those lands would yield better metrics of fit with past data. Our results validate our hypothesis since two different metrics that evaluate goodness of fit both yielded higher values when differentially assessed lands are treated as excluded. This suggests that, at least in our study area, differential assessment, which protects farm and ranch lands for tenuous periods of time, has indeed allowed farmland to resist urban development. Including differentially assessed lands also yielded very different calibrated coefficients of growth as the model tried to account for the same growth patterns over two very different excluded areas. Excluded layer design can greatly affect model behavior. Since differentially assessed lands are quite common through the United States and are often ignored in urban growth modeling, the findings of this research can assist other urban growth modelers in designing excluded layers that result in more accurate model calibration and thus forecasting.