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Journal articles on the topic 'The next generation (Computer file)'

Author: Grafiati

Published: 4 June 2021

Last updated: 29 July 2025

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1

Ma, Yanjun. "rmvPFBAM: Removing Primers from BAM Files Based on Amplicon-Based Next-Generation Sequencing and Cloud Computing When Analyzing Personal Genome Data." Scientific Programming 2021 (November 16, 2021): 1–6. http://dx.doi.org/10.1155/2021/6536470.

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Personal genomic data constitute one important part of personal health data. However, due to the large amount of personal genomic data obtained by the next-generation sequencing technology, special tools are needed to analyze these data. In this article, we will explore a tool analyzing cloud-based large-scale genome sequencing data. Analyzing and identifying genomic variations from amplicon-based next-generation sequencing data are necessary for the clinical diagnosis and treatment of cancer patients. When processing the amplicon-based next-generation sequencing data, one essential step is re

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Vopson, Melvin M., Serban G. Lepadatu, Anna Vopson, and Szymon Łukaszyk. "Next-Generation Blockchain Technology: The Entropic Blockchain." Applied Sciences 14, no. 14 (2024): 6297. http://dx.doi.org/10.3390/app14146297.

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The storage, transmission, and processing of data become significant problems when large digital data files or databases are involved, as in the case of decentralized online global databases such as blockchain. Here, we propose a novel method that allows for the scalability of digital assets, including blockchain databases in the download, validation, and confidentiality processes, by developing a lightweight blockchain technology called Entropic Blockchain. This is a computer-implemented mathematical method by which to generate an information-entropic numerical barcode representation of a dig

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Roda-Casanova, Victor, Álvaro Zubizarreta-Macho, Francisco Sanchez-Marin, Óscar Alonso Ezpeleta, Alberto Albaladejo Martínez, and Agustín Galparsoro Catalán. "Computerized Generation and Finite Element Stress Analysis of Endodontic Rotary Files." Applied Sciences 11, no. 10 (2021): 4329. http://dx.doi.org/10.3390/app11104329.

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Introduction: The finite element method has been extensively used to analyze the mechanical behavior of endodontic rotary files under bending and torsional conditions. This methodology requires elevated computer-aided design skills to reproduce the geometry of the endodontic file, and also mathematical knowledge to perform the finite element analysis. In this study, an automated procedure is proposed for the computerized generation and finite element analysis of endodontic rotary files under bending and torsional conditions. Methods: An endodontic rotary file with a 25mm total length, 0.25mm a

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Shenoy, Prashant, Pawan Goyal, and Harrick M. Vin. "Architectural considerations for next-generation file systems." Multimedia Systems 8, no. 4 (2002): 270–83. http://dx.doi.org/10.1007/s005300100048.

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Maier, Martin, and Martin Herzog. "Online gaming and P2P file sharing in next-generation EPONs." IEEE Communications Magazine 48, no. 2 (2010): 48–55. http://dx.doi.org/10.1109/mcom.2010.5402663.

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Artimo, Panu, Séverine Duvaud, Mikhail Pachkov, Vassilios Ioannidis, Erik van Nimwegen, and Heinz Stockinger. "The ISMARA client." F1000Research 5 (December 15, 2016): 2851. http://dx.doi.org/10.12688/f1000research.9794.1.

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ISMARA (ismara.unibas.ch) automatically infers the key regulators and regulatory interactions from high-throughput gene expression or chromatin state data. However, given the large sizes of current next generation sequencing (NGS) datasets, data uploading times are a major bottleneck. Additionally, for proprietary data, users may be uncomfortable with uploading entire raw datasets to an external server. Both these problems could be alleviated by providing a means by which users could pre-process their raw data locally, transferring only a small summary file to the ISMARA server. We developed a

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Carpentieri, Bruno. "Compression of Next-Generation Sequencing Data and of DNA Digital Files." Algorithms 13, no. 6 (2020): 151. http://dx.doi.org/10.3390/a13060151.

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The increase in memory and in network traffic used and caused by new sequenced biological data has recently deeply grown. Genomic projects such as HapMap and 1000 Genomes have contributed to the very large rise of databases and network traffic related to genomic data and to the development of new efficient technologies. The large-scale sequencing of samples of DNA has brought new attention and produced new research, and thus the interest in the scientific community for genomic data has greatly increased. In a very short time, researchers have developed hardware tools, analysis software, algori

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Xie, Chao, Zhen Xuan Yeo, Marie Wong, et al. "Fast and accurate HLA typing from short-read next-generation sequence data with xHLA." Proceedings of the National Academy of Sciences 114, no. 30 (2017): 8059–64. http://dx.doi.org/10.1073/pnas.1707945114.

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The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99–100% four-digit typing accuracy for both class I and II HLA genes, taking only∼3 min to process a 30× whole-genome BAM file on a desktop computer.

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M.S. Tg Sulaiman, T., S. B. Mohamed, M. Minhat, A. S. Mohamed, and A. R. Mohamed. "Integrated Interface Development Environment using STEP Universal Data Structure." International Journal of Engineering & Technology 7, no. 2.15 (2018): 27. http://dx.doi.org/10.14419/ijet.v7i2.15.11194.

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Nowadays modern manufacturing demands advanced computer controller, having higher input language and less proprietary vendor dependencies. STEP stands for Standard for the Exchange of Product model data is the next generation of data model between CAD/CAM and CNC system. STEP is still under research and development all around the world. This paper describes the design, development and testing of an integrated Interface development environment for STEP file using Universal Data Structure, which aims to provide support for machining operation. The system also aims to provide function of reading

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Alukwe, Chrispus. "Enhancing Cybersecurity: Smart Intrusion Detection in File Server SYSTEMS." Journal of Science, Innovation and Creativity 2, no. 1 (2023): 1–6. http://dx.doi.org/10.58721/jsic.v2i1.287.

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System security is a major challenge worldwide, which has led to the increasing implementation of security surveillance systems in the public and private sectors. Likewise, it is inevitable to secure server-based systems that store vast amounts of sensitive data that is accessed from time to time. Intrusion Detection Systems (IDS) use metrics to detect anomalous activity on computers and computer networks. Modern detection algorithms try to reach detection metrics by acting as an antivirus. This is not enough, the need to explore more controlled, porous, and more secure systems is inevitable,

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Gao, Lei, Cong Wu, and Lin Liu. "AUSPP: A universal short-read pre-processing package." Journal of Bioinformatics and Computational Biology 17, no. 06 (2019): 1950037. http://dx.doi.org/10.1142/s0219720019500379.

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There are many short-read aligners that can map short reads to a reference genome/sequence, and most of them can directly accept a FASTQ file as the input query file. However, the raw data usually need to be pre-processed. Few software programs specialize in pre-processing raw data generated by a variety of next-generation sequencing (NGS) technologies. Here, we present AUSPP, a Perl script-based pipeline for pre-processing and automatic mapping of NGS short reads. This pipeline encompasses quality control, adaptor trimming, collapsing of reads, structural RNA removal, length selection, read m

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Zhang, Henry B., Minji Kim, Jeffrey H. Chuang, and Yijun Ruan. "pyBedGraph: a python package for fast operations on 1D genomic signal tracks." Bioinformatics 36, no. 10 (2020): 3234–35. http://dx.doi.org/10.1093/bioinformatics/btaa061.

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Abstract Motivation Modern genomic research is driven by next-generation sequencing experiments such as ChIP-seq and ChIA-PET that generate coverage files for transcription factor binding, as well as DHS and ATAC-seq that yield coverage files for chromatin accessibility. Such files are in a bedGraph text format or a bigWig binary format. Obtaining summary statistics in a given region is a fundamental task in analyzing protein binding intensity or chromatin accessibility. However, the existing Python package for operating on coverage files is not optimized for speed. Results We developed pyBedG

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Ishiya, Koji, and Shintaroh Ueda. "MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing." PeerJ 5 (May 30, 2017): e3406. http://dx.doi.org/10.7717/peerj.3406.

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Recent rapid advances in high-throughput, next-generation sequencing (NGS) technologies have promoted mitochondrial genome studies in the fields of human evolution, medical genetics, and forensic casework. However, scientists unfamiliar with computer programming often find it difficult to handle the massive volumes of data that are generated by NGS. To address this limitation, we developed MitoSuite, a user-friendly graphical tool for analysis of data from high-throughput sequencing of the human mitochondrial genome. MitoSuite generates a visual report on NGS data with simple mouse operations.

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Tsai, Ming-Hsin, Yen-Yi Liu, and Chih-Chieh Chen. "OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling." PeerJ 7 (August 28, 2019): e7600. http://dx.doi.org/10.7717/peerj.7600.

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With the evolution of next generation sequencing (NGS) technologies, whole-genome sequencing of bacterial isolates is increasingly employed to investigate epidemiology. Phylogenetic analysis is the common method for using NGS data, usually for comparing closeness between bacterial isolates to detect probable outbreaks. However, interpreting a phylogenetic tree is not easy without training in evolutionary biology. Therefore, developing an easy-to-use tool that can assist people who wish to use a phylogenetic tree to investigate epidemiological relatedness is crucial. In this paper, we present a

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Alabadi, Montdher, and Adib Habbal. "Next-generation predictive maintenance: leveraging blockchain and dynamic deep learning in a domain-independent system." PeerJ Computer Science 9 (December 6, 2023): e1712. http://dx.doi.org/10.7717/peerj-cs.1712.

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The fourth industrial revolution, often referred to as Industry 4.0, has revolutionized the manufacturing sector by integrating emerging technologies such as artificial intelligence (AI), machine and deep learning, Industrial Internet of Things (IIoT), cloud computing, cyber physical systems (CPSs) and cognitive computing, throughout the production life cycle. Predictive maintenance (PdM) emerges as a critical component, utilizing data analytic to track machine health and proactively detect machinery failures. Deep learning (DL), is pivotal in this context, offering superior accuracy in predic

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Iwao, Hirohide. "6 Next Generation TV Program Exchange System "FileX"." Journal of the Institute of Image Information and Television Engineers 67, no. 5 (2013): 379–82. http://dx.doi.org/10.3169/itej.67.379.

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Qur'ana, Tri Wahyu, Al Fath Riza Kholdani, and Hayati Noor. "Pelatihan Merakit dan Instalasi Laptop/Komputer pada Santri Yayasan Pendidikan Islam Pondok Pesantren Wali Songo Banjarbaru." PengabdianMu: Jurnal Ilmiah Pengabdian kepada Masyarakat 5, no. 4 (2020): 383–87. http://dx.doi.org/10.33084/pengabdianmu.v5i4.1270.

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Assembling a computer is a stage of bringing together the components needed to run correctly. To understand the correct computer assembly process, an understanding of computer hardware is required both logically and physically. Meanwhile, so that the computer can be operated according to its function, it is necessary to install it. Computer installation is installing a program (software) into a computer. All software (e.g., Microsoft Windows, Microsoft Office, and others) apart from that, also install functions to match the program with the tools installed on the computer and parse the compres

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Chun, Hein, and Sangwoo Kim. "BAMixChecker: an automated checkup tool for matched sample pairs in NGS cohort." Bioinformatics 35, no. 22 (2019): 4806–8. http://dx.doi.org/10.1093/bioinformatics/btz479.

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Abstract Summary Mislabeling in the process of next generation sequencing is a frequent problem that can cause an entire genomic analysis to fail, and a regular cohort-level checkup is needed to ensure that it has not occurred. We developed a new, automated tool (BAMixChecker) that accurately detects sample mismatches from a given BAM file cohort with minimal user intervention. BAMixChecker uses a flexible, data-specific set of single-nucleotide polymorphisms and detects orphan (unpaired) and swapped (mispaired) samples based on genotype-concordance score and entropy-based file name analysis.

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Chandak, Shubham, Kedar Tatwawadi, Idoia Ochoa, Mikel Hernaez, and Tsachy Weissman. "SPRING: a next-generation compressor for FASTQ data." Bioinformatics 35, no. 15 (2018): 2674–76. http://dx.doi.org/10.1093/bioinformatics/bty1015.

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Abstract Motivation High-Throughput Sequencing technologies produce huge amounts of data in the form of short genomic reads, associated quality values and read identifiers. Because of the significant structure present in these FASTQ datasets, general-purpose compressors are unable to completely exploit much of the inherent redundancy. Although there has been a lot of work on designing FASTQ compressors, most of them lack in support of one or more crucial properties, such as support for variable length reads, scalability to high coverage datasets, pairing-preserving compression and lossless com

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Urgese, Gianvito, Emanuele Parisi, Orazio Scicolone, Santa Di Cataldo, and Elisa Ficarra. "BioSeqZip: a collapser of NGS redundant reads for the optimization of sequence analysis." Bioinformatics 36, no. 9 (2020): 2705–11. http://dx.doi.org/10.1093/bioinformatics/btaa051.

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Abstract Motivation High-throughput next-generation sequencing can generate huge sequence files, whose analysis requires alignment algorithms that are typically very demanding in terms of memory and computational resources. This is a significant issue, especially for machines with limited hardware capabilities. As the redundancy of the sequences typically increases with coverage, collapsing such files into compact sets of non-redundant reads has the 2-fold advantage of reducing file size and speeding-up the alignment, avoiding to map the same sequence multiple times. Method BioSeqZip generates

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Jurczak, Mateusz, and Jakub Młyńczak. "Method for automation of generation of interlocking tables for station traffic control devices." WUT Journal of Transportation Engineering 131 (December 1, 2020): 45–58. http://dx.doi.org/10.5604/01.3001.0014.8100.

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On account of the growing number of railway upgrading projects implemented in Poland, numerous problems are emerging when prepared and performed. While preparing detailed plans and specifications for railway traffic control devices intended to secure traffic at a railway station, one must deal with numerous alterations related to the work's phasing directly linked with the said equipment. Consequently, the variety of elements subject to change includes the schematic plan and the relevant interlocking tables for railway traffic control systems. This article aims to discuss the authors’ original

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Khan, Nauman, Imran Ali Khan, Jawad Usman Arshed, Mehtab Afzal, Muhammad Masroor Ahmed, and Muhammad Arif. "5G-EECC: Energy-Efficient Collaboration-Based Content Sharing Strategy in Device-to-Device Communication." Security and Communication Networks 2022 (January 25, 2022): 1–13. http://dx.doi.org/10.1155/2022/1354238.

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In the past few years, mobile data traffic has seen exponential growth due to the emergence of smart applications. Although throughput enhancement techniques such as macro- and femtocells reduce cell size, they are relatively expensive to implement. Mobile device-to-device (D2D) communication has emerged as a solution to support the growing popularity of multimedia content for local service in next-generation 5G cellular networks. Content sharing is the prominent feature, which helps D2D communication in reducing offload traffic on the network, improving the energy efficiency of the device, an

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Fernández-Blanco, Gabriel, Iván Froiz-Míguez, Paula Fraga-Lamas, and Tiago M. Fernández-Caramés. "Design, Implementation and Practical Energy-Efficiency Evaluation of a Blockchain Based Academic Credential Verification System for Low-Power Nodes." Applied Sciences 15, no. 12 (2025): 6596. https://doi.org/10.3390/app15126596.

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The educational system manages extensive documentation and paperwork, which can lead to human errors and sometimes abuse or fraud, such as the falsification of diplomas, certificates or other credentials. In fact, in recent years, multiple cases of fraud have been detected, representing a significant cost to society, since fraud harms the trustworthiness of certificates and academic institutions. To tackle such an issue, this article proposes a solution aimed at recording and verifying academic records through a decentralized application that is supported by a smart contract deployed in the Et

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Jain, Prashant Udaychand, and Vinaykumar Tomar. "Expanded Noise Margin 10T SRAM Cell using Finfet Device." International Journal on Recent and Innovation Trends in Computing and Communication 11, no. 9s (2023): 767–76. http://dx.doi.org/10.17762/ijritcc.v11i9s.7959.

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Static random access memory (SRAM) cells are being improved in order to increase resistance to device level changes and satisfy the requirements of low-power applications. A unique 10-transistor FinFET-based SRAM cell with single-ended read and differential write functionality is presented in this study. This cutting-edge architecture is more power-efficient than ST (Schmitt trigger) 10T or traditional 6T SRAM cells, using only 1.87 and 1.6 units of power respectively during read operations. The efficiency is attributable to a lower read activity factor, which saves electricity. The read stati

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Deschamps-Francoeur, Gabrielle, Vincent Boivin, Sherif Abou Elela, and Michelle S. Scott. "CoCo: RNA-seq read assignment correction for nested genes and multimapped reads." Bioinformatics 35, no. 23 (2019): 5039–47. http://dx.doi.org/10.1093/bioinformatics/btz433.

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Abstract Motivation Next-generation sequencing techniques revolutionized the study of RNA expression by permitting whole transcriptome analysis. However, sequencing reads generated from nested and multi-copy genes are often either misassigned or discarded, which greatly reduces both quantification accuracy and gene coverage. Results Here we present count corrector (CoCo), a read assignment pipeline that takes into account the multitude of overlapping and repetitive genes in the transcriptome of higher eukaryotes. CoCo uses a modified annotation file that highlights nested genes and proportiona

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Lu, Peng, Jingjing Jin, Zefeng Li, et al. "PGcloser: Fast Parallel Gap-Closing Tool Using Long-Reads or Contigs to Fill Gaps in Genomes." Evolutionary Bioinformatics 16 (January 2020): 117693432091385. http://dx.doi.org/10.1177/1176934320913859.

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Assembled draft genomes usually contain many gaps because of the length limit of next-generation sequencing. Although many gap-closing tools have been developed, most of them still attempt to fill gaps on the basis of next-generation sequencing reads (always < 200 bp). Hence, the gap-filling effect is inferior. Several tools that use long-reads to close gaps have recently been created. However, they require extensive runtimes, which may not be suitable for large genomes. We describe a gap-closing tool called PGcloser, which supports parallel mode and adopts long-reads/contigs to fill gaps i

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Yu, Rongshan, and Wenxian Yang. "ScaleQC: a scalable lossy to lossless solution for NGS data compression." Bioinformatics 36, no. 17 (2020): 4551–59. http://dx.doi.org/10.1093/bioinformatics/btaa543.

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Abstract Motivation Per-base quality values in Next Generation Sequencing data take a significant portion of storage even after compression. Lossy compression technologies could further reduce the space used by quality values. However, in many applications, lossless compression is still desired. Hence, sequencing data in multiple file formats have to be prepared for different applications. Results We developed a scalable lossy to lossless compression solution for quality values named ScaleQC (Scalable Quality value Compression). ScaleQC is able to provide the so-called bit-stream level scalabi

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Li, Sun, Chang, Cai, Hong, and Zhou. "Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)." Genes 10, no. 7 (2019): 554. http://dx.doi.org/10.3390/genes10070554.

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Understanding chromatin interactions is important because they create chromosome conformation and link the cis- and trans- regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing is a genome-wide high-throughput technology that detects chromatin interactions associated with a specific protein of interest. We developed ChIA-PET Tool for ChIA-PET data analysis in 2010. Here, we present the updated version of ChIA-PET Tool (V3) as a computational package to process the next-generation sequence data generate

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Patria, Rida. "Educate Children's Character With Finding Nemo Film Media." Journal of Literature Language and Academic Studies 2, no. 01 (2023): 19–22. https://doi.org/10.56855/jllans.v2i1.280.

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Children as the next generation of the nation, need to get serious attention, because the progress of a country will depend on the current and future generations. In this article, the author will conduct a review of an animated children's film Finding Nemo as a positive viewing medium to educate children's character as the nation's successor. Finding Nemo is a computer graphic animated film made in the United States which won an Academy Award. Released on May 30, 2003 in Canada and the United States. The main players are Albert Brooks, Ellen DeGeneres, Alexander Gould, Willem Dafoe, and many m

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Mendis, Dinusha. "‘Clone Wars’ Episode II—The Next Generation: The Copyright Implications Relating to 3D Printing and Computer-Aided Design (CAD) Files." Law, Innovation and Technology 6, no. 2 (2014): 265–81. http://dx.doi.org/10.5235/17579961.6.2.265.

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Jirotka, M., A. C. Simpson, R. P. Highnam, et al. "Digital Mammography: A World without Film?" Methods of Information in Medicine 44, no. 02 (2005): 168–71. http://dx.doi.org/10.1055/s-0038-1633939.

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Summary Objectives: eDiaMoND is a next generation Internet (”Grid”) multidisciplinary research project funded by the UK e-Science Programme with the following objectives; the development of a next generation Internet enabled prototype to demonstrate the potential benefits of a national infrastructure to support digital mammography; the exploration of potential benefits for digital mammography systems, with particular emphasis being placed on selected applications, namely, screening, training, computer-aided detection and appropriate support for epidemiological studies. Methods: EDiaMoND has wo

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Costanza, Pascal, Charlotte Herzeel, and Wilfried Verachtert. "Comparing Ease of Programming in C++, Go, and Java for Implementing a Next-Generation Sequencing Tool." Evolutionary Bioinformatics 15 (January 2019): 117693431986901. http://dx.doi.org/10.1177/1176934319869015.

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elPrep is an extensible multithreaded software framework for efficiently processing Sequence Alignment/Map (SAM)/Binary Alignment/Map (BAM) files in next-generation sequencing pipelines. Similar to other SAM/BAM tools, a key challenge in elPrep is memory management, as such programs need to manipulate large amounts of data. We therefore investigated 3 programming languages with support for assisted or automated memory management for implementing elPrep, namely C++, Go, and Java. We implemented a nontrivial subset of elPrep in all 3 programming languages and compared them by benchmarking their

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Botacin, Marcus, Hojjat Aghakhani, Stefano Ortolani, et al. "One Size Does Not Fit All." ACM Transactions on Privacy and Security 24, no. 2 (2021): 1–31. http://dx.doi.org/10.1145/3429741.

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Malware analysis is an essential task to understand infection campaigns, the behavior of malicious codes, and possible ways to mitigate threats. Malware analysis also allows better assessment of attackers’ capabilities, techniques, and processes. Although a substantial amount of previous work provided a comprehensive analysis of the international malware ecosystem, research on regionalized, country-, and population-specific malware campaigns have been scarce. Moving towards addressing this gap, we conducted a longitudinal (2012-2020) and comprehensive (encompassing an entire population of onli

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Ji, Mingeun, Yejin Kan, Dongyeon Kim, Jaehee Jung, and Gangman Yi. "cPlot: Contig-Plotting Visualization for the Analysis of Short-Read Nucleotide Sequence Alignments." International Journal of Molecular Sciences 23, no. 19 (2022): 11484. http://dx.doi.org/10.3390/ijms231911484.

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Advances in the next-generation sequencing technology have led to a dramatic decrease in read-generation cost and an increase in read output. Reconstruction of short DNA sequence reads generated by next-generation sequencing requires a read alignment method that reconstructs a reference genome. In addition, it is essential to analyze the results of read alignments for a biologically meaningful inference. However, read alignment from vast amounts of genomic data from various organisms is challenging in that it involves repeated automatic and manual analysis steps. We, here, devised cPlot softwa

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Lee, Chien‐Cheng, Pau‐Choo Chung, Dyi‐Rong Duh, Yunghsiang S. Han, and Chi‐Wei Lin. "A practice of a collaborative multipoint medical teleconsultation system on broadband network." Journal of High Speed Networks 13, no. 3 (2004): 207–22. https://doi.org/10.3233/hsn-2004-244.

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The paper presents and discusses a collaborative teleconsultation system built on next generation network (NGN) transmission considerations. Considering the capability of merging medical images with multimedia data and real‐time video conferencing in transmission provided by NGN networks, the system is built with computer‐supported cooperative work (CSCW), DICOM standard, security functions, and image processing/analysis tools. The built‐in CSCW creates a collaborative consultation environment for synchronous interactive face‐to‐face discussion. The security functions provide the privacy and i

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Sarkar, Nurul I., Osman Mussa, and Sonia Gul. "Impact of People’s Movement on Wi-Fi Link Throughput in Indoor Propagation Environments: An Empirical Study." Electronics 10, no. 7 (2021): 856. http://dx.doi.org/10.3390/electronics10070856.

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There has been tremendous growth in the deployment of Wi-Fi 802.11-based networks in recent years. Many researchers have been investigating the performance of the Wi-Fi 802.11-based networks by exploring factors such as signal interference, radio propagation environments, and wireless protocols. However, exploring the effect of people’s movement on the Wi-Fi link throughout the performance is still a potential area yet to be explored. This paper investigates the impact of people’s movement on Wi-Fi link throughput. This is achieved by setting up experimental scenarios by using a pair of wirele

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Yang, Rui, Marshall Ward, and Ben Evans. "Parallel I∕O in Flexible Modelling System (FMS) and Modular Ocean Model 5 (MOM5)." Geoscientific Model Development 13, no. 4 (2020): 1885–902. http://dx.doi.org/10.5194/gmd-13-1885-2020.

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Abstract. We present an implementation of parallel I∕O in the Modular Ocean Model (MOM), a numerical ocean model used for climate forecasting, and determine its optimal performance over a range of tuning parameters. Our implementation uses the parallel API of the netCDF library, and we investigate the potential bottlenecks associated with the model configuration, netCDF implementation, the underpinning MPI-IO library/implementations and Lustre filesystem. We investigate the performance of a global 0.25∘ resolution model using 240 and 960 CPUs. The best performance is observed when we limit the

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Liu, Yuansheng, and Jinyan Li. "Hamming-shifting graph of genomic short reads: Efficient construction and its application for compression." PLOS Computational Biology 17, no. 7 (2021): e1009229. http://dx.doi.org/10.1371/journal.pcbi.1009229.

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Graphs such as de Bruijn graphs and OLC (overlap-layout-consensus) graphs have been widely adopted for the de novo assembly of genomic short reads. This work studies another important problem in the field: how graphs can be used for high-performance compression of the large-scale sequencing data. We present a novel graph definition named Hamming-Shifting graph to address this problem. The definition originates from the technological characteristics of next-generation sequencing machines, aiming to link all pairs of distinct reads that have a small Hamming distance or a small shifting offset or

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Rausch, Tobias, Markus Hsi-Yang Fritz, Jan O. Korbel, and Vladimir Benes. "Alfred: interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencing." Bioinformatics 35, no. 14 (2018): 2489–91. http://dx.doi.org/10.1093/bioinformatics/bty1007.

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Abstract Summary Harmonizing quality control (QC) of large-scale second and third-generation sequencing datasets is key for enabling downstream computational and biological analyses. We present Alfred, an efficient and versatile command-line application that computes multi-sample QC metrics in a read-group aware manner, across a wide variety of sequencing assays and technologies. In addition to standard QC metrics such as GC bias, base composition, insert size and sequencing coverage distributions it supports haplotype-aware and allele-specific feature counting and feature annotation. The vers

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Majeed, Mohammed Abdul, Rossilawati Sulaiman, Zarina Shukur, and Mohammad Kamrul Hasan. "A Review on Text Steganography Techniques." Mathematics 9, no. 21 (2021): 2829. http://dx.doi.org/10.3390/math9212829.

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There has been a persistent requirement for safeguarding documents and the data they contain, either in printed or electronic form. This is because the fabrication and faking of documents is prevalent globally, resulting in significant losses for individuals, societies, and industrial sectors, in addition to national security. Therefore, individuals are concerned about protecting their work and avoiding these unlawful actions. Different techniques, such as steganography, cryptography, and coding, have been deployed to protect valuable information. Steganography is an appropriate method, in whi

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Buonomenna, Maria Giovanna. "Inorganic Thin-Film Solar Cells: Challenges at the Terawatt-Scale." Symmetry 15, no. 9 (2023): 1718. http://dx.doi.org/10.3390/sym15091718.

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Thin-film solar cells have been referred to as second-generation solar photovoltaics (PV) or next-generation solutions for the renewable energy industry. The layer of absorber materials used to produce thin-film cells can vary in thickness, from nanometers to a few micrometers. This is much thinner than conventional solar cells. This review focuses on inorganic thin films and, therefore, hybrid inorganic–organic perovskite, organic solar cells, etc., are excluded from the discussion. Two main families of thin-film solar cells, i.e., silicon-based thin films (amorphous (a-Si) and micromorph sil

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Crippa, Paolo, Giorgio Biagetti, Lorenzo Minelli, et al. "Next-Generation Hybrid RF Front-End with MoS2-FET Supply Management Circuit, CNT-FET Amplifiers, and Graphene Thin-Film Antennas." Electronics 11, no. 22 (2022): 3708. http://dx.doi.org/10.3390/electronics11223708.

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One-dimensional (1D) and two-dimensional (2D) materials represent the emerging technologies for transistor electronics in view of their attractive electrical (high power gain, high cut-off frequency, low power dissipation) and mechanical properties. This work investigates the integration of carbon-nanotube-based field-effect transistors (CNT-FETs) and molybdenum disulphide (MoS2)-based FETs with standard CMOS technology for designing a simple analog system integrating a power switching circuit for the supply management of a 10 GHz transmitting/receiving (T/R) module that embeds a low-noise amp

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Bader, Wahiba, Jeremy Delerce, Sarah Aherfi, Bernard La Scola, and Philippe Colson. "Quasispecies Analysis of SARS-CoV-2 of 15 Different Lineages during the First Year of the Pandemic Prompts Scratching under the Surface of Consensus Genome Sequences." International Journal of Molecular Sciences 23, no. 24 (2022): 15658. http://dx.doi.org/10.3390/ijms232415658.

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The tremendous majority of SARS-CoV-2 genomic data so far neglected intra-host genetic diversity. Here, we studied SARS-CoV-2 quasispecies based on data generated by next-generation sequencing (NGS) of complete genomes. SARS-CoV-2 raw NGS data had been generated for nasopharyngeal samples collected between March 2020 and February 2021 by the Illumina technology on a MiSeq instrument, without prior PCR amplification. To analyze viral quasispecies, we designed and implemented an in-house Excel file (“QuasiS”) that can characterize intra-sample nucleotide diversity along the genomes using data of

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Gai, Cuili, Jigang Wang, Yongsheng Wang, and Junming Li. "The Low-Dimensional Three-Dimensional Tin Halide Perovskite: Film Characterization and Device Performance." Energies 13, no. 1 (2019): 2. http://dx.doi.org/10.3390/en13010002.

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Halide perovskite solar cells (PSCs) are considered as one of the most promising candidates for the next generation solar cells as their power conversion efficiency (PCE) has rapidly increased up to 25.2%. However, the most efficient halide perovskite materials all contain toxic lead. Replacing the lead cation with environmentally friendly tin (Sn) is proposed as an important alternative. Today, the inferior performance of Sn-based PSCs mainly due to two challenging issues, namely the facile oxidation of Sn2+ to Sn4+ and the low formation energies of Sn vacancies. Two-dimensional (2D) halide p

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Pathak, Sudipta, and Sanguthevar Rajasekaran. "RETRACTED: LFQC: a lossless compression algorithm for FASTQ files." Bioinformatics 35, no. 9 (2014): e1-e7. http://dx.doi.org/10.1093/bioinformatics/btu701.

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Abstract Motivation Next-generation sequencing (NGS) technologies have revolutionized genomic research by reducing the cost of whole-genome sequencing. One of the biggest challenges posed by modern sequencing technology is economic storage of NGS data. Storing raw data is infeasible because of its enormous size and high redundancy. In this article, we address the problem of storage and transmission of large Fastq files using innovative compression techniques. Results We introduce a new lossless non-reference-based fastq compression algorithm named lossless FastQ compressor. We have compared ou

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Moore, Joshua, and Nicholas Sofroniew. "Next Generation File Formats and Platforms." Microscopy and Microanalysis 27, S1 (2021): 2842. http://dx.doi.org/10.1017/s1431927621009922.

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Chang, Yeoungjin, Ravindra Naik Bukke, Youngoo Kim, Kiwan Ahn, Jinbaek Bae, and Jin Jang. "High-Performance Amorphous InGaSnO Thin-Film Transistor with ZrAlOx Gate Insulator by Spray Pyrolysis." Electronics 12, no. 3 (2023): 688. http://dx.doi.org/10.3390/electronics12030688.

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Here, we report the high-performance amorphous gallium indium tin oxide (a-IGTO) thin-film transistor (TFT) with zirconium aluminum oxide (ZAO) gate insulator by spray pyrolysis. The Ga ratio in the IGTO precursor solution varied up to 20%. The spray pyrolyzed a-IGTO with a high-k ZAO gate insulator (GI) exhibits the field-effect mobility (μFE) of 16 cm2V−1s−1, threshold voltage (VTH) of −0.45 V subthreshold swing (SS) of 133 mV/dec., and ON/OFF current ratio of ~108. The optimal a-IGTO TFT shows excellent stability under positive-bias-temperature stress (PBTS) with a small ΔVTH shift of 0.35

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Nakano, Kosei, Hiroyuki Motozuka, Gaius Yao Huang Wee, et al. "High-Capacity Data Collection Platform for Smart Cities Using IEEE 802.11ad-Based Millimeter-Wave V2X Communication." Wireless Communications and Mobile Computing 2022 (July 9, 2022): 1–13. http://dx.doi.org/10.1155/2022/3909685.

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The collection and utilization of huge sensor data from vehicles for visualizing the city is expected to realize various enhanced services for smart cities. A next-generation gigabit vehicle-to-everything (V2X) data collection platform based on 60 GHz millimeter-wave (mmWave) small cell radio access has been proposed in the previous work for enabling efficient and high-capacity data upload from vehicles to the cloud. This paper presents further analysis of the initial link setup delay to evaluate the effectiveness of the fast initial V2X link setup method proposed, which is suitable for 60 GHz

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Lee, Se-Hyeong, So-Young Bak, and Moonsuk Yi. "Improved Performance and Bias Stability of Al2O3/IZO Thin-Film Transistors with Vertical Diffusion." Electronics 11, no. 14 (2022): 2263. http://dx.doi.org/10.3390/electronics11142263.

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Several studies on amorphous oxide semiconductor thin-film transistors (TFTs) applicable to next-generation display devices have been conducted. To improve the poor switching characteristics and gate bias stability of co-sputtered aluminum–indium–zinc oxide (AIZO) TFTs, we fabricate Al2O3/indium–zinc oxide (IZO) dual-active-layer TFTs. By varying the Al2O3 target power and oxygen partial pressure in the chamber during Al2O3 back-channel deposition, we optimize the electrical characteristics and gate bias stability of the Al2O3/IZO TFTs. The Al2O3/IZO TFTs, which are fabricated under 50 W Al2O3

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Ward, Christopher M., Thu-Hien To, and Stephen M. Pederson. "ngsReports: a Bioconductor package for managing FastQC reports and other NGS related log files." Bioinformatics 36, no. 8 (2019): 2587–88. http://dx.doi.org/10.1093/bioinformatics/btz937.

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Abstract Motivation High throughput next generation sequencing (NGS) has become exceedingly cheap, facilitating studies to be undertaken containing large sample numbers. Quality control (QC) is an essential stage during analytic pipelines and the outputs of popular bioinformatics tools such as FastQC and Picard can provide information on individual samples. Although these tools provide considerable power when carrying out QC, large sample numbers can make inspection of all samples and identification of systemic bias a challenge. Results We present ngsReports, an R package designed for the mana

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