Data has an undoubtable impact on society. Storing and processing large amounts of available data is currently one of the key success factors for an organization. Nonetheless, we are recently witnessing a change represented by huge and heterogeneous amounts of data. Indeed, 90% of the data in the world has been generated in the last two years. Thus, in order to carry on these data exploitation tasks, organizations must first perform data integration combining data from multiple sources to yield a unified view over them. Yet, the integration of massive and heterogeneous amounts of data requires revisiting the traditional integration assumptions to cope with the new requirements posed by such data-intensive settings.This PhD thesis aims to provide a novel framework for data integration in the context of data-intensive ecosystems, which entails dealing with vast amounts of heterogeneous data, from multiple sources and in their original format. To this end, we advocate for an integration process consisting of sequential activities governed by a semantic layer, implemented via a shared repository of metadata. From an stewardship perspective, this activities are the deployment of a data integration architecture, followed by the population of such shared metadata. From a data consumption perspective, the activities are virtual and materialized data integration, the former an exploratory task and the latter a consolidation one. Following the proposed framework, we focus on providing contributions to each of the four activities.We begin proposing a software reference architecture for semantic-aware data-intensive systems. Such architecture serves as a blueprint to deploy a stack of systems, its core being the metadata repository. Next, we propose a graph-based metadata model as formalism for metadata management. We focus on supporting schema and data source evolution, a predominant factor on the heterogeneous sources at hand. For virtual integration, we propose query rewriting algorithms that rely on the previously proposed metadata model. We additionally consider semantic heterogeneities in the data sources, which the proposed algorithms are capable of automatically resolving. Finally, the thesis focuses on the materialized integration activity, and to this end, proposes a method to select intermediate results to materialize in data-intensive flows. Overall, the results of this thesis serve as contribution to the field of data integration in contemporary data-intensive ecosystems. / Doctorat en Sciences de l'ingénieur et technologie / info:eu-repo/semantics/nonPublished

Modern manufacturing processes are becoming more integrated and relying on measuring performance to better identify ways of improvement. The AEC industry is now moving in this direction through IT-based Design and Construction Integration (ITDCI). ITDCI is a collaborative knowledge-based activity in which each participant continuously and timely contributes and shares his/her knowledge to realize a specific goal, bonded by a unified and cohesive culture with the use of the supportive IT-tools. Executing the project in an ITDCI fashion requires the satisfaction of these conditions. This research developed a formal model that consists of 75 ITDCI mechanisms distributed over the different phases of the facility development process within colleges and universities to enable the knowledge transfer process and achieve the highest level of integration. The level of ITDCI involved in a particular project can be then measured by quantifying the number of ITDCI mechanisms introduced. The research methodology included the following activities: reviewing the related literature, developing and validating a scenario for the facility development process within typical colleges and universities through literature review and interviews, providing a definition for each phase of the process to be executed in an ITDCI fashion and finally identifying actions or mechanisms that have to be activated to obtain the highest level of ITDCI. The model was validated through an online survey that targeted the members of the Society of Colleges and Universities (SCUP) and a case study. WPI's new East Hall residence facility was used as a case study to validate the model. This model is a significant contribution to the construction industry because it acts as a measuring tool to assess the corresponding level of ITDCI in the facility development process. It also helps to develop a common understanding among industry practitioners on what is required to achieve a desired level of ITDCI in their project. This comprehension would guide them to a better recognition of the benefits and consequences of each specific level of IT-based integration on their project outcomes. It will also enable them to execute more accurate cost/benefit analyses and eventually opt for the optimum ITDCI level. For future work, the model could be expanded to include other types of facilities, such as residential, healthcare and commercial facilities to achieve wider adoption within the AEC industry.

The continuing threats from viral infectious diseases highlight the need for new tools to study viral interactions with host cells. Understanding how these viruses interact and respond to their environment can help predict outbreaks, shed insight on the most likely strains to emerge, and determine which viruses have the potential to cause significant human illness. Animal studies provide a wealth of information, but the interpretation of results is confounded by the large number of uncontrolled or unknown variables in complex living systems. In contrast, traditional tissue culture approaches have provided investigators a valuable platform with a high degree of experimental control and flexibility, but the static nature of flask-based cell culture makes it difficult to study viral evolution. Serial passaging introduces un-physiological perturbations to cell and virus populations by drastically reducing the number of species with each passage. Low copy, high fitness viral variants maybe eliminated, while in vivo these variants would be essential in determining the virus’ evolutionary fate. Bridging technologies are urgently needed to mitigate the unrealistic dynamics in static flask-based cultures, and the complexity and expense of in vivo experiments. This thesis details the development of a continuous perfusion platform capable of more closely mimicking in vivo cell-virus dynamics, while surpassing the experimental control and flexibility of standard cell culture. First, a microfluidic flow through acoustic device is optimized to enable efficient and controllable separation of cells and viruses. Repeatable isolation of cell and virus species is demonstrated with both a well-characterized virus, Dengue Virus (DENV), and the novel Golden Gate Virus. Next, a platform is built around this device to enable controllable, automated, continuous cell culture. Beads are used to assess system performance and optimize operation. Subsequently, the platform is used to culture both murine hybridoma (4G2) and human monocyte (THP-1) cell lines for over one month, and demonstrate the ability to manipulate population dynamics. Finally, we use the platform to establish a multispecies culture with THP-1 cells and Sindbis Virus (SINV). This work integrates distinct engineering feats to create a platform capable of enhancing existing cell virus studies and opening the door to a variety of high-impact investigations.

How does the brain convert sensory information into abstract representations that can support complex behaviours? The rodent head-direction (HD) system, whose cell ensembles represent head direction in the horizontal plane, is a striking example of a “cognitive” representation without a direct sensory correlate. It can be updated by sensory inputs fromdifferentmodalities, yet persists in the absence of external input. Together with cells tuned for place, the HD system is thought to be fundamental for navigation and spatial information processing. However, relatively few studies have sought to characterise the connection between the HD system and spatial behaviour directly, and their overall outcome has been inconclusive. In the experiments that make up the first part of this thesis, we approach this issue by isolating the self-motion component of the HDsystem. We developed an (angular) path integration task in which we show that rats rely on their internal sense of direction to return to a trial-unique starting location, allowing us to investigate the contribution of the HD system to this behaviour without influences from uncontrolled external cues. Using this path integration task, we show that rats with bilateral lesions of the lateral mammillary nuclei (LMN) are significantly impaired compared to sham-operated controls. Lesions of the LMN, which contains HDcells, are known to abolish directional firing in downstream HD areas, suggesting that impairment on the task is due to loss of HD activity. We also recorded HD cell activity as rats are performing the path integration task, and found the HD representation to correlate with the rats’ choice of return journey. Thus, we provide both causal and correlational experimental evidence for a critical role of the HD system in path integration. For the second part of this thesis, we implemented a computational model of how the HD system is updated by head movements during path integration, providing a novel explanation for HD cells’ ability to anticipate the animal’s head direction. The model predicts that such anticipatory time intervals (ATIs) should depend on the frequency spectrum of the rats’ head movements. In direct comparison with experimental recording data, we show that the model can explain up to 80% of the experimentally observed variance, where none was explained by previous models. We also consider the effects of propagating the HD signal through multiple layers, identifying several potential sources of anticipation and lag. In summary, this thesis provides behavioural, lesion, and unit-recording evidence that during path integration, rats use a directional signal provided by the head direction system. The neural mechanisms responsible for the generation and maintenance of this signal are explored computationally. The finding that ATIs depend on the statistics of head movements has methodological implications and constrains models of the HD system.

Faculty of Humanities School of Social Sciences 9003886p mashikel@social.wits.ac.za / Using in-depth interviews with key informants, participant observation, an analysis of documentary and archival sources, and a survey of a national sample of 395 former APLA and MK soldiers, this study analyses the process of demobilisation in South Africa between 1994 and 2004. The key questions are: why and how was the demobilisation process conducted and what were its consequences? Demobilisation is a shorthand term for the multi-staged process of converting a soldier to a civilian. This encompasses the release of soldiers from a statutory force or guerrilla group and their reintegration into civilian society. Reintegration is defined as “the process of facilitating the ex-soldiers’ transition to civilian life” (Clark, 1995: 50). In South Africa, demobilisation was envisaged as the last phase in the process of forming the South African National Defence Force (SANDF). The Interim Constitution (Act No. 200 of 1993) made provision for three phases in the formation of the SANDF. First was the integration of various armed forces. This was followed by a process of consolidation, which included the completion of bridging training by former members of the Azanian People’s Liberation Army (APLA) and uMKhonto we Sizwe (MK). The final phase was the reduction of the size of the integrated SANDF, known as rationalisation. However, the concept held the same meaning as demobilisation. The thesis of this study is that the reduction of the size of the SANDF (known as rationalisation) was necessary for two reasons. First was the perceived and real improvement in the national and regional security environment. Second was the perceived economic and development impact of the reduction of defence expenditure. These were informed by the broadened concept of security, which was popularised by non-governmental organisations such as the Military Research Group. However, while rationalisation was postponed and anticipated as the final phase in the process of forming the SANDF, the presence of military “misfits” among former APLA and MK soldiers (the aged, the sick and those who lacked the necessary educational qualifications) led to the introduction of a process of excluding these categories from the process of integration. The process became known as demobilisation and was introduced without adequate planning. It differed from the anticipated rationalisation process which was meant to apply to all members of the integrated SANDF. Various factors pointed to the lack of adequate planning. First, demobilisation was introduced before the finalisation of the relevant legislation, and consequently the process was halted in 1995. Second, the demobilisation of former APLA and MK soldiers was not accompanied by effective reintegration programmes. The reintegration programme that was assembled consisted of a once-off demobilisation gratuity, a voluntary two-week counselling programme and an option to join the Service Corps for an eighteen-month vocational training programme. Third, while the Service Corps was part of the reintegration programme, it was not operational when demobilisation began. When it became operational, it was ineffective as an institution to provide for the re-skilling of demobilised former APLA and MK soldiers. The lack of adequate planning for the demobilisation and reintegration of former APLA and MK soldiers has hindered their full social and economic reintegration into civilian society. Following an analysis of the socio-economic needs of a national sample of 395 former APLA and MK soldiers, it is argued that they have not achieved economic reintegration in the sense of achieving a productive livelihood. Furthermore, it is argued that while respondents have achieved social reintegration some of them continue to see themselves as a distinct group different from other members of the society. Thus, demobilised soldiers may threaten the consolidation of democracy in South Africa and destabilise the region. The proliferation of light weapons throughout the region following the end of armed conflict and the lack of effective disarmament in South Africa increases the potential not only for violent crime but also for serious political and social disruptions.

Caviomorph rodents arrived from Africa as sweepstakes colonists to the South American island continent between 54 and 37 Ma, and subsequently underwent a rapid and widespread adaptive radiation beginning in the middle Eocene. The geographic isolation of South America gave rise to a number of endemic mammal species that filled a wide variety of ecological niches. The resulting size of caviomorph rodents spanned over three orders of magnitude, making them an intriguing lineage to explore the morphological and ecological implications of size evolution. Here, I explore the morphological cranial patterns of extinct and extant caviomorph taxa using 2D landmark-based geometric morphometric analysis. Results are key to advancing our understanding of the effects phylogeny and body size have on cranial morphology of caviomorphs (and more broadly, mammals). This study indicates a deviation from the mammalian modular patterns determined a priori, suggesting unique evolutionary processes at play during the caviomorph adaptive radiation.

Small and medium enterprises (SMEs) are becoming increasingly engaged in B2B interactions. The ubiquitousness of the Internet and the quasi-reliance on electronic document exchanges with larger trading partners have fostered this move. The main technical challenge that this brings to SMEs is that of business document integration: they need to exchange business documents with heterogeneous document formats and also integrate these documents with internal information systems. Often they can not afford using expensive, customized and proprietary solutions for document exchange and storage. Rather they need cost-effective approaches designed based on open standards and backed with easy-to-use information systems. In this dissertation, we investigate the problem of business document integration for SMEs following a design science methodology. We propose a framework and conceptual architecture for a business document integration system (BDIS). By studying existing business document formats, we recommend using the GS1 XML standard format as the intermediate format for business documents in BDIS. The GS1 standards are widely used in supply chains and logistics globally. We present an architecture for BDIS consisting of two layers: one for the design of internal information system based on relational databases, capable of storing XML business documents, and the other enabling the exchange of heterogeneous business documents at runtime. For the design layer, we leverage existing XML schema conversion approaches, and extend them, to propose a customized and novel approach for converting GS1 XML document schemas into relational schemas. For the runtime layer, we propose wrappers as architectural components for the conversion of various electronic documents formats into the GS1 XML format. We demonstrate our approach through a case study involving a GS1 XML business document. We have implemented a prototype BDIS. We have evaluated and compared it with existing research and commercial tools for XML to relational schema conversion. The results show that it generates operational and simpler relational schemas for GS1 XML documents. In conclusion, the proposed framework enables SMEs to engage effectively in electronic business.

Master of Science / Phylogenetic tree reconstruction is a prominent problem in computational biology. Currently, all computational methods have their limitations and work well only for simple problems of small size. No existing method can guarantee that trees constructed for real-world problems are true phylogenetic trees for large and complex problems mainly because the existing computational models are not very biologically realistic. It has become a serious issue for many important real-life applications which often desire accurate results from phylogenetic analysis. Thus, it is very crucial to effectively incorporate multi-disciplinary analyses and synthesize results from various sources when answering real-life questions. In this thesis, a novel web-based phylogeny reconstruction system with a real-time interactive environment, called Qphyl (short for quartet-based phylogenetic analysis) is introduced. The Qphyl system uses a new interactive approach to enable biologists to greatly improve the final results through effectively dynamic interaction with the computation, e.g., to move the computation back and forth to different stages so users can check the intermediate results, compare results from different methods and carry out certain manual refinements using their biological domain-specific knowledge in the decision making on how a tree should be reconstructed. Currently the alpha version of this web-based interactive system has been released and accessible through the URL: http://ww-test.it.usyd.edu.au/sogrid/qphyl/.

Individualisation has become an ambiguous feature of late modern societies. It carries a sense of liberation, yet individuals are compelled to cope with a fragmented and pluralised social order largely by themselves. While the advance of individual freedoms is taken-for-granted, the seemingly unnoticed structural imposition to individually negotiate the boundaries between systemic and normative processes is portrayed as individual freedom and social integration. This thesis explores the ambiguities underpinning individualisation as they emerge from contemporary transformations of capitalism and work. As a result of a hyper-differentiated late modern social order the interface between functional and normative processes shifts from an institutional and organisational level to an individual one. Individualisation can no longer sufficiently be described as 'institutionalised individualism', either in respect to the realisation of a rather consistent normative infrastructure, or as mere individual responses to systemic dependencies. I argue that under the contemporary conditions of marketisation individuals increasingly become the focal point for the negotiation of systemic and normative processes. Substantiated by the theoretical argument of 'corporatisation' and the analysis of interviews with managers from international corporations, I contend that various workorganisational developments transform the subtle pressures to individually negotiate the demarcations between systems and lifeworld into an organising principle. I describe the emerging ambiguities with which individuals struggle, in particular at the workplace, as 'organised individualisation'. Individuals become 'active hubs' not only for the coordination but also for the reproduction of their own systemic dependencies which are organisationally pre-defined. While the responsibility to pseudo-negotiate systemic processes is put on individuals, the lack of opportunities to publicly debate and contest society's normative underpinnings generates deficiencies in social integration.

<p>Syftet med denna uppsats är att beskriva hur den rådande etniska boendesegregationen ser ut i Halmstads innerstad samt att förklara hur denna har uppstått. Som synes är syftet tvådelat där den ena delen är beskrivande och har som mål att beskriva den rådande etniska boendesegregationen i Halmstad. Den andra delen av syftet är av förklarande natur då jag kommer att försöka förklara varför den rådande boendestrukturen ser ut som den gör i Halmstad.</p><p>För att kunna strukturera materialet på ett lämpligt sätt, och för att kunna uppnå den eftersträvade överskådligheten kommer jag främst att genomföra statistiska bearbetningar och analyser av det insamlade materialet. </p><p>Resultaten </p><p>Denna uppsats behandlar den etniska boendesegregationen i Halmstad. Det övergripande syftet är att beskriva hur den rådande etniska boendesegregationen ser ut i Halmstad samt att förklara hur denna har uppstått. </p><p>Med uppsatsens empiri som stöd finns det skäl att hävda att Halmstad har en relativt långt gången etnisk boendesegregation. Det har kunnat påvisas att det förekommit flyttningar mellan Halmstads delområden som skapat en uppdelning på bostadsmarknaden mellan olika etniska grupper, och det är delområdena Andersberg, Linehed, Vallås V. och Nyhem som är de hårdast drabbade. </p><p>Förklaringarna till varför den ovan beskrivna etniska boendesegregationen ser ut som den gör är många, och inom ramen för denna uppsats har med säkerhet inte samtliga bakomliggande variabler till situationen funnits. Utifrån uppsatsens teori och empiriska material har det dock kunnat konstateras att följande förklaringar till finns till varför den etniska boendesegregationen ser ut som den gör i Halmstad:</p><p>Det har uppstått segregationsgenererade flyttningarna till följd av att förhållandena i förskolorna och skolorna på Anderberg, Linehed, Vallås V. och Nyhem skiljer sig betydligt från övriga skolor i Halmstad. Antalet hemspråksberättigade elever är mycket högt och det är troligt att detta har lett till att de svenska hushållen uppfattat att barnens språkutveckling och inlärning skulle bli sämre om de gick kvar i skolorna. Av denna anledning valde de att flytta till områden där det var en lägre andel barn med utländsk bakgrund. Det är viktigt att betona att det inte kan påvisas om situationen i skolorna på Anderberg, Linehed, Vallås V. och Nyhem ger sämre förutsättningar än övriga skolor i Halmstad. Detta är dock inte det viktiga, utan centralt är istället att de svenska hushållen troligtvis upplevde att situationen kunde förvärras för deras barn om de stannade i delområdet. </p><p>De segregationsgenererade flyttningarna har också uppstått till följd av att andelen begångna brott i de etniskt segregerade delområdena är betydligt högre än i övriga delar av Halmstad. Den försämrade tryggheten som detta innebär leder att man väljer att flytta till något annat delområde. </p><p>Det har också uppstått flyttningar mellan delområdena som beror på de institutionella förhållandena på bostadsmarknaden. Bostadspolitiken kring Miljonprogrammet medförde att det upprättades bostadsområden som uppfattats som mindre attraktiva än andra bostadsområden. I Halmstad är dessa bostadsområden främst lokaliserade till de etniskt segregerade delområdena. Samtidigt har andra institutionella förhållanden, så som arbetsmarknadspolitiken och den generella välfärdspolitiken, medfört att det förekommer en stor spridning mellan olika hushåll avseende resurser. I Halmstad har de resurssvagare hushållen därmed blivit mer eller mindre hänvisade till de etniskt segregerade bostadsområdena där de mindre attraktiva bostadsområdena finns, medan de resursstarkare hushållen har haft större valmöjligheter i sitt boende. </p><p>Ovanstående faktorer är de viktigaste till varför den etniska boendesegregationen ser ut som den gör i Halmstad.</p>