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Phylogenetic models generally assume a homogeneous, time reversible, stationary process. These assumptions are often violated by the real, far more complex, evolutionary process. This thesis is centered on non-homogeneous, lineage-specific, properties of molecular sequences. It consist several related but independent studies. LineageSpecificSeqgen, an extension to the Seq-Gen program, which allows generation of sequences with changes in the proportion of variable sites, is introduced. This program is then used in a simulation study showing that changes in the proportion of variable sites can hinder tree estimation accuracy, and that tree reconstruction under the best-fit model chosen using a relative test can result in a wrong tree. In this case, the less commonly used absolute model-fit was a better predictor of tree estimation accuracy. This study found that increased taxon sampling of lineages that have undergone a change in the proportion of variable sites was critical for accurate tree reconstruction and that, in contrast to some earlier findings, the accuracy of maximum parsimony is adversely affected by such changes. This thesis also addresses the well-known long-branch attraction artifact. A nonparametric bootstrap test to identify changes in the substitution process is introduced, validated, and applied to the case of Microsporidia, a highly reduced intracellular parasite. Microsporidia was first thought to be an early branching eukaryote, but is now believed to be sister to, or included within, fungi. Its apparent basal eukaryote position is considered a result of long-branch attraction due to an elevated evolutionary rate in the microsporidian lineage. This study shows that long-branch estimates and basal positioning of Microsporidia both correlate with increased proportions of radical substitutions in the microsporidian lineage. In simulated data, such increased proportions of radical substitutions leads to erroneous long-branch estimates. These results suggest that the long microsporidian branch is likely to be a result of an increased proportion of radical substitutions on that branch, rather than increased evolutionary rate per se. The focus of the last study is the intriguing case of Mesostigma, a fresh water green alga for which contradicting phylogenetic relationships were inferred. While some studies placed Mesostigma within the Streptophyta lineage (which includes land plants), others placed it as the deepest green algae divergence. This basal positioning is regarded as a result of long-branch attraction due to poor taxon sampling. Reinvestigation of a 13- taxon mitochondrial amino acid dataset and a sub-dataset of 8 taxa reveals that site sampling, and in particular the treatment of missing data, is just as important a factor for accurate tree reconstruction as taxon sampling. This study identifies a difficulty in recreating the long-branch attraction observed for the 8-taxon dataset in simulated data. The cause is likely to be the smaller number of amino acid characters per site in simulated data compared to real data, highlighting the fact that there are properties of the evolutionary process that are yet to be accurately modeled.

Phylogenetic models generally assume a homogeneous, time reversible, stationary process. These assumptions are often violated by the real, far more complex, evolutionary process. This thesis is centered on non-homogeneous, lineage-specific, properties of molecular sequences. It consist several related but independent studies. LineageSpecificSeqgen, an extension to the Seq-Gen program, which allows generation of sequences with changes in the proportion of variable sites, is introduced. This program is then used in a simulation study showing that changes in the proportion of variable sites can hinder tree estimation accuracy, and that tree reconstruction under the best-fit model chosen using a relative test can result in a wrong tree. In this case, the less commonly used absolute model-fit was a better predictor of tree estimation accuracy. This study found that increased taxon sampling of lineages that have undergone a change in the proportion of variable sites was critical for accurate tree reconstruction and that, in contrast to some earlier findings, the accuracy of maximum parsimony is adversely affected by such changes. This thesis also addresses the well-known long-branch attraction artifact. A nonparametric bootstrap test to identify changes in the substitution process is introduced, validated, and applied to the case of Microsporidia, a highly reduced intracellular parasite. Microsporidia was first thought to be an early branching eukaryote, but is now believed to be sister to, or included within, fungi. Its apparent basal eukaryote position is considered a result of long-branch attraction due to an elevated evolutionary rate in the microsporidian lineage. This study shows that long-branch estimates and basal positioning of Microsporidia both correlate with increased proportions of radical substitutions in the microsporidian lineage. In simulated data, such increased proportions of radical substitutions leads to erroneous long-branch estimates. These results suggest that the long microsporidian branch is likely to be a result of an increased proportion of radical substitutions on that branch, rather than increased evolutionary rate per se. The focus of the last study is the intriguing case of Mesostigma, a fresh water green alga for which contradicting phylogenetic relationships were inferred. While some studies placed Mesostigma within the Streptophyta lineage (which includes land plants), others placed it as the deepest green algae divergence. This basal positioning is regarded as a result of long-branch attraction due to poor taxon sampling. Reinvestigation of a 13- taxon mitochondrial amino acid dataset and a sub-dataset of 8 taxa reveals that site sampling, and in particular the treatment of missing data, is just as important a factor for accurate tree reconstruction as taxon sampling. This study identifies a difficulty in recreating the long-branch attraction observed for the 8-taxon dataset in simulated data. The cause is likely to be the smaller number of amino acid characters per site in simulated data compared to real data, highlighting the fact that there are properties of the evolutionary process that are yet to be accurately modeled.

Master of Industrial Relations / Australia, during the twenty five years that followed the end of the Second World War, experienced increased prosperity and a stable industrial relations system in which the Commonwealth Conciliation and Arbitration Commission (the federal commission) played a dominant and authoritative role. The NSW building boom which began in the latter part of the 1950s introduced new technology, concentrated building workers in the central business district of Sydney, and broadened the range of skills required of builders' labourers. The major NSW building tradesmen's union, the Building Workers' Industrial Union (NSW/BWIU), had a communist leadership. The national body of that union lost its federal industrial registration in 1948, and the NSW/BWIU moderated its behaviour after it nearly lost its own, NSW state, registration in 1957. The Australian Building Construction Employees and Builders' Labourers Federation (ABLF) had a federal award under which most of the members of its NSW branch (NSW/BLF) were employed. The leadership of both the ABLF and of the NSW/BLF were communist. The Communist Party of Australia (CPA) suffered a defection by the ABLF leadership in the early 1960s to a communist party which endorsed Marxist- Leninist policies. The BWIU leadership also left the CPA (and formed the Socialist Party of Australia) following an announced shift in policy direction by the CPA in 1969. That shift in policy abandoned the `united front' concept and adopted ultra-left policies which advocated vanguard action by small groups. The announcement by the CPA of its new policies occurred after the gaoling of a Victorian union leader which signalled the virtual collapse of the previously authoritative, and punitive, role of the federal commission. The structure and politics of society underwent enormous change during the 1960s and early 1970s which was an era of protest during which various social movements were formed. The NSW/BLF became a major participant in those protests and movements, and conducted various industrial and social campaigns during the first half of the 1970s. Those campaigns were conducted in line with the ultra-left policies of the CPA, and this isolated the NSW/BLF from its federal body and from the trade union movement generally. This thesis analyses some of the campaigns conducted by the NSW/BLF during the period 1970-1974 and the various responses by the Master Builders Association of NSW (MBA/NSW) to those campaigns. The MBA/NSW broadened its membership base during the 1950s, and the effect that its new membership structure had on its decision-making processes is also considered.

Este trabalho apresenta proposta de modelo matemático para o problema de expansão do sistema de transmissão baseado no fluxo de carga CC considerando a utilização de links CC e FACTS resolvido através de metodologia de solução que considera a primeira e a segunda lei de Kirchhoff em processo enumerativo de branch-and-bound adaptado. A abordagem possui dois pontos em destaque: i) apresenta uma proposta de modelo matemático com possibilidade da utilização direta em problemas de expansão de linhas de transmissão que possuem tanto linhas de transmissão CA, transformadores, links CC e dispositivos FACTS e ii) é um método exato de solução do problema que garante a otimalidade da resposta e traz uma contribuição ao tradicional método branch-and-bound por incluir relaxações adicionais. O método aplicado aos sistemas de 6 barras de Garver e sistema Sul sudeste Brasileiro de 46 barras apresenta respostas adequadas e o modelo matemático testado em um sistema Garver modificado apresenta novas configurações possíveis com redução do custo total do investimento. / This work proposes a mathematical model to the transmission expansion system problem based on the DC power flow model considering the use of DC links and FACTS that is solved using a solution method considering the first and second Kirchhoff’s Law in an enumerative adapted branch-and-bound process. It is possible to highlight two key aspects of the proposed approach: i) presents a mathematical model that can be directly used on expansion transmission systems problems that have AC transmission lines, transformers, DC links and FACTS and ii) is an exact solution method that guarantees the optimum problems’s solutions and contributes to the traditional branch-and-bound method bringing additional relaxations. The solution method applied to Garver’s six-bus network and southeast Brazilian 46 bus network provides correct answers and the mathematical model tested on a modified Garver’s six-bus network presents new possible configurations that enables overall cost reduction to the problem.

Dans cette thèse, nous étudions trois problèmes d'ordonnancement de la chaîne logistique dans le modèle de production à la demande. Le premier problème est un problème d'ordonnancement de production et de distribution intermédiaire dans une chaîne logistique avec un producteur et un prestataire logistique. Le deuxième problème est un problème d'ordonnancement de production et de distribution aval avec des dates de début au plus tôt et des dates limites de livraison dans une chaîne logistique avec un producteur, un prestataire logistique et un client. Le troisième problème est un problème d'ordonnancement de production et de distribution aval avec des temps de réglage et des fenêtres de temps de livraison dans une chaîne logistique avec un producteur, un prestataire logistique et plusieurs clients. Pour les trois problèmes, nous étudions les problèmes d'ordonnancement individuels et les problèmes d'ordonnancement coordonnés. Nous proposons des algorithmes polynomiaux ou prouvons la NP-Complétude de ces problèmes, et développons des algorithmes exacts ou heuristiques pour résoudre les problèmes NP-Difficiles. Nous proposons des mécanismes de coordination et évaluons le bénéfice de la coordination. / In this dissertation, we aim at investigating three supply chain scheduling problems in the make-To-Order business model. The first problem is a production and interstage distribution scheduling problem in a supply chain with a manufacturer and a third-Party logistics (3PL) provider. The second problem is a production and outbound distribution scheduling problem with release dates and deadlines in a supply chain with a manufacturer, a 3PL provider and a customer. The third problem is a production and outbound distribution scheduling problem with setup times and delivery time windows in a supply chain with a manufacturer, a 3PL provider and several customers. For the three problems, we study their individual scheduling problems and coordinated scheduling problems: we propose polynomial-Time algorithms or prove the intractability of these problems, and develop exact algorithms or heuristics to solve the NP-Hard problems. We establish mechanisms of coordination and evaluate the benefits of coordination.