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Journal articles on the topic 'Predicted frames sequence'

Author: Grafiati

Published: 30 May 2022

Last updated: 31 July 2025

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1

Gu, Ming Ming, and Qi Jing. "Compressed Sensing with Generalized Hebbian Algorithm in Video Frame Prediction." Applied Mechanics and Materials 397-400 (September 2013): 2167–70. http://dx.doi.org/10.4028/www.scientific.net/amm.397-400.2167.

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Compressed Sensing with Generalized Hebbian Algorithm (GHA) in Video Frame Prediction is proposed in the paper. After analyzing the inter-frame correlation among the images of video sequences, GHA, as neural network algorithm of PCA, is adopted to remove the transform coefficients with lower value according in order to implement video compressed sensing. Furthermore, for statistics of the adjacent frames are similar enough, the algorithm processes superiority in video frame prediction. Simulation results show that, the proposed algorithm can not only improve the reconstructed quality and the v

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2

Chen, Xinyi, Weimin Lei, Wei Zhang, Yanwen Wang, and Mingxin Liu. "Ultra-Low Bitrate Predictive Portrait Video Compression with Diffusion Models." Symmetry 17, no. 6 (2025): 913. https://doi.org/10.3390/sym17060913.

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Deep neural video compression codecs have shown great promise in recent years. However, there are still considerable challenges for ultra-low bitrate video coding. Inspired by recent diffusion models for image and video compression attempts, we attempt to leverage diffusion models for ultra-low bitrate portrait video compression. In this paper, we propose a predictive portrait video compression method that leverages the temporal prediction capabilities of diffusion models. Specifically, we develop a temporal diffusion predictor based on a conditional latent diffusion model, with the predicted

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VERMA, NISHCHAL K., and SHIKHA SINGH. "IMAGE SEQUENCE PREDICTION USING ANN AND RBFNN." International Journal of Image and Graphics 13, no. 02 (2013): 1340006. http://dx.doi.org/10.1142/s0219467813400068.

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A novel approach to predict future image frame of an image sequence is being presented. First, a method to predict the future position of a moving object in an image sequence is discussed using artificial neural network (ANN). Second, optical flow concept is used for generating complete image frame by calculating velocity of each pixel on both axes. A separate ANN (both sigmoidal and radial basis function neural network) is modeled for each pixel's velocity and predicted velocity of each pixel is then mapped to its future values and image frames are generated. The quality evaluations of predic

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Elton, Debra M., William A. Bonass, Richard A. Killington, David M. Meredith, and Ian W. Halliburton. "Location of open reading frames coding for equine herpesvirus type-1 glycoproteins with homology to gE and gI of herpes simplex virus." American Journal of Veterinary Research 52, no. 8 (1991): 1252–57. http://dx.doi.org/10.2460/ajvr.1991.52.08.1252.

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Summary The dna fragments representing the entire short unique region and part of the repeat sequences of the equine herpesvirus type-1 genome were cloned into plasmid vectors. The approximate positions of the junctions between the short unique region and the inverted repeats were then located by restriction endonuclease mapping. Two open reading frames coding for potential glycoproteins have been identified within the short unique region, using dna sequence analysis. The predicted amino acid sequences of these open reading frames had extensive homology to the herpes simplex virus glycoprotein

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Duffy, Simon P., Aaron M. Young, Benoit Morin, Christopher J. Lucarotti, Ben F. Koop, and David B. Levin. "Sequence Analysis and Organization of the Neodiprion abietis Nucleopolyhedrovirus Genome." Journal of Virology 80, no. 14 (2006): 6952–63. http://dx.doi.org/10.1128/jvi.00187-06.

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ABSTRACT Of 30 baculovirus genomes that have been sequenced to date, the only nonlepidopteran baculoviruses include the dipteran Culex nigripalpus nucleopolyhedrovirus and two hymenopteran nucleopolyhedroviruses that infect the sawflies Neodiprion lecontei (NeleNPV) and Neodiprion sertifer (NeseNPV). This study provides a complete sequence and genome analysis of the nucleopolyhedrovirus that infects the balsam fir sawfly Neodiprion abietis (Hymenoptera, Symphyta, Diprionidae). The N. abietis nucleopolyhedrovirus (NeabNPV) is 84,264 bp in size, with a G+C content of 33.5%, and contains 93 predi

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Liu, Xiaoying, Rolf Sommer Kaas, Peter Ruhdal Jensen, and Mhairi Workman. "Draft Genome Sequence of the Yeast Pachysolen tannophilus CBS 4044/NRRL Y-2460." Eukaryotic Cell 11, no. 6 (2012): 827. http://dx.doi.org/10.1128/ec.00114-12.

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ABSTRACT A draft genome sequence of the yeast Pachysolen tannophilus CBS 4044/NRRL Y-2460 is presented. The organism has the potential to be developed as a cell factory for biorefineries due to its ability to utilize waste feedstocks. The sequenced genome size was 12,238,196 bp, consisting of 34 scaffolds. A total of 4,463 genes from 5,346 predicted open reading frames were annotated with function.

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Furnari, Gabriele, Cristian Secchi, and Federica Ferraguti. "Sequence-based imitation learning for surgical robot operations." Artificial Intelligence Surgery 5, no. 1 (2025): 103–15. https://doi.org/10.20517/ais.2024.32.

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Aim This paper aims to advance autonomous surgical operations through imitation learning from video demonstrations. Methods To address this objective, we propose two main contributions: (1) We introduce a new dataset of virtual kidney tumor environments to train our model on. The dataset is composed of video demonstrations of tumor removal from the kidney, executed in a virtual environment, and kinematic data of the robot tools; (2) We employed an imitation learning architecture composed of vision transformers (ViT) to handle the frames extracted from the videos and of a long short-term memory

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8

Murdiyatmo, U., W. Asmara, J. S. H. Tsang, A. J. Baines, A. T. Bull, and D. J. Hardman. "Molecular biology of the 2-haloacid halidohydrolase IVa from Pseudomonas cepacia MBA4." Biochemical Journal 284, no. 1 (1992): 87–93. http://dx.doi.org/10.1042/bj2840087.

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The structural gene (hdl IVa) for the Pseudomonas cepacia MBA4 2-haloacid halidohydrolase IVa (Hdl IVa) was isolated on a 1.6 kb fragment of Ps. cepacia MBA4 chromosomal DNA. The recombinant halidohydrolase was expressed in Escherichia coli and Pseudomonas putida and the structural gene was subcloned on to the tac expression vector pBTac1. High-level expression from the tac promoter was seen to be temperature-dependent, a consequence of the nucleotide sequence adjacent to the fragment encoding the halidohydrolase. The nucleotide sequence of the fragment encoding the Hdl IVa was determined and

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9

Тимочко, О. І., В. В. Ларін, Ю. І. Шевяков, and А. Абдалла. "Investigation of the mechanism for processing predicted frames in the technology of compression of transformed images in computer systems and special purpose networks." Системи обробки інформації, no. 4(163), (October 28, 2020): 87–93. http://dx.doi.org/10.30748/soi.2020.163.09.

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The analysis of image processing technologies shows the main practice way to improve the quality of image processing. It is a preliminary analysis and subsequent image processing. It depends on the result of the preliminary analysis (filtration, sharpening, noise reduction, etc.). However, when selection of the method of preliminary analysis, an intermediate evaluation of results, selection of the subsequent processing method, etc. decision makers involved. This is not acceptable for practical implementation in automatic processing and transmission of video information systems. The main diffic

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10

Yan, Bo, Chuming Lin, and Weimin Tan. "Frame and Feature-Context Video Super-Resolution." Proceedings of the AAAI Conference on Artificial Intelligence 33 (July 17, 2019): 5597–604. http://dx.doi.org/10.1609/aaai.v33i01.33015597.

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For video super-resolution, current state-of-the-art approaches either process multiple low-resolution (LR) frames to produce each output high-resolution (HR) frame separately in a sliding window fashion or recurrently exploit the previously estimated HR frames to super-resolve the following frame. The main weaknesses of these approaches are: 1) separately generating each output frame may obtain high-quality HR estimates while resulting in unsatisfactory flickering artifacts, and 2) combining previously generated HR frames can produce temporally consistent results in the case of short informat

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11

Jungblut, Peter R., Eva-Christina Müller, Jens Mattow, and Stefan H. E. Kaufmann. "Proteomics Reveals Open Reading Frames inMycobacterium tuberculosis H37Rv Not Predicted by Genomics." Infection and Immunity 69, no. 9 (2001): 5905–7. http://dx.doi.org/10.1128/iai.69.9.5905-5907.2001.

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ABSTRACT Genomics revealed the sequence of 3924 genes of the H37Rv strain ofMycobacterium tuberculosis. Proteomics complements genomics in showing which genes are really expressed, and here we show the expression of six genes not predicted by genomics, as proved by two-dimensional electrophoresis and matrix-assisted laser desorption ionization and nano-electrospray mass spectrometry.

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Rancurel, Corinne, Mahvash Khosravi, A. Keith Dunker, Pedro R. Romero, and David Karlin. "Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation." Journal of Virology 83, no. 20 (2009): 10719–36. http://dx.doi.org/10.1128/jvi.00595-09.

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ABSTRACT It is widely assumed that new proteins are created by duplication, fusion, or fission of existing coding sequences. Another mechanism of protein birth is provided by overlapping genes. They are created de novo by mutations within a coding sequence that lead to the expression of a novel protein in another reading frame, a process called “overprinting.” To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes. Overlapping proteins have a sequence composition gl

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Ismail, Ahmed, Tanuj Saini, Ahmed Al Qaffas, et al. "Evidence of a Set of Core-Function Genes in 16 Bacillus Podoviral Genomes with Considerable Genomic Diversity." Viruses 15, no. 2 (2023): 276. http://dx.doi.org/10.3390/v15020276.

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Bacteriophage genomes represent an enormous level of genetic diversity and provide considerable potential to acquire new insights about viral genome evolution. In this study, the genome sequences of sixteen Bacillus-infecting bacteriophages were explored through comparative genomics approaches to reveal shared and unique characteristics. These bacteriophages are in the Salasmaviridae family with small (18,548–27,206 bp) double-stranded DNA genomes encoding 25–46 predicted open reading frames. We observe extensive nucleotide and amino acid sequence divergence among a set of core-function genes

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14

Arsenault, Danielle, Sophia P. Gosselin, and Johann Peter Gogarten. "An Actively Homing Insertion Element in a Phage Methylase Contains a Hidden HNH Endonuclease." Genes 16, no. 2 (2025): 178. https://doi.org/10.3390/genes16020178.

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Background/Objectives: The ShiLan domain was previously identified as an insertion sequence in a phage DNA methylase gene that exhibited similar evolutionary patterns to that of an active intein or self-splicing intron but could not be identified as either. It produces no internal stop codons when read in frame with its host methylase gene, leading to the thought that it may not be an intron and rather be an abnormal type of intein. However, the sequence has no detectable self-splicing domains, which are essential for intein persistence, as preventing an intein from successfully splicing is of

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15

Thekke-Veetil, Thanuja, Nancy K. McCoppin, Houston A. Hobbs, et al. "Discovery of a Novel Member of the Carlavirus Genus from Soybean (Glycine max L. Merr.)." Pathogens 10, no. 2 (2021): 223. http://dx.doi.org/10.3390/pathogens10020223.

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A novel member of the Carlavirus genus, provisionally named soybean carlavirus 1 (SCV1), was discovered by RNA-seq analysis of randomly collected soybean leaves in Illinois, USA. The SCV1 genome contains six open reading frames that encode a viral replicase, triple gene block proteins, a coat protein (CP) and a nucleic acid binding protein. The proteins showed highest amino acid sequence identities with the corresponding proteins of red clover carlavirus A (RCCVA). The predicted amino acid sequence of the SCV1 replicase was only 60.6% identical with the replicase of RCCVA, which is below the d

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16

Denis-Larose, Claude, Hélène Bergeron, Diane Labbé, et al. "Characterization of the Basic Replicon ofRhodococcus Plasmid pSOX and Development of aRhodococcus-Escherichia coli Shuttle Vector†." Applied and Environmental Microbiology 64, no. 11 (1998): 4363–67. http://dx.doi.org/10.1128/aem.64.11.4363-4367.1998.

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ABSTRACT The replication region of a 100-kb desulfurization plasmid (pSOX) from Rhodococcus sp. strain X309 was localized to a 4-kbKpnI fragment, and its sequence was determined. The amino acid sequence of one of the predicted open reading frames (ORFs) was related to the putative replication (Rep) protein sequences of the mycobacterial pLR7 family of plasmids. Three of the five predicted ORF products were identified by radiolabelling with the Escherichia coli T7 polymerase/promoter system. In E. coli, the Rep protein of pSOX was apparently synthesized in a shortened form, 21.3 kDa instead of

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Wang, Qiang, Liuyang Jiang, Xuebin Sun, Jingbo Zhao, Zhaopeng Deng, and Shizhong Yang. "An Efficient LiDAR Point Cloud Map Coding Scheme Based on Segmentation and Frame-Inserting Network." Sensors 22, no. 14 (2022): 5108. http://dx.doi.org/10.3390/s22145108.

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In this article, we present an efficient coding scheme for LiDAR point cloud maps. As a point cloud map consists of numerous single scans spliced together, by recording the time stamp and quaternion matrix of each scan during map building, we cast the point cloud map compression into the point cloud sequence compression problem. The coding architecture includes two techniques: intra-coding and inter-coding. For intra-frames, a segmentation-based intra-prediction technique is developed. For inter-frames, an interpolation-based inter-frame coding network is explored to remove temporal redundancy

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18

Bork, Peer, Christos Ouzounis, Chris Sander, Michael Scharf, Reinhard Schneider, and Erik Sonnhammer. "Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III." Protein Science 1, no. 12 (1992): 1677–90. http://dx.doi.org/10.1002/pro.5560011216.

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19

Okinaka, R. T., K. Cloud, O. Hampton, et al. "Sequence and Organization of pXO1, the Large Bacillus anthracis Plasmid Harboring the Anthrax Toxin Genes." Journal of Bacteriology 181, no. 20 (1999): 6509–15. http://dx.doi.org/10.1128/jb.181.20.6509-6515.1999.

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ABSTRACT The Bacillus anthracis Sterne plasmid pXO1 was sequenced by random, “shotgun” cloning. A circular sequence of 181,654 bp was generated. One hundred forty-three open reading frames (ORFs) were predicted using GeneMark and GeneMark.hmm, comprising only 61% (110,817 bp) of the pXO1 DNA sequence. The overall guanine-plus-cytosine content of the plasmid is 32.5%. The most recognizable feature of the plasmid is a “pathogenicity island,” defined by a 44.8-kb region that is bordered by inverted IS1627 elements at each end. This region contains the three toxin genes (cya, lef, and pagA), regul

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Singh Raghava, Gajendra Pal, Da Jeong Hwang, and Joon Hee Han. "ECGpred: Correlation and Prediction of Gene Expression from Nucleotide Sequence." Open Bioinformatics Journal 2, no. 1 (2008): 64–71. http://dx.doi.org/10.2174/1875036200802010064.

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Development of gene expression prediction systems from huge amount of microarray data is an inevitable problem. In the present study a support vector machine (SVM) based method has been developed to predict expression of genes from its nucleotide sequence. In this method, SVM was trained on microarray data of genes and trained SVM was used to predict the expression of other genes of the same organism under the same condition. The SVM models were developed using nucleotide, dinucleotide, and trinucleotide composition of genes and achieved correlation coefficients (r) 0.25, 0.70, 0.82 respective

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Salmi, Daniel, Vincent Magrini, Patricia L. Hartzell, and Philip Youderian. "Genetic Determinants of Immunity and Integration of Temperate Myxococcus xanthus Phage Mx8." Journal of Bacteriology 180, no. 3 (1998): 614–21. http://dx.doi.org/10.1128/jb.180.3.614-621.1998.

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ABSTRACT An 8.1-kb fragment of the temperate Myxococcus xanthusphage Mx8 genome, when cloned into a plasmid vector, permits site-specific integration of the plasmid and confers superinfection immunity. Sequence analysis of a 9.5-kb region of Mx8 DNA containing this fragment reveals 19 densely packed open reading frames, four of which have predicted products with known or suspected activities. The Mx8 imm gene, required for superinfection immunity, has a sequence similar to that of Arabidopsis thalianaG-box-binding factor 1. Mx8 makes a DNA adenine methylase, Mox, and integrase, Int, related to

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Chang, Yijan E., Laura Menotti, Felix Filatov, Gabriella Campadelli-Fiume та Bernard Roizman. "UL27.5 Is a Novel γ2 Gene Antisense to the Herpes Simplex Virus 1 Gene Encoding Glycoprotein B". Journal of Virology 72, № 7 (1998): 6056–64. http://dx.doi.org/10.1128/jvi.72.7.6056-6064.1998.

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ABSTRACT An antibody made against the herpes simplex virus 1 US5 gene predicted to encode glycoprotein J was found to react strongly with two proteins, one with an apparent M r of 23,000 and mapping in the S component and one with a herpes simplex virus protein with an apparent M r of 43,000. The antibody also reacted with herpes simplex virus type 2 proteins forming several bands with apparent M rs ranging from 43,000 to 50,000. Mapping studies based on intertypic recombinants, analyses of deletion mutants, and ultimately, reaction of the antibody with a chimeric protein expressed by in-frame

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Gruidl, Michael E., and Gisela Mosig. "SEQUENCE AND TRANSCRIPTS OF THE BACTERIOPHAGE T4 DNA REPAIR GENE uvsY." Genetics 114, no. 4 (1986): 1061–79. http://dx.doi.org/10.1093/genetics/114.4.1061.

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ABSTRACT We have cloned, sequenced and analyzed transcription of the phage T4 uvsY gene. This gene is transcribed from a single gp MotA-dependent middle promoter to give a major transcript of approximately 930 nucleotides and a minor transcript of approximately 620 nucleotides. All in vivo and in vitro uvsY transcripts show anomalous migration in agarose gels. The uvsY transcript contains an open reading frame coding for an 137 amino acid [15.8 kilodaltons (kD)] UvsY protein and two unidentified open reading frames, ORF UvsY.-1 (9.0 kD) and ORF UvsY.-2 (6.0 kD). Our DNA sequence differs in onl

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Gubser, Caroline, and Geoffrey L. Smith. "The sequence of camelpox virus shows it is most closely related to variola virus, the cause of smallpox." Journal of General Virology 83, no. 4 (2002): 855–72. http://dx.doi.org/10.1099/0022-1317-83-4-855.

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Camelpox virus (CMPV) and variola virus (VAR) are orthopoxviruses (OPVs) that share several biological features and cause high mortality and morbidity in their single host species. The sequence of a virulent CMPV strain was determined; it is 202182 bp long, with inverted terminal repeats (ITRs) of 6045 bp and has 206 predicted open reading frames (ORFs). As for other poxviruses, the genes are tightly packed with little non-coding sequence. Most genes within 25 kb of each terminus are transcribed outwards towards the terminus, whereas genes within the centre of the genome are transcribed from e

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Klupp, Barbara G., Christoph J. Hengartner, Thomas C. Mettenleiter, and Lynn W. Enquist. "Complete, Annotated Sequence of the Pseudorabies Virus Genome." Journal of Virology 78, no. 1 (2004): 424–40. http://dx.doi.org/10.1128/jvi.78.1.424-440.2004.

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ABSTRACT We have obtained the complete DNA sequence of pseudorabies virus (PRV), an alphaherpesvirus also known as Aujeszky's disease virus or suid herpesvirus 1, using sequence fragments derived from six different strains (Kaplan, Becker, Rice, Indiana-Funkhauser, NIA-3, and TNL). The assembled PRV genome sequence comprises 143,461 nucleotides. As expected, it matches the predicted gene arrangement, genome size, and restriction enzyme digest patterns. More than 70 open reading frames were identified with homologs in related alphaherpesviruses; none were unique to PRV. RNA polymerase II transc

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Miyazawa, Daisuke, Le Thi Ha Thanh, Akio Tani, et al. "Isolation and Characterization of Genes Responsible for Naphthalene Degradation from Thermophilic Naphthalene Degrader, Geobacillus sp. JF8." Microorganisms 8, no. 1 (2019): 44. http://dx.doi.org/10.3390/microorganisms8010044.

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Geobacillus sp. JF8 is a thermophilic biphenyl and naphthalene degrader. To identify the naphthalene degradation genes, cis-naphthalene dihydrodiol dehydrogenase was purified from naphthalene-grown cells, and its N-terminal amino acid sequence was determined. Using a DNA probe encoding the N-terminal region of the dehydrogenase, a 10-kb DNA fragment was isolated. Upstream of nahB, a gene for dehydrogenase, there were two open reading frames which were designated as nahAc and nahAd, respectively. The products of nahAc and nahAd were predicted to be alpha and beta subunit of ring-hydroxylating d

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Ling, Kai-Shu, Hai-Ying Zhu, and Dennis Gonsalves. "Complete nucleotide sequence and genome organization of Grapevine leafroll-associated virus 3, type member of the genus Ampelovirus." Journal of General Virology 85, no. 7 (2004): 2099–102. http://dx.doi.org/10.1099/vir.0.80007-0.

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This study reports on the complete genome sequence of Grapevine leafroll-associated virus 3, the type member of the genus Ampelovirus. The genome is 17 919 nt in size and contains 13 open reading frames (ORFs). Previously, the sequence of 13 154 nt of the 3′-terminal of the genome was reported. The newly sequenced portion contains a 158 nt 5′ UTR, a single papain-like protease and a methyltransferase-like (MT) domain. ORF1a encodes a large polypeptide with a molecular mass of 245 kDa. With a predicted +1 frameshift, the large fusion protein generated from ORF1a/1b would produce a 306 kDa polyp

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Fisseha, Makda, Dvora Biran та Lee Kroos. "Identification of the Ω4499 Regulatory Region Controlling Developmental Expression of a Myxococcus xanthus Cytochrome P-450 System". Journal of Bacteriology 181, № 17 (1999): 5467–75. http://dx.doi.org/10.1128/jb.181.17.5467-5475.1999.

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ABSTRACT Ω4499 is the site of a Tn5 lac insertion in theMyxococcus xanthus chromosome that fuses lacZexpression to a developmentally regulated promoter. Cell-cell interactions that occur during development, including C signaling, are required for normal expression of Tn5 lac Ω4499. The DNA upstream of the Ω4499 insertion has been cloned, and the promoter has been localized. Analysis of the DNA sequence downstream of the promoter revealed one complete open reading frame and a second partial open reading frame that is interrupted by Tn5 lac Ω4499. The predicted products of these open reading fra

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Treger, J. M., and K. McEntee. "Structure of the DNA damage-inducible gene DDR48 and evidence for its role in mutagenesis in Saccharomyces cerevisiae." Molecular and Cellular Biology 10, no. 6 (1990): 3174–84. http://dx.doi.org/10.1128/mcb.10.6.3174-3184.1990.

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The DDR48 gene of Saccharomyces cerevisiae is a member of a set of genes that displays increased transcription in response to treatments that produce DNA lesions or to heat-shock stress. Other members of this group include the DDRA2 and UBI4 genes. DNA sequence analysis of the DDR48 gene demonstrates the presence of two overlapping open reading frames, each of which has the capacity to encode a protein with a molecular mass of approximately 45 kilodaltons. Fusions of the DDR48 coding sequences to lacZ demonstrates that only one of these frames is expressed in yeast cells. The protein predicted

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Treger, J. M., and K. McEntee. "Structure of the DNA damage-inducible gene DDR48 and evidence for its role in mutagenesis in Saccharomyces cerevisiae." Molecular and Cellular Biology 10, no. 6 (1990): 3174–84. http://dx.doi.org/10.1128/mcb.10.6.3174.

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The DDR48 gene of Saccharomyces cerevisiae is a member of a set of genes that displays increased transcription in response to treatments that produce DNA lesions or to heat-shock stress. Other members of this group include the DDRA2 and UBI4 genes. DNA sequence analysis of the DDR48 gene demonstrates the presence of two overlapping open reading frames, each of which has the capacity to encode a protein with a molecular mass of approximately 45 kilodaltons. Fusions of the DDR48 coding sequences to lacZ demonstrates that only one of these frames is expressed in yeast cells. The protein predicted

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Monteiro-Vitorello, Claudia B., Luis E. A. Camargo, Marie A. Van Sluys, et al. "The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. xyli." Molecular Plant-Microbe Interactions® 17, no. 8 (2004): 827–36. http://dx.doi.org/10.1094/mpmi.2004.17.8.827.

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The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli

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McGhee, Gayle C., and Alan L. Jones. "Complete Nucleotide Sequence of Ubiquitous Plasmid pEA29 fromErwinia amylovora Strain Ea88: Gene Organization and Intraspecies Variation." Applied and Environmental Microbiology 66, no. 11 (2000): 4897–907. http://dx.doi.org/10.1128/aem.66.11.4897-4907.2000.

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ABSTRACT The complete sequence of plasmid pEA29 from Erwinia amylovora strain Ea88 consists of 28,185 bp with a 50.2% G+C content. As deletions and insertions were detected in other derivatives of pEA29, its size actually varied from 27.6 to 34.9 kb. Thirteen open reading frames that encoded predicted proteins with similarities to known proteins from other bacteria were identified along with two open reading frames related to hypothetical proteins found in GenBank and six open reading frames with no similarities to existing GenBank entries. Predicted products of open reading frames with simila

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Braid, Michael D., Jennifer L. Silhavy, Christopher L. Kitts, Raul J. Cano, and Martha M. Howe. "Complete Genomic Sequence of Bacteriophage B3, a Mu-Like Phage of Pseudomonas aeruginosa." Journal of Bacteriology 186, no. 19 (2004): 6560–74. http://dx.doi.org/10.1128/jb.186.19.6560-6574.2004.

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ABSTRACT Bacteriophage B3 is a transposable phage of Pseudomonas aeruginosa. In this report, we present the complete DNA sequence and annotation of the B3 genome. DNA sequence analysis revealed that the B3 genome is 38,439 bp long with a G+C content of 63.3%. The genome contains 59 proposed open reading frames (ORFs) organized into at least three operons. Of these ORFs, the predicted proteins from 41 ORFs (68%) display significant similarity to other phage or bacterial proteins. Many of the predicted B3 proteins are homologous to those encoded by the early genes and head genes of Mu and Mu-lik

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Aigner, Sandra, and Marco Körner. "The Importance of Loss Functions for Increasing the Generalization Abilities of a Deep Learning-Based Next Frame Prediction Model for Traffic Scenes." Machine Learning and Knowledge Extraction 2, no. 2 (2020): 78–98. http://dx.doi.org/10.3390/make2020006.

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This paper analyzes in detail how different loss functions influence the generalization abilities of a deep learning-based next frame prediction model for traffic scenes. Our prediction model is a convolutional long-short term memory (ConvLSTM) network that generates the pixel values of the next frame after having observed the raw pixel values of a sequence of four past frames. We trained the model with 21 combinations of seven loss terms using the Cityscapes Sequences dataset and an identical hyper-parameter setting. The loss terms range from pixel-error based terms to adversarial terms. To a

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Zrelovs, Nikita, Andris Dislers, and Andris Kazaks. "Genome Characterization of Nocturne116, Novel Lactococcus lactis-Infecting Phage Isolated from Moth." Microorganisms 9, no. 7 (2021): 1540. http://dx.doi.org/10.3390/microorganisms9071540.

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While looking for novel insect-associated phages, a unique siphophage, Nocturne116, was isolated from a deceased local moth specimen along with its host, which was identified by 16S rRNA gene sequencing as a strain of Lactococcus lactis. Next-generation sequencing and the subsequent genome annotation elaborated on herein revealed that the genome of Nocturne116 is a 25,554 bp long dsDNA molecule with 10 bp long 3′ cos overhangs and a GC content of 37.99%, comprising 52 predicted open reading frames. The complete nucleotide sequence of phage Nocturne116 genome is dissimilar to any of the already

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Wallace, Edward W. J., Corinne Maufrais, Jade Sales-Lee, et al. "Quantitative global studies reveal differential translational control by start codon context across the fungal kingdom." Nucleic Acids Research 48, no. 5 (2020): 2312–31. http://dx.doi.org/10.1093/nar/gkaa060.

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Abstract Eukaryotic protein synthesis generally initiates at a start codon defined by an AUG and its surrounding Kozak sequence context, but the quantitative importance of this context in different species is unclear. We tested this concept in two pathogenic Cryptococcus yeast species by genome-wide mapping of translation and of mRNA 5′ and 3′ ends. We observed thousands of AUG-initiated upstream open reading frames (uORFs) that are a major contributor to translation repression. uORF use depends on the Kozak sequence context of its start codon, and uORFs with strong contexts promote nonsense-m

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Akiyoshi, Donna E., Maria Denaro, Haihong Zhu, Julia L. Greenstein, Papia Banerjee, and Jay A. Fishman. "Identification of a Full-Length cDNA for an Endogenous Retrovirus of Miniature Swine." Journal of Virology 72, no. 5 (1998): 4503–7. http://dx.doi.org/10.1128/jvi.72.5.4503-4507.1998.

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ABSTRACT Endogenous retroviruses of swine are a concern in the use of pig-derived tissues for xenotransplantation into humans. The nucleotide sequence of porcine endogenous retrovirus taken from lymphocytes of miniature swine (PERV-MSL) has been characterized. PERV-MSL is a type C retrovirus of 8,132 bp with the greatest nucleic acid sequence identity to gibbon ape leukemia virus and murine leukemia virus. Constitutive production of PERV-MSL RNA has been detected in normal leukocytes and in multiple organs of swine. The copy numbers of full-length PERV sequences per genome (approximately 8 to

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Bérard, Jacques, and Gabriel Gingras. "The puh structural gene coding for the H subunit of the Rhodospirillum rubrum photoreaction center." Biochemistry and Cell Biology 69, no. 2-3 (1991): 122–31. http://dx.doi.org/10.1139/o91-019.

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The Rhodospirillum rubrum structural gene puh, coding for the photoreaction center H polypeptide, and three other putative genes that surround puh were cloned and sequenced. The deduced 257 amino acid H polypeptide has a molecular weight of 27 909, in close agreement with polyacrylamide gel electrophoresis determination. Hydropathy plots predict a single hydrophobic α helix. The H polypeptide of Rhodospirillum rubrum shares only 23% of its residues with all three of the H polypeptides from Rhodopseudomonas viridis, Rhodobacter capsulatus, and Rhodobacter sphaeroides. Despite this apparent low

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Kuriyama, R., P. Savereide, P. Lefebvre, and S. Dasgupta. "The predicted amino acid sequence of a centrosphere protein in dividing sea urchin eggs is similar to elongation factor (EF-1 alpha)." Journal of Cell Science 95, no. 2 (1990): 231–36. http://dx.doi.org/10.1242/jcs.95.2.231.

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Monoclonal antibody (SU5), prepared from isolated mitotic spindles of sea urchin eggs, stained centrospheres preferentially and recognized a 50K (K = 10(3) Mr) polypeptide on immunoblots. Three positive clones were isolated by screening a lambda gt11 cDNA expression library prepared from sea urchin egg mRNA with SU5. One clone containing a 1.8-kb (1 kb = 10(3) base-pairs) insert was selected for further characterization. The beta-galactosidase fusion protein encoded by the cDNA clone had an apparent relative molecular mass of 150K, indicating that the inserted cDNA produced an estimated 34K of

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Zeng, F. Y., C. W. M. Chan, M. N. Chan, et al. "The Complete Genome Sequence of Severe Acute Respiratory Syndrome Coronavirus Strain HKU-39849 (HK-39)." Experimental Biology and Medicine 228, no. 7 (2003): 866–73. http://dx.doi.org/10.1177/15353702-0322807-13.

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The complete genomic nucleotide sequence (29.7kb) of a Hong Kong severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) strain HK-39 is determined. Phylogenetic analysis of the genomic sequence reveals it to be a distinct member of the Coronaviridae family. 5′ RACE assay confirms the presence of at least six subgenomic transcripts all containing the predicted intergenic sequences. Five open reading frames (ORFs), namely ORF1a, 1b, S, M, and N, are found to be homologues to other CoV members, and three more unknown ORFs (X1, X2, and X3) are unparalleled in all other known CoV species.

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Gigante, Gao, Tang, et al. "Genome of Alaskapox Virus, A Novel Orthopoxvirus Isolated from Alaska." Viruses 11, no. 8 (2019): 708. http://dx.doi.org/10.3390/v11080708.

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Since the eradication of smallpox, there have been increases in poxvirus infections and the emergence of several novel poxviruses that can infect humans and domestic animals. In 2015, a novel poxvirus was isolated from a resident of Alaska. Diagnostic testing and limited sequence analysis suggested this isolate was a member of the Orthopoxvirus (OPXV) genus but was highly diverged from currently known species, including Akhmeta virus. Here, we present the complete 210,797 bp genome sequence of the Alaska poxvirus isolate, containing 206 predicted open reading frames. Phylogenetic analysis of t

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Vedantam, Gayatri, Thomas J. Novicki, and David W. Hecht. "Bacteroides fragilis Transfer Factor Tn5520: the Smallest Bacterial Mobilizable Transposon Containing Single Integrase and Mobilization Genes That Function inEscherichia coli." Journal of Bacteriology 181, no. 8 (1999): 2564–71. http://dx.doi.org/10.1128/jb.181.8.2564-2571.1999.

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ABSTRACT Many bacterial genera, including Bacteroides spp., harbor mobilizable transposons, a class of transfer factors that carry genes for conjugal DNA transfer and, in some cases, antibiotic resistance. Mobilizable transposons are capable of inserting into and mobilizing other, nontransferable plasmids and are implicated in the dissemination of antibiotic resistance. This paper presents the isolation and characterization of Tn5520, a new mobilizable transposon from Bacteroides fragilis LV23. At 4,692 bp, it is the smallest mobilizable transposon reported from any bacterial genus. Tn5520 was

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Ashraf, Muhammad Aleem, Judith K. Brown, Muhammad Shahzad Iqbal, and Naitong Yu. "Genome-Wide Identification of Cotton MicroRNAs Predicted for Targeting Cotton Leaf Curl Kokhran Virus-Lucknow." Microbiology Research 15, no. 1 (2023): 1–19. http://dx.doi.org/10.3390/microbiolres15010001.

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Cotton leaf curl Kokhran virus (CLCuKoV) (genus, Begomovirus; family, Geminiviridae) is one of several plant virus pathogens of cotton (Gossypium hirsutum L.) that cause cotton leaf curl disease in Pakistan. Begomoviruses are transmitted by the whitefly Bemisia tabaci cryptic species group and cause economic losses in cotton and other crops worldwide. The CLCuKoV strain, referred to as CLCuKoV-Bur, emerged in the vicinity of Burewala, Pakistan, and was the primary causal virus associated with the second CLCuD epidemic in Pakistan. The monopartite ssDNA genome of (2.7 Kb) contains six open read

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Gould, Phillip S., and Andrew J. Easton. "Coupled Translation of the Respiratory Syncytial Virus M2 Open Reading Frames Requires Upstream Sequences." Journal of Biological Chemistry 280, no. 23 (2005): 21972–80. http://dx.doi.org/10.1074/jbc.m502276200.

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We have investigated the mechanism of the translation of the second open reading frame (ORF) of the respiratory syncytial virus M2 transcript that uses a novel coupled translation process requiring prior translation of the upstream ORF. The second M2-2 ORF sequences play no role in the coupling process and can be replaced with other gene sequences. Surprisingly, the overlap region of the two ORFs alone was not sufficient for coupled translation to occur. An analysis of the sequences required for the coupling process showed that portions of the transcript located along the length of the first O

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Garsin, Danielle A., Jonathan Urbach, Jose C. Huguet-Tapia, Joseph E. Peters, and Frederick M. Ausubel. "Construction of an Enterococcus faecalis Tn917-Mediated-Gene-Disruption Library Offers Insight into Tn917 Insertion Patterns." Journal of Bacteriology 186, no. 21 (2004): 7280–89. http://dx.doi.org/10.1128/jb.186.21.7280-7289.2004.

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ABSTRACT Sequencing the insertion sites of 8,865 Tn917 insertions in Enterococcus faecalis strain OG1RF identified a hot spot in the replication terminus region corresponding to 6% of the genome where 65% of the transposons had inserted. In E. faecalis, Tn917 preferentially inserted at a 29-bp consensus sequence centered on TATAA, a 5-bp sequence that is duplicated during insertion. The regional insertion site preference at the chromosome terminus was not observed in another low-G+C gram-positive bacterium, Listeria monocytogenes, although the consensus insertion sequence was the same. The 8,8

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"Frame Prediction- Noise Removal using Denoising Autoencoders." International Journal of Innovative Technology and Exploring Engineering 9, no. 2 (2019): 5296–99. http://dx.doi.org/10.35940/ijitee.b7135.129219.

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In the current times, tasks like Object Detection, Object tracking, Gesture prediction, Video prediction in computer vision are being solved effectively with models of deep learning . Video frame prediction involves predicting the next few frames of a video given the previous frame or frames as input. Currently, the challenge in video frame prediction is that the predicted future frames are blurry. This paper focuses on the removal of noise from the predicted image using Denoising Autoencoders, solve the above-addressed issue. The proposed work, trains LSTM model which generates future frames

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Andrade-Domínguez, Andrés, Roberto Kolter, and Lori R. Shapiro. "Complete Genome Sequence of EtG, the First Phage Sequenced from Erwinia tracheiphila." Genome Announcements 6, no. 8 (2018). http://dx.doi.org/10.1128/genomea.00127-18.

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ABSTRACT Erwinia tracheiphila is the causal agent of bacterial wilt of cucurbits. Here, we report the genome sequence of the temperate phage EtG, which was isolated from an E. tracheiphila -infected cucumber plant. Phage EtG has a linear 30,413-bp double-stranded DNA genome with cohesive ends and 45 predicted open reading frames.

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Schneider, William L., Aaron J. Sechler, and Elizabeth E. Rogers. "Complete Genome Sequence of Rathayibacter toxicus Phage NCPPB3778." Genome Announcements 5, no. 42 (2017). http://dx.doi.org/10.1128/genomea.00671-17.

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ABSTRACT The phage NCPPB3778 was isolated from Rathayibacter toxicus strain CS14, and the genomic DNA was sequenced. The genome is similar to siphoviruses, consisting of 44,520 bases including 77 predicted open reading frames. Portions of the genome are annotated as typical phage proteins, but much of the genome sequence is unique from other bacteriophages.

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Sarker, Subir, Sally R. Isberg, Ajani Athukorala, et al. "Characterization of a Complete Genome Sequence of Molluscum Contagiosum Virus from an Adult Woman in Australia." Microbiology Resource Announcements 10, no. 1 (2021). http://dx.doi.org/10.1128/mra.00939-20.

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ABSTRACT The complete genome sequence of molluscum contagiosum virus 1 (MOCV1) isolate NT2017 was sequenced from a tissue sample from an Australian woman. The genome consisted of 185,655 bp encoding 169 predicted open reading frames. Phylogenetically, isolate NT2017 was most closely related to an MOCV1 strain from Slovenia.

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Kingry, Luke C., Dhwani Batra, Adam Replogle, et al. "Chromosome and Linear Plasmid Sequences of a 2015 Human Isolate of the Tick-Borne Relapsing Fever Spirochete, Borrelia turicatae." Genome Announcements 4, no. 4 (2016). http://dx.doi.org/10.1128/genomea.00655-16.

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The sequences of the complete linear chromosome and 7 linear plasmids of the relapsing fever spirochete Borrelia turicatae are presented in this report. The 925,547 bp of chromosome and 380,211 bp of plasmid sequence were predicted to contain a total of 1,131 open reading frames, with an average G+C content of 29.7%.

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