Dissertations / Theses on the topic 'Pathways'

The challenge with todays microarray experiments is to infer biological conclusions from them. There are two crucial difficulties to be surmounted in this challenge:(1) A lack of suitable biological repository that can be easily integrated into computational algorithms. (2) Contemporary algorithms used to analyze microarray data are unable to draw consistent biological results from diverse datasets of the same disease. To deal with the first difficulty, we believe a core database that unifies available biological repositories is important. Towards this end, we create a unified biological database from three popular biological repositories (KEGG, Ingenuity and Wikipathways). This database provides computer scientists the flexibility of easily integrating biological information using simple API calls or SQL queries. To deal with the second difficulty of deriving consistent biological results from the experiments, we first conceptualize the notion of “subnetworks”, which refers to a connected portion in a biological pathway. Then we propose a method that identifies subnetworks that are consistently expressed by patients of he same disease phenotype. We test our technique on independent datasets of several diseases, including ALL, DMD and lung cancer. For each of these diseases, we obtain two independent microarray datasets produced by distinct labs on distinct platforms. In each case, our technique consistently produces overlapping lists of significant nontrivial subnetworks from two independent sets of microarray data. The gene-level agreement of these significant subnetworks is between 66.67% to 91.87%. In contrast, when the same pairs of microarray datasets were analysed using GSEA and t-test, this percentage fell between 37% to 55.75% (GSEA) and between 2.55% to 19.23% (t-test). Furthermore, the genes selected using GSEA and t-test do not form subnetworks of substantial size. Thus it is more probable that the subnetworks selected by our technique can provide the researcher with more descriptive information on the portions of the pathway which actually associates with the disease. Keywords: pathway analysis, microarray

Detta examensarbete granskar analysverktyg ur ett tvärvetenskapligt perspektiv. Det finns en hel del olika analysverktyg idag som analyserar specifika typer av omik data och därför undersöker vi hur många det finns samt vad de kan göra. Genom att definiera ett antal specifika krav såsom hur många typer av omik data den kan hantera, noggrannhet av verktygets analys så kan man se vilka som är mest lämpliga analysverktygen när det gäller kartläggning av omik data. Resultaten visar att det idag inte finns analysverktyg som uppfyller de specifikt angivna kraven eller huvudsyftet genom testning av programvaran. Ingenuity analysverktyget är det närmaste vi kan komma för de krav som vi söker. På begäran av slutanvändaren testades två analysverktyg för att se om en kombination av dessa kan uppfylla slut användarens krav. Analysverktyget Uniprot batch converter testas med FEvER men resultat är inte framgångsrikt, då kombinationen av dessa verktyg inte är bättre än Ingenuity analysverktyget. Fokus vänds mot en alternativ kombination som är en hemsida och heter NCBI. Hemsidan har en sökmotor kopplad till flera olika analysverktyg som är gratis att använda. Genom sökmotorn kan ”omik” data kombineras och mer än ett inmatat värde kan hanteras i taget. Eftersom tekniken snabbt går framåt innebär det däremot att nya analysverktyg behövs för data hantering och inom en snar framtid så har vi kanske ett analysverktyg som uppfyller kraven av slutanvändarna.
This thesis examines PATs from a multidisciplinary view. There are a lot of PAT's existing today analyzing specific type of omics data, therefore we investigate them and what they can do. By defining some specific requirements such as how many omics data types it can handle, the accuracy of the PAT can be obtained to get the most suitable PAT when it comes to mapping omics data to pathways. Results show that no PATs found today fulfills the specific set of requirements or the main goal though software testing. The Ingenuity PAT is the closest to fulfill the requirements. Requested by the end user, two PATs are tested in combination to see if these can fulfill the requirements of the end user. Uniprot batch converter was tested with FEvER and results did not turn out successfully since the combination of the two PATs is no better than the Ingenuity PAT. Focus then turned to an alternative combination, a homepage called NCBI that have search engines connected to several free PATs available thus fulfilling the requirements. Through the search engine “omics” data can be combined and more than one input can be taken at a time. Since technology is rapidly moving forward, the need for new tools for data interpretation also grows. It means that in a near future we may be able to find a PAT that fulfills the requirements of the end users.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2017.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 86-91).
Metabolic engineering efforts have so far focused on strain optimization through careful metabolic modeling and tinkering with host genomes, through gene knockouts or knockins, to direct flux in desired channels. These efforts have borne fruit with the development of large manufacturing processes for numerous chemicals. The next challenge for metabolic engineering, however, lies in tackling issues associated with construction of more complex pathways, such as those that directly interfere with host metabolism, have branchpoints with promiscuous enzymes, or synthesize toxic intermediates or products. Dynamic metabolic engineering has emerged as a new frontier for tool development to allow regulation and control of native and cellular pathways during the course of a production run. Advantages in dynamic strategies are especially apparent in the aforementioned examples where traditional static strategies of gene knockouts or knockins are not an option. Instead, it is necessary to be able to control when certain genes are expressed, such as to build biomass before switching on growth-limiting production pathways, or accumulating intermediates to drive the reaction of a promiscuous enzyme along a certain branch. In this thesis, we propose enzyme control strategies that are independent of any biosynthetic pathway of interest. Therefore, they can theoretically be applied to a wide variety of contexts in a "plug-and-play" fashion to control pathway enzyme expression. After initial work to understand the limitations of nutrient starvation strategies to induce genetic circuits, we decided to use quorum sensing circuitry to create circuits that can be autonomously induced. We used parts of the Esa QS system (derived from Pantoea stewartii) to create circuit variants in the Lscherichia cohi genome, which switch off expression of the targeted gene at various times and cell densities. Switching times were varied by modulating the expression of the AHL synthase, and therefore the production rate of AHL, the quorum sensing molecule. Switching dynamics were characterized and ranked for the entire library of circuit variants using fluorescent reporters. The characterized device was used to identify optimal switching times for redirection of glycolytic fluxes into heterologous pathways, resulting in a 5.5-fold boost in myo-inositol (MI) and increasing glucaric acid titers from unmeasurable quantities up to >0.8 g/L. With a focus on industrial application, consistency of device performance was verified in benchtop bioreactors, achieving nearly 10-fold and 5-fold boosts in specific titers of myoinositol and glucaric acid, respectively. To demonstrate broad utility and "off-the-shelf" applicability, the control module was applied to dynamic downregulation of flux into aromatic amino acid biosynthesis to accumulate the industrially-relevant intermediate, shikimate, resulting in an increase in titers from unmeasurable quantities to >100 mg/L. Finally, this QS device was coupled with a MI-biosensor circuit to institute two layers of dynamic regulation and further improve glucaric acid titers. Production trials in these composite strains resulted in the highest glucaric titers (-2 g/L) reported to date from E. coli K-strains. This work reports the first completely autonomous dynamic regulation module and its application in bioproduction of multiple products from different metabolic pathways. We envision that the strategy presented here may be adapted to any pathway context and gene of interest. With increased prevalence of dynamic regulation, the relevant strategies may become standardized for general use.
by Apoorv Gupta.
Ph. D.

Against the background of increasing multidisciplinarity as well as the focus on quality, transparency and economic efficiency of medical services, clinical pathways (CPs) have been established as a promising tool at the organizational level in recent years. They are primarily intended to ensure an adequate description of the care processes and to manage the balance between best treatment practice and economic viability. CPs standardize the internal care services by explicating the institution-specific knowledge with regard to recommendations for action, service portfolio, organizational structures, infrastructure, etc. of a specific service provider. The development of hospital information systems (HIS) has so far been characterized by an evolutionary development of modules in the field of laboratory, radiology, nursing and picture archiving systems as well as in the area of administrative systems. As one result of this development, the HIS usually comprises a heterogeneous network of software systems of different types and manufacturers. However, the actual control of patients by means of evidence-based processes and integration of CPs into HIS was not addressed until the recent years, when HIS manufacturers started developing modules for CP modeling and workflow support. The objective of this thesis is to provide a holistic methodical support for the description of clinical pathways and their integration into a hospital information system to finally improve the compliance of daily care to standard process definitions. Therefore, conceptual models provide an adequate mean to describe and communicate complex matters in a comprehensible form as well as to configure IT systems due to their semi-formal nature. Hence, a first research thread investigates the question, how clinical pathways can be described adequately using conceptual models. This results in an iterative design of adequate modeling languages for clinical pathways. A second research thread further investigates the question, how conceptual models of clinical pathways can be used to configure process-oriented application systems in health care. This thread therefore describes the design of a model-based method, that enables a consecutive transformation of CPs into technical (workflow) specifications, based on the principles of the Model-Driven Architecture.

This research utilised a range of deterministic and stochastic analyses to establish whether Queensland's juvenile justice system processes Aboriginal and non-Aboriginal young male offenders differently. The impetus for this research stemmed from the continued high rates of Aboriginal over-representation within Australia's criminal justice system, despite diversionary measures to reduce such over-representation, and a commitment by the Queensland Government to reduce by 50% the number of Aboriginal peoples in custody by the year 2011. There are two competing hypotheses concerning the cause of this over-representation, (i) external factors such as socioeconomic disadvantage, unemployment or substance abuse, or (ii) systemic disparity within the criminal justice system. For this research, disparity is defined as the unacceptable use of discrimination; discrimination can be appropriate if it is used to define or enhance a situation, such as discriminating between offenders who are recidivists and those who are first time offenders. The inappropriate use of discrimination occurs for example, when harsher sentences are issued to offenders based on non-legal factors such as race or gender. Systemic disparity is therefore used here to represent the inappropriate use of discrimination against an offender by the criminal justice system. The second hypothesis, one of systemic disparity, provided the framework for this research, which posed the following primary question: Is there quantifiable evidence to support the existence of disparity acting against young male Aboriginal offenders within Queensland's juvenile justice system? Two separate but complementary studies were designed to address this issue: the pathways study and the trajectory study. The pathways study utilised 20,648 finalised appearances for Aboriginal and non-Aboriginal young male offenders in Queensland's juvenile courts, during 1999 to 2003. Three custodial decision-making stages (police custody, remand, and sentencing) were examined and two questions initially posed: Does the custodial decision made at one stage of the juvenile justice system impact on a subsequent custodial decision-making stage? Does criminal history, Aboriginal status, offence type or an interaction of these factors significantly influence the probability of (i) detention in police custody (ii) court remand (iii) a custodial order at sentencing? It was recognised that other legally relevant factors such as family structure and stability, school attendance and community ties might also influence these custodial decisions; however, for the purposes of this research it was not possible to include these variables in the analyses. Controlling for criminal history, findings from logistic regression analyses indicated that being detained in police custody increased the odds of being remanded into custody, and being remanded into custody increased the odds of a custodial order. Whilst Aboriginal status was not a consistent factor at any of these three custodial stages, there was clear evidence of disparity acting against the young male Aboriginal offender, particularly early in their criminal career. To examine these disparities further, these three custodial stages were modeled as eight processing pathways: four of which resulted in a custodial order and four in a noncustodial order. Using this processing model, a third question was posed: Do young Aboriginal and non-Aboriginal male offenders have different custodial pathways? Findings indicated that Aboriginal and non-Aboriginal young male offenders were in general, processed along similar custodial pathways that did not include police custody, remand or a custodial order. However, young male Aboriginal offenders were less likely than equivalent non-Aboriginal offenders to have been processed along this pathway and more likely to be processed along the pathways that included remand. It was found that young offenders with a chronic criminal history were more likely to be processed along these remand pathways, and Aboriginal offenders were more likely to have a chronic criminal history than non-Aboriginal offenders; there was clear evidence of disparity at specific custodial stages of the system. In addition, as young male Aboriginal offenders progressed deeper into the system there was evidence of cumulative disparity, particularly along the remand pathways, meaning that the probability of being in custody increases as the offender progresses from one custodial stage to the next custodial stage. Given the existence of disparity, acting within the juvenile justice system and against the young male Aboriginal offender, it was important to formulate viable solutions to such disparity, particularly in light of the Queensland government's commitment to reduce Aboriginal offenders in custody by 50%. Deterministic analyses and computer simulations were used to test the viability of various reduction scenarios suggested by the data. Despite in some instances, different results from the deterministic analyses and the computer simulations, overall findings indicated that to reduce custodial disparity whether at the remand stage, the custodial order stage, or in custody overall (the summation of police custody, remand and custodial orders) that reducing remand, regardless of whether the young offender had been in police custody or not, was the best overall solution. The trajectory study built on the findings of the pathways study, which had identified criminal history as an important factor in the processing pathways of young male Aboriginal and non-Aboriginal offenders. Using the semi-parametric group based method, the criminal trajectories of Aboriginal and non-Aboriginal young male offenders in Queensland were modeled. These trajectories were based on the finalised appearances of two cohorts of young offenders aged 10 to 17 years of age: those born in 1983 and 1984 and who had turned 18 years of age in 2001 and 2002 respectively. All of these young male offenders had entered the adult system when they turned 17 years of age, and this data provided their complete juvenile history in Queensland. Prior analyses using this method had not considered Aboriginal status or race as a determining factor in these trajectory models, nor had these models been validated either internally or externally in published works. For this research, internal validity was considered as the correct classification of offenders into trajectory groups, and external validity as the ability to reproduce these results in a second or subsequent sample of juvenile offenders. Two questions were therefore posed in the trajectory study: Do young Aboriginal and non-Aboriginal male offenders have different criminal trajectories? Can the predicted model(s) be validated, both internally and externally? Initial findings indicated that the optimal trajectory models selected on prior knowledge and the Bayesian Information Criterion did not validate internally. This finding brought into question the trajectory results of other published works that had not internally validated their models. The models finally selected as optimal indicated that Aboriginal and non-Aboriginal young male offenders did not have a common criminal trajectory and could not be modeled as one population. Both Aboriginal and non-Aboriginal young offenders were modeled by a low-frequency group, a late-onset group, and a chronic trajectory group. However, the young male Aboriginal offender was more likely than the non-Aboriginal to have been in the chronic or the late onset group and less likely to have been in the lowfrequency group. External validation utilised an innovative but simple method that utilised all of the data in the modeling process along with a sample of this same data for validation purposes: 10% of the criminal profiles, which were characteristic of the trajectory groups, and a further 5% of randomly selected profiles were chosen for validation. All of the characteristic profiles, but only 50% of the randomly selected profiles were validated, and of the latter, the majority not validated was in the late-onset group. In total, 79.2% of the Aboriginal trajectories and 85.6% of the non-Aboriginal criminal trajectories were correctly externally validated. Overall, there are two important implications from this research for government. First, even though young male Aboriginal offenders are more likely to have a chronic criminal history than non-Aboriginal offenders, this factor does not account for all of the observed disparity acting against the young Aboriginal offender within Queensland's juvenile justice system: there is evidence of disparity within the system that is unaccounted for by either offence type or criminal history. Second, given this chronic criminal history, systemic solutions to systemic disparity whilst viable, will not ultimately resolve this problem: they are only short-term measures at the end of a very long justice system. Longer-term solutions are needed to address external factors such as socio-economic disadvantage, unemployment and substance abuse in Aboriginal communities, before these young people are exposed to the system. Continuing to concentrate on systemic solutions, to such an entrenched problem as Aboriginal overrepresentation and disparity, is a misdirection of system resources and is inconsistent with social justice.

[Truncated abstract] Hypothesis: There is deficiency in the evidence base and scientific underpinning of existing diagnostic imaging pathways (DIP) for diagnostic endpoints. Objective: a) To carry out systematic review of literature in relation to use of diagnostic imaging tests for diagnosis and investigation of 78 common clinical problems, b) To identify deficiencies and controversies in existing diagnostic imaging pathways, and to develop a new set of consensus based pathways for diagnostic imaging (DIP) supported by evidence as an education and decision support tool for hospital based doctors and general practitioners, c) To carry out a trial dissemination, implementation and evaluation of DIP. Methods: 78 common clinical presentations were chosen for development of DIP. For general practitioners, clinical topics were selected based on the following criteria: common clinical problem, complex in regards to options available for imaging, subject to inappropriate imaging resulting in unnecessary expenditure and /or radiation exposure, and new options for imaging of which general practitioners may not be aware. For hospital based junior doctors and medical students, additional criteria included: acute presentation when immediate access to expert radiological opinion may be lacking and clinical problem for which there is a need for education. Systematic review of the literature in relation to each of the 78 topics was carried out using Ovid, Pubmed and Cochrane Database of Systematic Reviews. ... The electronic environment and the method of delivery provided a satisfactory medium for dissemination. Getting DIP implemented required vigorous effort. Knowledge of diagnostic imaging and requesting behaviour tended to become more aligned with DIP following a period of intensive marketing. Conclusions: Systematic review of literature and input and feedback from various clinicians and radiologists led to the development of 78 consensus based Diagnostic Imaging Pathways supported by evidence. These pathways are a valuable decision support tool and are a definite step towards incorporating evidence based medicine in patient management. The clinical and academic content of DIP is of practical use to a wide range of clinicians in hospital and general practice settings. It is source of high level knowledge; a reference tool for the latest available and most effective imaging test for a particular clinical problem. In addition, it is an educational tool for medical students, junior doctors, medical imaging technologists, and allied health care personnel.

A qualitative descriptive approach was undertaken to research what was available within the areas of advice and guidance for potential principals who wish to achieve the position of principal at secondary schools in Aotearoa New Zealand. The literature review for this study uncovered very little in the way of New Zealand-based professional advice and guidance for potential principals, despite there being some leadership development programmes such as the Principal Preparation Programmes for Aspiring Principals (University of Auckland, Centre for Educational Leadership). However, the international literature revealed a greater wealth of data on existing principal preparation programmes, and the phenomenon of leadership. In terms of the methodology, case studies and interviews of six participants were undertaken. Six current principals of provincial North Island secondary schools in New Zealand were interviewed face-to-face. Their stories were audio-taped and transcribed. The interviews were essentially rich narratives of leadership stories and were somewhat akin to individual case studies of the participants' own leadership and principal development. Content and thematic analysis of the data revealed eight aspects of principal development which were distilled to four main themes: historical career pathway; managing the journey; handing over the knowledge; and personal costs to the participants. The findings from this research showed that few principals followed planned career pathways or had access to advice, guidance or formal training for principalship. Participants generally gained principal positions through good luck rather than good management. The increasing complexity of the principal's role, combined with a projected shortage of competent candidates, requires that preparation for principalship needs to be implemented as a well-structured, rigorous programme. A framework for such a programme is proposed.

A fundamental research question in regional economic development, is why some regions are able to diversify into new products and industries, while others continue to face challenges in diversification? This doctorate research explores the different pathways to diversification. It follows the three-stage modular structure of DBA for Cranfield School of Management. This thesis consists of a systematic literature review, a single qualitative case study on UAE, and a research synthesis of published cases on Singapore, Norway and UAE. The linking document provides a summary of the three projects and consolidates findings and contributions into a path creation model that provides new understanding on the pathways to regional diversifications. This research integrates existing theoretical foundations of evolutionary economic geography, institutional economic geography, path dependence, industry relatedness, economic complexity, and path creation into a unified conceptual path creation model. It generates propositions, builds a framework and develops a matrix for path creation that integrate context, actors, factors, mechanisms and outcomes shaping regional diversification. It finds that in the context of path dependence and existing conditions of a region, economic actors undertake strategic measures to influence the institutional capabilities to accumulate knowledge and trigger indigenous creation, anchoring, branching, and clustering diversification mechanisms to create complex varieties of related and unrelated diversification outcomes. The institutional collaboration capabilities are found to be instrumental in accumulating knowledge and determining the relatedness and complexity of diversification outcomes. This research further provides a set of integrated platform strategies to guide policy-makers on setting up the pathways to regional diversification.

This research utilised a range of deterministic and stochastic analyses to establish whether Queensland's juvenile justice system processes Aboriginal and non-Aboriginal young male offenders differently. The impetus for this research stemmed from the continued high rates of Aboriginal over-representation within Australia's criminal justice system, despite diversionary measures to reduce such over-representation, and a commitment by the Queensland Government to reduce by 50% the number of Aboriginal peoples in custody by the year 2011. There are two competing hypotheses concerning the cause of this over-representation, (i) external factors such as socioeconomic disadvantage, unemployment or substance abuse, or (ii) systemic disparity within the criminal justice system. For this research, disparity is defined as the unacceptable use of discrimination; discrimination can be appropriate if it is used to define or enhance a situation, such as discriminating between offenders who are recidivists and those who are first time offenders. The inappropriate use of discrimination occurs for example, when harsher sentences are issued to offenders based on non-legal factors such as race or gender. Systemic disparity is therefore used here to represent the inappropriate use of discrimination against an offender by the criminal justice system. The second hypothesis, one of systemic disparity, provided the framework for this research, which posed the following primary question: Is there quantifiable evidence to support the existence of disparity acting against young male Aboriginal offenders within Queensland's juvenile justice system? Two separate but complementary studies were designed to address this issue: the pathways study and the trajectory study. The pathways study utilised 20,648 finalised appearances for Aboriginal and non-Aboriginal young male offenders in Queensland's juvenile courts, during 1999 to 2003. Three custodial decision-making stages (police custody, remand, and sentencing) were examined and two questions initially posed: Does the custodial decision made at one stage of the juvenile justice system impact on a subsequent custodial decision-making stage? Does criminal history, Aboriginal status, offence type or an interaction of these factors significantly influence the probability of (i) detention in police custody (ii) court remand (iii) a custodial order at sentencing? It was recognised that other legally relevant factors such as family structure and stability, school attendance and community ties might also influence these custodial decisions; however, for the purposes of this research it was not possible to include these variables in the analyses. Controlling for criminal history, findings from logistic regression analyses indicated that being detained in police custody increased the odds of being remanded into custody, and being remanded into custody increased the odds of a custodial order. Whilst Aboriginal status was not a consistent factor at any of these three custodial stages, there was clear evidence of disparity acting against the young male Aboriginal offender, particularly early in their criminal career. To examine these disparities further, these three custodial stages were modeled as eight processing pathways: four of which resulted in a custodial order and four in a noncustodial order. Using this processing model, a third question was posed: Do young Aboriginal and non-Aboriginal male offenders have different custodial pathways? Findings indicated that Aboriginal and non-Aboriginal young male offenders were in general, processed along similar custodial pathways that did not include police custody, remand or a custodial order. However, young male Aboriginal offenders were less likely than equivalent non-Aboriginal offenders to have been processed along this pathway and more likely to be processed along the pathways that included remand. It was found that young offenders with a chronic criminal history were more likely to be processed along these remand pathways, and Aboriginal offenders were more likely to have a chronic criminal history than non-Aboriginal offenders; there was clear evidence of disparity at specific custodial stages of the system. In addition, as young male Aboriginal offenders progressed deeper into the system there was evidence of cumulative disparity, particularly along the remand pathways, meaning that the probability of being in custody increases as the offender progresses from one custodial stage to the next custodial stage. Given the existence of disparity, acting within the juvenile justice system and against the young male Aboriginal offender, it was important to formulate viable solutions to such disparity, particularly in light of the Queensland government's commitment to reduce Aboriginal offenders in custody by 50%. Deterministic analyses and computer simulations were used to test the viability of various reduction scenarios suggested by the data. Despite in some instances, different results from the deterministic analyses and the computer simulations, overall findings indicated that to reduce custodial disparity whether at the remand stage, the custodial order stage, or in custody overall (the summation of police custody, remand and custodial orders) that reducing remand, regardless of whether the young offender had been in police custody or not, was the best overall solution. The trajectory study built on the findings of the pathways study, which had identified criminal history as an important factor in the processing pathways of young male Aboriginal and non-Aboriginal offenders. Using the semi-parametric group based method, the criminal trajectories of Aboriginal and non-Aboriginal young male offenders in Queensland were modeled. These trajectories were based on the finalised appearances of two cohorts of young offenders aged 10 to 17 years of age: those born in 1983 and 1984 and who had turned 18 years of age in 2001 and 2002 respectively. All of these young male offenders had entered the adult system when they turned 17 years of age, and this data provided their complete juvenile history in Queensland. Prior analyses using this method had not considered Aboriginal status or race as a determining factor in these trajectory models, nor had these models been validated either internally or externally in published works. For this research, internal validity was considered as the correct classification of offenders into trajectory groups, and external validity as the ability to reproduce these results in a second or subsequent sample of juvenile offenders. Two questions were therefore posed in the trajectory study: Do young Aboriginal and non-Aboriginal male offenders have different criminal trajectories? Can the predicted model(s) be validated, both internally and externally? Initial findings indicated that the optimal trajectory models selected on prior knowledge and the Bayesian Information Criterion did not validate internally. This finding brought into question the trajectory results of other published works that had not internally validated their models. The models finally selected as optimal indicated that Aboriginal and non-Aboriginal young male offenders did not have a common criminal trajectory and could not be modeled as one population. Both Aboriginal and non-Aboriginal young offenders were modeled by a low-frequency group, a late-onset group, and a chronic trajectory group. However, the young male Aboriginal offender was more likely than the non-Aboriginal to have been in the chronic or the late onset group and less likely to have been in the lowfrequency group. External validation utilised an innovative but simple method that utilised all of the data in the modeling process along with a sample of this same data for validation purposes: 10% of the criminal profiles, which were characteristic of the trajectory groups, and a further 5% of randomly selected profiles were chosen for validation. All of the characteristic profiles, but only 50% of the randomly selected profiles were validated, and of the latter, the majority not validated was in the late-onset group. In total, 79.2% of the Aboriginal trajectories and 85.6% of the non-Aboriginal criminal trajectories were correctly externally validated. Overall, there are two important implications from this research for government. First, even though young male Aboriginal offenders are more likely to have a chronic criminal history than non-Aboriginal offenders, this factor does not account for all of the observed disparity acting against the young Aboriginal offender within Queensland's juvenile justice system: there is evidence of disparity within the system that is unaccounted for by either offence type or criminal history. Second, given this chronic criminal history, systemic solutions to systemic disparity whilst viable, will not ultimately resolve this problem: they are only short-term measures at the end of a very long justice system. Longer-term solutions are needed to address external factors such as socio-economic disadvantage, unemployment and substance abuse in Aboriginal communities, before these young people are exposed to the system. Continuing to concentrate on systemic solutions, to such an entrenched problem as Aboriginal overrepresentation and disparity, is a misdirection of system resources and is inconsistent with social justice.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Criminology and Criminal Justice
Full Text

Oxygen and nitric oxide reductases are enzymes found in aerobic and anaerobic respiration, respectively. Both enzyme groups belong to the superfamily of Heme-Copper Oxidases, which is further divided into several subgroups: oxygen-reducing enzymes into A-, B- and C-type and nitric oxide reductases into qNORs and cNORs. Oxygen reducing enzymes use the energy released from oxygen reduction to take up electrons and protons from different sides of the membrane. Additionally, protons are pumped. These processes produce a membrane potential, which is used by the ATP-synthase to produce ATP, the universal energy currency of the cell. Nitric oxide reductases are not known to conserve the energy from nitric oxide reduction, although the reaction is highly exergonic. Here, the detailed mechanism of a B-type oxidase is studied with special interest in an element involved in proton pumping (proton loading site, PLS). The study supports the hypothesis that the PLS is protonated in one and deprotonated in the consecutive step of the oxidative catalytic cycle, and that a proton is pumped during the final oxidation phase. It further strengthens the previous suggestion that the PLS is a cluster instead of a single residue or heme propionate. Additionally, it is proposed that the residue Asp372, which is in vicinity of the heme a3 propionates previously suggested as PLS, is part of this cluster. In another study, we show that the Glu15II at the entry of the proton pathway in the B-type oxidase is the only crucial residue for proton uptake, while Tyr248 is or is close to the internal proton donor responsible for coupling proton pumping to oxygen reduction. The thesis also includes studies on the mechanism and electrogenicity of qNOR. We show that there is a difference in the proton-uptake reaction between qNOR and the non-electrogenic homolog cNOR, hinting at a different reaction mechanism. Further, studies on a qNOR from a different host showed that qNOR is indeed electrogenic. This surprising result opens up new discussions on the evolution of oxygen and nitric oxide reductases, and about how energy conservation can be achieved.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

The rapid convergence of technologies of communication into a multimedia environment taking place over the last decade has created a new interest in the possibilities offered by videoconferencing systems. We are thus beginning to see the expansion of the potential for various levels of human interaction mediated by video in both business and educational domains. Through the support of the technologically mediated environment, people now have the capability to travel across time and space, meeting with other individuals, seemingly as if face-to-face. The purpose of this thesis is to explore more fully some of the issues of the new communication technologies (differences between face-to-face and mediated communication, changes to our conceptions of time and space, and problems of privacy and surveillance) and specifically how they apply to various videoconferencing scenarios as well as to a more detailed case study of a teleteaching experiment conducted recently at a French research institute.

Energy metabolism plays a vital role in normal physiology, adaptive responses and host defense mechanisms. Research throughout the last decade has shown evidence that immune pathways communicate with metabolic pathways to alter the metabolic status in response to physiological or pathological signals. In this thesis, I will explore how immunomodulatory molecules affect metabolic homeostasis and conversely, how metabolic sensing pathways modulate immune responses. The first part my work utilizes an immunomodulatory sugar motif to determine mechanisms by which immune cells influence metabolism. Specifically, I show in chapter 2 that lacto-N-fucopentaose III (LNFPIII), a motif used by pathogens to attenuate inflammation, is capable of improving systemic insulin sensitivity by increasing Il-10 production in macrophages and dendritic cells and subsequently improving white adipose tissue insulin sensitivity. Chapter 3 will address the observation that this same glycan is capable of directly activating Fxra in hepatocytes. This direct effect manifests as a reduction in high-fat-diet-induced hepatic triglyceride accumulation and improvement in liver function. Lastly, in chapter 4, I will discuss the role of metabolic regulators in the macrophage and how this affects the ability of the macrophage to kill bacteria. Specifically, I will show that lipid sensing nuclear receptors, such as Ppard and Pparg, are critical regulators of phagosomal function and bacterial killing. Macrophage-specific deletion of these receptors prevents efficient killing of Streptococcus pneumoniae, the causative bacterium in many cases of respiratory pneumonia. Ligand activation improves survival, suggesting a potential therapeutic role for Ppar activation during infection. Taken together, all the data suggest a critical role for the evolutionary interaction between metabolic and immune pathways. These interactions may be important when developing new therapeutics for complex metabolic and immunological dysfunctions.

The conceptual foundation for my creative thesis work is based in research into the development of science, particularly the field of cosmology, and its related visual vocabulary. Three interrelated projects encompass my interests in unique artists' books and variable editions, research based projects, codified presentation of data, and universal interconnectedness, or oneness in all things, that was at the heart of medieval cosmology and is embraced by some 21st century subcultures. The thematic timeline of the artwork spans developments in the Early Middle Ages related to astronomy and cosmology and through 20th century guidebooks and NASA's social media accounts. The resulting artwork includes an artist's book, sculptural bookwork, monoprints, and an edition of broadsides.

Includes abstract.
Includes bibliographical references.
Due to high incidence rates and the development of new drug-resistant or multidrug-resistant strains of TB, the development of new medicines and treatments for tuberculosis is a necessity. In order to develop these drugs, Mycobacterium tuberculosis (Mtb) needs to be studied more completely; this study performs a characterisation of the metabolome of Mtb and comparison across the phylogenetic profile to identify notable pathways.

In the present study, we designed a new chemical template that contains an oxindole moiety as potential dual-pathway inhibitors of the Raf/MEK/ERK and PI3K/Akt signaling pathways. The design hypothesis is to evaluate whether the oxindole ring system will approximately orient functional groups in a similar manner to the thiazolidinedione moiety, and thus maintain biological activity as dual-pathway inhibitors of the Raf/MEK/ERK and PI3K/Akt signaling pathways. Furthermore, the oxindole ring will provide the flexibility to allow the introduction of various substituents on the oxindole moiety, thereby facilitating comprehensive SAR studies to further explore the biological activity.

AbstractBrand love has become an increasingly interesting area of research for academics and marketing practitioners alike, as it has shown to drive consumer behaviours such as brand loyalty, positive word-of-mouth and negative information resistance (Batra et al., 2012). However, the focus has primarily been on brand love as a concept and how it drives consumer behaviour from a company perspective, and to a lesser extent on the antecedent pathways that lead to it from a consumer perspective. Based on extant research concerning brand love and its antecedents, this study tries to shed more light on the pathways that lead to brand love out of a consumer perspective. This study builds on extant research in brand love by connecting a brand love prototype model (ibid.), with anthropomorphism as an additional antecedent (Rauschnabel & Ahuvia, 2014), and attempts to extend earlier findings regarding the antecedents of brand love by describing how the antecedents form a pathway to brand love as seen out of a consumer’s point of view. The research was carried out by the use of a deductive, qualitative approach and thematical analysis. The data collection was done through the use of unstructured interviews. This study finds that the pathways to brand love can vary and be triggered from different angles, but that the key factors to brand love are anthropomorphism of the brand and integration of the brand into the self. This research is limited by the fact that the pathways are described through the use of a thematical analysis and that the respondents were selected as a result of a convenience selection. It would therefore be prudent to test the findings with a quantitative method and also to extend the number of respondents. This study is the first to qualitatively investigate the pathways between the antecedents of brand love out of a consumer perspective and will contribute to brand love literature by providing new insight into the antecedent pathways of brand love.

To determine parameter values for models of reactions in the human body, like the glycolysis, good methods of parameter estimation are needed. Those models are often non-linear and estimation of the parameters can be very time consuming if it is possible at all. The goal of this work is to test different methods to improve the calculation speed of the parameter estimation of an example system. If the parameter estimation speed for the example system can be improved it is likely that the method could also be useful for systems similar to the example system.

One approach to improve the calculation speed is to construct a new cost function whose evaluation does not require any simulation of the system. Simulation free parameter estimation can be much quicker than using simulations to evaluate the cost function since the cost function is evaluated many times. Also a modication of the simulated annealing optimization method has been implemented and tested.

It turns out that some of the methods significantly reduced the time needed for the parameter estimations. However the quick methods have disadvantages in the form of reduced robustness. The most successful method was using a spline approximation together with a separation of the model into several submodels, and repeated use of the simulated annealing optimization algorithm to estimate the parameters.

The regulation of microvascular survival impacts both developmental remodelling of the vasculature, and various pathologies. The aim of this thesis was to examine the role of a recently identified A20 binding inhibitor of NF-kB, a zinc finger protein termed ABIN-2 in endothelial protection. More specifically, looking at its effects on inflammation and apoptosis in endothelia both at the cellular level and in vivo. The involvement of ABIN-2 in the Tie2 receptor pathway was also examined. Tie2 is an endothelial receptor essential for blood vessel formation and promotes endothelial survival. A transfection protocol was established allowing expression ABIN-2 in up to 90% of endothelial cells. ABIN-2 was shown to reduce apoptosis in endothelial cells as well as improve cell survival following growth factor deprivation. This effect was inhibited by Wortmannin and LY294002 which are known inhibitors of phatidylinositol-3 kinase. Expression of the truncated form of ABIN-2 lacking the carboxy terminal of ABIN-2 did not protect cells from apoptosis. In addition, expression of the truncated form prevented cell rescue by angiopoeitin-1 from apoptosis. The chick chorioallantoic membrane was used as an in vivo model for testing the role of ABIN-2 in vessel inflammation. It was possible to use this model to transfect plasmids into live microvessels using electroporation resulting in high yield expression of target protein. This model was adapted to look at microvessel inflammation and apoptosis. Expression of ABIN-2 in microvessels reduced leukocyte rolling following tumour necrosis factor-a and lipopolysaccharide induced inflammation. The truncated form of ABIN-2 lacking the carboxy terminal did not reduce microvessel inflammation. The NF-kB inhibitor PTDC was found to suppress leukocyte rolling. ABIN-2 expression also appeared to give limited protection against apoptosis in vivo.

Thesis (Ph.D.)--University of Melbourne, The National Vision Research Institute of Australia and Dept. of Optometry & Vision Sciences, 2007.
Typescript. Includes bibliographical references (leaves 95-111).

Rapid advancements in experimental techniques have benefited molecular biology in many ways. The experiments once considered impossible due to the lack of resources can now be performed with relative ease in an acceptable time-span; monitoring simultaneous expressions of thousands of genes at a given time point is one of them. Microarray technology is the most popular method in biological sciences to observe the simultaneous expression levels of a large number of genes. The large amount of data produced by a microarray experiment requires considerable computational analysis before some biologically meaningful hypothesis can be drawn. In contrast to a single time-point microarray experiment, the temporal microarray experiments enable us to understand the dynamics of the underlying system. Such information, if properly utilized, can provide vital clues about the structure and functioning of the system under study. This dissertation introduces some new computational techniques to process temporal microarray data. We focus on three broad stages of microarray data analysis - normalization, clustering and inference of gene-regulatory networks. We explain our methods using various synthesized datasets and a real biological dataset, produced in-house, to monitor the leaf senescence process in Arabidopsis thaliana.

Noxious stimuli have a profound influence on motor behaviour, but there is a paucity of information regarding how somatosensory information is transformed into a motor output. The cerebellum is the largest sensorimotor control structure within the brain and previous electrophysiological studies have demonstrated that climbing fibres, one of its major sources of afferent input, are activated in response to a noxious pinch stimulus. This thesis investigates the anatomical pathways by which nociceptive information may reach the cerebellum, with a particular focus upon the olivo-cerebellar system, the sole source of climbing fibres.

The brown planthopper, Nilaparvata lugens, is a pest of rice in tropical regions. Its direct feeding results in loss in yield and plant death ("hopper bum"). Several compounds that stimulate insect attraction have been detected in rice plants colonised by N. lugens, including 1,2-dimethoxybenzene or veratrole. Electro-physiological studies and highresolution gas chromatography have identified veratrole as an attractant of N. lugens. Veratrole is a product of salicylic acid, a derivative of the phenyl propanoid pathway. Salicylic acid is decarboxylated to catechol, a step which is encoded by salicylate hydroxylase. Catechol is subsequently methylated to veratrole, which is released as a volatile compound from rice leaves. Mature scutellum-derived rice calli from (Oryza sativa) cv.Taipei 309 were transformed, using microprojectile bombardment, with pROB5 containing the hpt gene conferring resistance to the antibiotic hygromycin and pSLJ7307 carrying the nahG gene derived from Pseudomonas putida and coding for the enzyme salicylate hydroxylase. Following selection on hygromycin-containing medium, 17 independent transgenic rice plants were regenerated from >3600 bombarded calli, with a transformation frequency of 0.47%. Transgenic plants were confirmed by RT-PCR. Plant lines were classified as high expressors (10 lines) and low expressors (7 lines) depending on salicylate hydroxylase production. All transgenic lines exhibited higher enzyme activity than wild-type plants. Transgenic plants produced had altered metabolism for antioxidant enzymes such as catalase, ascorbate peroxidase and superoxide dismutase and reactive oxygen species such as hydrogen peroxide. Plants unable to accumulate salicylic acid exhibited delayed transcription of pathogenesis related genes and may therefore be compromised in their ability to respond to pathogen attack and mechanical wounding. Enhanced veratrole production was corroborated using gas chromatography of volatiles released from transgenic undamaged and mechanically damaged plants. Bioassays indicated that N. lugens were more attracted to high expressing plants than to wild-type plants, making more visits to areas containing transgenic rice leaves than areas containing non-transformed leaves and spending longer in these areas. Manipulating the production of veratrole by enhancing salicylate hydroxylase activity has therefore modified attraction of the N. lugens for high expressing nahG positive rice plants.

The primary subject of this thesis is the study of warm dense hydrogen by means of pulsed laser heating in the pressure region 1 to 2 Mbar and temperatures above the melting line, where a liquid-liquid phase transition from the insulating molecular fluid to a conducting atomic hydrogen fluid, so called plasma phase transition (PPT), was predicted to take place. The first evidence of the PPT under static compression is reported. The observations are in agreement with the negative slope phase line predicted by ab initio methods.
Physics

PONTIFÍCIA UNIVERSIDADE CATÓLICA DO RIO DE JANEIRO
COORDENAÇÃO DE APERFEIÇOAMENTO DO PESSOAL DE ENSINO SUPERIOR
A presente pesquisa tem como tema o processo de ensino e aprendizagem de geometria analítica, assunto no qual os alunos do ensino médio têm apresentado dificuldades. Por isto se faz necessário que o professor utilize um maior número de ferramentas pedagógicas, explorando os caminhos algébrico e geométrico para resolução de problemas. O objetivo deste estudo é propor caminhos para o ensino da geometria analítica tendo como base três eixos norteadores: A história das geometrias, a proposição de problemas matemáticos que podem ser resolvidos tanto pela geometria plana como pela geometria analítica e o uso da ferramenta tecnológica através do software Geogebra. Utilizamos neste trabalho materiais didáticos disponibilizados em escolas públicas estaduais do Estado do Rio de Janeiro, material voltado para a formação do professor de matemática e livros sobre a história da matemática.
The topic of this research is the process of teaching and learning analytical geometry, aThe topic of this research is the process of teaching and learning analytical geometry, a theme in which the students from high school have great difficulties. It is necessary that the teacher use a greater number of educational tools, exploring the algebraic and geometric aspects for problem solving. The aim of this study is to propose new methods for teaching analytical geometry based on three guiding principles: The history of geometry, the proposition of mathematical problems that can be solved either by analytical geometry or by plane geometry and the use of a technological tool, the software Geogebra. In this work, we use teaching materials available in public schools of the state of Rio de Janeiro, material focused in the training of mathematical teachers and books of history of mathematics.

Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2009.
Cataloged from PDF version of thesis.
Includes bibliographical references.
In title on title page, the word "Mitochondrial" is spelled "Mitochondial."
Mitochondria are cellular compartments that perform essential roles in energy metabolism, ion homeostasis, and apoptosis. Mitochondrial dysfunction causes disease in 1 in 5,000 live births and also has been associated with aging, neurodegeneration, cancer, and diabetes. To systematically explore the function of mitochondria in health and in disease, it is necessary to identify all of the proteins resident in this organelle and to understand how they integrate into pathways. However, traditional molecular and biochemistry methods have identified only half of the estimated 1200 mitochondrial proteins, including the 13 encoded by the tiny mitochondrial genome. Now, newly available genomic technologies make it possible to identify the remainder and explore their roles in cellular pathways and disease. Toward this goal, we performed mass spectrometry, GFP tagging, and machine learning on multiple genomic datasets to create a mitochondrial compendium of 1098 genes and their protein expression across 14 mouse tissues. We linked poorly characterized proteins in this inventory to known mitochondrial pathways by virtue of shared evolutionary history. We additionally used our matched mRNA and protein measurements to demonstrate a widespread role of upstream open reading frames (uORFs) in blunting translation of mitochondrial and other cellular proteins. Next we used the mitochondrial protein inventory to identify genes underlying inherited diseases of mitochondrial dysfunction. In collaboration with clinicians, we identified causal mutations in five genes underlying diseases including hepatocerebral mtDNA depletion syndrome, autosomal dominant mitochondrial myopathy, and several forms of inherited complex I deficiency. These discoveries have enabled the development of diagnostic tests now widely available. More broadly, the mitochondrial compendium provides a foundation for systematically exploring the organelle's contribution to both basic cellular biology and human disease.
by Sarah E. Calvo.
Ph.D.

This study tests the predictions made by several causal theories proposing different etiologies for childhood-onset and adolescent-onset conduct problems. It investigates a variety of causal factors proven to be important for the development of antisocial behaviors, specifically neuropsychological/cognitive deficits, temperamental vulnerabilities, dysfunctional parenting, deviant peers, and rebelliousness. Current theories generally agree that the early onset pathway is distinguished by interactions between a child with a difficult temperament and dysfunctional parent-child interactions. However, theories differ as to whether they emphasize the temperament and neurocognitive deficits of the child, or the parenting behaviors. In the adolescent onset pathway, theories typically focus on the importance of affiliation with deviant peers but differ as to whether this is attributed to a personality characterized by the rejection of traditional values and rebelliousness as leading to this association or failures in parenting practices. Seventy-eight pre-adjudicated adolescent (ranging in age from 11 to 18) boys housed in two short-term detention facilities and one outpatient program for boys at risk for involvement in the juvenile justice system in southeastern Louisiana participated in the current study. The sample was ethnically diverse (56% African-American) and largely came from facilities serving either a large urban or a largely suburban and rural region of the state. The sample was divided into two groups based on the youngest age of a self-reported delinquent act or parent-reported severe conduct problem. The childhoodonset group (n =47) displayed at least one serious antisocial behavior prior to age 12, whereas the adolescent-onset group (n =31) did not. As predicted, the childhood-onset group showed greater levels of dysfunctional parenting and CU traits. Contrary to predictions, however, this group also showed the strongest affiliation with deviant peers. The only variable strongly associated with the adolescent onset group was lower scores on a measure of traditionalism which indicates less endorsement of traditional values and status hierarchies. The implications of these results for understanding different causal trajectories to antisocial behavior and for designing better prevention and treatment programs for antisocial youth are discussed.

The aim of this doctoral thesis is to increase the understanding of the causes of homelessness in later life, by identifying how antecedents, states and events interact and both trigger and contribute to homelessness, and the processes and pathways involved in the transition to homelessness. Using present theories, concepts and empirical evidence as a foundation, the thesis is largely informed by an intensive ethnographic field study which lasted for 15 months and was carried out in London, Sheffield, Leeds and Manchester. It involved 225 respondents over the age of 55 years, the majority of whom were homeless when interviewed. Through depth interviewing and the compilation of partial life histories, it was possible to collect objective information which enabled some quantitative comparisons and statistical analysis, and qualitative data which enabled analyses using detailed case study reports. A descriptive profile of the characteristics of the respondents and their histories of homelessness identifies the distinctive features of this group. Although some had been homeless since early adulthood and were in a state of chronic homelessness, others had experienced homelessness for the first time in old age. Four commonly-reported situations preceding homelessness are identified, and these are examined in depth and provide the core of the qualitative analyses. These are mobile work histories, bereavement, the breakdown of intimate relationships, and mental illness. The thesis demonstrates that the origins of homelessness are complex, and deepseated, they are intricately related to psychological and sociological factors, and that homelessness extends far beyond a lack of housing. By increasing the knowledge of the aetiology of homelessness, the thesis also makes a contribution to the understanding of the problems and needs of older homeless people and is thus informative to welfare policy and practice.

Amorphous silica is one of the most common phases to precipitate from geothermal fluids. It precipitates by self-assembly of monomeric silica (H4SiO4) via heterogeneous and homogeneous nucleation and subsequent growth of nuclei by addition of dissolved silica. The mechanism and the factors controlling the individual steps of silica precipitation have been studied in numerous laboratory experiments over the last decades and are, despite their complexity, well understood. However, due to the higher complexity of natural geothermal fluids (e.g high fluid flow rates, microbial activity or complex fluid chemistries), these findings cannot be directly applied to the study of silica scaling inside geothermal power plants and silica sinters around hot springs. In the first part of this thesis we present the results from the first ever time-resolved study of silica precipitation inside in-use geothermal pipelines. Silica scales formed primarily via heterogeneous nucleation on steel surfaces, resulting in a silica layer rapidly covering these surfaces. This pathway of silica deposition was controlled by surface roughness, total silica concentration and temperature and allowed the deposition of up to 1 g of silica per day and m2. Homogeneous nucleation also occurred and lead to the formation of silica microspheres which were deposited preferentially into depressions and along edges or were aggregated to fan- and ridge-shaped structures growing towards the flow, depending on the fluid flow regime. While the 3D structures could result in more turbulent flow, decreasing the flow rate, the formation of the silica layer could potentially even be beneficial for the operation of a geothermal power plant as it passivates the surface against corrosion. For the second part of this thesis, we studied the interaction of a silica solution with a protein (=lysozyme), during which hybrid composites were formed. By investigating these final products in detail, we determined that, depending on the timing of the silica-lysozyme interactions (during or after silica polymerisation) and the ratio of silica-to-protein, the resulting composites showed different structures and surface properties. This is of interest for biomineralisation as it elucidates how biomolecules interact with dissolved silica and how microorganisms can control this process.

Microbial metabolism can be tailored to meet human specifications, but the degree to which these living systems can be repurposed is still unknown. Artificial biological control strategies are being developed with the goal of enabling the predictable implementation of novel biological functions (e.g., engineered metabolism). This dissertation project contributes genetic tools useful for modulating gene expression levels (extending promoters with UP elements) and isolating transcription and translation of engineered DNA from the endogenous cellular network (expression by orthogonal cellular machinery), which have been demonstrated in Escherichia coli for the production of lycopene, a 40-carbon tetraterpene carotenoid with antioxidant activity and a number of other desirable properties.

Stroke is a common neurological event which often results in motor deficits of the hand and arm. The reticulospinal tract (RST) may partly underlie residual hand and arm movement ability after a stroke but remains poorly characterised. A greater understanding of the RST could inform work to improve motor recovery. Additionally, the development of non-invasive methods of probing the RST in humans should allow comparison of the characteristics of the RST across species. It has been suggested that the RST is involved in mediating muscle responses to auditory startle, experimentally known as the StartReact paradigm. However, it was not clear how this pathway was involved. A human experiment presented here suggests that the RST comprises the final pathway in the StartReact effect, confirming it as a technique to probe the RST in humans. Other factors such as habituation and the validity of a marker of the StartReact effect were also further explored; these findings may inform future use of the technique. The output divergence, co-activation patterns, level of fractionation and synergies produced by the RST were further characterised in macaques and baboons; these factors had previously been mostly unexplored. In macaques, two subdivisions of primary motor cortex (M1) were also characterised in order to compare to the RST. These subdivisions are based upon the presence of corticomotoneuronal (CM) cells, and consist of ‘old’ (CM cells absent) and ‘new’ (CM cells present) M1. Stimulation of new M1 produced a higher level of fractionation of movement than stimulation of old M1 and the reticular formation (RF). The RF is suggested to produce slightly more fractionated behaviour than old M1, though the baboon RF responses may be less fractionated than those from macaque old M1. Output divergence of the RF as well as old and new M1 was also explored. However, methodological limitations may have biased the results towards muscles with more excitable motoneurons, or monosynaptic connections. Abstract ii In baboons, threshold stimulation elicited responses in upper limb and axial muscles only, with higher stimulation intensities or trains of pulses required to activate leg muscles. In contrast to long-held beliefs about RST output, distal upper limb muscles were more commonly activated than proximal ones. Previously reported attempts to record natural electromyography (EMG) data from macaques were limited to controlled experimental settings, and hence may have differed from EMG observed during truly natural behaviours. Here, EMG was recorded from 18 muscles in one macaque over several hours of natural, untrained activity in her home cage. Two matrix decomposition algorithms extracted three to four dominant synergies from the data. This number is comparable to that previously described for ‘natural’ behaviour in more controlled conditions, suggesting that it accurately reflects the dominant synergies used across both conditions. Future work should aim to delineate the respective contributions of the RST and corticospinal tract to natural movement and to develop approaches to manipulate RST projections in humans to improve post-stroke motor outcomes.

Formation of cadherin-based adhesive structures at sites of cell-cell contact leads to activation of several signalling pathways inside the cell. In order to examine the molecular mechanisms involved in these pathways, my project focused on two binding partners of cadherin, pi20 catenin and Hakai. pi20 catenin (pi20) is an Armadillo family member, which binds to the cytoplasmic tail of cadherins at sites of cell-cell contact. It has been implicated in regulation of cell- cell adhesion by modulating cadherin trafficking, and also in the regulation of actin dynamics through its association with members of the Rho-GTPase family. The presence of pi20 in the nucleus observed for a number of cell lines indicates an additional nuclear function for this protein. A number of biochemical assays show that pi20 can bind to the transcription factor Glis2. In addition, pi20 expression can induce C-terminal cleavage of the Glis2 protein. This cleavage is increased by the overexpression of Src, suggesting a role for Src-mediated tyrosine phosphorylation of pi20. Since Glis2 has been shown to have a role in neuronal differentiation, an investigation was carried out on the effect of overexpressing Glis2 in the neural tube of developing chick embryos. Interestingly, overexpressing Glis2 inhibited neuronal differentiation. A similar effect was also observed when the cleaved form of Glis2 was co-expressed with pi20. These results suggest a nuclear role for pi20 by modulating the cleavage of the transcription factor Glis2, and potentially altering the transcription of genes in the neuronal differentiation pathway. Hakai is an E3 ubiquitin ligase for the E-cadherin complex, which competes for binding on the E-cadherin intracellular tail with pi20. As Hakai is ubiquitously expressed, it is likely that Hakai has other substrates in the cell. Using the results of a previously completed yeast two-hybrid screen, several potential binding partners for Hakai have been identified.