Relevant bibliographies by topics / Mutation database

Academic literature on the topic 'Mutation database'

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Published: 9 March 2023
Last updated: 10 March 2023

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Journal articles on the topic "Mutation database"

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Gottlieb, Bruce, Lenore K. Beitel, and Mark A. Trifiro. "Variable expressivity and mutation databases: The androgen receptor gene mutations database." Human Mutation 17, no. 5 (2001): 382–88. http://dx.doi.org/10.1002/humu.1113.

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Lee, Joon-Hyop, Jiyoung Ahn, Won Seo Park, Eun Kyung Choe, Eunyoung Kim, Rumi Shin, Seung Chul Heo, et al. "Colorectal Cancer Prognosis is Not Associated with BRAF and KRAS Mutations-A STROBE Compliant Study." Journal of Clinical Medicine 8, no. 1 (January 17, 2019): 111. http://dx.doi.org/10.3390/jcm8010111.

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Background: We investigated the associations between v-Raf murine sarcoma viral oncogene homolog B1 (BRAFV600E, henceforth BRAF) and v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations and colorectal cancer (CRC) prognosis, using The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GSE39582) datasets. Materials and Methods: The effects of BRAF and KRAS mutations on overall survival (OS) and disease-free survival (DFS) of CRC were evaluated. Results: The mutational status of BRAF and KRAS genes was not associated with overall survival (OS) or DFS of the CRC patients drawn from the TCGA database. The 3-year OS and DFS rates of the BRAF mutation (+) vs. mutation (−) groups were 92.6% vs. 90.4% and 79.7% vs. 68.4%, respectively. The 3-year OS and DFS rates of the KRAS mutation (+) vs. mutation (−) groups were 90.4% vs. 90.5% and 65.3% vs. 73.5%, respectively. In stage II patients, however, the 3-year OS rate was lower in the BRAF mutation (+) group than in the mutation (−) group (85.5% vs. 97.7%, p <0.001). The mutational status of BRAF genes of 497 CRC patients drawn from the GSE39582 database was not associated with OS or DFS. The 3-year OS and DFS rates of BRAF mutation (+) vs. mutation (−) groups were 75.7% vs. 78.9% and 73.6% vs. 71.1%, respectively. However, KRAS mutational status had an effect on 3-year OS rate (71.9% mutation (+) vs. 83% mutation (−), p = 0.05) and DFS rate (66.3% mutation (+) vs. 74.6% mutation (−), p = 0.013). Conclusions: We found no consistent association between the mutational status of BRAF nor KRAS and the OS and DFS of CRC patients from the TCGA and GSE39582 databases. Studies with longer-term records and larger patient numbers may be necessary to expound the influence of BRAF and KRAS mutations on the outcomes of CRC.
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Stenson, P. D., E. Ball, K. Howells, A. Phillips, M. Mort, and D. N. Cooper. "Human Gene Mutation Database: towards a comprehensive central mutation database." Journal of Medical Genetics 45, no. 2 (September 24, 2007): 124–26. http://dx.doi.org/10.1136/jmg.2007.055210.

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Ping, Jie, Olufunmilola Oyebamiji, Hui Yu, Scott Ness, Jeremy Chien, Fei Ye, Huining Kang, et al. "MutEx: a multifaceted gateway for exploring integrative pan-cancer genomic data." Briefings in Bioinformatics 21, no. 4 (October 7, 2019): 1479–86. http://dx.doi.org/10.1093/bib/bbz084.

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Abstract Somatic mutation and gene expression dysregulation are considered two major tumorigenesis factors. While independent investigations of either factor pervade, studies of associations between somatic mutations and gene expression changes have been sporadic and nonsystematic. Utilizing genomic data collected from 11 315 subjects of 33 distinct cancer types, we constructed MutEx, a pan-cancer integrative genomic database. This database records the relationships among gene expression, somatic mutation and survival data for cancer patients. MutEx can be used to swiftly explore the relationship between these genomic/clinic features within and across cancer types and, more importantly, search for corroborating evidence for hypothesis inception. Our database also incorporated Gene Ontology and several pathway databases to enhance functional annotation, and elastic net and a gene expression composite score to aid in survival analysis. To demonstrate the usability of MutEx, we provide several application examples, including top somatic mutations associated with the most extensive expression dysregulation in breast cancer, differential mutational burden downstream of DNA mismatch repair gene mutations and composite gene expression score-based survival difference in breast cancer. MutEx can be accessed at http://www.innovebioinfo.com/Databases/Mutationdb_About.php.
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Nebel, Istvan T., Barbara Trültsch, and Ralf Paschke. "TSH Receptor Mutation Database." Journal of Clinical Endocrinology & Metabolism 84, no. 6 (June 1999): 2263. http://dx.doi.org/10.1210/jcem.84.6.5809-9.

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Cooper, D. N., and Michael Krawczak. "Human Gene Mutation Database." Human Genetics 98, no. 5 (September 26, 1996): 629. http://dx.doi.org/10.1007/s004390050272.

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Niesler, Beate, Christine Fischer, and Gudrun A. Rappold. "The humanSHOX mutation database." Human Mutation 20, no. 5 (October 25, 2002): 338–41. http://dx.doi.org/10.1002/humu.10125.

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Beysen, Diane, Jo Vandesompele, Ludwine Messiaen, Anne De Paepe, and Elfride De Baere. "The humanFOXL2 mutation database." Human Mutation 24, no. 3 (2004): 189–93. http://dx.doi.org/10.1002/humu.20079.

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Wertheim-Tysarowska, Katarzyna, Agnieszka Sobczyńska-Tomaszewska, Cezary Kowalewski, Michał Skroński, Grzegorz Święćkowski, Anna Kutkowska-Kaźmierczak, Katarzyna Woźniak, and Jerzy Bal. "The COL7A1 mutation database." Human Mutation 33, no. 2 (December 20, 2011): 327–31. http://dx.doi.org/10.1002/humu.21651.

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Shemansky, Jennifer M., Lea Patrice McDaniel, Christopher Klimas, Stephen D. Dertinger, Vasily N. Dobrovolsky, Takafumi Kimoto, Katsuyoshi Horibata, James E. Polli, and Robert H. Heflich. "Pig‐agene mutation database." Environmental and Molecular Mutagenesis 60, no. 8 (June 7, 2019): 759–62. http://dx.doi.org/10.1002/em.22298.

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Dissertations / Theses on the topic "Mutation database"

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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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Books on the topic "Mutation database"

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L, Mendelsohn Mortimer, and Albertini Richard J, eds. Mutation and the environment: Proceedings of the Fifth International Conference on Environmental Mutagens, held in Cleveland, Ohio, July 10-15, 1989. New York: Wiley-Liss, 1990.

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Wong, W. Eric. Mutation Testing for the New Century (Advances in Database Systems). Springer, 2001.

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Richards, G., and O. Oud. Mutations: An Interactive Education Tool for Secondary Schools and Undergraduates University Teaching (World Biodiversity Database Electronic Series). UNESCO, 2003.

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Book chapters on the topic "Mutation database"

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Collod-Béroud, Gwenaëlle, and Catherine Boileau. "The Marfan Mutation Database." In Marfan Syndrome: A Primer for Clinicians and Scientists, 101–12. Boston, MA: Springer US, 2004. http://dx.doi.org/10.1007/978-1-4419-9013-6_9.

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Do, Van-Nho, Quang-Vu Nguyen, and Thanh-Binh Nguyen. "Evaluating Mutation Operator and Test Case Effectiveness by Means of Mutation Testing." In Intelligent Information and Database Systems, 837–50. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-73280-6_66.

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Masrom, S., Siti Z. Z. Abidin, N. Omar, and K. Nasir. "Time-Varying Mutation in Particle Swarm Optimization." In Intelligent Information and Database Systems, 31–40. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-36546-1_4.

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Nguyen, Quang Vu, and Lech Madeyski. "Higher Order Mutation Testing to Drive Development of New Test Cases: An Empirical Comparison of Three Strategies." In Intelligent Information and Database Systems, 235–44. Berlin, Heidelberg: Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/978-3-662-49381-6_23.

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Nguyen, Quang Vu, and Lech Madeyski. "On the Relationship Between the Order of Mutation Testing and the Properties of Generated Higher Order Mutants." In Intelligent Information and Database Systems, 245–54. Berlin, Heidelberg: Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/978-3-662-49381-6_24.

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Cruts, Marc, and Christine Van Broeckhoven. "Data Mining: Applying the AD&FTD Mutation Database to Progranulin." In Methods in Molecular Biology, 81–92. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8559-3_6.

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Hu, Peng, Yongli Wang, Hening Wang, Ruxin Zhao, Chi Yuan, Yi Zheng, Qianchun Lu, Yanchao Li, and Isma Masood. "ALO-DM: A Smart Approach Based on Ant Lion Optimizer with Differential Mutation Operator in Big Data Analytics." In Database Systems for Advanced Applications, 64–73. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-91455-8_6.

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Sevanthi, Amitha Mithra V., Prashant Kale, Chandra Prakash, M. K. Ramkumar, Neera Yadav, V. Sureshkumar, Yugandhar Poli, et al. "National repository of EMS induced mutants of an upland rice cultivar Nagina 22: progress update on characterization and utilization." In Mutation breeding, genetic diversity and crop adaptation to climate change, 290–302. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0030.

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Abstract The Indian initiative for creating mutant resources in rice has generated 87,000 mutants in the background of a popular drought- and heat-tolerant upland cultivar, Nagina 22 (N22), through EMS mutagenesis. So far, 541 macro-mutants from this resource have been identified, maintained in the mutant garden and characterized in detail based on 44 descriptors pertaining to distinctness, uniformity and stability (DUS) of rice and other agronomic parameters. The similarity index of the mutants was more than 0.6 for nearly 90% of the mutants with respect to DUS descriptors, further establishing the validity of the mutants. The available high-quality sequence resource of N22 has been improved by reducing the gaps by 0.02% in the coding sequence (CDS) region. This was made possible using the newly synthesized whole-genome data of N22 which helped to remove 9006 'Ns' and replace 12,746 existing nucleotides with the accurate ones. These sequence and morphological details have been updated in the mutant database 'EMSgardeN22'. Further, 1058 mutants have been identified for low-P tolerance, tolerance to sheath blight, blast, drought, heat, higher photosynthetic efficiency and agronomic and root traits from this resource. A novel herbicide-tolerant (imazethapyr) mutant earlier identified and characterized from this resource is now being used in introgressing the herbicide-tolerant trait in eight major rice varieties in India. Further, robust and simpler screening systems have been tested for studying low-P tolerance of the mutants. A grain-size mutant, heat-tolerant mutant, drought-tolerant mutant, stay-green mutant and low-P tolerant and water-use efficient high-root-volume mutants have been characterized at morphological and molecular levels. A brief account of all these mutants, the entire mutant resource and the elaborate trait-based screenings is presented in this chapter.
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Zatkova, Andrea, Tatiana Sedlackova, Jan Radvansky, Helena Polakova, Martina Nemethova, Robert Aquaron, Ismail Dursun, Jeannette L. Usher, and Ludevit Kadasi. "Identification of 11 Novel Homogentisate 1,2 Dioxygenase Variants in Alkaptonuria Patients and Establishment of a Novel LOVD-Based HGD Mutation Database." In JIMD Reports, 55–65. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/8904_2011_68.

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Anagnostopoulos, Anna V. "TBASE : The Relationalized Database of Transgenic Animals and Targeted Mutations." In Transgenic Animals, 533–52. London: CRC Press, 2022. http://dx.doi.org/10.1201/9781003211099-99.

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Conference papers on the topic "Mutation database"

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Tuya, Javier, Ma Jose Suarez-Cabal, and Claudio de la Riva. "SQLMutation: A tool to generate mutants of SQL database queries." In Second Workshop on Mutation Analysis (Mutation 2006 - ISSRE Workshops 2006). IEEE, 2006. http://dx.doi.org/10.1109/mutation.2006.13.

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Cabeca, Andrea Gonçalves, Mario Jino, and Plinio S. Leitao-Junior. "Mutation Analysis for SQL Database Applications." In 2009 Fourth International Conference on Software Engineering Advances (ICSEA). IEEE, 2009. http://dx.doi.org/10.1109/icsea.2009.30.

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Zhou, Chixiang, and Phyllis Frankl. "Mutation Testing for Java Database Applications." In 2009 International Conference on Software Testing Verification and Validation (ICST). IEEE, 2009. http://dx.doi.org/10.1109/icst.2009.43.

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McMinn, Phil, Gregory M. Kapfhammer, and Chris J. Wright. "Virtual mutation analysis of relational database schemas." In the 11th International Workshop. New York, New York, USA: ACM Press, 2016. http://dx.doi.org/10.1145/2896921.2896933.

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Toledo, Ludmila I., Celso G. Camilo, and Cassio Leonardo Rodrigues. "MutShrink: a Mutation-based Test Database Shrinking Method." In 2020 IEEE International Conference on Systems, Man, and Cybernetics (SMC). IEEE, 2020. http://dx.doi.org/10.1109/smc42975.2020.9283198.

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Pant, Millie, Radha Thangaraj, and Ajith Abraham. "Particle Swarm Optimization Using Adaptive Mutation." In 2008 19th International Conference on Database and Expert Systems Applications (DEXA). IEEE, 2008. http://dx.doi.org/10.1109/dexa.2008.70.

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Pan, Kai, Xintao Wu, and Tao Xie. "Automatic test generation for mutation testing on database applications." In 2013 8th International Workshop on Automation of Software Test (AST). IEEE, 2013. http://dx.doi.org/10.1109/iwast.2013.6595801.

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Shahriar, Hossain, and Sheetal Batchu. "Towards mutation-based testing of column-oriented database queries." In the 2014 ACM Southeast Regional Conference. New York, New York, USA: ACM Press, 2014. http://dx.doi.org/10.1145/2638404.2638470.

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McCormick, Donald W., William B. Frakes, and Reghu Anguswamy. "A comparison of database fault detection capabilities using mutation testing." In the ACM-IEEE international symposium. New York, New York, USA: ACM Press, 2012. http://dx.doi.org/10.1145/2372251.2372310.

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Moncao, Ana Claudia B. Loureiro, Celso G. Camilo, Leonardo T. Queiroz, Cassio L. Rodrigues, Plinio de Sa Leitao, and Auri M. R. Vincenzi. "Shrinking a database to perform SQL mutation tests using an evolutionary algorithm." In 2013 IEEE Congress on Evolutionary Computation. IEEE, 2013. http://dx.doi.org/10.1109/cec.2013.6557874.

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Reports on the topic "Mutation database"

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Juvik, John A., Avri Bar Zur, and Torbert R. Rocheford. Breeding for Quality in Vegetable Maize Using Linked Molecular Markers. United States Department of Agriculture, January 1993. http://dx.doi.org/10.32747/1993.7568764.bard.

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Recently, the vegetable corn industry has shifted from the use of traditional cultivars with the sugary1 (su1) endosperm mutation to newer hybrids homozygous for the shrunken2 (sh2) or sugary enhancer1 (se1) genes. With greater kernel sucrose content, these hybrids are preferred by consumers and retain sugar for longer post harvest periods, providing the industry with more time to marker products with superior quality. Commercialization has been hindered, however, by reduced field emergence, and the establishment of stands with heterogeneous uniformity and maturities. This investigation was conducted to identify key biochemical and physiological characteristics in sh2 and se1 maize kernels associated with improved emergence, and stand establishment; and in immature ears at fresh harvest maturity, properties associated with eating quality. The location of genes or QTL controlling these kernel characteristics and other traits were then mapped to specific chromosomal regions by their linkage to molecular markers using two segregating F2:3 populations. This database was used to compare the efficiency of marker-assisted selection of key alleles with phenotypic selection for trait improvement. A model designed to uncover and quantify digenic interaction was applied to the datasets to evaluate the role of epistasis in the inheritance of quantitative traits.
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Zhao, Lili, Tao Li, Meijuan Dang, Ye Li, Hong Fan, Qian Hao, Dingli Song, et al. Association of methylenetetrahydrofolate reductase (MTHFR) C677T gene polymorphism with ischemic stroke risk in different populations: an updated meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, November 2022. http://dx.doi.org/10.37766/inplasy2022.11.0037.

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Review question / Objective: Recently, increasing evidence has implicated methylenetetrahydrofolate reductase (MTHFR) gene mutation as a risk factor for ischemic stroke (IS) in the general population. However, studies have been inconclusive and lack evidence on specific populations. We aim to determine whether the MTHFR C677T variant is linked to an increased risk of IS in different age groups andregions. Information sources: A systematic search of PubMed, EMBASE, Cochrane Library, Web of Science, and CNKI databases for relevant observational studies will be undertaken.
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Gelb, Jr., Jack, Yoram Weisman, Brian Ladman, and Rosie Meir. Identification of Avian Infectious Brochitis Virus Variant Serotypes and Subtypes by PCR Product Cycle Sequencing for the Rational Selection of Effective Vaccines. United States Department of Agriculture, December 2003. http://dx.doi.org/10.32747/2003.7586470.bard.

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Objectives 1. Determine the serotypic identities of 40 recent IBV isolates from commercial chickens raised in the USA and Israel. 2. Sequence all IBV field isolates using PCR product cycle sequencing and analyze their S 1 sequence to detennine their homology to other strains in the Genbank and EMBL databases. 3. Select vaccinal strains with the highest S 1 sequence homology to the field isolates and perform challenge of immunity studies in chickens in laboratory trials to detennine level of protection afforded by the vaccines. Background Infectious bronchitis (IB) is a common, economically important disease of the chicken. IB occurs as a respiratory form, associated with airsacculitis, condemnation, and mortality of meat-type broilers, a reproductive form responsible for egg production losses in layers and breeders, and a renal form causing high mortality in broilers and pullets. The causative agent is avian coronavirus infectious bronchitis virus (IBV). Replication of the virus' RNA genome is error-prone and mutations commonly result. A major target for mutation is the gene encoding the spike (S) envelope protein used by the virus to attach and infect the host cell. Mutations in the S gene result in antigenic changes that can lead to the emergence of variant serotypes. The S gene is able to tolerate numerous mutations without compromising the virus' ability to replicate and cause disease. An end result of the virus' "flexibility" is that many strains of IBV are capable of existing in nature. Once formed, new mutant strains, often referred to as variants, are soon subjected to immunological selection so that only the most antigenically novel variants survive in poultry populations. Many novel antigenic variant serotypes and genotypes have been isolated from commercial poultry flocks. Identification of the field isolates of IBV responsible for outbreaks is critical for selecting the appropriate strain(s) for vaccination. Reverse transcriptase polymerase chain reaction (RT-PCR) of the Sl subunit of the envelope spike glycoprotein gene has been a common method used to identify field strains, replacing other time-consuming or less precise tests. Two PCR approaches have been used for identification, restriction fragment length polymorphism (RFLP) and direct automated cycle sequence analysis of a diagnostically relevant hypervariab1e region were compared in our BARD research. Vaccination for IB, although practiced routinely in commercial flocks, is often not protective. Field isolates responsible for outbreaks may be unrelated to the strain(s) used in the vaccination program. However, vaccines may provide varying degrees of cross- protection vs. unrelated field strains so vaccination studies should be performed. Conclusions RFLP and S1 sequence analysis methods were successfully performed using the field isolates from the USA and Israel. Importantly, the S1 sequence analysis method enabled a direct comparison of the genotypes of the field strains by aligning them to sequences in public databases e.g. GenBank. Novel S1 gene sequences were identified in both USA and Israel IBVs but greater diversity was observed in the field isolates from the USA. One novel genotype, characterized in this project, Israel/720/99, is currently being considered for development as an inactivated vaccine. Vaccination with IBV strains in the US (Massachusetts, Arkansas, Delaware 072) or in Israel (Massachusetts, Holland strain) provided higher degrees of cross-protection vs. homologous than heterologous strain challenge. In many cases however, vaccination with two strains (only studies with US strains) produced reasonable cross-protection against heterologous field isolate challenge. Implications S1 sequence analysis provides numerical similarity values and phylogenetic information that can be useful, although by no means conclusive, in developing vaccine control strategies. Identification of many novel S1 genotypes of IBV in the USA is evidence that commercial flocks will be challenged today and in the future with strains unrelated to vaccines. In Israel, monitoring flocks for novel IBV field isolates should continue given the identification of Israel/720/99, and perhaps others in the future. Strains selected for vaccination of commercial flocks should induce cross- protection against unrelated genotypes. Using diverse genotypes for vaccination may result in immunity against unrelated field strains.
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Rodriguez Muxica, Natalia. Open configuration options Bioinformatics for Researchers in Life Sciences: Tools and Learning Resources. Inter-American Development Bank, February 2022. http://dx.doi.org/10.18235/0003982.

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The COVID-19 pandemic has shown that bioinformatics--a multidisciplinary field that combines biological knowledge with computer programming concerned with the acquisition, storage, analysis, and dissemination of biological data--has a fundamental role in scientific research strategies in all disciplines involved in fighting the virus and its variants. It aids in sequencing and annotating genomes and their observed mutations; analyzing gene and protein expression; simulation and modeling of DNA, RNA, proteins and biomolecular interactions; and mining of biological literature, among many other critical areas of research. Studies suggest that bioinformatics skills in the Latin American and Caribbean region are relatively incipient, and thus its scientific systems cannot take full advantage of the increasing availability of bioinformatic tools and data. This dataset is a catalog of bioinformatics software for researchers and professionals working in life sciences. It includes more than 300 different tools for varied uses, such as data analysis, visualization, repositories and databases, data storage services, scientific communication, marketplace and collaboration, and lab resource management. Most tools are available as web-based or desktop applications, while others are programming libraries. It also includes 10 suggested entries for other third-party repositories that could be of use.
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Friedman, Haya, Julia Vrebalov, James Giovannoni, and Edna Pesis. Unravelling the Mode of Action of Ripening-Specific MADS-box Genes for Development of Tools to Improve Banana Fruit Shelf-life and Quality. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592116.bard.

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Fruit deterioration is a consequence of a genetically-determined fruit ripening and senescence programs, in which developmental factors lead to a climacteric rise of ethylene production in ethylene-sensitive fruits such as tomato and banana. Breeding of tomato with extended fruit shelf life involves the incorporation of a mutation in RIN, a MADS-box transcription factor participating in developmental control signalling of ripening. The RIN mode of action is not fully understood, and it may be predicted to interact with other MADS-box genes to execute its effects. The overall goal of this study was to demonstrate conservation of ripening control functions between banana and tomato and thus, the potential to genetically extend shelf-life in banana based on tools developed in tomato. The specific objectives were: 1. To increase the collection of potential RIN-like genes from banana; 2. To verify their action as developmental regulators; 3. To elucidate MADS-box gene mode of action in ripening control; 4. To create transgenic banana plants that express low levels of endogenous Le-RIN- like, MaMADS- gene(s). We have conducted experiments in banana as well as in tomato. In tomato we have carried out the transformation of the tomato rin mutant with the MaMADS1 and MaMADS2 banana genes. We have also developed a number of domain swap constructs to functionally examine the ripening-specific aspects of the RIN gene. Our results show the RIN-C terminal region is essential for the gene to function in the ripening signalling pathway. We have further explored the tomato genome databases and recovered an additional MADS-box gene necessary for fruit ripening. This gene has been previously termed TAGL1 but has not been functionally characterized in transgenic plants. TAGL1 is induced during ripening and we have shown via RNAi repression that it is necessary for both fleshy fruit expansion and subsequent ripening. In banana we have cloned the full length of six MaMADS box genes from banana and determined their spatial and temporal expression patterns. We have created antibodies to MaMADS2 and initiated ChI assay. We have created four types of transgenic banana plants designed to reduce the levels of two of the MaMADS box genes. Our results show that the MaMADS-box genes expression in banana is dynamically changing after harvest and most of them are induced at the onset of the climacteric peak. Most likely, different MaMADS box genes are active in the pulp and peel and they are differently affected by ethylene. Only the MaMADS2 box gene expression is not affected by ethylene indicating that this gene might act upstream to the ethylene response pathway. The complementation analysis in tomato revealed that neither MaMADS1 nor MaMADS2 complement the rin mutation suggesting that they have functionally diverged sufficiently to not be able to interact in the context of the tomato ripening regulatory machinery. The developmental signalling pathways controlling ripening in banana and tomato are not identical and/or have diverged through evolution. Nevertheless, at least the genes MaMADS1 and MaMADS2 constitute part of the developmental control of ripening in banana, since transgenic banana plants with reduced levels of these genes are delayed in ripening. The detailed effect on peel and pulp, of these transgenic plants is underway. So far, these transgenic bananas can respond to exogenous ethylene, and they seem to ripen normally. The response to ethylene suggest that in banana the developmental pathway of ripening is different than that in tomato, because rin tomatoes do not ripen in response to exogenous ethylene, although they harbor the ethylene response capability This study has a major contribution both in scientific and agricultural aspects. Scientifically, it establishes the role of MaMADS box genes in a different crop-the banana. The developmental ripening pathway in banana is similar, but yet different from that of the model plant tomato and one of the major differences is related to ethylene effect on this pathway in banana. In addition, we have shown that different components of the MaMADS-box genes are employed in peel and pulp. The transgenic banana plants created can help to further study the ripening control in banana. An important and practical outcome of this project is that we have created several banana transgenic plants with fruit of extended shelf life. These bananas clearly demonstrate the potential of MaMADS gene control for extending shelf-life, enhancing fruit quality, increasing yield in export systems and for improving food security in areas where Musaspecies are staple food crops.
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