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Dissertations / Theses on the topic 'MinION sequencing'

Author: Grafiati

Published: 11 March 2023

Last updated: 19 July 2025

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1

Sim, Justin. "The evaluation of in-field whole genome sequencing using the minION™ nanopore sequencer for forensic DNA applications." Thesis, Sim, Justin (2018) The evaluation of in-field whole genome sequencing using the minION™ nanopore sequencer for forensic DNA applications. Masters by Coursework thesis, Murdoch University, 2018. https://researchrepository.murdoch.edu.au/id/eprint/41414/.

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In-field whole genome sequencing has been made possible by the introduction of the MinION™ DNA sequencer by Oxford Nanopore Technologies. Current forensic DNA analysis requires samples to be sent to a dedicated lab offsite. Depending on the location this process can take time. The evaluation of alternatives such as field sequencing using the MinION™, with the possibility of providing access to results in a shorter time with lower costs, should be researched and validated. The potential applications of the MinION™ in forensic scenarios have not been studied partly due to the recent release of t

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2

Cain, Elizabeth. "Targeted STR and SNP in-field sequencing by Oxford Nanopore MinION™ for the identification of an individual in a military scenario." Thesis, Cain, Elizabeth (2019) Targeted STR and SNP in-field sequencing by Oxford Nanopore MinION™ for the identification of an individual in a military scenario. Masters by Coursework thesis, Murdoch University, 2019. https://researchrepository.murdoch.edu.au/id/eprint/49630/.

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The requirement for DNA evidence in forensics has increased, meaning the demand for DNA typing has also increased. Current analytical processes for DNA evidence are known to be costly and time-consuming and traditionally occur at a centralised laboratory which can impact on the amount of time from sample collection to DNA profile generation. Therefore, research has focused on creating technologies that are capable of in-field analysis. Oxford Nanopore Technologies developed MinION™, a portable, cost-effective nanopore sequencer that is capable of in-field analysis. The development of in-field

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3

Fruchard, Cécile. "Étude des chromosomes sexuels et du déterminisme du sexe chez les plantes : comparaison des systèmes Silene et Coccinia." Thesis, Lyon, 2018. http://www.theses.fr/2018LYSE1108/document.

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Bien que les sexes séparés (dioecie) soient plus rares que chez les animaux, ∼15 600 espèces dioiques ont évolué chez les angiospermes (∼6% de l'ensemble des espèces). La manière dont le sexe de ces plantes est contrôlé est une question centrale de la biologie végétale, mais également de l'agronomie car de nombreuses plantes cultivées sont des plantes dioiques (∼20% des espèces cultivées) mais dont un seul sexe (généralement les femelles) présente un intérêt agronomique. Pourtant, seulement trois gènes du déterminisme du sexe ont été identifiés à ce jour chez les plantes dioiques, chez le kaki

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4

Ulrich, Kristina. "Molecular epidemiological study on Infectious Pancreatic Necrosis Virus isolates from aquafarms in Scotland over three decades." Thesis, University of Stirling, 2018. http://hdl.handle.net/1893/28340.

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Introduction: RNA viruses are economically important pathogens of fish, and among these viruses, infectious pancreatic necrosis virus (IPNV) is of particular concern for the aquaculture industry, especially for farmed rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). This non-enveloped aquatic virus, which was first isolated in the UK in 1971, belongs to the family of Birnaviridae and has a bi-segmented dsRNA genome of about 6kb. IPNV is classified in 6 genogroups with correspondence to 10 known serotypes and an additional proposed genogroup of marine aquabirnaviruses (MAB

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5

Ilango, Sankaralingam. "Computer-aided underground mining machine sequencing." Ohio : Ohio University, 1987. http://www.ohiolink.edu/etd/view.cgi?ohiou1183047349.

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6

Pelley, Charles W. "A study of sequencing strategy for steep, tabular, hardrock orebodies." Thesis, McGill University, 1994. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=41746.

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This thesis reviews, analyses and classifies extraction methods and sequences used in steep, tabular orebodies in Ontario hardrock mines and how new bulk mining techniques have affected them.<br>The thesis examines, as a case study, the complexities of sequencing the extraction of the Hemlo orebody through three adjacent mines and details the planning and monitoring of extracting one section of the David Bell orebody. It examines the use of numerical modelling as a tool in extraction sequence planning and demonstrates how, in conjunction with an instrumentation program, the results assist succ

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7

Smoljanovic, Muñoz Milivoj Antonio. "Optimum sequencing of underground ore reserves for different mining systems." Tesis, Universidad de Chile, 2012. http://www.repositorio.uchile.cl/handle/2250/111985.

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Magíster en Minería<br>Ingeniero Civil de Minas<br>Currently, mine plans are optimized by using many criteria, such as profit, life of mine, concentration of some pollutants, mining costs, confidence level or mineral resources, while attending constraints related to production rates, plant capacities and grades. Whilst this approach is successful in terms of producing high value production schedules, it uses a static sequence of production units (for open pit and underground mine) and therefore the optimization is performed within the level of freedom left by the original opening schedule and

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8

Quan, Aaron. "Batch Sequencing Methods for Computer Experiments." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1401462464.

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9

Mousavi, Nogholi Amin Alah. "Optimisation of open pit mine block sequencing." Thesis, Queensland University of Technology, 2015. https://eprints.qut.edu.au/86697/1/Amin%20Alah_Mousavi%20Nogholi_Thesis.pdf.

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This study presents a comprehensive mathematical model for open pit mine block sequencing problem which considers technical aspects of real-life mine operations. As the open pit block sequencing problem is an NP-hard, state-of-the-art heuristics algorithms, including constructive heuristic, local search, simulated annealing, and tabu search are developed and coded using MATLAB programming language. Computational experiments show that the proposed algorithms are satisfactory to solve industrial-scale instances. Numerical investigation and sensitivity analysis based on real-world data are also c

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10

桂宏胜 and Hongsheng Gui. "Data mining of post genome-wide association studies and next generation sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/193431.

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11

Giollo, Manuel. "Computational Approaches to Address the Next-Generation Sequencing Era." Doctoral thesis, Università degli studi di Padova, 2015. http://hdl.handle.net/11577/3424280.

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In this thesis, I propose new algorithms and models to address biological problems. Computer science in fact plays a key role in proteomics and genetics research due to the advent of big datasets. In the context of protein study, I developed new methods for protein function prediction based on information retrieval principles. By using heterogeneous source of knowledge, like graph search and sequence similarity, I designed a tool called INGA that can be used to annotate entire genomes. It has been benchmarked during the Critical Assessment of Function Annotation challenge, and it proved to be

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Bly, Elizabeth 1981. "Effects of reduced IFR arrival-arrival wake vortex separation minima and improved runaway operations sequencing on flight delay." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/28908.

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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2005.<br>Includes bibliographical references (p. 99-101).<br>(cont.) 65.6% and 67.0% and the average NAS delay by 24.3% and 24.7% relative to the FIFO and Serve-the-Longest-Queue algorithms respectively.<br>Two methods to improve runway throughput are evaluated in this thesis. The first, increasing runway capacity during periods of bad weather by reducing IFR arrival-arrival wake vortex separations. The second, increasing runway efficiency in all weather conditions using event sequencing algorithms. Tw

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13

Ferrarini, Margherita. "From exome to whole genome sequencing: mining for inconsistencies and functional elements in coding and non-coding regions." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3424933.

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Over the last two decades the advancement in DNA sequencing technologies has enormously increased the amount of sequencing data available to researchers and geneticists. This has been accompanied by the development of tools for sequencing data analysis, including the human reference genome, that is undoubtedly an indispensable resource. It is known that the reference genome does not always represent the real consensus sequence of the human population, due to the inclusion of rare alleles and sequencing errors. Moreover, genomic duplications are often misassembled and, as a result, they may be

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14

Fontes, Marcélio Prado. "Influência do nível freático no sequenciamento de lavra aplicado ao planejamento estratégico de lavra." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2016. http://hdl.handle.net/10183/142459.

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Desenvolver o sequenciamento de mina envolve muitos fatores e uma grande quantidade de informações, consequentemente, a rentabilidade do projeto dependerá fortemente do cronograma de produção. Um projeto de mineração pode estar condicionado ao sequenciamento não ideal, o que afeta os resultados econômicos do projeto e também leva a uma utilização inadequada dos recursos minerais. Durante o sequenciamento da mina é necessário tomar decisões para cada bloco durante a extração, tais como: 1) Se um determinado bloco deve ou não ser minerado; 2) Se minerado, quando deveria ser extraído; 3) Uma vez

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15

Chennen, Kirsley. "Maladies rares et "Big Data" : solutions bioinformatiques vers une analyse guidée par les connaissances : applications aux ciliopathies." Thesis, Strasbourg, 2016. http://www.theses.fr/2016STRAJ076/document.

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Au cours de la dernière décennie, la recherche biomédicale et la pratique médicale ont été révolutionné par l'ère post-génomique et l'émergence des « Big Data » en biologie. Il existe toutefois, le cas particulier des maladies rares caractérisées par la rareté, allant de l’effectif des patients jusqu'aux connaissances sur le domaine. Néanmoins, les maladies rares représentent un réel intérêt, car les connaissances fondamentales accumulées en temps que modèle d'études et les solutions thérapeutique qui en découlent peuvent également bénéficier à des maladies plus communes. Cette thèse porte sur

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16

Qin, Yu. "Computations and Algorithms in Physical and Biological Problems." Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11478.

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This dissertation presents the applications of state-of-the-art computation techniques and data analysis algorithms in three physical and biological problems: assembling DNA pieces, optimizing self-assembly yield, and identifying correlations from large multivariate datasets. In the first topic, in-depth analysis of using Sequencing by Hybridization (SBH) to reconstruct target DNA sequences shows that a modified reconstruction algorithm can overcome the theoretical boundary without the need for different types of biochemical assays and is robust to error. In the second topic, consistent with t

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17

Diedrich, Cássio. "Incorporação da variabilidade dos teores para análise de risco de recursos minerais e sequenciamento de lavra." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2012. http://hdl.handle.net/10183/61134.

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A indústria de mineração investiga continuamente processos de reconciliação e técnicas adequadas para mapear possíveis riscos na recuperação do minério e no planejamento de lavra. Um estudo de caso em uma mina de cobre brasileira investiga a adequação do uso de teores simulados para a definição de áreas de risco que afetam o planejamento mineiro e as reservas minerais definidas. Simulações condicionais foram usadas para derivar múltiplos modelos de teores de cobre dentro de um típico corpo de minério do depósito e esses modelos foram comparados com os dados reais de produção (reconciliação). A

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18

Alaimo, Salvatore. "From diagnosis to therapy: algorithmic methodologies for precision medicine." Doctoral thesis, Università di Catania, 2016. http://hdl.handle.net/10761/3731.

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In recent years, it has become established the idea of a novel medicine where a patient is the center around which multidisciplinary teams (made up of physicians, statisticians and bioinformaticians) sew targeted treatments. Precision medicine involves the use of detailed patient-specific molecular information for diagnosing, categorizing and guiding treatment of a disease, with the main purpose of improving the clinical outcome compared to a more classical approach. In precision medicine it is supposed that the cause of a disease is at least partially attributable to specific genetic or epige

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19

Tramonte, Keila Modesto. "Estudo da disponibilidade de metais em sedimentos do Sistema Cananéia-Iguape." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/21/21137/tde-24032015-152819/.

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O Sistema Cananéia-Iguape sofreu importantes alterações ambientais devido à abertura do canal do Valo Grande que o conectou ao rio Ribeira de Iguape. Com a intensa atividade de mineração ocorrida no Vale do Ribeira, a bacia do rio Ribeira foi afetada, atingindo o Sistema através desse canal. Diante desse cenário, o principal objetivo deste estudo foi avaliar a disponibilidade de Cu, Pb e Zn no Sistema Cananéia-Iguape, a partir do teor associado aos principais componentes dos sedimentos. Para estimar a contaminação química, o teor desses elementos foi comparado aos limites canadenses (ISQG e PE

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20

Ferreira, Marcos Manoel. "Estudo da mobilidade e da biodisponibilidade do arsênio em solos e sedimentos de Paracatu-MG." Niterói, 2016. https://app.uff.br/riuff/handle/1/1666.

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Submitted by Biblioteca de Pós-Graduação em Geoquímica BGQ (bgq@ndc.uff.br) on 2016-04-29T16:38:13Z No. of bitstreams: 1 TESE Marcos Ferreira Final.pdf: 14202319 bytes, checksum: 0a3e4b766ed3761f565f902e1f0d9730 (MD5)<br>Made available in DSpace on 2016-04-29T16:38:13Z (GMT). No. of bitstreams: 1 TESE Marcos Ferreira Final.pdf: 14202319 bytes, checksum: 0a3e4b766ed3761f565f902e1f0d9730 (MD5)<br>Coordenação de Aperfeiçoamento de Pessoal de Nível Superior<br>Universidade Federal Fluminense. Instituto de Química. Programa de Pós-Graduação em Geociências-Geoquímica. Niterói, RJ<br>Este estudo b

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21

Simões, Cláudia Sofia Lola. "Modelação da erosão do solo numa região de forte impacte de actividades mineiras e estudo geoquímico das zonas mais vulneráveis, com vista à sua remediação e reabilitação. Estudo de uma área piloto da Bacia do rio Paraopeba (Bacia do Rio Paraopeba - MG, Brasil)." Doctoral thesis, Universidade de Évora, 2015. http://hdl.handle.net/10174/16404.

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A erosão acelerada resulta em graves consequências para a qualidade do solo e da água, assim como para a sustentabilidade dos sistemas agrários. Para caso de estudo seleccionou-se a bacia hidrográfica do Rio Paraopeba, localizada na região sudoeste do Brasil, na área denominada de Quadrilátero Ferrífero, onde a intensa actividade mineira, se reflecte, não apenas no agravamento dos processos erosivos, mas também, na qualidade da água e do solo. No trabalho desenvolvido, identificaram-se as zonas mais vulneráveis aos processos erosivos, tendo como base metodologias de modelagem matemática comput

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22

Maestri, Simone. "Development of novel bioinformatic pipelines for MinION-based DNA barcoding." Doctoral thesis, 2021. http://hdl.handle.net/11562/1042782.

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DNA-barcoding is the process of taxonomic identification based on the sequence of a marker gene. When complex samples are analysed, we refer in particular to meta-barcoding. Barcoding has traditionally been performed with Sanger sequencing platform. The emergence of second-generation sequencing platforms, mainly represented by Illumina, enabled the high-throughput sequencing of hundreds of samples, and allowed the characterization of complex samples through meta-barcoding experiments. However, fragments sequenced with the Illumina platform are shorter than 600 bp, and this greatly limits taxon

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23

Hansen, Sören. "High resolution differentiation of infectious agents at the level of antibody and nucleic acid by using peptide microarray and nanopore sequencing." Thesis, 2019. http://hdl.handle.net/21.11130/00-1735-0000-0003-C18C-5.

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24

Lin, Yen-Yu, and 林延諭. "SSR marker mining and its strategy under low-coverage shotgun sequencing." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/21440621910411303220.

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碩士<br>國立臺灣大學<br>農藝學研究所<br>100<br>Simple sequence repeat (SSR) markers have been widely used in many areas of genetic research due to their codominance, ease of use, multiallelic nature, and abundance characteristics in the genome. Though various SSR markers in pepper have been published, it is still not sufficient to create a highly saturated linkage map. Here we utilized the 454 pyrosequencing technique to perform whole genome shotgun sequencing for pepper (Capsicum annuum). Tandem Repeats Finder (TRF) was applied to identify SSRs followed by primer design using Primer3. A Perl script was wri

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25

Wang, Ying-Tsui, and 王瀅翠. "The Effect of Sequencing Coverage on Mining Simple Sequence Repeats by Simulation." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/66611629874821750641.

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碩士<br>國立臺灣大學<br>農藝學研究所<br>100<br>Microsatellites or simple sequence repeats (SSRs) are tandem repeats distributed across genomes with 1 to 6 nucleotide motifs. Because of their genomic abundance and high level of polymorphism, SSRs is designed as molecular markers to apply in a variety of researches. In recent year, the rapidly-developing next generation sequencing technology (NGST) has impacted the ways of mining SSRs. NGST not only has the advantage of higher speed and lower cost but also offers the opportunities to discover novel SSRs. However, in a pilot study, the budget may be limited an

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26

"Establishing an Integrated SNV Mining and Utilization Pipeline for Next Generation Sequencing Studies." 2016. http://repository.lib.cuhk.edu.hk/en/item/cuhk-1292604.

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27

Yu, Hui-Ju, and 余惠茹. "A Study of Using Learning Path Mining to Assist the Design of SCORM Teaching Material of Sequencing." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/92673373000164313843.

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碩士<br>大葉大學<br>資訊管理學系碩士班<br>93<br>With the development of information technology, the trend of e-learning has been improved. E-learning has some problems about the uncorrected guideline of learning path. The e-learning content standard SCORM has also considered the sequencing and navigation of learning object and made clear defined in relation standard. But how to plan the suitable arranges the sequencing strategies, accord with the learner's degree, cognitive style and demand, it is the key point of influencing the quality of the teaching material. So this research will use the data mining to

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28

Gomes, Margarida de Sousa. "Peptone from casein: its influence in the transcription of lanthipeptides and the proteome of Pedobacter lusitanus NL19." Master's thesis, 2021. http://hdl.handle.net/10773/30990.

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Pedobacter lusitanus NL19 is a Gram -negative bacterium from the famil y Sphingobacteriaceae, which was isolated from a deactivated uranium mine in Portugal. This strain produces non ribosomal peptides (NRPs), calle d pedopeptins. The production of these peptides is repressed by high concentrations of peptone from casein (PC). In addition to biosynthetic gene clusters (BGCs) encoding NRPs, the NL19 strain genome also has BGCs of other secondary metabolites (SMs), incl uding lanthipeptides (4 BGCs: ped8, ped 14, ped15 and ped17). Lanthipeptides are ribosomally synthesized and post -translationa

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29

Ibrahim, A. "Effective Characterization of Sequence Data through Frequent Episodes." Thesis, 2015. http://etd.iisc.ac.in/handle/2005/3969.

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Pattern discovery is an important area of data mining referring to a class of techniques designed for the extraction of interesting patterns from the data. A pattern is some kind of a local structure that captures correlations and dependencies present in the elements of the data. In general, pattern discovery is about finding all patterns of `interest' in the data and a popular measure of interestingness for a pattern is its frequency of occurrence in the data. Thus the problem of frequent pattern discovery is to find all patterns in the data whose frequency of occurrence exceeds some user def

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Ibrahim, A. "Effective Characterization of Sequence Data through Frequent Episodes." Thesis, 2015. http://etd.iisc.ernet.in/2005/3969.

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Pattern discovery is an important area of data mining referring to a class of techniques designed for the extraction of interesting patterns from the data. A pattern is some kind of a local structure that captures correlations and dependencies present in the elements of the data. In general, pattern discovery is about finding all patterns of `interest' in the data and a popular measure of interestingness for a pattern is its frequency of occurrence in the data. Thus the problem of frequent pattern discovery is to find all patterns in the data whose frequency of occurrence exceeds some user def

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31

Silva, Mónica Alexandra Andrade. "Assessing potential impacts of deep-sea mining on dispersal and population connectivity of the vent mussel Bathymodiolus azoricus." Master's thesis, 2016. http://hdl.handle.net/10400.3/3938.

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Dissertação de Mestrado, Estudos Integrados dos Oceanos, 19 de Outubro de 2016, Universidade dos Açores.<br>Os campos hidrotermais são caracterizados por serem ambientes únicos, por terem características físico-químicas extremas, assim como composições únicas de espécies biológicas. Bathymodiolus azoricus é um bivalve de mar profundo predominante dos campos hidrotermais ao longo da Crista Médio-Atlântica (CMA). Ainda muito pouco é conhecido sobre a estrutura genética tanto como a existência de conectividade desta espécie. Desse modo, o objetivo deste estudo foi identificar escalas e padrões es

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Frazao, Rodolfo. "Analyse du métabolisme du soufre de la bactérie autotrophique acidophile Acidithiobacillus thiooxidans ATCC 19377." Thèse, 2015. http://hdl.handle.net/1866/13859.

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Les impacts environnementaux dues à l'extraction minière sont considérables. C'est l'action des microorganismes, en utilisant leur métabolisme du soufre sur les déchets miniers, qui engendre les plus grands défis. Jusqu'à présent, peu de recherches ont été effectués sur les microorganismes environnementaux pour la compréhension globale de l'action du métabolisme du soufre dans une optique de prévention et de rémédiation des impacts environnementaux de l'extraction minière. Dans cette étude, nous avons étudié une bactérie environnementale, Acidithiobacillus thiooxidans, dans le but de comprendr

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Sweeting, Alice. "Discovering the Movement Sequences of Elite and Junior Elite Netball Athletes." Thesis, 2017. https://vuir.vu.edu.au/34111/.

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This thesis investigated the movement sequences of elite and junior-elite female netball athletes using a local positioning system (LPS). Study one determined the indoor validity of an LPS, specifically the Wireless ad hoc System for Positioning (WASP), for measuring distance, velocity and angular velocity whilst sprinting and walking five nonlinear courses. The criterion measure used to assess WASP validity was Vicon, a motion analysis system. During all sprinting and walking drills, WASP had an acceptable accuracy for measuring total distance covered (coefficient of variation, CV; < 5

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