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Wright, Christopher. "Mutation analysis of relational database schemas." Thesis, University of Sheffield, 2015. http://etheses.whiterose.ac.uk/12059/.
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The schema is the key artefact used to describe the structure of a relational database, specifying how data will be stored and the integrity constraints used to ensure it is valid. It is therefore surprising that to date little work has addressed the problem of schema testing, which aims to identify mistakes in the schema early in software development. Failure to do so may lead to critical faults, which may cause data loss or degradation of data quality, remaining undetected until later when they will prove much more costly to fix. This thesis explores how mutation analysis – a technique commonly used in software testing to evaluate test suite quality – can be applied to evaluate data generated to exercise the integrity constraints of a relational database schema. By injecting faults into the constraints, modelling both faults of omission and commission, this enables the fault-finding capability of test suites generated by different techniques to be compared. This is essential to empirically evaluate further schema testing research, providing a means of assessing the effectiveness of proposed techniques. To mutate the integrity constraints of a schema, a collection of novel mutation operators are proposed and implementation described. These allow an empirical evaluation of an existing data generation approach, demonstrating the effectiveness of the mutation analysis technique and identifying a configuration that killed 94% of mutants on average. Cost-effective algorithms for automatically removing equivalent mutants and other ineffective mutants are then proposed and evaluated, revealing a third of mutation scores to be mutation adequate and reducing time taken by an average of 7%. Finally, the execution cost problem is confronted, with a range of optimisation strategies being applied that consistently improve efficiency, reducing the time taken by several hours in the best case and as high as 99% on average for one DBMS.
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Wu, Yongjian. "An empirical study of the use of conceptual models for mutation testing of database application programs." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B37599434.
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Wu, Yongjian, and 吳勇堅. "An empirical study of the use of conceptual models for mutation testing of database application programs." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2006. http://hub.hku.hk/bib/B37599434.
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Kamanu, Frederick Kinyua. "Computational Verification of Published Human Mutations." Thesis, University of the Western Cape, 2008. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_2906_1269551415.
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The completion of the Human Genome Project, a remarkable feat by any measure, has provided over three billion bases of reference nucleotides for comparative studies. The next, and perhaps more challenging step is to analyse sequence variation and relate this information to important phenotypes. Most human sequence variations are characterized by structural complexity and, are hence, associated with abnormal functional dynamics. This thesis covers the assembly of a computational platform for verifying these variations, based on accurate, published, experimental data.
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Sevinc, Ender. "Genetic Algorithms For Distributed Database Design And Distributed Database Query Optimization." Phd thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/3/12611194/index.pdf.
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The increasing performance of computers, reduced prices and ability to connect systems with low cost gigabit ethernet LAN and ATM WAN networks make distributed database systems an attractive research area. However, the complexity of
distributed database query optimization is still a limiting factor. Optimal techniques, such as dynamic programming, used in centralized database query optimization are not feasible because of the increased problem size. The recently developed genetic algorithm (GA) based optimization techniques presents a promising alternative. We compared the best known GA with a random algorithm and showed that it achieves almost no improvement over the random search algorithm generating an equal number of random solutions. Then, we analyzed a set of possible GA parameters and determined that two-point truncate technique using GA gives the best results.
New mutation and crossover operators defined in our GA are experimentally analyzed within a synthetic distributed database having increasing the numbers of relations and nodes. The designed synthetic database replicated relations, but there was no horizontal/vertical fragmentation. We can translate a select-project-join query including a fragmented relation with N fragments into a corresponding query with N relations. Comparisons with optimal results found by exhaustive search are only 20% off the results produced by our new GA formulation showing a 50% improvement over the previously known GA based algorithm.
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Nowacki, Piotr Marek. "Design, development, and deployment of a locus specific mutation database : the PAHdb example." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0004/MQ44234.pdf.
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McCormick, II Donald W. "Towards A Sufficient Set of Mutation Operators for Structured Query Language (SQL)." Thesis, Virginia Tech, 2010. http://hdl.handle.net/10919/32526.
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Test suites for database applications depend on adequate test data and real-world test faults for success. An automated tool is available that quantifies test data coverage for database queries written in SQL. An automated tool is also available that mimics real-world faults by mutating SQL, however tests have revealed that these simulated faults do not completely represent real-world faults. This paper demonstrates how half of the mutation operators used by the SQL mutation tool in real-world test suites generated significantly lower detection scores than those from research test suites. Three revised mutation operators are introduced that improve detection scores and contribute toward re-defining a sufficient set of mutation operators for SQL. Finally, a procedure is presented that reduces the test burden by automatically comparing SQL mutants with their original queries.Master of Science
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Kang, Ce. "Investigating the Genetic Basis of the Spastic-Ataxias using Next Generation Sequencing and a Mutation Database." Thesis, The University of Sydney, 2021. https://hdl.handle.net/2123/27330.
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Introduction: “Spastic-ataxias” are a group of conditions that are characterised by spasticity as well as ataxia. They are usually hereditary in nature, and demonstrate widespread genetic heterogeneity and phenotypical variance. In this thesis, I seek to draw meaningful genotype-phenotype relationship in two disorders – Hereditary Cerebellar Ataxia (HCA) and Hereditary Spastic Paraplegia (HSP).
Method: We undertook separate studies for each disorder. The first study is a retrospective review of HCA cases referred to the Neurogenetics Clinic at Royal North Shore Hospital over a 15-year period. Here, the patient’s signs and symptoms are analysed with their mode of genetic investigation. The second study is a systemic review of all published HSP cases in the PubMed database until April 2018. For this study, the cases of HSP are limited to patients with mutations in ATL1, SPAST, and REEP1, the most common autosomal dominant variants of HSP. The signs and symptoms of these cases were analysed along with the genetic and mutational data.
Results: For the HCA study, we reviewed 87 cases, and found routine repeat expansion panels have a detection rate of 13.8%, with next-generation sequencing (NGS) yielded a further 34.4% (11/32). NGS and whole genome sequencing together improve the overall diagnostic rate to 28.8%, and detected several novel variants. For the HSP study, we reviewed 1642 cases, and found several key phenotypic differences amongst the three variants. We found loss-of-function variants to be more frequent in SPAST and REEP1, and is associated with more severe disease in SPAST.
Discussion: Our studies highlight the genetic and phenotypic heterogeneity of HCA and HSP. In HCA, we support the use of NGS approaches for individuals who were negative on repeat expansion testing. In HSP, we found several key differences amongst the variants to have implication for clinical diagnosis. These studies have contributed key findings to the literature of “spastic-ataxia”.
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Venkatesan, Lavanya. "Identifying and Tracking the Evolution of Mutations in the SARS-CoV-2 Virus." Thesis, Virginia Tech, 2021. http://hdl.handle.net/10919/103939.
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SARS-CoV-2 is caused by a pathogenic and highly transmissible beta coronavirus leading to severe infections in immuno-compromised individuals. This study first evaluates the primers used in the Reverse Transcription Polymerase Chain Reaction (RT-PCR) to detect SARS-CoV-2 by understanding how mutations might affect the primer efficiency with the SARS-CoV-2 sequences. Mutations on the Spike protein of SARS-CoV-2 are the most important as the spike protein mediates the viral entry into host cells. This study tracks the course of mutations on the spike protein by focusing on the haplogroups of the sequences across the world. A comprehensive database linking three important, currently available databases is curated as part of this study to fill the gaps caused by sequencing errors. Further, this study exploits the data generated by the Illumina and Oxford Nanopore next generation sequencing methods to study the evolution of mutations in a single Septuagenarian patient over an infection period of 102 days using the gene analysis software Geneious Prime.Master of Science
A novel corona virus named Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has taken down the entire world by causing Covid-19 pandemic. Initially detected in Wuhan, China, the virus has now made its way to more than 200 countries with a heavy death toll. Understanding the virus through mutation tracking and improving diagnostics and vaccine design have now become the top priority of researchers. Most of these researchers depend on quality viral sequence datasets to identify and track mutations. One aim of this study is to provide a comprehensive dataset linking the GISAID (Global Initiative on Sharing All Influenza Data), NCBI (National Center for Biological Information) and the SRA (Sequence Read Archive) sequences. The dataset can be used for genome analysis and mutation tracking which can provide important insights for vaccine design and in improving diagnostic assays. In addition, this study provides an analysis of viral mutations in in the genomic regions targeted by commonly used primers in the RT-PCR tests for SARS-CoV-2 that may affect the efficiency of detection. This study also uses the haplogroup information of people across the world to track the D614G mutation on the S gene of SARS-CoV-2 as it may be associated with increased transmissibility. To track the course of mutations in SARS-CoV-2, it is important to analyze the sequencing data provided by the Illumina and Oxford Nanopore next generation sequencing methods. We present a case study to investigate the course of SARS-CoV-2 mutations in a single septuagenarian patient over a period of 102days using the Sequence Read Archive (SRA) data generated by two Next Generation Sequencing methods and compare the advantages that one has over the other.
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MOROSINI, SARA. "Integrated genetic diagnosis of neurofibromatosis type 1 (NF1) and molecular characterization of one case of compound heterozygosity." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2014. http://hdl.handle.net/10281/83314.
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Genetic analysis of Neurofibromatosis type 1 (NF1) may facilitate the identification of patients in early phases of the disease. Here, we present an overview of our diagnostic research spanning the last eleven years, with a focus on the description of 225 NF1 mutations, 126 of which are novel, found in a series of 605 patients (513 unrelated) in Italy. Between 2003 and 2013, 443 unrelated patients were profiled by DHPLC analysis of 60 amplicons derived from genomic NF1 DNA and subsequent sequencing of heterozygotic PCR products. In addition, a subset of patients was studied by MLPA to identify any duplications, large deletions or microdeletions present at the locus. Over the last year, 70 unrelated patients were investigated by MLPA and sequencing of 22 amplicons spanning the entire NF1 cDNA. Mutations were found in 70% of the 293 patients studied by DHPLC, thereby fulfilling the NIH criterion for the clinical diagnosis of NF1 (detection rate: 70%); furthermore, 87% of the patients studied by RNA sequencing were genetically characterized. Mutations were also found in 36 of the 159 patients not fulfilling the NIH clinical criteria. These data support the use of RNA-based methods for genetic analysis and provide novel information for relevant for improving the management of symptoms in oligosymptomatic patients.
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Fischer, Liane, Caroline Wilde, Torsten Schöneberg, and Ines Liebscher. "Functional relevance of naturally occurring mutations in adhesion G protein-coupled receptor ADGRD1 (GPR133)." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-208803.
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Background: A large number of human inherited and acquired diseases and phenotypes are caused by mutations in G protein-coupled receptors (GPCR). Genome-wide association studies (GWAS) have shown that variations in the ADGRD1 (GPR133) locus are linked with differences in metabolism, human height and heart frequency. ADGRD1 is a Gs protein-coupled receptor belonging to the class of adhesion GPCRs. Results: Analysis of more than 1000 sequenced human genomes revealed approximately 9000 single nucleotide polymorphisms (SNPs) in the human ADGRD1 as listed in public data bases. Approximately 2.4 % of these SNPs are located in exons resulting in 129 non-synonymous SNPs (nsSNPs) at 119 positions of ADGRD1. However, the functional relevance of those variants is unknown. In-depth characterization of these amino acid changes revealed several nsSNPs (A448D, Q600stop, C632fs [frame shift], A761E, N795K) causing full or partial loss of receptor function, while one nsSNP (F383S) significantly increased basal activity of ADGRD1. Conclusion: Our results show that a broad spectrum of functionally relevant ADGRD1 variants is present in the human population which may cause clinically relevant phenotypes, while being compatible with life when heterozygous.
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Connell, Jasmine. "Multigenerational mtGenome analysis for identification of historical military remains." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/210165/1/Jasmine_Connell_Thesis.pdf.
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Using the unique Norfolk Island pedigree, this dissertation focused on extended pedigree analysis to evaluate the suitability of whole mitochondrial genome analysis for historical casework, and to provide one of the first mutation rate estimates for the entire mitochondrial genome. This research also provided a mitochondrial DNA control region database representing World War II-era Australian soldiers that has been used by the Australian Defence Force for human identification. It is expected that this work will help to reduce the incorrect identification of military remains and will assist the forensic community for cases involving familial matching.
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BARILARO, MARIA ROSA. "Polimorfismi del DNA mitocondriale: implicazioni analitiche e forensi." Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2010. http://hdl.handle.net/2108/1390.
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La tipizzazione del DNA mitocondriale (mtDNA) ha trovato un’importante nicchia nell’analisi forense dei campioni degradati, dei capelli ed al verificarsi dei disastri di massa. Attualmente la maggior parte dei laboratori forensi, che si occupano di mtDNA, si focalizzano sull’informazione che deriva dal sequenziamento delle due regioni ipervariabili (HVI ed HVII), dell’estensione di oltre 600 paia di basi, poste all’interno della Regione di Controllo. Una limitazione dell’analisi del DNA mitocondriale è rappresentata dal basso potere di discriminazione associato ai tipi comuni HVI/HVII: ad esempio nel database forense relativo ai Caucasici Europei ci sono circa 20 tipi comuni HVI/HVII, condivisi da circa il 21% della popolazione ivi rappresentata.
Abbiamo sequenziato l’intero genoma mitocondriale di 40 individui Italiani, suddivisi in base alle differenti aree di provenienza (Nord, Centro, Sud ed Isole) al fine di individuare polimorfismi a singolo nucleotide (SNPs), all’interno della Regione Codificante, utili per una ulteriore discriminazione (nella definizione degli aplogruppi) e, se presente, in relazione alle differenti aree. Abbiamo posto particolare attenzione ai siti condivisi, neutrali e non ridondanti ed abbiamo verificato il riscontro in letteratura.
Abbiamo descritto 8 nuovi polimorfismi, 4 mutazioni private che potenzialmente potrebbero essere dei siti discriminanti, un nuovo polimorfismo di lunghezza in HVIII, una nuova inserzione, una nuova delezione e 2 eteroplasmie di sequenza, in precedenza descritte come semplici transizioni; abbiamo individuato 7 individui, caratterizzati da altrettanti aplogruppi particolari, uno dei quali è anche interessante da un punto di vista genetico-medico. La rimanente quantità di variazione individuata è già stata descritta in letteratura e le frequenze concordano con quelle dei Caucasici: una notevole varietà tra gli aplogruppi rappresentati è stata osservata nel Sud Italia, come atteso dal pattern dei flussi migratori.
Il nostro lavoro ha mostrato l’enorme variabilità, peraltro insita nel DNA mitocondriale, perfino in un piccolo campione di individui ed ha dimostrato l’utilità degli SNPs nella definizione degli aplotipi individuali, ma nel contempo ha sottolineato l’utilità di potenziare la ricerca nella migliore definizione delle malattie associate al DNA mitocondriale. Dall’altro lato, sostiene fortemente la necessità di migliorare il database forense per il DNA mitocondriale, non soltanto relativamente alla regione di controllo ma anche, come in Gene Bank, relativamente a quella codificante. Questo potrà essere ottenuto incoraggiando l’inserimento delle nuove sequenze prodotte in Gene Bank, ottenute in base alle linee guida standard per l’alta qualità dei dati, che attualmente sono in via di definizione, ed eseguendo il sequenziamento dell’intero genoma mediante tecnologie universali ed innovative (NGS, Next Generation Sequences o tecnologie di Sequenziamento di Prossima Generazione).Mitochondrial DNA (mtDNA) typing has found an important niche in the forensic testing of degraded samples, hairs and in the evenience of mass disasters. Currently, most forensic mtDNA laboratories focus on sequence information within the two hypervariable regions (HVI and HVII) of >600 bases within the control region. One limitation of mtDNA testing is the low power of discrimination associated with common HVI/HVII types: for example, in the European Caucasian forensic database, there are approximately twenty common HVI/HVII types, matching about twenty-one percent of the population. We have sequenced the entire mtDNA genome of 40 Italian individuals, classified according to the different areas of origin (North, Center, South and Insulae), in order to search for single nucleotide polymorphisms (SNPs) in the coding region, useful for additional discrimination (in haplogroup defining) and, if any, according to the different areas. In particular, we have payed attention to SNPs which were shared, neutral and non redundant and we have checked for previous descriptions in literature. We have described 8 new polymorphisms, 4 private mutations which could reveal to be useful discriminating SNPs, a new length polymorphism in HVIII, a new insertion, a new deletion and 2 sequence heteroplasmies, previously described as simple transitions; we have identified 7 individuals, harbouring particular haplotypes, one of whom is also interesting by a medical-genetic point of view. The other bulk of variation we have found has already been described and frequencies agree with those of Caucasians: a notable variability among represented haplogroups has been detected in the South of Italy, as could be expected by the pattern of migrations. Our work has shown the enormous variability, which is typical of mtDNA, even in a small sample of individuals and has demonstrated the utility of SNPs in defining the individual haplotypes, but has also pointed out the usefulness of increasing research in better defining mtDNA-associated diseases. On the other hand, it strongly supports the need for the improvement of the forensic database for mitochondrial DNA, not only regarding the control region, but also, as Gene Bank does, regarding the coding region. This may be reached by encouraging the submission of the newly described sequences to Gene Bank, issued according to standard guidelines for high quality data, which are currently been developed, and performing the whole Genome sequencing by universal, new technologies (NGS, Next Generation Sequencing).
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Leyland, Nicola Ruth. "Characterisation of null mutations in genes encoding components of antioxidant metabolism in Arabidopsis thaliana." Thesis, University of East Anglia, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.268507.
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Gardner, Allison. "Characterising and predicting amyloid mutations in proteins." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/characterising-and-predicting-amyloid-mutations-in-proteins(5fb5b725-ac9e-499b-81ee-f9ce7cbcb19e).html.
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A database, AmyProt, was developed that collated details of 32 human amyloid proteins associated with disease and 488 associated mutations and polymorphisms, of which 316 are classified as amyloid. A detailed profile of the mutations was developed in terms of location within domains and secondary structures of the proteins and functional effects of the mutations. The data was used to test the hypothesis that mutations enhance amyloidosis in human amyloid proteins have distinctive characteristics, in terms of specific location within proteins and physico-chemical characteristics, which differentiate them from non-amyloid forming polymorphisms in amyloid proteins and from disease mutations and polymorphisms in non-amyloid disease linked proteins. The aim was to use these characteristics to train a prediction algorithm for amyloid mutations that will provide a more accurate prediction than current general disease prediction tools and amyloid prediction tools that focus on aggregating regions. 66 location specific features and changes upon mutation of 366 amino acids propensities, derived from the amino acid index database AAindex, were analysed. A significant proportion of mutations were located with aggregating regions, however the majority of mutations were not associated with these regions. An analysis of motifs showed that amyloid mutations had a significant association with transmembrane helix motifs such as GxxxG. Statistical analysis of substitutions mutations, using substitution matrices, showed that amyloid mutations have a decrease in α-helix propensity and overall secondary structure propensity compared to the disease mutations and disease and amyloid polymorphisms. Machine learning was used to reduce the large set of features to a set of 18 features. These included location near transmembrane helices, secondary structure features; transmembrane and extracellular domains and 4 amino acid propensities: knowledge-based membrane propensity scale from 3D helix; α-helix propensity; partition coefficient; normalized frequency of coil. The AmyProt mutations and non-amyloid polymorphisms were used to train and test the novel amyloid mutation prediction tool, AmyPred, the first tool developed purely to predict amyloid mutations. AmyPred predicts the amyloidogenicity of mutations as a consensus by majority vote (CMV) and mean probability (CMP) of 5 classifiers. Validation of AmyPred with 27 amyloid mutations and 20 non-amyloid mutations from APP, Tau and TTR proteins, gave classification accuracies of 0.7/0.71 (CMV/CMP) and with an MCC of 0.4 (CMV) and 0.41 (CMP). AmyPred out performed other tools such as SIFT (0.37) and PolyPhen (0.36) and the amyloid consensus prediction tool, MetAmyl (0.13). Finally, AmyPred was used to analyse p53 mutations to characterize amyloid and non-amyloid mutations within this protein.
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Jansson, Bertheussen Nina, and Lina Welander. "Databas i Microsoft Access för forskningsstudie angående ärftlig mutation i genen TP53." Thesis, KTH, Skolan för teknik och hälsa (STH), 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-190874.
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I det här projektet har en databas byggts till ett nationellt forskningsprojekt angående nedärvda mutationer i genen TP53. Forskningsprojektets syfte är att få en större förståelse för mutationer i TP53 och dess effekt på den ökade förekomster av cancersjukdomar hos personer med den här mutationen. Eftersom det inom forskningsprojektet kommer samlas ihop mycket information som behöver lagras på ett överskådligt sätt finns ett behov av en användarvänlig databas som uppfyller deras krav. Målet med det här projektet var att bygga en databas i programmet Microsoft Access för att användas i det här forskningsprojektet. Databasen skulle kunna lagra, filtrera och sortera stora mängder information. Uppdragsgivarna önskade att databasen skulle vara ''lättanvänd och överskådlig'', samt att det skulle vara ''svårt att göra fel''. Efter många möten med uppdragsgivarna där databasen har demonstrerats och förklarats har ändringar och uppdateringar gjorts löpande för att nå upp till uppdragsgivarnas önskemål och krav. En färdig databas fanns tillgänglig till uppdragsgivarna när projektet var färdigt och vi anser att målen är uppfyllda, även om det finns säkerhets- och sekretessaspekter för uppdragsgivarna att arbeta vidare med innan databasen kan implementeras fullt ut i forskningsprojektet.In this project, a data base have been built for a national research project regarding effects of heritage germline mutations in the gene TP53. The aim of the study is to get a greater understanding about the mutations in TP53 and its effects on the increased presence of tumours and cancer diseases in people with this kind of mutation. Since a lot of data is being collected there is a need for a simple and user friendly data base to store all the information. The aim of this project was to create a data base in Microsoft Access that can be used in the research project for storing data and also to simplify analyses of the results. The employer of this project wanted a ''simple-to-use and easily managed'' data base, and that it should be ''hard to make a mistake''. Muliple demonstration and explanatory meetings were held to update the employer regularly and to get important feedback about changes and other requests. A ready-to-use data base was handed to the employer at the end of the project and we consider that the demands where met, even though there is still a safety and secrecy issue that the employer needs to take care of before the data base can be fully operational.
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Toledo, Ludmila Irineu. "MutShrink: um método de redução de banco de dados de teste baseado em mutação." Universidade Federal de Goiás, 2017. http://repositorio.bc.ufg.br/tede/handle/tede/7737.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
Regression testing for database applications can be a computationally costly task as it often deals with databases with large volumes of data and complex SQL statements (for example, nested queries, set comparisons, use of functions and operators). In this context, some works only select a subset of the database for testing purposes, that is, select data to create a test database and thus improve test efficiency. But usually, the selection of test data is also a complex optimization problem. Thus, this work proposes a method of selecting test data for regression testing on SQL statements based on mutation analysis, called MutShrink. The goal is to minimize the cost of testing by reducing the size of the database while maintaining the same effectiveness as the original database. MutShrink consists of using the result of the generated mutants to evaluate the database and select tuples using filters in these results, selecting reduced sets of test data. Experiments were performed using a benchmark with complex SQLs and database with large data volume. We compared our proposal with the QAShrink tool and the results revealed that MutShrink overcame the QAShrink tool in 92.85 % of cases when evaluated by the Mutation Score metric and 57.14 % of cases when evaluated by the metric Full Predicate Coverage.
O teste de regressão para aplicações de banco de dados pode ser uma tarefa computacionalmente custosa, pois frequentemente lida com bancos de dados com grandes volumes de dados e instruções SQL com estruturas complexas (por exemplo, consultas aninhadas, comparação de conjuntos, uso de funções e operadores). Neste contexto, alguns trabalhos realizam seleção apenas de um subconjunto do banco de dados para fins de teste, ou seja, selecionam dados para criar um banco de dados de teste e assim, melhorar a eficiência do teste. Mas, normalmente, a seleção de dados de teste também é um problema complexo de otimização. Assim, este trabalho propõe um método de seleção de dados de teste para teste de regressão em instruções SQLs baseado em análise de mutação, chamado MutShrink. O objetivo é minimizar o custo do teste reduzindo o tamanho do banco de dados, mantendo a eficácia semelhante ao banco original. O MutShrink consiste em utilizar o resultado dos mutantes gerados para avaliar o banco de dados e selecionar tuplas a partir de filtros nestes resultados, selecionando conjuntos reduzidos de dados de teste. Foram realizados experimentos usando um benchmark com SQLs de estruturas complexas e banco de dados com grande volume de dados. Comparamos nossa proposta com a ferramenta QAShrink e os resultados revelaram que o MutShrink superou a ferramenta QAShrink em 92,85% dos casos quando avaliada pela métrica Escore de Mutação e em 57,14% dos casos quando avaliada pela métrica Full Predicate Coverage.
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Rallapalli, P. M. "Interactive locus-specific databases and evolutionary aspects of the mutations in coagulation proteins." Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1458877/.
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Blood coagulation occurs through a cascade of enzymes and cofactors that produces a fibrin clot, while otherwise maintaining haemostasis. The 11 human coagulation factors (FG, FII-FXIII) are associated with thousands of mutations. Variations caused by these mutations are the basis for evolutionary consequences and several of these mutations are also associated with clinically diagnosable bleeding disorders. Trailing the success of sequencing and diagnostic methods, increasing numbers of mutations are being compiled in order to present a more detailed patient-specific description of the disease. This thesis describes an interactive locus-specific database system in which the mutations in patients with haemophilia (A and B) are presented in searchable formats, and viewed in comparisons against protein structures and sequence alignments. The approach used within these databases are set up in a way that they could be extended and combined with a database management system to design a mutation database for the other bleeding disorders of the coagulation system. Our main focus was to correlate the protein sequence and structure with their functional interactions, also keeping in mind the evolutionary selective pressure at the mutation sites. We evaluated the strength of selective pressures on the 11 coagulation factors during vertebrate evolution, and compared these with human mutations in FVIII, FIX and FXI. We have showed that the coagulation system in vertebrates was under strong selective pressures, perhaps to adapt against blood-invading pathogens. It was concluded that when a site was under positive selection, it was less likely to be associated with disease-causing mutations. In contrast, sites under negative selection were more likely to be associated with disease-causing mutations and be destabilizing. The scientific design of the databases with improved understanding of evolutionary changes will lead to a more comprehensive comparative understanding of the genetic factors that influence bleeding risk thus providing optimised genetic services.
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Romanet, Pauline. "Etiologies héréditaires et somatiques des adénomes hypophysaires : étude du gène Men1 et du locus Gnas." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0278/document.
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La Néoplasie Endocrinienne Multiple de type 1 (NEM1) est une maladie génétique qui associe hyperparathyroïdie primaire, tumeurs neuroendocrines digestives et adénomes hypophysaires. Elle est due à des mutations non récurrentes du gène MEN1, parfois difficile à classer. Nous avons rassemblé et analysé les données cliniques et génétiques de 1676 patients français porteurs d’une variation de MEN1 des 4 laboratoires experts du groupe TENGEN. De ce travail, nous avons alimenté une base de données de variants (UMD MEN1) et établir le profil mutationnel de MEN1 en France. Dans une seconde partie, nous avons établi des recommandations pour la classification des variants faux sens de MEN1 en adaptant les Guidelines de l’ACMG-AMP (American College of Medical Genetics).Le Syndrome de McCune-Albright (SMA) est du à des mutations postzygotiques activatrices récurrentes du gène GNAS, responsables d’un mosaïcisme somatique, souvent indétectables dans le sang. En utilisant une technique de PCR quantitative ultrasensible, le taux de détection des mutations R201C et R201H est de 50% dans le sang de 16 patients présentant 1 à 3 lésions majeures du SMA. Pour la 1ere fois, nous avons retrouvé ces mutations dans l’ADN circulant de 3/4 patients testés.Ces mutations sont retrouvées aussi dans 30 à 40% des adénomes somatotropes. Le locus GNAS est soumis à empreinte parentale, responsable d’une expression mono-allélique de GNAS dans certains tissus comme l’hypophyse. Dans une série de 57 adénomes somatotropes nous avons montré une perturbation de l’empreinte de GNAS, associée à une relâche de l’empreinte mais n’entraînait pas d’augmentation de l’expression du gène GNASThe Multiple Endocrine Neoplasia 1 (MEN1) is due to MEN1 mutations and characterized by a broad spectrum of lesions including hyperparathyroidism, pituitary adenomas and neuroendocrine tumors. Missense variants are frequent and could lead wrong interpretation. We collected and analyzed all the 370 variants of 1676 patients sequenced for ten years by the TENGEN network (French oncogenetics of neuroendocrine tumors). We registered them in the UMD MEN1 database. Then, consensus was reached to validate adjustments to the ACMG-AMP guidelines for MEN1 locus-specific interpretation of missense variants. The McCune-Albright syndrome (MAS) is a rare pediatric mosaic genetic disorder. MAS results from recurrent post-zygotic GNAS mutations, not detectable in blood DNA by Sanger. We develop an ultrasensitive quantitative PCR using digital droplet PCR™ (ddPCR™) in order to target the R201C and R201H GNAS mutations. After a validation study, we clinically evaluated ddPCR™ in the whole blood DNA or circulating cell-free DNA (ccfDNA) of patients presented with at least 1 MAS lesion. First we detected in ccfDNA the mosaic somatic GNAS mutant. The ddPCR™ showed a mutation detection rate of 50% in blood DNA of the 16 included patients and 3/4 in ccfDNA.GNAS mutations are also reported in 30 to 40% of somatotroph tumors. GNAS is encoded by an imprinted locus, responsible for a mono-allelic expression in pituitary. We explored the GNAS locus methylation status of 57 somatotroph adenomas and showed disturbance. We studied the impact on GNAS, SST2R and AIP expression of this disturbance. We showed an imprinting relaxation not associated with an increased expression of GNAS
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Lopes, Andreia Sofia dos Santos. "Genetic basis of congenital Erythrocytosis: search for new mutations and associated genes and update of online databases." Master's thesis, Universidade de Aveiro, 2017. http://hdl.handle.net/10773/22704.
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Mestrado em Bioquímica - Bioquímica ClínicaEritrocitose Congénita (EC) designa um grupo de patologias que podem ser primárias ou secundárias, sendo classificadas com base nos níveis de eritropoietina (EPO). A EC primária, devida a alterações nos percursores eritroides, é causada por alterações no recetor da eritropoietina (EpoR) devido a mutações nos genes EPOR e SH2B3. O EpoR fica permanentemente ativado, o que leva à diminuição dos níveis de EPO. A EC secundária pode ser causada por alterações de componentes na via de sensibilização ao oxigénio, devido a mutações nos genes VHL, EGLN1 e EPAS1, ou devido a hemoglobinas de alta afinidade para o oxigénio em consequência de mutações nos genes HBA, HBB e BPGM. Mutações nestes genes promovem um aumento dos níveis de EPO. Apesar de já estarem descritas causas moleculares para a origem da EC, cerca de 70% dos doentes ainda permanecem sem uma causa genética identificada. Neste estudo foram analisadas 125 amostras de indivíduos com suspeita de EC, seguidos no Centro Hospitalar e Universitário de Coimbra ou enviados de outros hospitais portugueses/internacionais. Os testes laboratoriais foram orientados com base na história clínica e familiar e nos níveis de EPO, e incluíram a sequenciação dos genes: EPOR, SH2B3, VHL, EGLN1, EPAS1, HBA, HBB, BPGM. Foram identificadas 5 mutações: 3 no gene VHL (c.74C>T, p.Pro25Leu; c.154G>T, p.Glu52*; c.241C>T, p.Pro81Ser), 1 no gene EGLN1 (c.1216G>C, p.Gly406Arg) e 1 no gene HBB (Hb San Diego [HBB: c.328G>A, p.Val110Met]). Mutações no gene VHL têm uma transmissão autossómica recessiva estando descritos casos esporádicos em que se encontra apenas uma mutação, também neste estudo todas as mutações encontradas estão em heterozigotia. O mecanismo subjacente nestes casos ainda permanece por elucidar. A mutação encontrada no gene EGLN1 não está descrita na literatura, segundo a análise in sílico é uma variante patogénica, pelo que deverá ser a causa da EC. No gene HBB a variante foi identificada num individuo de origem turca, sendo a primeira descrição desta variante na Turquia. Concluindo, neste estudo foi possível identificar a causa molecular da EC em 5/125 doentes estudados. Foram encontradas 4 mutações descritas e 1 nova mutação. No entanto, 120 doentes ainda permanecem sem diagnóstico molecular. Isto demonstra que mais estudos são necessários para entender esta doença. O uso da tecnologia de Next Generation Sequencing (NGS) pode ser uma ferramenta valiosa no estudo da EC, uma vez que pode identificar outros genes que possam estar envolvidos na EC.
Congenital Erythrocytosis (CE) belongs to a diseases group that can be primary or secondary, and are classified based on EPO levels. Primary CE, due to mutations in the erythroid precursors, is caused by changes in EPO receptor (EpoR) due to mutations in EPOR and SH2B3 genes. EpoR is permanently activated, which leads to a decrease in EPO levels. Secondary CE can be caused by defects in the components of the oxygen-sensing pathway, namely mutations in VHL, EGLN1 and EPAS1, or due to congenital defects such as Hbs with increased oxygen affinity, due to mutations in the HBB, HBA or BPGM. Mutations in these genes leads to an increase of EPO levels. Despite important discoveries in the molecular pathogenesis of CE, in about 70% of the patients the genetic causes remain to be identified. In this study were analysed 125 samples of individuals with suspicious of CE, followed in Centro Hospitalar e Universitário de Coimbra or from other Portuguese/international hospitals. Laboratory testing was guided by clinical and familiarhistory and EPO levels, and included: EPOR, SH2B3, VHL, EGLN1, EPAS1, HBA, HBB, BPGM sequencing. Were identified 5 mutations: 3 in VHL gene (c.74C>T, p.Pro25Leu; c.154G>T, p.Glu52*; c.241C>T, p.Pro81Ser), 1 in EGLN1 gene (c.1216G>C, p.Gly406Arg) and 1 in HBB gene (Hb San Diego [HBB: c.328G>A, p.Val110Met]). Mutations in VHL gene have an autosomal recessive inheritance, with sporadic cases in which only one mutation is found, also in this study all the mutations found are in heterozygosity. The underlying mechanism in these cases still remains to be elucidated. The mutation found in the EGLN1 gene is not described in the literature, according to in silico analysis it is a pathogenic variant and should therefore be the cause of CE. In the HBB gene the variant was identified in an individual of Turkish origin, the first description of this variant in Turkey In conclusion, in this study was possible to identify the CE molecular aetiology in 5/125 patients studied. It was found 4 described mutations and 1 new mutation. However, 120 patients still remain without molecular diagnosis. This demonstrates that more studies are needed to understand this disease. The use of Next Generation Sequencing (NGS) technology can be a valuable tool in the study of CE as it can identify other genes that may be involved in CE.
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Dúbrava, Juraj Ondrej. "Interaktivní databáze pro úschovu a údržbu biologických dat." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2021. http://www.nusl.cz/ntk/nusl-445536.
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Cieľom tejto práce je vytvorenie novej databázy dát pre proteínovú stabilitu, ktorá bude udržiavať a poskytovať experimentálne dáta. Výsledkom práce je databáza FireProtDB, ktorá poskytuje manuálne overené experimentálne dáta z dostupných zdrojov a implementuje grafické užívateľské rozhranie, ktoré poskytuje dôležité informácie o dátach spoločne s možnosťou vyhľadávania umožňujúcim vytvárať dotazy na mieru a cieliacim na užívateľov, ktorí hľadajú dáta pre vytváranie dátových sád pre nástroje využívajúce strojové učenie.
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Oliveros, Marcia Perez Resende. ""Prevalência e covariação de mutações relacionadas à resistência aos inibidores de protease no subtipo F do HIV-1"." Universidade de São Paulo, 2005. http://www.teses.usp.br/teses/disponiveis/5/5160/tde-19102005-105311/.
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Cada subtipo de HIV-1 tem um padrão mutacional próprio. Dados sobre mutações de resistência aos antiretrovirais foram obtidos com o subtipo B, primeiro em prevalência no Brasil. O segundo em algumas regiões é o subtipo F. Foram analisados padrões mutacionais em seqüências brasileiras de protease do subtipo F e levantou as seqüências deste subtipo disponíveis na base de dados de Stanford. A análise de dois grupos de seqüências (pacientes não tratados e tratados com inibidores de protease) mostrou 19 mutações associadas ao tratamento comuns ao subtipo B e 17 duplas de mutações associadas ao tratamento que diferem das descritas para o subtipo B, indicando a necessidade de estudos sobre rotas mutacionais no subtipo F.Each HIV-1 subtype has a specific mutation pattern. Data on HIV-1 antiretroviral resistance mutations were obtained with subtype B, the first in prevalence in Brazil. The second in some regions is subtype F. Mutation patterns of Brazilian subtype F protease sequences were analyzed and performed a research of the sequences of Stanford Database. The analysis of two groups of sequences (untreated and treated patients with protease inhibitors) showed 19 treatment associated mutations also common in subtype B and 17 combinations of statistically treatment associated mutations that were quite different to those described for subtype B, indicating the need of studies to evaluate specific mutation pathways of subtype F.
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Pinard, Amélie. "Le syndrome de Marfan et pathologies associées : identification de nouveaux gènes impliqués dans la bicuspidie de la valve aortique." Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM5022.
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Le syndrome de Marfan (MFS) est une maladie génétique rare. Les signes cliniques sont principalement squelettiques, oculaires et cardiovasculaires. Le premier gène identifié est FBN1. Une LSDB UMD créée en 1995 a permis de colliger les mutations identifiées chez les patients. D’autres gènes ont été identifiés comme causant des syndromes apparentés : FBN2, TGFBR1, TGFBR2, ACTA2, SMAD3, MYH11 et MYLK. Ma thèse avait pour but de mettre à jour ces différentes bases et de créer celles des nouveaux gènes. Les techniques de séquençage nouvelle génération dans la pratique clinique amènent des médecins non spécialistes à rapporter des variations secondaires dans ces gènes « actionable ». Il s’agit de la ressource la plus complète pour les cliniciens et les généticiens pour interpréter les variants associés au MFS et ses pathologies associées pour les variants primaires et secondaires.La bicuspidie de la valve aortique (2 feuillets au lieu de 3) est la malformation cardiovasculaire la plus fréquente touchant 0,6 à 2 % de la population. Ma thèse avait pour but d’identifier de nouveaux gènes impliqués dans la BAV. Grâce à une cohorte de 200 patients, le gène HOXA1, un facteur de transcription, a pu être examiné de manière plus approfondie. Alors qu’il contient une répétition de 10 histidines, les individus hétérozygotes mutés en présentent 11. Mes études ont permis de démontrer l’imputabilité de cette mutation. Dans un second temps, un séquençage d’exomes entiers a permis de mettre en évidence de nouveaux variants prédits pathogènes. Ces données permettront de mieux comprendre le rôle physiologique d’HOXA1 et des nouveaux gènes candidats dans la pathogénèse de la BAV chez l’humainMarfan Syndrome is a rare genetic disorder. Clinical signs are mainly skeletal, ocular and cardiovascular. The first gene identified is FBN1. A LSDB UMD was created in 1995 to colligate all the mutations identified in. Thereafter, several others genes were identified involved in related disorders : FBN2, TGFBR1 and TGFBR2, ACTA2, SMAD3, MYH11 and MYLK. The objectives of my PhD were to update these databases and to create new ones for genes. Next generation sequencing in clinical practice leads non-specialized doctors to report pathogenic secondary variants in “actionable” genes. Our databases are the only resources providing access to the full spectrum of known pathogenic mutations with checked and interpreted data from many reference diagnostic laboratories and research centers worldwide, and the most comprehensive resources for clinicians and geneticists to interpret variations linked to Marfan syndrome and related disorders not only primary but also secondary variants.Bicuspid Aortic Valve is the most common cardiovascular malformation affecting 0.6-2% of the population (2 leaflets instead of 3). Thanks to a cohort of 200 BAV patients, HOXA1 gene, a transcription factor, has been screened. While HOXA1 contains a string of 10 histidine repeats, these individuals are heterozygous for an 11 histidine repeat variant. My studies showed the imputability of this mutation. In a second phase, whole exome sequencing allow us to highlight new variants predicted pathogenic. Studies are still ongoing to confirm their imputability. These data contribute to our better understanding of the physiological of HOXA1 and new candidate genes in the pathogenesis of BAV disease in humans
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Al, Hawajri Abd Al Nasser. "Etude du polymorphisme et des mutations associées à la résistance dans les gènes codant la Protéase, la Reverse Transcriptase et la gp-41 du virus HIV-1 chez les patients naîfs et multitraités de Seine Saint-Denis et à partir des données d'une database internationale : différences entre les sous-types B et non -B." Paris 13, 2005. http://www.theses.fr/2005PA132036.
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Khawaja, Anas Ahmad. "Studie rozmanitosti HCV IRES: propojení experimentálního přístupu s přípravou a hodnocením rozsáhlé databáze mutací." Doctoral thesis, 2016. http://www.nusl.cz/ntk/nusl-351519.
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Translation initiation in the hepatitis C virus (HCV) occurs through a cap- independent mechanism that involves an internal ribosome entry site (IRES) capable of interaction with and utilization of the eukaryotic translational machinery. We focused on the structural configuration of the different HCV-IRES domains and the impact of IRES primary sequence variations on secondary structure conservation and function. For this purpose we introduced into our laboratory, methods such as denaturing gradient and temperature gradient gel electrophoresis for screening the degree of heterogeneity and total amount of HCV-IRES variability accumulated in HCV infected patients over a period of time. The selected samples showed variable migration pattern of the HCV-IRES (from all the patients) visualized in DGGE and TGGE, were sequenced and evaluated for translation efficiency using flow cytometry. In some cases, we discovered that multiple mutations, even those scattered across different domains of HCV-IRES, led to restoration of the HCV-IRES translational activity, although the individual occurrences of these mutations were found to be deleterious. We propose that such observation may be attributed to probable long- range inter- and/or intra-domain functional interactions. We established a large-scale HCV-IRES...
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Mayne, Christopher G. "BAFF-R mutation : a novel contributor to systemic autoimmunity /." 2008. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Amack, Jeffrey D. "Development and characterization of a cell culture model of the myotonic dystrophy trinucleotide (CTG) repeat expansion mutation /." 2002. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Gottwald, Jennifer Rose. "Mutational analysis of proteins involved in phloem transport in Arabidopsis." 2000. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Bua, Entela A. "The role of MTDNA deletion mutations, electron transport system abnormalities and calorie restriction on sarcopenia." 2004. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Vega, Amanda L. "Arrhythmia mutations in the cardiac inward rectifying potassium channel Kir2.1 (KCNJ2) : mechanisms for molecular and cellular phenotypes /." 2008. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Muangprom, Amorntip. "A novel dwarfing mutation in a "Green Revolution" gene in Brassica rapa : its role in the gibberellin pathway and its potential use in agriculture /." 2004. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Wanagat, Jonathan. "The role of mitochondrial DNA deletion mutations in the pathogenesis of aging : studies in rodent heart and skeletal muscle /." 2000. http://www.library.wisc.edu/databases/connect/dissertations.html.
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Ye, Bin. "Structure-function of the cardiac sodium channel (SCN5A/Nav1.5) - the common background sequence and the effects of naturally occuring (pathogenic and non-pathogenic) and designed mutations /." 2002. http://www.library.wisc.edu/databases/connect/dissertations.html.
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