STUDIES ON THE PATTERNS OF NUCLEOTIDE AND AMINO ACID SUBSTITUTION (ELECTROPHORESIS, MUTATION RATE, SELECTION, BASE, COMPOSITION)

Theoretical and empirical studies were conducted on the pattern of nucleotide and amino acid substitution in evolution, taking into account the effects of mutation at the nucleotide level and purifying selection at the amino acid level. A theoretical model for predicting the evolutionary change in electrophoretic mobility of a protein was also developed by using information on the pattern of amino acid substitution. The specific problems studied and the main results obtained are as follows: (1) Estimation of the pattern of nucleotide substitution in DNA nuclear genomes. The pattern of point mutations and nucleotide substitutions among the four different nucleotides are inferred from the evolutionary changes of pseudogenes and functional genes, respectively. Both patterns are non-random, the rate of change varying considerably with nucleotide pair, and that in both cases transitions occur somewhat more frequently than transversions. In protein evolution, substitution occurs more often between amino acids with similar physico-chemical properties than between dissimilar amino acids. (2) Estimation of the pattern of nucleotide substitution in RNA genomes. The majority of mutations in retroviruses accumulate at the reverse transcription stage. Selection at the amino acid level is very weak, and almost non-existent between synonymous codons. The pattern of mutation is very different from that in DNA genomes. Nevertheless, the pattern of purifying selection at the amino acid level is similar to that in DNA genomes, although selection intensity is much weaker. (3) Evaluation of the determinants of molecular evolutionary rates in protein-coding genes. Based on rates of nucleotide substitution for mammalian genes, the rate of amino acid substitution of a protein is determined by its amino acid composition. The content of glycine is shown to correlate strongly and negatively with the rate of substitution. Empirical formulae, called indices of mutability, are developed in order to predict the rate of molecular evolution of a protein from data on its amino acid sequence. (4) Studies on the evolutionary patterns of electrophoretic mobility of proteins. A theoretical model was constructed that predicts the electric charge of a protein at any given pH and its isoelectric point from data on its primary and quaternary structures. Using this model, the evolutionary change in electrophoretic mobilities of different proteins and the expected amount of electrophoretically hidden genetic variation were studied. In the absence of selection for the pI value, proteins will on the average evolve toward a mildly basic pI. (Abstract shortened with permission of author.) ^

Estimating parameters in Markov models for longitudinal studies with missing data or surrogate outcomes

The discrete-time Markov chain is commonly used in describing changes of health states for chronic diseases in a longitudinal study. Statistical inferences on comparing treatment effects or on finding determinants of disease progression usually require estimation of transition probabilities. In many situations when the outcome data have some missing observations or the variable of interest (called a latent variable) can not be measured directly, the estimation of transition probabilities becomes more complicated. In the latter case, a surrogate variable that is easier to access and can gauge the characteristics of the latent one is usually used for data analysis. ^ This dissertation research proposes methods to analyze longitudinal data (1) that have categorical outcome with missing observations or (2) that use complete or incomplete surrogate observations to analyze the categorical latent outcome. For (1), different missing mechanisms were considered for empirical studies using methods that include EM algorithm, Monte Carlo EM and a procedure that is not a data augmentation method. For (2), the hidden Markov model with the forward-backward procedure was applied for parameter estimation. This method was also extended to cover the computation of standard errors. The proposed methods were demonstrated by the Schizophrenia example. The relevance of public health, the strength and limitations, and possible future research were also discussed. ^

An Empirical Comparison of Reuse in Embedded and Nonembedded Systems

High-quality software, delivered on time and budget, constitutes a critical part of most products and services in modern society. Our government has invested billions of dollars to develop software assets, often to redevelop the same capability many times. Recognizing the waste involved in redeveloping these assets, in 1992 the Department of Defense issued the Software Reuse Initiative. The vision of the Software Reuse Initiative was "To drive the DoD software community from its current "re-invent the software" cycle to a process-driven, domain-specific, architecture-centric, library-based way of constructing software.'' Twenty years after issuing this initiative, there is evidence of this vision beginning to be realized in nonembedded systems. However, virtually every large embedded system undertaken has incurred large cost and schedule overruns. Investigations into the root cause of these overruns implicates reuse. Why are we seeing improvements in the outcomes of these large scale nonembedded systems and worse outcomes in embedded systems? This question is the foundation for this research. The experiences of the Aerospace industry have led to a number of questions about reuse and how the industry is employing reuse in embedded systems. For example, does reuse in embedded systems yield the same outcomes as in nonembedded systems? Are the outcomes positive? If the outcomes are different, it may indicate that embedded systems should not use data from nonembedded systems for estimation. Are embedded systems using the same development approaches as nonembedded systems? Does the development approach make a difference? If embedded systems develop software differently from nonembedded systems, it may mean that the same processes do not apply to both types of systems. What about the reuse of different artifacts? Perhaps there are certain artifacts that, when reused, contribute more or are more difficult to use in embedded systems. Finally, what are the success factors and obstacles to reuse? Are they the same in embedded systems as in nonembedded systems? The research in this dissertation is comprised of a series of empirical studies using professionals in the aerospace and defense industry as its subjects. The main focus has been to investigate the reuse practices of embedded systems professionals and nonembedded systems professionals and compare the methods and artifacts used against the outcomes. The research has followed a combined qualitative and quantitative design approach. The qualitative data were collected by surveying software and systems engineers, interviewing senior developers, and reading numerous documents and other studies. Quantitative data were derived from converting survey and interview respondents' answers into coding that could be counted and measured. From the search of existing empirical literature, we learned that reuse in embedded systems are in fact significantly different from nonembedded systems, particularly in effort in model based development approach and quality where the development approach was not specified. The questionnaire showed differences in the development approach used in embedded projects from nonembedded projects, in particular, embedded systems were significantly more likely to use a heritage/legacy development approach. There was also a difference in the artifacts used, with embedded systems more likely to reuse hardware, test products, and test clusters. Nearly all the projects reported using code, but the questionnaire showed that the reuse of code brought mixed results. One of the differences expressed by the respondents to the questionnaire was the difficulty in reuse of code for embedded systems when the platform changed. The semistructured interviews were performed to tell us why the phenomena in the review of literature and the questionnaire were observed. We asked respected industry professionals, such as senior fellows, fellows and distinguished members of technical staff, about their experiences with reuse. We learned that many embedded systems used heritage/legacy development approaches because their systems had been around for many years, before models and modeling tools became available. We learned that reuse of code is beneficial primarily when the code does not require modification, but, especially in embedded systems, once it has to be changed, reuse of code yields few benefits. Finally, while platform independence is a goal for many in nonembedded systems, it is certainly not a goal for the embedded systems professionals and in many cases it is a detriment. However, both embedded and nonembedded systems professionals endorsed the idea of platform standardization. Finally, we conclude that while reuse in embedded systems and nonembedded systems is different today, they are converging. As heritage embedded systems are phased out, models become more robust and platforms are standardized, reuse in embedded systems will become more like nonembedded systems.

Statistical racing techniques for improved empirical evaluation of evolutionary algorithms

In empirical studies of Evolutionary Algorithms, it is usually desirable to evaluate and compare algorithms using as many different parameter settings and test problems as possible, in border to have a clear and detailed picture of their performance. Unfortunately, the total number of experiments required may be very large, which often makes such research work computationally prohibitive. In this paper, the application of a statistical method called racing is proposed as a general-purpose tool to reduce the computational requirements of large-scale experimental studies in evolutionary algorithms. Experimental results are presented that show that racing typically requires only a small fraction of the cost of an exhaustive experimental study.

Is there a special kind of "reading" for translation? An empirical investigation of reading in the translation process

The role of reading in translation is rarely discussed in the literature. Translation has mainly been discussed within a product-oriented framework. The more process-oriented approaches of recent years have taken notice of reading as a component activity of the translation process. However, few empirical studies have been completed which address the role of reading in translation. The way a person reads, and the result of that reading (some sort of mental representation of the text or text segment), will depend on the reader's purposes and motivations. The present empirical study indicates that while the translator's reading of a text may be to some extent more thorough and deliberate than that of an ordinary reader, it is not likely to be markedly so. The study also indicates a significant variability in the way translators "read for translation". This suggests the existence of alternate strategies in this kind of reading.

Empirical research into white racialized identities in Britain

The intellectual project of using whiteness as an explicit tool of analysis is not one that has taken root in Britain. However, there are a number of empirical studies that investigate the racialization of white identities. In this article, I look at some empirical sociological fieldwork carried out on white identities in Britain since the early 1990s and identify the key themes arising. These themes are (in)visibility, norms and values, cultural capital and integration, contingent hierarchies and Empire in the present. In Britain, a pertinent distinction is between rural and urban settings for the enactment of white identities vis-a`-vis those of minorities, and there is an exploration of some of the contingency that draws the boundary between ‘white’ and ‘Other’ in different places. Areas of commonality and distinctiveness are noted in terms of the American work. In the last section, I argue that there are a number of issues to resolve around continuing such studies, including linking the micro-level to the macro-level analysis, and expanding to international comparative work.

Strategic sourcing supplier selection misalignment with critical success factors:findings from multiple case studies in Germany and the United Kingdom

Strategic sourcing plays an important role in organisations' performance. Strategic sourcing has been researched extensively using empirical studies as well as review work, such as strategic sourcing importance, issues and challenges, processes, source selection criteria and framework. However, there is no research on critical success factors for strategic sourcing specific to industry and country. This research aims to qualitatively evaluate and understand the current role of strategic sourcing, the critical success factors for business performance and its relationship with strategic sourcing, and strategic supplier evaluation criteria from multiple stakeholders' perspectives specific to industry and country. This research studies twenty organisations from Germany and the United Kingdom (UK) covering two industry sectors - electronics manufacturing and construction. We consider five organisations from each industry sector and each country. The findings from twenty case studies reveal comparative analysis of strategic sourcing practices of two countries and two industries.

Revisiting the lean agile paradigm:an empirical study in the aerospace industry

Much has been written about the potential impact of Lean Agile paradigm on firm's supply chain performance. However, most of the existing studies mainly pointed out Lean is for cost reduction, whereas Agility is for attaining flexibility. There are little empirical studies in literature that examined how Lean Agile paradigm impacts on supply chain performance. This paper aims to address this gap by studying the influence of Lean and Agility paradigms on a single commodity supply chain delivery performance in the aerospace industry. Data was collected from four separate 'Rigid pipes' supply chains to study how manufacturing alignment impacts on the delivery performance. Implications of the study to practitioners and academia are discussed and future research outlined.

The determinants of R&D investment: A survey of the empirical research

This paper offers an extensive survey and a critical discussion of the empirical literature on the driving factors of R&D. These factors are subsumed under five broad types. The paper first summarises the key predictions from theory regarding each type's R&D effect. It then examines for which factors differences in the theoretical predictions can also be found in empirical studies, and for which factors the empirical evidence is more unanimous. As the focus is on the empirical literature, methodological issues are also highlighted. The major factor types identified in the literature are, individual firm or industry characteristics, particularly internal finance and sales; competition in product markets; R&D tax credits and subsidies; location and resource related factors, such as spillovers from university research within close geographic proximity, membership of a research joint venture and cooperation with research centres, and the human capital embodied in knowledge workers; and spillovers from foreign R&D. Although on balance there is a consensus regarding the R&D effects of most factors, there is also variation in results. Recent work suggests that accounting for non-linearities is one area of research that may explain and encompass contradictory findings.

Self-cutting and prospective repetition of self-harm: studies of emergency department presentations in Ireland

Background Self-harm places an individual at increased risk of future self-harm and suicide, and indicates distress and maladaptive coping. Those who present to hospital with self-cutting form a significant minority of self-harm patients who are at increased risk of prospective repetition of self-harm and suicide compared with those presenting with intentional overdose. In addition to increased risk, there is emerging evidence of demographic, psychological, clinical, and social differences between those presenting with self-cutting and those presenting with overdose. Aim and Key Objectives The aim of the current doctoral work was to examine in detail the association between presenting with self-cutting and risk of prospective repetition. The objectives were: to identify evidence-based risk factors for repetition of self-harm among those presenting to emergency departments with self-harm; to compare demographic and presentation characteristics and prospective repetition across presentations of self-cutting only, self-cutting plus intentional overdose, and intentional overdose only; to compare prospective repetition and other characteristics within self-cutting presentations based on the type of treatment received; to compare self-cutting and intentional overdose patients on psychological risk and protective factors for repetition; and to examine the lived experience of engaging in repeated overdose and self-cutting. Methods The current doctoral work used a mixed-methods approach and is comprised of one systematic review and four empirical studies. The empirical studies were two registry-based prospective studies of Irish hospital presentations of self-harm, one prospective structured interview study, and one qualitative study using Interpretative Phenomenological Analysis. Results The systematic review identified several consistent and emerging risk factors for repetition of self-harm, compared to which self-cutting had a medium-sized effect. The registry studies demonstrated that the involvement of self-cutting, particularly less medically severe selfcutting, confers an increased risk of 1-month and 12-month repetition among Irish index selfharm presentations. The structured psychological study detected higher hopelessness and lower non-reactivity to inner experience among those presenting with self-cutting, and higher depression among those who repeated self-harm. Repeaters had lower baseline levels of protective psychological factors than non-repeaters and continued to have higher depression and hopelessness at follow-up. Finally, the qualitative study indicated that self-harm is a purposeful action taken in response to an overwhelming situation and is evaluated afterwards in terms of personal and social effects. Chosen method of self-harm seemed to be influenced by the desired outcome of the self-harm act, capability, accessibility and previous experience. Conclusion Despite limitations in terms of recruitment rates, the work presented in this thesis is innovative in examining the issue of the association between self-cutting and repetition from multiple perspectives. No one factor can reliably predict all repetition but self-cutting represents one consistent and easily detected risk factor for repetition. Those who present with self-cutting exhibit significant differences on demographic, clinical, and psychological variables compared with those presenting with intentional overdose, and seem to exhibit a more vulnerable profile. However, those who present with self-cutting do not form a discrete or homogenous group, and self-harm methods and levels of suicidal intent are liable to fluctuate over time.

Introduction: Exploring the Comparative in Socio-Legal Studies

Among the diverse approaches to comparison in socio-legal studies those that employ qualitative research, richness of detail, and attention to context are the focus of this special issue. The Introduction draws on comparative law and social science literature to argue that comparison amongst studies of laws in contexts can follow different trajectories: the comparison may start from an assumption of similarity—in form, purposes, or context—in order to identify significant differences; or it may identify significant similarity across social and cultural divides. What unites many of the projects of comparison undertaken by qualitative empirical researchers is that the points of relevant comparison are identified within the complexity of the empirical studies at hand; and they are allowed to emerge, or change, as the researcher comes to understand the facts and issues more deeply.

The impact of mindfulness on the wellbeing and performance of educators: A systematic review of the empirical literature

Given the potentially demanding nature of teaching, efforts are underway to develop practices that can improve the wellbeing of educators, including interventions based on mindfulness meditation. We performed systematic review of empirical studies featuring analyses of mindfulness in teaching contexts. Databases were reviewed from the start of records to January 2016. Eligibility criteria included empirical analyses of mindfulness and wellbeing outcomes acquired in relation to practice. A total of 19 papers met the eligibility criteria and were included in the systematic review, consisting of a total 1,981 participants. Studies were principally examined for outcomes such as burnout, anxiety, depression and stress, as well as more positive wellbeing measures (e.g., life satisfaction). The systematic review revealed that mindfulness was generally associated with positive outcomes in relation to most measures. However, the quality of the studies was inconsistent, and so further research is needed, particularly involving high-quality randomised control trials.

Understanding import diversification: an empirical analysis

This paper analyzes import diversification in an aggregated perspective -- Using a dataset for 60 countries covering the period 1995-2010, we study the main determinants of import diversification -- We expect to contribute to the current literature, taking into account that there have been few empirical studies addressing import diversification and more specifically, at the cross-country level -- We take into account variables classified into four categories: Structural factors, macroeconomic factors, international trade factors and political factors -- We find robust evidence that total factor productivity (TFP), capital stock, real Exchange rates and terms of trade are key drivers of import diversification -- On the other hand, domestic consumption and trade openness exert an effect leading to import concentration -- We interpret this finding, taking into account the theoretical framework provided by the international trade and growth theories

Entrepreneurship in project management systems: proposal of a model and preliminary empirical evidence

This study analyzes the manifestation of the dimensions of Entrepreneurial Orientation (EO) and Project Management Systems (PMS). We used a qualitative approach to conduct exploratory research through a study in literature and a pilot case in a software company. Data was collected from semi structured interviews, documents, and records on file, then triangulated and treated with content analysis. The model proposed for the relationship between the types of PMS (ad hoc, Classic PM, innovation, entrepreneurship/intrapreneurship) and the dimensions of EO (innovativeness, risk-taking, proactiveness, competitive aggressiveness, and autonomy), was partially corroborated by empirical studies. New studies are suggested to validate the applicability and setup of the model.

Price manipulation: theoretical models and empirical investigation

Understanding why market manipulation is conducted, under which conditions it is the most profitable and investigating the magnitude of these practices are crucial questions for financial regulators. Closing price manipulation induced by derivatives’ expiration is the primary subject of this thesis. The first chapter provides a mathematical framework in continuous time to study the incentive to manipulate a set of securities induced by a derivative position. An agent holding a European-type contingent claim, depending on the price of a basket of underlying securities, is considered. The agent can affect the price of the underlying securities by trading on each of them before expiration. The elements of novelty are at least twofold: (1) a multi-asset market is considered; (2) the problem is solved by means of both classic optimisation and stochastic control techniques. Both linear and option payoffs are considered. In the second chapter an empirical investigation is conducted on the existence of expiration day effects on the UK equity market. Intraday data on FTSE 350 stocks over a six-year period from 2015-2020 are used. The results show that the expiration of index derivatives is associated with a rise in both trading activity and volatility, together with significant price distortions. The expiration of single stock options appears to have little to no impact on the underlying securities. The last chapter examines the existence of patterns in line with closing price manipulation of UK stocks on option expiration days. The main contributions are threefold: (1) this is one of the few empirical studies on manipulation induced by the options market; (2) proprietary equity orderbook and transaction data sets are used to define manipulation proxies, providing a more detailed analysis; (3) the behaviour of proprietary trading firms is studied. Despite the industry concerns, no evidence is found of this type of manipulative behaviour.