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identification</title> <meta name="description" content="Search results for: genomic identification"> <meta name="keywords" content="genomic identification"> <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1, maximum-scale=1, user-scalable=no"> <meta charset="utf-8"> <link href="https://cdn.waset.org/favicon.ico" type="image/x-icon" rel="shortcut icon"> <link href="https://cdn.waset.org/static/plugins/bootstrap-4.2.1/css/bootstrap.min.css" rel="stylesheet"> <link href="https://cdn.waset.org/static/plugins/fontawesome/css/all.min.css" rel="stylesheet"> <link href="https://cdn.waset.org/static/css/site.css?v=150220211555" rel="stylesheet"> </head> <body> <header> <div class="container"> <nav class="navbar navbar-expand-lg navbar-light"> <a class="navbar-brand" href="https://waset.org"> <img src="https://cdn.waset.org/static/images/wasetc.png" alt="Open Science Research Excellence" title="Open Science Research Excellence" /> </a> <button class="d-block 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action="https://publications.waset.org/abstracts/search"> <div id="custom-search-input"> <div class="input-group"> <i class="fas fa-search"></i> <input type="text" class="search-query" name="q" placeholder="Author, Title, Abstract, Keywords" value="genomic identification"> <input type="submit" class="btn_search" value="Search"> </div> </div> </form> </div> </div> <div class="row mt-3"> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Commenced</strong> in January 2007</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Frequency:</strong> Monthly</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Edition:</strong> International</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Paper Count:</strong> 3161</div> </div> </div> </div> <h1 class="mt-3 mb-3 text-center" style="font-size:1.6rem;">Search results for: genomic identification</h1> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3161</span> The Various Legal Dimensions of Genomic Data</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Amy%20Gooden">Amy Gooden</a> </p> <p class="card-text"><strong>Abstract:</strong></p> When human genomic data is considered, this is often done through only one dimension of the law, or the interplay between the various dimensions is not considered, thus providing an incomplete picture of the legal framework. This research considers and analyzes the various dimensions in South African law applicable to genomic sequence data – including property rights, personality rights, and intellectual property rights. The effective use of personal genomic sequence data requires the acknowledgement and harmonization of the rights applicable to such data. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=artificial%20intelligence" title="artificial intelligence">artificial intelligence</a>, <a href="https://publications.waset.org/abstracts/search?q=data" title=" data"> data</a>, <a href="https://publications.waset.org/abstracts/search?q=law" title=" law"> law</a>, <a href="https://publications.waset.org/abstracts/search?q=genomics" title=" genomics"> genomics</a>, <a href="https://publications.waset.org/abstracts/search?q=rights" title=" rights"> rights</a> </p> <a href="https://publications.waset.org/abstracts/153282/the-various-legal-dimensions-of-genomic-data" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/153282.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">138</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3160</span> Suppression Subtractive Hybridization Technique for Identification of the Differentially Expressed Genes</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Tuhina-khatun">Tuhina-khatun</a>, <a href="https://publications.waset.org/abstracts/search?q=Mohamed%20Hanafi%20Musa"> Mohamed Hanafi Musa</a>, <a href="https://publications.waset.org/abstracts/search?q=Mohd%20Rafii%20Yosup"> Mohd Rafii Yosup</a>, <a href="https://publications.waset.org/abstracts/search?q=Wong%20Mui%20Yun"> Wong Mui Yun</a>, <a href="https://publications.waset.org/abstracts/search?q=Aktar-uz-Zaman"> Aktar-uz-Zaman</a>, <a href="https://publications.waset.org/abstracts/search?q=Mahbod%20Sahebi"> Mahbod Sahebi</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Suppression subtractive hybridization (SSH) method is valuable tool for identifying differentially regulated genes in disease specific or tissue specific genes important for cellular growth and differentiation. It is a widely used method for separating DNA molecules that distinguish two closely related DNA samples. SSH is one of the most powerful and popular methods for generating subtracted cDNA or genomic DNA libraries. It is based primarily on a suppression polymerase chain reaction (PCR) technique and combines normalization and subtraction in a solitary procedure. The normalization step equalizes the abundance of DNA fragments within the target population, and the subtraction step excludes sequences that are common to the populations being compared. This dramatically increases the probability of obtaining low-abundance differentially expressed cDNAs or genomic DNA fragments and simplifies analysis of the subtracted library. SSH technique is applicable to many comparative and functional genetic studies for the identification of disease, developmental, tissue specific, or other differentially expressed genes, as well as for the recovery of genomic DNA fragments distinguishing the samples under comparison. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=suppression%20subtractive%20hybridization" title="suppression subtractive hybridization">suppression subtractive hybridization</a>, <a href="https://publications.waset.org/abstracts/search?q=differentially%20expressed%20genes" title=" differentially expressed genes"> differentially expressed genes</a>, <a href="https://publications.waset.org/abstracts/search?q=disease%20specific%20genes" title=" disease specific genes"> disease specific genes</a>, <a href="https://publications.waset.org/abstracts/search?q=tissue%20specific%20genes" title=" tissue specific genes"> tissue specific genes</a> </p> <a href="https://publications.waset.org/abstracts/36148/suppression-subtractive-hybridization-technique-for-identification-of-the-differentially-expressed-genes" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/36148.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">433</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3159</span> Genomic Evidence for Ancient Human Migrations Along South America's East Coast</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Andre%20Luiz%20Campelo%20dos%20Santos">Andre Luiz Campelo dos Santos</a>, <a href="https://publications.waset.org/abstracts/search?q=Amanda%20Owings"> Amanda Owings</a>, <a href="https://publications.waset.org/abstracts/search?q=Henry%20Socrates%20Lavalle%20Sullasi"> Henry Socrates Lavalle Sullasi</a>, <a href="https://publications.waset.org/abstracts/search?q=Omer%20Gokcumen"> Omer Gokcumen</a>, <a href="https://publications.waset.org/abstracts/search?q=Michael%20DeGiorgio"> Michael DeGiorgio</a>, <a href="https://publications.waset.org/abstracts/search?q=John%20Lindo"> John Lindo</a> </p> <p class="card-text"><strong>Abstract:</strong></p> An increasing body of archaeological and genomic evidence have indicated a complex settlement process of the Americas. Here, four newly sequenced ancient genomes from Northeast Brazil and Uruguay are reported to share strong relationships with previously published samples from Panama and Southeast Brazil. Moreover, an unexpected high genomic affinity with present-day Onge is found in ancient individuals unearthed along the northern portion of South America’s Atlantic coast. These results provide genomic evidence for ancient migrations along South America’s Atlantic coast. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=archaeogenomics" title="archaeogenomics">archaeogenomics</a>, <a href="https://publications.waset.org/abstracts/search?q=atlantic%20coast" title=" atlantic coast"> atlantic coast</a>, <a href="https://publications.waset.org/abstracts/search?q=paleomigrations" title=" paleomigrations"> paleomigrations</a>, <a href="https://publications.waset.org/abstracts/search?q=South%20America" title=" South America"> South America</a> </p> <a href="https://publications.waset.org/abstracts/148451/genomic-evidence-for-ancient-human-migrations-along-south-americas-east-coast" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/148451.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">241</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3158</span> Isolation and Identification of Diacylglycerol Acyltransferase Type-2 (GAT2) Genes from Three Egyptian Olive Cultivars</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Yahia%20I.%20Mohamed">Yahia I. Mohamed</a>, <a href="https://publications.waset.org/abstracts/search?q=Ahmed%20I.%20Marzouk"> Ahmed I. Marzouk</a>, <a href="https://publications.waset.org/abstracts/search?q=Mohamed%20A.%20Yacout"> Mohamed A. Yacout</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Aim of this work was to study the genetic basis for oil accumulation in olive fruit via tracking DGAT2 (Diacylglycerol acyltransferase type-2) gene in three Egyptian Origen Olive cultivars namely Toffahi, Hamed and Maraki using molecular marker techniques and bioinformatics tools. Results illustrate that, firstly: specific genomic band of Maraki cultivars was identified as DGAT2 (Diacylglycerol acyltransferase type-2) and identical for this gene in Olea europaea with 100 % of similarity. Secondly, differential genomic band of Maraki cultivars which produced from RAPD fingerprinting technique reflected predicted distinguished sequence which identified as DGAT2 (Diacylglycerol acyltransferase type-2) in Fragaria vesca subsp. Vesca with 76% of sequential similarity. Third and finally, specific genomic specific band of Hamed cultivars was indentified as two fragments, 1-Olea europaea cultivar Koroneiki diacylglycerol acyltransferase type 2 mRNA, complete cds with two matches regions with 99% or 2-PREDICTED: Fragaria vesca subsp. vesca diacylglycerol O-acyltransferase 2-like (LOC101313050), mRNA with 86% of similarity. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=Olea%20europaea" title="Olea europaea">Olea europaea</a>, <a href="https://publications.waset.org/abstracts/search?q=fingerprinting" title=" fingerprinting"> fingerprinting</a>, <a href="https://publications.waset.org/abstracts/search?q=diacylglycerol%20acyltransferase%20type-2%20%28DGAT2%29" title=" diacylglycerol acyltransferase type-2 (DGAT2)"> diacylglycerol acyltransferase type-2 (DGAT2)</a>, <a href="https://publications.waset.org/abstracts/search?q=Egypt" title=" Egypt"> Egypt</a> </p> <a href="https://publications.waset.org/abstracts/15700/isolation-and-identification-of-diacylglycerol-acyltransferase-type-2-gat2-genes-from-three-egyptian-olive-cultivars" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/15700.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">503</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3157</span> Genomic Prediction Reliability Using Haplotypes Defined by Different Methods</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Sohyoung%20Won">Sohyoung Won</a>, <a href="https://publications.waset.org/abstracts/search?q=Heebal%20Kim"> Heebal Kim</a>, <a href="https://publications.waset.org/abstracts/search?q=Dajeong%20Lim"> Dajeong Lim</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Genomic prediction is an effective way to measure the abilities of livestock for breeding based on genomic estimated breeding values, statistically predicted values from genotype data using best linear unbiased prediction (BLUP). Using haplotypes, clusters of linked single nucleotide polymorphisms (SNPs), as markers instead of individual SNPs can improve the reliability of genomic prediction since the probability of a quantitative trait loci to be in strong linkage disequilibrium (LD) with markers is higher. To efficiently use haplotypes in genomic prediction, finding optimal ways to define haplotypes is needed. In this study, 770K SNP chip data was collected from Hanwoo (Korean cattle) population consisted of 2506 cattle. Haplotypes were first defined in three different ways using 770K SNP chip data: haplotypes were defined based on 1) length of haplotypes (bp), 2) the number of SNPs, and 3) k-medoids clustering by LD. To compare the methods in parallel, haplotypes defined by all methods were set to have comparable sizes; in each method, haplotypes defined to have an average number of 5, 10, 20 or 50 SNPs were tested respectively. A modified GBLUP method using haplotype alleles as predictor variables was implemented for testing the prediction reliability of each haplotype set. Also, conventional genomic BLUP (GBLUP) method, which uses individual SNPs were tested to evaluate the performance of the haplotype sets on genomic prediction. Carcass weight was used as the phenotype for testing. As a result, using haplotypes defined by all three methods showed increased reliability compared to conventional GBLUP. There were not many differences in the reliability between different haplotype defining methods. The reliability of genomic prediction was highest when the average number of SNPs per haplotype was 20 in all three methods, implying that haplotypes including around 20 SNPs can be optimal to use as markers for genomic prediction. When the number of alleles generated by each haplotype defining methods was compared, clustering by LD generated the least number of alleles. Using haplotype alleles for genomic prediction showed better performance, suggesting improved accuracy in genomic selection. The number of predictor variables was decreased when the LD-based method was used while all three haplotype defining methods showed similar performances. This suggests that defining haplotypes based on LD can reduce computational costs and allows efficient prediction. Finding optimal ways to define haplotypes and using the haplotype alleles as markers can provide improved performance and efficiency in genomic prediction. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=best%20linear%20unbiased%20predictor" title="best linear unbiased predictor">best linear unbiased predictor</a>, <a href="https://publications.waset.org/abstracts/search?q=genomic%20prediction" title=" genomic prediction"> genomic prediction</a>, <a href="https://publications.waset.org/abstracts/search?q=haplotype" title=" haplotype"> haplotype</a>, <a href="https://publications.waset.org/abstracts/search?q=linkage%20disequilibrium" title=" linkage disequilibrium"> linkage disequilibrium</a> </p> <a href="https://publications.waset.org/abstracts/99642/genomic-prediction-reliability-using-haplotypes-defined-by-different-methods" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/99642.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">141</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3156</span> Sparse Modelling of Cancer Patients’ Survival Based on Genomic Copy Number Alterations</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Khaled%20M.%20Alqahtani">Khaled M. Alqahtani</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Copy number alterations (CNA) are variations in the structure of the genome, where certain regions deviate from the typical two chromosomal copies. These alterations are pivotal in understanding tumor progression and are indicative of patients' survival outcomes. However, effectively modeling patients' survival based on their genomic CNA profiles while identifying relevant genomic regions remains a statistical challenge. Various methods, such as the Cox proportional hazard (PH) model with ridge, lasso, or elastic net penalties, have been proposed but often overlook the inherent dependencies between genomic regions, leading to results that are hard to interpret. In this study, we enhance the elastic net penalty by incorporating an additional penalty that accounts for these dependencies. This approach yields smooth parameter estimates and facilitates variable selection, resulting in a sparse solution. Our findings demonstrate that this method outperforms other models in predicting survival outcomes, as evidenced by our simulation study. Moreover, it allows for a more meaningful interpretation of genomic regions associated with patients' survival. We demonstrate the efficacy of our approach using both real data from a lung cancer cohort and simulated datasets. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=copy%20number%20alterations" title="copy number alterations">copy number alterations</a>, <a href="https://publications.waset.org/abstracts/search?q=cox%20proportional%20hazard" title=" cox proportional hazard"> cox proportional hazard</a>, <a href="https://publications.waset.org/abstracts/search?q=lung%20cancer" title=" lung cancer"> lung cancer</a>, <a href="https://publications.waset.org/abstracts/search?q=regression" title=" regression"> regression</a>, <a href="https://publications.waset.org/abstracts/search?q=sparse%20solution" title=" sparse solution"> sparse solution</a> </p> <a href="https://publications.waset.org/abstracts/185477/sparse-modelling-of-cancer-patients-survival-based-on-genomic-copy-number-alterations" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/185477.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">45</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3155</span> The Identification of Combined Genomic Expressions as a Diagnostic Factor for Oral Squamous Cell Carcinoma</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Ki-Yeo%20Kim">Ki-Yeo Kim</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Trends in genetics are transforming in order to identify differential coexpressions of correlated gene expression rather than the significant individual gene. Moreover, it is known that a combined biomarker pattern improves the discrimination of a specific cancer. The identification of the combined biomarker is also necessary for the early detection of invasive oral squamous cell carcinoma (OSCC). To identify the combined biomarker that could improve the discrimination of OSCC, we explored an appropriate number of genes in a combined gene set in order to attain the highest level of accuracy. After detecting a significant gene set, including the pre-defined number of genes, a combined expression was identified using the weights of genes in a gene set. We used the Principal Component Analysis (PCA) for the weight calculation. In this process, we used three public microarray datasets. One dataset was used for identifying the combined biomarker, and the other two datasets were used for validation. The discrimination accuracy was measured by the out-of-bag (OOB) error. There was no relation between the significance and the discrimination accuracy in each individual gene. The identified gene set included both significant and insignificant genes. One of the most significant gene sets in the classification of normal and OSCC included MMP1, SOCS3 and ACOX1. Furthermore, in the case of oral dysplasia and OSCC discrimination, two combined biomarkers were identified. The combined genomic expression achieved better performance in the discrimination of different conditions than in a single significant gene. Therefore, it could be expected that accurate diagnosis for cancer could be possible with a combined biomarker. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=oral%20squamous%20cell%20carcinoma" title="oral squamous cell carcinoma">oral squamous cell carcinoma</a>, <a href="https://publications.waset.org/abstracts/search?q=combined%20biomarker" title=" combined biomarker"> combined biomarker</a>, <a href="https://publications.waset.org/abstracts/search?q=microarray%20dataset" title=" microarray dataset"> microarray dataset</a>, <a href="https://publications.waset.org/abstracts/search?q=correlated%20genes" title=" correlated genes"> correlated genes</a> </p> <a href="https://publications.waset.org/abstracts/35990/the-identification-of-combined-genomic-expressions-as-a-diagnostic-factor-for-oral-squamous-cell-carcinoma" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/35990.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">423</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3154</span> Genomic Identification of Anisakis Simplex Larvae by PCR-RAPD</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Fumiko%20Kojima">Fumiko Kojima</a>, <a href="https://publications.waset.org/abstracts/search?q=Shuji%20Fujimoto"> Shuji Fujimoto</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Anisakiasis is a disease caused by infection with an anisakid larvae, mostly Anisakis simplex. The larvae commonly infect in marine fish and the disease is frequently reported in areas of the world where fish is consumed raw, lightly pickled or salted. In Japan, people have the habit of eating raw fish such as ‘sushi’ or ‘sashimi’, so they have more chance of infection with larvae of anisakid nematodes. There are three sibling species in A. simplex larvae, namely, A. simplex sensu stricto (Asss), A. pegreffii (Ap) and A. simplex C. It was revealed that Ap is dominant among the larvae from fish (Scomber japonics) in the Japan Sea side and Asss is dominant among those of the Pacific Ocean side conversely. Although anisakiasis has happened in Japan among both the Japan Sea side area and the Pacific Ocean side area. The aim of this study was to investigate genetic variations between the siblings (Asss and Ap) and within the same sibling species by random amplified polymorphic DNA (RAPD) technique. In order to investigate the genetic difference among the each A. simplex larvae, we used RAPD technique to differentiate individuals of A. simplex obtained from Scomber japonics fish those were caught in the Japan sea (Goto Islands in Nagasaki Prefecture) and the cost of Pacific Ocean (Kanagawa Prefecture). The RAPD patterns of the control DNA (Genus Raphidascaris) were markedly different from those of the A. simplex. There were differences in amplification patterns between Asss and Ap. The RAPD patterns for larvae obtained from fish of the same sea were somewhat different and variations were detected even among larvae from the same fish. These results suggest the considerable high genetic variability between Asss and Ap and the possible existence of genetic variation within the sibling species. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=Anisakiasis%20in%20Japan" title="Anisakiasis in Japan">Anisakiasis in Japan</a>, <a href="https://publications.waset.org/abstracts/search?q=Anisakis%20simplex" title=" Anisakis simplex"> Anisakis simplex</a>, <a href="https://publications.waset.org/abstracts/search?q=genomic%20identification" title=" genomic identification"> genomic identification</a>, <a href="https://publications.waset.org/abstracts/search?q=PCR-RAPD" title=" PCR-RAPD"> PCR-RAPD</a> </p> <a href="https://publications.waset.org/abstracts/55789/genomic-identification-of-anisakis-simplex-larvae-by-pcr-rapd" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/55789.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">181</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3153</span> Genomic Resilience and Ecological Vulnerability in Coffea Arabica: Insights from Whole Genome Resequencing at Its Center of Origin</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Zewdneh%20Zana%20Zate">Zewdneh Zana Zate</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The study focuses on the evolutionary and ecological genomics of both wild and cultivated Coffea arabica L. at its center of origin, Ethiopia, aiming to uncover how this vital species may withstand future climate changes. Utilizing bioclimatic models, we project the future distribution of Arabica under varied climate scenarios for 2050 and 2080, identifying potential conservation zones and immediate risk areas. Through whole-genome resequencing of accessions from Ethiopian gene banks, this research assesses genetic diversity and divergence between wild and cultivated populations. It explores relationships, demographic histories, and potential hybridization events among Coffea arabica accessions to better understand the species' origins and its connection to parental species. This genomic analysis also seeks to detect signs of natural or artificial selection across populations. Integrating these genomic discoveries with ecological data, the study evaluates the current and future ecological and genomic vulnerabilities of wild Coffea arabica, emphasizing necessary adaptations for survival. We have identified key genomic regions linked to environmental stress tolerance, which could be crucial for breeding more resilient Arabica varieties. Additionally, our ecological modeling predicted a contraction of suitable habitats, urging immediate conservation actions in identified key areas. This research not only elucidates the evolutionary history and adaptive strategies of Arabica but also informs conservation priorities and breeding strategies to enhance resilience to climate change. By synthesizing genomic and ecological insights, we provide a robust framework for developing effective management strategies aimed at sustaining Coffea arabica, a species of profound global importance, in its native habitat under evolving climatic conditions. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=coffea%20arabica" title="coffea arabica">coffea arabica</a>, <a href="https://publications.waset.org/abstracts/search?q=climate%20change%20adaptation" title=" climate change adaptation"> climate change adaptation</a>, <a href="https://publications.waset.org/abstracts/search?q=conservation%20strategies" title=" conservation strategies"> conservation strategies</a>, <a href="https://publications.waset.org/abstracts/search?q=genomic%20resilience" title=" genomic resilience"> genomic resilience</a> </p> <a href="https://publications.waset.org/abstracts/185493/genomic-resilience-and-ecological-vulnerability-in-coffea-arabica-insights-from-whole-genome-resequencing-at-its-center-of-origin" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/185493.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">40</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3152</span> TARF: Web Toolkit for Annotating RNA-Related Genomic Features</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Jialin%20Ma">Jialin Ma</a>, <a href="https://publications.waset.org/abstracts/search?q=Jia%20Meng"> Jia Meng</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Genomic features, the genome-based coordinates, are commonly used for the representation of biological features such as genes, RNA transcripts and transcription factor binding sites. For the analysis of RNA-related genomic features, such as RNA modification sites, a common task is to correlate these features with transcript components (5'UTR, CDS, 3'UTR) to explore their distribution characteristics in terms of transcriptomic coordinates, e.g., to examine whether a specific type of biological feature is enriched near transcription start sites. Existing approaches for performing these tasks involve the manipulation of a gene database, conversion from genome-based coordinate to transcript-based coordinate, and visualization methods that are capable of showing RNA transcript components and distribution of the features. These steps are complicated and time consuming, and this is especially true for researchers who are not familiar with relevant tools. To overcome this obstacle, we develop a dedicated web app TARF, which represents web toolkit for annotating RNA-related genomic features. TARF web tool intends to provide a web-based way to easily annotate and visualize RNA-related genomic features. Once a user has uploaded the features with BED format and specified a built-in transcript database or uploaded a customized gene database with GTF format, the tool could fulfill its three main functions. First, it adds annotation on gene and RNA transcript components. For every features provided by the user, the overlapping with RNA transcript components are identified, and the information is combined in one table which is available for copy and download. Summary statistics about ambiguous belongings are also carried out. Second, the tool provides a convenient visualization method of the features on single gene/transcript level. For the selected gene, the tool shows the features with gene model on genome-based view, and also maps the features to transcript-based coordinate and show the distribution against one single spliced RNA transcript. Third, a global transcriptomic view of the genomic features is generated utilizing the Guitar R/Bioconductor package. The distribution of features on RNA transcripts are normalized with respect to RNA transcript landmarks and the enrichment of the features on different RNA transcript components is demonstrated. We tested the newly developed TARF toolkit with 3 different types of genomics features related to chromatin H3K4me3, RNA N6-methyladenosine (m6A) and RNA 5-methylcytosine (m5C), which are obtained from ChIP-Seq, MeRIP-Seq and RNA BS-Seq data, respectively. TARF successfully revealed their respective distribution characteristics, i.e. H3K4me3, m6A and m5C are enriched near transcription starting sites, stop codons and 5’UTRs, respectively. Overall, TARF is a useful web toolkit for annotation and visualization of RNA-related genomic features, and should help simplify the analysis of various RNA-related genomic features, especially those related RNA modifications. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=RNA-related%20genomic%20features" title="RNA-related genomic features">RNA-related genomic features</a>, <a href="https://publications.waset.org/abstracts/search?q=annotation" title=" annotation"> annotation</a>, <a href="https://publications.waset.org/abstracts/search?q=visualization" title=" visualization"> visualization</a>, <a href="https://publications.waset.org/abstracts/search?q=web%20server" title=" web server"> web server</a> </p> <a href="https://publications.waset.org/abstracts/59044/tarf-web-toolkit-for-annotating-rna-related-genomic-features" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/59044.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">208</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3151</span> Evaluation of Four Different DNA Targets in Polymerase Chain Reaction for Detection and Genotyping of Helicobacter pylori</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Abu%20Salim%20Mustafa">Abu Salim Mustafa</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Polymerase chain reaction (PCR) assays targeting genomic DNA segments have been established for the detection of <em>Helicobacter pylori</em> in clinical specimens. However, the data on comparative evaluations of various targets in detection of <em>H. pylori</em> are limited. Furthermore, the frequencies of <em>vacA</em> (<em>s1</em> and <em>s2</em>) and <em>cagA </em>genotypes, which are suggested to be involved in the pathogenesis of <em>H. pylori</em> in other parts of the world, are not well studied in Kuwait. The aim of this study was to evaluate PCR assays for the detection and genotyping of <em>H. pylori</em> by targeting the amplification of DNA targets from four genomic segments. The genomic DNA were isolated from 72 clinical isolates of <em>H. pylori</em> and tested in PCR with four pairs of oligonucleotides primers, i.e. ECH-U/ECH-L, ET-5U/ET-5L, CagAF/CagAR and Vac1F/Vac1XR, which were expected to amplify targets of various sizes (471 bp, 230 bp, 183 bp and 176/203 bp, respectively) from the genomic DNA of <em>H. pylori.</em> The PCR-amplified DNA were analyzed by agarose gel electrophoresis. PCR products of expected size were obtained with all primer pairs by using genomic DNA isolated from <em>H. pylori</em>. DNA dilution experiments showed that the most sensitive PCR target was 471 bp DNA amplified by the primers ECH-U/ECH-L, followed by the targets of Vac1F/Vac1XR (176 bp/203 DNA), CagAF/CagAR (183 bp DNA) and ET-5U/ET-5L (230 bp DNA). However, when tested with undiluted genomic DNA isolated from single colonies of all isolates, the Vac1F/Vac1XR target provided the maximum positive results (71/72 (99% positives)), followed by ECH-U/ECH-L (69/72 (93% positives)), ET-5U/ET-5L (51/72 (71% positives)) and CagAF/CagAR (26/72 (46% positives)). The results of genotyping experiments showed that <em>vacA s1</em> (46% positive) and <em>vacA s2</em> (54% positive) genotypes were almost equally associated with VaCA+/CagA- isolates (P > 0.05), but with VacA+/CagA+ isolates, S1 genotype (92% positive) was more frequently detected than S2 genotype (8% positive) (P< 0.0001). In conclusion, among the primer pairs tested, Vac1F/Vac1XR provided the best results for detection of <em>H. pylori</em>. The genotyping experiments showed that <em>vacA s1</em> and <em>vacA s2</em> genotypes were almost equally associated with <em>vaCA<sup>+</sup>/cagA<sup>- </sup></em>isolates, but <em>vacA s1</em> genotype had a significantly increased association with <em>vacA<sup>+</sup>/cagA<sup>+ </sup></em>isolates. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=H.%20pylori" title="H. pylori">H. pylori</a>, <a href="https://publications.waset.org/abstracts/search?q=PCR" title=" PCR"> PCR</a>, <a href="https://publications.waset.org/abstracts/search?q=detection" title=" detection"> detection</a>, <a href="https://publications.waset.org/abstracts/search?q=genotyping" title=" genotyping"> genotyping</a> </p> <a href="https://publications.waset.org/abstracts/98742/evaluation-of-four-different-dna-targets-in-polymerase-chain-reaction-for-detection-and-genotyping-of-helicobacter-pylori" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/98742.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">133</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3150</span> Genomic Analysis of Whole Genome Sequencing of Leishmania Major</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Fatimazahrae%20Elbakri">Fatimazahrae Elbakri</a>, <a href="https://publications.waset.org/abstracts/search?q=Azeddine%20Ibrahimi"> Azeddine Ibrahimi</a>, <a href="https://publications.waset.org/abstracts/search?q=Meryem%20Lemrani"> Meryem Lemrani</a>, <a href="https://publications.waset.org/abstracts/search?q=Dris%20Belghyti"> Dris Belghyti</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Leishmaniasis represents a major public health problem because of the number of cases recorded each year and the wide distribution of the disease. It is a parasitic disease of flagellated protozoa transmitted by the bite of certain species of sandfly, causing a spectrum of clinical pathology in humans ranging from disfiguring skin lesions to fatal visceral leishmaniasis. Cutaneous leishmaniasis due to Leishmania major is a polymorphic disease; in fact, the infection can be asymptomatic, localized, or disseminated. The objective of this work is to determine the genomic diversity that contributes to clinical variability by trying to identify the variation in chromosome number and to extract SNPs and SNPs and InDels; it is based on four sequences (WGS) of Leishmania major available on NCBI in Fastq form, from three countries: Tunisia, Algeria, and Israel, the analysis is set up from a pipeline to facilitate the discovery of genetic diversity, in particular SNP and chromosomal somy. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=Leshmania%20major" title="Leshmania major">Leshmania major</a>, <a href="https://publications.waset.org/abstracts/search?q=cutaneous%20Leishmania" title=" cutaneous Leishmania"> cutaneous Leishmania</a>, <a href="https://publications.waset.org/abstracts/search?q=NGS" title=" NGS"> NGS</a>, <a href="https://publications.waset.org/abstracts/search?q=genomic" title=" genomic"> genomic</a>, <a href="https://publications.waset.org/abstracts/search?q=somy" title=" somy"> somy</a>, <a href="https://publications.waset.org/abstracts/search?q=variant%20calling" title=" variant calling"> variant calling</a> </p> <a href="https://publications.waset.org/abstracts/170783/genomic-analysis-of-whole-genome-sequencing-of-leishmania-major" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/170783.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">79</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3149</span> Breeding Cotton for Annual Growth Habit: Remobilizing End-of-season Perennial Reserves for Increased Yield</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Salman%20Naveed">Salman Naveed</a>, <a href="https://publications.waset.org/abstracts/search?q=Nitant%20Gandhi"> Nitant Gandhi</a>, <a href="https://publications.waset.org/abstracts/search?q=Grant%20Billings"> Grant Billings</a>, <a href="https://publications.waset.org/abstracts/search?q=Zachary%20Jones"> Zachary Jones</a>, <a href="https://publications.waset.org/abstracts/search?q=B.%20Todd%20Campbell"> B. Todd Campbell</a>, <a href="https://publications.waset.org/abstracts/search?q=Michael%20Jones"> Michael Jones</a>, <a href="https://publications.waset.org/abstracts/search?q=Sachin%20Rustgi"> Sachin Rustgi</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Cotton (Gossypium spp.) is the primary source of natural fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified markers associated with the gene expression traits via genome-wide association analysis using a 63K SNP Array (Hulse-Kemp et al. 2015 G3 5:1187). Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed association with expression traits. Out of these 396 markers, 159 mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated via virus-induced gene silencing. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=cotton" title="cotton">cotton</a>, <a href="https://publications.waset.org/abstracts/search?q=GWAS" title=" GWAS"> GWAS</a>, <a href="https://publications.waset.org/abstracts/search?q=QTL" title=" QTL"> QTL</a>, <a href="https://publications.waset.org/abstracts/search?q=expression%20traits" title=" expression traits"> expression traits</a> </p> <a href="https://publications.waset.org/abstracts/143604/breeding-cotton-for-annual-growth-habit-remobilizing-end-of-season-perennial-reserves-for-increased-yield" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/143604.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">151</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3148</span> Resequencing and Genomic Study of Wild Coffea Arabica Unveils Genetic Groups at Its Origin and Their Geographic Distribution</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Zate%20Zewdneh%20Zana">Zate Zewdneh Zana</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Coffea arabica (Arabica coffee), a cornerstone of the global beverage industry, necessitates rigorous genetic conservation due to its economic significance and genetic complexity. In this study, we performed whole-genome resequencing of wild species collected from its birthplace, Ethiopia. Advanced Illumina sequencing technology facilitated the mapping of a high percentage of clean reads to the C. arabica reference genome, revealing a substantial number of genetic variants, predominantly SNPs. Our comprehensive analysis not only uncovered a notable distribution of genomic variants across the coffee genome but also identified distinct genetic groups through phylogenetic and population structure analyses. This genomic study provides invaluable insights into the genetic diversity of C. arabica, highlighting the potential of identified SNPs and InDels in enhancing our understanding of key agronomic traits. The findings contribute significantly to genetic studies and support strategic breeding and conservation efforts essential for sustaining the global coffee industry. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=population%20genetics" title="population genetics">population genetics</a>, <a href="https://publications.waset.org/abstracts/search?q=wild%20species" title=" wild species"> wild species</a>, <a href="https://publications.waset.org/abstracts/search?q=evolutionary%20study" title=" evolutionary study"> evolutionary study</a>, <a href="https://publications.waset.org/abstracts/search?q=coffee%20plant" title=" coffee plant"> coffee plant</a> </p> <a href="https://publications.waset.org/abstracts/187447/resequencing-and-genomic-study-of-wild-coffea-arabica-unveils-genetic-groups-at-its-origin-and-their-geographic-distribution" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/187447.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">40</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3147</span> Genetic Instabilities in Marine Bivalve Following Benzo(α)pyrene Exposure: Utilization of Combined Random Amplified Polymorphic DNA and Comet Assay</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Mengjie%20Qu">Mengjie Qu</a>, <a href="https://publications.waset.org/abstracts/search?q=Yi%20Wang"> Yi Wang</a>, <a href="https://publications.waset.org/abstracts/search?q=Jiawei%20Ding"> Jiawei Ding</a>, <a href="https://publications.waset.org/abstracts/search?q=Siyu%20Chen"> Siyu Chen</a>, <a href="https://publications.waset.org/abstracts/search?q=Yanan%20Di"> Yanan Di</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Marine ecosystem is facing intensified multiple stresses caused by environmental contaminants from human activities. Xenobiotics, such as benzo(α)pyrene (BaP) have been discharged into marine environment and cause hazardous impacts on both marine organisms and human beings. As a filter-feeder, marine mussels, Mytilus spp., has been extensively used to monitor the marine environment. However, their genomic alterations induced by such xenobiotics are still kept unknown. In the present study, gills, as the first defense barrier in mussels, were selected to evaluate the genetic instability alterations induced by the exposure to BaP both in vivo and in vitro. Both random amplified polymorphic DNA (RAPD) assay and comet assay were applied as the rapid tools to assess the environmental stresses due to their low money- and time-consumption. All mussels were identified to be the single species of Mytilus coruscus before used in BaP exposure at the concentration of 56 μg/l for 1 & 3 days (in vivo exposure) or 1 & 3 hours (in vitro). Both RAPD and comet assay results were showed significantly increased genomic instability with time-specific altering pattern. After the recovery period in 'in vivo' exposure, the genomic status was as same as control condition. However, the relative higher genomic instabilities were still observed in gill cells after the recovery from in vitro exposure condition. Different repair mechanisms or signaling pathway might be involved in the isolated gill cells in the comparison with intact tissues. The study provides the robust and rapid techniques to exam the genomic stability in marine organisms in response to marine environmental changes and provide basic information for further mechanism research in stress responses in marine organisms. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=genotoxic%20impacts" title="genotoxic impacts">genotoxic impacts</a>, <a href="https://publications.waset.org/abstracts/search?q=in%20vivo%2Fvitro%20exposure" title=" in vivo/vitro exposure"> in vivo/vitro exposure</a>, <a href="https://publications.waset.org/abstracts/search?q=marine%20mussels" title=" marine mussels"> marine mussels</a>, <a href="https://publications.waset.org/abstracts/search?q=RAPD%20and%20comet%20assay" title=" RAPD and comet assay"> RAPD and comet assay</a> </p> <a href="https://publications.waset.org/abstracts/84882/genetic-instabilities-in-marine-bivalve-following-benzoapyrene-exposure-utilization-of-combined-random-amplified-polymorphic-dna-and-comet-assay" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/84882.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">279</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3146</span> Allelic Diversity of Productive, Reproductive and Fertility Traits Genes of Buffalo and Cattle</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=M.%20Moaeen-ud-Din">M. Moaeen-ud-Din</a>, <a href="https://publications.waset.org/abstracts/search?q=G.%20Bilal"> G. Bilal</a>, <a href="https://publications.waset.org/abstracts/search?q=M.%20Yaqoob"> M. Yaqoob</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Identification of genes of importance regarding production traits in buffalo is impaired by a paucity of genomic resources. Choice to fill this gap is to exploit data available for cow. The cross-species application of comparative genomics tools is potential gear to investigate the buffalo genome. However, this is dependent on nucleotide sequences similarity. In this study gene diversity between buffalo and cattle was determined by using 86 gene orthologues. There was about 3% difference in all genes in term of nucleotide diversity; and 0.267±0.134 in amino acids indicating the possibility for successfully using cross-species strategies for genomic studies. There were significantly higher non synonymous substitutions both in cattle and buffalo however, there was similar difference in term of dN – dS (4.414 vs 4.745) in buffalo and cattle respectively. Higher rate of non-synonymous substitutions at similar level in buffalo and cattle indicated a similar positive selection pressure. Results for relative rate test were assessed with the chi-squared test. There was no significance difference on unique mutations between cattle and buffalo lineages at synonymous sites. However, there was a significance difference on unique mutations for non synonymous sites indicating ongoing mutagenic process that generates substitutional mutation at approximately the same rate at silent sites. Moreover, despite of common ancestry, our results indicate a different divergent time among genes of cattle and buffalo. This is the first demonstration that variable rates of molecular evolution may be present within the family Bovidae. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=buffalo" title="buffalo">buffalo</a>, <a href="https://publications.waset.org/abstracts/search?q=cattle" title=" cattle"> cattle</a>, <a href="https://publications.waset.org/abstracts/search?q=gene%20diversity" title=" gene diversity"> gene diversity</a>, <a href="https://publications.waset.org/abstracts/search?q=molecular%20evolution" title=" molecular evolution"> molecular evolution</a> </p> <a href="https://publications.waset.org/abstracts/26997/allelic-diversity-of-productive-reproductive-and-fertility-traits-genes-of-buffalo-and-cattle" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/26997.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">489</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3145</span> Analysis of Saudi Breast Cancer Patients’ Primary Tumors using Array Comparative Genomic Hybridization</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=L.%20M.%20Al-Harbi">L. M. Al-Harbi</a>, <a href="https://publications.waset.org/abstracts/search?q=A.%20M.%20Shokry"> A. M. Shokry</a>, <a href="https://publications.waset.org/abstracts/search?q=J.%20S.%20M.%20Sabir"> J. S. M. Sabir</a>, <a href="https://publications.waset.org/abstracts/search?q=A.%20Chaudhary"> A. Chaudhary</a>, <a href="https://publications.waset.org/abstracts/search?q=J.%20Manikandan"> J. Manikandan</a>, <a href="https://publications.waset.org/abstracts/search?q=K.%20S.%20Saini"> K. S. Saini</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Breast cancer is the second most common cause of cancer death worldwide and is the most common malignancy among Saudi females. During breast carcinogenesis, a wide-array of cytogenetic changes involving deletions, or amplification, or translocations, of part or whole of chromosome regions have been observed. Because of the limitations of various earlier technologies, newer tools are developed to scan for changes at the genomic level. Recently, Array Comparative Genomic Hybridization (aCGH) technique has been applied for detecting segmental genomic alterations at molecular level. In this study, aCGH was performed on twenty breast cancer tumors and their matching non-tumor (normal) counterparts using the Agilent 2x400K. Several regions were identified to be either amplified or deleted in a tumor-specific manner. Most frequent alterations were amplification of chromosome 1q, chromosome 8q, 20q, and deletions at 16q were also detected. The amplification of genetic events at 1q and 8q were further validated using FISH analysis using probes targeting 1q25 and 8q (MYC gene). The copy number changes at these loci can potentially cause a significant change in the tumor behavior, as deletions in the E-Cadherin (CDH1)-tumor suppressor gene as well as amplification of the oncogenes-Aurora Kinase A. (AURKA) and MYC could make these tumors highly metastatic. This study validates the use of aCGH in Saudi breast cancer patients and sets the foundations necessary for performing larger cohort studies searching for ethnicity-specific biomarkers and gene copy number variations. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=breast%20cancer" title="breast cancer">breast cancer</a>, <a href="https://publications.waset.org/abstracts/search?q=molecular%20biology" title=" molecular biology"> molecular biology</a>, <a href="https://publications.waset.org/abstracts/search?q=ecology" title=" ecology"> ecology</a>, <a href="https://publications.waset.org/abstracts/search?q=environment" title=" environment"> environment</a> </p> <a href="https://publications.waset.org/abstracts/5124/analysis-of-saudi-breast-cancer-patients-primary-tumors-using-array-comparative-genomic-hybridization" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/5124.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">376</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3144</span> Disability, Stigma and In-Group Identification: An Exploration across Different Disability Subgroups</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Sharmila%20Rathee">Sharmila Rathee</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Individuals with disability/ies often face negative attitudes, discrimination, exclusion, and inequality of treatment due to stigmatization and stigmatized treatment. While a significant number of studies in field of stigma suggest that group-identification has positive consequences for stigmatized individuals, ironically very miniscule empirical work in sight has attempted to investigate in-group identification as a coping measure against stigma, humiliation and related experiences among disability group. In view of death of empirical research on in-group identification among disability group, through present work, an attempt has been made to examine the experiences of stigma, humiliation, and in-group identification among disability group. Results of the study suggest that use of in-group identification as a coping strategy is not uniform across members of disability group and degree of in-group identification differs across different sub-groups of disability groups. Further, in-group identification among members of disability group depends on variables like degree and impact of disability, factors like onset of disability, nature, and visibility of disability, educational experiences and resources available to deal with disabling conditions. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=disability" title="disability">disability</a>, <a href="https://publications.waset.org/abstracts/search?q=stigma" title=" stigma"> stigma</a>, <a href="https://publications.waset.org/abstracts/search?q=in-group%20identification" title=" in-group identification"> in-group identification</a>, <a href="https://publications.waset.org/abstracts/search?q=social%20identity" title=" social identity"> social identity</a> </p> <a href="https://publications.waset.org/abstracts/48888/disability-stigma-and-in-group-identification-an-exploration-across-different-disability-subgroups" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/48888.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">324</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3143</span> Forensic Challenges in Source Device Identification for Digital Videos</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Mustapha%20Aminu%20Bagiwa">Mustapha Aminu Bagiwa</a>, <a href="https://publications.waset.org/abstracts/search?q=Ainuddin%20Wahid%20Abdul%20Wahab"> Ainuddin Wahid Abdul Wahab</a>, <a href="https://publications.waset.org/abstracts/search?q=Mohd%20Yamani%20Idna%20Idris"> Mohd Yamani Idna Idris</a>, <a href="https://publications.waset.org/abstracts/search?q=Suleman%20Khan"> Suleman Khan</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Video source device identification has become a problem of concern in numerous domains especially in multimedia security and digital investigation. This is because videos are now used as evidence in legal proceedings. Source device identification aim at identifying the source of digital devices using the content they produced. However, due to affordable processing tools and the influx in digital content generating devices, source device identification is still a major problem within the digital forensic community. In this paper, we discuss source device identification for digital videos by identifying techniques that were proposed in the literature for model or specific device identification. This is aimed at identifying salient open challenges for future research. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=video%20forgery" title="video forgery">video forgery</a>, <a href="https://publications.waset.org/abstracts/search?q=source%20camcorder" title=" source camcorder"> source camcorder</a>, <a href="https://publications.waset.org/abstracts/search?q=device%20identification" title=" device identification"> device identification</a>, <a href="https://publications.waset.org/abstracts/search?q=forgery%20detection" title=" forgery detection "> forgery detection </a> </p> <a href="https://publications.waset.org/abstracts/21641/forensic-challenges-in-source-device-identification-for-digital-videos" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/21641.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">631</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3142</span> Copy Number Variants in Children with Non-Syndromic Congenital Heart Diseases from Mexico</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Maria%20Lopez-Ibarra">Maria Lopez-Ibarra</a>, <a href="https://publications.waset.org/abstracts/search?q=Ana%20Velazquez-Wong"> Ana Velazquez-Wong</a>, <a href="https://publications.waset.org/abstracts/search?q=Lucelli%20Ya%C3%B1ez-Gutierrez"> Lucelli Yañez-Gutierrez</a>, <a href="https://publications.waset.org/abstracts/search?q=Maria%20Araujo-Solis"> Maria Araujo-Solis</a>, <a href="https://publications.waset.org/abstracts/search?q=Fabio%20Salamanca-Gomez"> Fabio Salamanca-Gomez</a>, <a href="https://publications.waset.org/abstracts/search?q=Alfonso%20Mendez-Tenorio"> Alfonso Mendez-Tenorio</a>, <a href="https://publications.waset.org/abstracts/search?q=Hayde%C3%A9%20Rosas-Vargas"> Haydeé Rosas-Vargas</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Congenital heart diseases (CHD) are the most common congenital abnormalities. These conditions can occur as both an element of distinct chromosomal malformation syndromes or as non-syndromic forms. Their etiology is not fully understood. Genetic variants such copy number variants have been associated with CHD. The aim of our study was to analyze these genomic variants in peripheral blood from Mexican children diagnosed with non-syndromic CHD. We included 16 children with atrial and ventricular septal defects and 5 healthy subjects without heart malformations as controls. To exclude the most common heart disease-associated syndrome alteration, we performed a fluorescence in situ hybridization test to identify the 22q11.2, responsible for congenital heart abnormalities associated with Di-George Syndrome. Then, a microarray based comparative genomic hybridization was used to identify global copy number variants. The identification of copy number variants resulted from the comparison and analysis between our results and data from main genetic variation databases. We identified copy number variants gain in three chromosomes regions from pediatric patients, 4q13.2 (31.25%), 9q34.3 (25%) and 20q13.33 (50%), where several genes associated with cellular, biosynthetic, and metabolic processes are located, UGT2B15, UGT2B17, SNAPC4, SDCCAG3, PMPCA, INPP6E, C9orf163, NOTCH1, C20orf166, and SLCO4A1. In addition, after a hierarchical cluster analysis based on the fluorescence intensity ratios from the comparative genomic hybridization, two congenital heart disease groups were generated corresponding to children with atrial or ventricular septal defects. Further analysis with a larger sample size is needed to corroborate these copy number variants as possible biomarkers to differentiate between heart abnormalities. Interestingly, the 20q13.33 gain was present in 50% of children with these CHD which could suggest that alterations in both coding and non-coding elements within this chromosomal region may play an important role in distinct heart conditions. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=aCGH" title="aCGH">aCGH</a>, <a href="https://publications.waset.org/abstracts/search?q=bioinformatics" title=" bioinformatics"> bioinformatics</a>, <a href="https://publications.waset.org/abstracts/search?q=congenital%20heart%20diseases" title=" congenital heart diseases"> congenital heart diseases</a>, <a href="https://publications.waset.org/abstracts/search?q=copy%20number%20variants" title=" copy number variants"> copy number variants</a>, <a href="https://publications.waset.org/abstracts/search?q=fluorescence%20in%20situ%20hybridization" title=" fluorescence in situ hybridization"> fluorescence in situ hybridization</a> </p> <a href="https://publications.waset.org/abstracts/53721/copy-number-variants-in-children-with-non-syndromic-congenital-heart-diseases-from-mexico" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/53721.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">292</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3141</span> Evolutionary Genomic Analysis of Adaptation Genomics </h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Agostinho%20Antunes">Agostinho Antunes</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=adaptation" title="adaptation">adaptation</a>, <a href="https://publications.waset.org/abstracts/search?q=animals" title=" animals"> animals</a>, <a href="https://publications.waset.org/abstracts/search?q=evolution" title=" evolution"> evolution</a>, <a href="https://publications.waset.org/abstracts/search?q=genomics" title=" genomics"> genomics</a> </p> <a href="https://publications.waset.org/abstracts/23726/evolutionary-genomic-analysis-of-adaptation-genomics" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/23726.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">429</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3140</span> Identification of Dynamic Friction Model for High-Precision Motion Control</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Martin%20Goubej">Martin Goubej</a>, <a href="https://publications.waset.org/abstracts/search?q=Tomas%20Popule"> Tomas Popule</a>, <a href="https://publications.waset.org/abstracts/search?q=Alois%20Krejci"> Alois Krejci</a> </p> <p class="card-text"><strong>Abstract:</strong></p> This paper deals with experimental identification of mechanical systems with nonlinear friction characteristics. Dynamic LuGre friction model is adopted and a systematic approach to parameter identification of both linear and nonlinear subsystems is given. The identification procedure consists of three subsequent experiments which deal with the individual parts of plant dynamics. The proposed method is experimentally verified on an industrial-grade robotic manipulator. Model fidelity is compared with the results achieved with a static friction model. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=mechanical%20friction" title="mechanical friction">mechanical friction</a>, <a href="https://publications.waset.org/abstracts/search?q=LuGre%20model" title=" LuGre model"> LuGre model</a>, <a href="https://publications.waset.org/abstracts/search?q=friction%20identification" title=" friction identification"> friction identification</a>, <a href="https://publications.waset.org/abstracts/search?q=motion%20control" title=" motion control"> motion control</a> </p> <a href="https://publications.waset.org/abstracts/51897/identification-of-dynamic-friction-model-for-high-precision-motion-control" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/51897.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">413</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3139</span> Benefit Sharing of Research Participants in Human Genomic Research: Ethical Concerns and Ramifications</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Tamanda%20Kamwendo">Tamanda Kamwendo</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The concept of benefit sharing has been a prominent global debate in the world, gaining traction in human research ethics. Despite its prevalence, the concept of benefit sharing is not without controversy over its meaning and justification. This is due to the fact that it lacks a broadly accepted definition and many proponents discuss benefit sharing by arguing for its necessity rather than engaging in critical intellectual engagement with technical issues such as what it implies. What is clear in the literature is that the underlying premise of benefit-sharing is that research involving underprivileged and marginalized people is currently unjust and inequitable because these people are denied access to these gains; thus, benefit-sharing arrangements are required for these research projects to be just and equitable. This paper, therefore, investigates the discourses and justifications behind the concept of benefit sharing to human participants, particularly when dealing with human genomics research. Furthermore, considering that benefit sharing is generally viewed as a transaction between research organizations and research participants, it raises ethical concerns concerning the commodification of human material and undermines the sanctity of the human genome. This is predicated on the idea that research sponsors would be compelled to deliver a minimum set of possible benefits to research participants and communities in exchange for their involvement in the study. There is, therefore, need to protect benefit-sharing practices in international health research by developing a governance legal framework. A legal framework of benefit sharing will also dispel the issue of commodification of human material where human genomic research is done. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=benefit%20sharing" title="benefit sharing">benefit sharing</a>, <a href="https://publications.waset.org/abstracts/search?q=human%20participants" title=" human participants"> human participants</a>, <a href="https://publications.waset.org/abstracts/search?q=human%20genomic%20research" title=" human genomic research"> human genomic research</a>, <a href="https://publications.waset.org/abstracts/search?q=ethical%20concerns" title=" ethical concerns"> ethical concerns</a> </p> <a href="https://publications.waset.org/abstracts/170678/benefit-sharing-of-research-participants-in-human-genomic-research-ethical-concerns-and-ramifications" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/170678.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">76</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3138</span> Identification of Nonlinear Systems Structured by Hammerstein-Wiener Model </h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=A.%20Brouri">A. Brouri</a>, <a href="https://publications.waset.org/abstracts/search?q=F.%20Giri"> F. Giri</a>, <a href="https://publications.waset.org/abstracts/search?q=A.%20Mkhida"> A. Mkhida</a>, <a href="https://publications.waset.org/abstracts/search?q=A.%20Elkarkri"> A. Elkarkri</a>, <a href="https://publications.waset.org/abstracts/search?q=M.%20L.%20Chhibat"> M. L. Chhibat</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Standard Hammerstein-Wiener models consist of a linear subsystem sandwiched by two memoryless nonlinearities. Presently, the linear subsystem is allowed to be parametric or not, continuous- or discrete-time. The input and output nonlinearities are polynomial and may be noninvertible. A two-stage identification method is developed such the parameters of all nonlinear elements are estimated first using the Kozen-Landau polynomial decomposition algorithm. The obtained estimates are then based upon in the identification of the linear subsystem, making use of suitable pre-ad post-compensators. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=nonlinear%20system%20identification" title="nonlinear system identification">nonlinear system identification</a>, <a href="https://publications.waset.org/abstracts/search?q=Hammerstein-Wiener%20systems" title=" Hammerstein-Wiener systems"> Hammerstein-Wiener systems</a>, <a href="https://publications.waset.org/abstracts/search?q=frequency%20identification" title=" frequency identification"> frequency identification</a>, <a href="https://publications.waset.org/abstracts/search?q=polynomial%20decomposition" title=" polynomial decomposition"> polynomial decomposition</a> </p> <a href="https://publications.waset.org/abstracts/7969/identification-of-nonlinear-systems-structured-by-hammerstein-wiener-model" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/7969.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">511</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3137</span> Genomics of Adaptation in the Sea</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Agostinho%20Antunes">Agostinho Antunes</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=marine%20genomics" title="marine genomics">marine genomics</a>, <a href="https://publications.waset.org/abstracts/search?q=evolutionary%20bioinformatics" title=" evolutionary bioinformatics"> evolutionary bioinformatics</a>, <a href="https://publications.waset.org/abstracts/search?q=human%20genome%20sequencing" title=" human genome sequencing"> human genome sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=genomic%20analyses" title=" genomic analyses"> genomic analyses</a> </p> <a href="https://publications.waset.org/abstracts/20910/genomics-of-adaptation-in-the-sea" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/20910.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">611</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3136</span> Gene Prediction in DNA Sequences Using an Ensemble Algorithm Based on Goertzel Algorithm and Anti-Notch Filter</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Hamidreza%20Saberkari">Hamidreza Saberkari</a>, <a href="https://publications.waset.org/abstracts/search?q=Mousa%20Shamsi"> Mousa Shamsi</a>, <a href="https://publications.waset.org/abstracts/search?q=Hossein%20Ahmadi"> Hossein Ahmadi</a>, <a href="https://publications.waset.org/abstracts/search?q=Saeed%20Vaali"> Saeed Vaali</a>, <a href="https://publications.waset.org/abstracts/search?q="></a>, <a href="https://publications.waset.org/abstracts/search?q=MohammadHossein%20Sedaaghi">MohammadHossein Sedaaghi</a> </p> <p class="card-text"><strong>Abstract:</strong></p> In the recent years, using signal processing tools for accurate identification of the protein coding regions has become a challenge in bioinformatics. Most of the genomic signal processing methods is based on the period-3 characteristics of the nucleoids in DNA strands and consequently, spectral analysis is applied to the numerical sequences of DNA to find the location of periodical components. In this paper, a novel ensemble algorithm for gene selection in DNA sequences has been presented which is based on the combination of Goertzel algorithm and anti-notch filter (ANF). The proposed algorithm has many advantages when compared to other conventional methods. Firstly, it leads to identify the coding protein regions more accurate due to using the Goertzel algorithm which is tuned at the desired frequency. Secondly, faster detection time is achieved. The proposed algorithm is applied on several genes, including genes available in databases BG570 and HMR195 and their results are compared to other methods based on the nucleotide level evaluation criteria. Implementation results show the excellent performance of the proposed algorithm in identifying protein coding regions, specifically in identification of small-scale gene areas. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=protein%20coding%20regions" title="protein coding regions">protein coding regions</a>, <a href="https://publications.waset.org/abstracts/search?q=period-3" title=" period-3"> period-3</a>, <a href="https://publications.waset.org/abstracts/search?q=anti-notch%20filter" title=" anti-notch filter"> anti-notch filter</a>, <a href="https://publications.waset.org/abstracts/search?q=Goertzel%20algorithm" title=" Goertzel algorithm"> Goertzel algorithm</a> </p> <a href="https://publications.waset.org/abstracts/10286/gene-prediction-in-dna-sequences-using-an-ensemble-algorithm-based-on-goertzel-algorithm-and-anti-notch-filter" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/10286.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">387</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3135</span> Prediction of Ionizing Radiation Doses in Irradiated red Pepper (Capsicum annuum) and Mint (Mentha piperita) by Gel Electrophoresis</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=%C5%9Eeyma%20%C3%96z%C3%A7irak%20Erg%C3%BCn">Şeyma Özçirak Ergün</a>, <a href="https://publications.waset.org/abstracts/search?q=Erg%C3%BCn%20%C5%9Eakalar"> Ergün Şakalar</a>, <a href="https://publications.waset.org/abstracts/search?q=Emrah%20Yalazi%CC%87"> Emrah Yalazi̇</a>, <a href="https://publications.waset.org/abstracts/search?q=Nebahat%20%C5%9Eahi%CC%87n"> Nebahat Şahi̇n</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Food irradiation is a usage of exposing food to ionising radiation (IR) such as gamma rays. IR has been used to decrease the number of harmful microorganisms in the food such as spices. Excessive usage of IR can cause damage to both food and people who consuming food. And also it causes to damages on food DNA. Generally, IR detection techniques were utilized in literature for spices are Electron Spin Resonance (ESR), Thermos Luminescence (TL). Storage creates negative effect on IR detection method then analyses of samples have been performed without storage in general. In the experimental part, red pepper (Capsicum annuum) and mint (Mentha piperita) as spices were exposed to 0, 0.272, 0.497, 1.06, 3.64, 8.82, and 17.42 kGy ionize radiation. ESR was applied to samples irradiated. DNA isolation from irradiated samples was performed using GIDAGEN Multi Fast DNA isolation kit. The DNA concentration was measured using a microplate reader spectrophotometer (Infinite® 200 PRO-Life Science–Tecan). The concentration of each DNA was adjusted to 50 ng/µL. Genomic DNA was imaged by UV transilluminator (Gel Doc XR System, Bio-Rad) for the estimation of genomic DNA bp-fragment size after IR. Thus, agarose gel profiles of irradiated spices were obtained to determine the change of band profiles. Besides, samples were examined at three different time periods (0, 3, 6 months storage) to show the feasibility of developed method. Results of gel electrophoresis showed especially degradation of DNA of irradiated samples. In conclusion, this study with gel electrophoresis can be used as a basis for the identification of the dose of irradiation by looking at degradation profiles at specific amounts of irradiation. Agarose gel results of irradiated samples were confirmed with ESR analysis. This method can be applied widely to not only food products but also all biological materials containing DNA to predict radiation-induced damage of DNA. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=DNA" title="DNA">DNA</a>, <a href="https://publications.waset.org/abstracts/search?q=electrophoresis" title=" electrophoresis"> electrophoresis</a>, <a href="https://publications.waset.org/abstracts/search?q=gel%20electrophoresis" title=" gel electrophoresis"> gel electrophoresis</a>, <a href="https://publications.waset.org/abstracts/search?q=ionizeradiation" title=" ionizeradiation"> ionizeradiation</a> </p> <a href="https://publications.waset.org/abstracts/53071/prediction-of-ionizing-radiation-doses-in-irradiated-red-pepper-capsicum-annuum-and-mint-mentha-piperita-by-gel-electrophoresis" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/53071.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">259</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3134</span> Antibody Reactivity of Synthetic Peptides Belonging to Proteins Encoded by Genes Located in Mycobacterium tuberculosis-Specific Genomic Regions of Differences</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Abu%20Salim%20Mustafa">Abu Salim Mustafa</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The comparisons of mycobacterial genomes have identified several <em>Mycobacterium tuberculosis</em>-specific genomic regions that are absent in other mycobacteria and are known as regions of differences. Due to <em>M. tuberculosis</em>-specificity, the peptides encoded by these regions could be useful in the specific diagnosis of tuberculosis. To explore this possibility, overlapping synthetic peptides corresponding to 39 proteins predicted to be encoded by genes present in regions of differences were tested for antibody-reactivity with sera from tuberculosis patients and healthy subjects. The results identified four immunodominant peptides corresponding to four different proteins, with three of the peptides showing significantly stronger antibody reactivity and rate of positivity with sera from tuberculosis patients than healthy subjects. The fourth peptide was recognized equally well by the sera of tuberculosis patients as well as healthy subjects. Predication of antibody epitopes by bioinformatics analyses using ABCpred server predicted multiple linear epitopes in each peptide. Furthermore, peptide sequence analysis for sequence identity using BLAST suggested <em>M. tuberculosis</em>-specificity for the three peptides that had preferential reactivity with sera from tuberculosis patients, but the peptide with equal reactivity with sera of TB patients and healthy subjects showed significant identity with sequences present in nob-tuberculous mycobacteria. The three identified <em>M. tuberculosis</em>-specific immunodominant peptides may be useful in the serological diagnosis of tuberculosis. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=genomic%20regions%20of%20differences" title="genomic regions of differences">genomic regions of differences</a>, <a href="https://publications.waset.org/abstracts/search?q=Mycobacterium%20tuberculossis" title=" Mycobacterium tuberculossis"> Mycobacterium tuberculossis</a>, <a href="https://publications.waset.org/abstracts/search?q=peptides" title=" peptides"> peptides</a>, <a href="https://publications.waset.org/abstracts/search?q=serodiagnosis" title=" serodiagnosis"> serodiagnosis</a> </p> <a href="https://publications.waset.org/abstracts/83354/antibody-reactivity-of-synthetic-peptides-belonging-to-proteins-encoded-by-genes-located-in-mycobacterium-tuberculosis-specific-genomic-regions-of-differences" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/83354.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">183</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3133</span> Genomic Sequence Representation Learning: An Analysis of K-Mer Vector Embedding Dimensionality</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=James%20Jr.%20Mashiyane">James Jr. Mashiyane</a>, <a href="https://publications.waset.org/abstracts/search?q=Risuna%20Nkolele"> Risuna Nkolele</a>, <a href="https://publications.waset.org/abstracts/search?q=Stephanie%20J.%20M%C3%BCller"> Stephanie J. Müller</a>, <a href="https://publications.waset.org/abstracts/search?q=Gciniwe%20S.%20Dlamini"> Gciniwe S. Dlamini</a>, <a href="https://publications.waset.org/abstracts/search?q=Rebone%20L.%20Meraba"> Rebone L. Meraba</a>, <a href="https://publications.waset.org/abstracts/search?q=Darlington%20S.%20Mapiye"> Darlington S. Mapiye</a> </p> <p class="card-text"><strong>Abstract:</strong></p> When performing language tasks in natural language processing (NLP), the dimensionality of word embeddings is chosen either ad-hoc or is calculated by optimizing the Pairwise Inner Product (PIP) loss. The PIP loss is a metric that measures the dissimilarity between word embeddings, and it is obtained through matrix perturbation theory by utilizing the unitary invariance of word embeddings. Unlike in natural language, in genomics, especially in genome sequence processing, unlike in natural language processing, there is no notion of a “word,” but rather, there are sequence substrings of length k called k-mers. K-mers sizes matter, and they vary depending on the goal of the task at hand. The dimensionality of word embeddings in NLP has been studied using the matrix perturbation theory and the PIP loss. In this paper, the sufficiency and reliability of applying word-embedding algorithms to various genomic sequence datasets are investigated to understand the relationship between the k-mer size and their embedding dimension. This is completed by studying the scaling capability of three embedding algorithms, namely Latent Semantic analysis (LSA), Word2Vec, and Global Vectors (GloVe), with respect to the k-mer size. Utilising the PIP loss as a metric to train embeddings on different datasets, we also show that Word2Vec outperforms LSA and GloVe in accurate computing embeddings as both the k-mer size and vocabulary increase. Finally, the shortcomings of natural language processing embedding algorithms in performing genomic tasks are discussed. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=word%20embeddings" title="word embeddings">word embeddings</a>, <a href="https://publications.waset.org/abstracts/search?q=k-mer%20embedding" title=" k-mer embedding"> k-mer embedding</a>, <a href="https://publications.waset.org/abstracts/search?q=dimensionality%0D%0Areduction" title=" dimensionality reduction"> dimensionality reduction</a> </p> <a href="https://publications.waset.org/abstracts/151370/genomic-sequence-representation-learning-an-analysis-of-k-mer-vector-embedding-dimensionality" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/151370.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">138</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3132</span> Structural Damage Detection Using Sensors Optimally Located</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Carlos%20Alberto%20Riveros">Carlos Alberto Riveros</a>, <a href="https://publications.waset.org/abstracts/search?q=Edwin%20Fabi%C3%A1n%20Garc%C3%ADa"> Edwin Fabián García</a>, <a href="https://publications.waset.org/abstracts/search?q=Javier%20Enrique%20Rivero"> Javier Enrique Rivero</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The measured data obtained from sensors in continuous monitoring of civil structures are mainly used for modal identification and damage detection. Therefore when modal identification analysis is carried out the quality in the identification of the modes will highly influence the damage detection results. It is also widely recognized that the usefulness of the measured data used for modal identification and damage detection is significantly influenced by the number and locations of sensors. The objective of this study is the numerical implementation of two widely known optimum sensor placement methods in beam-like structures <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=optimum%20sensor%20placement" title="optimum sensor placement">optimum sensor placement</a>, <a href="https://publications.waset.org/abstracts/search?q=structural%20damage%20detection" title=" structural damage detection"> structural damage detection</a>, <a href="https://publications.waset.org/abstracts/search?q=modal%20identification" title=" modal identification"> modal identification</a>, <a href="https://publications.waset.org/abstracts/search?q=beam-like%20structures." title=" beam-like structures. "> beam-like structures. </a> </p> <a href="https://publications.waset.org/abstracts/15240/structural-damage-detection-using-sensors-optimally-located" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/15240.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">431</span> </span> </div> </div> <ul class="pagination"> <li class="page-item disabled"><span class="page-link">&lsaquo;</span></li> <li class="page-item active"><span class="page-link">1</span></li> <li class="page-item"><a class="page-link" href="https://publications.waset.org/abstracts/search?q=genomic%20identification&page=2">2</a></li> <li class="page-item"><a class="page-link" href="https://publications.waset.org/abstracts/search?q=genomic%20identification&page=3">3</a></li> <li class="page-item"><a class="page-link" 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