Over the past several years, new DNA sequencing technologies have led to a great in- crease in the quantity of biological sequence data that can be generated. Typically there may be millions or even billions of short reads sequences of a few hundred base pairs that are to some degree redundant: the data fall naturally into clusters of sequences that are highly similar to each other. In order to reduce the time required for analysis of the data, it therefore becomes of interest to compute representatives of these clusters, based on some definition of similarity. In this thesis we examine two clustering software packages, USEARCH and DNACLUST, that seek to perform this clustering task efficiently. We provide an overview of the techniques used by these two packages; we compare and evaluate them both from a methodological and experimental perspective, and draw conclusions about their effectiveness and utility. / Thesis / Master of Science (MSc)

We perform N-body simulations of star clusters in time-dependant galactic potentials. Since the Milky Way was built up through mergers with dwarf galaxies, its globular cluster population is made up of clusters formed both during the initial collapse of the Galaxy and in dwarf galaxies that were later accreted. Throughout a dwarf Milky Way merger, dwarf galaxy clusters are subject to a changing galactic potential. We investigate how this changing galactic potential affects the evolution of a cluster's half-mass radius. In particular, we simulate clusters on circular orbits around a dwarf galaxy that either falls into the Milky Way or evaporates as it orbits the Milky Way. We find that the dynamical evolution of a star cluster is determined by whichever galaxy has the strongest tidal field at the position of the cluster. Thus, clusters entering the Milky Way undergo changes in size as the Milky Way tidal field becomes stronger and that of the dwarf diminishes. We find that ultimately accreted clusters become the same size as a cluster born in the Milky Way on the same orbit. The change in size for accreted clusters occurs on a short time-scale, comparable to 1-2 cluster half-mass relaxation times. Assuming their initial sizes are similar, clusters born in the Galaxy and those that are accreted cannot be separated based on their current size alone. / Thesis / Master of Science (MSc)

No description available.

Iron sulfur [Fe-S] proteins are essential components of many major biological processes including electron transport, respiration, photosynthesis, hormone biosynthesis, and environmental sensing. The process of [Fe-S] cluster assembly in living cells is a controlled mechanism that is highly conserved across all kingdoms. Considerable progress has been made in deciphering this mechanism in bacteria, yeast, and mammals. The key players are the NifS/IscS/SufS proteins, which act as the sulfur donor, and the NifU/IscU/SufU proteins, which serve as a scaffold that binds Fe and upon which the cluster is assembled. Additional proteins are involved in the maturation and transport of the clusters. In eukaryotes there is redundancy in the proteins involved in this mechanism and the process is compartmentalized. Not much is known about the [Fe-S] cluster assembly mechanism in plants. In addition to the redundancy and compartmentalization seen in this machinery in eukaryotes, plants present a further challenge by offering chloroplasts as an additional site for [Fe-S] cluster assembly. The objective of this project has been to characterize Arabidopsis AtNFS1 and AtISU1-3, which show high homology to NifS/IscS and NifU/IscU, respectively, and are hypothesized to be key players in [Fe-S] cluster biogenesis in plants. Subcellular localization results of the AtNFS1 and AtISU1-3 proteins fused to GFP from this study are consistent with the presence of dual machinery in plants, with both mitochondria and chloroplasts as sites for [Fe-S] cluster assembly. Furthermore, observations also showed that AtISU2 mRNA may be unstable. The results of these experiments, together with promoter analysis described in this dissertation using GUS fusions suggested that the genes encoding the AtISU scaffold proteins are regulated at the transcriptional and probably also at the posttranscriptional level. Gene silencing experiments performed in this dissertation research using antisense and RNAi constructs indicated that these genes have the potential to impact respiration, photosynthesis, phytohormone biosynthesis, and environmental sensing, diverse processes that rely on [Fe-S] proteins. These observations, together with previous in vitro evidence that AtNFS1 and AtISU1 can participate in [Fe-S] cluster assembly, provide strong evidence that these proteins are part of two distinct cluster assembly systems that function in different subcellular locations and perhaps under different environmental conditions. Information gathered here has made it possible to begin developing a detailed model of [Fe-S] cluster biogenesis in plants. / Ph. D.

We present new deep photometry of the rich globular cluster (GC) systems around the Brightest Cluster Galaxies UGC 9799 (Abell 2052) and UGC 10143 (Abell 2147), obtained with the Hubble Space Telescope (HST) ACS and WFC3 cameras. For comparison, we also present new reductions of similar HST/ACS data for the Coma supergiants NGC 4874 and 4889. All four of these galaxies have huge cluster populations (to the radial limits of our data, comprising from 12,000 to 23,000 clusters per galaxy). The metallicity distribution functions (MDFs) of the GCs can still be matched by a bimodal-Gaussian form where the metal-rich and metal-poor modes are separated by similar or equal to 0.8 dex, but the internal dispersions of each mode are so large that the total MDF becomes very broad and nearly continuous from [Fe/H] similar or equal to-2.4 to solar. There are, however, significant differences between galaxies in the relative numbers of metal-rich clusters, suggesting that they underwent significantly different histories of mergers with massive gas-rich halos. Last, the proportion of metal-poor GCs rises especially rapidly outside projected radii R >= 4 R-eff, suggesting the importance of accreted dwarf satellites in the outer halo. Comprehensive models for the formation of GCs as part of the hierarchical formation of their parent galaxies will be needed to trace the systematic change in structure of the MDF with galaxy mass, from the distinctly bimodal form in smaller galaxies up to the broad continuum that we see in the very largest systems.

SPIDERS (The SPectroscopic IDentification of eROSITA Sources) is a programme dedicated to the homogeneous and complete spectroscopic follow-up of X-ray active galactic nuclei and galaxy clusters over a large area (similar to 7500 deg(2)) of the extragalactic sky. SPIDERS is part of the Sloan Digital Sky Survey (SDSS)-IV project, together with the Extended Baryon Oscillation Spectroscopic Survey and the Time-Domain Spectroscopic Survey. This paper describes the largest project within SPIDERS before the launch of eROSITA: an optical spectroscopic survey of X-ray-selected, massive (similar to 10(14)-10(15) M-circle dot) galaxy clusters discovered in ROSAT and XMM-Newton imaging. The immediate aim is to determine precise (Delta(z) similar to 0.001) redshifts for 4000-5000 of these systems out to z similar to 0.6. The scientific goal of the program is precision cosmology, using clusters as probes of large-scale structure in the expanding Universe. We present the cluster samples, target selection algorithms and observation strategies. We demonstrate the efficiency of selecting targets using a combination of SDSS imaging data, a robust red-sequence finder and a dedicated prioritization scheme. We describe a set of algorithms and work-flow developed to collate spectra and assign cluster membership, and to deliver catalogues of spectroscopically confirmed clusters. We discuss the relevance of line-of-sight velocity dispersion estimators for the richer systems. We illustrate our techniques by constructing a catalogue of 230 spectroscopically validated clusters (0.031 < z < 0.658), found in pilot observations. We discuss two potential science applications of the SPIDERS sample: the study of the X-ray luminosity-velocity dispersion (L-X-sigma) relation and the building of stacked phase-space diagrams.

NGC 5986 is a poorly studied but relatively massive Galactic globular cluster that shares several physical and morphological characteristics with "iron-complex" clusters known to exhibit significant metallicity and heavy-element dispersions. In order to determine whether NGC 5986 joins the iron-complex cluster class, we investigated the chemical composition of 25 red giant branch and asymptotic giant branch cluster stars using high-resolution spectra obtained with the Magellan-M2FS instrument. Cluster membership was verified using a combination of radial velocity and [Fe/H] measurements, and we found the cluster to have a mean heliocentric radial velocity of +99.76 km s(-1) (sigma = 7.44 km s(-1)). We derived a mean metallicity of [Fe/H] = -1.54 dex (sigma = 0.08 dex), but the cluster's small dispersion in [Fe/H] and low [La/Eu] abundance preclude it from being an iron-complex cluster. NGC 5986 has <[Eu/Fe]> = +0.76 dex (sigma = 0.08 dex), which is among the highest ratios detected in a Galactic cluster, but the small [Eu/Fe] dispersion is puzzling because such high values near [Fe/H] similar to -1.5 are typically only found in dwarf galaxies exhibiting large [Eu/Fe] variations. NGC 5986 exhibits classical globular cluster characteristics, such as uniformly enhanced [alpha/Fe] ratios, a small dispersion in Fe-peak abundances, and (anti) correlated light-element variations. Similar to NGC 2808, we find evidence that NGC 5986 may host at least four to five populations with distinct light-element compositions, and the presence of a clear Mg-Al anticorrelation along with an Al-Si correlation suggests that the cluster gas experienced processing at temperatures. greater than or similar to 65-70 MK. However, the current data do not support burning temperatures exceeding similar to 100 MK. We find some evidence that the first-and second-generation stars in NGC 5986 may be fully spatially mixed, which could indicate that the cluster has lost a significant fraction of its original mass.

Este trabalho procura averiguar as dificuldades e os problemas envolvidos na especificação e implementação de uma arquitetura de objetos de serviço para gerenciamento e suporte a aplicações distribuídas em uma plataforma de computadores em configuração tipo cluster, em particular daqueles que devem cumprir requisitos de alta disponibilidade. Tal arquitetura deve apresentar-se como uma infra-estrutura distribuída de serviços e compor uma camada intermediária entre as partes das aplicações distribuídas e os recursos do cluster, compondo desse modo uma camada de middleware. Uma arquitetura de gerenciamento e de suporte a aplicações distribuídas, para que possa atingir plenamente seus objetivos, deve ser projetada como uma infra-estrutura distribuída de serviços de modo a oferecer acesso fácil e eficiente a estes. Neste trabalho, investigamos a possibilidade de se implementar tal infra-estrutura utilizando a arquitetura de objetos distribuídos OMG CORBA, a qual tem por objetivo facilitar a especificação, implementação e o acesso a interfaces de serviços de objetos distribuídos. Uma infra-estrutura de serviços de suporte a aplicações e de gerenciamento de cluster- é composta de dezenas de interfaces dos mais diversos tipos e finalidades, compondo vários sistemas e subsistemas distribuídos cujos serviços devem ser fácil e transparentemente acessíveis através da rede de comunicação que interconecta os nós do cluster. Essa rede tipicamente utiliza os protocolos de comunicação Ethernet IEEE 802.3, IP e TCP/UDP em seus níveis de enlace, rede e transporte, respectivamente. Por essa ótica, CORBA atende de antemão vários dos requisitos necessários, porém em diversos aspectos da arquitetura e dos serviços houve necessidade de se averiguar com mais profundidade a capacidade de CORBA de atendê-los. Como por exemplo, averiguou-se a capacidade de CORBA lidar com problemas ligados à falhas parciais de comunicação, comunicação em grupo, comunicação não-bloqueante e outras. Um dos desafios da abordagem utilizando CORBA reside no fato de que se tem o pré-requisito de alta disponibilidade. A arquitetura proposta deve ser projetada levando-se em conta que certas partes do sistema, tais como subsistemas de armazenamento, processamento, rede, aplicações e outros podem , a qualquer momento, falhar ou tornar-se inoperantes. O grande desafio deste trabalho consiste assim em averiguar quais são as dificuldades de se utilizar CORBA como parte central da arquitetura, uma vez que a infra-estrutura obtida necessita ser ela própria um conjunto de serviços de alta disponibilidade, caso contrário ela não conseguirá cumprir seus objetivos. Investigaremos então possíveis modos de implementação de objetos CORBA que venham a cumprir os requisitos de alta disponibilidade necessários. Por fim, este trabalho procura averiguar a possibilidade de se implementar tal arquitetura em clusters baseados em elementos de hardware e software disponíveis em larga escala e a baixo custo no mercado tais como PCs ou servidores baseados em processador Intel rodando os sistemas operacionais Linux ou FreeBSD e interconectados por redes locais de baixo custo. Tais plataformas são popularmente conhecidas como Beowulf Clusters. Este aspecto da investigação terá influência no projeto da arquitetura proposta, uma vez que procuramos enfocar aspectos de alta escalabilidade para o cluster, uma tendência para o uso desse tipo de cluster em aplicações de alta demanda de processamento e recursos, tais servidores web e de banco de dados de grandes provedores de conteúdo e serviços da Internet / This work intends to investigate for the difficulties and problems involved in the specification and implementation of an object-oriented architecture of services for management and support of distributed applications in a platform of computers in cluster configuration, in particular for those that must fulfill requirements of high availability. Such architecture must present itself as a infrastructure of distributed services and should compose an intermediate layer between the parts of the cluster distributed applications and the cluster resources, composing in this way a middleware layer. In order to reach its objectives, this support and management architecture must be designed as a distributed infrastructure of services. By this way, it can offer easy and efficient access to its services. In this text, we investigate the possibility of implementing such infrastructure of services using the distributed object architecture proposed by OMG, the so-called CORBA architecture. CORBA has many objectives and features as to facilitate the specification, implementation and access to distributed service objects. An infrastructure of services for the support and management of clusters and cluster applications is composed of a set of interfaces of the most diverse types and purposes, composing some distributed systems and subsystems whose services must be easy and transparently accessible through the communication networks that interconnects the cluster computer nodes. Cluster networks typically uses standard communication protocols such as Ethernet IEEE 802.3 at the data-link layer, the Internet Protocol (IP) at the network layer and TCP/UDP at the transport layer. In these aspects CORBA takes care on beforehand of severa1 of these requirements. However, for many service requirements of the proposed architecture it was necessary inquiring in more depth the CORBA capabilities to accomplish them. As an example, it was investigated the CORBA capabilities to deal with problems related to partial communication failures, communication for object groups, non-blocking and asynchronous communication and others. One of the challenges of the CORBA approach for the proposed architecture inhabits in the fact that the system must accomplish the prerequisite of high availability. The architecture proposal must be designed taking in account that certain parts of the system, such as storage subsystems, processors, network, applications and others can, at any time, fail or become inoperative. The great challenge of this proposal work consists thus inquiring the difficulties of adopting CORBA as a central part of the architecture, since the gotten infrastructure needss to be a proper high availability set of services. In contrary case, it will not fulfill its primary objectives. We will investigate possible ways of implementing CORBA objects in such a way that they fulfill the necessary high availability requirements. Finally, this work looks for the possibility of implementing the proposed system in clusters built with wide scale and low cost hardware and software elements available in the market, such as Intel-processor-based PCs and servers running open-source and low-cost operating systems such as Linux or FreeBSD and interconnected by low cost local area networks. Such platforms are popularly known as Beowulf Clusters. This aspect of The inquiry will have influence in the architecture proposal, once we are focusing aspects of high scalability for the cluster since there is a trend for the use of this type of cluster in applications of high demand of processing and resources, such as web servers for great suppliers of content and services on the Internet

O surgimento de novos serviços e aplicações baseados na Web tem provocado um aumento desenfreado na quantidade de usuários da World Wide Web que, por sua vez, se torna cada vez mais popular no mundo dos negócios. Sites de e-commerce, que demandam grande tráfego de requisições, têm adotado sistemas de servidores Web distribuídos, como a arquitetura Web Cluster. Isso se deve ao fato de enfrentarem frequentemente situações de sobrecarga, durante as quais podem deixar de atender requisições de transação (com grande probabilidade de gerar renda) por conta do aumento na demanda de requisições de navegação (geram renda apenas de forma indireta). A utilização ineficiente de recursos pode comprometer o desempenho do sistema e é nesse contexto que este trabalho se insere. Neste trabalho foi desenvolvido um modelo de Servidor Web para E-Commerce (SWE-C),validado por meio de um modelo de simulação e uma carga sintética gerada a partir de um modelo desenvolvido com os principais tipos de requisições que caracterizam um site de e-commerce. Foram realizadas simulações no sistema com diversas combinações de algoritmos de escalonamento e disciplinas de atendimentos para filas, dentre as quais de destaca uma nova disciplina que utiliza um mecanismo de prioridades orientado ao consumo de CPU proposto neste trabalho. O objetivo é aumentar o throughput de requisições de transação e melhorar os tempos de resposta em situações de sobrecarga. Uma avaliação de desempenho foi realizado e constatou-se que o mecanismo de prioridades proposto é adequado às necessidades de um site de e-commerce. / The appearance of new services and applications based on the web has causing a wild increase in the amount of users of the World Wide Web that becomes more popular in the business world. E-commerce sites that demand great request traffic has adopted a distributed web servers system, such as the Web Cluster. This occurs because this sites frequently are on overloaded situations, leaving to serve request transactions (with large probability of generate income) due to increasing demand of navigation requests (generates income only indirectly). The low resource utilization can compromise the system performance. This work is inserted in this context. In this master thesis has been developed a Web server model for E-Commerce (WSE-C). It is validated with a simulation model using a synthetic workload characterized with the main types of equest identified from e-commerce sites. Several simulations were accomplished in the system, combining the scheduling algorithms, the queue attendances disciplines and the use of a new priority mechanism oriented to the CPU utilization. The aim of this work is increase the request throughput and to obtain a better response time on overload situation. A performance evaluation was conducted and shown that priority mechanisms is adequate to a e-commerce site.

Esta tese teve como objetivo apresentar quais os elementos que devem constar em um modelo descritivo para representar o que ocorre na realidade na governança em clusters. Para atingir este objetivo desenvolveu-se uma pesquisa para compreender que elementos eram considerados por pesquisadores ao escreveram sobre a governança de aglomerados produtivos. De posse destes dados, o material resultante foi classificado considerando sua natureza. Se descritivos ou normativos. Assim foram constituídos os Elementos da Governança em Cluster com sua conceituação a partir do que indica a literatura da área. Os Elementos da Governança, a saber: Estrutura da Governança, Funções da Governança, Mecanismos /Meios da Governança, Objetivos da Governança, Agentes da Governança e Requisitos da governança. Após, para atingir o objetivo da Tese, fez-se necessária a confrontação das informações teóricas com dados empíricos. Então se desenvolveu pesquisa em 5 Clusters no Estado Rio Grande do Sul. Foram estudados os seguintes casos: Cluster de Doces, na região de Pelotas-RS; Cluster Bovinocultura de Corte, na região da Campanha Gaúcha; Cluster Vitivinícola, na Região da Fronteira Oeste de Campanha; Cluster Moveleiro, na Região Central do Estado; e Cluster Metal-Mecânico. Na Serra Gaúcha. Os dados coletados constituíram-se em um modelo descritivo visando representar como estão apresentados os Elementos da Governança na realidade. A Estrutura da Governança foi definida como a forma como se organiza a governança em um cluster. De forma hierárquica ou heterárquica, apresentando firmas independentes que operam como uma entidade única. A Função da Governança foi definida como o ato de influenciar a tomada de decisão das empresas no aglomerado, indicando formas de interação entre as organizações. Os Mecanismos da Governança foram definidos como contratos formais e informais que organizam o relacionamento entre organizações em um cluster. O Objetivo da Governança foi definido como Garantir vitalidade do agrupamento compondo competitividade e maximização do valor para toda a cadeia de produção. Os Agentes da Governança foram definidos como empresas independentes, ligadas por vínculos de proximidade geográfica, relacionamento transacional, processos competitivos e/ou cooperativos, governo local, instituições científicas e de apoio. Como requisito para a existência de Governança foi definido que a confiança é o principal atributo. / This thesis aims to show what elements should be included in a descriptive model to represent what actually occurs in governance in clusters. To achieve this goal developed a survey to understand what factors were considered by the researchers wrote about the governance of production clusters. Using these data, the resulting material was classified considering their nature. If descriptive or normative. Thus were formed the Elements of Governance Cluster with its concept from the literature would suggest the area. Elements of Governance, namely: Governance Structure, Functions Governance Mechanisms / Media Governance, Governance Goals, Agents and Governance Requirements governance. After, to achieve the objective of the thesis, it was necessary to confrontation of theoretical information with empirical data. Then developed in 5 research clusters in Rio Grande do Sul state the following cases were studied: Cluster Candy, in the region of Pelotas; Cluster Beef Cattle in the Campanha Gaucha region; Wine Cluster in the Border Campaign West Region; Cluster Furniture in the State Central Region; Cluster and Metal-mechanic. In the Serra Gaucha. The data collected consisted of a descriptive model, to represent how the elements are shown Governance in reality. The Structure of Governance was defined as how governance is organized in a cluster. Hierarchical or heterarchical form, with independent firms that operate as a single entity. The Role of Governance has been defined as the act of influencing the decision making of firms in the cluster, indicating ways of interaction between organizations. The Mechanisms of Governance were defined as formal and informal contracts that organize the relationship between organizations in a cluster. The Purpose of the Governance was set to ensure the vitality and competitiveness cluster composing maximizing value for the whole chain of production. Agents of the Governance were defined as independent companies linked by bonds of geographical proximity, transactional relationships, competitive and / or cooperative processes, local government, scientific institutions and support. As a requirement for the existence of Governance has been defined that trust is the main attribute.