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metagenomic sequence analysis</title> <meta name="description" content="Search results for: shotgun metagenomic sequence analysis"> <meta name="keywords" content="shotgun metagenomic sequence analysis"> <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 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method="get" 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="shotgun metagenomic sequence analysis"> <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> 28586</div> </div> </div> </div> <h1 class="mt-3 mb-3 text-center" style="font-size:1.6rem;">Search results for: shotgun metagenomic sequence analysis</h1> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">28586</span> TAXAPRO, A Streamlined Pipeline to Analyze Shotgun Metagenomes</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Sofia%20Sehli">Sofia Sehli</a>, <a href="https://publications.waset.org/abstracts/search?q=Zainab%20El%20Ouafi"> Zainab El Ouafi</a>, <a href="https://publications.waset.org/abstracts/search?q=Casey%20Eddington"> Casey Eddington</a>, <a href="https://publications.waset.org/abstracts/search?q=Soumaya%20Jbara"> Soumaya Jbara</a>, <a href="https://publications.waset.org/abstracts/search?q=Kasambula%20Arthur%20Shem"> Kasambula Arthur Shem</a>, <a href="https://publications.waset.org/abstracts/search?q=Islam%20El%20Jaddaoui"> Islam El Jaddaoui</a>, <a href="https://publications.waset.org/abstracts/search?q=Ayorinde%20Afolayan"> Ayorinde Afolayan</a>, <a href="https://publications.waset.org/abstracts/search?q=Olaitan%20I.%20Awe"> Olaitan I. Awe</a>, <a href="https://publications.waset.org/abstracts/search?q=Allissa%20Dillman"> Allissa Dillman</a>, <a href="https://publications.waset.org/abstracts/search?q=Hassan%20Ghazal"> Hassan Ghazal</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The ability to promptly sequence whole genomes at a relatively low cost has revolutionized the way we study the microbiome. Microbiologists are no longer limited to studying what can be grown in a laboratory and instead are given the opportunity to rapidly identify the makeup of microbial communities in a wide variety of environments. Analyzing whole genome sequencing (WGS) data is a complex process that involves multiple moving parts and might be rather unintuitive for scientists that don’t typically work with this type of data. Thus, to help lower the barrier for less-computationally inclined individuals, TAXAPRO was developed at the first Omics Codeathon held virtually by the African Society for Bioinformatics and Computational Biology (ASBCB) in June 2021. TAXAPRO is an advanced metagenomics pipeline that accurately assembles organelle genomes from whole-genome sequencing data. TAXAPRO seamlessly combines WGS analysis tools to create a pipeline that automatically processes raw WGS data and presents organism abundance information in both a tabular and graphical format. TAXAPRO was evaluated using COVID-19 patient gut microbiome data. Analysis performed by TAXAPRO demonstrated a high abundance of Clostridia and Bacteroidia genera and a low abundance of Proteobacteria genera relative to others in the gut microbiome of patients hospitalized with COVID-19, consistent with the original findings derived using a different analysis methodology. This provides crucial evidence that the TAXAPRO workflow dispenses reliable organism abundance information overnight without the hassle of performing the analysis manually. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=metagenomics" title="metagenomics">metagenomics</a>, <a href="https://publications.waset.org/abstracts/search?q=shotgun%20metagenomic%20sequence%20analysis" title=" shotgun metagenomic sequence analysis"> shotgun metagenomic sequence analysis</a>, <a href="https://publications.waset.org/abstracts/search?q=COVID-19" title=" COVID-19"> COVID-19</a>, <a href="https://publications.waset.org/abstracts/search?q=pipeline" title=" pipeline"> pipeline</a>, <a href="https://publications.waset.org/abstracts/search?q=bioinformatics" title=" bioinformatics"> bioinformatics</a> </p> <a href="https://publications.waset.org/abstracts/147152/taxapro-a-streamlined-pipeline-to-analyze-shotgun-metagenomes" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/147152.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">221</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">28585</span> Towards End-To-End Disease Prediction from Raw Metagenomic Data</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Maxence%20Queyrel">Maxence Queyrel</a>, <a href="https://publications.waset.org/abstracts/search?q=Edi%20Prifti"> Edi Prifti</a>, <a href="https://publications.waset.org/abstracts/search?q=Alexandre%20Templier"> Alexandre Templier</a>, <a href="https://publications.waset.org/abstracts/search?q=Jean-Daniel%20Zucker"> Jean-Daniel Zucker</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=deep%20learning" title="deep learning">deep learning</a>, <a href="https://publications.waset.org/abstracts/search?q=disease%20prediction" title=" disease prediction"> disease prediction</a>, <a href="https://publications.waset.org/abstracts/search?q=end-to-end%20machine%20learning" title=" end-to-end machine learning"> end-to-end machine learning</a>, <a href="https://publications.waset.org/abstracts/search?q=metagenomics" title=" metagenomics"> metagenomics</a>, <a href="https://publications.waset.org/abstracts/search?q=multiple%20instance%20learning" title=" multiple instance learning"> multiple instance learning</a>, <a href="https://publications.waset.org/abstracts/search?q=precision%20medicine" title=" precision medicine"> precision medicine</a> </p> <a href="https://publications.waset.org/abstracts/131509/towards-end-to-end-disease-prediction-from-raw-metagenomic-data" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/131509.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">125</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">28584</span> Viral Metagenomics Revealed a Novel Cardiovirus in Feces of Wild Rats</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Asif%20Mahmood">Asif Mahmood</a>, <a href="https://publications.waset.org/abstracts/search?q=Shama%20Shama"> Shama Shama</a>, <a href="https://publications.waset.org/abstracts/search?q=Hao%20Ni"> Hao Ni</a>, <a href="https://publications.waset.org/abstracts/search?q=Hao%20Wang"> Hao Wang</a>, <a href="https://publications.waset.org/abstracts/search?q=Yu%20Ling"> Yu Ling</a>, <a href="https://publications.waset.org/abstracts/search?q=Hui%20Xu"> Hui Xu</a>, <a href="https://publications.waset.org/abstracts/search?q=Shixing%20Yang"> Shixing Yang</a>, <a href="https://publications.waset.org/abstracts/search?q=Qais%20Ahmad%20Naseer"> Qais Ahmad Naseer</a>, <a href="https://publications.waset.org/abstracts/search?q=Wen%20Zhang"> Wen Zhang</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Cardiovirus is a genus of viruses belonging to the family Picornaviridae. Here, we used viral metagenomic techniques to detect the viral nucleic acid in the fecal samples from wild rats in Zhenjiang city in China. Fecal samples were collected from 20 wild rats and pooled into four sample pools and then subjected to libraries construction which were then sequenced on Illumina MiSeq platform. The sequenced reads were analyzed using viral metagenomic analysis pipeline. A novel cardiovirus from feces of a wild rat was identified, named amzj-2018, of which the complete genome was acquired. Phylogenetic analysis based on the complete amino acid sequence of polyprotein revealed that amzj-2018 formed a separate branch located between clusters of Saffold virus and Rat Theilovirus 1 (RTV-1). Phylogenetic analysis based on different regions of the polyproteins, including P1, P2, P3, and P2+P3, respectively, showed discordant trees, where the tree based on P3 region indicated that amzj-2018 clustered separately between Theiler's murine encephalomyelitis virus and RTV-1. The complete genome of a cardiovirus was determined from the feces of wild rats which belonged to a novel type of cardiovirus based on phylogenetic analysis. Whether it is associated with disease needs further investigation. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=cardiovirus" title="cardiovirus">cardiovirus</a>, <a href="https://publications.waset.org/abstracts/search?q=viral%20metagenomics" title=" viral metagenomics"> viral metagenomics</a>, <a href="https://publications.waset.org/abstracts/search?q=genomic%20organization" title=" genomic organization"> genomic organization</a>, <a href="https://publications.waset.org/abstracts/search?q=phylogenetic%20analysis" title=" phylogenetic analysis"> phylogenetic analysis</a> </p> <a href="https://publications.waset.org/abstracts/192230/viral-metagenomics-revealed-a-novel-cardiovirus-in-feces-of-wild-rats" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/192230.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">18</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">28583</span> Analysis of Taxonomic Compositions, Metabolic Pathways and Antibiotic Resistance Genes in Fish Gut Microbiome by Shotgun Metagenomics</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Anuj%20Tyagi">Anuj Tyagi</a>, <a href="https://publications.waset.org/abstracts/search?q=Balwinder%20Singh"> Balwinder Singh</a>, <a href="https://publications.waset.org/abstracts/search?q=Naveen%20Kumar%20B.%20T."> Naveen Kumar B. T.</a>, <a href="https://publications.waset.org/abstracts/search?q=Niraj%20K.%20Singh"> Niraj K. Singh</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Characterization of diverse microbial communities in specific environment plays a crucial role in the better understanding of their functional relationship with the ecosystem. It is now well established that gut microbiome of fish is not the simple replication of microbiota of surrounding local habitat, and extensive species, dietary, physiological and metabolic variations in fishes may have a significant impact on its composition. Moreover, overuse of antibiotics in human, veterinary and aquaculture medicine has led to rapid emergence and propagation of antibiotic resistance genes (ARGs) in the aquatic environment. Microbial communities harboring specific ARGs not only get a preferential edge during selective antibiotic exposure but also possess the significant risk of ARGs transfer to other non-resistance bacteria within the confined environments. This phenomenon may lead to the emergence of habitat-specific microbial resistomes and subsequent emergence of virulent antibiotic-resistant pathogens with severe fish and consumer health consequences. In this study, gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. Metagenomic DNA, extracted from the fish gut, was subjected to sequencing on Illumina NextSeq to generate paired-end (PE) 2 x 150 bp sequencing reads. After the QC of raw sequencing data by Trimmomatic, taxonomic analysis by Kraken2 taxonomic sequence classification system revealed the presence of 36 phyla, 326 families and 985 genera in the fish gut microbiome. At phylum level, Proteobacteria accounted for more than three-fourths of total bacterial populations followed by Actinobacteria (14%) and Cyanobacteria (3%). Commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) were found to be very less prevalent in fish gut. After sequencing data assembly by MEGAHIT v1.1.2 assembler and PROKKA automated analysis pipeline, pathway analysis revealed the presence of 1,608 Metacyc pathways in the fish gut microbiome. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy-metabolism (4%) and fermentation (2%). Almost one-third (33%) of biosynthesis pathways were involved in the synthesis of secondary metabolites. Metabolic pathways for the biosynthesis of 35 antibiotic types were also present, and these accounted for 5% of overall metabolic pathways in the fish gut microbiome. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. More than 90% ARGs in fish gut microbiome were against beta-lactams (penicillins, cephalosporins, penems, and monobactams). Resistance against tetracycline, macrolides, fluoroquinolones, and phenicols ranged from 0.7% to 1.3%. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=antibiotic%20resistance" title="antibiotic resistance">antibiotic resistance</a>, <a href="https://publications.waset.org/abstracts/search?q=fish%20gut" title=" fish gut"> fish gut</a>, <a href="https://publications.waset.org/abstracts/search?q=metabolic%20pathways" title=" metabolic pathways"> metabolic pathways</a>, <a href="https://publications.waset.org/abstracts/search?q=microbial%20diversity" title=" microbial diversity"> microbial diversity</a> </p> <a href="https://publications.waset.org/abstracts/99462/analysis-of-taxonomic-compositions-metabolic-pathways-and-antibiotic-resistance-genes-in-fish-gut-microbiome-by-shotgun-metagenomics" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/99462.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">144</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">28582</span> Merging Sequence Diagrams Based Slicing</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Bouras%20Zine%20Eddine">Bouras Zine Eddine</a>, <a href="https://publications.waset.org/abstracts/search?q=Talai%20Abdelouaheb"> Talai Abdelouaheb</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The need to merge software artifacts seems inherent to modern software development. Distribution of development over several teams and breaking tasks into smaller, more manageable pieces are an effective means to deal with the kind of complexity. In each case, the separately developed artifacts need to be assembled as efficiently as possible into a consistent whole in which the parts still function as described. Also, earlier changes are introduced into the life cycle and easier is their management by designers. Interaction-based specifications such as UML sequence diagrams have been found effective in this regard. As a result, sequence diagrams can be used not only for capturing system behaviors but also for merging changes in order to create a new version. The objective of this paper is to suggest a new approach to deal with the problem of software merging at the level of sequence diagrams by using the concept of dependence analysis that captures, formally, all mapping and differences between elements of sequence diagrams and serves as a key concept to create a new version of sequence diagram. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=system%20behaviors" title="system behaviors">system behaviors</a>, <a href="https://publications.waset.org/abstracts/search?q=sequence%20diagram%20merging" title=" sequence diagram merging"> sequence diagram merging</a>, <a href="https://publications.waset.org/abstracts/search?q=dependence%20analysis" title=" dependence analysis"> dependence analysis</a>, <a href="https://publications.waset.org/abstracts/search?q=sequence%20diagram%20slicing" title=" sequence diagram slicing"> sequence diagram slicing</a> </p> <a href="https://publications.waset.org/abstracts/29735/merging-sequence-diagrams-based-slicing" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/29735.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">340</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">28581</span> In Agile Projects - Arithmetic Sequence is More Effective than Fibonacci Sequence to Use for Estimating the Implementation Effort of User Stories</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Khaled%20Jaber">Khaled Jaber</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The estimation of effort in software development is a complex task. The traditional Waterfall approach used to develop software systems requires a lot of time to estimate the effort needed to implement user requirements. Agile manifesto, however, is currently more used in the industry than the Waterfall to develop software systems. In Agile, the user requirement is referred to as a user story. Agile teams mostly use the Fibonacci sequence 1, 2, 3, 5, 8, 11, etc. in estimating the effort needed to implement the user story. This work shows through analysis that the Arithmetic sequence, e.g., 3, 6, 9, 12, etc., is more effective than the Fibonacci sequence in estimating the user stories. This paper mathematically and visually proves the effectiveness of the Arithmetic sequence over the FB sequence. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=agie" title="agie">agie</a>, <a href="https://publications.waset.org/abstracts/search?q=scrum" title=" scrum"> scrum</a>, <a href="https://publications.waset.org/abstracts/search?q=estimation" title=" estimation"> estimation</a>, <a href="https://publications.waset.org/abstracts/search?q=fibonacci%20sequence" title=" fibonacci sequence"> fibonacci sequence</a> </p> <a href="https://publications.waset.org/abstracts/145354/in-agile-projects-arithmetic-sequence-is-more-effective-than-fibonacci-sequence-to-use-for-estimating-the-implementation-effort-of-user-stories" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/145354.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">206</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">28580</span> 16s rRNA Based Metagenomic Analysis of Palm Sap Samples From Bangladesh</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=%C3%81gota%20%C3%81brah%C3%A1m">Ágota Ábrahám</a>, <a href="https://publications.waset.org/abstracts/search?q=Md%20Nurul%20Islam"> Md Nurul Islam</a>, <a href="https://publications.waset.org/abstracts/search?q=Karimane%20Zeghbib"> Karimane Zeghbib</a>, <a href="https://publications.waset.org/abstracts/search?q=G%C3%A1bor%20Kemenesi"> Gábor Kemenesi</a>, <a href="https://publications.waset.org/abstracts/search?q=Sazeda%20Akter"> Sazeda Akter</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Collecting palm sap as a food source is an everyday practice in some parts of the world. However, the consumption of palm juice has been associated with regular infections and epidemics in parts of Bangladesh. This is attributed to fruit-eating bats and other vertebrates or invertebrates native to the area, contaminating the food with their body secretions during the collection process. The frequent intake of palm juice, whether as a processed food product or in its unprocessed form, is a common phenomenon in large areas. The range of pathogens suitable for human infection resulting from this practice is not yet fully understood. Additionally, the high sugar content of the liquid makes it an ideal culture medium for certain bacteria, which can easily propagate and potentially harm consumers. Rapid diagnostics, especially in remote locations, could mitigate health risks associated with palm juice consumption. The primary objective of this research is the rapid genomic detection and risk assessment of bacteria that may cause infections in humans through the consumption of palm juice. Utilizing state-of-the-art third-generation Nanopore metagenomic sequencing technology based on 16S rRNA, and identified bacteria primarily involved in fermenting processes. The swift metagenomic analysis, coupled with the widespread availability and portability of Nanopore products (including real-time analysis options), proves advantageous for detecting harmful pathogens in food sources without relying on extensive industry resources and testing. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=raw%20date%20palm%20sap" title="raw date palm sap">raw date palm sap</a>, <a href="https://publications.waset.org/abstracts/search?q=NGS" title=" NGS"> NGS</a>, <a href="https://publications.waset.org/abstracts/search?q=metabarcoding" title=" metabarcoding"> metabarcoding</a>, <a href="https://publications.waset.org/abstracts/search?q=food%20safety" title=" food safety"> food safety</a> </p> <a href="https://publications.waset.org/abstracts/178944/16s-rrna-based-metagenomic-analysis-of-palm-sap-samples-from-bangladesh" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/178944.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">56</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">28579</span> Toward Particular Series with (k,h)-Jacobsthal Sequence</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Seyyd%20Hossein%20Jafari-Petroudi">Seyyd Hossein Jafari-Petroudi</a>, <a href="https://publications.waset.org/abstracts/search?q=Maryam%20Pirouz"> Maryam Pirouz</a> </p> <p class="card-text"><strong>Abstract:</strong></p> This note is devoted to (k; h)-Jacobsthal sequence as a general term of particular series. More formulas for nth term and sum of the first n terms of series that their general terms are (k; h)-Jacobsthal sequence and (k; h)-Jacobsthal-Petroudi sequence are derived. Finally other properties of these sequences are represented. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=%28k" title="(k">(k</a>, <a href="https://publications.waset.org/abstracts/search?q=h%29-Jacobsthal%20sequence" title="h)-Jacobsthal sequence">h)-Jacobsthal sequence</a>, <a href="https://publications.waset.org/abstracts/search?q=%28k" title="(k">(k</a>, <a href="https://publications.waset.org/abstracts/search?q=h%29-Jacobsthal%20Petroudisequence" title="h)-Jacobsthal Petroudisequence">h)-Jacobsthal Petroudisequence</a>, <a href="https://publications.waset.org/abstracts/search?q=recursive%20relation" title=" recursive relation"> recursive relation</a>, <a href="https://publications.waset.org/abstracts/search?q=sum" title=" sum"> sum</a> </p> <a href="https://publications.waset.org/abstracts/40044/toward-particular-series-with-kh-jacobsthal-sequence" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/40044.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">393</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">28578</span> Bioinformatic Screening of Metagenomic Fosmid Libraries for Identification of Biosynthetic Pathways Derived from the Colombian Soils</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Mar%C3%ADa%20Fernanda%20Quiceno%20Vallejo">María Fernanda Quiceno Vallejo</a>, <a href="https://publications.waset.org/abstracts/search?q=Patricia%20del%20Portillo"> Patricia del Portillo</a>, <a href="https://publications.waset.org/abstracts/search?q=Mar%C3%ADa%20Mercedes%20Zambrano"> María Mercedes Zambrano</a>, <a href="https://publications.waset.org/abstracts/search?q=Jeisson%20Alejandro%20Triana"> Jeisson Alejandro Triana</a>, <a href="https://publications.waset.org/abstracts/search?q=Dayana%20Calderon"> Dayana Calderon</a>, <a href="https://publications.waset.org/abstracts/search?q=Juan%20Manuel%20Anzola"> Juan Manuel Anzola</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Microorganisms from tropical ecosystems can be novel in terms of adaptations and conservation. Given the macrodiversity of Colombian ecosystems, it is possible that this diversity is also present in Colombian soils. Tropical soil bacteria could offer a potentially novel source of bioactive compounds. In this study we analyzed a metagenomic fosmid library constructed with tropical bacterial DNAs with the aim of understanding its underlying diversity and functional potential. 8640 clones from the fosmid library were sequenced by NANOPORE MiniOn technology, then analyzed with bioinformatic tools such as Prokka, AntiSMASH and Bagel4 in order to identify functional biosynthetic pathways in the sequences. The strains showed ample difference when it comes to biosynthetic pathways. In total we identified 4 pathways related to aryl polyene synthesis, 12 related to terpenes, 22 related to NRPs (Non ribosomal peptides), 11 related PKs (Polyketide synthases) and 7 related to RiPPs (bacteriocins). We designed primers for the metagenomic clones with the most BGCs (sample 6 and sample 2). Results show the biotechnological / pharmacological potential of tropical ecosystems. Overall, this work provides an overview of the genomic and functional potential of Colombian soil and sets the groundwork for additional exploration of tropical metagenomic sequencing. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=bioactives" title="bioactives">bioactives</a>, <a href="https://publications.waset.org/abstracts/search?q=biosyntethic%20pathways" title=" biosyntethic pathways"> biosyntethic pathways</a>, <a href="https://publications.waset.org/abstracts/search?q=bioinformatic" title=" bioinformatic"> bioinformatic</a>, <a href="https://publications.waset.org/abstracts/search?q=bacterial%20gene%20clusters" title=" bacterial gene clusters"> bacterial gene clusters</a>, <a href="https://publications.waset.org/abstracts/search?q=secondary%20metabolites" title=" secondary metabolites"> secondary metabolites</a> </p> <a href="https://publications.waset.org/abstracts/144224/bioinformatic-screening-of-metagenomic-fosmid-libraries-for-identification-of-biosynthetic-pathways-derived-from-the-colombian-soils" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/144224.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">165</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">28577</span> On the Analysis of Pseudorandom Partial Quotient Sequences Generated from Continued Fractions</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=T.%20Padma">T. Padma</a>, <a href="https://publications.waset.org/abstracts/search?q=Jayashree%20S.%20Pillai"> Jayashree S. Pillai</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Random entities are an essential component in any cryptographic application. The suitability of a number theory based novel pseudorandom sequence called Pseudorandom Partial Quotient Sequence (PPQS) generated from the continued fraction expansion of irrational numbers, in cryptographic applications, is analyzed in this paper. An approach to build the algorithm around a hard mathematical problem has been considered. The PQ sequence is tested for randomness and its suitability as a cryptographic key by performing randomness analysis, key sensitivity and key space analysis, precision analysis and evaluating the correlation properties is established. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=pseudorandom%20sequences" title="pseudorandom sequences">pseudorandom sequences</a>, <a href="https://publications.waset.org/abstracts/search?q=key%20sensitivity" title=" key sensitivity"> key sensitivity</a>, <a href="https://publications.waset.org/abstracts/search?q=correlation" title=" correlation"> correlation</a>, <a href="https://publications.waset.org/abstracts/search?q=security%20analysis" title=" security analysis"> security analysis</a>, <a href="https://publications.waset.org/abstracts/search?q=randomness%20analysis" title=" randomness analysis"> randomness analysis</a>, <a href="https://publications.waset.org/abstracts/search?q=sensitivity%20analysis" title=" sensitivity analysis"> sensitivity analysis</a> </p> <a href="https://publications.waset.org/abstracts/26665/on-the-analysis-of-pseudorandom-partial-quotient-sequences-generated-from-continued-fractions" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/26665.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">591</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">28576</span> Primer Design for the Detection of Secondary Metabolite Biosynthetic Pathways in Metagenomic Data</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Jeisson%20Alejandro%20Triana">Jeisson Alejandro Triana</a>, <a href="https://publications.waset.org/abstracts/search?q=Maria%20Fernanda%20Quiceno%20Vallejo"> Maria Fernanda Quiceno Vallejo</a>, <a href="https://publications.waset.org/abstracts/search?q=Patricia%20del%20Portillo"> Patricia del Portillo</a>, <a href="https://publications.waset.org/abstracts/search?q=Juan%20Manuel%20Anzola"> Juan Manuel Anzola</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Most of the known antimicrobials so far discovered are secondary metabolites. The potential for new natural products of this category increases as new microbial genomes and metagenomes are being sequenced. Despite the advances, there is no systematic way to interrogate metagenomic clones for their potential to contain clusters of genes related to these pathways. Here we analyzed 52 biosynthetic pathways from the AntiSMASH database at the protein domain level in order to identify domains of high specificity and sensitivity with respect to specific biosynthetic pathways. These domains turned out to have various degrees of divergence at the DNA level. We propose PCR assays targetting such domains in-silico and corroborated one by Sanger sequencing. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=bioinformatic" title="bioinformatic">bioinformatic</a>, <a href="https://publications.waset.org/abstracts/search?q=anti%20smash" title=" anti smash"> anti smash</a>, <a href="https://publications.waset.org/abstracts/search?q=antibiotics" title=" antibiotics"> antibiotics</a>, <a href="https://publications.waset.org/abstracts/search?q=secondary%20metabolites" title=" secondary metabolites"> secondary metabolites</a>, <a href="https://publications.waset.org/abstracts/search?q=natural%20products" title=" natural products"> natural products</a>, <a href="https://publications.waset.org/abstracts/search?q=protein%20domains" title=" protein domains"> protein domains</a> </p> <a href="https://publications.waset.org/abstracts/144241/primer-design-for-the-detection-of-secondary-metabolite-biosynthetic-pathways-in-metagenomic-data" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/144241.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">180</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">28575</span> A Similarity/Dissimilarity Measure to Biological Sequence Alignment</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Muhammad%20A.%20Khan">Muhammad A. Khan</a>, <a href="https://publications.waset.org/abstracts/search?q=Waseem%20Shahzad"> Waseem Shahzad</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Analysis of protein sequences is carried out for the purpose to discover their structural and ancestry relationship. Sequence similarity determines similar protein structures, similar function, and homology detection. Biological sequences composed of amino acid residues or nucleotides provide significant information through sequence alignment. In this paper, we present a new similarity/dissimilarity measure to sequence alignment based on the primary structure of a protein. The approach finds the distance between the two given sequences using the novel sequence alignment algorithm and a mathematical model. The algorithm runs at a time complexity of O(n²). A distance matrix is generated to construct a phylogenetic tree of different species. The new similarity/dissimilarity measure outperforms other existing methods. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=alignment" title="alignment">alignment</a>, <a href="https://publications.waset.org/abstracts/search?q=distance" title=" distance"> distance</a>, <a href="https://publications.waset.org/abstracts/search?q=homology" title=" homology"> homology</a>, <a href="https://publications.waset.org/abstracts/search?q=mathematical%20model" title=" mathematical model"> mathematical model</a>, <a href="https://publications.waset.org/abstracts/search?q=phylogenetic%20tree" title=" phylogenetic tree"> phylogenetic tree</a> </p> <a href="https://publications.waset.org/abstracts/95183/a-similaritydissimilarity-measure-to-biological-sequence-alignment" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/95183.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">178</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">28574</span> Metagenomic Analysis and Pharmacokinetics of Phage Therapy in the Treatment of Bovine Subclinical Mastitis</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Vaibhav%20D.%20Bhatt">Vaibhav D. Bhatt</a>, <a href="https://publications.waset.org/abstracts/search?q=Anju%20P.%20Kunjadia"> Anju P. Kunjadia</a>, <a href="https://publications.waset.org/abstracts/search?q=D.%20S.%20Nauriyal"> D. S. Nauriyal</a>, <a href="https://publications.waset.org/abstracts/search?q=Bhumika%20J.%20Joshi"> Bhumika J. Joshi</a>, <a href="https://publications.waset.org/abstracts/search?q=Chaitanya%20G.%20Joshi"> Chaitanya G. Joshi</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Metagenomic analysis of milk samples collected from local cattle breed, kankrej (Bos indicus), Gir (Bos indicus) and Crossbred (Bos indicus X Bos taurus) cattle harbouring subclinical mastitis was carried out by next-generation sequencing (NGS) 454 GS-FLX technology. Around 56 different species including members of Enterobacteriales, Pseudomonadales, Bacillales and Lactobacillales with varying abundance were detected in infected milk. The interesting presence of bacteriophages against Staphylococcus aureus, Escherichia coli, Enterobacter and Yersinia species were observed, especially Enterobacteria and E. coli phages (0∙32%) in Kankrej, Enterobacteria and Staphylococcus phages (1∙05%) in Gir and Staphylococcus phages (2∙32%) in crossbred cattle. NGS findings suggest that phages may be involved in imparting natural resistance of the cattle against pathogens. Further infected milk samples were subjected for bacterial isolation. Fourteen different isolates were identified, and DNA was extracted. Genes (Tet-K, Msr-A, and Mec-A) providing antibiotic resistance to the bacteria were screened by Polymerase Chain Reaction and results were validated with traditional antibiotic assay. Total 3 bacteriophages were isolated from nearby environment of the cattle farm. The efficacy of phages was checked against multi-drug resistant bacteria, identified by PCR. In-vivo study was carried out for phage therapy in mammary glands of female rats “Wister albino”. Mammary glands were infused with MDR isolates for 3 consecutive days. Recovery was observed in infected rats after intramammary infusion of sterile phage suspension. From day 4th onwards, level of C-reactive protein was significant increases up to day 12th . However, significant reduction was observed between days 12th to 18th post treatment. Bacteriophages have significant potential as antibacterial agents and their ability to replicate exponentially within their hosts and their specificity, make them ideal candidates for more sustainable mastitis control. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=bacteriophages" title="bacteriophages">bacteriophages</a>, <a href="https://publications.waset.org/abstracts/search?q=c-reactive%20protein" title=" c-reactive protein"> c-reactive protein</a>, <a href="https://publications.waset.org/abstracts/search?q=mastitis" title=" mastitis"> mastitis</a>, <a href="https://publications.waset.org/abstracts/search?q=metagenomic%20analysis" title=" metagenomic analysis"> metagenomic analysis</a> </p> <a href="https://publications.waset.org/abstracts/65533/metagenomic-analysis-and-pharmacokinetics-of-phage-therapy-in-the-treatment-of-bovine-subclinical-mastitis" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/65533.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">315</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">28573</span> Influence of Stacking Sequence and Temperature on Buckling Resistance of GFRP Infill Panel</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Viriyavudh%20Sim">Viriyavudh Sim</a>, <a href="https://publications.waset.org/abstracts/search?q=SeungHyun%20Kim"> SeungHyun Kim</a>, <a href="https://publications.waset.org/abstracts/search?q=JungKyu%20Choi"> JungKyu Choi</a>, <a href="https://publications.waset.org/abstracts/search?q=WooYoung%20Jung"> WooYoung Jung</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Glass Fiber Reinforced Polymer (GFRP) is a major evolution for energy dissipation when used as infill material for seismic retrofitting of steel frame, a basic PMC infill wall system consists of two GFRP laminates surrounding an infill of foam core. This paper presents numerical analysis in terms of buckling resistance of GFRP sandwich infill panels system under the influence of environment temperature and stacking sequence of laminate skin. Mode of failure under in-plane compression is studied by means of numerical analysis with ABAQUS platform. Parameters considered in this study are contact length between infill and frame, laminate stacking sequence of GFRP skin and variation of mechanical properties due to increment of temperature. The analysis is done with four cases of simple stacking sequence over a range of temperature. The result showed that both the effect of temperature and stacking sequence alter the performance of entire panel system. The rises of temperature resulted in the decrements of the panel’s strength. This is due to the polymeric nature of this material. Additionally, the contact length also displays the effect on the performance of infill panel. Furthermore, the laminate stiffness can be modified by orientation of laminate, which can increase the infill panel strength. Hence, optimal performance of the entire panel system can be obtained by comparing different cases of stacking sequence. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=buckling%20resistance" title="buckling resistance">buckling resistance</a>, <a href="https://publications.waset.org/abstracts/search?q=GFRP%20infill%20panel" title=" GFRP infill panel"> GFRP infill panel</a>, <a href="https://publications.waset.org/abstracts/search?q=stacking%20sequence" title=" stacking sequence"> stacking sequence</a>, <a href="https://publications.waset.org/abstracts/search?q=temperature%20dependent" title=" temperature dependent"> temperature dependent</a> </p> <a href="https://publications.waset.org/abstracts/47887/influence-of-stacking-sequence-and-temperature-on-buckling-resistance-of-gfrp-infill-panel" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/47887.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">374</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">28572</span> Metagenomic Assessment of the Effects of Genetically Modified Crops on Microbial Ecology and Physicochemical Properties of Soil</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Falana%20Yetunde%20Olaitan">Falana Yetunde Olaitan</a>, <a href="https://publications.waset.org/abstracts/search?q=Ijah%20%20U.%20J.%20J"> Ijah U. J. J</a>, <a href="https://publications.waset.org/abstracts/search?q=Solebo%20Shakirat%20O."> Solebo Shakirat O.</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Genetically modified crops are already phenomenally successful and are grown worldwide in more than eighteen countries on more than 67 million hectares. Nigeria, in October 2018, approved Bacillus thuringiensis (Bt) cotton and maize; therefore, the need to carry out environmental risk assessment studies. A total of 15 4L octagonal ceramic pots were filled with 4kg of soil and placed on the bench in 2 rows of 10 pots each and the 3rd row of 5 pots, 1st-row pots were used to plant GM cotton seeds, while the 2nd-row pots were used for non-GM cotton seeds and the 3rd row of 5 pots served as control, all in the screen house. Soil samples for metagenomic DNA extraction were collected at random and at the monthly interval after planting at a distance of 2mm from the plant’s root and at a depth of 10cm using a sterile spatula. Soil samples for physicochemical analysis were collected before planting and after harvesting the GM and non-GM crops as well as from the control soil. The DNA was extracted, quantified and sequenced; Sample 1A (DNA from GM cotton Soil at 1st interval) gave the lowest sequence read with 0.853M while sample 2B (DNA from GM cotton Soil at 2nd interval) gave the highest with 5.785M, others gave between 1.8M and 4.7M. The samples treatment were grouped into four, Group 1 (GM cotton soil from 1 to 3 intervals) had between 800,000 and 5,700,000 strains of microbes (SOM), Group 2 (non GM cotton soil from 1 to 3 intervals) had between 1,400,600 and 4,200,000 SOM, Group 3 (control soil) had between 900,000 and 3,600,000 SOM and Group 4 (initial soil) had between 3,700,000 and 4,000,000 SOM. The microbes observed were predominantly bacteria (including archaea), fungi, dark matter alongside protists and phages. The predominant bacterial groups were the Terrabacteria (Bacillus funiculus, Bacillus sp.), the Proteobacteria (Microvirga massiliensis, sphingomonas sp.) and the Archaea (Nitrososphaera sp.), while the fungi were Aspergillus fischeri and Fusarium falciforme. The comparative analysis between groups was done using JACCARD PERMANOVA beta diversity analysis at P-value not more than 0.76 and there was no significant pair found. The pH for initial, GM cotton, non-GM cotton and control soil were 6.28, 6.26, 7.25, 8.26 and the percentage moisture was 0.63, 0.78, 0.89 and 0.82, respectively, while the percentage Nitrogen was observed to be 17.79, 1.14, 1.10 and 0.56 respectively. Other parameters include, varying concentrations of Potassium (0.46, 1,284.47, 1,785.48, 1,252.83 mg/kg) and Phosphorus (18.76, 17.76, 16.87, 15.23 mg/kg) were recorded for the four treatments respectively. The soil consisted mainly of silt (32.09 to 34.66%) and clay (58.89 to 60.23%), reflecting the soil texture as silty – clay. The results were then tested with ANOVA at less than 0.05 P-value and no pair was found to be significant as well. The results suggest that the GM crops have no significant effect on microbial ecology and physicochemical properties of the soil and, in turn, no direct or indirect effects on human health. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=genetically%20modified%20crop" title="genetically modified crop">genetically modified crop</a>, <a href="https://publications.waset.org/abstracts/search?q=microbial%20ecology" title=" microbial ecology"> microbial ecology</a>, <a href="https://publications.waset.org/abstracts/search?q=physicochemical%20properties" title=" physicochemical properties"> physicochemical properties</a>, <a href="https://publications.waset.org/abstracts/search?q=metagenomics" title=" metagenomics"> metagenomics</a>, <a href="https://publications.waset.org/abstracts/search?q=DNA" title=" DNA"> DNA</a>, <a href="https://publications.waset.org/abstracts/search?q=soil" title=" soil"> soil</a> </p> <a href="https://publications.waset.org/abstracts/144917/metagenomic-assessment-of-the-effects-of-genetically-modified-crops-on-microbial-ecology-and-physicochemical-properties-of-soil" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/144917.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">145</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">28571</span> Applications of Out-of-Sequence Thrust Movement for Earthquake Mitigation: A Review</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Rajkumar%20Ghosh">Rajkumar Ghosh</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The study presents an overview of the many uses and approaches for estimating out-of-sequence thrust movement in earthquake mitigation. The study investigates how knowing and forecasting thrust movement during seismic occurrences might assist to effective earthquake mitigation measures. The review begins by discussing out-of-sequence thrust movement and its importance in earthquake mitigation strategies. It explores how typical techniques of estimating thrust movement may not capture the full complexity of seismic occurrences and emphasizes the benefits of include out-of-sequence data in the analysis. A thorough review of existing research and studies on out-of-sequence thrust movement estimates for earthquake mitigation. The study demonstrates how to estimate out-of-sequence thrust movement using multiple data sources such as GPS measurements, satellite imagery, and seismic recordings. The study also examines the use of out-of-sequence thrust movement estimates in earthquake mitigation measures. It investigates how precise calculation of thrust movement may help improve structural design, analyse infrastructure risk, and develop early warning systems. The potential advantages of using out-of-sequence data in these applications to improve the efficiency of earthquake mitigation techniques. The difficulties and limits of estimating out-of-sequence thrust movement for earthquake mitigation. It addresses data quality difficulties, modelling uncertainties, and computational complications. To address these obstacles and increase the accuracy and reliability of out-of-sequence thrust movement estimates, the authors recommend topics for additional study and improvement. The study is a helpful resource for seismic monitoring and earthquake risk assessment researchers, engineers, and policymakers, supporting innovations in earthquake mitigation measures based on a better knowledge of thrust movement dynamics. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=earthquake%20mitigation" title="earthquake mitigation">earthquake mitigation</a>, <a href="https://publications.waset.org/abstracts/search?q=out-of-sequence%20thrust" title=" out-of-sequence thrust"> out-of-sequence thrust</a>, <a href="https://publications.waset.org/abstracts/search?q=satellite%20imagery" title=" satellite imagery"> satellite imagery</a>, <a href="https://publications.waset.org/abstracts/search?q=seismic%20recordings" title=" seismic recordings"> seismic recordings</a>, <a href="https://publications.waset.org/abstracts/search?q=GPS%20measurements" title=" GPS measurements"> GPS measurements</a> </p> <a href="https://publications.waset.org/abstracts/168985/applications-of-out-of-sequence-thrust-movement-for-earthquake-mitigation-a-review" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/168985.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">85</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">28570</span> Encryption and Decryption of Nucleic Acid Using Deoxyribonucleic Acid Algorithm</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Iftikhar%20A.%20Tayubi">Iftikhar A. Tayubi</a>, <a href="https://publications.waset.org/abstracts/search?q=Aabdulrahman%20Alsubhi"> Aabdulrahman Alsubhi</a>, <a href="https://publications.waset.org/abstracts/search?q=Abdullah%20Althrwi"> Abdullah Althrwi</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The deoxyribonucleic acid text provides a single source of high-quality Cryptography about Deoxyribonucleic acid sequence for structural biologists. We will provide an intuitive, well-organized and user-friendly web interface that allows users to encrypt and decrypt Deoxy Ribonucleic Acid sequence text. It includes complex, securing by using Algorithm to encrypt and decrypt Deoxy Ribonucleic Acid sequence. The utility of this Deoxy Ribonucleic Acid Sequence Text is that, it can provide a user-friendly interface for users to Encrypt and Decrypt store the information about Deoxy Ribonucleic Acid sequence. These interfaces created in this project will satisfy the demands of the scientific community by providing fully encrypt of Deoxy Ribonucleic Acid sequence during this website. We have adopted a methodology by using C# and Active Server Page.NET for programming which is smart and secure. Deoxy Ribonucleic Acid sequence text is a wonderful piece of equipment for encrypting large quantities of data, efficiently. The users can thus navigate from one encoding and store orange text, depending on the field for user’s interest. Algorithm classification allows a user to Protect the deoxy ribonucleic acid sequence from change, whether an alteration or error occurred during the Deoxy Ribonucleic Acid sequence data transfer. It will check the integrity of the Deoxy Ribonucleic Acid sequence data during the access. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=algorithm" title="algorithm">algorithm</a>, <a href="https://publications.waset.org/abstracts/search?q=ASP.NET" title=" ASP.NET"> ASP.NET</a>, <a href="https://publications.waset.org/abstracts/search?q=DNA" title=" DNA"> DNA</a>, <a href="https://publications.waset.org/abstracts/search?q=encrypt" title=" encrypt"> encrypt</a>, <a href="https://publications.waset.org/abstracts/search?q=decrypt" title=" decrypt"> decrypt</a> </p> <a href="https://publications.waset.org/abstracts/95200/encryption-and-decryption-of-nucleic-acid-using-deoxyribonucleic-acid-algorithm" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/95200.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">234</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">28569</span> Metagenomics Analysis on Microbial Communities of Sewage Sludge from Nyeri-Kangemi Wastewater Treatment Plant, Nyeri County-Kenya</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Allan%20Kiptanui%20Kimisto">Allan Kiptanui Kimisto</a>, <a href="https://publications.waset.org/abstracts/search?q=Geoffrey%20Odhiambo%20Ongondo"> Geoffrey Odhiambo Ongondo</a>, <a href="https://publications.waset.org/abstracts/search?q=Anastasia%20Wairimu%20Muia"> Anastasia Wairimu Muia</a>, <a href="https://publications.waset.org/abstracts/search?q=Cyrus%20Ndungu%20Kimani"> Cyrus Ndungu Kimani</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The major challenge to proper sewage sludge treatment processes is the poor understanding of sludge microbiome diversities. This study applied the whole-genome. shotgun metagenomics technique to profile the microbial composition of sewage sludge in two active digestion lagoons at the Nyeri-Kangemi Wastewater Treatment Plant in Nyeri County, Kenya. Total microbial community DNA was extracted from samples using the available ZymoBIOMICS™ DNA Miniprep Kit and sequenced using Shotgun metagenomics. Samples were analyzed using MG-RAST software (Project ID: mgp100988), which allowed for comparing taxonomic diversity before β-diversities studies for Bacteria, Archaea and Eukaryotes. The study identified 57 phyla, 145 classes, 301 orders, 506 families, 963 genera, and 1980 species. Bacteria dominated the microbes and comprised 28 species, 51 classes, 110 orders, 243 families, 597 genera, and 1518 species. The Bacteroides(6.77%) were dominant, followed by Acinetobacter(1.44%) belonging to the Gammaproteobacteria and Acidororax (1.36%), Bacillus (1.24%) and Clostridium (1.02%) belonging to Betaproteobacteria. Archaea recorded 5 phyla, 13 classes, 19 orders, 29 families, 60 genera,and87 species, with the dominant genera being Methanospirillum (16.01%), methanosarcina (15.70%), and Methanoregula(14.80%) and Methanosaeta (8.74%), Methanosphaerula(5.48%) and Methanobrevibacter(5.03%) being the subdominant group. The eukaryotes were the least in abundance and comprised 24 phyla, 81 classes, 301 orders, 506 families, 963 genera, and 980 species. Arabidopsis (4.91%) and Caenorhabditis (4.81%) dominated the eukaryotes, while Dityostelium (3.63%) and Drosophila(2.08%) were the subdominant genera. All these microbes play distinct roles in the anaerobic treatment process of sewage sludge. The local sludge microbial composition and abundance variations may be due to age difference differences between the two digestion lagoons in operation at the plant and the different degradation rales played by the taxa. The information presented in this study can help in the genetic manipulation or formulation of optimal microbial ratios to improve their effectiveness in sewage sludge treatment. This study recommends further research on how the different taxa respond to environmental changes over time and space. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=shotgun%20metagenomics" title="shotgun metagenomics">shotgun metagenomics</a>, <a href="https://publications.waset.org/abstracts/search?q=sludge" title=" sludge"> sludge</a>, <a href="https://publications.waset.org/abstracts/search?q=bacteria" title=" bacteria"> bacteria</a>, <a href="https://publications.waset.org/abstracts/search?q=archaea" title=" archaea"> archaea</a>, <a href="https://publications.waset.org/abstracts/search?q=eukaryotes" title=" eukaryotes"> eukaryotes</a> </p> <a href="https://publications.waset.org/abstracts/157198/metagenomics-analysis-on-microbial-communities-of-sewage-sludge-from-nyeri-kangemi-wastewater-treatment-plant-nyeri-county-kenya" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/157198.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">101</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">28568</span> Constructing Orthogonal De Bruijn and Kautz Sequences and Applications</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Yaw-Ling%20Lin">Yaw-Ling Lin</a> </p> <p class="card-text"><strong>Abstract:</strong></p> A de Bruijn graph of order k is a graph whose vertices representing all length-k sequences with edges joining pairs of vertices whose sequences have maximum possible overlap (length k−1). Every Hamiltonian cycle of this graph defines a distinct, minimum length de Bruijn sequence containing all k-mers exactly once. A Kautz sequence is the minimal generating sequence so as the sequence of minimal length that produces all possible length-k sequences with the restriction that every two consecutive alphabets in the sequences must be different. A collection of de Bruijn/Kautz sequences are orthogonal if any two sequences are of maximally differ in sequence composition; that is, the maximum length of their common substring is k. In this paper, we discuss how such a collection of (maximal) orthogonal de Bruijn/Kautz sequences can be made and use the algorithm to build up a web application service for the synthesized DNA and other related biomolecular sequences. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=biomolecular%20sequence%20synthesis" title="biomolecular sequence synthesis">biomolecular sequence synthesis</a>, <a href="https://publications.waset.org/abstracts/search?q=de%20Bruijn%20sequences" title=" de Bruijn sequences"> de Bruijn sequences</a>, <a href="https://publications.waset.org/abstracts/search?q=Eulerian%20cycle" title=" Eulerian cycle"> Eulerian cycle</a>, <a href="https://publications.waset.org/abstracts/search?q=Hamiltonian%20cycle" title=" Hamiltonian cycle"> Hamiltonian cycle</a>, <a href="https://publications.waset.org/abstracts/search?q=Kautz%20sequences" title=" Kautz sequences"> Kautz sequences</a>, <a href="https://publications.waset.org/abstracts/search?q=orthogonal%20sequences" title=" orthogonal sequences"> orthogonal sequences</a> </p> <a href="https://publications.waset.org/abstracts/121912/constructing-orthogonal-de-bruijn-and-kautz-sequences-and-applications" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/121912.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">167</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">28567</span> Comparing the Sequence and Effectiveness of Teaching the Four Basic Operations and Mathematics in Primary Schools</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Abubakar%20Sadiq%20Mensah">Abubakar Sadiq Mensah</a>, <a href="https://publications.waset.org/abstracts/search?q=Hassan%20Usman"> Hassan Usman </a> </p> <p class="card-text"><strong>Abstract:</strong></p> The study compared the effectiveness of Audition, Multiplication, subtraction and Division (AMSD) and Addition, subtraction, Multiplication and Division (ASMD), sequence of teaching these four basic operations in mathematics to primary one pupil’s in Katsina Local Government, Katsina State. The study determined the sequence that was more effective and mostly adopted by teachers of the operations. One hundred (100) teachers and sixty pupils (60) from primary one were used for the study. The pupils were divided into two equal groups. The researcher taught these operations to each group separately for four weeks (4 weeks). Group one was taught using the ASMD sequence, while group two was taught using ASMD sequence. In order to generate the needed data for the study, questionnaires and tests were administered on the samples. Data collected were analyzed and major findings were arrived at: (i) Two primary mathematics text books were used in all the primary schools in the area; (ii) Each of the textbooks contained the ASMD sequence; (iii) 73% of the teachers sampled adopted the ASMD sequence of teaching these operations; and (iv) Group one of the pupils (taught using AMSD sequence) performed significantly better than their counter parts in group two (taught using AMSD sequence). On the basis of this, the researcher concluded that the AMSD sequence was more effective in teaching the operations than the ASMD sequence. Consequently, the researcher concluded that primary schools teachers, authors of primary mathematics textbooks, and curriculum planner should adopt the AMSD sequence of teaching these operations. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=matematic" title="matematic">matematic</a>, <a href="https://publications.waset.org/abstracts/search?q=high%20school" title=" high school"> high school</a>, <a href="https://publications.waset.org/abstracts/search?q=four%20basic%20operations" title=" four basic operations"> four basic operations</a>, <a href="https://publications.waset.org/abstracts/search?q=effectiveness%20of%20teaching" title=" effectiveness of teaching"> effectiveness of teaching</a> </p> <a href="https://publications.waset.org/abstracts/8847/comparing-the-sequence-and-effectiveness-of-teaching-the-four-basic-operations-and-mathematics-in-primary-schools" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/8847.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">253</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">28566</span> On Paranorm Zweier I-Convergent Sequence Spaces</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Nazneen%20Khan">Nazneen Khan</a>, <a href="https://publications.waset.org/abstracts/search?q=Vakeel%20A.%20Khan"> Vakeel A. Khan</a> </p> <p class="card-text"><strong>Abstract:</strong></p> In this article we introduce the Paranorm Zweier I-convergent sequence spaces, for a sequence of positive real numbers. We study some topological properties, prove the decomposition theorem and study some inclusion relations on these spaces. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=ideal" title="ideal">ideal</a>, <a href="https://publications.waset.org/abstracts/search?q=%0Cfilter" title=" filter"> filter</a>, <a href="https://publications.waset.org/abstracts/search?q=I-convergence" title=" I-convergence"> I-convergence</a>, <a href="https://publications.waset.org/abstracts/search?q=I-nullity" title=" I-nullity"> I-nullity</a>, <a href="https://publications.waset.org/abstracts/search?q=paranorm" title=" paranorm"> paranorm</a> </p> <a href="https://publications.waset.org/abstracts/9634/on-paranorm-zweier-i-convergent-sequence-spaces" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/9634.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">481</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">28565</span> High-Throughput Mechanized Microfluidic Test Groundwork for Precise Microbial Genomics</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Pouya%20Karimi">Pouya Karimi</a>, <a href="https://publications.waset.org/abstracts/search?q=Ramin%20Gasemi%20Shayan"> Ramin Gasemi Shayan</a>, <a href="https://publications.waset.org/abstracts/search?q=Parsa%20Sheykhzade"> Parsa Sheykhzade</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Ease shotgun DNA sequencing is changing the microbial sciences. Sequencing instruments are compelling to the point that example planning is currently the key constraining element. Here, we present a microfluidic test readiness stage that incorporates the key strides in cells to grouping library test groundwork for up to 96 examples and decreases DNA input prerequisites 100-overlay while keeping up or improving information quality. The universally useful microarchitecture we show bolsters work processes with subjective quantities of response and tidy up or catch steps. By decreasing the example amount necessities, we empowered low-input (∼10,000 cells) entire genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil miniaturized scale settlements with prevalent outcomes. We additionally utilized the upgraded throughput to succession ∼400 clinical Pseudomonas aeruginosa libraries and exhibit magnificent single-nucleotide polymorphism discovery execution that clarified phenotypically watched anti-toxin opposition. Completely coordinated lab-on-chip test arrangement beats specialized boundaries to empower more extensive organization of genomics across numerous fundamental research and translational applications. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=clinical%20microbiology" title="clinical microbiology">clinical microbiology</a>, <a href="https://publications.waset.org/abstracts/search?q=DNA" title=" DNA"> DNA</a>, <a href="https://publications.waset.org/abstracts/search?q=microbiology" title=" microbiology"> microbiology</a>, <a href="https://publications.waset.org/abstracts/search?q=microbial%20genomics" title=" microbial genomics"> microbial genomics</a> </p> <a href="https://publications.waset.org/abstracts/127020/high-throughput-mechanized-microfluidic-test-groundwork-for-precise-microbial-genomics" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/127020.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">123</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">28564</span> Finding the Longest Common Subsequence in Normal DNA and Disease Affected Human DNA Using Self Organizing Map</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=G.%20Tamilpavai">G. Tamilpavai</a>, <a href="https://publications.waset.org/abstracts/search?q=C.%20Vishnuppriya"> C. Vishnuppriya</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Bioinformatics is an active research area which combines biological matter as well as computer science research. The longest common subsequence (LCSS) is one of the major challenges in various bioinformatics applications. The computation of the LCSS plays a vital role in biomedicine and also it is an essential task in DNA sequence analysis in genetics. It includes wide range of disease diagnosing steps. The objective of this proposed system is to find the longest common subsequence which presents in a normal and various disease affected human DNA sequence using Self Organizing Map (SOM) and LCSS. The human DNA sequence is collected from National Center for Biotechnology Information (NCBI) database. Initially, the human DNA sequence is separated as k-mer using k-mer separation rule. Mean and median values are calculated from each separated k-mer. These calculated values are fed as input to the Self Organizing Map for the purpose of clustering. Then obtained clusters are given to the Longest Common Sub Sequence (LCSS) algorithm for finding common subsequence which presents in every clusters. It returns nx(n-1)/2 subsequence for each cluster where n is number of k-mer in a specific cluster. Experimental outcomes of this proposed system produce the possible number of longest common subsequence of normal and disease affected DNA data. Thus the proposed system will be a good initiative aid for finding disease causing sequence. Finally, performance analysis is carried out for different DNA sequences. The obtained values show that the retrieval of LCSS is done in a shorter time than the existing system. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=clustering" title="clustering">clustering</a>, <a href="https://publications.waset.org/abstracts/search?q=k-mers" title=" k-mers"> k-mers</a>, <a href="https://publications.waset.org/abstracts/search?q=longest%20common%20subsequence" title=" longest common subsequence"> longest common subsequence</a>, <a href="https://publications.waset.org/abstracts/search?q=SOM" title=" SOM"> SOM</a> </p> <a href="https://publications.waset.org/abstracts/90640/finding-the-longest-common-subsequence-in-normal-dna-and-disease-affected-human-dna-using-self-organizing-map" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/90640.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">267</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">28563</span> Towards the Reverse Engineering of UML Sequence Diagrams Using Petri Nets</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=C.%20Baidada">C. Baidada</a>, <a href="https://publications.waset.org/abstracts/search?q=M.%20H.%20Abidi"> M. H. Abidi</a>, <a href="https://publications.waset.org/abstracts/search?q=A.%20Jakimi"> A. Jakimi</a>, <a href="https://publications.waset.org/abstracts/search?q=E.%20H.%20El%20Kinani"> E. H. El Kinani</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Reverse engineering has become a viable method to measure an existing system and reconstruct the necessary model from tis original. The reverse engineering of behavioral models consists in extracting high-level models that help understand the behavior of existing software systems. In this paper, we propose an approach for the reverse engineering of sequence diagrams from the analysis of execution traces produced dynamically by an object-oriented application using petri nets. Our methods show that this approach can produce state diagrams in reasonable time and suggest that these diagrams are helpful in understanding the behavior of the underlying application. Finally we will discuss approachs and tools that are needed in the process of reverse engineering UML behavior. This work is a substantial step towards providing high-quality methodology for effectiveand efficient reverse engineering of sequence diagram. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=reverse%20engineering" title="reverse engineering">reverse engineering</a>, <a href="https://publications.waset.org/abstracts/search?q=UML%20behavior" title="UML behavior">UML behavior</a>, <a href="https://publications.waset.org/abstracts/search?q=sequence%20diagram" title=" sequence diagram"> sequence diagram</a>, <a href="https://publications.waset.org/abstracts/search?q=execution%20traces" title=" execution traces"> execution traces</a>, <a href="https://publications.waset.org/abstracts/search?q=petri%20nets" title="petri nets">petri nets</a> </p> <a href="https://publications.waset.org/abstracts/35341/towards-the-reverse-engineering-of-uml-sequence-diagrams-using-petri-nets" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/35341.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">446</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">28562</span> Phenotype Prediction of DNA Sequence Data: A Machine and Statistical Learning Approach</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Mpho%20Mokoatle">Mpho Mokoatle</a>, <a href="https://publications.waset.org/abstracts/search?q=Darlington%20Mapiye"> Darlington Mapiye</a>, <a href="https://publications.waset.org/abstracts/search?q=James%20Mashiyane"> James Mashiyane</a>, <a href="https://publications.waset.org/abstracts/search?q=Stephanie%20Muller"> Stephanie Muller</a>, <a href="https://publications.waset.org/abstracts/search?q=Gciniwe%20Dlamini"> Gciniwe Dlamini</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=AWD-LSTM" title="AWD-LSTM">AWD-LSTM</a>, <a href="https://publications.waset.org/abstracts/search?q=bootstrapping" title=" bootstrapping"> bootstrapping</a>, <a href="https://publications.waset.org/abstracts/search?q=k-mers" title=" k-mers"> k-mers</a>, <a href="https://publications.waset.org/abstracts/search?q=next%20generation%20sequencing" title=" next generation sequencing"> next generation sequencing</a> </p> <a href="https://publications.waset.org/abstracts/122679/phenotype-prediction-of-dna-sequence-data-a-machine-and-statistical-learning-approach" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/122679.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">167</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">28561</span> Phenotype Prediction of DNA Sequence Data: A Machine and Statistical Learning Approach</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Darlington%20Mapiye">Darlington Mapiye</a>, <a href="https://publications.waset.org/abstracts/search?q=Mpho%20Mokoatle"> Mpho Mokoatle</a>, <a href="https://publications.waset.org/abstracts/search?q=James%20Mashiyane"> James Mashiyane</a>, <a href="https://publications.waset.org/abstracts/search?q=Stephanie%20Muller"> Stephanie Muller</a>, <a href="https://publications.waset.org/abstracts/search?q=Gciniwe%20Dlamini"> Gciniwe Dlamini</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=AWD-LSTM" title="AWD-LSTM">AWD-LSTM</a>, <a href="https://publications.waset.org/abstracts/search?q=bootstrapping" title=" bootstrapping"> bootstrapping</a>, <a href="https://publications.waset.org/abstracts/search?q=k-mers" title=" k-mers"> k-mers</a>, <a href="https://publications.waset.org/abstracts/search?q=next%20generation%20sequencing" title=" next generation sequencing"> next generation sequencing</a> </p> <a href="https://publications.waset.org/abstracts/122670/phenotype-prediction-of-dna-sequence-data-a-machine-and-statistical-learning-approach" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/122670.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">159</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">28560</span> The Influence of Music Education and the Order of Sounds on the Grouping of Sounds into Sequences of Six Tones</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Adam%20Rosi%C5%84ski">Adam Rosiński</a> </p> <p class="card-text"><strong>Abstract:</strong></p> This paper discusses an experiment conducted with two groups of participants, composed of musicians and non-musicians, in order to investigate the impact of the speed of a sound sequence and the order of sounds on the grouping of sounds into sequences of six tones. Significant differences were observed between musicians and non-musicians with respect to the threshold sequence speed at which the sequence was split into two streams. The differences in the results for the two groups suggest that the musical education of the participating listeners may be a vital factor. The criterion of musical education should be taken into account during experiments so that the results obtained are reliable, uniform, and free from interpretive errors. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=auditory%20scene%20analysis" title="auditory scene analysis">auditory scene analysis</a>, <a href="https://publications.waset.org/abstracts/search?q=education" title=" education"> education</a>, <a href="https://publications.waset.org/abstracts/search?q=hearing" title=" hearing"> hearing</a>, <a href="https://publications.waset.org/abstracts/search?q=psychoacoustics" title=" psychoacoustics"> psychoacoustics</a> </p> <a href="https://publications.waset.org/abstracts/158683/the-influence-of-music-education-and-the-order-of-sounds-on-the-grouping-of-sounds-into-sequences-of-six-tones" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/158683.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">102</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">28559</span> Human Microbiome Hidden Association with Chronic and Autoimmune Diseases</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Elmira%20Davasaz%20Tabrizi">Elmira Davasaz Tabrizi</a>, <a href="https://publications.waset.org/abstracts/search?q=Mu%CC%88s%CC%A7teba%20Sevil"> Müşteba Sevil</a>, <a href="https://publications.waset.org/abstracts/search?q=Ercan%20Arican"> Ercan Arican</a> </p> <p class="card-text"><strong>Abstract:</strong></p> In recent decades, there has been a sharp increase in the prevalence of several unrelated chronic diseases. The use of long-term antibiotics for chronic illnesses is increasing. The antibiotic resistance occurrence and its relationship with host microbiomes are still unclear. Properties of the identifying antibodies have been the focus of chronic disease research, such as prostatitis or autoimmune. The immune system is made up of a complicated but well-organized network of cell types that constantly monitor and maintain their surroundings. The regulated homeostatic interaction between immune system cells and their surrounding environment shapes the microbial flora. Researchers believe that the disappearance of special bacterial species from our ancestral microbiota might have altered the body flora that can cause a rise in disease during the human life span. This unpleasant pattern demonstrates the importance of focusing on discovering and revealing the root causes behind the disappearance or alteration of our microbiota. In this review, we gathered the results of some studies that reveal changes in the diversity and quantity of microorganisms that may affect chronic and autoimmune diseases. Additionally, a Ph.D. thesis that is still in process as Metagenomic studies in chronic prostatitis samples is mentioned. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=metagenomic" title="metagenomic">metagenomic</a>, <a href="https://publications.waset.org/abstracts/search?q=autoimmune" title=" autoimmune"> autoimmune</a>, <a href="https://publications.waset.org/abstracts/search?q=prostatitis" title=" prostatitis"> prostatitis</a>, <a href="https://publications.waset.org/abstracts/search?q=microbiome" title=" microbiome"> microbiome</a> </p> <a href="https://publications.waset.org/abstracts/159476/human-microbiome-hidden-association-with-chronic-and-autoimmune-diseases" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/159476.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">96</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">28558</span> Radio Frequency Identification Encryption via Modified Two Dimensional Logistic Map</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Hongmin%20Deng">Hongmin Deng</a>, <a href="https://publications.waset.org/abstracts/search?q=Qionghua%20Wang"> Qionghua Wang</a> </p> <p class="card-text"><strong>Abstract:</strong></p> A modified two dimensional (2D) logistic map based on cross feedback control is proposed. This 2D map exhibits more random chaotic dynamical properties than the classic one dimensional (1D) logistic map in the statistical characteristics analysis. So it is utilized as the pseudo-random (PN) sequence generator, where the obtained real-valued PN sequence is quantized at first, then applied to radio frequency identification (RFID) communication system in this paper. This system is experimentally validated on a cortex-M<sub>0</sub> development board, which shows the effectiveness in key generation, the size of key space and security. At last, further cryptanalysis is studied through the test suite in the National Institute of Standards and Technology (NIST). <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=chaos%20encryption" title="chaos encryption">chaos encryption</a>, <a href="https://publications.waset.org/abstracts/search?q=logistic%20map" title=" logistic map"> logistic map</a>, <a href="https://publications.waset.org/abstracts/search?q=pseudo-random%20sequence" title=" pseudo-random sequence"> pseudo-random sequence</a>, <a href="https://publications.waset.org/abstracts/search?q=RFID" title=" RFID"> RFID</a> </p> <a href="https://publications.waset.org/abstracts/46725/radio-frequency-identification-encryption-via-modified-two-dimensional-logistic-map" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/46725.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">401</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">28557</span> Prediction and Identification of a Permissive Epitope Insertion Site for St Toxoid in cfaB from Enterotoxigenic Escherichia coli</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=N.%20Zeinalzadeh">N. Zeinalzadeh</a>, <a href="https://publications.waset.org/abstracts/search?q=Mahdi%20Sadeghi"> Mahdi Sadeghi</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Enterotoxigenic Escherichia coli (ETEC) is the most common cause of non-inflammatory diarrhea in the developing countries, resulting in approximately 20% of all diarrheal episodes in children in these areas. ST is one of the most important virulence factors and CFA/I is one of the frequent colonization factors that help to process of ETEC infection. ST and CfaB (CFA/I subunit) are among vaccine candidates against ETEC. So, ST because of its small size is not a good immunogenic in the natural form. However to increase its immunogenic potential, here we explored candidate positions for ST insertion in CfaB sequence. After bioinformatics analysis, one of the candidate positions was selected and the chimeric gene (cfaB*st) sequence was synthesized and expressed in E. coli BL21 (DE3). The chimeric recombinant protein was purified with Ni-NTA columns and characterized with western blot analysis. The residue 74-75 of CfaB sequence could be a good candidate position for ST and other epitopes insertion. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=bioinformatics" title="bioinformatics">bioinformatics</a>, <a href="https://publications.waset.org/abstracts/search?q=CFA%2FI" title=" CFA/I"> CFA/I</a>, <a href="https://publications.waset.org/abstracts/search?q=enterotoxigenic%20E.%20coli" title=" enterotoxigenic E. coli"> enterotoxigenic E. coli</a>, <a href="https://publications.waset.org/abstracts/search?q=ST%20toxoid" title=" ST toxoid"> ST toxoid</a> </p> <a href="https://publications.waset.org/abstracts/41728/prediction-and-identification-of-a-permissive-epitope-insertion-site-for-st-toxoid-in-cfab-from-enterotoxigenic-escherichia-coli" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/41728.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info 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