Durant la última dècada, la demanda d’emmagatzematge de dades ha anat creixent exponencialment any rere any. Apart de demanar més capacitat d’emmagatzematge, el usuaris actualment també demanen poder accedir a les seves dades des de qualsevol lloc i des de qualsevol dispositiu. Degut a aquests nous requeriments, els usuaris estan actualment movent les seves dades personals (correus electrònics, documents, fotografies, etc.) cap a serveis d’emmagatzematge en línia com ara Gmail, Facebook, Flickr o Dropbox. Malauradament, aquests serveis d’emmagatzematge en línia estan sostinguts per unes grans infraestructures informàtiques que poques empreses poden finançar. Per tal de reduir el costs d’aquestes grans infraestructures informàtiques, ha sorgit una nova onada de serveis d’emmagatzematge en línia que obtenen grans infraestructures d’emmagatzematge a base d’integrar els recursos petits centres de dades, o fins i tot a base d’integrar els recursos d’emmagatzematge del usuaris finals. No obstant això, els recursos que formen aquestes noves infraestructures d’emmagatzematge són molt heterogenis, cosa que planteja un repte per al dissenyadors d’aquests sistemes: Com es poden dissenyar sistemes d’emmagatzematge en línia, fiables i eficients, quan la infraestructura emprada és tan heterogènia? Aquesta tesis presenta un estudi dels principals problemes que sorgeixen quan un vol respondre a aquesta pregunta. A més proporciona diferents eines per tal d’optimitzar el disseny de sistemes d’emmagatzematge distribuïts i heterogenis. Les principals contribucions són: Primer, creem un marc d’anàlisis per estudiar els efectes de la redundància de dades en el cost dels sistemes d’emmagatzematge distribuïts. Donat un esquema de redundància específic, el marc d’anàlisis presentat permet predir el cost mitjà d’emmagatzematge i el cost mitjà de comunicació d’un sistema d’emmagatzematge implementat sobre qualsevol infraestructura informàtica distribuïda. Segon, analitzem els impactes que la redundància de dades té en la disponibilitat de les dades, i en els temps de recuperació. Donada una redundància, i donat un sistema d’emmagatzematge heterogeni, creem un grup d’algorismes per a determinar la disponibilitat de les dades esperada, i els temps de recuperació esperats. Tercer, dissenyem diferents polítiques d’assignació de dades per a diferents sistemes d’emmagatzematge. Diferenciem entre aquells escenaris on la totalitat de la infraestructura està administrada per una sola organització, i els escenaris on diferents parts auto administrades contribueixen els seus recursos. Els objectius de les nostres polítiques d’assignació de dades són: (i) minimitzar la redundància necessària, (ii) garantir la equitat entre totes les parts que participen al sistema, i (iii) incentivar a les parts perquè contribueixin els seus recursos al sistema. / Over the last decade, users’ storage demands have been growing exponentially year over year. Besides demanding more storage capacity and more data reliability, today users also demand the possibility to access their data from any location and from any device. These new needs encourage users to move their personal data (e.g., E-mails, documents, pictures, etc.) to online storage services such as Gmail, Facebook, Flickr or Dropbox. Unfortunately, these online storage services are built upon expensive large datacenters that only a few big enterprises can afford. To reduce the costs of these large datacenters, a new wave of online storage services has recently emerged integrating storage resources from different small datacenters, or even integrating user storage resources into the provider’s storage infrastructure. However, the storage resources that compose these new storage infrastructures are highly heterogeneous, which poses a challenging problem to storage systems designers: How to design reliable and efficient distributed storage systems over heterogeneous storage infrastructures? This thesis provides an analysis of the main problems that arise when one aims to answer this question. Besides that, this thesis provides different tools to optimize the design of heterogeneous distributed storage systems. The contribution of this thesis is threefold: First, we provide a novel framework to analyze the effects that data redundancy has on the storage and communication costs of distributed storage systems. Given a generic redundancy scheme, the presented framework can predict the average storage costs and the average communication costs of a storage system deployed over a specific storage infrastructure. Second, we analyze the impacts that data redundancy has on data availability and retrieval times. For a given redundancy and a heterogeneous storage infrastructure, we provide a set of algorithms that allow to determine the expected data availability and expected retrieval times. Third, we design different data assignment policies for different storage scenarios. We differentiate between scenarios where the entire storage infrastructure is managed by the same organization, and scenarios where different parties contribute their storage resources. The aims of our assignment policies are: (i) to minimize the required redundancy, (ii) to guarantee fairness among all parties, and (iii) to encourage different parties to contribute their local storage resources to the system.

This dissertation investigates the effects of foreign direct investment (FDI) and international trade on firm level decisions and examines the effect of policy changes on aggregate productivity and welfare in open economies. The first two chapters build an open economy model of FDI and trade where heterogeneous firms make simultaneous foreign investment and export decisions. The theoretical model is estimated using Indonesian manufacturing data. The estimated model is then used to perform a variety of counterfactual experiments to assess the positive and normative effects of international barriers to trade and FDI. I find that the impact of FDI on aggregate productivity is at least three times the impact of international trade on aggregate productivity. The third chapter, co-authored with Hiroyuki Kasahara, investigates whether importing intermediate goods improves plant performance. While addressing the issue of simultaneity between productivity shocks and the decision to import intermediates, we estimate the impact of the use of foreign intermediates on plants' productivity using plant-level Chilean manufacturing panel data. We find that by importing foreign intermediates, manufacturing plants can improve productivity. / Thesis (Ph.D, Economics) -- Queen's University, 2008-06-20 10:21:01.069

While much evidence suggests that ecosystem functioning is closely related to biodiversity, present rates of biodiversity loss are high. With the emergence of the metacommunity concept ecologists have become increasingly aware that both local processes (e.g. competition, predation), and regional processes (e.g. dispersal and regional heterogeneity) affect ecological communities at multiple spatial scales. I experimentally investigated the effects of habitat connectivity and regional heterogeneity on biodiversity, community composition, and ecosystem functioning of artificial pond metacommunities of freshwater invertebrates at the local (α), among-community (β), and regional (γ) spatial levels. There was a significant effect of habitat connectivity on mean local richness, but mean local Simpson diversity, mean local functional diversity (FD), and all the three indices of ecosystem functioning investigated (regional abundance, invertebrate biomass, and chlorophyll a concentration) were unaffected by connectivity levels. Regional heterogeneity had no effect on local diversity, but enhanced both among-community richness and among-community Simpson diversity. Conversely, connectivity reduced among-community Simpson diversity. All indices of regional diversity were unaffected by either connectivity or heterogeneity. Despite expectations that there would be strong interactions between the effects of connectivity and heterogeneity on species richness, there were no interactions for any index of biodiversity at any spatial scale. Invertebrate community composition was unaffected by either connectivity or heterogeneity, though there was a significant effect of heterogeneity on its variance. Neither connectivity nor heterogeneity had significant effects on any index of ecosystem functioning, nor among-community coefficients of variation of ecosystem functioning. Connectivity appears to act mainly as a force homogenizing habitat patches in a region, as opposed to having strong effects in and of itself on communities. Conversely, heterogeneity acts largely as a diversifying force, maintaining differences between communities within a region, but, similar to connectivity, it does not have clear effects on communities at the local scale. Despite the different processes expected to act in homogeneous and heterogeneous regions, it does not appear that connectivity and heterogeneity interact strongly. / Thesis (Master, Biology) -- Queen's University, 2008-10-16 09:06:33.103

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Determining the factors responsible for the origin and maintenance of diversity remains a difficult problem in evolutionary biology. There is extensive theoretical work which suggests that environmental heterogeneity plays a major role. This theory argues that diversification is ultimately due to divergent natural selection for alternative resources. In this thesis I investigate adaptation and the evolution of diversity in experimental populations of the asexual bacterium Pseudomonas fluorescens. In all experiments I introduce clonal isolates of Pseudomonas to a novel environment and allow evolution to occur through the substitution of random mutations. Adaptation can then be quantified by comparing evolved genotypes to the ancestor. These experiments show that when Pseudomonas is selected in a complex environment containing several resources, sympatric genotypes adapt to use different resources, leading to the evolution of genetically diverse populations. In environments containing just a single resource, most genotypes adapt to use the same resource and no such diversity is observed. Adaptation in the experimental populations is caused by the fixation of beneficial mutations of intermediate fitness effect. My results highlight the value of microbial model systems for answering evolutionary questions and provide strong evidence for the role of ecological factors in the origin of diversity.

Cancer is a complex and deadly disease that is caused by genetic lesions in somatic cells. Further research in computational methodology for detecting and characterizing somatic mutations is necessary in order to understand the comprehensive systems level model of the roles of those lesions in cancer development. In the first project, I trained a list of supervised machine learning classifiers that classify false positive versus true positive somatic single nucleotide variants (SNVs). I was able to show an improvement of somatic SNV detection on the data set over the reported classifier. In the second project, we developed PhyloSub model that uses a nonparametric Bayesian prior over a set of trees to cluster SNVs, and infer the subclonal phylogenetic structure of tumors with uncertainty from SNV sequencing data. Experiments showed that PhyloSub model could infer the subclonal phylogenetic structure from both single and multiple tumor samples.

Cancer is a complex and deadly disease that is caused by genetic lesions in somatic cells. Further research in computational methodology for detecting and characterizing somatic mutations is necessary in order to understand the comprehensive systems level model of the roles of those lesions in cancer development. In the first project, I trained a list of supervised machine learning classifiers that classify false positive versus true positive somatic single nucleotide variants (SNVs). I was able to show an improvement of somatic SNV detection on the data set over the reported classifier. In the second project, we developed PhyloSub model that uses a nonparametric Bayesian prior over a set of trees to cluster SNVs, and infer the subclonal phylogenetic structure of tumors with uncertainty from SNV sequencing data. Experiments showed that PhyloSub model could infer the subclonal phylogenetic structure from both single and multiple tumor samples.

Abstract Senecio is one of the largest genera in the Asteraceae family with 28 Senecio species in New Zealand and over 1200 species worldwide. Native Senecio in the Canterbury region are typically naturally uncommon and exhibit extreme fluctuations in population size. Contrary to native Senecio, exotic Senecio in the Canterbury region are thriving. Why some exotic species thrive in a novel environment while native species decline has been an area of intense study since the era of Darwin. However, despite extensive study, we are still unsure about the underlying mechanisms of this phenomenon. This thesis looks at several hypotheses that have been proposed to explain differences in success between native and exotic species including four that have been frequently mentioned in the literature: phylogenetics, natural enemy release and biotic resistance, allopolyploidy and habitat modification. In order to determine if phylogenetic relatedness influences the abundance and distribution of Senecio species in Canterbury, DNA phylogenies of New Zealand’s Senecio were constructed using nuclear (ITS, ETS) and plastid (trnL, trnL-F and psbA-trnH) DNA sequences. The resulting cladograms were used to determine the areas of origin of New Zealand’s Senecio lineages, the identity of their closest relatives and lineages and species that are of allopolyploid origin. The data provided by the phylogenetic analyses was to provide context for analyses of ecological data of 86 native and exotic Senecio populations from the Canterbury region. My results indicate that phylogenetic relatedness is a poor predictor of the amount of folivory experienced by Senecio, although some natural enemies of native and exotic Senecio displayed a positive preference for Senecio depending on their clade. The strongest effects on Senecio and the occurrences of their natural enemies came from the surrounding land use which influenced the amount of folivory and the abundances of natural enemies on Senecio. Enemy release and biotic resistance were land use specific within Canterbury and by themselves cannot explain the variance in folivory when applied to a landscape scale. According to my results, the biggest factor influencing Senecio folivory, abundance and distribution in the Canterbury region is change in the surrounding land use.

While the virtues of social capital in democracies are widely recognized, previous studies have repeatedly shown that social capital is in short supply in heterogeneous communities with ethnic minorities. Against the view that levels of social capital are culturally predetermined, I argue that it is possible to generate social capital by carefully formulating political institutions. Drawing from theories of institutional management of ethnic conflict and theories of institutional learning, I construct an integrated theory of social capital which hypothesizes that citizens learn to trust one another based on their experiences with political institutions during an extended period of democratic rule. To test this integrated model of social capital, I use a probit analysis to examine how democratic longevity in different institutional settings (e.g., majoritarian vs. consensus) influences social capital. To overcome the endogeneity problem that exists between social capital and democratic longevity, I adopt an instrumental variables approach, drawing on theories in international relations. My analysis of World Values Survey data yields three main conclusions concerning the institutional arrangements that foster social capital. First, I find that democratic longevity fosters higher levels of trust in countries with consensus institutions containing powersharing arrangements through cabinets, executive-legislative balances, party systems, and electoral systemspresumably because cooperation among different groups enhances social capital. Second, a longer period of democratic rule in highly federal institutions undermines trust, as the devolution of powers through territorial units is thought to fragment the political system and society. Finally, consistent with the theoretical expectations, I find that these two conclusions hold only among ethnic minorities. Among ethnic majorities, the effect of democratic longevity disappears once we purge the endogenous component (i.e., the effect of social capital on democratic longevity), using an instrumental variables approach. Case studies of the Baltic States, the Canadian province of Quebec, and Malaysia corroborated the findings from the statistical analyses. By uncovering a mechanism through which social capital can be generated in multiethnic states, this study makes an important contribution to the literature.