WorldWideScience

Sample records for dsrna genomic segments

  1. Construction of carrier state viruses with partial genomes of the segmented dsRNA bacteriophages

    International Nuclear Information System (INIS)

    Sun Yang; Qiao Xueying; Mindich, Leonard

    2004-01-01

    The cystoviridae are bacteriophages with genomes of three segments of dsRNA enclosed within a polyhedral capsid. Two members of this family, PHI6 and PHI8, have been shown to form carrier states in which the virus replicates as a stable episome in the host bacterium while expressing reporter genes such as kanamycin resistance or lacα. The carrier state does not require the activity of all the genes necessary for phage production. It is possible to generate carrier states by infecting cells with virus or by electroporating nonreplicating plasmids containing cDNA copies of the viral genomes into the host cells. We have found that carrier states in both PHI6 and PHI8 can be formed at high frequency with all three genomic segments or with only the large and small segments. The large genomic segment codes for the proteins that constitute the inner core of the virus, which is the structure responsible for the packaging and replication of the genome. In PHI6, a carrier state can be formed with the large and middle segment if mutations occur in the gene for the major structural protein of the inner core. In PHI8, carrier state formation requires the activity of genes 8 and 12 of segment S

  2. Identification and Characterization of a Novel Hepta-Segmented dsRNA Virus From the Phytopathogenic Fungus Colletotrichum fructicola

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    Lifeng Zhai

    2018-04-01

    Full Text Available A novel hepta-segmented double-stranded RNA (dsRNA virus was isolated and characterized from the strain FJ-4 of the phytopathogenic fungus Colletotrichum fructicola, and was named Colletotrichum fructicola chrysovirus 1 (CfCV1. The full-length cDNAs of dsRNA1–7 were 3620, 2801, 2687, 2437, 1750, 1536, and 1211 bp, respectively. The 5′- and 3′-untranslated regions of the seven dsRNAs share highly similar internal sequence and contain conserved sequence stretches, indicating that they have a common virus origin. The 5′-and 3′-UTRs of the seven dsRNAs were predicted to fold into stable stem-loop structures. CfCV1 contains spherical virions that are 35 nm in diameter consisting of seven segments. The largest dsRNA of CfCV1 encodes an RNA-dependent RNA polymerase (RdRp, and the second dsRNA encodes a viral capsid protein (CP. The dsRNA5 encodes a C2H2-type zinc finger protein containing an R-rich region and a G-rich region. The smallest dsRNA is a satellite-like RNA. The functions of the other proteins encoded by dsRNA3, dsRNA4, dsRNA6 are unknown. Phylogenetic analysis, based on RdRp and CP, indicated that CfCV1 is phylogenetically related to Botryosphaeria dothidea chrysovirus 1 (BdCV1, and Penicillium janczewskii chrysovirus 2 (PjCV2, a cluster of an independent cluster II group in the family Chrysoviridae. Importantly, all the seven segments of CfCV1 were transmitted successfully to other virus-free strains with an all-or-none fashion. CfCV1 exerts minor influence on the growth of C. fructicola but can confer hypovirulence to the fungal host. To our knowledge, this is the first report of a hepta-segmented tentative chrysovirus in C. fructicola.

  3. In vivo studies of genomic packaging in the dsRNA bacteriophage Φ8

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    Mindich Leonard

    2005-03-01

    Full Text Available Abstract Background Φ8 is a bacteriophage containing a genome of three segments of double-stranded RNA inside a polyhedral capsid enveloped in a lipid-containing membrane. Plus strand RNA binds and is packaged by empty procapsids. Whereas Φ6, another member of the Cystoviridae, shows high stringency, serial dependence and precision in its genomic packaging in vitro and in vivo, Φ8 packaging is more flexible. Unique sequences (pac near the 5' ends of plus strands are necessary and sufficient for Φ6 genomic packaging and the RNA binding sites are located on P1, the major structural protein of the procapsid. Results In this paper the boundaries of the Φ8 pac sequences have been explored by testing the in vivo packaging efficacy of transcripts containing deletions or changes in the RNA sequences. The pac sequences have been localized to the 5' untranslated regions of the viral transcripts. Major changes in the pac sequences are either tolerated or ameliorated by suppressor mutations in the RNA sequence. Changes in the genomic packaging program can be established as a result of mutations in P1, the major structural protein of the procapsid and the determinant of RNA binding specificity. Conclusion Although Φ8 is distantly related to bacteriophage Φ6, and does not show sequence similarity, it has a similar genomic packaging program. This program, however, is less stringent than that of Φ6.

  4. Exploratory analysis of genomic segmentations with Segtools

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    Buske Orion J

    2011-10-01

    Full Text Available Abstract Background As genome-wide experiments and annotations become more prevalent, researchers increasingly require tools to help interpret data at this scale. Many functional genomics experiments involve partitioning the genome into labeled segments, such that segments sharing the same label exhibit one or more biochemical or functional traits. For example, a collection of ChlP-seq experiments yields a compendium of peaks, each labeled with one or more associated DNA-binding proteins. Similarly, manually or automatically generated annotations of functional genomic elements, including cis-regulatory modules and protein-coding or RNA genes, can also be summarized as genomic segmentations. Results We present a software toolkit called Segtools that simplifies and automates the exploration of genomic segmentations. The software operates as a series of interacting tools, each of which provides one mode of summarization. These various tools can be pipelined and summarized in a single HTML page. We describe the Segtools toolkit and demonstrate its use in interpreting a collection of human histone modification data sets and Plasmodium falciparum local chromatin structure data sets. Conclusions Segtools provides a convenient, powerful means of interpreting a genomic segmentation.

  5. Comparing genomes with rearrangements and segmental duplications.

    Science.gov (United States)

    Shao, Mingfu; Moret, Bernard M E

    2015-06-15

    Large-scale evolutionary events such as genomic rearrange.ments and segmental duplications form an important part of the evolution of genomes and are widely studied from both biological and computational perspectives. A basic computational problem is to infer these events in the evolutionary history for given modern genomes, a task for which many algorithms have been proposed under various constraints. Algorithms that can handle both rearrangements and content-modifying events such as duplications and losses remain few and limited in their applicability. We study the comparison of two genomes under a model including general rearrangements (through double-cut-and-join) and segmental duplications. We formulate the comparison as an optimization problem and describe an exact algorithm to solve it by using an integer linear program. We also devise a sufficient condition and an efficient algorithm to identify optimal substructures, which can simplify the problem while preserving optimality. Using the optimal substructures with the integer linear program (ILP) formulation yields a practical and exact algorithm to solve the problem. We then apply our algorithm to assign in-paralogs and orthologs (a necessary step in handling duplications) and compare its performance with that of the state-of-the-art method MSOAR, using both simulations and real data. On simulated datasets, our method outperforms MSOAR by a significant margin, and on five well-annotated species, MSOAR achieves high accuracy, yet our method performs slightly better on each of the 10 pairwise comparisons. http://lcbb.epfl.ch/softwares/coser. © The Author 2015. Published by Oxford University Press.

  6. Discovery of a dsRNA virus infecting the marine photosynthetic protist Micromonas pusilla

    International Nuclear Information System (INIS)

    Brussaard, C.P.D.; Noordeloos, A.A.M.; Sandaa, R.-A.; Heldal, M.; Bratbak, G.

    2004-01-01

    We report the isolation of the first double-stranded (ds) RNA virus in the family Reoviridae that infects a protist (microalga Micromonas pusilla, Prasinophyceae). The dsRNA genome was composed of 11 segments ranging between 0.8 and 5.8 kb, with a total size of approximately 25.5 kb. The virus (MpRNAV-01B) could not be assigned to the genus level because host type, genome size, and number of segments smaller than 2 kb did not correspond to either of the two existing 11-segmented dsRNA genera Rotavirus and Aquareovirus. MpRNAV-01B has a particle size of 65-80 nm, a narrow host range, a latent period of 36 h, and contains five major proteins (120, 95, 67, 53, and 32 kDa). MpRNAV-01B was stable to freeze-thawing, resistant to chloroform, ether, nonionic detergents, chelating and reducing agents. The virus was inactivated at temperatures above 35 deg. C and by ionic detergent, ethanol, acetone, and acidic conditions (pH 2-5)

  7. Structural constraints in the packaging of bluetongue virus genomic segments

    OpenAIRE

    Burkhardt, Christiane; Sung, Po-Yu; Celma, Cristina C.; Roy, Polly

    2014-01-01

    : The mechanism used by bluetongue virus (BTV) to ensure the sorting and packaging of its 10 genomic segments is still poorly understood. In this study, we investigated the packaging constraints for two BTV genomic segments from two different serotypes. Segment 4 (S4) of BTV serotype 9 was mutated sequentially and packaging of mutant ssRNAs was investigated by two newly developed RNA packaging assay systems, one in vivo and the other in vitro. Modelling of the mutated ssRNA followed by bioche...

  8. Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments

    NARCIS (Netherlands)

    Wichgers Schreur, Paul J.; Kortekaas, Jeroen

    2016-01-01

    The bunyavirus genome comprises a small (S), medium (M), and large (L) RNA segment of negative polarity. Although genome segmentation confers evolutionary advantages by enabling genome reassortment events with related viruses, genome segmentation also complicates genome replication and packaging.

  9. Spectral entropy criteria for structural segmentation in genomic DNA sequences

    International Nuclear Information System (INIS)

    Chechetkin, V.R.; Lobzin, V.V.

    2004-01-01

    The spectral entropy is calculated with Fourier structure factors and characterizes the level of structural ordering in a sequence of symbols. It may efficiently be applied to the assessment and reconstruction of the modular structure in genomic DNA sequences. We present the relevant spectral entropy criteria for the local and non-local structural segmentation in DNA sequences. The results are illustrated with the model examples and analysis of intervening exon-intron segments in the protein-coding regions

  10. Structural constraints in the packaging of bluetongue virus genomic segments.

    Science.gov (United States)

    Burkhardt, Christiane; Sung, Po-Yu; Celma, Cristina C; Roy, Polly

    2014-10-01

    The mechanism used by bluetongue virus (BTV) to ensure the sorting and packaging of its 10 genomic segments is still poorly understood. In this study, we investigated the packaging constraints for two BTV genomic segments from two different serotypes. Segment 4 (S4) of BTV serotype 9 was mutated sequentially and packaging of mutant ssRNAs was investigated by two newly developed RNA packaging assay systems, one in vivo and the other in vitro. Modelling of the mutated ssRNA followed by biochemical data analysis suggested that a conformational motif formed by interaction of the 5' and 3' ends of the molecule was necessary and sufficient for packaging. A similar structural signal was also identified in S8 of BTV serotype 1. Furthermore, the same conformational analysis of secondary structures for positive-sense ssRNAs was used to generate a chimeric segment that maintained the putative packaging motif but contained unrelated internal sequences. This chimeric segment was packaged successfully, confirming that the motif identified directs the correct packaging of the segment. © 2014 The Authors.

  11. Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments.

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    Paul J Wichgers Schreur

    2016-08-01

    Full Text Available The bunyavirus genome comprises a small (S, medium (M, and large (L RNA segment of negative polarity. Although genome segmentation confers evolutionary advantages by enabling genome reassortment events with related viruses, genome segmentation also complicates genome replication and packaging. Accumulating evidence suggests that genomes of viruses with eight or more genome segments are incorporated into virions by highly selective processes. Remarkably, little is known about the genome packaging process of the tri-segmented bunyaviruses. Here, we evaluated, by single-molecule RNA fluorescence in situ hybridization (FISH, the intracellular spatio-temporal distribution and replication kinetics of the Rift Valley fever virus (RVFV genome and determined the segment composition of mature virions. The results reveal that the RVFV genome segments start to replicate near the site of infection before spreading and replicating throughout the cytoplasm followed by translocation to the virion assembly site at the Golgi network. Despite the average intracellular S, M and L genome segments approached a 1:1:1 ratio, major differences in genome segment ratios were observed among cells. We also observed a significant amount of cells lacking evidence of M-segment replication. Analysis of two-segmented replicons and four-segmented viruses subsequently confirmed the previous notion that Golgi recruitment is mediated by the Gn glycoprotein. The absence of colocalization of the different segments in the cytoplasm and the successful rescue of a tri-segmented variant with a codon shuffled M-segment suggested that inter-segment interactions are unlikely to drive the copackaging of the different segments into a single virion. The latter was confirmed by direct visualization of RNPs inside mature virions which showed that the majority of virions lack one or more genome segments. Altogether, this study suggests that RVFV genome packaging is a non-selective process.

  12. Use of bacterially expressed dsRNA to downregulate Entamoeba histolytica gene expression.

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    Carlos F Solis

    Full Text Available BACKGROUND: Modern RNA interference (RNAi methodologies using small interfering RNA (siRNA oligonucleotide duplexes or episomally synthesized hairpin RNA are valuable tools for the analysis of gene function in the protozoan parasite Entamoeba histolytica. However, these approaches still require time-consuming procedures including transfection and drug selection, or costly synthetic molecules. PRINCIPAL FINDINGS: Here we report an efficient and handy alternative for E. histolytica gene down-regulation mediated by bacterial double-stranded RNA (dsRNA targeting parasite genes. The Escherichia coli strain HT115 which is unable to degrade dsRNA, was genetically engineered to produce high quantities of long dsRNA segments targeting the genes that encode E. histolytica beta-tubulin and virulence factor KERP1. Trophozoites cultured in vitro were directly fed with dsRNA-expressing bacteria or soaked with purified dsRNA. Both dsRNA delivery methods resulted in significant reduction of protein expression. In vitro host cell-parasite assays showed that efficient downregulation of kerp1 gene expression mediated by bacterial dsRNA resulted in significant reduction of parasite adhesion and lytic capabilities, thus supporting a major role for KERP1 in the pathogenic process. Furthermore, treatment of trophozoites cultured in microtiter plates, with a repertoire of eighty-five distinct bacterial dsRNA segments targeting E. histolytica genes with unknown function, led to the identification of three genes potentially involved in the growth of the parasite. CONCLUSIONS: Our results showed that the use of bacterial dsRNA is a powerful method for the study of gene function in E. histolytica. This dsRNA delivery method is also technically suitable for the study of a large number of genes, thus opening interesting perspectives for the identification of novel drug and vaccine targets.

  13. Detection and analysis of ancient segmental duplications in mammalian genomes.

    Science.gov (United States)

    Pu, Lianrong; Lin, Yu; Pevzner, Pavel A

    2018-05-07

    Although segmental duplications (SDs) represent hotbeds for genomic rearrangements and emergence of new genes, there are still no easy-to-use tools for identifying SDs. Moreover, while most previous studies focused on recently emerged SDs, detection of ancient SDs remains an open problem. We developed an SDquest algorithm for SD finding and applied it to analyzing SDs in human, gorilla, and mouse genomes. Our results demonstrate that previous studies missed many SDs in these genomes and show that SDs account for at least 6.05% of the human genome (version hg19), a 17% increase as compared to the previous estimate. Moreover, SDquest classified 6.42% of the latest GRCh38 version of the human genome as SDs, a large increase as compared to previous studies. We thus propose to re-evaluate evolution of SDs based on their accurate representation across multiple genomes. Toward this goal, we analyzed the complex mosaic structure of SDs and decomposed mosaic SDs into elementary SDs, a prerequisite for follow-up evolutionary analysis. We also introduced the concept of the breakpoint graph of mosaic SDs that revealed SD hotspots and suggested that some SDs may have originated from circular extrachromosomal DNA (ecDNA), not unlike ecDNA that contributes to accelerated evolution in cancer. © 2018 Pu et al.; Published by Cold Spring Harbor Laboratory Press.

  14. Analysis Of Segmental Duplications In The Pig Genome Based On Next-Generation Sequencing

    DEFF Research Database (Denmark)

    Fadista, João; Bendixen, Christian

    Segmental duplications are >1kb segments of duplicated DNA present in a genome with high sequence identity (>90%). They are associated with genomic rearrangements and provide a significant source of gene and genome evolution within mammalian genomes. Although segmental duplications have been...... extensively studied in other organisms, its analysis in pig has been hampered by the lack of a complete pig genome assembly. By measuring the depth of coverage of Illumina whole-genome shotgun sequencing reads of the Tabasco animal aligned to the latest pig genome assembly (Sus scrofa 10 – based also...... and their associated copy number alterations, focusing on the global organization of these segments and their possible functional significance in porcine phenotypes. This work provides insights into mammalian genome evolution and generates a valuable resource for porcine genomics research...

  15. RNA structural constraints in the evolution of the influenza A virus genome NP segment

    NARCIS (Netherlands)

    A.P. Gultyaev (Alexander); A. Tsyganov-Bodounov (Anton); M.I. Spronken (Monique); S. Van Der Kooij (Sander); R.A.M. Fouchier (Ron); R.C.L. Olsthoorn (René)

    2014-01-01

    textabstractConserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length,

  16. Avian reovirus L2 genome segment sequences and predicted structure/function of the encoded RNA-dependent RNA polymerase protein

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    Xu Wanhong

    2008-12-01

    Full Text Available Abstract Background The orthoreoviruses are infectious agents that possess a genome comprised of 10 double-stranded RNA segments encased in two concentric protein capsids. Like virtually all RNA viruses, an RNA-dependent RNA polymerase (RdRp enzyme is required for viral propagation. RdRp sequences have been determined for the prototype mammalian orthoreoviruses and for several other closely-related reoviruses, including aquareoviruses, but have not yet been reported for any avian orthoreoviruses. Results We determined the L2 genome segment nucleotide sequences, which encode the RdRp proteins, of two different avian reoviruses, strains ARV138 and ARV176 in order to define conserved and variable regions within reovirus RdRp proteins and to better delineate structure/function of this important enzyme. The ARV138 L2 genome segment was 3829 base pairs long, whereas the ARV176 L2 segment was 3830 nucleotides long. Both segments were predicted to encode λB RdRp proteins 1259 amino acids in length. Alignments of these newly-determined ARV genome segments, and their corresponding proteins, were performed with all currently available homologous mammalian reovirus (MRV and aquareovirus (AqRV genome segment and protein sequences. There was ~55% amino acid identity between ARV λB and MRV λ3 proteins, making the RdRp protein the most highly conserved of currently known orthoreovirus proteins, and there was ~28% identity between ARV λB and homologous MRV and AqRV RdRp proteins. Predictive structure/function mapping of identical and conserved residues within the known MRV λ3 atomic structure indicated most identical amino acids and conservative substitutions were located near and within predicted catalytic domains and lining RdRp channels, whereas non-identical amino acids were generally located on the molecule's surfaces. Conclusion The ARV λB and MRV λ3 proteins showed the highest ARV:MRV identity values (~55% amongst all currently known ARV and MRV

  17. Efficient Algorithms for Analyzing Segmental Duplications, Deletions, and Inversions in Genomes

    Science.gov (United States)

    Kahn, Crystal L.; Mozes, Shay; Raphael, Benjamin J.

    Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics consisting of pieces of multiple other segmental duplications. This complex genomic organization complicates analysis of the evolutionary history of these sequences. Earlier, we introduced a genomic distance, called duplication distance, that computes the most parsimonious way to build a target string by repeatedly copying substrings of a source string. We also showed how to use this distance to describe the formation of segmental duplications according to a two-step model that has been proposed to explain human segmental duplications. Here we describe polynomial-time exact algorithms for several extensions of duplication distance including models that allow certain types of substring deletions and inversions. These extensions will permit more biologically realistic analyses of segmental duplications in genomes.

  18. An Inhibitory Motif on the 5’UTR of Several Rotavirus Genome Segments Affects Protein Expression and Reverse Genetics Strategies

    Science.gov (United States)

    Papa, Guido; Eichwald, Catherine; Burrone, Oscar R.

    2016-01-01

    Rotavirus genome consists of eleven segments of dsRNA, each encoding one single protein. Viral mRNAs contain an open reading frame (ORF) flanked by relatively short untranslated regions (UTRs), whose role in the viral cycle remains elusive. Here we investigated the role of 5’UTRs in T7 polymerase-driven cDNAs expression in uninfected cells. The 5’UTRs of eight genome segments (gs3, gs5-6, gs7-11) of the simian SA11 strain showed a strong inhibitory effect on the expression of viral proteins. Decreased protein expression was due to both compromised transcription and translation and was independent of the ORF and the 3’UTR sequences. Analysis of several mutants of the 21-nucleotide long 5’UTR of gs 11 defined an inhibitory motif (IM) represented by its primary sequence rather than its secondary structure. IM was mapped to the 5’ terminal 6-nucleotide long pyrimidine-rich tract 5’-GGY(U/A)UY-3’. The 5’ terminal position within the mRNA was shown to be essentially required, as inhibitory activity was lost when IM was moved to an internal position. We identified two mutations (insertion of a G upstream the 5’UTR and the U to A mutation of the fifth nucleotide of IM) that render IM non-functional and increase the transcription and translation rate to levels that could considerably improve the efficiency of virus helper-free reverse genetics strategies. PMID:27846320

  19. Detection and correction of false segmental duplications caused by genome mis-assembly

    Science.gov (United States)

    2010-01-01

    Diploid genomes with divergent chromosomes present special problems for assembly software as two copies of especially polymorphic regions may be mistakenly constructed, creating the appearance of a recent segmental duplication. We developed a method for identifying such false duplications and applied it to four vertebrate genomes. For each genome, we corrected mis-assemblies, improved estimates of the amount of duplicated sequence, and recovered polymorphisms between the sequenced chromosomes. PMID:20219098

  20. biomvRhsmm: Genomic Segmentation with Hidden Semi-Markov Model

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    Yang Du

    2014-01-01

    Full Text Available High-throughput technologies like tiling array and next-generation sequencing (NGS generate continuous homogeneous segments or signal peaks in the genome that represent transcripts and transcript variants (transcript mapping and quantification, regions of deletion and amplification (copy number variation, or regions characterized by particular common features like chromatin state or DNA methylation ratio (epigenetic modifications. However, the volume and output of data produced by these technologies present challenges in analysis. Here, a hidden semi-Markov model (HSMM is implemented and tailored to handle multiple genomic profile, to better facilitate genome annotation by assisting in the detection of transcripts, regulatory regions, and copy number variation by holistic microarray or NGS. With support for various data distributions, instead of limiting itself to one specific application, the proposed hidden semi-Markov model is designed to allow modeling options to accommodate different types of genomic data and to serve as a general segmentation engine. By incorporating genomic positions into the sojourn distribution of HSMM, with optional prior learning using annotation or previous studies, the modeling output is more biologically sensible. The proposed model has been compared with several other state-of-the-art segmentation models through simulation benchmarking, which shows that our efficient implementation achieves comparable or better sensitivity and specificity in genomic segmentation.

  1. Deciphering the assembly of multi-segment genome complexes in influenza A virus

    OpenAIRE

    Prisner, Simon

    2017-01-01

    Influenza A besitzt ein segmentiertes, achtsträngiges Genom in negativer Orientierung. Die einzelnen Segmente sind in virale Ribonukleoproteinkomplexe (vRNPs) verpackt. Genomische Segmentierung erlaubt es Influenza, zwischen verschiedenen Stämmen Reassortierung zu betreiben, was zur Entstehung von hochgradig virulenten und potentiell pandemischen neuen Stämmen führen kann. Die Existenz eines Packungsmechanismus wird vermutet, der sicherstellt dass exakt ein Segment jeden Typs in neu knospe...

  2. Analysis of high-identity segmental duplications in the grapevine genome

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    Carelli Francesco N

    2011-08-01

    Full Text Available Abstract Background Segmental duplications (SDs are blocks of genomic sequence of 1-200 kb that map to different loci in a genome and share a sequence identity > 90%. SDs show at the sequence level the same characteristics as other regions of the human genome: they contain both high-copy repeats and gene sequences. SDs play an important role in genome plasticity by creating new genes and modeling genome structure. Although data is plentiful for mammals, not much was known about the representation of SDs in plant genomes. In this regard, we performed a genome-wide analysis of high-identity SDs on the sequenced grapevine (Vitis vinifera genome (PN40024. Results We demonstrate that recent SDs (> 94% identity and >= 10 kb in size are a relevant component of the grapevine genome (85 Mb, 17% of the genome sequence. We detected mitochondrial and plastid DNA and genes (10% of gene annotation in segmentally duplicated regions of the nuclear genome. In particular, the nine highest copy number genes have a copy in either or both organelle genomes. Further we showed that several duplicated genes take part in the biosynthesis of compounds involved in plant response to environmental stress. Conclusions These data show the great influence of SDs and organelle DNA transfers in modeling the Vitis vinifera nuclear DNA structure as well as the impact of SDs in contributing to the adaptive capacity of grapevine and the nutritional content of grape products through genome variation. This study represents a step forward in the full characterization of duplicated genes important for grapevine cultural needs and human health.

  3. Segment-specific terminal sequences of Bunyamwera bunyavirus regulate genome replication

    International Nuclear Information System (INIS)

    Barr, John N.; Elliott, Richard M.; Dunn, Ewan F.; Wertz, Gail W.

    2003-01-01

    Bunyamwera virus (BUNV) is the prototype of both the Orthobunyavirus genus and the Bunyaviridae family of segmented negative sense RNA viruses. The tripartite BUNV genome consists of small (S), medium (M), and large (L) segments that are transcribed to give a single mRNA and replicated to generate an antigenome that is the template for synthesis of further genomic RNA strands. We modified an existing cDNA-derived RNA synthesis system to allow identification of BUNV RNA replication and transcription products by direct metabolic labeling. Direct RNA analysis allowed us to distinguish between template activities that affected either RNA replication or mRNA transcription, an ability that was not possible using previous reporter gene expression assays. We generated genome analogs containing the entire nontranslated terminal sequences of the S, M, and L BUNV segments surrounding a common sequence. Analysis of RNAs synthesized from these templates revealed that the relative abilities of BUNV segments to perform RNA replication was M > L > S. Exchange of segment-specific terminal nucleotides identified a 12-nt region located within both the 3' and 5' termini of the M segment that correlated with its high replication ability

  4. Studies on the Virome of the Entomopathogenic Fungus Beauveria bassiana Reveal Novel dsRNA Elements and Mild Hypervirulence.

    Science.gov (United States)

    Kotta-Loizou, Ioly; Coutts, Robert H A

    2017-01-01

    The entomopathogenic fungus Beauveria bassiana has a wide host range and is used as a biocontrol agent against arthropod pests. Mycoviruses have been described in phytopathogenic fungi while in entomopathogenic fungi their presence has been reported only rarely. Here we show that 21.3% of a collection of B. bassiana isolates sourced from worldwide locations, harbor dsRNA elements. Molecular characterization of these elements revealed the prevalence of mycoviruses belonging to the Partitiviridae and Totiviridae families, the smallest reported virus to date, belonging to the family Narnaviridae, and viruses unassigned to a family or genus. Of particular importance is the discovery of members of a newly proposed family Polymycoviridae in B. bassiana. Polymycoviruses, previously designated as tetramycoviruses, consist of four non-conventionally encapsidated capped dsRNAs. The presence of additional non-homologous genomic segments in B. bassiana polymycoviruses and other fungi illustrates the unprecedented dynamic nature of the viral genome. Finally, a comparison of virus-free and virus-infected isogenic lines derived from an exemplar B. bassiana isolate revealed a mild hypervirulent effect of mycoviruses on the growth of their host isolate and on its pathogenicity against the greater wax moth Galleria mellonella, highlighting for the first time the potential of mycoviruses as enhancers of biocontrol agents.

  5. Segmenting the human genome based on states of neutral genetic divergence.

    Science.gov (United States)

    Kuruppumullage Don, Prabhani; Ananda, Guruprasad; Chiaromonte, Francesca; Makova, Kateryna D

    2013-09-03

    Many studies have demonstrated that divergence levels generated by different mutation types vary and covary across the human genome. To improve our still-incomplete understanding of the mechanistic basis of this phenomenon, we analyze several mutation types simultaneously, anchoring their variation to specific regions of the genome. Using hidden Markov models on insertion, deletion, nucleotide substitution, and microsatellite divergence estimates inferred from human-orangutan alignments of neutrally evolving genomic sequences, we segment the human genome into regions corresponding to different divergence states--each uniquely characterized by specific combinations of divergence levels. We then parsed the mutagenic contributions of various biochemical processes associating divergence states with a broad range of genomic landscape features. We find that high divergence states inhabit guanine- and cytosine (GC)-rich, highly recombining subtelomeric regions; low divergence states cover inner parts of autosomes; chromosome X forms its own state with lowest divergence; and a state of elevated microsatellite mutability is interspersed across the genome. These general trends are mirrored in human diversity data from the 1000 Genomes Project, and departures from them highlight the evolutionary history of primate chromosomes. We also find that genes and noncoding functional marks [annotations from the Encyclopedia of DNA Elements (ENCODE)] are concentrated in high divergence states. Our results provide a powerful tool for biomedical data analysis: segmentations can be used to screen personal genome variants--including those associated with cancer and other diseases--and to improve computational predictions of noncoding functional elements.

  6. Nuclear factor 90 uses an ADAR2-like binding mode to recognize specific bases in dsRNA.

    Science.gov (United States)

    Jayachandran, Uma; Grey, Heather; Cook, Atlanta G

    2016-02-29

    Nuclear factors 90 and 45 (NF90 and NF45) form a protein complex involved in the post-transcriptional control of many genes in vertebrates. NF90 is a member of the dsRNA binding domain (dsRBD) family of proteins. RNA binding partners identified so far include elements in 3' untranslated regions of specific mRNAs and several non-coding RNAs. In NF90, a tandem pair of dsRBDs separated by a natively unstructured segment confers dsRNA binding activity. We determined a crystal structure of the tandem dsRBDs of NF90 in complex with a synthetic dsRNA. This complex shows surprising similarity to the tandem dsRBDs from an adenosine-to-inosine editing enzyme, ADAR2 in complex with a substrate RNA. Residues involved in unusual base-specific recognition in the minor groove of dsRNA are conserved between NF90 and ADAR2. These data suggest that, like ADAR2, underlying sequences in dsRNA may influence how NF90 recognizes its target RNAs. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

    NARCIS (Netherlands)

    Uwimana, B.; Smulders, M.J.M.; Hooftman, D.A.P.; Hartman, Y.; van Tienderen, P.H.; Jansen, J.; McHale, L.K.; Michelmore, R.W.; Visser, R.G.F.; van de Wiel, C.C.M.

    2012-01-01

    Background: After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural

  8. Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

    NARCIS (Netherlands)

    Uwimana, B.; Smulders, M.J.M.; Hooftman, D.A.P.; Hartman, Y.; Tienderen, van P.H.; Jansen, J.; McHale, L.K.; Michelmore, R.; Visser, R.G.F.; Wiel, van de C.C.M.

    2012-01-01

    After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The

  9. Assignment of simian rotavirus SA11 temperature-sensitive mutant groups B and E to genome segments

    International Nuclear Information System (INIS)

    Gombold, J.L.; Estes, M.K.; Ramig, R.F.

    1985-01-01

    Recombinant (reassortant) viruses were selected from crosses between temperature-sensitive (ts) mutants of simian rotavirus SA11 and wild-type human rotavirus Wa. The double-stranded genome RNAs of the reassortants were examined by electrophoresis in Tris-glycine-buffered polyacrylamide gels and by dot hybridization with a cloned DNA probe for genome segment 2. Analysis of replacements of genome segments in the reassortants allowed construction of a map correlating genome segments providing functions interchangeable between SA11 and Wa. The reassortants revealed a functional correspondence in order of increasing electrophoretic mobility of genome segments. Analysis of the parental origin of genome segments in ts+ SA11/Wa reassortants derived from the crosses SA11 tsB(339) X Wa and SA11 tsE(1400) X Wa revealed that the group B lesion of tsB(339) was located on genome segment 3 and the group E lesion of tsE(1400) was on segment 8

  10. Assignment of simian rotavirus SA11 temperature-sensitive mutant groups B and E to genome segments

    Energy Technology Data Exchange (ETDEWEB)

    Gombold, J.L.; Estes, M.K.; Ramig, R.F.

    1985-05-01

    Recombinant (reassortant) viruses were selected from crosses between temperature-sensitive (ts) mutants of simian rotavirus SA11 and wild-type human rotavirus Wa. The double-stranded genome RNAs of the reassortants were examined by electrophoresis in Tris-glycine-buffered polyacrylamide gels and by dot hybridization with a cloned DNA probe for genome segment 2. Analysis of replacements of genome segments in the reassortants allowed construction of a map correlating genome segments providing functions interchangeable between SA11 and Wa. The reassortants revealed a functional correspondence in order of increasing electrophoretic mobility of genome segments. Analysis of the parental origin of genome segments in ts+ SA11/Wa reassortants derived from the crosses SA11 tsB(339) X Wa and SA11 tsE(1400) X Wa revealed that the group B lesion of tsB(339) was located on genome segment 3 and the group E lesion of tsE(1400) was on segment 8.

  11. Dicer uses distinct modules for recognizing dsRNA termini.

    Science.gov (United States)

    Sinha, Niladri K; Iwasa, Janet; Shen, Peter S; Bass, Brenda L

    2018-01-19

    Invertebrates rely on Dicer to cleave viral double-stranded RNA (dsRNA), and Drosophila Dicer-2 distinguishes dsRNA substrates by their termini. Blunt termini promote processive cleavage, while 3' overhanging termini are cleaved distributively. To understand this discrimination, we used cryo-electron microscopy to solve structures of Drosophila Dicer-2 alone and in complex with blunt dsRNA. Whereas the Platform-PAZ domains have been considered the only Dicer domains that bind dsRNA termini, unexpectedly, we found that the helicase domain is required for binding blunt, but not 3' overhanging, termini. We further showed that blunt dsRNA is locally unwound and threaded through the helicase domain in an adenosine triphosphate-dependent manner. Our studies reveal a previously unrecognized mechanism for optimizing antiviral defense and set the stage for the discovery of helicase-dependent functions in other Dicers. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  12. Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments

    LENUS (Irish Health Repository)

    OhEigeartaigh, Sean S

    2011-07-26

    Abstract Background In standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline similarity in a BLAST search, the discovery that the genes are located within a region of conserved gene order (synteny) can provide additional evidence that they are orthologs. Thus, for interpreting borderline search results, it would be useful to know whether the syntenic context of a database hit is similar to that of the query. This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically. Results We made use of the synteny information contained in the Yeast Gene Order Browser database for 11 yeast species to carry out a systematic search for protein-coding genes that were overlooked in the original annotations of one or more yeast genomes but which are syntenic with their orthologs. Such genes tend to have been overlooked because they are short, highly divergent, or contain introns. The key features of our software - called SearchDOGS - are that the database entries are classified into sets of genomic segments that are already known to be orthologous, and that very weak BLAST hits are retained for further analysis if their genomic location is similar to that of the query. Using SearchDOGS we identified 595 additional protein-coding genes among the 11 yeast species, including two new genes in Saccharomyces cerevisiae. We found additional genes for the mating pheromone a-factor in six species including Kluyveromyces lactis. Conclusions SearchDOGS has proven highly successful for identifying overlooked genes in the yeast genomes. We anticipate that our approach can be adapted for study of further groups of species, such as bacterial genomes. More generally, the concept of doing sequence similarity searches against databases to which external

  13. Non-canonical ribosomal DNA segments in the human genome, and nucleoli functioning.

    Science.gov (United States)

    Kupriyanova, Natalia S; Netchvolodov, Kirill K; Sadova, Anastasia A; Cherepanova, Marina D; Ryskov, Alexei P

    2015-11-10

    Ribosomal DNA (rDNA) in the human genome is represented by tandem repeats of 43 kb nucleotide sequences that form nucleoli organizers (NORs) on each of five pairs of acrocentric chromosomes. RDNA-similar segments of different lengths are also present on (NOR)(-) chromosomes. Many of these segments contain nucleotide substitutions, supplementary microsatellite clusters, and extended deletions. Recently, it was shown that, in addition to ribosome biogenesis, nucleoli exhibit additional functions, such as cell-cycle regulation and response to stresses. In particular, several stress-inducible loci located in the ribosomal intergenic spacer (rIGS) produce stimuli-specific noncoding nucleolus RNAs. By mapping the 5'/3' ends of the rIGS segments scattered throughout (NOR)(-) chromosomes, we discovered that the bonds in the rIGS that were most often susceptible to disruption in the rIGS were adjacent to, or overlapped with stimuli-specific inducible loci. This suggests the interconnection of the two phenomena - nucleoli functioning and the scattering of rDNA-like sequences on (NOR)(-) chromosomes. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Genome-wide signatures of 'rearrangement hotspots' within segmental duplications in humans.

    Directory of Open Access Journals (Sweden)

    Mohammed Uddin

    Full Text Available The primary objective of this study was to create a genome-wide high resolution map (i.e., >100 bp of 'rearrangement hotspots' which can facilitate the identification of regions capable of mediating de novo deletions or duplications in humans. A hierarchical method was employed to fragment segmental duplications (SDs into multiple smaller SD units. Combining an end space free pairwise alignment algorithm with a 'seed and extend' approach, we have exhaustively searched 409 million alignments to detect complex structural rearrangements within the reference-guided assembly of the NA18507 human genome (18× coverage, including the previously identified novel 4.8 Mb sequence from de novo assembly within this genome. We have identified 1,963 rearrangement hotspots within SDs which encompass 166 genes and display an enrichment of duplicated gene nucleotide variants (DNVs. These regions are correlated with increased non-allelic homologous recombination (NAHR event frequency which presumably represents the origin of copy number variations (CNVs and pathogenic duplications/deletions. Analysis revealed that 20% of the detected hotspots are clustered within the proximal and distal SD breakpoints flanked by the pathogenic deletions/duplications that have been mapped for 24 NAHR-mediated genomic disorders. FISH Validation of selected complex regions revealed 94% concordance with in silico localization of the highly homologous derivatives. Other results from this study indicate that intra-chromosomal recombination is enhanced in genic compared with agenic duplicated regions, and that gene desert regions comprising SDs may represent reservoirs for creation of novel genes. The generation of genome-wide signatures of 'rearrangement hotspots', which likely serve as templates for NAHR, may provide a powerful approach towards understanding the underlying mutational mechanism(s for development of constitutional and acquired diseases.

  15. Characterization of gene expression on genomic segment 7 of infectious salmon anaemia virus

    Directory of Open Access Journals (Sweden)

    Qian Biao

    2007-03-01

    Full Text Available Abstract Background Infectious salmon anaemia (ISA virus (ISAV, an important pathogen of fish that causes disease accompanied by high mortality in marine-farmed Atlantic salmon, is the only species in the genus Isavirus, one of the five genera of the Orthomyxoviridae family. The Isavirus genome consists of eight single-stranded RNA species, and the virions have two surface glycoproteins; haemagglutinin-esterase (HE protein encoded on segment 6 and fusion (F protein encoded on segment 5. Based on the initial demonstration of two 5'-coterminal mRNA transcripts by RT-PCR, ISAV genomic segment 7 was suggested to share a similar coding strategy with segment 7 of influenza A virus, encoding two proteins. However, there appears to be confusion as to the protein sizes predicted from the two open reading frames (ORFs of ISAV segment 7 which has in turn led to confusion of the predicted protein functions. The primary goal of the present work was to clone and express these two ORFs in order to assess whether the predicted protein sizes match those of the expressed proteins so as to clarify the coding assignments, and thereby identify any additional structural proteins of ISAV. Results In the present study we show that ISAV segment 7 encodes 3 proteins with estimated molecular masses of 32, 18, and 9.5 kDa. The 18-kDa and 9.5-kDa products are based on removal of an intron each from the primary transcript (7-ORF1 so that the translation continues in the +2 and +3 reading frames, respectively. The segment 7-ORF1/3 product is variably truncated in the sequence of ISAV isolates of the European genotype. All three proteins are recognized by rabbit antiserum against the 32-kDa product of the primary transcript, as they all share the N-terminal 22 amino acids. This antiserum detected a single 35-kDa protein in Western blots of purified virus, and immunoprecipitated a 32-kDa protein in ISAV-infected TO cells. Immunofluorescence staining of infected cells with the

  16. The Consequences of Reconfiguring the Ambisense S Genome Segment of Rift Valley Fever Virus on Viral Replication in Mammalian and Mosquito Cells and for Genome Packaging

    Science.gov (United States)

    Elliott, Richard M.

    2014-01-01

    Rift Valley fever virus (RVFV, family Bunyaviridae) is a mosquito-borne pathogen of both livestock and humans, found primarily in Sub-Saharan Africa and the Arabian Peninsula. The viral genome comprises two negative-sense (L and M segments) and one ambisense (S segment) RNAs that encode seven proteins. The S segment encodes the nucleocapsid (N) protein in the negative-sense and a nonstructural (NSs) protein in the positive-sense, though NSs cannot be translated directly from the S segment but rather from a specific subgenomic mRNA. Using reverse genetics we generated a virus, designated rMP12:S-Swap, in which the N protein is expressed from the NSs locus and NSs from the N locus within the genomic S RNA. In cells infected with rMP12:S-Swap NSs is expressed at higher levels with respect to N than in cells infected with the parental rMP12 virus. Despite NSs being the main interferon antagonist and determinant of virulence, growth of rMP12:S-Swap was attenuated in mammalian cells and gave a small plaque phenotype. The increased abundance of the NSs protein did not lead to faster inhibition of host cell protein synthesis or host cell transcription in infected mammalian cells. In cultured mosquito cells, however, infection with rMP12:S-Swap resulted in cell death rather than establishment of persistence as seen with rMP12. Finally, altering the composition of the S segment led to a differential packaging ratio of genomic to antigenomic RNA into rMP12:S-Swap virions. Our results highlight the plasticity of the RVFV genome and provide a useful experimental tool to investigate further the packaging mechanism of the segmented genome. PMID:24550727

  17. Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations.

    Science.gov (United States)

    Uwimana, Brigitte; Smulders, Marinus J M; Hooftman, Danny A P; Hartman, Yorike; van Tienderen, Peter H; Jansen, Johannes; McHale, Leah K; Michelmore, Richard W; Visser, Richard G F; van de Wiel, Clemens C M

    2012-03-26

    After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F(1) hybrid was backcrossed to L. serriola to generate BC(1) and BC(2) populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC(1)S(1) and BC(2)S(1)). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC(1)S(1) and BC(2)S(1) hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC(1) and BC(2) hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. As it was shown that the crop contributed QTLs with either a positive

  18. Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

    Directory of Open Access Journals (Sweden)

    Uwimana Brigitte

    2012-03-01

    Full Text Available Abstract Background After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (transgenes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1. Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency. Results Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. Conclusion As it was shown that the crop

  19. Crop to wild introgression in lettuce: following the fate of crop genome segments in backcross populations

    Science.gov (United States)

    2012-01-01

    Background After crop-wild hybridization, some of the crop genomic segments may become established in wild populations through selfing of the hybrids or through backcrosses to the wild parent. This constitutes a possible route through which crop (trans)genes could become established in natural populations. The likelihood of introgression of transgenes will not only be determined by fitness effects from the transgene itself but also by the crop genes linked to it. Although lettuce is generally regarded as self-pollinating, outbreeding does occur at a low frequency. Backcrossing to wild lettuce is a likely pathway to introgression along with selfing, due to the high frequency of wild individuals relative to the rarely occurring crop-wild hybrids. To test the effect of backcrossing on the vigour of inter-specific hybrids, Lactuca serriola, the closest wild relative of cultivated lettuce, was crossed with L. sativa and the F1 hybrid was backcrossed to L. serriola to generate BC1 and BC2 populations. Experiments were conducted on progeny from selfed plants of the backcrossing families (BC1S1 and BC2S1). Plant vigour of these two backcrossing populations was determined in the greenhouse under non-stress and abiotic stress conditions (salinity, drought, and nutrient deficiency). Results Despite the decreasing contribution of crop genomic blocks in the backcross populations, the BC1S1 and BC2S1 hybrids were characterized by a substantial genetic variation under both non-stress and stress conditions. Hybrids were identified that performed equally or better than the wild genotypes, indicating that two backcrossing events did not eliminate the effect of the crop genomic segments that contributed to the vigour of the BC1 and BC2 hybrids. QTLs for plant vigour under non-stress and the various stress conditions were detected in the two populations with positive as well as negative effects from the crop. Conclusion As it was shown that the crop contributed QTLs with either a

  20. A novel monopartite dsRNA virus isolated from the entomopathogenic and nematophagous fungus Purpureocillium lilacinum.

    Science.gov (United States)

    Herrero, Noemi

    2016-12-01

    Purpureocillium lilacinum is a ubiquitous saprophytic fungus commonly isolated from soils and widely known as a biological control agent against phytopathogenic nematodes and pest insects. Mycoviruses infect a wide number of fungal species, but the study of viruses infecting entomopathogenic fungi is still quite recent. In this study, a total of 86 P. lilacinum isolates collected from soil in natural and cultivated habitats throughout the Czech Republic were analyzed; 22 % of the isolates harbored double-stranded RNA (dsRNA) elements with viral characteristics. These results suggest that mycoviruses are common in P. lilacinum. One of the most common dsRNA elements detected in the survey was completely sequenced and corresponded to the 2,864-bp genome of a previously undescribed mycovirus, designated Purpureocillium lilacinum nonsegmented virus 1 (PlNV-1). Phylogenetic analysis of the RNA-dependent RNA polymerase of PlNV-1 indicated that this virus might belong to a new taxon related to the family Partitiviridae.

  1. The most conserved genome segments for life detection on Earth and other planets.

    Science.gov (United States)

    Isenbarger, Thomas A; Carr, Christopher E; Johnson, Sarah Stewart; Finney, Michael; Church, George M; Gilbert, Walter; Zuber, Maria T; Ruvkun, Gary

    2008-12-01

    On Earth, very simple but powerful methods to detect and classify broad taxa of life by the polymerase chain reaction (PCR) are now standard practice. Using DNA primers corresponding to the 16S ribosomal RNA gene, one can survey a sample from any environment for its microbial inhabitants. Due to massive meteoritic exchange between Earth and Mars (as well as other planets), a reasonable case can be made for life on Mars or other planets to be related to life on Earth. In this case, the supremely sensitive technologies used to study life on Earth, including in extreme environments, can be applied to the search for life on other planets. Though the 16S gene has become the standard for life detection on Earth, no genome comparisons have established that the ribosomal genes are, in fact, the most conserved DNA segments across the kingdoms of life. We present here a computational comparison of full genomes from 13 diverse organisms from the Archaea, Bacteria, and Eucarya to identify genetic sequences conserved across the widest divisions of life. Our results identify the 16S and 23S ribosomal RNA genes as well as other universally conserved nucleotide sequences in genes encoding particular classes of transfer RNAs and within the nucleotide binding domains of ABC transporters as the most conserved DNA sequence segments across phylogeny. This set of sequences defines a core set of DNA regions that have changed the least over billions of years of evolution and provides a means to identify and classify divergent life, including ancestrally related life on other planets.

  2. Incompatibility and competitive exclusion of genomic segments between sibling Drosophila species.

    Science.gov (United States)

    Fang, Shu; Yukilevich, Roman; Chen, Ying; Turissini, David A; Zeng, Kai; Boussy, Ian A; Wu, Chung-I

    2012-06-01

    The extent and nature of genetic incompatibilities between incipient races and sibling species is of fundamental importance to our view of speciation. However, with the exception of hybrid inviability and sterility factors, little is known about the extent of other, more subtle genetic incompatibilities between incipient species. Here we experimentally demonstrate the prevalence of such genetic incompatibilities between two young allopatric sibling species, Drosophila simulans and D. sechellia. Our experiments took advantage of 12 introgression lines that carried random introgressed D. sechellia segments in different parts of the D. simulans genome. First, we found that these introgression lines did not show any measurable sterility or inviability effects. To study if these sechellia introgressions in a simulans background contained other fitness consequences, we competed and genetically tracked the marked alleles within each introgression against the wild-type alleles for 20 generations. Strikingly, all marked D. sechellia introgression alleles rapidly decreased in frequency in only 6 to 7 generations. We then developed computer simulations to model our competition results. These simulations indicated that selection against D. sechellia introgression alleles was high (average s = 0.43) and that the marker alleles and the incompatible alleles did not separate in 78% of the introgressions. The latter result likely implies that most introgressions contain multiple genetic incompatibilities. Thus, this study reveals that, even at early stages of speciation, many parts of the genome diverge to a point where introducing foreign elements has detrimental fitness consequences, but which cannot be seen using standard sterility and inviability assays.

  3. An efficient and high fidelity method for amplification, cloning and sequencing of complete tospovirus genomic RNA segments

    Science.gov (United States)

    Amplification and sequencing of the complete M- and S-RNA segments of Tomato spotted wilt virus and Impatiens necrotic spot virus as a single fragment is useful for whole genome sequencing of tospoviruses co-infecting a single host plant. It avoids issues associated with overlapping amplicon-based ...

  4. Occurrence of dsRNA Mycovirus (LeV-FMRI0339 in the Edible Mushroom Lentinula edodes and Meiotic Stability of LeV-FMRI0339 among Monokaryotic Progeny

    Directory of Open Access Journals (Sweden)

    Jung-Mi Kim

    2013-12-01

    Full Text Available dsRNA was found in malformed cultures of Lentinula edodes strain FMRI0339, one of the three most popular sawdust cultivated commercial strains of shiitake, and was also found in healthy-looking fruiting bodies and actively growing mycelia. Cloning of the partial genome of the dsRNA revealed the presence of the RdRp sequence of a novel L. edodes mycovirus (LeV, and sequence comparison of the cloned amplicon showed identical sequences sequence to known RNA-dependent RNA polymerase genes of LeV found in strain HKA. The meiotic stability of dsRNA was examined by measuring the ratio of the presence of dsRNA among sexual monokaryotic progeny. More than 40% of the monokaryotic progeny still contained the dsRNA, indicating the persistence of dsRNA during sexual reproduction. Comparing the mycelia growth of monokaryotic progeny suggested that there appeared to be a tendency toward a lower frequency of virus incidence in actively growing progeny.

  5. Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage

    International Nuclear Information System (INIS)

    Lisal, Jiri; Kainov, Denis E.; Lam, TuKiet T.; Emmett, Mark R.; Wei Hui; Gottlieb, Paul; Marshall, Alan G.; Tuma, Roman

    2006-01-01

    Many viruses employ molecular motors to package their genomes into preformed empty capsids (procapsids). In dsRNA bacteriophages the packaging motor is a hexameric ATPase P4, which is an integral part of the multisubunit procapsid. Structural and biochemical studies revealed a plausible RNA-translocation mechanism for the isolated hexamer. However, little is known about the structure and regulation of the hexamer within the procapsid. Here we use hydrogen-deuterium exchange and mass spectrometry to delineate the interactions of the P4 hexamer with the bacteriophage phi12 procapsid. P4 associates with the procapsid via its C-terminal face. The interactions also stabilize subunit interfaces within the hexamer. The conformation of the virus-bound hexamer is more stable than the hexamer in solution, which is prone to spontaneous ring openings. We propose that the stabilization within the viral capsid increases the packaging processivity and confers selectivity during RNA loading

  6. Molecular Characterization of Bombyx mori Cytoplasmic Polyhedrosis Virus Genome Segment 4

    Science.gov (United States)

    Ikeda, Keiko; Nagaoka, Sumiharu; Winkler, Stefan; Kotani, Kumiko; Yagi, Hiroaki; Nakanishi, Kae; Miyajima, Shigetoshi; Kobayashi, Jun; Mori, Hajime

    2001-01-01

    The complete nucleotide sequence of the genome segment 4 (S4) of Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) was determined. The 3,259-nucleotide sequence contains a single long open reading frame which spans nucleotides 14 to 3187 and which is predicted to encode a protein with a molecular mass of about 130 kDa. Western blot analysis showed that S4 encodes BmCPV protein VP3, which is one of the outer components of the BmCPV virion. Sequence analysis of the deduced amino acid sequence of BmCPV VP3 revealed possible sequence homology with proteins from rice ragged stunt virus (RRSV) S2, Nilaparvata lugens reovirus S4, and Fiji disease fijivirus S4. This may suggest that plant reoviruses originated from insect viruses and that RRSV emerged more recently than other plant reoviruses. A chimeric protein consisting of BmCPV VP3 and green fluorescent protein (GFP) was constructed and expressed with BmCPV polyhedrin using a baculovirus expression vector. The VP3-GFP chimera was incorporated into BmCPV polyhedra and released under alkaline conditions. The results indicate that specific interactions occur between BmCPV polyhedrin and VP3 which might facilitate BmCPV virion occlusion into the polyhedra. PMID:11134312

  7. Engineered chloroplast dsRNA silences cytochrome p450 monooxygenase, V-ATPase and chitin synthase genes in the insect gut and disrupts Helicoverpa zea larval development and pupation.

    Science.gov (United States)

    Jin, Shuangxia; Singh, Nameirakpam D; Li, Lebin; Zhang, Xianlong; Daniell, Henry

    2015-04-01

    In the past two decades, chloroplast genetic engineering has been advanced to achieve high-level protein accumulation but not for down-regulation of targeted genes. Therefore, in this report, lepidopteran chitin synthase (Chi), cytochrome P450 monooxygenase (P450) and V-ATPase dsRNAs were expressed via the chloroplast genome to study RNA interference (RNAi) of target genes in intended hosts. PCR and Southern blot analysis confirmed homoplasmy and site-specific integration of transgene cassettes into the chloroplast genomes. Northern blots and real-time qRT-PCR confirmed abundant processed and unprocessed dsRNA transcripts (up to 3.45 million copies of P450 dsRNAs/μg total RNA); the abundance of cleaved dsRNA was greater than the endogenous psbA transcript. Feeding of leaves expressing P450, Chi and V-ATPase dsRNA decreased transcription of the targeted gene to almost undetectable levels in the insect midgut, likely after further processing of dsRNA in their gut. Consequently, the net weight of larvae, growth and pupation rates were significantly reduced by chloroplast-derived dsRNAs. Taken together, successful expression of dsRNAs via the chloroplast genome for the first time opens the door to study RNA interference/processing within plastids. Most importantly, dsRNA expressed in chloroplasts can be utilized for gene inactivation to confer desired agronomic traits or for various biomedical applications, including down-regulation of dysfunctional genes in cancer or autoimmune disorders, after oral delivery of dsRNA bioencapsulated within plant cells. © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  8. Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses

    Directory of Open Access Journals (Sweden)

    Atkins John F

    2009-03-01

    Full Text Available Abstract The plant-infecting members of the genus Fijivirus (family Reoviridae have linear dsRNA genomes divided into 10 segments, two of which contain two substantial and non-overlapping ORFs, while the remaining eight are apparently monocistronic. However, one of these – namely segment 5 – contains a second long ORF (~200+ codons that overlaps the 3' end of the major ORF (~920–940 codons in the +1 reading frame. In this report, we use bioinformatic techniques to analyze the pattern of base variations across an alignment of fijivirus segment 5 sequences, and show that this 3' ORF has a strong coding signature. Possible translation mechanisms for this unusually positioned ORF are discussed.

  9. The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics.

    Science.gov (United States)

    Dorfman, Kevin D

    2018-02-01

    The development of bright bisintercalating dyes for deoxyribonucleic acid (DNA) in the 1990s, most notably YOYO-1, revolutionized the field of polymer physics in the ensuing years. These dyes, in conjunction with modern molecular biology techniques, permit the facile observation of polymer dynamics via fluorescence microscopy and thus direct tests of different theories of polymer dynamics. At the same time, they have played a key role in advancing an emerging next-generation method known as genome mapping in nanochannels. The effect of intercalation on the bending energy of DNA as embodied by a change in its statistical segment length (or, alternatively, its persistence length) has been the subject of significant controversy. The precise value of the statistical segment length is critical for the proper interpretation of polymer physics experiments and controls the phenomena underlying the aforementioned genomics technology. In this perspective, we briefly review the model of DNA as a wormlike chain and a trio of methods (light scattering, optical or magnetic tweezers, and atomic force microscopy (AFM)) that have been used to determine the statistical segment length of DNA. We then outline the disagreement in the literature over the role of bisintercalation on the bending energy of DNA, and how a multiscale biomechanical approach could provide an important model for this scientifically and technologically relevant problem.

  10. Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent.

    Directory of Open Access Journals (Sweden)

    Abdulahi Alfonso-Morales

    Full Text Available Infectious bursal disease (IBD is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV strains worldwide.Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population.This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for

  11. Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent.

    Science.gov (United States)

    Alfonso-Morales, Abdulahi; Rios, Liliam; Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L; Bertran, Kateri; Frías, Maria T; Ganges, Llilianne; Díaz de Arce, Heidy; Majó, Natàlia; Núñez, José I; Pérez, Lester J

    2015-01-01

    Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population. This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for molecular

  12. Molecular characterization of genome segments 1 and 3 encoding two capsid proteins of Antheraea mylitta cytoplasmic polyhedrosis virus

    Directory of Open Access Journals (Sweden)

    Chakrabarti Mrinmay

    2010-08-01

    Full Text Available Abstract Background Antheraea mylitta cytoplasmic polyhedrosis virus (AmCPV, a cypovirus of Reoviridae family, infects Indian non-mulberry silkworm, Antheraea mylitta, and contains 11 segmented double stranded RNA (S1-S11 in its genome. Some of its genome segments (S2 and S6-S11 have been previously characterized but genome segments encoding viral capsid have not been characterized. Results In this study genome segments 1 (S1 and 3 (S3 of AmCPV were converted to cDNA, cloned and sequenced. S1 consisted of 3852 nucleotides, with one long ORF of 3735 nucleotides and could encode a protein of 1245 amino acids with molecular mass of ~141 kDa. Similarly, S3 consisted of 3784 nucleotides having a long ORF of 3630 nucleotides and could encode a protein of 1210 amino acids with molecular mass of ~137 kDa. BLAST analysis showed 20-22% homology of S1 and S3 sequence with spike and capsid proteins, respectively, of other closely related cypoviruses like Bombyx mori CPV (BmCPV, Lymantria dispar CPV (LdCPV, and Dendrolimus punctatus CPV (DpCPV. The ORFs of S1 and S3 were expressed as 141 kDa and 137 kDa insoluble His-tagged fusion proteins, respectively, in Escherichia coli M15 cells via pQE-30 vector, purified through Ni-NTA chromatography and polyclonal antibodies were raised. Immunoblot analysis of purified polyhedra, virion particles and virus infected mid-gut cells with the raised anti-p137 and anti-p141 antibodies showed specific immunoreactive bands and suggest that S1 and S3 may code for viral structural proteins. Expression of S1 and S3 ORFs in insect cells via baculovirus recombinants showed to produce viral like particles (VLPs by transmission electron microscopy. Immunogold staining showed that S3 encoded proteins self assembled to form viral outer capsid and VLPs maintained their stability at different pH in presence of S1 encoded protein. Conclusion Our results of cloning, sequencing and functional analysis of AmCPV S1 and S3 indicate that S3

  13. How clonal is clonal? Genome plasticity across multicellular segments of a "Candidatus Marithrix sp." filament from sulfidic, briny seafloor sediments in the Gulf of Mexico

    Directory of Open Access Journals (Sweden)

    Verena Salman-Carvalho

    2016-08-01

    Full Text Available Candidatus Marithrix is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria. This group of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 µm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, Candidatus Marithrix was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the Candidatus Marithrix genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98-100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes - the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or 'intrasegmental sequence heterogeneity' (ISH events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament.

  14. Delivery of dsRNA through topical feeding for RNA interference in the citrus sap piercing-sucking hemipteran, Diaphorina citri.

    Science.gov (United States)

    Killiny, Nabil; Kishk, Abdelaziz

    2017-06-01

    RNA interference (RNAi) is a powerful means to study functional genomics in insects. The delivery of dsRNA is a challenging step in the development of RNAi assay. Here, we describe a new delivery method to increase the effectiveness of RNAi in the Asian citrus psyllid Diaphorina citri. Bromophenol blue droplets were topically applied to fifth instar nymphs and adults on the ventral side of the thorax between the three pairs of legs. In addition to video recordings that showed sucking of the bromophenol blue by the stylets, dissected guts turned blue indicating that the uptake was through feeding. Thus, we called the method topical feeding. We targeted the abnormal wing disc gene (awd), also called nucleoside diphosphate kinase (NDPK), as a reporter gene to prove the uptake of dsRNA via this method of delivery. Our results showed that dsRNA-awd caused reduction of awd expression and nymph mortality. Survival and lifespan of adults emerged from treated nymphs and treated adults were affected. Silencing awd caused wing malformation in the adults emerged from treated nymphs. Topical feeding as a delivery of dsRNA is highly efficient for both nymphs and adults. The described method could be used to increase the efficiency of RNAi in D. citri and other sap piercing-sucking hemipterans. © 2017 Wiley Periodicals, Inc.

  15. Segmental allotetraploidy and allelic interactions in buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.) as revealed by genome mapping.

    Science.gov (United States)

    Jessup, R W; Burson, B L; Burow, O; Wang, Y W; Chang, C; Li, Z; Paterson, A H; Hussey, M A

    2003-04-01

    Linkage analyses increasingly complement cytological and traditional plant breeding techniques by providing valuable information regarding genome organization and transmission genetics of complex polyploid species. This study reports a genome map of buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.). Maternal and paternal maps were constructed with restriction fragment length polymorphisms (RFLPs) segregating in 87 F1 progeny from an intraspecific cross between two heterozygous genotypes. A survey of 862 heterologous cDNAs and gDNAs from across the Poaceae, as well as 443 buffelgrass cDNAs, yielded 100 and 360 polymorphic probes, respectively. The maternal map included 322 RFLPs, 47 linkage groups, and 3464 cM, whereas the paternal map contained 245 RFLPs, 42 linkage groups, and 2757 cM. Approximately 70 to 80% of the buffelgrass genome was covered, and the average marker spacing was 10.8 and 11.3 cM on the respective maps. Preferential pairing was indicated between many linkage groups, which supports cytological reports that buffelgrass is a segmental allotetraploid. More preferential pairing (disomy) was found in the maternal than paternal parent across linkage groups (55 vs. 38%) and loci (48 vs. 15%). Comparison of interval lengths in 15 allelic bridges indicated significantly less meiotic recombination in paternal gametes. Allelic interactions were detected in four regions of the maternal map and were absent in the paternal map.

  16. Structural Basis for dsRNA Recognition by NS1 Protein of Influenza A Virus

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, A.; Wong, S; Yuan, Y

    2009-01-01

    Influenza A viruses are important human pathogens causing periodic pandemic threats. Nonstructural protein 1 (NS1) protein of influenza A virus (NS1A) shields the virus against host defense. Here, we report the crystal structure of NS1A RNA-binding domain (RBD) bound to a double-stranded RNA (dsRNA) at 1.7A. NS1A RBD forms a homodimer to recognize the major groove of A-form dsRNA in a length-independent mode by its conserved concave surface formed by dimeric anti-parallel alpha-helices. dsRNA is anchored by a pair of invariable arginines (Arg38) from both monomers by extensive hydrogen bonds. In accordance with the structural observation, isothermal titration calorimetry assay shows that the unique Arg38-Arg38 pair and two Arg35-Arg46 pairs are crucial for dsRNA binding, and that Ser42 and Thr49 are also important for dsRNA binding. Agrobacterium co-infiltration assay further supports that the unique Arg38 pair plays important roles in dsRNA binding in vivo.

  17. Statistical properties of thermodynamically predicted RNA secondary structures in viral genomes

    Science.gov (United States)

    Spanò, M.; Lillo, F.; Miccichè, S.; Mantegna, R. N.

    2008-10-01

    By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a simple random null hypothesis. The detected hairpin structures of RNA secondary structures are present both in coding and in noncoding regions for the four groups of viruses categorized as dsDNA, dsRNA, ssDNA and ssRNA. For all groups, hairpin structures of RNA secondary structures are detected more frequently than expected for a random null hypothesis in noncoding rather than in coding regions. However, potential RNA secondary structures are also present in coding regions of dsDNA group. In fact, we detect evolutionary conserved RNA secondary structures in conserved coding and noncoding regions of a large set of complete genomes of dsDNA herpesviruses.

  18. Increased RNAi Efficacy in Spodoptera exigua via the Formulation of dsRNA With Guanylated Polymers

    Directory of Open Access Journals (Sweden)

    Olivier Christiaens

    2018-04-01

    Full Text Available Lepidoptera comprise some of the most devastating herbivorous pest insects worldwide. One of the most promising novel pest control strategies is exploiting the RNA interference (RNAi mechanism to target essential genes for knockdown and incite toxic effects in the target species without harming other organisms in the ecosystem. However, many insects are refractory to oral RNAi, often due to rapid degradation of ingested dsRNA in their digestive system. This is the case for many lepidopteran insects, including the beet armyworm Spodoptera exigua, which is characterized by a very alkaline gut environment (pH > 9.0 and a strong intestinal nucleolytic activity. In this research, guanidine-containing polymers were developed to protect dsRNA against nucleolytic degradation, specifically in high pH environments. First, their ability to protect dsRNA against nucleolytic degradation in gut juice of the beet armyworm S. exigua was investigated ex vivo. Polymers with high guanidine content provided a strong protection against nucleolytic degradation at pH 11, protecting the dsRNA for up to 30 h. Next, cellular uptake of the dsRNA and the polyplexes in lepidopteran CF203 midgut cells was investigated by confocal microscopy, showing that the polymer also enhanced cellular uptake of the dsRNA. Finally, in vivo feeding RNAi bioassays demonstrated that using these guanidine-containing polymer nanoparticles led to an increased RNAi efficiency in S. exigua. Targeting the essential gene chitin synthase B, we observed that the mortality increased to 53% in the polymer-protected dsRNA treatment compared to only 16% with the naked dsRNA and found that polymer-protected dsRNA completely halted the development of the caterpillars. These results show that using guanylated polymers as a formulation strategy can prevent degradation of dsRNA in the alkaline and strongly nucleolytic gut of lepidopteran insects. Furthermore, the polymer also enhances cellular uptake in

  19. Ebolavirus VP35 uses a bimodal strategy to bind dsRNA for innate immune suppression

    Energy Technology Data Exchange (ETDEWEB)

    Kimberlin, Christopher R.; Bornholdt, Zachary A.; Li, Sheng; Woods, Jr., Virgil L.; MacRae, Ian J.; Saphire, Erica Ollmann (Scripps); (UCSD)

    2010-03-12

    Ebolavirus causes a severe hemorrhagic fever and is divided into five distinct species, of which Reston ebolavirus is uniquely nonpathogenic to humans. Disease caused by ebolavirus is marked by early immunosuppression of innate immune signaling events, involving silencing and sequestration of double-stranded RNA (dsRNA) by the viral protein VP35. Here we present unbound and dsRNA-bound crystal structures of the dsRNA-binding domain of Reston ebolavirus VP35. The structures show that VP35 forms an unusual, asymmetric dimer on dsRNA binding, with each of the monomers binding dsRNA in a different way: one binds the backbone whereas the other caps the terminus. Additional SAXS, DXMS, and dsRNA-binding experiments presented here support a model of cooperative dsRNA recognition in which binding of the first monomer assists binding of the next monomer of the oligomeric VP35 protein. This work illustrates how ebolavirus VP35 could mask key recognition sites of molecules such as RIG-I, MDA-5, and Dicer to silence viral dsRNA in infection.

  20. dsRNA binding properties of RDE-4 and TRBP reflect their distinct roles in RNAi.

    Science.gov (United States)

    Parker, Greg S; Maity, Tuhin Subhra; Bass, Brenda L

    2008-12-26

    Double-stranded RNA (dsRNA)-binding proteins facilitate Dicer functions in RNA interference. Caenorhabditis elegans RDE-4 facilitates cleavage of long dsRNA to small interfering RNA (siRNA), while human trans-activation response RNA-binding protein (TRBP) functions downstream to pass siRNA to the RNA-induced silencing complex. We show that these distinct in vivo roles are reflected in in vitro binding properties. RDE-4 preferentially binds long dsRNA, while TRBP binds siRNA with an affinity that is independent of dsRNA length. These properties are mechanistically based on the fact that RDE-4 binds cooperatively, via contributions from multiple domains, while TRBP binds noncooperatively. Our studies offer a paradigm for how dsRNA-binding proteins, which are not sequence specific, discern dsRNA length. Additionally, analyses of the ability of RDE-4 deletion constructs and RDE-4/TRBP chimeras to reconstitute Dicer activity suggest RDE-4 promotes activity using its dsRNA-binding motif 2 to bind dsRNA, its linker region to interact with Dicer, and its C-terminus for Dicer activation.

  1. dsRNA binding characterization of full length recombinant wild type and mutants Zaire ebolavirus VP35.

    Science.gov (United States)

    Zinzula, Luca; Esposito, Francesca; Pala, Daniela; Tramontano, Enzo

    2012-03-01

    The Ebola viruses (EBOVs) VP35 protein is a multifunctional major virulence factor involved in EBOVs replication and evasion of the host immune system. EBOV VP35 is an essential component of the viral RNA polymerase, it is a key participant of the nucleocapsid assembly and it inhibits the innate immune response by antagonizing RIG-I like receptors through its dsRNA binding function and, hence, by suppressing the host type I interferon (IFN) production. Insights into the VP35 dsRNA recognition have been recently revealed by structural and functional analysis performed on its C-terminus protein. We report the biochemical characterization of the Zaire ebolavirus (ZEBOV) full-length recombinant VP35 (rVP35)-dsRNA binding function. We established a novel in vitro magnetic dsRNA binding pull down assay, determined the rVP35 optimal dsRNA binding parameters, measured the rVP35 equilibrium dissociation constant for heterologous in vitro transcribed dsRNA of different length and short synthetic dsRNA of 8bp, and validated the assay for compound screening by assessing the inhibitory ability of auryntricarboxylic acid (IC(50) value of 50μg/mL). Furthermore, we compared the dsRNA binding properties of full length wt rVP35 with those of R305A, K309A and R312A rVP35 mutants, which were previously reported to be defective in dsRNA binding-mediated IFN inhibition, showing that the latter have measurably increased K(d) values for dsRNA binding and modified migration patterns in mobility shift assays with respect to wt rVP35. Overall, these results provide the first characterization of the full-length wt and mutants VP35-dsRNA binding functions. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

    Directory of Open Access Journals (Sweden)

    Eichler Evan E

    2008-08-01

    Full Text Available Abstract Background It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs. This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements. Results Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA. Conclusion We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.

  3. RDE-4 preferentially binds long dsRNA and its dimerization is necessary for cleavage of dsRNA to siRNA.

    Science.gov (United States)

    Parker, Greg S; Eckert, Debra M; Bass, Brenda L

    2006-05-01

    In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA-binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not required in subsequent steps, and how RDE-4 distinguishes between long dsRNA and short siRNA is unclear. We report the first detailed analysis of RDE-4 binding, using purified recombinant RDE-4 and various truncated proteins. We find that, similar to other dsRBPs, RDE-4 is not sequence-specific. However, consistent with its in vivo roles, RDE-4 binds with higher affinity to long dsRNA. We also observe that RDE-4 is a homodimer in solution, and that the C-terminal domain of the protein is required for dimerization. Using extracts from wild-type and rde-4 mutant C. elegans, we show that the C-terminal dimerization domain is required for the production of siRNA. Our findings suggest a model for RDE-4 function during the initiation of RNAi.

  4. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

    International Nuclear Information System (INIS)

    Cheng, Xiaofei; Deng, Ping; Cui, Hongguang; Wang, Aiming

    2015-01-01

    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  5. Visualizing double-stranded RNA distribution and dynamics in living cells by dsRNA binding-dependent fluorescence complementation

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Xiaofei [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang 310036 (China); Deng, Ping; Cui, Hongguang [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada); Wang, Aiming, E-mail: aiming.wang@agr.gc.ca [Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario N5V 4T3 (Canada)

    2015-11-15

    Double-stranded RNA (dsRNA) is an important type of RNA that plays essential roles in diverse cellular processes in eukaryotic organisms and a hallmark in infections by positive-sense RNA viruses. Currently, no in vivo technology has been developed for visualizing dsRNA in living cells. Here, we report a dsRNA binding-dependent fluorescence complementation (dRBFC) assay that can be used to efficiently monitor dsRNA distribution and dynamics in vivo. The system consists of two dsRNA-binding proteins, which are fused to the N- and C-terminal halves of the yellow fluorescent protein (YFP). Binding of the two fusion proteins to a common dsRNA brings the split YFP halves in close proximity, leading to the reconstitution of the fluorescence-competent structure and restoration of fluorescence. Using this technique, we were able to visualize the distribution and trafficking of the replicative RNA intermediates of positive-sense RNA viruses in living cells. - Highlights: • A live-cell imaging system was developed for visualizing dsRNA in vivo. • It uses dsRNA binding proteins fused with two halves of a fluorescent protein. • Binding to a common dsRNA enables the reporter to become fluorescent. • The system can efficiently monitor viral RNA replication in living cells.

  6. Sequence analysis of the PIP5K locus in Eimeria maxima provides further evidence for eimerian genome plasticity and segmental organization.

    Science.gov (United States)

    Song, B K; Pan, M Z; Lau, Y L; Wan, K L

    2014-07-29

    Commercial flocks infected by Eimeria species parasites, including Eimeria maxima, have an increased risk of developing clinical or subclinical coccidiosis; an intestinal enteritis associated with increased mortality rates in poultry. Currently, infection control is largely based on chemotherapy or live vaccines; however, drug resistance is common and vaccines are relatively expensive. The development of new cost-effective intervention measures will benefit from unraveling the complex genetic mechanisms that underlie host-parasite interactions, including the identification and characterization of genes encoding proteins such as phosphatidylinositol 4-phosphate 5-kinase (PIP5K). We previously identified a PIP5K coding sequence within the E. maxima genome. In this study, we analyzed two bacterial artificial chromosome clones presenting a ~145-kb E. maxima (Weybridge strain) genomic region spanning the PIP5K gene locus. Sequence analysis revealed that ~95% of the simple sequence repeats detected were located within regions comparable to the previously described feature-rich segments of the Eimeria tenella genome. Comparative sequence analysis with the orthologous E. maxima (Houghton strain) region revealed a moderate level of conserved synteny. Unique segmental organizations and telomere-like repeats were also observed in both genomes. A number of incomplete transposable elements were detected and further scrutiny of these elements in both orthologous segments revealed interesting nesting events, which may play a role in facilitating genome plasticity in E. maxima. The current analysis provides more detailed information about the genome organization of E. maxima and may help to reveal genotypic differences that are important for expression of traits related to pathogenicity and virulence.

  7. The variability of the large genomic segment of Tahyna orthobunyavirus and an all-atom exploration of its anti-viral drug resistance

    Czech Academy of Sciences Publication Activity Database

    Kilian, Patrik; Valdés, James J.; Lecina-Casas, D.; Chrudimský, T.; Růžek, Daniel

    2013-01-01

    Roč. 20, 2013-Dec (2013), s. 304-311 ISSN 1567-1348 R&D Projects: GA ČR GAP502/11/2116; GA MŠk(CZ) EE2.3.30.0032 Institutional support: RVO:60077344 Keywords : Tahyna virus * Orthobunyavirus * California complex * Genetic variability * Large genomic segment Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.264, year: 2013

  8. Production and application of long dsRNA in mammalian cells

    Czech Academy of Sciences Publication Activity Database

    Chalupníková, Kateřina; Nejepínská, Jana; Svoboda, Petr

    2013-01-01

    Roč. 942, 20.2.2013 (2013), s. 291-314 ISSN 1940-6029 Institutional support: RVO:68378050 Keywords : dsRNA * RNAi * IFN response * transgenic RNAi * OAS (2′5′-oligoadenylate synthetase) Subject RIV: EB - Genetics ; Molecular Biology

  9. Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity.

    Science.gov (United States)

    Fajardo, Teodoro; Sung, Po-Yu; Roy, Polly

    2015-12-01

    Bluetongue virus (BTV) causes hemorrhagic disease in economically important livestock. The BTV genome is organized into ten discrete double-stranded RNA molecules (S1-S10) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly. To substantiate and extend these studies, we have investigated the RNA sorting and packaging mechanisms with a new experimental approach using inhibitory oligonucleotides. Putative packaging signals present in the 3'untranslated regions of BTV segments were targeted by a number of nuclease resistant oligoribonucleotides (ORNs) and their effects on virus replication in cell culture were assessed. ORNs complementary to the 3' UTR of BTV RNAs significantly inhibited virus replication without affecting protein synthesis. Same ORNs were found to inhibit complex formation when added to a novel RNA-RNA interaction assay which measured the formation of supramolecular complexes between and among different RNA segments. ORNs targeting the 3'UTR of BTV segment 10, the smallest RNA segment, were shown to be the most potent and deletions or substitution mutations of the targeted sequences diminished the RNA complexes and abolished the recovery of viable viruses using reverse genetics. Cell-free capsid assembly/RNA packaging assay also confirmed that the inhibitory ORNs could interfere with RNA packaging and further substitution mutations within the putative RNA packaging sequence have identified the recognition sequence concerned. Exchange of 3'UTR between segments have further demonstrated that RNA recognition was segment specific, most likely acting as part of the secondary structure of the entire genomic segment. Our data confirm that genome packaging in this segmented dsRNA virus occurs via the formation of supramolecular complexes formed by the interaction of specific sequences located in the 3' UTRs. Additionally, the inhibition of packaging in-trans with inhibitory ORNs

  10. Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments.

    Science.gov (United States)

    Kargarfard, Fatemeh; Sami, Ashkan; Mohammadi-Dehcheshmeh, Manijeh; Ebrahimie, Esmaeil

    2016-11-16

    Recent (2013 and 2009) zoonotic transmission of avian or porcine influenza to humans highlights an increase in host range by evading species barriers. Gene reassortment or antigenic shift between viruses from two or more hosts can generate a new life-threatening virus when the new shuffled virus is no longer recognized by antibodies existing within human populations. There is no large scale study to help understand the underlying mechanisms of host transmission. Furthermore, there is no clear understanding of how different segments of the influenza genome contribute in the final determination of host range. To obtain insight into the rules underpinning host range determination, various supervised machine learning algorithms were employed to mine reassortment changes in different viral segments in a range of hosts. Our multi-host dataset contained whole segments of 674 influenza strains organized into three host categories: avian, human, and swine. Some of the sequences were assigned to multiple hosts. In point of fact, the datasets are a form of multi-labeled dataset and we utilized a multi-label learning method to identify discriminative sequence sites. Then algorithms such as CBA, Ripper, and decision tree were applied to extract informative and descriptive association rules for each viral protein segment. We found informative rules in all segments that are common within the same host class but varied between different hosts. For example, for infection of an avian host, HA14V and NS1230S were the most important discriminative and combinatorial positions. Host range identification is facilitated by high support combined rules in this study. Our major goal was to detect discriminative genomic positions that were able to identify multi host viruses, because such viruses are likely to cause pandemic or disastrous epidemics.

  11. Genomic segments RNA1 and RNA2 of Prunus necrotic ringspot virus codetermine viral pathogenicity to adapt to alternating natural Prunus hosts.

    Science.gov (United States)

    Cui, Hongguang; Hong, Ni; Wang, Guoping; Wang, Aiming

    2013-05-01

    Prunus necrotic ringspot virus (PNRSV) affects Prunus fruit production worldwide. To date, numerous PNRSV isolates with diverse pathological properties have been documented. To study the pathogenicity of PNRSV, which directly or indirectly determines the economic losses of infected fruit trees, we have recently sequenced the complete genome of peach isolate Pch12 and cherry isolate Chr3, belonging to the pathogenically aggressive PV32 group and mild PV96 group, respectively. Here, we constructed the Chr3- and Pch12-derived full-length cDNA clones that were infectious in the experimental host cucumber and their respective natural Prunus hosts. Pch12-derived clones induced much more severe symptoms than Chr3 in cucumber, and the pathogenicity discrepancy between Chr3 and Pch12 was associated with virus accumulation. By reassortment of genomic segments, swapping of partial genomic segments, and site-directed mutagenesis, we identified the 3' terminal nucleotide sequence (1C region) in RNA1 and amino acid K at residue 279 in RNA2-encoded P2 as the severe virulence determinants in Pch12. Gain-of-function experiments demonstrated that both the 1C region and K279 of Pch12 were required for severe virulence and high levels of viral accumulation. Our results suggest that PNRSV RNA1 and RNA2 codetermine viral pathogenicity to adapt to alternating natural Prunus hosts, likely through mediating viral accumulation.

  12. Non-Invasive Delivery of dsRNA into De-Waxed Tick Eggs by Electroporation

    Science.gov (United States)

    Ruiz, Newton; de Abreu, Leonardo Araujo; Parizi, Luís Fernando; Kim, Tae Kwon; Mulenga, Albert; Braz, Gloria Regina Cardoso; Vaz, Itabajara da Silva; Logullo, Carlos

    2015-01-01

    RNA interference-mediated gene silencing was shown to be an efficient tool for validation of targets that may become anti-tick vaccine components. Here, we demonstrate the application of this approach in the validation of components of molecular signaling cascades, such as the Protein Kinase B (AKT) / Glycogen Synthase Kinase (GSK) axis during tick embryogenesis. It was shown that heptane and hypochlorite treatment of tick eggs can remove wax, affecting corium integrity and but not embryo development. Evidence of AKT and GSK dsRNA delivery into de-waxed eggs of via electroporation is provided. Primers designed to amplify part of the dsRNA delivered into the electroporated eggs dsRNA confirmed its entry in eggs. In addition, it was shown that electroporation is able to deliver the fluorescent stain, 4',6-diamidino-2-phenylindole (DAPI). To confirm gene silencing, a second set of primers was designed outside the dsRNA sequence of target gene. In this assay, the suppression of AKT and GSK transcripts (approximately 50% reduction in both genes) was demonstrated in 7-day-old eggs. Interestingly, silencing of GSK in 7-day-old eggs caused 25% reduction in hatching. Additionally, the effect of silencing AKT and GSK on embryo energy metabolism was evaluated. As expected, knockdown of AKT, which down regulates GSK, the suppressor of glycogen synthesis, decreased glycogen content in electroporated eggs. These data demonstrate that electroporation of de-waxed R. microplus eggs could be used for gene silencing in tick embryos, and improve the knowledge about arthropod embryogenesis. PMID:26091260

  13. Accumulation of dsRNA in endosomes contributes to inefficient RNA interference in the fall armyworm, Spodoptera frugiperda.

    Science.gov (United States)

    Yoon, June-Sun; Gurusamy, Dhandapani; Palli, Subba Reddy

    2017-11-01

    RNA interference (RNAi) efficiency varies among insects studied. The barriers for successful RNAi include the presence of double-stranded ribonucleases (dsRNase) in the lumen and hemolymph that could potentially digest double-stranded RNA (dsRNA) and the variability in the transport of dsRNA into and within the cells. We recently showed that the dsRNAs are transported into lepidopteran cells, but they are not processed into small interference RNAs (siRNAs) because they are trapped in acidic bodies. In the current study, we focused on the identification of acidic bodies in which dsRNAs accumulate in Sf9 cells. Time-lapse imaging studies showed that dsRNAs enter Sf9 cells and accumulate in acidic bodies within 20 min after their addition to the medium. CypHer-5E-labeled dsRNA also accumulated in the midgut and fat body dissected from Spodoptera frugiperda larvae with similar patterns observed in Sf9 cells. Pharmacological inhibitor assays showed that the dsRNAs use clathrin mediated endocytosis pathway for transport into the cells. We investigated the potential dsRNA accumulation sites employing LysoTracker and double labeling experiments using the constructs to express a fusion of green fluorescence protein with early or late endosomal marker proteins and CypHer-5E-labeled dsRNA. Interestingly, CypHer-5E-labeled dsRNA accumulated predominantly in early and late endosomes. These data suggest that entrapment of internalized dsRNA in endosomes is one of the major factors contributing to inefficient RNAi response in lepidopteran insects. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Optimization of recombinant bacteria expressing dsRNA to enhance insecticidal activity against a lepidopteran insect, Spodoptera exigua.

    Directory of Open Access Journals (Sweden)

    Mohammad Vatanparast

    Full Text Available Double-stranded RNA (dsRNA has been applied to control insect pests due to its induction of RNA interference (RNAi of a specific target gene expression. However, developing dsRNA-based insecticidal agent has been a great challenge especially against lepidopteran insect pests due to variations in RNAi efficiency. The objective of this study was to screen genes of chymotrypsins (SeCHYs essential for the survival of the beet armyworm, Spodoptera exigua, to construct insecticidal dsRNA. In addition, an optimal oral delivery method was developed using recombinant bacteria. At least 7 SeCHY genes were predicted from S. exigua transcriptomes. Subsequent analyses indicated that SeCHY2 was widely expressed in different developmental stages and larval tissues by RT-PCR and its expression knockdown by RNAi caused high mortality along with immunosuppression. However, a large amount of dsRNA was required to efficiently kill late instars of S. exigua because of high RNase activity in their midgut lumen. To minimize dsRNA degradation, bacterial expression and formulation of dsRNA were performed in HT115 Escherichia coli using L4440 expression vector. dsRNA (300 bp specific to SeCHY2 overexpressed in E. coli was toxic to S. exigua larvae after oral administration. To enhance dsRNA release from E. coli, bacterial cells were sonicated before oral administration. RNAi efficiency of sonicated bacteria was significantly increased, causing higher larval mortality at oral administration. Moreover, targeting young larvae possessing weak RNase activity in the midgut lumen significantly enhanced RNAi efficiency and subsequent insecticidal activity against S. exigua.

  15. Viral Delivery of dsRNA for Control of Insect Agricultural Pests and Vectors of Human Disease: Prospects and Challenges

    Directory of Open Access Journals (Sweden)

    Anna Kolliopoulou

    2017-06-01

    Full Text Available RNAi is applied as a new and safe method for pest control in agriculture but efficiency and specificity of delivery of dsRNA trigger remains a critical issue. Various agents have been proposed to augment dsRNA delivery, such as engineered micro-organisms and synthetic nanoparticles, but the use of viruses has received relatively little attention. Here we present a critical view of the potential of the use of recombinant viruses for efficient and specific delivery of dsRNA. First of all, it requires the availability of plasmid-based reverse genetics systems for virus production, of which an overview is presented. For RNA viruses, their application seems to be straightforward since dsRNA is produced as an intermediate molecule during viral replication, but DNA viruses also have potential through the production of RNA hairpins after transcription. However, application of recombinant virus for dsRNA delivery may not be straightforward in many cases, since viruses can encode RNAi suppressors, and virus-induced silencing effects can be determined by the properties of the encoded RNAi suppressor. An alternative is virus-like particles that retain the efficiency and specificity determinants of natural virions but have encapsidated non-replicating RNA. Finally, the use of viruses raises important safety issues which need to be addressed before application can proceed.

  16. Effect of PEG biofunctional spacers and TAT peptide on dsRNA loading on gold nanoparticles

    International Nuclear Information System (INIS)

    Sanz, Vanesa; Conde, João; Hernández, Yulán; Baptista, Pedro V.; Ibarra, M. R.; Fuente, Jesús M. de la

    2012-01-01

    The surface chemistry of gold nanoparticles (AuNPs) plays a critical role in the self-assembly of thiolated molecules and in retaining the biological function of the conjugated biomolecules. According to the well-established gold–thiol interaction the undefined ionic species on citrate-reduced gold nanoparticle surface can be replaced with a self-assembled monolayer of certain thiolate derivatives and other biomolecules. Understanding the effect of such derivatives in the functionalization of several types of biomolecules, such as PEGs, peptides or nucleic acids, has become a significant challenge. Here, an approach to attach specific biomolecules to the AuNPs (∼14 nm) surface is presented together with a study of their effect in the functionalization with other specific derivatives. The effect of biofunctional spacers such as thiolated poly(ethylene glycol) (PEG) chains and a positive peptide, TAT, in dsRNA loading on AuNPs is reported. Based on the obtained data, we hypothesize that loading of oligonucleotides onto the AuNP surface may be controlled by ionic and weak interactions positioning the entry of the oligo through the PEG layer. We demonstrate that there is a synergistic effect of the TAT peptide and PEG chains with specific functional groups on the enhancement of dsRNA loading onto AuNPs.

  17. Effect of PEG biofunctional spacers and TAT peptide on dsRNA loading on gold nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Sanz, Vanesa; Conde, Joao; Hernandez, Yulan [Universidad de Zaragoza, Instituto de Nanociencia de Aragon (Spain); Baptista, Pedro V. [Universidade Nova de Lisboa, Departamento de Ciencias da Vida, Faculdade de Ciencias e Tecnologia, Centro de Investigacao em Genetica Molecular Humana (Portugal); Ibarra, M. R.; Fuente, Jesus M. de la, E-mail: jmfuente@unizar.es [Universidad de Zaragoza, Instituto de Nanociencia de Aragon (Spain)

    2012-06-15

    The surface chemistry of gold nanoparticles (AuNPs) plays a critical role in the self-assembly of thiolated molecules and in retaining the biological function of the conjugated biomolecules. According to the well-established gold-thiol interaction the undefined ionic species on citrate-reduced gold nanoparticle surface can be replaced with a self-assembled monolayer of certain thiolate derivatives and other biomolecules. Understanding the effect of such derivatives in the functionalization of several types of biomolecules, such as PEGs, peptides or nucleic acids, has become a significant challenge. Here, an approach to attach specific biomolecules to the AuNPs ({approx}14 nm) surface is presented together with a study of their effect in the functionalization with other specific derivatives. The effect of biofunctional spacers such as thiolated poly(ethylene glycol) (PEG) chains and a positive peptide, TAT, in dsRNA loading on AuNPs is reported. Based on the obtained data, we hypothesize that loading of oligonucleotides onto the AuNP surface may be controlled by ionic and weak interactions positioning the entry of the oligo through the PEG layer. We demonstrate that there is a synergistic effect of the TAT peptide and PEG chains with specific functional groups on the enhancement of dsRNA loading onto AuNPs.

  18. Molecular evolution of avian reovirus: evidence for genetic diversity and reassortment of the S-class genome segments and multiple cocirculating lineages

    International Nuclear Information System (INIS)

    Liu, Hung J.; Lee, Long H.; Hsu, Hsiao W.; Kuo, Liam C.; Liao, Ming H.

    2003-01-01

    Nucleotide sequences of the S-class genome segments of 17 field-isolates and vaccine strains of avian reovirus (ARV) isolated over a 23-year period from different hosts, pathotypes, and geographic locations were examined and analyzed to define phylogenetic profiles and evolutionary mechanism. The S1 genome segment showed noticeably higher divergence than the other S-class genes. The σC-encoding gene has evolved into six distinct lineages. In contrast, the other S-class genes showed less divergence than that of the σC-encoding gene and have evolved into two to three major distinct lineages, respectively. Comparative sequence analysis provided evidence indicating extensive sequence divergence between ARV and other orthoreoviruses. The evolutionary trees of each gene were distinct, suggesting that these genes evolve in an independent manner. Furthermore, variable topologies were the result of frequent genetic reassortment among multiple cocirculating lineages. Results showed genetic diversity correlated more closely with date of isolation and geographic sites than with host species and pathotypes. This is the first evidence demonstrating genetic variability among circulating ARVs through a combination of evolutionary mechanisms involving multiple cocirculating lineages and genetic reassortment. The evolutionary rates and patterns of base substitutions were examined. The evolutionary rate for the σC-encoding gene and σC protein was higher than for the other S-class genes and other family of viruses. With the exception of the σC-encoding gene, which nonsynonymous substitutions predominate over synonymous, the evolutionary process of the other S-class genes can be explained by the neutral theory of molecular evolution. Results revealed that synonymous substitutions predominate over nonsynonymous in the S-class genes, even though genetic diversity and substitution rates vary among the viruses

  19. Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers.

    Science.gov (United States)

    Edet, Offiong Ukpong; Kim, June-Sik; Okamoto, Masanori; Hanada, Kousuke; Takeda, Tomoyuki; Kishii, Masahiro; Gorafi, Yasir Serag Alnor; Tsujimoto, Hisashi

    2018-03-27

    The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses. We generated de novo DNA and mRNA sequence information of L. racemosus and developed 110 polymorphic PCR-based markers from the data, and to complement the PCR markers, DArT-seq genotyping was applied to develop additional 9990 SNP markers. Approximately 52% of all the markers enabled us to clearly genotype 22 wheat-L. racemosus chromosome introgression lines, and L. racemosus chromosome-specific markers were highly efficient in detailed characterization of the translocation and recombination lines analyzed. A further analysis revealed remarkable transferability of the PCR markers to three other important Triticeae perennial species: L. mollis, Psathyrostachys huashanica and Elymus ciliaris, indicating their suitability for characterizing wheat-alien chromosome introgressions carrying chromosomes of these genomes. The efficiency of the markers in characterizing wheat-L. racemosus chromosome introgression lines proves their reliability, and their high transferability further broadens their scope of application. This is the first report on sequencing and development of markers from L. racemosus genome and the application of DArT-seq to develop markers from a perennial wild relative of wheat, marking a paradigm shift from the seeming concentration of the technology on cultivated species. Integration of these markers with appropriate cytogenetic methods would accelerate development and characterization of wheat-alien chromosome introgression lines.

  20. Genomes

    National Research Council Canada - National Science Library

    Brown, T. A. (Terence A.)

    2002-01-01

    ... of genome expression and replication processes, and transcriptomics and proteomics. This text is richly illustrated with clear, easy-to-follow, full color diagrams, which are downloadable from the book's website...

  1. The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans.

    Science.gov (United States)

    Tabara, Hiroaki; Yigit, Erbay; Siomi, Haruhiko; Mello, Craig C

    2002-06-28

    Double-stranded (ds) RNA induces potent gene silencing, termed RNA interference (RNAi). At an early step in RNAi, an RNaseIII-related enzyme, Dicer (DCR-1), processes long-trigger dsRNA into small interfering RNAs (siRNAs). DCR-1 is also required for processing endogenous regulatory RNAs called miRNAs, but how DCR-1 recognizes its endogenous and foreign substrates is not yet understood. Here we show that the C. elegans RNAi pathway gene, rde-4, encodes a dsRNA binding protein that interacts during RNAi with RNA identical to the trigger dsRNA. RDE-4 protein also interacts in vivo with DCR-1, RDE-1, and a conserved DExH-box helicase. Our findings suggest a model in which RDE-4 and RDE-1 function together to detect and retain foreign dsRNA and to present this dsRNA to DCR-1 for processing.

  2. Evaluation of deoxynivalenol production in dsRNA Carrying and Cured Fusarium graminearum isolates by AYT1 expressing transformed tobacco

    Directory of Open Access Journals (Sweden)

    Samira Shahbazi

    2015-12-01

    Full Text Available Introduction: Fusarium head blight (FHB, is the most destructive disease of wheat, producing the mycotoxin deoxynivalenol, a protein synthesis inhibitor, which is harmful to humans and livestock. dsRNAmycoviruses-infected-isolates of Fusariumgraminearum, showed changes in morphological and pathogenicity phenotypes including reduced virulence towards wheat and decreased production of trichothecene mycotoxin (deoxynivalenol: DON. Materials and methods: Previous studies indicated that over expression of yeast acetyl transferase gene (ScAYT1 encoding a 3-O trichothecene acetyl transferase that converts deoxynivalenol to a less toxic acetylated form, leads to suppression of the deoxynivalenol sensitivity in pdr5 yeast mutants. To identify whether ScAYT1 over-expression in transgenic tobacco plants can deal with mycotoxin (deoxynivalenol in fungal extract and studying the effect of dsRNA contamination on detoxification and resistance level, we have treated T1 AYT1 transgenic tobacco seedlings with complete extraction of normal F. graminearum isolate carrying dsRNA metabolites. First, we introduced AYT1into the model tobacco plants through Agrobacterium-mediated transformation in an attempt to detoxify deoxynivalenol. Results: In vitro tests with extraction of dsRNA carrying and cured isolates of F. graminearum and 10 ppm of deoxynivalenol indicated variable resistance levels in transgenic plants. Discussion and conclusion: The results of this study indicate that the transgene expression AYT1 and Fusarium infection to dsRNA can induce tolerance to deoxynivalenol, followed by increased resistance to Fusarium head blight disease of wheat.

  3. Grass genomes

    OpenAIRE

    Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

    1998-01-01

    For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

  4. Temporal analysis of reassortment and molecular evolution of Cucumber mosaic virus: Extra clues from its segmented genome

    Energy Technology Data Exchange (ETDEWEB)

    Ohshima, Kazusato, E-mail: ohshimak@cc.saga-u.ac.jp [Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga (Japan); The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima (Japan); Matsumoto, Kosuke [Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga (Japan); Yasaka, Ryosuke [Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga (Japan); The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima (Japan); Nishiyama, Mai; Soejima, Kenta [Laboratory of Plant Virology, Faculty of Agriculture, Saga University, Saga (Japan); Korkmaz, Savas [Department of Plant Protection, Faculty of Agriculture, University of Canakkale Onsekiz Mart, Canakkale (Turkey); Ho, Simon Y.W. [School of Biological Sciences, University of Sydney, Sydney, New South Wales (Australia); Gibbs, Adrian J. [Emeritus Faculty, Australian National University, Canberra (Australia); Takeshita, Minoru [Laboratory of Plant Pathology, Faculty of Agriculture, University of Miyazaki, Miyazaki (Japan)

    2016-01-15

    Cucumber mosaic virus (CMV) is a damaging pathogen of over 200 mono- and dicotyledonous crop species worldwide. It has the broadest known host range of any virus, but the timescale of its evolution is unknown. To investigate the evolutionary history of this virus, we obtained the genomic sequences of 40 CMV isolates from brassicas sampled in Iran, Turkey and Japan, and combined them with published sequences. Our synonymous ('silent') site analyses revealed that the present CMV population is the progeny of a single ancestor existing 1550–2600 years ago, but that the population mostly radiated 295–545 years ago. We found that the major CMV lineages are not phylogeographically confined, but that recombination and reassortment is restricted to local populations and that no reassortant lineage is more than 251 years old. Our results highlight the different evolutionary patterns seen among viral pathogens of brassica crops across the world. - Highlights: • Present-day CMV lineages had a most recent common ancestor 1550–2600 years ago. • The CMV population mostly radiated less than 295–545 years ago. • No reassortant found in the present populations is more than 251 years old. • The open-reading frames evolve at around 2.3–4.7×10{sup −4} substitutions/site/year. • Synonymous codons of CMV seem to have a more precise temporal signal than all codons.

  5. Marburg virus VP35 can both fully coat the backbone and cap the ends of dsRNA for interferon antagonism.

    Directory of Open Access Journals (Sweden)

    Shridhar Bale

    2012-09-01

    Full Text Available Filoviruses, including Marburg virus (MARV and Ebola virus (EBOV, cause fatal hemorrhagic fever in humans and non-human primates. All filoviruses encode a unique multi-functional protein termed VP35. The C-terminal double-stranded (dsRNA-binding domain (RBD of VP35 has been implicated in interferon antagonism and immune evasion. Crystal structures of the VP35 RBD from two ebolaviruses have previously demonstrated that the viral protein caps the ends of dsRNA. However, it is not yet understood how the expanses of dsRNA backbone, between the ends, are masked from immune surveillance during filovirus infection. Here, we report the crystal structure of MARV VP35 RBD bound to dsRNA. In the crystal structure, molecules of dsRNA stack end-to-end to form a pseudo-continuous oligonucleotide. This oligonucleotide is continuously and completely coated along its sugar-phosphate backbone by the MARV VP35 RBD. Analysis of dsRNA binding by dot-blot and isothermal titration calorimetry reveals that multiple copies of MARV VP35 RBD can indeed bind the dsRNA sugar-phosphate backbone in a cooperative manner in solution. Further, MARV VP35 RBD can also cap the ends of the dsRNA in solution, although this arrangement was not captured in crystals. Together, these studies suggest that MARV VP35 can both coat the backbone and cap the ends, and that for MARV, coating of the dsRNA backbone may be an essential mechanism by which dsRNA is masked from backbone-sensing immune surveillance molecules.

  6. Whole-Genome Analysis of a Novel Fish Reovirus (MsReV Discloses Aquareovirus Genomic Structure Relationship with Host in Saline Environments

    Directory of Open Access Journals (Sweden)

    Zhong-Yuan Chen

    2015-08-01

    Full Text Available Aquareoviruses are serious pathogens of aquatic animals. Here, genome characterization and functional gene analysis of a novel aquareovirus, largemouth bass Micropterus salmoides reovirus (MsReV, was described. It comprises 11 dsRNA segments (S1–S11 covering 24,024 bp, and encodes 12 putative proteins including the inclusion forming-related protein NS87 and the fusion-associated small transmembrane (FAST protein NS22. The function of NS22 was confirmed by expression in fish cells. Subsequently, MsReV was compared with two representative aquareoviruses, saltwater fish turbot Scophthalmus maximus reovirus (SMReV and freshwater fish grass carp reovirus strain 109 (GCReV-109. MsReV NS87 and NS22 genes have the same structure and function with those of SMReV, whereas GCReV-109 is either missing the coiled-coil region in NS79 or the gene-encoding NS22. Significant similarities are also revealed among equivalent genome segments between MsReV and SMReV, but a difference is found between MsReV and GCReV-109. Furthermore, phylogenetic analysis showed that 13 aquareoviruses could be divided into freshwater and saline environments subgroups, and MsReV was closely related to SMReV in saline environments. Consequently, these viruses from hosts in saline environments have more genomic structural similarities than the viruses from hosts in freshwater. This is the first study of the relationships between aquareovirus genomic structure and their host environments.

  7. In C. elegans, high levels of dsRNA allow RNAi in the absence of RDE-4.

    Science.gov (United States)

    Habig, Jeffrey W; Aruscavage, P Joseph; Bass, Brenda L

    2008-01-01

    C. elegans Dicer requires an accessory double-stranded RNA binding protein, RDE-4, to enact the first step of RNA interference, the cleavage of dsRNA to produce siRNA. While RDE-4 is typically essential for RNAi, we report that in the presence of high concentrations of trigger dsRNA, rde-4 deficient animals are capable of silencing a transgene. By multiple criteria the silencing occurs by the canonical RNAi pathway. For example, silencing is RDE-1 dependent and exhibits a decrease in the targeted mRNA in response to an increase in siRNA. We also find that high concentrations of dsRNA trigger lead to increased accumulation of primary siRNAs, consistent with the existence of a rate-limiting step during the conversion of primary to secondary siRNAs. Our studies also revealed that transgene silencing occurs at low levels in the soma, even in the presence of ADARs, and that at least some siRNAs accumulate in a temperature-dependent manner. We conclude that an RNAi response varies with different conditions, and this may allow an organism to tailor a response to specific environmental signals.

  8. In C. elegans, high levels of dsRNA allow RNAi in the absence of RDE-4.

    Directory of Open Access Journals (Sweden)

    Jeffrey W Habig

    Full Text Available C. elegans Dicer requires an accessory double-stranded RNA binding protein, RDE-4, to enact the first step of RNA interference, the cleavage of dsRNA to produce siRNA. While RDE-4 is typically essential for RNAi, we report that in the presence of high concentrations of trigger dsRNA, rde-4 deficient animals are capable of silencing a transgene. By multiple criteria the silencing occurs by the canonical RNAi pathway. For example, silencing is RDE-1 dependent and exhibits a decrease in the targeted mRNA in response to an increase in siRNA. We also find that high concentrations of dsRNA trigger lead to increased accumulation of primary siRNAs, consistent with the existence of a rate-limiting step during the conversion of primary to secondary siRNAs. Our studies also revealed that transgene silencing occurs at low levels in the soma, even in the presence of ADARs, and that at least some siRNAs accumulate in a temperature-dependent manner. We conclude that an RNAi response varies with different conditions, and this may allow an organism to tailor a response to specific environmental signals.

  9. Structure of RDE-4 dsRBDs and mutational studies provide insights into dsRNA recognition in the Caenorhabditis elegans RNAi pathway.

    Science.gov (United States)

    Chiliveri, Sai Chaitanya; Deshmukh, Mandar V

    2014-02-15

    The association of RDE-4 (RNAi defective 4), a protein containing two dsRBDs (dsRNA-binding domains), with long dsRNA and Dcr-1 (Dicer1 homologue) initiates the siRNA pathway in Caenorhabditis elegans. Unlike its homologues in higher eukaryotes, RDE-4 dsRBDs possess weak (micromolar) affinity for short dsRNA. With increasing length of dsRNA, RDE-4 exhibits enhanced affinity due to co-operativity. The linker and dsRBD2 are indispensable for RDE-4's simultaneous interaction with dsRNA and Dcr-1. In the present study, we have determined the solution structures of RDE-4 constructs that contain both dsRBDs and the linker region. In addition to the canonical dsRBD fold, both dsRBDs of RDE-4 show modified structural features such as truncation in the β1-β2 loop that rationalize RDE-4's relatively weak dsRNA affinity. Structure and binding studies demonstrate that dsRBD2 plays a decisive role in the RDE-4-dsRNA interaction; however, in contrast with previous findings, we found ephemeral interaction of RDE-4 dsRBD1 with dsRNA. More importantly, mutations in two tandem lysine residues (Lys217 and Lys218) in dsRBD2 impair RDE-4's dsRNA-binding ability and could obliterate RNAi initiation in C. elegans. Additionally, we postulate a structural basis for the minimal requirement of linker and dsRBD2 for RDE-4's association with dsRNA and Dcr-1.

  10. Identification and differentiation of the twenty six bluetongue virus serotypes by RT-PCR amplification of the serotype-specific genome segment 2.

    Directory of Open Access Journals (Sweden)

    Narender S Maan

    Full Text Available Bluetongue (BT is an arthropod-borne viral disease, which primarily affects ruminants in tropical and temperate regions of the world. Twenty six bluetongue virus (BTV serotypes have been recognised worldwide, including nine from Europe and fifteen in the United States. Identification of BTV serotype is important for vaccination programmes and for BTV epidemiology studies. Traditional typing methods (virus isolation and serum or virus neutralisation tests (SNT or VNT are slow (taking weeks, depend on availability of reference virus-strains or antisera and can be inconclusive. Nucleotide sequence analyses and phylogenetic comparisons of genome segment 2 (Seg-2 encoding BTV outer-capsid protein VP2 (the primary determinant of virus serotype were completed for reference strains of BTV-1 to 26, as well as multiple additional isolates from different geographic and temporal origins. The resulting Seg-2 database has been used to develop rapid (within 24 h and reliable RT-PCR-based typing assays for each BTV type. Multiple primer-pairs (at least three designed for each serotype were widely tested, providing an initial identification of serotype by amplification of a cDNA product of the expected size. Serotype was confirmed by sequencing of the cDNA amplicons and phylogenetic comparisons to previously characterised reference strains. The results from RT-PCR and sequencing were in perfect agreement with VNT for reference strains of all 26 BTV serotypes, as well as the field isolates tested. The serotype-specific primers showed no cross-amplification with reference strains of the remaining 25 serotypes, or multiple other isolates of the more closely related heterologous BTV types. The primers and RT-PCR assays developed in this study provide a rapid, sensitive and reliable method for the identification and differentiation of the twenty-six BTV serotypes, and will be updated periodically to maintain their relevance to current BTV distribution and

  11. An accessory to the 'Trinity': SR-As are essential pathogen sensors of extracellular dsRNA, mediating entry and leading to subsequent type I IFN responses.

    Directory of Open Access Journals (Sweden)

    Stephanie J DeWitte-Orr

    2010-03-01

    Full Text Available Extracellular RNA is becoming increasingly recognized as a signaling molecule. Virally derived double stranded (dsRNA released into the extracellular space during virus induced cell lysis acts as a powerful inducer of classical type I interferon (IFN responses; however, the receptor that mediates this response has not been identified. Class A scavenger receptors (SR-As are likely candidates due to their cell surface expression and ability to bind nucleic acids. In this study, we investigated a possible role for SR-As in mediating type I IFN responses induced by extracellular dsRNA in fibroblasts, a predominant producer of IFNbeta. Fibroblasts were found to express functional SR-As, even SR-A species thought to be macrophage specific. SR-A specific competitive ligands significantly blocked extracellular dsRNA binding, entry and subsequent interferon stimulated gene (ISG induction. Candidate SR-As were systematically investigated using RNAi and the most dramatic inhibition in responses was observed when all candidate SR-As were knocked down in unison. Partial inhibition of dsRNA induced antiviral responses was observed in vivo in SR-AI/II(-/- mice compared with WT controls. The role of SR-As in mediating extracellular dsRNA entry and subsequent induced antiviral responses was observed in both murine and human fibroblasts. SR-As appear to function as 'carriers', facilitating dsRNA entry and delivery to the established dsRNA sensing receptors, specifically TLR3, RIGI and MDA-5. Identifying SR-As as gatekeepers of the cell, mediating innate antiviral responses, represents a novel function for this receptor family and provides insight into how cells recognize danger signals associated with lytic virus infections. Furthermore, the implications of a cell surface receptor capable of recognizing extracellular RNA may exceed beyond viral immunity to mediating other important innate immune functions.

  12. Complete Genome Sequence of a Double-Stranded RNA Virus from Avocado

    OpenAIRE

    Villanueva, Francisco; Sabanadzovic, Sead; Valverde, Rodrigo A.; Navas-Castillo, Jesús

    2012-01-01

    A number of avocado (Persea americana) cultivars are known to contain high-molecular-weight double-stranded RNA (dsRNA) molecules for which a viral nature has been suggested, although sequence data are not available. Here we report the cloning and complete sequencing of a 13.5-kbp dsRNA virus isolated from avocado and show that it corresponds to the genome of a new species of the genus Endornavirus (family Endornaviridae), tentatively named Persea americana endornavirus (PaEV).

  13. Complete Genome Sequence of a Double-Stranded RNA Virus from Avocado

    Science.gov (United States)

    Villanueva, Francisco; Sabanadzovic, Sead; Valverde, Rodrigo A.

    2012-01-01

    A number of avocado (Persea americana) cultivars are known to contain high-molecular-weight double-stranded RNA (dsRNA) molecules for which a viral nature has been suggested, although sequence data are not available. Here we report the cloning and complete sequencing of a 13.5-kbp dsRNA virus isolated from avocado and show that it corresponds to the genome of a new species of the genus Endornavirus (family Endornaviridae), tentatively named Persea americana endornavirus (PaEV). PMID:22205720

  14. Larval application of sodium channel homologous dsRNA restores pyrethroid insecticide susceptibility in a resistant adult mosquito population.

    Science.gov (United States)

    Bona, Ana Caroline Dalla; Chitolina, Rodrigo Faitta; Fermino, Marise Lopes; de Castro Poncio, Lisiane; Weiss, Avital; Lima, José Bento Pereira; Paldi, Nitzan; Bernardes, Emerson Soares; Henen, Jonathan; Maori, Eyal

    2016-07-14

    Mosquitoes host and pass on to humans a variety of disease-causing pathogens such as infectious viruses and other parasitic microorganisms. The emergence and spread of insecticide resistance is threatening the effectiveness of current control measures for common mosquito vector borne diseases, such as malaria, dengue and Zika. Therefore, the emerging resistance to the widely used pyrethroid insecticides is an alarming problem for public health. Herein we demonstrated the use of RNA interference (RNAi) to increase susceptibility of adult mosquitoes to a widely used pyrethroid insecticide. Experiments were performed on a field-collected pyrethroid resistant strain of Ae. aegypti (Rio de Janeiro; RJ). Larvae from the resistant Ae. aegypti population were soaked with double-stranded RNAs (dsRNAs) that correspond either to voltage-gate sodium channel (VGSC), P-glycoprotein, or P450 detoxification genes and reared to adulthood. Adult mortality rates in the presence of various Deltamethrin pyrethroid concentrations were used to assess mosquito insecticide susceptibility. We characterized the RJ Ae. aegypti strain with regard to its level of resistance to a pyrethroid insecticide and found that it was approximately 6 times more resistant to Deltamethrin compared to the laboratory Rockefeller strain. The RJ strain displayed a higher frequency of Val1016Ile and Phe1534Cys substitutions of the VGSC gene. The resistant strain also displayed a higher basal expression level of VGSC compared to the Rockefeller strain. When dsRNA-treated mosquitoes were subjected to a standard pyrethroid contact bioassay, only dsRNA targeting VGSC increased the adult mortality of the pyrethroid resistant strain. The dsRNA treatment proved effective in increasing adult mosquito susceptibility over a range of pyrethroid concentrations and these results were associated with dsRNA-specific small interfering RNAs in treated adults, and the corresponding specific down regulation of VGSC gene expression

  15. The Human dsRNA binding protein PACT is unable to functionally substitute for the Drosophila dsRNA binding protein R2D2 [v1; ref status: indexed, http://f1000r.es/201

    Directory of Open Access Journals (Sweden)

    Benjamin K Dickerman

    2013-10-01

    Full Text Available The primary function of the dsRNA binding protein (dsRBP PACT/RAX is to activate the dsRNA dependent protein kinase PKR in response to stress signals.  Additionally, it has been identified as a component of the small RNA processing pathway.  A role for PACT/RAX in this pathway represents an important interplay between two modes of post-transcriptional gene regulation.  The function of PACT/RAX in this context is poorly understood.  Thus, additional models are required to clarify the mechanism by which PACT/RAX functions.  In this study, Drosophila melanogaster was employed to identify functionally orthologous dsRNA-binding proteins.  Transgenic Drosophila expressing human PACT were generated to determine whether PACT is capable of functionally substituting for the Drosophila dsRBP R2D2, which has a well-defined role in small RNA biogenesis.  Results presented here indicate that PACT is unable to substitute for R2D2 at the whole organism level.

  16. Active Segmentation.

    Science.gov (United States)

    Mishra, Ajay; Aloimonos, Yiannis

    2009-01-01

    The human visual system observes and understands a scene/image by making a series of fixations. Every fixation point lies inside a particular region of arbitrary shape and size in the scene which can either be an object or just a part of it. We define as a basic segmentation problem the task of segmenting that region containing the fixation point. Segmenting the region containing the fixation is equivalent to finding the enclosing contour- a connected set of boundary edge fragments in the edge map of the scene - around the fixation. This enclosing contour should be a depth boundary.We present here a novel algorithm that finds this bounding contour and achieves the segmentation of one object, given the fixation. The proposed segmentation framework combines monocular cues (color/intensity/texture) with stereo and/or motion, in a cue independent manner. The semantic robots of the immediate future will be able to use this algorithm to automatically find objects in any environment. The capability of automatically segmenting objects in their visual field can bring the visual processing to the next level. Our approach is different from current approaches. While existing work attempts to segment the whole scene at once into many areas, we segment only one image region, specifically the one containing the fixation point. Experiments with real imagery collected by our active robot and from the known databases 1 demonstrate the promise of the approach.

  17. Specific RNA Interference in Caenorhabditis elegans by Ingested dsRNA Expressed in Bacillus subtilis

    NARCIS (Netherlands)

    Lezzerini, M.; van de Ven, K.; Veerman, M.; Brul, S.; Budovskaya, Y.V.

    2015-01-01

    In nematodes, genome-wide RNAi-screening has been widely used as a rapid and efficient method to identify genes involved in the aging processes. By far the easiest way of inducing RNA interference (RNAi) in Caenorhabditis elegans is by feeding Escherichia coli that expresses specific double stranded

  18. Segmentation: Identification of consumer segments

    DEFF Research Database (Denmark)

    Høg, Esben

    2005-01-01

    It is very common to categorise people, especially in the advertising business. Also traditional marketing theory has taken in consumer segments as a favorite topic. Segmentation is closely related to the broader concept of classification. From a historical point of view, classification has its...... origin in other sciences as for example biology, anthropology etc. From an economic point of view, it is called segmentation when specific scientific techniques are used to classify consumers to different characteristic groupings. What is the purpose of segmentation? For example, to be able to obtain...... a basic understanding of grouping people. Advertising agencies may use segmentation totarget advertisements, while food companies may usesegmentation to develop products to various groups of consumers. MAPP has for example investigated the positioning of fish in relation to other food products...

  19. Segmental Vitiligo.

    Science.gov (United States)

    van Geel, Nanja; Speeckaert, Reinhart

    2017-04-01

    Segmental vitiligo is characterized by its early onset, rapid stabilization, and unilateral distribution. Recent evidence suggests that segmental and nonsegmental vitiligo could represent variants of the same disease spectrum. Observational studies with respect to its distribution pattern point to a possible role of cutaneous mosaicism, whereas the original stated dermatomal distribution seems to be a misnomer. Although the exact pathogenic mechanism behind the melanocyte destruction is still unknown, increasing evidence has been published on the autoimmune/inflammatory theory of segmental vitiligo. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. A Single RNaseIII Domain Protein from Entamoeba histolytica Has dsRNA Cleavage Activity and Can Help Mediate RNAi Gene Silencing in a Heterologous System.

    Science.gov (United States)

    Pompey, Justine M; Foda, Bardees; Singh, Upinder

    2015-01-01

    Dicer enzymes process double-stranded RNA (dsRNA) into small RNAs that target gene silencing through the RNA interference (RNAi) pathway. Dicer enzymes are complex, multi-domain RNaseIII proteins, however structural minimalism of this protein has recently emerged in parasitic and fungal systems. The most minimal Dicer, Saccharomyces castellii Dicer1, has a single RNaseIII domain and two double stranded RNA binding domains. In the protozoan parasite Entamoeba histolytica 27nt small RNAs are abundant and mediate silencing, yet no canonical Dicer enzyme has been identified. Although EhRNaseIII does not exhibit robust dsRNA cleavage in vitro, it can process dsRNA in the RNAi-negative background of Saccharomyces cerevisiae, and in conjunction with S. castellii Argonaute1 can partially reconstitute the RNAi pathway. Thus, although EhRNaseIII lacks the domain architecture of canonical or minimal Dicer enzymes, it has dsRNA processing activity that contributes to gene silencing via RNAi. Our data advance the understanding of small RNA biogenesis in Entamoeba as well as broaden the spectrum of non-canonical Dicer enzymes that contribute to the RNAi pathway.

  1. A Single RNaseIII Domain Protein from Entamoeba histolytica Has dsRNA Cleavage Activity and Can Help Mediate RNAi Gene Silencing in a Heterologous System.

    Directory of Open Access Journals (Sweden)

    Justine M Pompey

    Full Text Available Dicer enzymes process double-stranded RNA (dsRNA into small RNAs that target gene silencing through the RNA interference (RNAi pathway. Dicer enzymes are complex, multi-domain RNaseIII proteins, however structural minimalism of this protein has recently emerged in parasitic and fungal systems. The most minimal Dicer, Saccharomyces castellii Dicer1, has a single RNaseIII domain and two double stranded RNA binding domains. In the protozoan parasite Entamoeba histolytica 27nt small RNAs are abundant and mediate silencing, yet no canonical Dicer enzyme has been identified. Although EhRNaseIII does not exhibit robust dsRNA cleavage in vitro, it can process dsRNA in the RNAi-negative background of Saccharomyces cerevisiae, and in conjunction with S. castellii Argonaute1 can partially reconstitute the RNAi pathway. Thus, although EhRNaseIII lacks the domain architecture of canonical or minimal Dicer enzymes, it has dsRNA processing activity that contributes to gene silencing via RNAi. Our data advance the understanding of small RNA biogenesis in Entamoeba as well as broaden the spectrum of non-canonical Dicer enzymes that contribute to the RNAi pathway.

  2. Computational sequence analysis of predicted long dsRNA transcriptomes of major crops reveals sequence complementarity with human genes.

    Science.gov (United States)

    Jensen, Peter D; Zhang, Yuanji; Wiggins, B Elizabeth; Petrick, Jay S; Zhu, Jin; Kerstetter, Randall A; Heck, Gregory R; Ivashuta, Sergey I

    2013-01-01

    Long double-stranded RNAs (long dsRNAs) are precursors for the effector molecules of sequence-specific RNA-based gene silencing in eukaryotes. Plant cells can contain numerous endogenous long dsRNAs. This study demonstrates that such endogenous long dsRNAs in plants have sequence complementarity to human genes. Many of these complementary long dsRNAs have perfect sequence complementarity of at least 21 nucleotides to human genes; enough complementarity to potentially trigger gene silencing in targeted human cells if delivered in functional form. However, the number and diversity of long dsRNA molecules in plant tissue from crops such as lettuce, tomato, corn, soy and rice with complementarity to human genes that have a long history of safe consumption supports a conclusion that long dsRNAs do not present a significant dietary risk.

  3. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome

    NARCIS (Netherlands)

    Sharp, Andrew J.; Hansen, Sierra; Selzer, Rebecca R.; Cheng, Ze; Regan, Regina; Hurst, Jane A.; Stewart, Helen; Price, Sue M.; Blair, Edward; Hennekam, Raoul C.; Fitzpatrick, Carrie A.; Segraves, Rick; Richmond, Todd A.; Guiver, Cheryl; Albertson, Donna G.; Pinkel, Daniel; Eis, Peggy S.; Schwartz, Stuart; Knight, Samantha J. L.; Eichler, Evan E.

    2006-01-01

    Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome, we investigated 130 regions that we hypothesized as candidates for previously undescribed genomic

  4. Mixed segmentation

    DEFF Research Database (Denmark)

    Hansen, Allan Grutt; Bonde, Anders; Aagaard, Morten

    content analysis and audience segmentation in a single-source perspective. The aim is to explain and understand target groups in relation to, on the one hand, emotional response to commercials or other forms of audio-visual communication and, on the other hand, living preferences and personality traits...

  5. A segment of the apospory-specific genomic region is highly microsyntenic not only between the apomicts Pennisetum squamulatum and buffelgrass, but also with a rice chromosome 11 centromeric-proximal genomic region.

    Science.gov (United States)

    Gualtieri, Gustavo; Conner, Joann A; Morishige, Daryl T; Moore, L David; Mullet, John E; Ozias-Akins, Peggy

    2006-03-01

    Bacterial artificial chromosome (BAC) clones from apomicts Pennisetum squamulatum and buffelgrass (Cenchrus ciliaris), isolated with the apospory-specific genomic region (ASGR) marker ugt197, were assembled into contigs that were extended by chromosome walking. Gene-like sequences from contigs were identified by shotgun sequencing and BLAST searches, and used to isolate orthologous rice contigs. Additional gene-like sequences in the apomicts' contigs were identified by bioinformatics using fully sequenced BACs from orthologous rice contigs as templates, as well as by interspecies, whole-contig cross-hybridizations. Hierarchical contig orthology was rapidly assessed by constructing detailed long-range contig molecular maps showing the distribution of gene-like sequences and markers, and searching for microsyntenic patterns of sequence identity and spatial distribution within and across species contigs. We found microsynteny between P. squamulatum and buffelgrass contigs. Importantly, this approach also enabled us to isolate from within the rice (Oryza sativa) genome contig Rice A, which shows the highest microsynteny and is most orthologous to the ugt197-containing C1C buffelgrass contig. Contig Rice A belongs to the rice genome database contig 77 (according to the current September 12, 2003, rice fingerprint contig build) that maps proximal to the chromosome 11 centromere, a feature that interestingly correlates with the mapping of ASGR-linked BACs proximal to the centromere or centromere-like sequences. Thus, relatedness between these two orthologous contigs is supported both by their molecular microstructure and by their centromeric-proximal location. Our discoveries promote the use of a microsynteny-based positional-cloning approach using the rice genome as a template to aid in constructing the ASGR toward the isolation of genes underlying apospory.

  6. A Segment of the Apospory-Specific Genomic Region Is Highly Microsyntenic Not Only between the Apomicts Pennisetum squamulatum and Buffelgrass, But Also with a Rice Chromosome 11 Centromeric-Proximal Genomic Region1[W

    Science.gov (United States)

    Gualtieri, Gustavo; Conner, Joann A.; Morishige, Daryl T.; Moore, L. David; Mullet, John E.; Ozias-Akins, Peggy

    2006-01-01

    Bacterial artificial chromosome (BAC) clones from apomicts Pennisetum squamulatum and buffelgrass (Cenchrus ciliaris), isolated with the apospory-specific genomic region (ASGR) marker ugt197, were assembled into contigs that were extended by chromosome walking. Gene-like sequences from contigs were identified by shotgun sequencing and BLAST searches, and used to isolate orthologous rice contigs. Additional gene-like sequences in the apomicts' contigs were identified by bioinformatics using fully sequenced BACs from orthologous rice contigs as templates, as well as by interspecies, whole-contig cross-hybridizations. Hierarchical contig orthology was rapidly assessed by constructing detailed long-range contig molecular maps showing the distribution of gene-like sequences and markers, and searching for microsyntenic patterns of sequence identity and spatial distribution within and across species contigs. We found microsynteny between P. squamulatum and buffelgrass contigs. Importantly, this approach also enabled us to isolate from within the rice (Oryza sativa) genome contig Rice A, which shows the highest microsynteny and is most orthologous to the ugt197-containing C1C buffelgrass contig. Contig Rice A belongs to the rice genome database contig 77 (according to the current September 12, 2003, rice fingerprint contig build) that maps proximal to the chromosome 11 centromere, a feature that interestingly correlates with the mapping of ASGR-linked BACs proximal to the centromere or centromere-like sequences. Thus, relatedness between these two orthologous contigs is supported both by their molecular microstructure and by their centromeric-proximal location. Our discoveries promote the use of a microsynteny-based positional-cloning approach using the rice genome as a template to aid in constructing the ASGR toward the isolation of genes underlying apospory. PMID:16415213

  7. Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments

    Directory of Open Access Journals (Sweden)

    Bruggmann Rémy

    2007-05-01

    Full Text Available Abstract Background Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL. To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite for that. QTL mapping in potato (Solanum tuberosum has identified a region on chromosome V tagged by DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late blight caused by the oomycete Phytophthora infestans and to root cyst nematodes. Results To obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial chromosome contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were assembled and annotated. Gene-by-gene co-linearity was disrupted by non-allelic insertions of retrotransposon elements, stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the sequence identified 48 putative open reading frames (ORF in one contig and 22 in the other, with an average of one ORF every 9 kbp. Ten ORFs were classified as resistance-gene-like, 11 as F-box-containing genes, 13 as transposable elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five micro-syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5. Conclusion Comparative sequence analysis revealed highly conserved collinear regions

  8. V-SINEs: A New Superfamily of Vertebrate SINEs That Are Widespread in Vertebrate Genomes and Retain a Strongly Conserved Segment within Each Repetitive Unit

    Science.gov (United States)

    Ogiwara, Ikuo; Miya, Masaki; Ohshima, Kazuhiko; Okada, Norihiro

    2002-01-01

    We have identified a new superfamily of vertebrate short interspersed repetitive elements (SINEs), designated V-SINEs, that are widespread in fishes and frogs. Each V-SINE includes a central conserved domain preceded by a 5′-end tRNA-related region and followed by a potentially recombinogenic (TG)n tract, with a 3′ tail derived from the 3′ untranslated region (UTR) of the corresponding partner long interspersed repetitive element (LINE) that encodes a functional reverse transcriptase. The central domain is strongly conserved and is even found in SINEs in the lamprey genome, suggesting that V-SINEs might be ∼550 Myr old or older in view of the timing of divergence of the lamprey lineage from the bony fish lineage. The central conserved domain might have been subject to some form of positive selection. Although the contemporary 3′ tails of V-SINEs differ from one another, it is possible that the original 3′ tail might have been replaced, via recombination, by the 3′ tails of more active partner LINEs, thereby retaining retropositional activity and the ability to survive for long periods on the evolutionary time scale. It seems plausible that V-SINEs may have some function(s) that have been maintained by the coevolution of SINEs and LINEs during the evolution of vertebrates. [The sequences reported in this paper have been deposited in the DDBJ/GenBank database under accession nos. AB072981–AB073004. Supplemental figures are available online at http://www.genome.org.] PMID:11827951

  9. Intracellular delivery of poly(I:C) induces apoptosis of fibroblast-like synoviocytes via an unknown dsRNA sensor

    Energy Technology Data Exchange (ETDEWEB)

    Karpus, Olga N.; Hsiao, Cheng-Chih; Kort, Hanneke de; Tak, Paul P.; Hamann, Jörg, E-mail: j.hamann@amc.uva.nl

    2016-08-26

    Fibroblast-like synoviocytes (FLS) express functional membranous and cytoplasmic sensors for double-stranded (ds)RNA. Notably, FLS undergo apoptosis upon transfection with the synthetic dsRNA analog poly(I:C). We here studied the mechanism of intracellular poly(I:C) recognition and subsequent cell death in FLS. FLS responded similarly to poly(I:C) or 3pRNA transfection; however, only intracellular delivery of poly(I:C) induced significant cell death, accompanied by upregulation of pro-apoptotic proteins Puma and Noxa, caspase 3 cleavage, and nuclear segregation. Knockdown of the DExD/H-box helicase MDA5 did not affect the response to intracellular poly(I:C); in contrast, knockdown of RIG-I abrogated the response to 3pRNA. Knockdown of the downstream adaptor proteins IPS, STING, and TRIF or inhibition of TBK1 did not affect the response to intracellular poly(I:C), while knockdown of IFNAR blocked intracellular poly(I:C)-mediated signaling and cell death. We conclude that a so far unknown intracellular sensor recognizes linear dsRNA and induces apoptosis in FLS. - Highlights: • Intracellular poly(I:C) and 3pRNA evoke immune responses in FLS. • Only intracellular delivery of poly(I:C) induces FLS apoptosis. • FLS do not require MDA5 for their response to intracellular poly(I:C). • FLS respond to intracellular poly(I:C) independent of IPS and STING. • An unknown intracellular sensor recognizes linear dsRNA in FLS.

  10. A member of the Tlr family is involved in dsRNA innate immune response in Paracentrotus lividus sea urchin.

    Science.gov (United States)

    Russo, Roberta; Chiaramonte, Marco; Matranga, Valeria; Arizza, Vincenzo

    2015-08-01

    The innate immune response involves proteins such as the membrane receptors of the Toll-like family (TLRs), which trigger different intracellular signalling pathways that are dependent on specific stimulating molecules. In sea urchins, TLR proteins are encoded by members of a large multigenic family composed of 60-250 genes in different species. Here, we report a newly identified mRNA sequence encoding a TLR protein (referred to as Pl-Tlr) isolated from Paracentrotus lividus immune cells. The partial protein sequence contained the conserved Toll/IL-1 receptor (TIR) domain, the transmembrane domain and part of the leucine repeats. Phylogenetic analysis of the Pl-Tlr protein was accomplished by comparing its sequence with those of TLRs from different classes of vertebrates and invertebrates. This analysis was suggestive of an evolutionary path that most likely represented the course of millions of years, starting from simple organisms and extending to humans. Challenge of the sea urchin immune system with poly-I:C, a chemical compound that mimics dsRNA, caused time-dependent Pl-Tlr mRNA up-regulation that was detected by QPCR. In contrast, bacterial LPS injury did not affect Pl-Tlr transcription. The study of the Tlr genes in the sea urchin model system may provide new perspectives on the role of Tlrs in the invertebrate immune response and clues concerning their evolution in a changing world. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Rapid RNase L-driven arrest of protein synthesis in the dsRNA response without degradation of translation machinery.

    Science.gov (United States)

    Donovan, Jesse; Rath, Sneha; Kolet-Mandrikov, David; Korennykh, Alexei

    2017-11-01

    Mammalian cells respond to double-stranded RNA (dsRNA) by activating a translation-inhibiting endoribonuclease, RNase L. Consensus in the field indicates that RNase L arrests protein synthesis by degrading ribosomal RNAs (rRNAs) and messenger RNAs (mRNAs). However, here we provide evidence for a different and far more efficient mechanism. By sequencing abundant RNA fragments generated by RNase L in human cells, we identify site-specific cleavage of two groups of noncoding RNAs: Y-RNAs, whose function is poorly understood, and cytosolic tRNAs, which are essential for translation. Quantitative analysis of human RNA cleavage versus nascent protein synthesis in lung carcinoma cells shows that RNase L stops global translation when tRNAs, as well as rRNAs and mRNAs, are still intact. Therefore, RNase L does not have to degrade the translation machinery to stop protein synthesis. Our data point to a rapid mechanism that transforms a subtle RNA cleavage into a cell-wide translation arrest. © 2017 Donovan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  12. Exposure to the viral by-product dsRNA or Coxsackievirus B5 triggers pancreatic beta cell apoptosis via a Bim / Mcl-1 imbalance.

    Directory of Open Access Journals (Sweden)

    Maikel L Colli

    2011-09-01

    Full Text Available The rise in type 1 diabetes (T1D incidence in recent decades is probably related to modifications in environmental factors. Viruses are among the putative environmental triggers of T1D. The mechanisms regulating beta cell responses to viruses, however, remain to be defined. We have presently clarified the signaling pathways leading to beta cell apoptosis following exposure to the viral mimetic double-stranded RNA (dsRNA and a diabetogenic enterovirus (Coxsackievirus B5. Internal dsRNA induces cell death via the intrinsic mitochondrial pathway. In this process, activation of the dsRNA-dependent protein kinase (PKR promotes eIF2α phosphorylation and protein synthesis inhibition, leading to downregulation of the antiapoptotic Bcl-2 protein myeloid cell leukemia sequence 1 (Mcl-1. Mcl-1 decrease results in the release of the BH3-only protein Bim, which activates the mitochondrial pathway of apoptosis. Indeed, Bim knockdown prevented both dsRNA- and Coxsackievirus B5-induced beta cell death, and counteracted the proapoptotic effects of Mcl-1 silencing. These observations indicate that the balance between Mcl-1 and Bim is a key factor regulating beta cell survival during diabetogenic viral infections.

  13. Brookhaven segment interconnect

    International Nuclear Information System (INIS)

    Morse, W.M.; Benenson, G.; Leipuner, L.B.

    1983-01-01

    We have performed a high energy physics experiment using a multisegment Brookhaven FASTBUS system. The system was composed of three crate segments and two cable segments. We discuss the segment interconnect module which permits communication between the various segments

  14. Nuclear Factor 90, a cellular dsRNA binding protein inhibits the HIV Rev-export function

    Directory of Open Access Journals (Sweden)

    St-Laurent Georges

    2006-11-01

    Full Text Available Abstract Background The HIV Rev protein is known to facilitate export of incompletely spliced and unspliced viral transcripts to the cytoplasm, a necessary step in virus life cycle. The Rev-mediated nucleo-cytoplasmic transport of nascent viral transcripts, dependents on interaction of Rev with the RRE RNA structural element present in the target RNAs. The C-terminal variant of dsRNA-binding nuclear protein 90 (NF90ctv has been shown to markedly attenuate viral replication in stably transduced HIV-1 target cell line. Here we examined a mechanism of interference of viral life cycle involving Rev-NF90ctv interaction. Results Since Rev:RRE complex formations depend on protein:RNA and protein:protein interactions, we investigated whether the expression of NF90ctv might interfere with Rev-mediated export of RRE-containing transcripts. When HeLa cells expressed both NF90ctv and Rev protein, we observed that NF90ctv inhibited the Rev-mediated RNA transport. In particular, three regions of NF90ctv protein are involved in blocking Rev function. Moreover, interaction of NF90ctv with the RRE RNA resulted in the expression of a reporter protein coding sequences linked to the RRE structure. Moreover, Rev influenced the subcellular localization of NF90ctv, and this process is leptomycin B sensitive. Conclusion The dsRNA binding protein, NF90ctv competes with HIV Rev function at two levels, by competitive protein:protein interaction involving Rev binding to specific domains of NF90ctv, as well as by its binding to the RRE-RNA structure. Our results are consistent with a model of Rev-mediated HIV-1 RNA export that envisions Rev-multimerization, a process interrupted by NF90ctv.

  15. The genomic and biological characterization of Citrullus lanatus cryptic virus infecting watermelon in China.

    Science.gov (United States)

    Xin, Min; Cao, Mengji; Liu, Wenwen; Ren, Yingdang; Lu, Chuantao; Wang, Xifeng

    2017-03-15

    A dsRNA virus was detected in the watermelon (Citrullus lanatus) samples collected from Kaifeng, Henan province, China through the use of next generation sequencing of small RNAs. The complete genome of this virus is comprised of dsRNA-1 (1603nt) and dsRNA-2 (1466nt), both of which are single open reading frames and potentially encode a 54.2kDa RNA-dependent RNA polymerase (RdRp) and a 45.9kDa coat protein (CP), respectively. The RdRp and CP share the highest amino acid identities 85.3% and 75.4% with a previously reported Israeli strain Citrullus lanatus cryptic virus (CiLCV), respectively. Genome comparisons indicate that this virus is the same species with CiLCV, whereas the reported sequences of the Israeli strain of CiLCV are partial, and our newly identified sequences can represent the complete genome of CiLCV. Futhermore, phylogenetic tree analyses based on the RdRp sequences suggest that CiLCV is one member in the genus Deltapartitivirus, family Partitiviridae. In addition, field investigation and seed-borne bioassays show that CiLCV commonly occurs in many varieties and is transmitted though seeds at a very high rate. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Influence of Bxpel1 Gene Silencing by dsRNA Interference on the Development and Pathogenicity of the Pine Wood Nematode, Bursaphelenchus xylophilus

    Science.gov (United States)

    Qiu, Xiu-Wen; Wu, Xiao-Qin; Huang, Lin; Ye, Jian-Ren

    2016-01-01

    As the causal agent of pine wilt disease (PWD), the pine wood nematode (PWN), Bursaphelenchus xylophilus, causes huge economic losses by devastating pine forests worldwide. The pectate lyase gene is essential for successful invasion of their host plants by plant-parasitic nematodes. To demonstrate the role of pectate lyase gene in the PWD process, RNA interference (RNAi) is used to analyze the function of the pectate lyase 1 gene in B. xylophilus (Bxpel1). The efficiency of RNAi was detected by real-time PCR. The result demonstrated that the quantity of B. xylophilus propagated with control solution treatment was 62 times greater than that soaking in double-stranded RNA (dsRNA) after B. xylophilus inoculation in Botrytis cinerea for the first generation (F1). The number of B. xylophilus soaking in control solution was doubled compared to that soaking in Bxpel1 dsRNA four days after inoculation in Pinus thunbergii. The quantity of B. xylophilus was reduced significantly (p < 0.001) after treatment with dsRNAi compared with that using a control solution treatment. Bxpel1 dsRNAi reduced the migration speed and reproduction of B. xylophilus in pine trees. The pathogenicity to P. thunbergii seedling of B. xylophilus was weaker after soaking in dsRNA solution compared with that after soaking in the control solution. Our results suggest that Bxpel1 gene is a significant pathogenic factor in the PWD process and this basic information may facilitate a better understanding of the molecular mechanism of PWD. PMID:26797602

  17. Pro-apoptotic signaling induced by Retinoic acid and dsRNA is under the control of Interferon Regulatory Factor-3 in breast cancer cells.

    Science.gov (United States)

    Bernardo, Ana R; Cosgaya, José M; Aranda, Ana; Jiménez-Lara, Ana M

    2017-07-01

    Breast cancer is one of the most lethal malignancies for women. Retinoic acid (RA) and double-stranded RNA (dsRNA) are considered signaling molecules with potential anticancer activity. RA, co-administered with the dsRNA mimic polyinosinic-polycytidylic acid (poly(I:C)), synergizes to induce a TRAIL (Tumor-Necrosis-Factor Related Apoptosis-Inducing Ligand)- dependent apoptotic program in breast cancer cells. Here, we report that RA/poly(I:C) co-treatment, synergically, induce the activation of Interferon Regulatory Factor-3 (IRF3) in breast cancer cells. IRF3 activation is mediated by a member of the pathogen recognition receptors, Toll-like receptor-3 (TLR3), since its depletion abrogates IRF3 activation by RA/poly(I:C) co-treatment. Besides induction of TRAIL, apoptosis induced by RA/poly(I:C) correlates with the increased expression of pro-apoptotic TRAIL receptors, TRAIL-R1/2, and the inhibition of the antagonistic receptors TRAIL-R3/4. IRF3 plays an important role in RA/poly(I:C)-induced apoptosis since IRF3 depletion suppresses caspase-8 and caspase-3 activation, TRAIL expression upregulation and apoptosis. Interestingly, RA/poly(I:C) combination synergizes to induce a bioactive autocrine/paracrine loop of type-I Interferons (IFNs) which is ultimately responsible for TRAIL and TRAIL-R1/2 expression upregulation, while inhibition of TRAIL-R3/4 expression is type-I IFN-independent. Our results highlight the importance of IRF3 and type-I IFNs signaling for the pro-apoptotic effects induced by RA and synthetic dsRNA in breast cancer cells.

  18. Exploring the molecular basis of dsRNA recognition by NS1 protein of influenza A virus using molecular dynamics simulation and free energy calculation.

    Science.gov (United States)

    Pan, Dabo; Sun, Huijun; Shen, Yulin; Liu, Huanxiang; Yao, Xiaojun

    2011-12-01

    The frequent outbreak of influenza pandemic and the limited available anti-influenza drugs highlight the urgent need for the development of new antiviral drugs. The dsRNA-binding surface of nonstructural protein 1 of influenza A virus (NS1A) is a promising target. The detailed understanding of NS1A-dsRNA interaction will be valuable for structure-based anti-influenza drug discovery. To characterize and explore the key interaction features between dsRNA and NS1A, molecular dynamics simulation combined with MM-GBSA calculations were performed. Based on the MM-GBSA calculations, we find that the intermolecular van der Waals interaction and the nonpolar solvation term provide the main driving force for the binding process. Meanwhile, 17 key residues from NS1A were identified to be responsible for the dsRNA binding. Compared with the wild type NS1A, all the studied mutants S42A, T49A, R38A, R35AR46A have obvious reduced binding free energies with dsRNA reflecting in the reduction of the polar and/or nonpolar interactions. In addition, the structural and energy analysis indicate the mutations have a small effect to the backbone structures but the loss of side chain interactions is responsible for the decrease of the binding affinity. The uncovering of NS1A-dsRNA recognition mechanism will provide some useful insights and new chances for the development of anti-influenza drugs. Copyright © 2011 Elsevier B.V. All rights reserved.

  19. Triggering of the dsRNA sensors TLR3, MDA5, and RIG-I induces CD55 expression in synovial fibroblasts.

    Directory of Open Access Journals (Sweden)

    Olga N Karpus

    Full Text Available CD55 (decay-accelerating factor is a complement-regulatory protein highly expressed on fibroblast-like synoviocytes (FLS. CD55 is also a ligand for CD97, an adhesion-type G protein-coupled receptor abundantly present on leukocytes. Little is known regarding the regulation of CD55 expression in FLS.FLS isolated from arthritis patients were stimulated with pro-inflammatory cytokines and Toll-like receptor (TLR ligands. Transfection with polyinosinic-polycytidylic acid (poly(I:C and 5'-triphosphate RNA were used to activate the cytoplasmic double-stranded (dsRNA sensors melanoma differentiation-associated gene 5 (MDA5 and retinoic acid-inducible gene-I (RIG-I. CD55 expression, cell viability, and binding of CD97-loaded beads were quantified by flow cytometry.CD55 was expressed at equal levels on FLS isolated from patients with rheumatoid arthritis (RA, osteoarthritis, psoriatic arthritis and spondyloarthritis. CD55 expression in RA FLS was significantly induced by IL-1β and especially by the TLR3 ligand poly(I:C. Activation of MDA5 and RIG-I also enhanced CD55 expression. Notably, activation of MDA5 dose-dependently induced cell death, while triggering of TLR3 or RIG-I had a minor effect on viability. Upregulation of CD55 enhanced the binding capacity of FLS to CD97-loaded beads, which could be blocked by antibodies against CD55.Activation of dsRNA sensors enhances the expression of CD55 in cultured FLS, which increases the binding to CD97. Our findings suggest that dsRNA promotes the interaction between FLS and CD97-expressing leukocytes.

  20. dsRNA silencing of an R2R3-MYB transcription factor affects flower cell shape in a Dendrobium hybrid.

    Science.gov (United States)

    Lau, Su-Ee; Schwarzacher, Trude; Othman, Rofina Yasmin; Harikrishna, Jennifer Ann

    2015-08-11

    The R2R3-MYB genes regulate pigmentation and morphogenesis of flowers, including flower and cell shape, and therefore have importance in the development of new varieties of orchids. However, new variety development is limited by the long breeding time required in orchids. In this study, we identified a cDNA, DhMYB1, that is expressed during flower development in a hybrid orchid, Dendrobium hybrida (Dendrobium bobby messina X Dendrobium chao phraya) then used the direct application of dsRNA to observe the effect of gene silencing on flower phenotype and floral epidermal cell shape. Flower bud development in the Dendrobium hybrid was characterised into seven stages and the time of meiosis was determined as between stages 3 to 5 when the bud is approximately half of the mature size. Scanning electron microscopy characterisation of adaxial epidermal cells of the flower perianth, showed that the petals and sepals each are divided into two distinct domains based on cell shape and size, while the labellum comprises seven domains. Thirty-two partial cDNA fragments representing R2R3-MYB gene sequences were isolated from D. hybrida. Phylogenetic analysis revealed that nine of the translated sequences were clustered with MYB sequences that are known to be involved in cell shape development and from these, DhMYB1 was selected for full length cDNA cloning and functional study. Direct application of a 430 bp dsRNA from the 3' region of DhMYB1 to emerging orchid flower buds reduced expression of DhMYB1 RNA compared with untreated control. Scanning electron microscopy of adaxial epidermal cells within domain one of the labellum of flowers treated with DhMYB1 dsRNA showed flattened epidermal cells whilst those of control flowers were conical. DhMYB1 is expressed throughout flower bud development and is involved in the development of the conical cell shape of the epidermal cells of the Dendrobium hybrida flower labellum. The direct application of dsRNA changed the phenotype of

  1. Molecular characterization of a new monopartite dsRNA mycovirus from mycorrhizal Thelephora terrestris (Ehrh.) and its detection in soil oribatid mites (Acari: Oribatida)

    Energy Technology Data Exchange (ETDEWEB)

    Petrzik, Karel, E-mail: petrzik@umbr.cas.cz [Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice (Czech Republic); Sarkisova, Tatiana [Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice (Czech Republic); Starý, Josef [Institute of Soil Biology, Biology Centre of the Czech Academy of Sciences, Na Sádkách 7, 370 05 České Budějovice (Czech Republic); Koloniuk, Igor [Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice (Czech Republic); and others

    2016-02-15

    A novel dsRNA virus was identified in the mycorrhizal fungus Thelephora terrestris (Ehrh.) and sequenced. This virus, named Thelephora terrestris virus 1 (TtV1), contains two reading frames in different frames but with the possibility that ORF2 could be translated as a fusion polyprotein after ribosomal -1 frameshifting. Picornavirus 2A-like motif, nudix hydrolase, phytoreovirus S7, and RdRp domains were found in a unique arrangement on the polyprotein. A new genus named Phlegivirus and containing TtV1, PgLV1, RfV1 and LeV is therefore proposed. Twenty species of oribatid mites were identified in soil material in the vicinity of T. terrestris. TtV1 was detected in large amounts in Steganacarus (Tropacarus) carinatus (C.L. Koch, 1841) and in much smaller amounts in Nothrus silvestris (Nicolet). This is the first description of mycovirus presence in oribatid mites. - Highlights: • A novel dsRNA virus was identified in the mycorrhizal fungus Thelephora terrestris. • A new virus genus Phlegivirus is proposed. • The mycovirus was firstly detected in oribatid mites.

  2. A mutation in the Arabidopsis HYL1 gene encoding a dsRNA binding protein affects responses to abscisic acid, auxin, and cytokinin

    Science.gov (United States)

    Lu, C.; Fedoroff, N.

    2000-01-01

    Both physiological and genetic evidence indicate interconnections among plant responses to different hormones. We describe a pleiotropic recessive Arabidopsis transposon insertion mutation, designated hyponastic leaves (hyl1), that alters the plant's responses to several hormones. The mutant is characterized by shorter stature, delayed flowering, leaf hyponasty, reduced fertility, decreased rate of root growth, and an altered root gravitropic response. It also exhibits less sensitivity to auxin and cytokinin and hypersensitivity to abscisic acid (ABA). The auxin transport inhibitor 2,3,5-triiodobenzoic acid normalizes the mutant phenotype somewhat, whereas another auxin transport inhibitor, N-(1-naph-thyl)phthalamic acid, exacerbates the phenotype. The gene, designated HYL1, encodes a 419-amino acid protein that contains two double-stranded RNA (dsRNA) binding motifs, a nuclear localization motif, and a C-terminal repeat structure suggestive of a protein-protein interaction domain. We present evidence that the HYL1 gene is ABA-regulated and encodes a nuclear dsRNA binding protein. We hypothesize that the HYL1 protein is a regulatory protein functioning at the transcriptional or post-transcriptional level.

  3. Molecular characterization of a new monopartite dsRNA mycovirus from mycorrhizal Thelephora terrestris (Ehrh.) and its detection in soil oribatid mites (Acari: Oribatida)

    International Nuclear Information System (INIS)

    Petrzik, Karel; Sarkisova, Tatiana; Starý, Josef; Koloniuk, Igor

    2016-01-01

    A novel dsRNA virus was identified in the mycorrhizal fungus Thelephora terrestris (Ehrh.) and sequenced. This virus, named Thelephora terrestris virus 1 (TtV1), contains two reading frames in different frames but with the possibility that ORF2 could be translated as a fusion polyprotein after ribosomal -1 frameshifting. Picornavirus 2A-like motif, nudix hydrolase, phytoreovirus S7, and RdRp domains were found in a unique arrangement on the polyprotein. A new genus named Phlegivirus and containing TtV1, PgLV1, RfV1 and LeV is therefore proposed. Twenty species of oribatid mites were identified in soil material in the vicinity of T. terrestris. TtV1 was detected in large amounts in Steganacarus (Tropacarus) carinatus (C.L. Koch, 1841) and in much smaller amounts in Nothrus silvestris (Nicolet). This is the first description of mycovirus presence in oribatid mites. - Highlights: • A novel dsRNA virus was identified in the mycorrhizal fungus Thelephora terrestris. • A new virus genus Phlegivirus is proposed. • The mycovirus was firstly detected in oribatid mites.

  4. Adaptive stress response in segmental progeria resembles long-lived dwarfism and calorie restriction in mice

    NARCIS (Netherlands)

    van de Ven, Marieke; Andressoo, Jaan-Olle; Holcomb, Valerie B.; von Lindern, Marieke; Jong, Willeke M. C.; de Zeeuw, Chris I.; Suh, Yousin; Hasty, Paul; Hoeijmakers, Jan H. J.; van der Horst, Gijsbertus T. J.; Mitchell, James R.

    2006-01-01

    How congenital defects causing genome instability can result in the pleiotropic symptoms reminiscent of aging but in a segmental and accelerated fashion remains largely unknown. Most segmental progerias are associated with accelerated fibroblast senescence, suggesting that cellular senescence is a

  5. Adaptive stress response in segmental progeria resembles long-lived dwarfism and calorie restriction in mice

    NARCIS (Netherlands)

    H.W.M. van de Ven (Marieke); J.-O. Andressoo (Jaan-Olle); V.B. Holcomb (Valerie); M.M. von Lindern (Marieke); W.M.C. Jong (Willeke); C.I. de Zeeuw (Chris); Y. Suh (Yousin); P. Hasty (Paul); J.H.J. Hoeijmakers (Jan); G.T.J. van der Horst (Gijsbertus); J.R. Mitchell (James)

    2006-01-01

    textabstractHow congenital defects causing genome instability can result in the pleiotropic symptoms reminiscent of aging but in a segmental and accelerated fashion remains largely unknown. Most segmental progerias are associated with accelerated fibroblast senescence, suggesting that cellular

  6. Chimaeric Virus-Like Particles Derived from Consensus Genome Sequences of Human Rotavirus Strains Co-Circulating in Africa

    Science.gov (United States)

    Jere, Khuzwayo C.; O'Neill, Hester G.; Potgieter, A. Christiaan; van Dijk, Alberdina A.

    2014-01-01

    Rotavirus virus-like particles (RV-VLPs) are potential alternative non-live vaccine candidates due to their high immunogenicity. They mimic the natural conformation of native viral proteins but cannot replicate because they do not contain genomic material which makes them safe. To date, most RV-VLPs have been derived from cell culture adapted strains or common G1 and G3 rotaviruses that have been circulating in communities for some time. In this study, chimaeric RV-VLPs were generated from the consensus sequences of African rotaviruses (G2, G8, G9 or G12 strains associated with either P[4], P[6] or P[8] genotypes) characterised directly from human stool samples without prior adaptation of the wild type strains to cell culture. Codon-optimised sequences for insect cell expression of genome segments 2 (VP2), 4 (VP4), 6 (VP6) and 9 (VP7) were cloned into a modified pFASTBAC vector, which allowed simultaneous expression of up to four genes using the Bac-to-Bac Baculovirus Expression System (BEVS; Invitrogen). Several combinations of the genome segments originating from different field strains were cloned to produce double-layered RV-VLPs (dRV-VLP; VP2/6), triple-layered RV-VLPs (tRV-VLP; VP2/6/7 or VP2/6/7/4) and chimaeric tRV-VLPs. The RV-VLPs were produced by infecting Spodoptera frugiperda 9 and Trichoplusia ni cells with recombinant baculoviruses using multi-cistronic, dual co-infection and stepwise-infection expression strategies. The size and morphology of the RV-VLPs, as determined by transmission electron microscopy, revealed successful production of RV-VLPs. The novel approach of producing tRV-VLPs, by using the consensus insect cell codon-optimised nucleotide sequence derived from dsRNA extracted directly from clinical specimens, should speed-up vaccine research and development by by-passing the need to adapt rotaviruses to cell culture. Other problems associated with cell culture adaptation, such as possible changes in epitopes, can also be circumvented

  7. Segmented trapped vortex cavity

    Science.gov (United States)

    Grammel, Jr., Leonard Paul (Inventor); Pennekamp, David Lance (Inventor); Winslow, Jr., Ralph Henry (Inventor)

    2010-01-01

    An annular trapped vortex cavity assembly segment comprising includes a cavity forward wall, a cavity aft wall, and a cavity radially outer wall there between defining a cavity segment therein. A cavity opening extends between the forward and aft walls at a radially inner end of the assembly segment. Radially spaced apart pluralities of air injection first and second holes extend through the forward and aft walls respectively. The segment may include first and second expansion joint features at distal first and second ends respectively of the segment. The segment may include a forward subcomponent including the cavity forward wall attached to an aft subcomponent including the cavity aft wall. The forward and aft subcomponents include forward and aft portions of the cavity radially outer wall respectively. A ring of the segments may be circumferentially disposed about an axis to form an annular segmented vortex cavity assembly.

  8. Pavement management segment consolidation

    Science.gov (United States)

    1998-01-01

    Dividing roads into "homogeneous" segments has been a major problem for all areas of highway engineering. SDDOT uses Deighton Associates Limited software, dTIMS, to analyze life-cycle costs for various rehabilitation strategies on each segment of roa...

  9. Speaker segmentation and clustering

    OpenAIRE

    Kotti, M; Moschou, V; Kotropoulos, C

    2008-01-01

    07.08.13 KB. Ok to add the accepted version to Spiral, Elsevier says ok whlile mandate not enforced. This survey focuses on two challenging speech processing topics, namely: speaker segmentation and speaker clustering. Speaker segmentation aims at finding speaker change points in an audio stream, whereas speaker clustering aims at grouping speech segments based on speaker characteristics. Model-based, metric-based, and hybrid speaker segmentation algorithms are reviewed. Concerning speaker...

  10. Spinal segmental dysgenesis

    Directory of Open Access Journals (Sweden)

    N Mahomed

    2009-06-01

    Full Text Available Spinal segmental dysgenesis is a rare congenital spinal abnormality , seen in neonates and infants in which a segment of the spine and spinal cord fails to develop normally . The condition is segmental with normal vertebrae above and below the malformation. This condition is commonly associated with various abnormalities that affect the heart, genitourinary, gastrointestinal tract and skeletal system. We report two cases of spinal segmental dysgenesis and the associated abnormalities.

  11. Automatic Melody Segmentation

    NARCIS (Netherlands)

    Rodríguez López, Marcelo

    2016-01-01

    The work presented in this dissertation investigates music segmentation. In the field of Musicology, segmentation refers to a score analysis technique, whereby notated pieces or passages of these pieces are divided into “units” referred to as sections, periods, phrases, and so on. Segmentation

  12. Gene conversion in the rice genome

    DEFF Research Database (Denmark)

    Xu, Shuqing; Clark, Terry; Zheng, Hongkun

    2008-01-01

    -chromosomal conversions distributed between chromosome 1 and 5, 2 and 6, and 3 and 5 are more frequent than genome average (Z-test, P ... is not tightly linked to natural selection in the rice genome. To assess the contribution of segmental duplication on gene conversion statistics, we determined locations of conversion partners with respect to inter-chromosomal segment duplication. The number of conversions associated with segmentation is less...... involved in conversion events. CONCLUSION: The evolution of gene families in the rice genome may have been accelerated by conversion with pseudogenes. Our analysis suggests a possible role for gene conversion in the evolution of pathogen-response genes....

  13. Short segment search method for phylogenetic analysis using nested sliding windows

    Science.gov (United States)

    Iskandar, A. A.; Bustamam, A.; Trimarsanto, H.

    2017-10-01

    To analyze phylogenetics in Bioinformatics, coding DNA sequences (CDS) segment is needed for maximal accuracy. However, analysis by CDS cost a lot of time and money, so a short representative segment by CDS, which is envelope protein segment or non-structural 3 (NS3) segment is necessary. After sliding window is implemented, a better short segment than envelope protein segment and NS3 is found. This paper will discuss a mathematical method to analyze sequences using nested sliding window to find a short segment which is representative for the whole genome. The result shows that our method can find a short segment which more representative about 6.57% in topological view to CDS segment than an Envelope segment or NS3 segment.

  14. GENOMIC FEATURES OF COTESIA PLUTELLAE POLYDNAVIRUS

    Institute of Scientific and Technical Information of China (English)

    LIUCai-ling; ZHUXiang-xiong; FuWen-jun; ZHAOMu-jun

    2003-01-01

    Polydnavirus was purified from the calyx fluid of Cotesia plutellae ovary. The genomic features of C. plutellae polydnavirus (CpPDV) were investigated. The viral genome consists of at least 12 different segments and the aggregate genome size is a lower estimate of 80kbp. By partial digestion of CpPDV DNA with BamHI and subsequent ligation with BamHI-cut plasmid Bluescript, a representative library of CpPDV genome was obtained.

  15. Transfected poly(I:C) activates different dsRNA receptors, leading to apoptosis or immunoadjuvant response in androgen-independent prostate cancer cells.

    Science.gov (United States)

    Palchetti, Sara; Starace, Donatella; De Cesaris, Paola; Filippini, Antonio; Ziparo, Elio; Riccioli, Anna

    2015-02-27

    Despite the effectiveness of surgery or radiation therapy for the treatment of early-stage prostate cancer (PCa), there is currently no effective strategy for late-stage disease. New therapeutic targets are emerging; in particular, dsRNA receptors Toll-like receptor 3 (TLR3) and cytosolic helicases expressed by cancer cells, once activated, exert a pro-apoptotic effect in different tumors. We previously demonstrated that the synthetic analog of dsRNA poly(I:C) induces apoptosis in the androgen-dependent PCa cell line LNCaP in a TLR3-dependent fashion, whereas only a weak apoptotic effect is observed in the more aggressive and androgen-independent PCa cells PC3 and DU145. In this paper, we characterize the receptors and the signaling pathways involved in the remarkable apoptosis induced by poly(I:C) transfected by Lipofectamine (in-poly(I:C)) compared with the 12-fold higher free poly(I:C) concentration in PC3 and DU145 cells. By using genetic inhibition of different poly(I:C) receptors, we demonstrate the crucial role of TLR3 and Src in in-poly(I:C)-induced apoptosis. Therefore, we show that the increased in-poly(I:C) apoptotic efficacy is due to a higher binding of endosomal TLR3. On the other hand, we show that in-poly(I:C) binding to cytosolic receptors MDA5 and RIG-I triggers IRF3-mediated signaling, leading uniquely to the up-regulation of IFN-β, which likely in turn induces increased TLR3, MDA5, and RIG-I proteins. In summary, in-poly(I:C) activates two distinct antitumor pathways in PC3 and DU145 cells: one mediated by the TLR3/Src/STAT1 axis, leading to apoptosis, and the other one mediated by MDA5/RIG-I/IRF3, leading to immunoadjuvant IFN-β expression. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. The infinite sites model of genome evolution.

    Science.gov (United States)

    Ma, Jian; Ratan, Aakrosh; Raney, Brian J; Suh, Bernard B; Miller, Webb; Haussler, David

    2008-09-23

    We formalize the problem of recovering the evolutionary history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement of segments of bases. The problem is examined in the limit as the number of bases in each genome goes to infinity. In this limit, the chromosomes are represented by continuous circles or line segments. For such an infinite-sites model, we present a polynomial-time algorithm to find the most parsimonious evolutionary history of any set of related present-day genomes.

  17. Segmentation, advertising and prices

    NARCIS (Netherlands)

    Galeotti, Andrea; Moraga González, José

    This paper explores the implications of market segmentation on firm competitiveness. In contrast to earlier work, here market segmentation is minimal in the sense that it is based on consumer attributes that are completely unrelated to tastes. We show that when the market is comprised by two

  18. Sipunculans and segmentation

    DEFF Research Database (Denmark)

    Wanninger, Andreas; Kristof, Alen; Brinkmann, Nora

    2009-01-01

    mechanisms may act on the level of gene expression, cell proliferation, tissue differentiation and organ system formation in individual segments. Accordingly, in some polychaete annelids the first three pairs of segmental peripheral neurons arise synchronously, while the metameric commissures of the ventral...

  19. Amplification of genome sections in mammalian somatic cells resistant to colchicine. VII. Localization of original and amplified copes of the mdr gene in the same segment of chromosome 4 of the Dzungarian hamster

    International Nuclear Information System (INIS)

    Sokova, O.I.; Siyanova, E.Yu.; Gudkov, A.V.; Kopnin, B.P.

    1988-01-01

    Using in situ hybridization, the mdr gene was mapped in chromosomes of Dzungarian hamster embryonic cells, amplification of which accompanies development of multidrug resistance (MDR). It was shown that the mdr gene is located in chromosome segment 4q15-21, in which, according to data obtained previously, amplified copes of open quotes MDR genes close quotes (mdr, et al.) are distributed, as a rule. Results obtained, as well as data of other investigators, attest to the fact that integration recombination of amplified copies of DNA occurs primarily at the site of disposition of homologous sequences

  20. A decision-theoretic approach for segmental classification

    OpenAIRE

    Yau, Christopher; Holmes, Christopher C.

    2013-01-01

    This paper is concerned with statistical methods for the segmental classification of linear sequence data where the task is to segment and classify the data according to an underlying hidden discrete state sequence. Such analysis is commonplace in the empirical sciences including genomics, finance and speech processing. In particular, we are interested in answering the following question: given data $y$ and a statistical model $\\pi(x,y)$ of the hidden states $x$, what should we report as the ...

  1. Pancreas and cyst segmentation

    Science.gov (United States)

    Dmitriev, Konstantin; Gutenko, Ievgeniia; Nadeem, Saad; Kaufman, Arie

    2016-03-01

    Accurate segmentation of abdominal organs from medical images is an essential part of surgical planning and computer-aided disease diagnosis. Many existing algorithms are specialized for the segmentation of healthy organs. Cystic pancreas segmentation is especially challenging due to its low contrast boundaries, variability in shape, location and the stage of the pancreatic cancer. We present a semi-automatic segmentation algorithm for pancreata with cysts. In contrast to existing automatic segmentation approaches for healthy pancreas segmentation which are amenable to atlas/statistical shape approaches, a pancreas with cysts can have even higher variability with respect to the shape of the pancreas due to the size and shape of the cyst(s). Hence, fine results are better attained with semi-automatic steerable approaches. We use a novel combination of random walker and region growing approaches to delineate the boundaries of the pancreas and cysts with respective best Dice coefficients of 85.1% and 86.7%, and respective best volumetric overlap errors of 26.0% and 23.5%. Results show that the proposed algorithm for pancreas and pancreatic cyst segmentation is accurate and stable.

  2. Segmentation of consumer's markets and evaluation of market's segments

    OpenAIRE

    ŠVECOVÁ, Iveta

    2013-01-01

    The goal of this bachelor thesis was to explain a possibly segmentation of consumer´s markets for a chosen company, and to present a suitable goods offer, so it would be suitable to the needs of selected segments. The work is divided into theoretical and practical part. First part describes marketing, segmentation, segmentation of consumer's markets, consumer's market, market's segments a other terms. Second part describes an evaluation of questionnaire survey, discovering of market's segment...

  3. MicroRNA and dsRNA targeting chitin synthase A reveal a great potential for pest management of the hemipteran insect Nilaparvata lugens.

    Science.gov (United States)

    Li, Tengchao; Chen, Jie; Fan, Xiaobin; Chen, Weiwen; Zhang, Wenqing

    2017-07-01

    Two RNA silencing pathways in insects are known to exist that are mediated by short interfering RNAs (siRNAs) and microRNAs (miRNAs), which have been hypothesised to be promising methods for insect pest control. However, a comparison between miRNA and siRNA in pest control is still unavailable, particularly in targeting chitin synthase gene A (CHSA). The dsRNA for Nilaparvata lugens CHSA (dsNlCHSA) and the microR-2703 (miR-2703) mimic targeting NlCHSA delivered via feeding affected the development of nymphs, reduced their chitin content and led to lethal phenotypes. The protein level of NlCHSA was downregulated after female adults were injected with dsNlCHSA or the miR-2703 mimic, but there were no significant differences in vitellogenin (NlVg) expression or in total oviposition relative to the control group. However, 90.68 and 46.13% of the eggs laid by the females injected with dsNlCHSA and miR-2703 mimic were unable to hatch, respectively. In addition, a second-generation miRNA and RNAi effect on N. lugens was observed. Ingested miR-2703 seems to be a good option for killing N. lugens nymphs, while NlCHSA may be a promising target for RNAi-based pest management. These findings provide important evidence for applications of small non-coding RNAs (snRNAs) in insect pest management. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  4. Gene silencing of mannose 6-phosphate reductase in the parasitic weed Orobanche aegyptiaca through the production of homologous dsRNA sequences in the host plant.

    Science.gov (United States)

    Aly, Radi; Cholakh, Hila; Joel, Daniel M; Leibman, Diana; Steinitz, Benjamin; Zelcer, Aaron; Naglis, Anna; Yarden, Oded; Gal-On, Amit

    2009-08-01

    Orobanche spp. (broomrape) are parasitic plants which subsist on the roots of a wide range of hosts, including tomato, causing severe losses in yield quality and quantity. Large amounts of mannitol accumulate in this parasitic weed during development. Mannose 6-phosphate reductase (M6PR) is a key enzyme in mannitol biosynthesis, and it has been suggested that mannitol accumulation may be very important for Orobanche development. Therefore, the Orobanche M6PR gene is a potential target for efforts to control this parasite. Transgenic tomato plants were produced bearing a gene construct containing a specific 277-bp fragment from Orobanche aegyptiaca M6PR-mRNA, in an inverted-repeat configuration. M6PR-siRNA was detected in three independent transgenic tomato lines in the R1 generation, but was not detected in the parasite. Quantitative RT-PCR analysis showed that the amount of endogenous M6PR mRNA in the tubercles and underground shoots of O. aegyptiaca grown on transgenic host plants was reduced by 60%-80%. Concomitant with M6PR mRNA suppression, there was a significant decrease in mannitol level and a significant increase in the percentage of dead O. aegyptiaca tubercles on the transgenic host plants. The detection of mir390, which is involved with cytoplasmic dsRNA processing, is the first indication of the existence of gene-silencing mechanisms in Orobanche spp. Gene silencing mechanisms are probably involved with the production of decreased levels of M6PR mRNA in the parasites grown on the transformed tomato lines.

  5. Genome instability in Lactobacillus rhamnosus GG

    NARCIS (Netherlands)

    Sybesma, W.; Molenaar, D.; IJcken, W. van; Venema, K.; Korta, R.

    2013-01-01

    We describe here a comparative genome analysis of three dairy product isolates of Lactobacillus rhamnosus GG (LGG) and the ATCC 53103 reference strain to the published genome sequence of L. rhamnosus GG. The analysis showed that in two of three isolates, major DNA segments were missing from the

  6. Identifying uniformly mutated segments within repeats.

    Science.gov (United States)

    Sahinalp, S Cenk; Eichler, Evan; Goldberg, Paul; Berenbrink, Petra; Friedetzky, Tom; Ergun, Funda

    2004-12-01

    Given a long string of characters from a constant size alphabet we present an algorithm to determine whether its characters have been generated by a single i.i.d. random source. More specifically, consider all possible n-coin models for generating a binary string S, where each bit of S is generated via an independent toss of one of the n coins in the model. The choice of which coin to toss is decided by a random walk on the set of coins where the probability of a coin change is much lower than the probability of using the same coin repeatedly. We present a procedure to evaluate the likelihood of a n-coin model for given S, subject a uniform prior distribution over the parameters of the model (that represent mutation rates and probabilities of copying events). In the absence of detailed prior knowledge of these parameters, the algorithm can be used to determine whether the a posteriori probability for n=1 is higher than for any other n>1. Our algorithm runs in time O(l4logl), where l is the length of S, through a dynamic programming approach which exploits the assumed convexity of the a posteriori probability for n. Our test can be used in the analysis of long alignments between pairs of genomic sequences in a number of ways. For example, functional regions in genome sequences exhibit much lower mutation rates than non-functional regions. Because our test provides means for determining variations in the mutation rate, it may be used to distinguish functional regions from non-functional ones. Another application is in determining whether two highly similar, thus evolutionarily related, genome segments are the result of a single copy event or of a complex series of copy events. This is particularly an issue in evolutionary studies of genome regions rich with repeat segments (especially tandemly repeated segments).

  7. Segmental tuberculosis verrucosa cutis

    Directory of Open Access Journals (Sweden)

    Hanumanthappa H

    1994-01-01

    Full Text Available A case of segmental Tuberculosis Verrucosa Cutis is reported in 10 year old boy. The condition was resembling the ascending lymphangitic type of sporotrichosis. The lesions cleared on treatment with INH 150 mg daily for 6 months.

  8. Chromosome condensation and segmentation

    International Nuclear Information System (INIS)

    Viegas-Pequignot, E.M.

    1981-01-01

    Some aspects of chromosome condensation in mammalians -humans especially- were studied by means of cytogenetic techniques of chromosome banding. Two further approaches were adopted: a study of normal condensation as early as prophase, and an analysis of chromosome segmentation induced by physical (temperature and γ-rays) or chemical agents (base analogues, antibiotics, ...) in order to show out the factors liable to affect condensation. Here 'segmentation' means an abnormal chromosome condensation appearing systematically and being reproducible. The study of normal condensation was made possible by the development of a technique based on cell synchronization by thymidine and giving prophasic and prometaphasic cells. Besides, the possibility of inducing R-banding segmentations on these cells by BrdU (5-bromodeoxyuridine) allowed a much finer analysis of karyotypes. Another technique was developed using 5-ACR (5-azacytidine), it allowed to induce a segmentation similar to the one obtained using BrdU and identify heterochromatic areas rich in G-C bases pairs [fr

  9. International EUREKA: Initialization Segment

    International Nuclear Information System (INIS)

    1982-02-01

    The Initialization Segment creates the starting description of the uranium market. The starting description includes the international boundaries of trade, the geologic provinces, resources, reserves, production, uranium demand forecasts, and existing market transactions. The Initialization Segment is designed to accept information of various degrees of detail, depending on what is known about each region. It must transform this information into a specific data structure required by the Market Segment of the model, filling in gaps in the information through a predetermined sequence of defaults and built in assumptions. A principal function of the Initialization Segment is to create diagnostic messages indicating any inconsistencies in data and explaining which assumptions were used to organize the data base. This permits the user to manipulate the data base until such time the user is satisfied that all the assumptions used are reasonable and that any inconsistencies are resolved in a satisfactory manner

  10. Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome.

    Science.gov (United States)

    Zhang, Wei; Zhang, Mingyi; Zhu, Xianwen; Cao, Yaping; Sun, Qing; Ma, Guojia; Chao, Shiaoman; Yan, Changhui; Xu, Steven S; Cai, Xiwen

    2018-02-01

    This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.

  11. Genome position specific priors for genomic prediction

    DEFF Research Database (Denmark)

    Brøndum, Rasmus Froberg; Su, Guosheng; Lund, Mogens Sandø

    2012-01-01

    casual mutation is different between the populations but affects the same gene. Proportions of a four-distribution mixture for SNP effects in segments of fixed size along the genome are derived from one population and set as location specific prior proportions of distributions of SNP effects...... for the target population. The model was tested using dairy cattle populations of different breeds: 540 Australian Jersey bulls, 2297 Australian Holstein bulls and 5214 Nordic Holstein bulls. The traits studied were protein-, fat- and milk yield. Genotypic data was Illumina 777K SNPs, real or imputed Results...

  12. Fluence map segmentation

    International Nuclear Information System (INIS)

    Rosenwald, J.-C.

    2008-01-01

    The lecture addressed the following topics: 'Interpreting' the fluence map; The sequencer; Reasons for difference between desired and actual fluence map; Principle of 'Step and Shoot' segmentation; Large number of solutions for given fluence map; Optimizing 'step and shoot' segmentation; The interdigitation constraint; Main algorithms; Conclusions on segmentation algorithms (static mode); Optimizing intensity levels and monitor units; Sliding window sequencing; Synchronization to avoid the tongue-and-groove effect; Accounting for physical characteristics of MLC; Importance of corrections for leaf transmission and offset; Accounting for MLC mechanical constraints; The 'complexity' factor; Incorporating the sequencing into optimization algorithm; Data transfer to the treatment machine; Interface between R and V and accelerator; and Conclusions on fluence map segmentation (Segmentation is part of the overall inverse planning procedure; 'Step and Shoot' and 'Dynamic' options are available for most TPS (depending on accelerator model; The segmentation phase tends to come into the optimization loop; The physical characteristics of the MLC have a large influence on final dose distribution; The IMRT plans (MU and relative dose distribution) must be carefully validated). (P.A.)

  13. Gamifying Video Object Segmentation.

    Science.gov (United States)

    Spampinato, Concetto; Palazzo, Simone; Giordano, Daniela

    2017-10-01

    Video object segmentation can be considered as one of the most challenging computer vision problems. Indeed, so far, no existing solution is able to effectively deal with the peculiarities of real-world videos, especially in cases of articulated motion and object occlusions; limitations that appear more evident when we compare the performance of automated methods with the human one. However, manually segmenting objects in videos is largely impractical as it requires a lot of time and concentration. To address this problem, in this paper we propose an interactive video object segmentation method, which exploits, on one hand, the capability of humans to identify correctly objects in visual scenes, and on the other hand, the collective human brainpower to solve challenging and large-scale tasks. In particular, our method relies on a game with a purpose to collect human inputs on object locations, followed by an accurate segmentation phase achieved by optimizing an energy function encoding spatial and temporal constraints between object regions as well as human-provided location priors. Performance analysis carried out on complex video benchmarks, and exploiting data provided by over 60 users, demonstrated that our method shows a better trade-off between annotation times and segmentation accuracy than interactive video annotation and automated video object segmentation approaches.

  14. Strategic market segmentation

    Directory of Open Access Journals (Sweden)

    Maričić Branko R.

    2015-01-01

    Full Text Available Strategic planning of marketing activities is the basis of business success in modern business environment. Customers are not homogenous in their preferences and expectations. Formulating an adequate marketing strategy, focused on realization of company's strategic objectives, requires segmented approach to the market that appreciates differences in expectations and preferences of customers. One of significant activities in strategic planning of marketing activities is market segmentation. Strategic planning imposes a need to plan marketing activities according to strategically important segments on the long term basis. At the same time, there is a need to revise and adapt marketing activities on the short term basis. There are number of criteria based on which market segmentation is performed. The paper will consider effectiveness and efficiency of different market segmentation criteria based on empirical research of customer expectations and preferences. The analysis will include traditional criteria and criteria based on behavioral model. The research implications will be analyzed from the perspective of selection of the most adequate market segmentation criteria in strategic planning of marketing activities.

  15. A conserved segmental duplication within ELA.

    Science.gov (United States)

    Brinkmeyer-Langford, C L; Murphy, W J; Childers, C P; Skow, L C

    2010-12-01

    The assembled genomic sequence of the horse major histocompatibility complex (MHC) (equine lymphocyte antigen, ELA) is very similar to the homologous human HLA, with the notable exception of a large segmental duplication at the boundary of ELA class I and class III that is absent in HLA. The segmental duplication consists of a ∼ 710 kb region of at least 11 repeated blocks: 10 blocks each contain an MHC class I-like sequence and the helicase domain portion of a BAT1-like sequence, and the remaining unit contains the full-length BAT1 gene. Similar genomic features were found in other Perissodactyls, indicating an ancient origin, which is consistent with phylogenetic analyses. Reverse-transcriptase PCR (RT-PCR) of mRNA from peripheral white blood cells of healthy and chronically or acutely infected horses detected transcription from predicted open reading frames in several of the duplicated blocks. This duplication is not present in the sequenced MHCs of most other mammals, although a similar feature at the same relative position is present in the feline MHC (FLA). Striking sequence conservation throughout Perissodactyl evolution is consistent with a functional role for at least some of the genes included within this segmental duplication. © 2010 The Authors, Journal compilation © 2010 Stichting International Foundation for Animal Genetics.

  16. Segmented block copolymers with monodisperse aramide end-segments

    NARCIS (Netherlands)

    Araichimani, A.; Gaymans, R.J.

    2008-01-01

    Segmented block copolymers were synthesized using monodisperse diaramide (TT) as hard segments and PTMO with a molecular weight of 2 900 g · mol-1 as soft segments. The aramide: PTMO segment ratio was increased from 1:1 to 2:1 thereby changing the structure from a high molecular weight multi-block

  17. Full Genome Characterization of Novel DS-1-Like G8P[8] Rotavirus Strains that Have Emerged in Thailand: Reassortment of Bovine and Human Rotavirus Gene Segments in Emerging DS-1-Like Intergenogroup Reassortant Strains.

    Directory of Open Access Journals (Sweden)

    Ratana Tacharoenmuang

    Full Text Available The emergence and rapid spread of unusual DS-1-like intergenogroup reassortant rotavirus strains have been recently reported in Asia, Australia, and Europe. During rotavirus surveillance in Thailand in 2013-2014, novel DS-1-like intergenogroup reassortant strains having G8P[8] genotypes (i.e., strains KKL-17, PCB-79, PCB-84, PCB-85, PCB-103, SKT-107, SWL-12, NP-130, PCB-656, SKT-457, SSKT-269, and SSL-55 were identified in stool samples from hospitalized children with severe diarrhea. In this study, we determined and characterized the complete genomes of these 12 strains (seven strains, KKL-17, PCB-79, PCB-84, PCB-85, PCB-103, SKT-107, and SWL-12, found in 2013 (2013 strains, and five, NP-130, PCB-656, SKT-457, SSKT-269, and SSL-55, in 2014 (2014 strains. On full genomic analysis, all 12 strains showed a unique genotype constellation comprising a mixture of genogroup 1 and 2 genes: G8-P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. With the exception of the G genotype, the unique genotype constellation of the 12 strains (P[8]-I2-R2-C2-M2-A2-N2-T2-E2-H2 was found to be shared with DS-1-like intergenogroup reassortant strains. On phylogenetic analysis, six of the 11 genes of the 2013 strains (VP4, VP2, VP3, NSP1, NSP3, and NSP5 appeared to have originated from DS-1-like intergenogroup reassortant strains, while the remaining four (VP7, VP6, VP1, and NSP2 and one (NSP4 gene appeared to be of bovine and human origin, respectively. Thus, the 2013 strains appeared to be reassortant strains as to DS-1-like intergenogroup reassortant, bovine, bovine-like human, and/or human rotaviruses. On the other hand, five of the 11 genes of the 2014 strains (VP4, VP2, VP3, NSP1, and NSP3 appeared to have originated from DS-1-like intergenogroup reassortant strains, while three (VP7, VP1, and NSP2 and one (NSP4 were assumed to be of bovine and human origin, respectively. Notably, the remaining two genes, VP6 and NSP5, of the 2014 strains appeared to have originated from locally

  18. Rediscovering market segmentation.

    Science.gov (United States)

    Yankelovich, Daniel; Meer, David

    2006-02-01

    In 1964, Daniel Yankelovich introduced in the pages of HBR the concept of nondemographic segmentation, by which he meant the classification of consumers according to criteria other than age, residence, income, and such. The predictive power of marketing studies based on demographics was no longer strong enough to serve as a basis for marketing strategy, he argued. Buying patterns had become far better guides to consumers' future purchases. In addition, properly constructed nondemographic segmentations could help companies determine which products to develop, which distribution channels to sell them in, how much to charge for them, and how to advertise them. But more than 40 years later, nondemographic segmentation has become just as unenlightening as demographic segmentation had been. Today, the technique is used almost exclusively to fulfill the needs of advertising, which it serves mainly by populating commercials with characters that viewers can identify with. It is true that psychographic types like "High-Tech Harry" and "Joe Six-Pack" may capture some truth about real people's lifestyles, attitudes, self-image, and aspirations. But they are no better than demographics at predicting purchase behavior. Thus they give corporate decision makers very little idea of how to keep customers or capture new ones. Now, Daniel Yankelovich returns to these pages, with consultant David Meer, to argue the case for a broad view of nondemographic segmentation. They describe the elements of a smart segmentation strategy, explaining how segmentations meant to strengthen brand identity differ from those capable of telling a company which markets it should enter and what goods to make. And they introduce their "gravity of decision spectrum", a tool that focuses on the form of consumer behavior that should be of the greatest interest to marketers--the importance that consumers place on a product or product category.

  19. Family genome browser: visualizing genomes with pedigree information.

    Science.gov (United States)

    Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

    2015-07-15

    Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  20. Scorpion image segmentation system

    Science.gov (United States)

    Joseph, E.; Aibinu, A. M.; Sadiq, B. A.; Bello Salau, H.; Salami, M. J. E.

    2013-12-01

    Death as a result of scorpion sting has been a major public health problem in developing countries. Despite the high rate of death as a result of scorpion sting, little report exists in literature of intelligent device and system for automatic detection of scorpion. This paper proposed a digital image processing approach based on the floresencing characteristics of Scorpion under Ultra-violet (UV) light for automatic detection and identification of scorpion. The acquired UV-based images undergo pre-processing to equalize uneven illumination and colour space channel separation. The extracted channels are then segmented into two non-overlapping classes. It has been observed that simple thresholding of the green channel of the acquired RGB UV-based image is sufficient for segmenting Scorpion from other background components in the acquired image. Two approaches to image segmentation have also been proposed in this work, namely, the simple average segmentation technique and K-means image segmentation. The proposed algorithm has been tested on over 40 UV scorpion images obtained from different part of the world and results obtained show an average accuracy of 97.7% in correctly classifying the pixel into two non-overlapping clusters. The proposed 1system will eliminate the problem associated with some of the existing manual approaches presently in use for scorpion detection.

  1. Organizational heterogeneity of vertebrate genomes.

    Science.gov (United States)

    Frenkel, Svetlana; Kirzhner, Valery; Korol, Abraham

    2012-01-01

    Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  2. Organizational heterogeneity of vertebrate genomes.

    Directory of Open Access Journals (Sweden)

    Svetlana Frenkel

    Full Text Available Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  3. Segmentation of complex document

    Directory of Open Access Journals (Sweden)

    Souad Oudjemia

    2014-06-01

    Full Text Available In this paper we present a method for segmentation of documents image with complex structure. This technique based on GLCM (Grey Level Co-occurrence Matrix used to segment this type of document in three regions namely, 'graphics', 'background' and 'text'. Very briefly, this method is to divide the document image, in block size chosen after a series of tests and then applying the co-occurrence matrix to each block in order to extract five textural parameters which are energy, entropy, the sum entropy, difference entropy and standard deviation. These parameters are then used to classify the image into three regions using the k-means algorithm; the last step of segmentation is obtained by grouping connected pixels. Two performance measurements are performed for both graphics and text zones; we have obtained a classification rate of 98.3% and a Misclassification rate of 1.79%.

  4. Genetic determinants of P wave duration and PR segment

    NARCIS (Netherlands)

    Verweij, Niek; Mateo Leach, Irene; van den Boogaard, Malou; van Veldhuisen, Dirk J.; Christoffels, Vincent M.; Hillege, Hans L.; van Gilst, Wiek H.; Barnett, Phil; de Boer, Rudolf A.; van der Harst, Pim

    2014-01-01

    The PR interval on the ECG reflects atrial depolarization and atrioventricular nodal delay which can be partially differentiated by P wave duration and PR segment, respectively. Genome-wide association studies have identified several genetic loci for PR interval, but it remains to be determined

  5. Genetic Determinants of P Wave Duration and PR Segment

    NARCIS (Netherlands)

    Verweij, Niek; Mateo Leach, Irene; van den Boogaard, Malou; van Veldhuisen, Dirk J.; Christoffels, Vincent M.; Hillege, Hans L.; van Gilst, Wiek H.; Barnett, Phil; de Boer, Rudolf A.; van der Harst, Pim

    Background-The PR interval on the ECG reflects atrial depolarization and atrioventricular nodal delay which can be partially differentiated by P wave duration and PR segment, respectively. Genome-wide association studies have identified several genetic loci for PR interval, but it remains to be

  6. Connecting textual segments

    DEFF Research Database (Denmark)

    Brügger, Niels

    2017-01-01

    history than just the years of the emergence of the web, the chapter traces the history of how segments of text have deliberately been connected to each other by the use of specific textual and media features, from clay tablets, manuscripts on parchment, and print, among others, to hyperlinks on stand......In “Connecting textual segments: A brief history of the web hyperlink” Niels Brügger investigates the history of one of the most fundamental features of the web: the hyperlink. Based on the argument that the web hyperlink is best understood if it is seen as another step in a much longer and broader...

  7. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae).

    Science.gov (United States)

    Schoville, Sean D; Chen, Yolanda H; Andersson, Martin N; Benoit, Joshua B; Bhandari, Anita; Bowsher, Julia H; Brevik, Kristian; Cappelle, Kaat; Chen, Mei-Ju M; Childers, Anna K; Childers, Christopher; Christiaens, Olivier; Clements, Justin; Didion, Elise M; Elpidina, Elena N; Engsontia, Patamarerk; Friedrich, Markus; García-Robles, Inmaculada; Gibbs, Richard A; Goswami, Chandan; Grapputo, Alessandro; Gruden, Kristina; Grynberg, Marcin; Henrissat, Bernard; Jennings, Emily C; Jones, Jeffery W; Kalsi, Megha; Khan, Sher A; Kumar, Abhishek; Li, Fei; Lombard, Vincent; Ma, Xingzhou; Martynov, Alexander; Miller, Nicholas J; Mitchell, Robert F; Munoz-Torres, Monica; Muszewska, Anna; Oppert, Brenda; Palli, Subba Reddy; Panfilio, Kristen A; Pauchet, Yannick; Perkin, Lindsey C; Petek, Marko; Poelchau, Monica F; Record, Éric; Rinehart, Joseph P; Robertson, Hugh M; Rosendale, Andrew J; Ruiz-Arroyo, Victor M; Smagghe, Guy; Szendrei, Zsofia; Thomas, Gregg W C; Torson, Alex S; Vargas Jentzsch, Iris M; Weirauch, Matthew T; Yates, Ashley D; Yocum, George D; Yoon, June-Sun; Richards, Stephen

    2018-01-31

    The Colorado potato beetle is one of the most challenging agricultural pests to manage. It has shown a spectacular ability to adapt to a variety of solanaceaeous plants and variable climates during its global invasion, and, notably, to rapidly evolve insecticide resistance. To examine evidence of rapid evolutionary change, and to understand the genetic basis of herbivory and insecticide resistance, we tested for structural and functional genomic changes relative to other arthropod species using genome sequencing, transcriptomics, and community annotation. Two factors that might facilitate rapid evolutionary change include transposable elements, which comprise at least 17% of the genome and are rapidly evolving compared to other Coleoptera, and high levels of nucleotide diversity in rapidly growing pest populations. Adaptations to plant feeding are evident in gene expansions and differential expression of digestive enzymes in gut tissues, as well as expansions of gustatory receptors for bitter tasting. Surprisingly, the suite of genes involved in insecticide resistance is similar to other beetles. Finally, duplications in the RNAi pathway might explain why Leptinotarsa decemlineata has high sensitivity to dsRNA. The L. decemlineata genome provides opportunities to investigate a broad range of phenotypes and to develop sustainable methods to control this widely successful pest.

  8. Viral replication kinetics and in vitro cytopathogenicity of parental and reassortant strains of bluetongue virus serotype 1, 6 and 8

    NARCIS (Netherlands)

    Coetzee, M.P.A.; Vuuren, van M.; Stokstad, M.; Myrmel, M.; Gennip, van H.G.P.; Rijn, van P.A.; Venter, E.H.

    2014-01-01

    Bluetongue virus (BTV), a segmented dsRNA virus, is the causative agent of bluetongue (BT), an economically important viral haemorrhagic disease of ruminants. Bluetongue virus can exchange its genome segments in mammalian or insect cells that have been co-infected with more than one strain of the

  9. Potential for La Crosse virus segment reassortment in nature

    Directory of Open Access Journals (Sweden)

    Geske Dave

    2008-12-01

    Full Text Available Abstract The evolutionary success of La Crosse virus (LACV, family Bunyaviridae is due to its ability to adapt to changing conditions through intramolecular genetic changes and segment reassortment. Vertical transmission of LACV in mosquitoes increases the potential for segment reassortment. Studies were conducted to determine if segment reassortment was occurring in naturally infected Aedes triseriatus from Wisconsin and Minnesota in 2000, 2004, 2006 and 2007. Mosquito eggs were collected from various sites in Wisconsin and Minnesota. They were reared in the laboratory and adults were tested for LACV antigen by immunofluorescence assay. RNA was isolated from the abdomen of infected mosquitoes and portions of the small (S, medium (M and large (L viral genome segments were amplified by RT-PCR and sequenced. Overall, the viral sequences from 40 infected mosquitoes and 5 virus isolates were analyzed. Phylogenetic and linkage disequilibrium analyses revealed that approximately 25% of infected mosquitoes and viruses contained reassorted genome segments, suggesting that LACV segment reassortment is frequent in nature.

  10. Adaptive stress response in segmental progeria resembles long-lived dwarfism and calorie restriction in mice

    OpenAIRE

    Ven, Marieke; Andressoo, Jaan-Olle; Holcomb, Valerie; Lindern, Marieke; Jong, Willeke; Zeeuw, Chris; Suh, Yousin; Hasty, Paul; Hoeijmakers, Jan; Horst, Gijsbertus; Mitchell, James

    2006-01-01

    textabstractHow congenital defects causing genome instability can result in the pleiotropic symptoms reminiscent of aging but in a segmental and accelerated fashion remains largely unknown. Most segmental progerias are associated with accelerated fibroblast senescence, suggesting that cellular senescence is a likely contributing mechanism. Contrary to expectations, neither accelerated senescence nor acute oxidative stress hypersensitivity was detected in primary fibroblast or erythroblast cul...

  11. Segmentation in cinema perception.

    Science.gov (United States)

    Carroll, J M; Bever, T G

    1976-03-12

    Viewers perceptually segment moving picture sequences into their cinematically defined units: excerpts that follow short film sequences are recognized faster when the excerpt originally came after a structural cinematic break (a cut or change in the action) than when it originally came before the break.

  12. Dictionary Based Image Segmentation

    DEFF Research Database (Denmark)

    Dahl, Anders Bjorholm; Dahl, Vedrana Andersen

    2015-01-01

    We propose a method for weakly supervised segmentation of natural images, which may contain both textured or non-textured regions. Our texture representation is based on a dictionary of image patches. To divide an image into separated regions with similar texture we use an implicit level sets...

  13. Unsupervised Image Segmentation

    Czech Academy of Sciences Publication Activity Database

    Haindl, Michal; Mikeš, Stanislav

    2014-01-01

    Roč. 36, č. 4 (2014), s. 23-23 R&D Projects: GA ČR(CZ) GA14-10911S Institutional support: RVO:67985556 Keywords : unsupervised image segmentation Subject RIV: BD - Theory of Information http://library.utia.cas.cz/separaty/2014/RO/haindl-0434412.pdf

  14. Metrics for image segmentation

    Science.gov (United States)

    Rees, Gareth; Greenway, Phil; Morray, Denise

    1998-07-01

    An important challenge in mapping image-processing techniques onto applications is the lack of quantitative performance measures. From a systems engineering perspective these are essential if system level requirements are to be decomposed into sub-system requirements which can be understood in terms of algorithm selection and performance optimization. Nowhere in computer vision is this more evident than in the area of image segmentation. This is a vigorous and innovative research activity, but even after nearly two decades of progress, it remains almost impossible to answer the question 'what would the performance of this segmentation algorithm be under these new conditions?' To begin to address this shortcoming, we have devised a well-principled metric for assessing the relative performance of two segmentation algorithms. This allows meaningful objective comparisons to be made between their outputs. It also estimates the absolute performance of an algorithm given ground truth. Our approach is an information theoretic one. In this paper, we describe the theory and motivation of our method, and present practical results obtained from a range of state of the art segmentation methods. We demonstrate that it is possible to measure the objective performance of these algorithms, and to use the information so gained to provide clues about how their performance might be improved.

  15. Extreme genomes

    OpenAIRE

    DeLong, Edward F

    2000-01-01

    The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

  16. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  17. Comparative genomics reveals insights into avian genome evolution and adaptation

    Science.gov (United States)

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

    2015-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

  18. Status of the segment interconnect, cable segment ancillary logic, and the cable segment hybrid driver projects

    International Nuclear Information System (INIS)

    Swoboda, C.; Barsotti, E.; Chappa, S.; Downing, R.; Goeransson, G.; Lensy, D.; Moore, G.; Rotolo, C.; Urish, J.

    1985-01-01

    The FASTBUS Segment Interconnect (SI) provides a communication path between two otherwise independent, asynchronous bus segments. In particular, the Segment Interconnect links a backplane crate segment to a cable segment. All standard FASTBUS address and data transactions can be passed through the SI or any number of SIs and segments in a path. Thus systems of arbitrary connection complexity can be formed, allowing simultaneous independent processing, yet still permitting devices associated with one segment to be accessed from others. The model S1 Segment Interconnect and the Cable Segment Ancillary Logic covered in this report comply with all the mandatory features stated in the FASTBUS specification document DOE/ER-0189. A block diagram of the SI is shown

  19. Market segmentation: Venezuelan ADRs

    Directory of Open Access Journals (Sweden)

    Urbi Garay

    2012-12-01

    Full Text Available The control on foreign exchange imposed by Venezuela in 2003 constitute a natural experiment that allows researchers to observe the effects of exchange controls on stock market segmentation. This paper provides empirical evidence that although the Venezuelan capital market as a whole was highly segmented before the controls were imposed, the shares in the firm CANTV were, through their American Depositary Receipts (ADRs, partially integrated with the global market. Following the imposition of the exchange controls this integration was lost. Research also documents the spectacular and apparently contradictory rise experienced by the Caracas Stock Exchange during the serious economic crisis of 2003. It is argued that, as it happened in Argentina in 2002, the rise in share prices occurred because the depreciation of the Bolívar in the parallel currency market increased the local price of the stocks that had associated ADRs, which were negotiated in dollars.

  20. Scintillation counter, segmented shield

    International Nuclear Information System (INIS)

    Olson, R.E.; Thumim, A.D.

    1975-01-01

    A scintillation counter, particularly for counting gamma ray photons, includes a massive lead radiation shield surrounding a sample-receiving zone. The shield is disassembleable into a plurality of segments to allow facile installation and removal of a photomultiplier tube assembly, the segments being so constructed as to prevent straight-line access of external radiation through the shield into radiation-responsive areas. Provisions are made for accurately aligning the photomultiplier tube with respect to one or more sample-transmitting bores extending through the shield to the sample receiving zone. A sample elevator, used in transporting samples into the zone, is designed to provide a maximum gamma-receiving aspect to maximize the gamma detecting efficiency. (U.S.)

  1. Head segmentation in vertebrates

    OpenAIRE

    Kuratani, Shigeru; Schilling, Thomas

    2008-01-01

    Classic theories of vertebrate head segmentation clearly exemplify the idealistic nature of comparative embryology prior to the 20th century. Comparative embryology aimed at recognizing the basic, primary structure that is shared by all vertebrates, either as an archetype or an ancestral developmental pattern. Modern evolutionary developmental (Evo-Devo) studies are also based on comparison, and therefore have a tendency to reduce complex embryonic anatomy into overly simplified patterns. Her...

  2. Video segmentation using keywords

    Science.gov (United States)

    Ton-That, Vinh; Vong, Chi-Tai; Nguyen-Dao, Xuan-Truong; Tran, Minh-Triet

    2018-04-01

    At DAVIS-2016 Challenge, many state-of-art video segmentation methods achieve potential results, but they still much depend on annotated frames to distinguish between background and foreground. It takes a lot of time and efforts to create these frames exactly. In this paper, we introduce a method to segment objects from video based on keywords given by user. First, we use a real-time object detection system - YOLOv2 to identify regions containing objects that have labels match with the given keywords in the first frame. Then, for each region identified from the previous step, we use Pyramid Scene Parsing Network to assign each pixel as foreground or background. These frames can be used as input frames for Object Flow algorithm to perform segmentation on entire video. We conduct experiments on a subset of DAVIS-2016 dataset in half the size of its original size, which shows that our method can handle many popular classes in PASCAL VOC 2012 dataset with acceptable accuracy, about 75.03%. We suggest widely testing by combining other methods to improve this result in the future.

  3. Market segmentation in behavioral perspective.

    OpenAIRE

    Wells, V.K.; Chang, S.W.; Oliveira-Castro, J.M.; Pallister, J.

    2010-01-01

    A segmentation approach is presented using both traditional demographic segmentation bases (age, social class/occupation, and working status) and a segmentation by benefits sought. The benefits sought in this case are utilitarian and informational reinforcement, variables developed from the Behavioral Perspective Model (BPM). Using data from 1,847 consumers and from a total of 76,682 individual purchases, brand choice and price and reinforcement responsiveness were assessed for each segment a...

  4. Segmentation of time series with long-range fractal correlations

    Science.gov (United States)

    Bernaola-Galván, P.; Oliver, J.L.; Hackenberg, M.; Coronado, A.V.; Ivanov, P.Ch.; Carpena, P.

    2012-01-01

    Segmentation is a standard method of data analysis to identify change-points dividing a nonstationary time series into homogeneous segments. However, for long-range fractal correlated series, most of the segmentation techniques detect spurious change-points which are simply due to the heterogeneities induced by the correlations and not to real nonstationarities. To avoid this oversegmentation, we present a segmentation algorithm which takes as a reference for homogeneity, instead of a random i.i.d. series, a correlated series modeled by a fractional noise with the same degree of correlations as the series to be segmented. We apply our algorithm to artificial series with long-range correlations and show that it systematically detects only the change-points produced by real nonstationarities and not those created by the correlations of the signal. Further, we apply the method to the sequence of the long arm of human chromosome 21, which is known to have long-range fractal correlations. We obtain only three segments that clearly correspond to the three regions of different G + C composition revealed by means of a multi-scale wavelet plot. Similar results have been obtained when segmenting all human chromosome sequences, showing the existence of previously unknown huge compositional superstructures in the human genome. PMID:23645997

  5. Segmentation of time series with long-range fractal correlations.

    Science.gov (United States)

    Bernaola-Galván, P; Oliver, J L; Hackenberg, M; Coronado, A V; Ivanov, P Ch; Carpena, P

    2012-06-01

    Segmentation is a standard method of data analysis to identify change-points dividing a nonstationary time series into homogeneous segments. However, for long-range fractal correlated series, most of the segmentation techniques detect spurious change-points which are simply due to the heterogeneities induced by the correlations and not to real nonstationarities. To avoid this oversegmentation, we present a segmentation algorithm which takes as a reference for homogeneity, instead of a random i.i.d. series, a correlated series modeled by a fractional noise with the same degree of correlations as the series to be segmented. We apply our algorithm to artificial series with long-range correlations and show that it systematically detects only the change-points produced by real nonstationarities and not those created by the correlations of the signal. Further, we apply the method to the sequence of the long arm of human chromosome 21, which is known to have long-range fractal correlations. We obtain only three segments that clearly correspond to the three regions of different G + C composition revealed by means of a multi-scale wavelet plot. Similar results have been obtained when segmenting all human chromosome sequences, showing the existence of previously unknown huge compositional superstructures in the human genome.

  6. Segmenting the Adult Education Market.

    Science.gov (United States)

    Aurand, Tim

    1994-01-01

    Describes market segmentation and how the principles of segmentation can be applied to the adult education market. Indicates that applying segmentation techniques to adult education programs results in programs that are educationally and financially satisfying and serve an appropriate population. (JOW)

  7. Market Segmentation for Information Services.

    Science.gov (United States)

    Halperin, Michael

    1981-01-01

    Discusses the advantages and limitations of market segmentation as strategy for the marketing of information services made available by nonprofit organizations, particularly libraries. Market segmentation is defined, a market grid for libraries is described, and the segmentation of information services is outlined. A 16-item reference list is…

  8. Albedo estimation for scene segmentation

    Energy Technology Data Exchange (ETDEWEB)

    Lee, C H; Rosenfeld, A

    1983-03-01

    Standard methods of image segmentation do not take into account the three-dimensional nature of the underlying scene. For example, histogram-based segmentation tacitly assumes that the image intensity is piecewise constant, and this is not true when the scene contains curved surfaces. This paper introduces a method of taking 3d information into account in the segmentation process. The image intensities are adjusted to compensate for the effects of estimated surface orientation; the adjusted intensities can be regarded as reflectivity estimates. When histogram-based segmentation is applied to these new values, the image is segmented into parts corresponding to surfaces of constant reflectivity in the scene. 7 references.

  9. FRAMEWORK FOR COMPARING SEGMENTATION ALGORITHMS

    Directory of Open Access Journals (Sweden)

    G. Sithole

    2015-05-01

    Full Text Available The notion of a ‘Best’ segmentation does not exist. A segmentation algorithm is chosen based on the features it yields, the properties of the segments (point sets it generates, and the complexity of its algorithm. The segmentation is then assessed based on a variety of metrics such as homogeneity, heterogeneity, fragmentation, etc. Even after an algorithm is chosen its performance is still uncertain because the landscape/scenarios represented in a point cloud have a strong influence on the eventual segmentation. Thus selecting an appropriate segmentation algorithm is a process of trial and error. Automating the selection of segmentation algorithms and their parameters first requires methods to evaluate segmentations. Three common approaches for evaluating segmentation algorithms are ‘goodness methods’, ‘discrepancy methods’ and ‘benchmarks’. Benchmarks are considered the most comprehensive method of evaluation. This paper shortcomings in current benchmark methods are identified and a framework is proposed that permits both a visual and numerical evaluation of segmentations for different algorithms, algorithm parameters and evaluation metrics. The concept of the framework is demonstrated on a real point cloud. Current results are promising and suggest that it can be used to predict the performance of segmentation algorithms.

  10. Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

    Directory of Open Access Journals (Sweden)

    Gendrault-Jacquemard A

    2005-07-01

    Full Text Available Abstract Background Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. Results Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. Conclusion The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

  11. Extreme-Scale De Novo Genome Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Georganas, Evangelos [Intel Corporation, Santa Clara, CA (United States); Hofmeyr, Steven [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.; Egan, Rob [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division; Buluc, Aydin [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.; Oliker, Leonid [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.; Rokhsar, Daniel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division; Yelick, Katherine [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.

    2017-09-26

    De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. Genome assembly software has many components, each of which stresses different components of a computer system. This chapter explains the computational challenges involved in each step of the HipMer pipeline, the key distributed data structures, and communication costs in detail. We present performance results of assembling the human genome and the large hexaploid wheat genome on large supercomputers up to tens of thousands of cores.

  12. Optimally segmented magnetic structures

    DEFF Research Database (Denmark)

    Insinga, Andrea Roberto; Bahl, Christian; Bjørk, Rasmus

    We present a semi-analytical algorithm for magnet design problems, which calculates the optimal way to subdivide a given design region into uniformly magnetized segments.The availability of powerful rare-earth magnetic materials such as Nd-Fe-B has broadened the range of applications of permanent...... is not available.We will illustrate the results for magnet design problems from different areas, such as electric motors/generators (as the example in the picture), beam focusing for particle accelerators and magnetic refrigeration devices.......We present a semi-analytical algorithm for magnet design problems, which calculates the optimal way to subdivide a given design region into uniformly magnetized segments.The availability of powerful rare-earth magnetic materials such as Nd-Fe-B has broadened the range of applications of permanent...... magnets[1][2]. However, the powerful rare-earth magnets are generally expensive, so both the scientific and industrial communities have devoted a lot of effort into developing suitable design methods. Even so, many magnet optimization algorithms either are based on heuristic approaches[3...

  13. Segmentation of the Infant Food Market

    OpenAIRE

    Hrůzová, Daniela

    2015-01-01

    The theoretical part covers general market segmentation, namely the marketing importance of differences among consumers, the essence of market segmentation, its main conditions and the process of segmentation, which consists of four consecutive phases - defining the market, determining important criteria, uncovering segments and developing segment profiles. The segmentation criteria, segmentation approaches, methods and techniques for the process of market segmentation are also described in t...

  14. Genome Imprinting

    Indian Academy of Sciences (India)

    the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

  15. Baculovirus Genomics

    NARCIS (Netherlands)

    Oers, van M.M.; Vlak, J.M.

    2007-01-01

    Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

  16. Genomic Testing

    Science.gov (United States)

    ... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

  17. Ancient genomes

    OpenAIRE

    Hoelzel, A Rus

    2005-01-01

    Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

  18. Phasing multi-segment undulators

    International Nuclear Information System (INIS)

    Chavanne, J.; Elleaume, P.; Vaerenbergh, P. Van

    1996-01-01

    An important issue in the manufacture of multi-segment undulators as a source of synchrotron radiation or as a free-electron laser (FEL) is the phasing between successive segments. The state of the art is briefly reviewed, after which a novel pure permanent magnet phasing section that is passive and does not require any current is presented. The phasing section allows the introduction of a 6 mm longitudinal gap between each segment, resulting in complete mechanical independence and reduced magnetic interaction between segments. The tolerance of the longitudinal positioning of one segment with respect to the next is found to be 2.8 times lower than that of conventional phasing. The spectrum at all gaps and useful harmonics is almost unchanged when compared with a single-segment undulator of the same total length. (au) 3 refs

  19. The LOFT Ground Segment

    DEFF Research Database (Denmark)

    Bozzo, E.; Antonelli, A.; Argan, A.

    2014-01-01

    targets per orbit (~90 minutes), providing roughly ~80 GB of proprietary data per day (the proprietary period will be 12 months). The WFM continuously monitors about 1/3 of the sky at a time and provides data for about ~100 sources a day, resulting in a total of ~20 GB of additional telemetry. The LOFT...... Burst alert System additionally identifies on-board bright impulsive events (e.g., Gamma-ray Bursts, GRBs) and broadcasts the corresponding position and trigger time to the ground using a dedicated system of ~15 VHF receivers. All WFM data are planned to be made public immediately. In this contribution...... we summarize the planned organization of the LOFT ground segment (GS), as established in the mission Yellow Book 1 . We describe the expected GS contributions from ESA and the LOFT consortium. A review is provided of the planned LOFT data products and the details of the data flow, archiving...

  20. Segmented heat exchanger

    Science.gov (United States)

    Baldwin, Darryl Dean; Willi, Martin Leo; Fiveland, Scott Byron; Timmons, Kristine Ann

    2010-12-14

    A segmented heat exchanger system for transferring heat energy from an exhaust fluid to a working fluid. The heat exchanger system may include a first heat exchanger for receiving incoming working fluid and the exhaust fluid. The working fluid and exhaust fluid may travel through at least a portion of the first heat exchanger in a parallel flow configuration. In addition, the heat exchanger system may include a second heat exchanger for receiving working fluid from the first heat exchanger and exhaust fluid from a third heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the second heat exchanger in a counter flow configuration. Furthermore, the heat exchanger system may include a third heat exchanger for receiving working fluid from the second heat exchanger and exhaust fluid from the first heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the third heat exchanger in a parallel flow configuration.

  1. International EUREKA: Market Segment

    International Nuclear Information System (INIS)

    1982-03-01

    The purpose of the Market Segment of the EUREKA model is to simultaneously project uranium market prices, uranium supply and purchasing activities. The regional demands are extrinsic. However, annual forward contracting activities to meet these demands as well as inventory requirements are calculated. The annual price forecast is based on relatively short term, forward balances between available supply and desired purchases. The forecasted prices and extrapolated price trends determine decisions related to exploration and development, new production operations, and the operation of existing capacity. Purchasing and inventory requirements are also adjusted based on anticipated prices. The calculation proceeds one year at a time. Conditions calculated at the end of one year become the starting conditions for the calculation in the subsequent year

  2. Probabilistic retinal vessel segmentation

    Science.gov (United States)

    Wu, Chang-Hua; Agam, Gady

    2007-03-01

    Optic fundus assessment is widely used for diagnosing vascular and non-vascular pathology. Inspection of the retinal vasculature may reveal hypertension, diabetes, arteriosclerosis, cardiovascular disease and stroke. Due to various imaging conditions retinal images may be degraded. Consequently, the enhancement of such images and vessels in them is an important task with direct clinical applications. We propose a novel technique for vessel enhancement in retinal images that is capable of enhancing vessel junctions in addition to linear vessel segments. This is an extension of vessel filters we have previously developed for vessel enhancement in thoracic CT scans. The proposed approach is based on probabilistic models which can discern vessels and junctions. Evaluation shows the proposed filter is better than several known techniques and is comparable to the state of the art when evaluated on a standard dataset. A ridge-based vessel tracking process is applied on the enhanced image to demonstrate the effectiveness of the enhancement filter.

  3. Segmented rail linear induction motor

    Science.gov (United States)

    Cowan, Jr., Maynard; Marder, Barry M.

    1996-01-01

    A segmented rail linear induction motor has a segmented rail consisting of a plurality of nonferrous electrically conductive segments aligned along a guideway. The motor further includes a carriage including at least one pair of opposed coils fastened to the carriage for moving the carriage. A power source applies an electric current to the coils to induce currents in the conductive surfaces to repel the coils from adjacent edges of the conductive surfaces.

  4. Segmentation-DrivenTomographic Reconstruction

    DEFF Research Database (Denmark)

    Kongskov, Rasmus Dalgas

    such that the segmentation subsequently can be carried out by use of a simple segmentation method, for instance just a thresholding method. We tested the advantages of going from a two-stage reconstruction method to a one stage segmentation-driven reconstruction method for the phase contrast tomography reconstruction......The tomographic reconstruction problem is concerned with creating a model of the interior of an object from some measured data, typically projections of the object. After reconstructing an object it is often desired to segment it, either automatically or manually. For computed tomography (CT...

  5. Automated medical image segmentation techniques

    Directory of Open Access Journals (Sweden)

    Sharma Neeraj

    2010-01-01

    Full Text Available Accurate segmentation of medical images is a key step in contouring during radiotherapy planning. Computed topography (CT and Magnetic resonance (MR imaging are the most widely used radiographic techniques in diagnosis, clinical studies and treatment planning. This review provides details of automated segmentation methods, specifically discussed in the context of CT and MR images. The motive is to discuss the problems encountered in segmentation of CT and MR images, and the relative merits and limitations of methods currently available for segmentation of medical images.

  6. ADVANCED CLUSTER BASED IMAGE SEGMENTATION

    Directory of Open Access Journals (Sweden)

    D. Kesavaraja

    2011-11-01

    Full Text Available This paper presents efficient and portable implementations of a useful image segmentation technique which makes use of the faster and a variant of the conventional connected components algorithm which we call parallel Components. In the Modern world majority of the doctors are need image segmentation as the service for various purposes and also they expect this system is run faster and secure. Usually Image segmentation Algorithms are not working faster. In spite of several ongoing researches in Conventional Segmentation and its Algorithms might not be able to run faster. So we propose a cluster computing environment for parallel image Segmentation to provide faster result. This paper is the real time implementation of Distributed Image Segmentation in Clustering of Nodes. We demonstrate the effectiveness and feasibility of our method on a set of Medical CT Scan Images. Our general framework is a single address space, distributed memory programming model. We use efficient techniques for distributing and coalescing data as well as efficient combinations of task and data parallelism. The image segmentation algorithm makes use of an efficient cluster process which uses a novel approach for parallel merging. Our experimental results are consistent with the theoretical analysis and practical results. It provides the faster execution time for segmentation, when compared with Conventional method. Our test data is different CT scan images from the Medical database. More efficient implementations of Image Segmentation will likely result in even faster execution times.

  7. Genomics of Escherichia and Shigella

    Science.gov (United States)

    Perna, Nicole T.

    The laboratory workhorse Escherichia coli K-12 is among the most intensively studied living organisms on earth, and this single strain serves as the model system behind much of our understanding of prokaryotic molecular biology. Dense genome sequencing and recent insightful comparative analyses are making the species E. coli, as a whole, an emerging system for studying prokaryotic population genetics and the relationship between system-scale, or genome-scale, molecular evolution and complex traits like host range and pathogenic potential. Genomic perspective has revealed a coherent but dynamic species united by intraspecific gene flow via homologous lateral or horizontal transfer and differentiated by content flux mediated by acquisition of DNA segments from interspecies transfers.

  8. Annotating non-coding regions of the genome.

    Science.gov (United States)

    Alexander, Roger P; Fang, Gang; Rozowsky, Joel; Snyder, Michael; Gerstein, Mark B

    2010-08-01

    Most of the human genome consists of non-protein-coding DNA. Recently, progress has been made in annotating these non-coding regions through the interpretation of functional genomics experiments and comparative sequence analysis. One can conceptualize functional genomics analysis as involving a sequence of steps: turning the output of an experiment into a 'signal' at each base pair of the genome; smoothing this signal and segmenting it into small blocks of initial annotation; and then clustering these small blocks into larger derived annotations and networks. Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis.

  9. Signals of historical interlocus gene conversion in human segmental duplications.

    Directory of Open Access Journals (Sweden)

    Beth L Dumont

    Full Text Available Standard methods of DNA sequence analysis assume that sequences evolve independently, yet this assumption may not be appropriate for segmental duplications that exchange variants via interlocus gene conversion (IGC. Here, we use high quality multiple sequence alignments from well-annotated segmental duplications to systematically identify IGC signals in the human reference genome. Our analysis combines two complementary methods: (i a paralog quartet method that uses DNA sequence simulations to identify a statistical excess of sites consistent with inter-paralog exchange, and (ii the alignment-based method implemented in the GENECONV program. One-quarter (25.4% of the paralog families in our analysis harbor clear IGC signals by the quartet approach. Using GENECONV, we identify 1477 gene conversion tracks that cumulatively span 1.54 Mb of the genome. Our analyses confirm the previously reported high rates of IGC in subtelomeric regions and Y-chromosome palindromes, and identify multiple novel IGC hotspots, including the pregnancy specific glycoproteins and the neuroblastoma breakpoint gene families. Although the duplication history of a paralog family is described by a single tree, we show that IGC has introduced incredible site-to-site variation in the evolutionary relationships among paralogs in the human genome. Our findings indicate that IGC has left significant footprints in patterns of sequence diversity across segmental duplications in the human genome, out-pacing the contributions of single base mutation by orders of magnitude. Collectively, the IGC signals we report comprise a catalog that will provide a critical reference for interpreting observed patterns of DNA sequence variation across duplicated genomic regions, including targets of recent adaptive evolution in humans.

  10. Herbarium genomics

    DEFF Research Database (Denmark)

    Bakker, Freek T.; Lei, Di; Yu, Jiaying

    2016-01-01

    Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

  11. Region segmentation along image sequence

    International Nuclear Information System (INIS)

    Monchal, L.; Aubry, P.

    1995-01-01

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs

  12. Market segmentation using perceived constraints

    Science.gov (United States)

    Jinhee Jun; Gerard Kyle; Andrew Mowen

    2008-01-01

    We examined the practical utility of segmenting potential visitors to Cleveland Metroparks using their constraint profiles. Our analysis identified three segments based on their scores on the dimensions of constraints: Other priorities--visitors who scored the highest on 'other priorities' dimension; Highly Constrained--visitors who scored relatively high on...

  13. Market Segmentation: An Instructional Module.

    Science.gov (United States)

    Wright, Peter H.

    A concept-based introduction to market segmentation is provided in this instructional module for undergraduate and graduate transportation-related courses. The material can be used in many disciplines including engineering, business, marketing, and technology. The concept of market segmentation is primarily a transportation planning technique by…

  14. IFRS 8 – OPERATING SEGMENTS

    Directory of Open Access Journals (Sweden)

    BOCHIS LEONICA

    2009-05-01

    Full Text Available Segment reporting in accordance with IFRS 8 will be mandatory for annual financial statements covering periods beginning on or after 1 January 2009. The standards replaces IAS 14, Segment Reporting, from that date. The objective of IFRS 8 is to require

  15. Reduplication Facilitates Early Word Segmentation

    Science.gov (United States)

    Ota, Mitsuhiko; Skarabela, Barbora

    2018-01-01

    This study explores the possibility that early word segmentation is aided by infants' tendency to segment words with repeated syllables ("reduplication"). Twenty-four nine-month-olds were familiarized with passages containing one novel reduplicated word and one novel non-reduplicated word. Their central fixation times in response to…

  16. The Importance of Marketing Segmentation

    Science.gov (United States)

    Martin, Gillian

    2011-01-01

    The rationale behind marketing segmentation is to allow businesses to focus on their consumers' behaviors and purchasing patterns. If done effectively, marketing segmentation allows an organization to achieve its highest return on investment (ROI) in turn for its marketing and sales expenses. If an organization markets its products or services to…

  17. Essays in international market segmentation

    NARCIS (Netherlands)

    Hofstede, ter F.

    1999-01-01

    The primary objective of this thesis is to develop and validate new methodologies to improve the effectiveness of international segmentation strategies. The current status of international market segmentation research is reviewed in an introductory chapter, which provided a number of

  18. Genome-Wide Characterization and Expression Profiling of Sugar Transporter Family in the Whitefly, Bemisia tabaci (Gennadius (Hemiptera: Aleyrodidae

    Directory of Open Access Journals (Sweden)

    Zezhong Yang

    2017-05-01

    Full Text Available Sugar transporters (STs play pivotal roles in the growth, development, and stress responses of phloem-sucking insects, such as the whitefly, Bemisia tabaci. In this study, 137 sugar transporters (STs were identified based on analysis of the genome and transcriptome of B. tabaci MEAM1. B. tabaci MEAM1 encodes a larger number of STs than other selected insects. Phylogenetic and molecular evolution analysis showed that the 137 STs formed three expanded clades and that the genes in Sternorrhyncha expanded clades had accelerated rates of evolution. B. tabaci sugar transporters (BTSTs were divided into three groups based on their expression profiles across developmental stages; however, no host-specific BTST was found in B. tabaci fed on different host plants. Feeding of B. tabaci adults with feeding diet containing dsRNA significantly reduced the transcript level of the target genes in B. tabaci and mortality was significantly improved in B. tabaci fed on dsRNA compared to the control, which indicates the sugar transporters may be used as potential RNAi targets for B. tabaci bio-control. These results provide a foundation for further studies of STs in B. tabaci.

  19. Segmental vitiligo with segmental morphea: An autoimmune link?

    Directory of Open Access Journals (Sweden)

    Pravesh Yadav

    2014-01-01

    Full Text Available An 18-year old girl with segmental vitiligo involving the left side of the trunk and left upper limb with segmental morphea involving the right side of trunk and right upper limb without any deeper involvement is illustrated. There was no history of preceding drug intake, vaccination, trauma, radiation therapy, infection, or hormonal therapy. Family history of stable vitiligo in her brother and a history of type II diabetes mellitus in the father were elicited. Screening for autoimmune diseases and antithyroid antibody was negative. An autoimmune link explaining the co-occurrence has been proposed. Cutaneous mosiacism could explain the presence of both the pathologies in a segmental distribution.

  20. Genomic profiling of plasmablastic lymphoma using array comparative genomic hybridization (aCGH: revealing significant overlapping genomic lesions with diffuse large B-cell lymphoma

    Directory of Open Access Journals (Sweden)

    Lu Xin-Yan

    2009-11-01

    Full Text Available Abstract Background Plasmablastic lymphoma (PL is a subtype of diffuse large B-cell lymphoma (DLBCL. Studies have suggested that tumors with PL morphology represent a group of neoplasms with clinopathologic characteristics corresponding to different entities including extramedullary plasmablastic tumors associated with plasma cell myeloma (PCM. The goal of the current study was to evaluate the genetic similarities and differences among PL, DLBCL (AIDS-related and non AIDS-related and PCM using array-based comparative genomic hybridization. Results Examination of genomic data in PL revealed that the most frequent segmental gain (> 40% include: 1p36.11-1p36.33, 1p34.1-1p36.13, 1q21.1-1q23.1, 7q11.2-7q11.23, 11q12-11q13.2 and 22q12.2-22q13.3. This correlated with segmental gains occurring in high frequency in DLBCL (AIDS-related and non AIDS-related cases. There were some segmental gains and some segmental loss that occurred in PL but not in the other types of lymphoma suggesting that these foci may contain genes responsible for the differentiation of this lymphoma. Additionally, some segmental gains and some segmental loss occurred only in PL and AIDS associated DLBCL suggesting that these foci may be associated with HIV infection. Furthermore, some segmental gains and some segmental loss occurred only in PL and PCM suggesting that these lesions may be related to plasmacytic differentiation. Conclusion To the best of our knowledge, the current study represents the first genomic exploration of PL. The genomic aberration pattern of PL appears to be more similar to that of DLBCL (AIDS-related or non AIDS-related than to PCM. Our findings suggest that PL may remain best classified as a subtype of DLBCL at least at the genome level.

  1. Using Predictability for Lexical Segmentation.

    Science.gov (United States)

    Çöltekin, Çağrı

    2017-09-01

    This study investigates a strategy based on predictability of consecutive sub-lexical units in learning to segment a continuous speech stream into lexical units using computational modeling and simulations. Lexical segmentation is one of the early challenges during language acquisition, and it has been studied extensively through psycholinguistic experiments as well as computational methods. However, despite strong empirical evidence, the explicit use of predictability of basic sub-lexical units in models of segmentation is underexplored. This paper presents an incremental computational model of lexical segmentation for exploring the usefulness of predictability for lexical segmentation. We show that the predictability cue is a strong cue for segmentation. Contrary to earlier reports in the literature, the strategy yields state-of-the-art segmentation performance with an incremental computational model that uses only this particular cue in a cognitively plausible setting. The paper also reports an in-depth analysis of the model, investigating the conditions affecting the usefulness of the strategy. Copyright © 2016 Cognitive Science Society, Inc.

  2. The Hierarchy of Segment Reports

    Directory of Open Access Journals (Sweden)

    Danilo Dorović

    2015-05-01

    Full Text Available The article presents an attempt to find the connection between reports created for managers responsible for different business segments. With this purpose, the hierarchy of the business reporting segments is proposed. This can lead to better understanding of the expenses under common responsibility of more than one manager since these expenses should be in more than one report. The structure of cost defined per business segment hierarchy with the aim of new, unusual but relevant cost structure for management can be established. Both could potentially bring new information benefits for management in the context of profit reporting.

  3. Segmental dilatation of the ileum

    Directory of Open Access Journals (Sweden)

    Tune-Yie Shih

    2017-01-01

    Full Text Available A 2-year-old boy was sent to the emergency department with the chief problem of abdominal pain for 1 day. He was just discharged from the pediatric ward with the diagnosis of mycoplasmal pneumonia and paralytic ileus. After initial examinations and radiographic investigations, midgut volvulus was impressed. An emergency laparotomy was performed. Segmental dilatation of the ileum with volvulus was found. The operative procedure was resection of the dilated ileal segment with anastomosis. The postoperative recovery was uneventful. The unique abnormality of gastrointestinal tract – segmental dilatation of the ileum, is described in details and the literature is reviewed.

  4. Accounting for segment correlations in segmented gamma-ray scans

    International Nuclear Information System (INIS)

    Sheppard, G.A.; Prettyman, T.H.; Piquette, E.C.

    1994-01-01

    In a typical segmented gamma-ray scanner (SGS), the detector's field of view is collimated so that a complete horizontal slice or segment of the desired thickness is visible. Ordinarily, the collimator is not deep enough to exclude gamma rays emitted from sample volumes above and below the segment aligned with the collimator. This can lead to assay biases, particularly for certain radioactive-material distributions. Another consequence of the collimator's low aspect ratio is that segment assays at the top and bottom of the sample are biased low because the detector's field of view is not filled. This effect is ordinarily countered by placing the sample on a low-Z pedestal and scanning one or more segment thicknesses below and above the sample. This takes extra time, however, We have investigated a number of techniques that both account for correlated segments and correct for end effects in SGS assays. Also, we have developed an algorithm that facilitates estimates of assay precision. Six calculation methods have been compared by evaluating the results of thousands of simulated, assays for three types of gamma-ray source distribution and ten masses. We will report on these computational studies and their experimental verification

  5. Molecular cloning and sequence analysis of VP6 gene of giant ...

    African Journals Online (AJOL)

    Rotavirus (family Reoviridae) is the leading cause of severe gastroenteritis in human and animals worldwide. The genome of rotavirus comprises of 11 segments of dsRNA and encodes six structural proteins (VP1 to VP4, VP6 and VP7) and six non structural proteins (NSP1 to NSP6). VP6 is a group of antigen of rotavirus ...

  6. Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.

    Science.gov (United States)

    Jeong, Young-Min; Kim, Namshin; Ahn, Byung Ohg; Oh, Mijin; Chung, Won-Hyong; Chung, Hee; Jeong, Seongmun; Lim, Ki-Byung; Hwang, Yoon-Jung; Kim, Goon-Bo; Baek, Seunghoon; Choi, Sang-Bong; Hyung, Dae-Jin; Lee, Seung-Won; Sohn, Seong-Han; Kwon, Soo-Jin; Jin, Mina; Seol, Young-Joo; Chae, Won Byoung; Choi, Keun Jin; Park, Beom-Seok; Yu, Hee-Ju; Mun, Jeong-Hwan

    2016-07-01

    This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

  7. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

  8. What are Segments in Google Analytics

    Science.gov (United States)

    Segments find all sessions that meet a specific condition. You can then apply this segment to any report in Google Analytics (GA). Segments are a way of identifying sessions and users while filters identify specific events, like pageviews.

  9. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  10. CLG for Automatic Image Segmentation

    OpenAIRE

    Christo Ananth; S.Santhana Priya; S.Manisha; T.Ezhil Jothi; M.S.Ramasubhaeswari

    2017-01-01

    This paper proposes an automatic segmentation method which effectively combines Active Contour Model, Live Wire method and Graph Cut approach (CLG). The aim of Live wire method is to provide control to the user on segmentation process during execution. Active Contour Model provides a statistical model of object shape and appearance to a new image which are built during a training phase. In the graph cut technique, each pixel is represented as a node and the distance between those nodes is rep...

  11. Market segmentation, targeting and positioning

    OpenAIRE

    Camilleri, Mark Anthony

    2017-01-01

    Businesses may not be in a position to satisfy all of their customers, every time. It may prove difficult to meet the exact requirements of each individual customer. People do not have identical preferences, so rarely does one product completely satisfy everyone. Many companies may usually adopt a strategy that is known as target marketing. This strategy involves dividing the market into segments and developing products or services to these segments. A target marketing strategy is focused on ...

  12. Recognition Using Classification and Segmentation Scoring

    National Research Council Canada - National Science Library

    Kimball, Owen; Ostendorf, Mari; Rohlicek, Robin

    1992-01-01

    .... We describe an approach to connected word recognition that allows the use of segmental information through an explicit decomposition of the recognition criterion into classification and segmentation scoring...

  13. Exposure to low-dose X-rays promotes peculiar autophagic cell death in Drosophila melanogaster, an effect that can be regulated by the inducible expression of Hml dsRNA

    Energy Technology Data Exchange (ETDEWEB)

    Kanao, Tomoko [Department of Radiological Sciences, International University of Health and Welfare, Kitakanemaru 2600-1, Ohtawara-shi, Tochigi-ken 324-8501 (Japan); Miyachi, Yukihisa [Department of Radiological Sciences, International University of Health and Welfare, Kitakanemaru 2600-1, Ohtawara-shi, Tochigi-ken 324-8501 (Japan)]. E-mail: ymiyachi@iuhw.ac.jp

    2006-03-20

    We previously reported that to induce an early emergence effect with low-dose X-irradiation in Drosophila, exposure during the prepupae stage is necessary. The present study examined the mechanism by which low-dose radiation rapidly eliminates larval cells and activates the formation of the imaginal discs during metamorphosis. Upon exposure to 0.5 Gy X-rays at 2 h after puparium formation (APF), the larval salivary glands swelled and were surrounded by remarkably thick structures containing an acid phosphatase (Acph) enzyme, implicating a peculiar autophagic cell death. TUNEL staining revealed the presence of DNA fragmentations compared with cells from sham controls which remained unchanged until 12 h APF. Additionally, the salivary glands of exposed flies were completely destroyed by 10 h APF. Furthermore, exposure to 0.5 Gy X-rays also facilitated the activity of the engulfment function of dendritic cells (DCs); they were generated in the larval salivary glands, engulfed the cell corpses and finally moved to the fat body. Data from an experiment demonstrating the inducible expression of Hml double-stranded RNA (dsRNA) indicate that a slow rate of engulfment of larval cells results in a longer time to emergence. Thus, the animals subjected to low-dose X-rays activated autophagic processes, resulting in significantly faster adult eclosion.

  14. Exposure to low-dose X-rays promotes peculiar autophagic cell death in Drosophila melanogaster, an effect that can be regulated by the inducible expression of Hml dsRNA

    International Nuclear Information System (INIS)

    Kanao, Tomoko; Miyachi, Yukihisa

    2006-01-01

    We previously reported that to induce an early emergence effect with low-dose X-irradiation in Drosophila, exposure during the prepupae stage is necessary. The present study examined the mechanism by which low-dose radiation rapidly eliminates larval cells and activates the formation of the imaginal discs during metamorphosis. Upon exposure to 0.5 Gy X-rays at 2 h after puparium formation (APF), the larval salivary glands swelled and were surrounded by remarkably thick structures containing an acid phosphatase (Acph) enzyme, implicating a peculiar autophagic cell death. TUNEL staining revealed the presence of DNA fragmentations compared with cells from sham controls which remained unchanged until 12 h APF. Additionally, the salivary glands of exposed flies were completely destroyed by 10 h APF. Furthermore, exposure to 0.5 Gy X-rays also facilitated the activity of the engulfment function of dendritic cells (DCs); they were generated in the larval salivary glands, engulfed the cell corpses and finally moved to the fat body. Data from an experiment demonstrating the inducible expression of Hml double-stranded RNA (dsRNA) indicate that a slow rate of engulfment of larval cells results in a longer time to emergence. Thus, the animals subjected to low-dose X-rays activated autophagic processes, resulting in significantly faster adult eclosion

  15. Comparative Genomics

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 8. Comparative Genomics - A Powerful New Tool in Biology. Anand K Bachhawat. General Article Volume 11 Issue 8 August 2006 pp 22-40. Fulltext. Click here to view fulltext PDF. Permanent link:

  16. Forces shaping the fastest evolving regions in the human genome

    DEFF Research Database (Denmark)

    Pollard, Katherine S; Salama, Sofie R; King, Bryan

    2006-01-01

    Comparative genomics allow us to search the human genome for segments that were extensively changed in the last approximately 5 million years since divergence from our common ancestor with chimpanzee, but are highly conserved in other species and thus are likely to be functional. We found 202...... genomic elements that are highly conserved in vertebrates but show evidence of significantly accelerated substitution rates in human. These are mostly in non-coding DNA, often near genes associated with transcription and DNA binding. Resequencing confirmed that the five most accelerated elements...... contributed to accelerated evolution of the fastest evolving elements in the human genome....

  17. Methods of evaluating segmentation characteristics and segmentation of major faults

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Kie Hwa; Chang, Tae Woo; Kyung, Jai Bok [Seoul National Univ., Seoul (Korea, Republic of)] (and others)

    2000-03-15

    Seismological, geological, and geophysical studies were made for reasonable segmentation of the Ulsan fault and the results are as follows. One- and two- dimensional electrical surveys revealed clearly the fault fracture zone enlarges systematically northward and southward from the vicinity of Mohwa-ri, indicating Mohwa-ri is at the seismic segment boundary. Field Geological survey and microscope observation of fault gouge indicates that the Quaternary faults in the area are reactivated products of the preexisting faults. Trench survey of the Chonbuk fault Galgok-ri revealed thrust faults and cumulative vertical displacement due to faulting during the late Quaternary with about 1.1-1.9 m displacement per event; the latest event occurred from 14000 to 25000 yrs. BP. The seismic survey showed the basement surface os cut by numerous reverse faults and indicated the possibility that the boundary between Kyeongsangbukdo and Kyeongsannamdo may be segment boundary.

  18. Segmentation by Large Scale Hypothesis Testing - Segmentation as Outlier Detection

    DEFF Research Database (Denmark)

    Darkner, Sune; Dahl, Anders Lindbjerg; Larsen, Rasmus

    2010-01-01

    a microscope and we show how the method can handle transparent particles with significant glare point. The method generalizes to other problems. THis is illustrated by applying the method to camera calibration images and MRI of the midsagittal plane for gray and white matter separation and segmentation......We propose a novel and efficient way of performing local image segmentation. For many applications a threshold of pixel intensities is sufficient but determine the appropriate threshold value can be difficult. In cases with large global intensity variation the threshold value has to be adapted...... locally. We propose a method based on large scale hypothesis testing with a consistent method for selecting an appropriate threshold for the given data. By estimating the background distribution we characterize the segment of interest as a set of outliers with a certain probability based on the estimated...

  19. Methods of evaluating segmentation characteristics and segmentation of major faults

    International Nuclear Information System (INIS)

    Lee, Kie Hwa; Chang, Tae Woo; Kyung, Jai Bok

    2000-03-01

    Seismological, geological, and geophysical studies were made for reasonable segmentation of the Ulsan fault and the results are as follows. One- and two- dimensional electrical surveys revealed clearly the fault fracture zone enlarges systematically northward and southward from the vicinity of Mohwa-ri, indicating Mohwa-ri is at the seismic segment boundary. Field Geological survey and microscope observation of fault gouge indicates that the Quaternary faults in the area are reactivated products of the preexisting faults. Trench survey of the Chonbuk fault Galgok-ri revealed thrust faults and cumulative vertical displacement due to faulting during the late Quaternary with about 1.1-1.9 m displacement per event; the latest event occurred from 14000 to 25000 yrs. BP. The seismic survey showed the basement surface os cut by numerous reverse faults and indicated the possibility that the boundary between Kyeongsangbukdo and Kyeongsannamdo may be segment boundary

  20. Copy number variation in the bovine genome

    DEFF Research Database (Denmark)

    Fadista, João; Thomsen, Bo; Holm, Lars-Erik

    2010-01-01

    to genetic variation in cattle. Results We designed and used a set of NimbleGen CGH arrays that tile across the assayable portion of the cattle genome with approximately 6.3 million probes, at a median probe spacing of 301 bp. This study reports the highest resolution map of copy number variation...... in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds. The CNVRs identified covered 0.68% (22 Mb) of the genome, and ranged in size from 1.7 to 2,031 kb (median size 16.7 kb). About 20% of the CNVs co-localized with segmental...... duplications, while 30% encompass genes, of which the majority is involved in environmental response. About 10% of the human orthologous of these genes are associated with human disease susceptibility and, hence, may have important phenotypic consequences. Conclusions Together, this analysis provides a useful...

  1. Personal genomics services: whose genomes?

    Science.gov (United States)

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

    New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

  2. Automatic segmentation of psoriasis lesions

    Science.gov (United States)

    Ning, Yang; Shi, Chenbo; Wang, Li; Shu, Chang

    2014-10-01

    The automatic segmentation of psoriatic lesions is widely researched these years. It is an important step in Computer-aid methods of calculating PASI for estimation of lesions. Currently those algorithms can only handle single erythema or only deal with scaling segmentation. In practice, scaling and erythema are often mixed together. In order to get the segmentation of lesions area - this paper proposes an algorithm based on Random forests with color and texture features. The algorithm has three steps. The first step, the polarized light is applied based on the skin's Tyndall-effect in the imaging to eliminate the reflection and Lab color space are used for fitting the human perception. The second step, sliding window and its sub windows are used to get textural feature and color feature. In this step, a feature of image roughness has been defined, so that scaling can be easily separated from normal skin. In the end, Random forests will be used to ensure the generalization ability of the algorithm. This algorithm can give reliable segmentation results even the image has different lighting conditions, skin types. In the data set offered by Union Hospital, more than 90% images can be segmented accurately.

  3. Dynamics of genome rearrangement in bacterial populations.

    Directory of Open Access Journals (Sweden)

    Aaron E Darling

    2008-07-01

    Full Text Available Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of "symmetric inversions"-inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings

  4. Skip segment Hirschsprung disease and Waardenburg syndrome

    Directory of Open Access Journals (Sweden)

    Erica R. Gross

    2015-04-01

    Full Text Available Skip segment Hirschsprung disease describes a segment of ganglionated bowel between two segments of aganglionated bowel. It is a rare phenomenon that is difficult to diagnose. We describe a recent case of skip segment Hirschsprung disease in a neonate with a family history of Waardenburg syndrome and the genetic profile that was identified.

  5. U.S. Army Custom Segmentation System

    Science.gov (United States)

    2007-06-01

    segmentation is individual or intergroup differences in response to marketing - mix variables. Presumptions about segments: •different demands in a...product or service category, •respond differently to changes in the marketing mix Criteria for segments: •The segments must exist in the environment

  6. Skip segment Hirschsprung disease and Waardenburg syndrome

    OpenAIRE

    Gross, Erica R.; Geddes, Gabrielle C.; McCarrier, Julie A.; Jarzembowski, Jason A.; Arca, Marjorie J.

    2015-01-01

    Skip segment Hirschsprung disease describes a segment of ganglionated bowel between two segments of aganglionated bowel. It is a rare phenomenon that is difficult to diagnose. We describe a recent case of skip segment Hirschsprung disease in a neonate with a family history of Waardenburg syndrome and the genetic profile that was identified.

  7. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

  8. A Novel Iris Segmentation Scheme

    Directory of Open Access Journals (Sweden)

    Chen-Chung Liu

    2014-01-01

    Full Text Available One of the key steps in the iris recognition system is the accurate iris segmentation from its surrounding noises including pupil, sclera, eyelashes, and eyebrows of a captured eye-image. This paper presents a novel iris segmentation scheme which utilizes the orientation matching transform to outline the outer and inner iris boundaries initially. It then employs Delogne-Kåsa circle fitting (instead of the traditional Hough transform to further eliminate the outlier points to extract a more precise iris area from an eye-image. In the extracted iris region, the proposed scheme further utilizes the differences in the intensity and positional characteristics of the iris, eyelid, and eyelashes to detect and delete these noises. The scheme is then applied on iris image database, UBIRIS.v1. The experimental results show that the presented scheme provides a more effective and efficient iris segmentation than other conventional methods.

  9. Translocations of chromosome end-segments and facultative heterochromatin promote meiotic ring formation in evening primroses.

    Science.gov (United States)

    Golczyk, Hieronim; Massouh, Amid; Greiner, Stephan

    2014-03-01

    Due to reciprocal chromosomal translocations, many species of Oenothera (evening primrose) form permanent multichromosomal meiotic rings. However, regular bivalent pairing is also observed. Chiasmata are restricted to chromosomal ends, which makes homologous recombination virtually undetectable. Genetic diversity is achieved by changing linkage relations of chromosomes in rings and bivalents via hybridization and reciprocal translocations. Although the structural prerequisite for this system is enigmatic, whole-arm translocations are widely assumed to be the mechanistic driving force. We demonstrate that this prerequisite is genome compartmentation into two epigenetically defined chromatin fractions. The first one facultatively condenses in cycling cells into chromocenters negative both for histone H3 dimethylated at lysine 4 and for C-banding, and forms huge condensed middle chromosome regions on prophase chromosomes. Remarkably, it decondenses in differentiating cells. The second fraction is euchromatin confined to distal chromosome segments, positive for histone H3 lysine 4 dimethylation and for histone H3 lysine 27 trimethylation. The end-segments are deprived of canonical telomeres but capped with constitutive heterochromatin. This genomic organization promotes translocation breakpoints between the two chromatin fractions, thus facilitating exchanges of end-segments. We challenge the whole-arm translocation hypothesis by demonstrating why reciprocal translocations of chromosomal end-segments should strongly promote meiotic rings and evolution toward permanent translocation heterozygosity. Reshuffled end-segments, each possessing a major crossover hot spot, can furthermore explain meiotic compatibility between genomes with different translocation histories.

  10. Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy

    DEFF Research Database (Denmark)

    Mefford, Heather C; Clauin, Severine; Sharp, Andrew J

    2007-01-01

    predisposed to recurrent rearrangement, by array-based comparative genomic hybridization. We found that 6% of fetal material showed evidence of microdeletion or microduplication, including three independent events that likely resulted from unequal crossing-over between segmental duplications. One...

  11. Document segmentation via oblique cuts

    Science.gov (United States)

    Svendsen, Jeremy; Branzan-Albu, Alexandra

    2013-01-01

    This paper presents a novel solution for the layout segmentation of graphical elements in Business Intelligence documents. We propose a generalization of the recursive X-Y cut algorithm, which allows for cutting along arbitrary oblique directions. An intermediate processing step consisting of line and solid region removal is also necessary due to presence of decorative elements. The output of the proposed segmentation is a hierarchical structure which allows for the identification of primitives in pie and bar charts. The algorithm was tested on a database composed of charts from business documents. Results are very promising.

  12. Optimally segmented permanent magnet structures

    DEFF Research Database (Denmark)

    Insinga, Andrea Roberto; Bjørk, Rasmus; Smith, Anders

    2016-01-01

    We present an optimization approach which can be employed to calculate the globally optimal segmentation of a two-dimensional magnetic system into uniformly magnetized pieces. For each segment the algorithm calculates the optimal shape and the optimal direction of the remanent flux density vector......, with respect to a linear objective functional. We illustrate the approach with results for magnet design problems from different areas, such as a permanent magnet electric motor, a beam focusing quadrupole magnet for particle accelerators and a rotary device for magnetic refrigeration....

  13. Intercalary bone segment transport in treatment of segmental tibial defects

    International Nuclear Information System (INIS)

    Iqbal, A.; Amin, M.S.

    2002-01-01

    Objective: To evaluate the results and complications of intercalary bone segment transport in the treatment of segmental tibial defects. Design: This is a retrospective analysis of patients with segmental tibial defects who were treated with intercalary bone segment transport method. Place and Duration of Study: The study was carried out at Combined Military Hospital, Rawalpindi from September 1997 to April 2001. Subjects and methods: Thirteen patients were included in the study who had developed tibial defects either due to open fractures with bone loss or subsequent to bone debridement of infected non unions. The mean bone defect was 6.4 cms and there were eight associated soft tissue defects. Locally made unilateral 'Naseer-Awais' (NA) fixator was used for bone segment transport. The distraction was done at the rate of 1mm/day after 7-10 days of osteotomy. The patients were followed-up fortnightly during distraction and monthly thereafter. The mean follow-up duration was 18 months. Results: The mean time in external fixation was 9.4 months. The m ean healing index' was 1.47 months/cm. Satisfactory union was achieved in all cases. Six cases (46.2%) required bone grafting at target site and in one of them grafting was required at the level of regeneration as well. All the wounds healed well with no residual infection. There was no residual leg length discrepancy of more than 20 mm nd one angular deformity of more than 5 degrees. The commonest complication encountered was pin track infection seen in 38% of Shanz Screws applied. Loosening occurred in 6.8% of Shanz screws, requiring re-adjustment. Ankle joint contracture with equinus deformity and peroneal nerve paresis occurred in one case each. The functional results were graded as 'good' in seven, 'fair' in four, and 'poor' in two patients. Overall, thirteen patients had 31 (minor/major) complications with a ratio of 2.38 complications per patient. To treat the bone defects and associated complications, a mean of

  14. Hydrophilic segmented block copolymers based on poly(ethylene oxide) and monodisperse amide segments

    NARCIS (Netherlands)

    Husken, D.; Feijen, Jan; Gaymans, R.J.

    2007-01-01

    Segmented block copolymers based on poly(ethylene oxide) (PEO) flexible segments and monodisperse crystallizable bisester tetra-amide segments were made via a polycondensation reaction. The molecular weight of the PEO segments varied from 600 to 4600 g/mol and a bisester tetra-amide segment (T6T6T)

  15. Dictionary Based Segmentation in Volumes

    DEFF Research Database (Denmark)

    Emerson, Monica Jane; Jespersen, Kristine Munk; Jørgensen, Peter Stanley

    Method for supervised segmentation of volumetric data. The method is trained from manual annotations, and these annotations make the method very flexible, which we demonstrate in our experiments. Our method infers label information locally by matching the pattern in a neighborhood around a voxel ...... to a dictionary, and hereby accounts for the volume texture....

  16. Multiple Segmentation of Image Stacks

    DEFF Research Database (Denmark)

    Smets, Jonathan; Jaeger, Manfred

    2014-01-01

    We propose a method for the simultaneous construction of multiple image segmentations by combining a recently proposed “convolution of mixtures of Gaussians” model with a multi-layer hidden Markov random field structure. The resulting method constructs for a single image several, alternative...

  17. Segmenting Trajectories by Movement States

    NARCIS (Netherlands)

    Buchin, M.; Kruckenberg, H.; Kölzsch, A.; Timpf, S.; Laube, P.

    2013-01-01

    Dividing movement trajectories according to different movement states of animals has become a challenge in movement ecology, as well as in algorithm development. In this study, we revisit and extend a framework for trajectory segmentation based on spatio-temporal criteria for this purpose. We adapt

  18. Segmental Colitis Complicating Diverticular Disease

    Directory of Open Access Journals (Sweden)

    Guido Ma Van Rosendaal

    1996-01-01

    Full Text Available Two cases of idiopathic colitis affecting the sigmoid colon in elderly patients with underlying diverticulosis are presented. Segmental resection has permitted close review of the histopathology in this syndrome which demonstrates considerable similarity to changes seen in idiopathic ulcerative colitis. The reported experience with this syndrome and its clinical features are reviewed.

  19. Leaf segmentation in plant phenotyping

    NARCIS (Netherlands)

    Scharr, Hanno; Minervini, Massimo; French, Andrew P.; Klukas, Christian; Kramer, David M.; Liu, Xiaoming; Luengo, Imanol; Pape, Jean Michel; Polder, Gerrit; Vukadinovic, Danijela; Yin, Xi; Tsaftaris, Sotirios A.

    2016-01-01

    Image-based plant phenotyping is a growing application area of computer vision in agriculture. A key task is the segmentation of all individual leaves in images. Here we focus on the most common rosette model plants, Arabidopsis and young tobacco. Although leaves do share appearance and shape

  20. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained...... by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans...

  1. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew David; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...

  2. Joint shape segmentation with linear programming

    KAUST Repository

    Huang, Qixing

    2011-01-01

    We present an approach to segmenting shapes in a heterogenous shape database. Our approach segments the shapes jointly, utilizing features from multiple shapes to improve the segmentation of each. The approach is entirely unsupervised and is based on an integer quadratic programming formulation of the joint segmentation problem. The program optimizes over possible segmentations of individual shapes as well as over possible correspondences between segments from multiple shapes. The integer quadratic program is solved via a linear programming relaxation, using a block coordinate descent procedure that makes the optimization feasible for large databases. We evaluate the presented approach on the Princeton segmentation benchmark and show that joint shape segmentation significantly outperforms single-shape segmentation techniques. © 2011 ACM.

  3. Complete genome sequence and phylogenetic analyses of an aquabirnavirus isolated from a diseased marbled eel culture in Taiwan.

    Science.gov (United States)

    Wen, Chiu-Ming

    2017-08-01

    An aquabirnavirus was isolated from diseased marbled eels (Anguilla marmorata; MEIPNV1310) with gill haemorrhages and associated mortality. Its genome segment sequences were obtained through next-generation sequencing and compared with published aquabirnavirus sequences. The results indicated that the genome sequence of MEIPNV1310 contains segment A (3099 nucleotides) and segment B (2789 nucleotides). Phylogenetic analysis showed that MEIPNV1310 is closely related to the infectious pancreatic necrosis Ab strain within genogroup II. This genome sequence is beneficial for studying the geographic distribution and evolution of aquabirnaviruses.

  4. Comparative genomic hybridization.

    Science.gov (United States)

    Pinkel, Daniel; Albertson, Donna G

    2005-01-01

    Altering DNA copy number is one of the many ways that gene expression and function may be modified. Some variations are found among normal individuals ( 14, 35, 103 ), others occur in the course of normal processes in some species ( 33 ), and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur prior to or shortly after fertilization, whereas DNA dosage alterations that occur in somatic cells are frequent contributors to cancer. Detecting these aberrations, and interpreting them within the context of broader knowledge, facilitates identification of critical genes and pathways involved in biological processes and diseases, and provides clinically relevant information. Over the past several years array comparative genomic hybridization (array CGH) has demonstrated its value for analyzing DNA copy number variations. In this review we discuss the state of the art of array CGH and its applications in medical genetics and cancer, emphasizing general concepts rather than specific results.

  5. Dictionary Based Segmentation in Volumes

    DEFF Research Database (Denmark)

    Emerson, Monica Jane; Jespersen, Kristine Munk; Jørgensen, Peter Stanley

    2015-01-01

    We present a method for supervised volumetric segmentation based on a dictionary of small cubes composed of pairs of intensity and label cubes. Intensity cubes are small image volumes where each voxel contains an image intensity. Label cubes are volumes with voxelwise probabilities for a given...... label. The segmentation process is done by matching a cube from the volume, of the same size as the dictionary intensity cubes, to the most similar intensity dictionary cube, and from the associated label cube we get voxel-wise label probabilities. Probabilities from overlapping cubes are averaged...... and hereby we obtain a robust label probability encoding. The dictionary is computed from labeled volumetric image data based on weighted clustering. We experimentally demonstrate our method using two data sets from material science – a phantom data set of a solid oxide fuel cell simulation for detecting...

  6. Compliance with Segment Disclosure Initiatives

    DEFF Research Database (Denmark)

    Arya, Anil; Frimor, Hans; Mittendorf, Brian

    2013-01-01

    Regulatory oversight of capital markets has intensified in recent years, with a particular emphasis on expanding financial transparency. A notable instance is efforts by the Financial Accounting Standards Board that push firms to identify and report performance of individual business units...... (segments). This paper seeks to address short-run and long-run consequences of stringent enforcement of and uniform compliance with these segment disclosure standards. To do so, we develop a parsimonious model wherein a regulatory agency promulgates disclosure standards and either permits voluntary...... by increasing transparency and leveling the playing field. However, our analysis also demonstrates that in the long run, if firms are unable to use discretion in reporting to maintain their competitive edge, they may seek more destructive alternatives. Accounting for such concerns, in the long run, voluntary...

  7. Segmental osteotomies of the maxilla.

    Science.gov (United States)

    Rosen, H M

    1989-10-01

    Multiple segment Le Fort I osteotomies provide the maxillofacial surgeon with the capabilities to treat complex dentofacial deformities existing in all three planes of space. Sagittal, vertical, and transverse maxillomandibular discrepancies as well as three-dimensional abnormalities within the maxillary arch can be corrected simultaneously. Accordingly, optimal aesthetic enhancement of the facial skeleton and a functional, healthy occlusion can be realized. What may be perceived as elaborate treatment plans are in reality conservative in terms of osseous stability and treatment time required. The close cooperation of an orthodontist well-versed in segmental orthodontics and orthognathic surgery is critical to the success of such surgery. With close attention to surgical detail, the complication rate inherent in such surgery can be minimized and the treatment goals achieved in a timely and predictable fashion.

  8. Segmented fuel and moderator rod

    International Nuclear Information System (INIS)

    Doshi, P.K.

    1987-01-01

    This patent describes a continuous segmented fuel and moderator rod for use with a water cooled and moderated nuclear fuel assembly. The rod comprises: a lower fuel region containing a column of nuclear fuel; a moderator region, disposed axially above the fuel region. The moderator region has means for admitting and passing the water moderator therethrough for moderating an upper portion of the nuclear fuel assembly. The moderator region is separated from the fuel region by a water tight separator

  9. Segmentation of sows in farrowing pens

    DEFF Research Database (Denmark)

    Tu, Gang Jun; Karstoft, Henrik; Pedersen, Lene Juul

    2014-01-01

    The correct segmentation of a foreground object in video recordings is an important task for many surveillance systems. The development of an effective and practical algorithm to segment sows in grayscale video recordings captured under commercial production conditions is described...

  10. Segmentation in local hospital markets.

    Science.gov (United States)

    Dranove, D; White, W D; Wu, L

    1993-01-01

    This study examines evidence of market segmentation on the basis of patients' insurance status, demographic characteristics, and medical condition in selected local markets in California in the years 1983 and 1989. Substantial differences exist in the probability patients may be admitted to particular hospitals based on insurance coverage, particularly Medicaid, and race. Segmentation based on insurance and race is related to hospital characteristics, but not the characteristics of the hospital's community. Medicaid patients are more likely to go to hospitals with lower costs and fewer service offerings. Privately insured patients go to hospitals offering more services, although cost concerns are increasing. Hispanic patients also go to low-cost hospitals, ceteris paribus. Results indicate little evidence of segmentation based on medical condition in either 1983 or 1989, suggesting that "centers of excellence" have yet to play an important role in patient choice of hospital. The authors found that distance matters, and that patients prefer nearby hospitals, moreso for some medical conditions than others, in ways consistent with economic theories of consumer choice.

  11. Roentgenological diagnoss of central segmental lung cancer

    International Nuclear Information System (INIS)

    Gurevich, L.A.; Fedchenko, G.G.

    1984-01-01

    Basing on an analysis of the results of clinicoroentgenological examination of 268 patments roentgenological semiotics of segmental lung cancer is presented. Some peculiarities of the X-ray picture of cancer of different segments of the lungs were revealed depending on tumor site and growth type. For the syndrome of segmental darkening the comprehensive X-ray methods where the chief method is tomography of the segmental bronchi are proposed

  12. Review of segmentation process in consumer markets

    OpenAIRE

    Veronika Jadczaková

    2013-01-01

    Although there has been a considerable debate on market segmentation over five decades, attention was merely devoted to single stages of the segmentation process. In doing so, stages as segmentation base selection or segments profiling have been heavily covered in the extant literature, whereas stages as implementation of the marketing strategy or market definition were of a comparably lower interest. Capitalizing on this shortcoming, this paper strives to close the gap and provide each step...

  13. Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4

    OpenAIRE

    Masuda, Shinji; Hori, Koichi; Maruyama, Fumito; Ren, Shukun; Sugimoto, Saori; Yamamoto, Nozomi; Mori, Hiroshi; Yamada, Takuji; Sato, Shusei; Tabata, Satoshi; Ohta, Hiroyuki; Kurokawa, Ken

    2013-01-01

    We report the draft genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum. The photosynthesis gene cluster comprises two segments?a unique feature among photosynthesis gene clusters of purple bacteria. The genome information will be useful for further analysis of bacterial photosynthesis.

  14. Complete Genome Sequence of a Novel Aquareovirus That Infects the Endangered Fountain Darter, Etheostoma fonticola.

    Science.gov (United States)

    Iwanowicz, Luke R; Iwanowicz, Deborah D; Adams, Cynthia R; Lewis, Teresa D; Brandt, Thomas M; Cornman, Robert S; Sanders, Lakyn

    2016-12-22

    Here, we report the complete genome of a novel aquareovirus isolated from clinically normal fountain darters, Etheostoma fonticola, inhabiting the San Marcos River, Texas, USA. The complete genome consists of 23,958 bp consisting of 11 segments that range from 783 bp (S11) to 3,866 bp (S1). Copyright © 2016 Iwanowicz et al.

  15. Complete Genome Sequence of a Novel Aquareovirus That Infects the Endangered Fountain Darter, Etheostoma fonticola

    OpenAIRE

    Iwanowicz, Luke R.; Iwanowicz, Deborah D.; Adams, Cynthia R.; Lewis, Teresa D.; Brandt, Thomas M.; Cornman, Robert S.; Sanders, Lakyn

    2016-01-01

    Here, we report the complete genome of a novel aquareovirus isolated from clinically normal fountain darters, Etheostoma fonticola, inhabiting the San Marcos River, Texas, USA. The complete genome consists of 23,958 bp consisting of 11 segments that range from 783 bp (S11) to 3,866 bp (S1).

  16. Complete genome sequence of a novel aquareovirus that infects the endangered fountain darter, Etheostoma fonticola

    Science.gov (United States)

    Iwanowicz, Luke R.; Iwanowicz, Deborah; Adams, Cynthia; Lewis, Teresa D.; Brandt, Thomas M.; Cornman, Robert S.; Sanders, Lakyn R.

    2016-01-01

    Here, we report the complete genome of a novel aquareovirus isolated from clinically normal fountain darters, Etheostoma fonticola, inhabiting the San Marcos River, Texas, USA. The complete genome consists of 23,958 bp consisting of 11 segments that range from 783 bp (S11) to 3,866 bp (S1).

  17. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

  19. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome.

    Science.gov (United States)

    Sharp, Andrew J; Hansen, Sierra; Selzer, Rebecca R; Cheng, Ze; Regan, Regina; Hurst, Jane A; Stewart, Helen; Price, Sue M; Blair, Edward; Hennekam, Raoul C; Fitzpatrick, Carrie A; Segraves, Rick; Richmond, Todd A; Guiver, Cheryl; Albertson, Donna G; Pinkel, Daniel; Eis, Peggy S; Schwartz, Stuart; Knight, Samantha J L; Eichler, Evan E

    2006-09-01

    Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome, we investigated 130 regions that we hypothesized as candidates for previously undescribed genomic disorders. We tested 290 individuals with mental retardation by BAC array comparative genomic hybridization and identified 16 pathogenic rearrangements, including de novo microdeletions of 17q21.31 found in four individuals. Using oligonucleotide arrays, we refined the breakpoints of this microdeletion, defining a 478-kb critical region containing six genes that were deleted in all four individuals. We mapped the breakpoints of this deletion and of four other pathogenic rearrangements in 1q21.1, 15q13, 15q24 and 17q12 to flanking segmental duplications, suggesting that these are also sites of recurrent rearrangement. In common with the 17q21.31 deletion, these breakpoint regions are sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions.

  20. Endogenous viral elements in animal genomes.

    Directory of Open Access Journals (Sweden)

    Aris Katzourakis

    2010-11-01

    Full Text Available Integration into the nuclear genome of germ line cells can lead to vertical inheritance of retroviral genes as host alleles. For other viruses, germ line integration has only rarely been documented. Nonetheless, we identified endogenous viral elements (EVEs derived from ten non-retroviral families by systematic in silico screening of animal genomes, including the first endogenous representatives of double-stranded RNA, reverse-transcribing DNA, and segmented RNA viruses, and the first endogenous DNA viruses in mammalian genomes. Phylogenetic and genomic analysis of EVEs across multiple host species revealed novel information about the origin and evolution of diverse virus groups. Furthermore, several of the elements identified here encode intact open reading frames or are expressed as mRNA. For one element in the primate lineage, we provide statistically robust evidence for exaptation. Our findings establish that genetic material derived from all known viral genome types and replication strategies can enter the animal germ line, greatly broadening the scope of paleovirological studies and indicating a more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized.

  1. Market Segmentation from a Behavioral Perspective

    Science.gov (United States)

    Wells, Victoria K.; Chang, Shing Wan; Oliveira-Castro, Jorge; Pallister, John

    2010-01-01

    A segmentation approach is presented using both traditional demographic segmentation bases (age, social class/occupation, and working status) and a segmentation by benefits sought. The benefits sought in this case are utilitarian and informational reinforcement, variables developed from the Behavioral Perspective Model (BPM). Using data from 1,847…

  2. Parallel fuzzy connected image segmentation on GPU

    OpenAIRE

    Zhuge, Ying; Cao, Yong; Udupa, Jayaram K.; Miller, Robert W.

    2011-01-01

    Purpose: Image segmentation techniques using fuzzy connectedness (FC) principles have shown their effectiveness in segmenting a variety of objects in several large applications. However, one challenge in these algorithms has been their excessive computational requirements when processing large image datasets. Nowadays, commodity graphics hardware provides a highly parallel computing environment. In this paper, the authors present a parallel fuzzy connected image segmentation algorithm impleme...

  3. LIFE-STYLE SEGMENTATION WITH TAILORED INTERVIEWING

    NARCIS (Netherlands)

    KAMAKURA, WA; WEDEL, M

    The authors present a tailored interviewing procedure for life-style segmentation. The procedure assumes that a life-style measurement instrument has been designed. A classification of a sample of consumers into life-style segments is obtained using a latent-class model. With these segments, the

  4. The Process of Marketing Segmentation Strategy Selection

    OpenAIRE

    Ionel Dumitru

    2007-01-01

    The process of marketing segmentation strategy selection represents the essence of strategical marketing. We present hereinafter the main forms of the marketing statategy segmentation: undifferentiated marketing, differentiated marketing, concentrated marketing and personalized marketing. In practice, the companies use a mix of these marketing segmentation methods in order to maximize the proffit and to satisfy the consumers’ needs.

  5. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Baumgarten Andrew

    2004-06-01

    Full Text Available Abstract Background Most genes in Arabidopsis thaliana are members of gene families. How do the members of gene families arise, and how are gene family copy numbers maintained? Some gene families may evolve primarily through tandem duplication and high rates of birth and death in clusters, and others through infrequent polyploidy or large-scale segmental duplications and subsequent losses. Results Our approach to understanding the mechanisms of gene family evolution was to construct phylogenies for 50 large gene families in Arabidopsis thaliana, identify large internal segmental duplications in Arabidopsis, map gene duplications onto the segmental duplications, and use this information to identify which nodes in each phylogeny arose due to segmental or tandem duplication. Examples of six gene families exemplifying characteristic modes are described. Distributions of gene family sizes and patterns of duplication by genomic distance are also described in order to characterize patterns of local duplication and copy number for large gene families. Both gene family size and duplication by distance closely follow power-law distributions. Conclusions Combining information about genomic segmental duplications, gene family phylogenies, and gene positions provides a method to evaluate contributions of tandem duplication and segmental genome duplication in the generation and maintenance of gene families. These differences appear to correspond meaningfully to differences in functional roles of the members of the gene families.

  6. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  7. Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica

    Science.gov (United States)

    2011-01-01

    Background Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these cannot easily explain, however, how the diverse mitotypes evolved within each genus or species. We analyzed the evolutionary relationships of Brassica mitotypes by sequencing. Results We sequenced the mitotypes of cam (Brassica rapa), ole (B. oleracea), jun (B. juncea), and car (B. carinata) and analyzed them together with two previously sequenced mitotypes of B. napus (pol and nap). The sizes of whole single circular genomes of cam, jun, ole, and car are 219,747 bp, 219,766 bp, 360,271 bp, and 232,241 bp, respectively. The mitochondrial genome of ole is largest as a resulting of the duplication of a 141.8 kb segment. The jun mitotype is the result of an inherited cam mitotype, and pol is also derived from the cam mitotype with evolutionary modifications. Genes with known functions are conserved in all mitotypes, but clear variation in open reading frames (ORFs) with unknown functions among the six mitotypes was observed. Sequence relationship analysis showed that there has been genome compaction and inheritance in the course of Brassica mitotype evolution. Conclusions We have sequenced four Brassica mitotypes, compared six Brassica mitotypes and suggested a mechanism for mitochondrial genome formation in Brassica, including evolutionary events such as inheritance, duplication, rearrangement, genome compaction, and mutation. PMID:21988783

  8. The structures of bovine herpesvirus 1 virion and concatemeric DNA: implications for cleavage and packaging of herpesvirus genomes

    International Nuclear Information System (INIS)

    Schynts, Frederic; McVoy, Michael A.; Meurens, Francois; Detry, Bruno; Epstein, Alberto L.; Thiry, Etienne

    2003-01-01

    Herpesvirus genomes are often characterized by the presence of direct and inverted repeats that delineate their grouping into six structural classes. Class D genomes consist of a long (L) segment and a short (S) segment. The latter is flanked by large inverted repeats. DNA replication produces concatemers of head-to-tail linked genomes that are cleaved into unit genomes during the process of packaging DNA into capsids. Packaged class D genomes are an equimolar mixture of two isomers in which S is in either of two orientations, presumably a consequence of homologous recombination between the inverted repeats. The L segment remains predominantly fixed in a prototype (P) orientation; however, low levels of genomes having inverted L (I L ) segments have been reported for some class D herpesviruses. Inefficient formation of class D I L genomes has been attributed to infrequent L segment inversion, but recent detection of frequent inverted L segments in equine herpesvirus 1 concatemers [Virology 229 (1997) 415-420] suggests that the defect may be at the level of cleavage and packaging rather than inversion. In this study, the structures of virion and concatemeric DNA of another class D herpesvirus, bovine herpesvirus 1, were determined. Virion DNA contained low levels of I L genomes, whereas concatemeric DNA contained significant amounts of L segments in both P and I L orientations. However, concatemeric termini exhibited a preponderance of L termini derived from P isomers which was comparable to the preponderance of P genomes found in virion DNA. Thus, the defect in formation of I L genomes appears to lie at the level of concatemer cleavage. These results have important implications for the mechanisms by which herpesvirus DNA cleavage and packaging occur

  9. Automatic segmentation of vertebrae from radiographs

    DEFF Research Database (Denmark)

    Mysling, Peter; Petersen, Peter Kersten; Nielsen, Mads

    2011-01-01

    Segmentation of vertebral contours is an essential task in the design of automatic tools for vertebral fracture assessment. In this paper, we propose a novel segmentation technique which does not require operator interaction. The proposed technique solves the segmentation problem in a hierarchical...... is constrained by a conditional shape model, based on the variability of the coarse spine location estimates. The technique is evaluated on a data set of manually annotated lumbar radiographs. The results compare favorably to the previous work in automatic vertebra segmentation, in terms of both segmentation...

  10. Color image Segmentation using automatic thresholding techniques

    International Nuclear Information System (INIS)

    Harrabi, R.; Ben Braiek, E.

    2011-01-01

    In this paper, entropy and between-class variance based thresholding methods for color images segmentation are studied. The maximization of the between-class variance (MVI) and the entropy (ME) have been used as a criterion functions to determine an optimal threshold to segment images into nearly homogenous regions. Segmentation results from the two methods are validated and the segmentation sensitivity for the test data available is evaluated, and a comparative study between these methods in different color spaces is presented. The experimental results demonstrate the superiority of the MVI method for color image segmentation.

  11. MOVING WINDOW SEGMENTATION FRAMEWORK FOR POINT CLOUDS

    Directory of Open Access Journals (Sweden)

    G. Sithole

    2012-07-01

    Full Text Available As lidar point clouds become larger streamed processing becomes more attractive. This paper presents a framework for the streamed segmentation of point clouds with the intention of segmenting unstructured point clouds in real-time. The framework is composed of two main components. The first component segments points within a window shifting over the point cloud. The second component stitches the segments within the windows together. In this fashion a point cloud can be streamed through these two components in sequence, thus producing a segmentation. The algorithm has been tested on airborne lidar point cloud and some results of the performance of the framework are presented.

  12. International team with Virginia Tech participation maps genome of dengue and yellow fever mosquito

    OpenAIRE

    Trulove, Susan

    2007-01-01

    Developing new strategies to prevent and control yellow fever and dengue fever has become more possible with the completion of the first draft of the genome sequence of Aedes aegypti mosquito by scientists led by Vishvanath Nene at The Institute for Genomic Research (TIGR) and David Severson at the University of Notre Dame. The genome is the complete set of genetic material including genes and other segments of DNA in an organism.

  13. The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

    OpenAIRE

    Elsik, Christine G.; Tellam, Ross L.; Worley, Kim C.; Gibbs, Richard A.; Abatepaulo, Antonio R. R.; Abbey, Colette A.; Adelson, David L.; Aerts, Jan; Ahola, Virpi; Alexander, Lee; Alioto, Tyler; Almeida, Iassudara G.; Amadio, Ariel F.; Anatriello, Elen; Antonarakis, Stylianos E.

    2009-01-01

    To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specifi...

  14. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  15. Unsupervised Performance Evaluation of Image Segmentation

    Directory of Open Access Journals (Sweden)

    Chabrier Sebastien

    2006-01-01

    Full Text Available We present in this paper a study of unsupervised evaluation criteria that enable the quantification of the quality of an image segmentation result. These evaluation criteria compute some statistics for each region or class in a segmentation result. Such an evaluation criterion can be useful for different applications: the comparison of segmentation results, the automatic choice of the best fitted parameters of a segmentation method for a given image, or the definition of new segmentation methods by optimization. We first present the state of art of unsupervised evaluation, and then, we compare six unsupervised evaluation criteria. For this comparative study, we use a database composed of 8400 synthetic gray-level images segmented in four different ways. Vinet's measure (correct classification rate is used as an objective criterion to compare the behavior of the different criteria. Finally, we present the experimental results on the segmentation evaluation of a few gray-level natural images.

  16. Efficient graph-cut tattoo segmentation

    Science.gov (United States)

    Kim, Joonsoo; Parra, Albert; Li, He; Delp, Edward J.

    2015-03-01

    Law enforcement is interested in exploiting tattoos as an information source to identify, track and prevent gang-related crimes. Many tattoo image retrieval systems have been described. In a retrieval system tattoo segmentation is an important step for retrieval accuracy since segmentation removes background information in a tattoo image. Existing segmentation methods do not extract the tattoo very well when the background includes textures and color similar to skin tones. In this paper we describe a tattoo segmentation approach by determining skin pixels in regions near the tattoo. In these regions graph-cut segmentation using a skin color model and a visual saliency map is used to find skin pixels. After segmentation we determine which set of skin pixels are connected with each other that form a closed contour including a tattoo. The regions surrounded by the closed contours are considered tattoo regions. Our method segments tattoos well when the background includes textures and color similar to skin.

  17. Metric Learning for Hyperspectral Image Segmentation

    Science.gov (United States)

    Bue, Brian D.; Thompson, David R.; Gilmore, Martha S.; Castano, Rebecca

    2011-01-01

    We present a metric learning approach to improve the performance of unsupervised hyperspectral image segmentation. Unsupervised spatial segmentation can assist both user visualization and automatic recognition of surface features. Analysts can use spatially-continuous segments to decrease noise levels and/or localize feature boundaries. However, existing segmentation methods use tasks-agnostic measures of similarity. Here we learn task-specific similarity measures from training data, improving segment fidelity to classes of interest. Multiclass Linear Discriminate Analysis produces a linear transform that optimally separates a labeled set of training classes. The defines a distance metric that generalized to a new scenes, enabling graph-based segmentation that emphasizes key spectral features. We describe tests based on data from the Compact Reconnaissance Imaging Spectrometer (CRISM) in which learned metrics improve segment homogeneity with respect to mineralogical classes.

  18. Interferon Induced Focal Segmental Glomerulosclerosis

    Directory of Open Access Journals (Sweden)

    Yusuf Kayar

    2016-01-01

    Full Text Available Behçet’s disease is an inflammatory disease of unknown etiology which involves recurring oral and genital aphthous ulcers and ocular lesions as well as articular, vascular, and nervous system involvement. Focal segmental glomerulosclerosis (FSGS is usually seen in viral infections, immune deficiency syndrome, sickle cell anemia, and hyperfiltration and secondary to interferon therapy. Here, we present a case of FSGS identified with kidney biopsy in a patient who had been diagnosed with Behçet’s disease and received interferon-alpha treatment for uveitis and presented with acute renal failure and nephrotic syndrome associated with interferon.

  19. A contrario line segment detection

    CERN Document Server

    von Gioi, Rafael Grompone

    2014-01-01

    The reliable detection of low-level image structures is an old and still challenging problem in computer vision. This?book leads a detailed tour through the LSD algorithm, a line segment detector designed to be fully automatic. Based on the a contrario framework, the algorithm works efficiently without the need of any parameter tuning. The design criteria are thoroughly explained and the algorithm's good and bad results are illustrated on real and synthetic images. The issues involved, as well as the strategies used, are common to many geometrical structure detection problems and some possible

  20. Did Globalization Lead to Segmentation?

    DEFF Research Database (Denmark)

    Di Vaio, Gianfranco; Enflo, Kerstin Sofia

    Economic historians have stressed that income convergence was a key feature of the 'OECD-club' and that globalization was among the accelerating forces of this process in the long-run. This view has however been challenged, since it suffers from an ad hoc selection of countries. In the paper......, a mixture model is applied to a sample of 64 countries to endogenously analyze the cross-country growth behavior over the period 1870-2003. Results show that growth patterns were segmented in two worldwide regimes, the first one being characterized by convergence, and the other one denoted by divergence...

  1. An overview on genome organization of marine organisms.

    Science.gov (United States)

    Costantini, Maria

    2015-12-01

    In this review we will concentrate on some general genome features of marine organisms and their evolution, ranging from vertebrate to invertebrates until unicellular organisms. Before genome sequencing, the ultracentrifugation in CsCl led to high resolution of mammalian DNA (without seeing at the sequence). The analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong in a small number of families characterized by different GC levels. The recent availability of a number of fully sequenced genomes allowed mapping very precisely the isochores, based on DNA sequences. Since isochores are tightly linked to biological properties such as gene density, replication timing and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function and evolution. This led the current level of knowledge and to further insights. Copyright © 2015. Published by Elsevier B.V.

  2. Transcriptional control in the segmentation gene network of Drosophila.

    Directory of Open Access Journals (Sweden)

    Mark D Schroeder

    2004-09-01

    Full Text Available The segmentation gene network of Drosophila consists of maternal and zygotic factors that generate, by transcriptional (cross- regulation, expression patterns of increasing complexity along the anterior-posterior axis of the embryo. Using known binding site information for maternal and zygotic gap transcription factors, the computer algorithm Ahab recovers known segmentation control elements (modules with excellent success and predicts many novel modules within the network and genome-wide. We show that novel module predictions are highly enriched in the network and typically clustered proximal to the promoter, not only upstream, but also in intronic space and downstream. When placed upstream of a reporter gene, they consistently drive patterned blastoderm expression, in most cases faithfully producing one or more pattern elements of the endogenous gene. Moreover, we demonstrate for the entire set of known and newly validated modules that Ahab's prediction of binding sites correlates well with the expression patterns produced by the modules, revealing basic rules governing their composition. Specifically, we show that maternal factors consistently act as activators and that gap factors act as repressors, except for the bimodal factor Hunchback. Our data suggest a simple context-dependent rule for its switch from repressive to activating function. Overall, the composition of modules appears well fitted to the spatiotemporal distribution of their positive and negative input factors. Finally, by comparing Ahab predictions with different categories of transcription factor input, we confirm the global regulatory structure of the segmentation gene network, but find odd skipped behaving like a primary pair-rule gene. The study expands our knowledge of the segmentation gene network by increasing the number of experimentally tested modules by 50%. For the first time, the entire set of validated modules is analyzed for binding site composition under a

  3. Genomics With Cloud Computing

    OpenAIRE

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

    Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

  4. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  5. Pathogenesis of Focal Segmental Glomerulosclerosis

    Directory of Open Access Journals (Sweden)

    Beom Jin Lim

    2016-11-01

    Full Text Available Focal segmental glomerulosclerosis (FSGS is characterized by focal and segmental obliteration of glomerular capillary tufts with increased matrix. FSGS is classified as collapsing, tip, cellular, perihilar and not otherwise specified variants according to the location and character of the sclerotic lesion. Primary or idiopathic FSGS is considered to be related to podocyte injury, and the pathogenesis of podocyte injury has been actively investigated. Several circulating factors affecting podocyte permeability barrier have been proposed, but not proven to cause FSGS. FSGS may also be caused by genetic alterations. These genes are mainly those regulating slit diaphragm structure, actin cytoskeleton of podocytes, and foot process structure. The mode of inheritance and age of onset are different according to the gene involved. Recently, the role of parietal epithelial cells (PECs has been highlighted. Podocytes and PECs have common mesenchymal progenitors, therefore, PECs could be a source of podocyte repopulation after podocyte injury. Activated PECs migrate along adhesion to the glomerular tuft and may also contribute to the progression of sclerosis. Markers of activated PECs, including CD44, could be used to distinguish FSGS from minimal change disease. The pathogenesis of FSGS is very complex; however, understanding basic mechanisms of podocyte injury is important not only for basic research, but also for daily diagnostic pathology practice.

  6. Brain Tumor Image Segmentation in MRI Image

    Science.gov (United States)

    Peni Agustin Tjahyaningtijas, Hapsari

    2018-04-01

    Brain tumor segmentation plays an important role in medical image processing. Treatment of patients with brain tumors is highly dependent on early detection of these tumors. Early detection of brain tumors will improve the patient’s life chances. Diagnosis of brain tumors by experts usually use a manual segmentation that is difficult and time consuming because of the necessary automatic segmentation. Nowadays automatic segmentation is very populer and can be a solution to the problem of tumor brain segmentation with better performance. The purpose of this paper is to provide a review of MRI-based brain tumor segmentation methods. There are number of existing review papers, focusing on traditional methods for MRI-based brain tumor image segmentation. this paper, we focus on the recent trend of automatic segmentation in this field. First, an introduction to brain tumors and methods for brain tumor segmentation is given. Then, the state-of-the-art algorithms with a focus on recent trend of full automatic segmentaion are discussed. Finally, an assessment of the current state is presented and future developments to standardize MRI-based brain tumor segmentation methods into daily clinical routine are addressed.

  7. A new framework for interactive images segmentation

    International Nuclear Information System (INIS)

    Ashraf, M.; Sarim, M.; Shaikh, A.B.

    2017-01-01

    Image segmentation has become a widely studied research problem in image processing. There exist different graph based solutions for interactive image segmentation but the domain of image segmentation still needs persistent improvements. The segmentation quality of existing techniques generally depends on the manual input provided in beginning, therefore, these algorithms may not produce quality segmentation with initial seed labels provided by a novice user. In this work we investigated the use of cellular automata in image segmentation and proposed a new algorithm that follows a cellular automaton in label propagation. It incorporates both the pixel's local and global information in the segmentation process. We introduced the novel global constraints in automata evolution rules; hence proposed scheme of automata evolution is more effective than the automata based earlier evolution schemes. Global constraints are also effective in deceasing the sensitivity towards small changes made in manual input; therefore proposed approach is less dependent on label seed marks. It can produce the quality segmentation with modest user efforts. Segmentation results indicate that the proposed algorithm performs better than the earlier segmentation techniques. (author)

  8. Delineating slowly and rapidly evolving fractions of the Drosophila genome.

    Science.gov (United States)

    Keith, Jonathan M; Adams, Peter; Stephen, Stuart; Mattick, John S

    2008-05-01

    Evolutionary conservation is an important indicator of function and a major component of bioinformatic methods to identify non-protein-coding genes. We present a new Bayesian method for segmenting pairwise alignments of eukaryotic genomes while simultaneously classifying segments into slowly and rapidly evolving fractions. We also describe an information criterion similar to the Akaike Information Criterion (AIC) for determining the number of classes. Working with pairwise alignments enables detection of differences in conservation patterns among closely related species. We analyzed three whole-genome and three partial-genome pairwise alignments among eight Drosophila species. Three distinct classes of conservation level were detected. Sequences comprising the most slowly evolving component were consistent across a range of species pairs, and constituted approximately 62-66% of the D. melanogaster genome. Almost all (>90%) of the aligned protein-coding sequence is in this fraction, suggesting much of it (comprising the majority of the Drosophila genome, including approximately 56% of non-protein-coding sequences) is functional. The size and content of the most rapidly evolving component was species dependent, and varied from 1.6% to 4.8%. This fraction is also enriched for protein-coding sequence (while containing significant amounts of non-protein-coding sequence), suggesting it is under positive selection. We also classified segments according to conservation and GC content simultaneously. This analysis identified numerous sub-classes of those identified on the basis of conservation alone, but was nevertheless consistent with that classification. Software, data, and results available at www.maths.qut.edu.au/-keithj/. Genomic segments comprising the conservation classes available in BED format.

  9. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  10. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  11. Hierarchical image segmentation for learning object priors

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, Lakshman [Los Alamos National Laboratory; Yang, Xingwei [TEMPLE UNIV.; Latecki, Longin J [TEMPLE UNIV.; Li, Nan [TEMPLE UNIV.

    2010-11-10

    The proposed segmentation approach naturally combines experience based and image based information. The experience based information is obtained by training a classifier for each object class. For a given test image, the result of each classifier is represented as a probability map. The final segmentation is obtained with a hierarchial image segmentation algorithm that considers both the probability maps and the image features such as color and edge strength. We also utilize image region hierarchy to obtain not only local but also semi-global features as input to the classifiers. Moreover, to get robust probability maps, we take into account the region context information by averaging the probability maps over different levels of the hierarchical segmentation algorithm. The obtained segmentation results are superior to the state-of-the-art supervised image segmentation algorithms.

  12. Image Segmentation Using Minimum Spanning Tree

    Science.gov (United States)

    Dewi, M. P.; Armiati, A.; Alvini, S.

    2018-04-01

    This research aim to segmented the digital image. The process of segmentation is to separate the object from the background. So the main object can be processed for the other purposes. Along with the development of technology in digital image processing application, the segmentation process becomes increasingly necessary. The segmented image which is the result of the segmentation process should accurate due to the next process need the interpretation of the information on the image. This article discussed the application of minimum spanning tree on graph in segmentation process of digital image. This method is able to separate an object from the background and the image will change to be the binary images. In this case, the object that being the focus is set in white, while the background is black or otherwise.

  13. Toxic Anterior Segment Syndrome (TASS

    Directory of Open Access Journals (Sweden)

    Özlem Öner

    2011-12-01

    Full Text Available Toxic anterior segment syndrome (TASS is a sterile intraocular inflammation caused by noninfectious substances, resulting in extensive toxic damage to the intraocular tissues. Possible etiologic factors of TASS include surgical trauma, bacterial endotoxin, intraocular solutions with inappropriate pH and osmolality, preservatives, denatured ophthalmic viscosurgical devices (OVD, inadequate sterilization, cleaning and rinsing of surgical devices, intraocular lenses, polishing and sterilizing compounds which are related to intraocular lenses. The characteristic signs and symptoms such as blurred vision, corneal edema, hypopyon and nonreactive pupil usually occur 24 hours after the cataract surgery. The differential diagnosis of TASS from infectious endophthalmitis is important. The main treatment for TASS formation is prevention. TASS is a cataract surgery complication that is more commonly seen nowadays. In this article, the possible underlying causes as well as treatment and prevention methods of TASS are summarized. (Turk J Oph thal mol 2011; 41: 407-13

  14. Translocations of Chromosome End-Segments and Facultative Heterochromatin Promote Meiotic Ring Formation in Evening Primroses[W][OPEN

    Science.gov (United States)

    Golczyk, Hieronim; Massouh, Amid; Greiner, Stephan

    2014-01-01

    Due to reciprocal chromosomal translocations, many species of Oenothera (evening primrose) form permanent multichromosomal meiotic rings. However, regular bivalent pairing is also observed. Chiasmata are restricted to chromosomal ends, which makes homologous recombination virtually undetectable. Genetic diversity is achieved by changing linkage relations of chromosomes in rings and bivalents via hybridization and reciprocal translocations. Although the structural prerequisite for this system is enigmatic, whole-arm translocations are widely assumed to be the mechanistic driving force. We demonstrate that this prerequisite is genome compartmentation into two epigenetically defined chromatin fractions. The first one facultatively condenses in cycling cells into chromocenters negative both for histone H3 dimethylated at lysine 4 and for C-banding, and forms huge condensed middle chromosome regions on prophase chromosomes. Remarkably, it decondenses in differentiating cells. The second fraction is euchromatin confined to distal chromosome segments, positive for histone H3 lysine 4 dimethylation and for histone H3 lysine 27 trimethylation. The end-segments are deprived of canonical telomeres but capped with constitutive heterochromatin. This genomic organization promotes translocation breakpoints between the two chromatin fractions, thus facilitating exchanges of end-segments. We challenge the whole-arm translocation hypothesis by demonstrating why reciprocal translocations of chromosomal end-segments should strongly promote meiotic rings and evolution toward permanent translocation heterozygosity. Reshuffled end-segments, each possessing a major crossover hot spot, can furthermore explain meiotic compatibility between genomes with different translocation histories. PMID:24681616

  15. Communication with market segments - travel agencies' perspective

    OpenAIRE

    Lorena Bašan; Jasmina Dlačić; Željko Trezner

    2013-01-01

    Purpose – The purpose of this paper is to research the travel agencies’ communication with market segments. Communication with market segments takes into account marketing communication means as well as the implementation of different business orientations. Design – Special emphasis is placed on the use of different marketing communication means and their efficiency. Research also explores business orientation adaptation when approaching different market segments. Methodology – In explo...

  16. Distance measures for image segmentation evaluation

    OpenAIRE

    Monteiro, Fernando C.; Campilho, Aurélio

    2012-01-01

    In this paper we present a study of evaluation measures that enable the quantification of the quality of an image segmentation result. Despite significant advances in image segmentation techniques, evaluation of these techniques thus far has been largely subjective. Typically, the effectiveness of a new algorithm is demonstrated only by the presentation of a few segmented images and is otherwise left to subjective evaluation by the reader. Such an evaluation criterion can be useful for differ...

  17. IFRS 8 Operating Segments - A Closer Look

    OpenAIRE

    Muthupandian, K S

    2008-01-01

    The International Accounting Standards Board issued the International Financial Reporting Standard 8 Operating Segments. Segment information is one of the most vital aspects of financial reporting for investors and other users. The IFRS 8 requires an entity to adopt the ‘management approach’ to reporting on the financial performance of its operating segments. This article presents a closer look of the standard (objective, scope, and disclosures).

  18. MRI Brain Tumor Segmentation Methods- A Review

    OpenAIRE

    Gursangeet, Kaur; Jyoti, Rani

    2016-01-01

    Medical image processing and its segmentation is an active and interesting area for researchers. It has reached at the tremendous place in diagnosing tumors after the discovery of CT and MRI. MRI is an useful tool to detect the brain tumor and segmentation is performed to carry out the useful portion from an image. The purpose of this paper is to provide an overview of different image segmentation methods like watershed algorithm, morphological operations, neutrosophic sets, thresholding, K-...

  19. Speaker Segmentation and Clustering Using Gender Information

    Science.gov (United States)

    2006-02-01

    used in the first stages of segmentation forder information in the clustering of the opposite-gender speaker diarization of news broadcasts. files, the...AFRL-HE-WP-TP-2006-0026 AIR FORCE RESEARCH LABORATORY Speaker Segmentation and Clustering Using Gender Information Brian M. Ore General Dynamics...COVERED (From - To) February 2006 ProceedinLgs 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Speaker Segmentation and Clustering Using Gender Information 5b

  20. Benchmarking of Remote Sensing Segmentation Methods

    Czech Academy of Sciences Publication Activity Database

    Mikeš, Stanislav; Haindl, Michal; Scarpa, G.; Gaetano, R.

    2015-01-01

    Roč. 8, č. 5 (2015), s. 2240-2248 ISSN 1939-1404 R&D Projects: GA ČR(CZ) GA14-10911S Institutional support: RVO:67985556 Keywords : benchmark * remote sensing segmentation * unsupervised segmentation * supervised segmentation Subject RIV: BD - Theory of Information Impact factor: 2.145, year: 2015 http://library.utia.cas.cz/separaty/2015/RO/haindl-0445995.pdf

  1. Genomics With Cloud Computing

    Directory of Open Access Journals (Sweden)

    Sukhamrit Kaur

    2015-04-01

    Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

  2. Track segment synthesis method for NTA film

    International Nuclear Information System (INIS)

    Kumazawa, Shigeru

    1980-03-01

    A method is presented for synthesizing track segments extracted from a gray-level digital picture of NTA film in automatic counting system. In order to detect each track in an arbitrary direction, even if it has some gaps, as a set of the track segments, the method links extracted segments along the track, in succession, to the linked track segments, according to whether each extracted segment bears a similarity of direction to the track or not and whether it is connected with the linked track segments or not. In the case of a large digital picture, the method is applied to each subpicture, which is a strip of the picture, and then concatenates subsets of track segments linked at each subpicture as a set of track segments belonging to a track. The method was applied to detecting tracks in various directions over the eight 364 x 40-pixel subpictures with the gray scale of 127/pixel (picture element) of the microphotograph of NTA film. It was proved to be able to synthesize track segments correctly for every track in the picture. (author)

  3. Segmenting hospitals for improved management strategy.

    Science.gov (United States)

    Malhotra, N K

    1989-09-01

    The author presents a conceptual framework for the a priori and clustering-based approaches to segmentation and evaluates them in the context of segmenting institutional health care markets. An empirical study is reported in which the hospital market is segmented on three state-of-being variables. The segmentation approach also takes into account important organizational decision-making variables. The sophisticated Thurstone Case V procedure is employed. Several marketing implications for hospitals, other health care organizations, hospital suppliers, and donor publics are identified.

  4. Prototype implementation of segment assembling software

    Directory of Open Access Journals (Sweden)

    Pešić Đorđe

    2018-01-01

    Full Text Available IT education is very important and a lot of effort is put into the development of tools for helping students to acquire programming knowledge and for helping teachers in automating the examination process. This paper describes a prototype of the program segment assembling software used in the context of making tests in the field of algorithmic complexity. The proposed new program segment assembling model uses rules and templates. A template is a simple program segment. A rule defines combining method and data dependencies if they exist. One example of program segment assembling by the proposed system is given. Graphical user interface is also described.

  5. Probabilistic Segmentation of Folk Music Recordings

    Directory of Open Access Journals (Sweden)

    Ciril Bohak

    2016-01-01

    Full Text Available The paper presents a novel method for automatic segmentation of folk music field recordings. The method is based on a distance measure that uses dynamic time warping to cope with tempo variations and a dynamic programming approach to handle pitch drifting for finding similarities and estimating the length of repeating segment. A probabilistic framework based on HMM is used to find segment boundaries, searching for optimal match between the expected segment length, between-segment similarities, and likely locations of segment beginnings. Evaluation of several current state-of-the-art approaches for segmentation of commercial music is presented and their weaknesses when dealing with folk music are exposed, such as intolerance to pitch drift and variable tempo. The proposed method is evaluated and its performance analyzed on a collection of 206 folk songs of different ensemble types: solo, two- and three-voiced, choir, instrumental, and instrumental with singing. It outperforms current commercial music segmentation methods for noninstrumental music and is on a par with the best for instrumental recordings. The method is also comparable to a more specialized method for segmentation of solo singing folk music recordings.

  6. Review of segmentation process in consumer markets

    Directory of Open Access Journals (Sweden)

    Veronika Jadczaková

    2013-01-01

    Full Text Available Although there has been a considerable debate on market segmentation over five decades, attention was merely devoted to single stages of the segmentation process. In doing so, stages as segmentation base selection or segments profiling have been heavily covered in the extant literature, whereas stages as implementation of the marketing strategy or market definition were of a comparably lower interest. Capitalizing on this shortcoming, this paper strives to close the gap and provide each step of the segmentation process with equal treatment. Hence, the objective of this paper is two-fold. First, a snapshot of the segmentation process in a step-by-step fashion will be provided. Second, each step (where possible will be evaluated on chosen criteria by means of description, comparison, analysis and synthesis of 32 academic papers and 13 commercial typology systems. Ultimately, the segmentation stages will be discussed with empirical findings prevalent in the segmentation studies and last but not least suggestions calling for further investigation will be presented. This seven-step-framework may assist when segmenting in practice allowing for more confidential targeting which in turn might prepare grounds for creating of a differential advantage.

  7. Interactive segmentation techniques algorithms and performance evaluation

    CERN Document Server

    He, Jia; Kuo, C-C Jay

    2013-01-01

    This book focuses on interactive segmentation techniques, which have been extensively studied in recent decades. Interactive segmentation emphasizes clear extraction of objects of interest, whose locations are roughly indicated by human interactions based on high level perception. This book will first introduce classic graph-cut segmentation algorithms and then discuss state-of-the-art techniques, including graph matching methods, region merging and label propagation, clustering methods, and segmentation methods based on edge detection. A comparative analysis of these methods will be provided

  8. DNABIT Compress - Genome compression algorithm.

    Science.gov (United States)

    Rajarajeswari, Pothuraju; Apparao, Allam

    2011-01-22

    Data compression is concerned with how information is organized in data. Efficient storage means removal of redundancy from the data being stored in the DNA molecule. Data compression algorithms remove redundancy and are used to understand biologically important molecules. We present a compression algorithm, "DNABIT Compress" for DNA sequences based on a novel algorithm of assigning binary bits for smaller segments of DNA bases to compress both repetitive and non repetitive DNA sequence. Our proposed algorithm achieves the best compression ratio for DNA sequences for larger genome. Significantly better compression results show that "DNABIT Compress" algorithm is the best among the remaining compression algorithms. While achieving the best compression ratios for DNA sequences (Genomes),our new DNABIT Compress algorithm significantly improves the running time of all previous DNA compression programs. Assigning binary bits (Unique BIT CODE) for (Exact Repeats, Reverse Repeats) fragments of DNA sequence is also a unique concept introduced in this algorithm for the first time in DNA compression. This proposed new algorithm could achieve the best compression ratio as much as 1.58 bits/bases where the existing best methods could not achieve a ratio less than 1.72 bits/bases.

  9. The diploid genome sequence of an individual human.

    Directory of Open Access Journals (Sweden)

    Samuel Levy

    2007-09-01

    Full Text Available Presented here is a genome sequence of an individual human. It was produced from approximately 32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel included 3,213,401 single nucleotide polymorphisms (SNPs, 53,823 block substitutions (2-206 bp, 292,102 heterozygous insertion/deletion events (indels(1-571 bp, 559,473 homozygous indels (1-82,711 bp, 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.

  10. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2002-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

  11. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  12. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  13. Multi-scale Gaussian representation and outline-learning based cell image segmentation

    Science.gov (United States)

    2013-01-01

    Background High-throughput genome-wide screening to study gene-specific functions, e.g. for drug discovery, demands fast automated image analysis methods to assist in unraveling the full potential of such studies. Image segmentation is typically at the forefront of such analysis as the performance of the subsequent steps, for example, cell classification, cell tracking etc., often relies on the results of segmentation. Methods We present a cell cytoplasm segmentation framework which first separates cell cytoplasm from image background using novel approach of image enhancement and coefficient of variation of multi-scale Gaussian scale-space representation. A novel outline-learning based classification method is developed using regularized logistic regression with embedded feature selection which classifies image pixels as outline/non-outline to give cytoplasm outlines. Refinement of the detected outlines to separate cells from each other is performed in a post-processing step where the nuclei segmentation is used as contextual information. Results and conclusions We evaluate the proposed segmentation methodology using two challenging test cases, presenting images with completely different characteristics, with cells of varying size, shape, texture and degrees of overlap. The feature selection and classification framework for outline detection produces very simple sparse models which use only a small subset of the large, generic feature set, that is, only 7 and 5 features for the two cases. Quantitative comparison of the results for the two test cases against state-of-the-art methods show that our methodology outperforms them with an increase of 4-9% in segmentation accuracy with maximum accuracy of 93%. Finally, the results obtained for diverse datasets demonstrate that our framework not only produces accurate segmentation but also generalizes well to different segmentation tasks. PMID:24267488

  14. Genetics in Ophthalmology III – Posterior Segment Diseases

    Directory of Open Access Journals (Sweden)

    Canan Aslı Utine

    2012-10-01

    Full Text Available Genetic diseases are congenital or acquired hereditary diseases that result from structural/functional disorders of the human genome. Today, the genetic factors that play a role in many diseases are being highlighted with the rapid progress in the field of genetics science. It becomes increasingly important that physicians from all disciplines have knowledge about the basic principles of genetics, patterns of inheritance, etc., so that they can follow the new developments. In genetic eye diseases, ophthalmologists should know the basic clinical and recently rapidly developing genetic characteristics of these diseases in order to properly approach the diagnosis and treatment and to provide genetic counseling. In this paper, posterior segment eye diseases of genetic origin are reviewed, and retinoblastoma, mitochondrial diseases, retinal dysplasia, retinitis pigmentosa, choroideremia, gyrate atrophy, Alström disease, ocular albinism, optic nerve hypoplasia, anophthalmia/microphthalmia and Leber’s congenital amaurosis are covered. (Turk J Ophthalmol 2012; 42: 386-92

  15. Segmentation of liver tumors on CT images

    International Nuclear Information System (INIS)

    Pescia, D.

    2011-01-01

    This thesis is dedicated to 3D segmentation of liver tumors in CT images. This is a task of great clinical interest since it allows physicians benefiting from reproducible and reliable methods for segmenting such lesions. Accurate segmentation would indeed help them during the evaluation of the lesions, the choice of treatment and treatment planning. Such a complex segmentation task should cope with three main scientific challenges: (i) the highly variable shape of the structures being sought, (ii) their similarity of appearance compared with their surrounding medium and finally (iii) the low signal to noise ratio being observed in these images. This problem is addressed in a clinical context through a two step approach, consisting of the segmentation of the entire liver envelope, before segmenting the tumors which are present within the envelope. We begin by proposing an atlas-based approach for computing pathological liver envelopes. Initially images are pre-processed to compute the envelopes that wrap around binary masks in an attempt to obtain liver envelopes from estimated segmentation of healthy liver parenchyma. A new statistical atlas is then introduced and used to segmentation through its diffeomorphic registration to the new image. This segmentation is achieved through the combination of image matching costs as well as spatial and appearance prior using a multi-scale approach with MRF. The second step of our approach is dedicated to lesions segmentation contained within the envelopes using a combination of machine learning techniques and graph based methods. First, an appropriate feature space is considered that involves texture descriptors being determined through filtering using various scales and orientations. Then, state of the art machine learning techniques are used to determine the most relevant features, as well as the hyper plane that separates the feature space of tumoral voxels to the ones corresponding to healthy tissues. Segmentation is then

  16. Visualization for genomics: the Microbial Genome Viewer.

    Science.gov (United States)

    Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

    2004-07-22

    A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

  17. Segment-Tube: Spatio-Temporal Action Localization in Untrimmed Videos with Per-Frame Segmentation

    OpenAIRE

    Le Wang; Xuhuan Duan; Qilin Zhang; Zhenxing Niu; Gang Hua; Nanning Zheng

    2018-01-01

    Inspired by the recent spatio-temporal action localization efforts with tubelets (sequences of bounding boxes), we present a new spatio-temporal action localization detector Segment-tube, which consists of sequences of per-frame segmentation masks. The proposed Segment-tube detector can temporally pinpoint the starting/ending frame of each action category in the presence of preceding/subsequent interference actions in untrimmed videos. Simultaneously, the Segment-tube detector produces per-fr...

  18. Genomic prediction using subsampling

    OpenAIRE

    Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

    2017-01-01

    Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

  19. CrusView: a Java-based visualization platform for comparative genomics analyses in Brassicaceae species.

    Science.gov (United States)

    Chen, Hao; Wang, Xiangfeng

    2013-09-01

    In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/.

  20. Mild toxic anterior segment syndrome mimicking delayed onset toxic anterior segment syndrome after cataract surgery

    Directory of Open Access Journals (Sweden)

    Su-Na Lee

    2014-01-01

    Full Text Available Toxic anterior segment syndrome (TASS is an acute sterile postoperative anterior segment inflammation that may occur after anterior segment surgery. I report herein a case that developed mild TASS in one eye after bilateral uneventful cataract surgery, which was masked during early postoperative period under steroid eye drop and mimicking delayed onset TASS after switching to weaker steroid eye drop.

  1. GeoSegmenter: A statistically learned Chinese word segmenter for the geoscience domain

    Science.gov (United States)

    Huang, Lan; Du, Youfu; Chen, Gongyang

    2015-03-01

    Unlike English, the Chinese language has no space between words. Segmenting texts into words, known as the Chinese word segmentation (CWS) problem, thus becomes a fundamental issue for processing Chinese documents and the first step in many text mining applications, including information retrieval, machine translation and knowledge acquisition. However, for the geoscience subject domain, the CWS problem remains unsolved. Although a generic segmenter can be applied to process geoscience documents, they lack the domain specific knowledge and consequently their segmentation accuracy drops dramatically. This motivated us to develop a segmenter specifically for the geoscience subject domain: the GeoSegmenter. We first proposed a generic two-step framework for domain specific CWS. Following this framework, we built GeoSegmenter using conditional random fields, a principled statistical framework for sequence learning. Specifically, GeoSegmenter first identifies general terms by using a generic baseline segmenter. Then it recognises geoscience terms by learning and applying a model that can transform the initial segmentation into the goal segmentation. Empirical experimental results on geoscience documents and benchmark datasets showed that GeoSegmenter could effectively recognise both geoscience terms and general terms.

  2. NUCLEAR SEGMENTATION IN MICROSCOPE CELL IMAGES: A HAND-SEGMENTED DATASET AND COMPARISON OF ALGORITHMS

    OpenAIRE

    Coelho, Luís Pedro; Shariff, Aabid; Murphy, Robert F.

    2009-01-01

    Image segmentation is an essential step in many image analysis pipelines and many algorithms have been proposed to solve this problem. However, they are often evaluated subjectively or based on a small number of examples. To fill this gap, we hand-segmented a set of 97 fluorescence microscopy images (a total of 4009 cells) and objectively evaluated some previously proposed segmentation algorithms.

  3. Robust shape regression for supervised vessel segmentation and its application to coronary segmentation in CTA

    DEFF Research Database (Denmark)

    Schaap, Michiel; van Walsum, Theo; Neefjes, Lisan

    2011-01-01

    This paper presents a vessel segmentation method which learns the geometry and appearance of vessels in medical images from annotated data and uses this knowledge to segment vessels in unseen images. Vessels are segmented in a coarse-to-fine fashion. First, the vessel boundaries are estimated...

  4. Ebolavirus comparative genomics

    DEFF Research Database (Denmark)

    Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

    2015-01-01

    The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

  5. Limb-segment selection in drawing behaviour

    NARCIS (Netherlands)

    Meulenbroek, R G; Rosenbaum, D A; Thomassen, A.J.W.M.; Schomaker, L R

    How do we select combinations of limb segments to carry out physical tasks? Three possible determinants of limb-segment selection are hypothesized here: (1) optimal amplitudes and frequencies of motion for the effectors; (2) preferred movement axes for the effectors; and (3) a tendency to continue

  6. LIMB-SEGMENT SELECTION IN DRAWING BEHAVIOR

    NARCIS (Netherlands)

    MEULENBROEK, RGJ; ROSENBAUM, DA; THOMASSEN, AJWM; SCHOMAKER, LRB; Schomaker, Lambertus

    How do we select combinations of limb segments to carry out physical tasks? Three possible determinants of limb-segment selection are hypothesized here: (1) optimal amplitudes and frequencies of motion for the effectors; (2) preferred movement axes for the effectors; and (3) a tendency to continue

  7. Handwriting segmentation of unconstrained Oriya text

    Indian Academy of Sciences (India)

    Based on vertical projection profiles and structural features of Oriya characters, text lines are segmented into words. For character segmentation, at first, the isolated and connected (touching) characters in a word are detected. Using structural, topological and water reservoir concept-based features, characters of the word ...

  8. Reflection symmetry-integrated image segmentation.

    Science.gov (United States)

    Sun, Yu; Bhanu, Bir

    2012-09-01

    This paper presents a new symmetry-integrated region-based image segmentation method. The method is developed to obtain improved image segmentation by exploiting image symmetry. It is realized by constructing a symmetry token that can be flexibly embedded into segmentation cues. Interesting points are initially extracted from an image by the SIFT operator and they are further refined for detecting the global bilateral symmetry. A symmetry affinity matrix is then computed using the symmetry axis and it is used explicitly as a constraint in a region growing algorithm in order to refine the symmetry of the segmented regions. A multi-objective genetic search finds the segmentation result with the highest performance for both segmentation and symmetry, which is close to the global optimum. The method has been investigated experimentally in challenging natural images and images containing man-made objects. It is shown that the proposed method outperforms current segmentation methods both with and without exploiting symmetry. A thorough experimental analysis indicates that symmetry plays an important role as a segmentation cue, in conjunction with other attributes like color and texture.

  9. Segmentation precedes face categorization under suboptimal conditions

    NARCIS (Netherlands)

    Van Den Boomen, Carlijn; Fahrenfort, Johannes J; Snijders, Tineke M; Kemner, Chantal

    2015-01-01

    Both categorization and segmentation processes play a crucial role in face perception. However, the functional relation between these subprocesses is currently unclear. The present study investigates the temporal relation between segmentation-related and category-selective responses in the brain,

  10. Bayesian segmentation of brainstem structures in MRI

    DEFF Research Database (Denmark)

    Iglesias, Juan Eugenio; Van Leemput, Koen; Bhatt, Priyanka

    2015-01-01

    the brainstem structures in novel scans. Thanks to the generative nature of the scheme, the segmentation method is robust to changes in MRI contrast or acquisition hardware. Using cross validation, we show that the algorithm can segment the structures in previously unseen T1 and FLAIR scans with great accuracy...

  11. Congenital segmental dilatation of the colon

    African Journals Online (AJOL)

    Congenital segmental dilatation of the colon is a rare cause of intestinal obstruction in neonates. We report a case of congenital segmental dilatation of the colon and highlight the clinical, radiological, and histopathological features of this entity. Proper surgical treatment was initiated on the basis of preoperative radiological ...

  12. 47 CFR 101.1505 - Segmentation plan.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Segmentation plan. 101.1505 Section 101.1505 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO SERVICES FIXED MICROWAVE SERVICES Service and Technical Rules for the 70/80/90 GHz Bands § 101.1505 Segmentation plan. (a) An entity...

  13. Market Segmentation Using Bayesian Model Based Clustering

    NARCIS (Netherlands)

    Van Hattum, P.

    2009-01-01

    This dissertation deals with two basic problems in marketing, that are market segmentation, which is the grouping of persons who share common aspects, and market targeting, which is focusing your marketing efforts on one or more attractive market segments. For the grouping of persons who share

  14. Convolutional Neural Networks for SAR Image Segmentation

    DEFF Research Database (Denmark)

    Malmgren-Hansen, David; Nobel-Jørgensen, Morten

    2015-01-01

    Segmentation of Synthetic Aperture Radar (SAR) images has several uses, but it is a difficult task due to a number of properties related to SAR images. In this article we show how Convolutional Neural Networks (CNNs) can easily be trained for SAR image segmentation with good results. Besides...

  15. Storing tooth segments for optimal esthetics

    NARCIS (Netherlands)

    Tuzuner, T.; Turgut, S.; Özen, B.; Kılınç, H.; Bagis, B.

    2016-01-01

    Objective: A fractured whole crown segment can be reattached to its remnant; crowns from extracted teeth may be used as pontics in splinting techniques. We aimed to evaluate the effect of different storage solutions on tooth segment optical properties after different durations. Study design: Sixty

  16. Benefit segmentation of the fitness market.

    Science.gov (United States)

    Brown, J D

    1992-01-01

    While considerate attention is being paid to the fitness and wellness needs of people by healthcare and related marketing organizations, little research attention has been directed to identifying the market segments for fitness based upon consumers' perceived benefits of fitness. This article describes three distinct segments of fitness consumers comprising an estimated 50 percent of households. Implications for marketing strategies are also presented.

  17. Moving window segmentation framework for point clouds

    NARCIS (Netherlands)

    Sithole, G.; Gorte, B.G.H.

    2012-01-01

    As lidar point clouds become larger streamed processing becomes more attractive. This paper presents a framework for the streamed segmentation of point clouds with the intention of segmenting unstructured point clouds in real-time. The framework is composed of two main components. The first

  18. Current segmented gamma-ray scanner technology

    International Nuclear Information System (INIS)

    Bjork, C.W.

    1987-01-01

    A new generation of segmented gamma-ray scanners has been developed at Los Alamos for scrap and waste measurements at the Savannah River Plant and the Los Alamos Plutonium Facility. The new designs are highly automated and exhibit special features such as good segmentation and thorough shielding to improve performance

  19. Creating Web Area Segments with Google Analytics

    Science.gov (United States)

    Segments allow you to quickly access data for a predefined set of Sessions or Users, such as government or education users, or sessions in a particular state. You can then apply this segment to any report within the Google Analytics (GA) interface.

  20. Unsupervised Retinal Vessel Segmentation Using Combined Filters.

    Directory of Open Access Journals (Sweden)

    Wendeson S Oliveira

    Full Text Available Image segmentation of retinal blood vessels is a process that can help to predict and diagnose cardiovascular related diseases, such as hypertension and diabetes, which are known to affect the retinal blood vessels' appearance. This work proposes an unsupervised method for the segmentation of retinal vessels images using a combined matched filter, Frangi's filter and Gabor Wavelet filter to enhance the images. The combination of these three filters in order to improve the segmentation is the main motivation of this work. We investigate two approaches to perform the filter combination: weighted mean and median ranking. Segmentation methods are tested after the vessel enhancement. Enhanced images with median ranking are segmented using a simple threshold criterion. Two segmentation procedures are applied when considering enhanced retinal images using the weighted mean approach. The first method is based on deformable models and the second uses fuzzy C-means for the image segmentation. The procedure is evaluated using two public image databases, Drive and Stare. The experimental results demonstrate that the proposed methods perform well for vessel segmentation in comparison with state-of-the-art methods.

  1. A NEW APPROACH TO SEGMENT HANDWRITTEN DIGITS

    NARCIS (Netherlands)

    Oliveira, L.S.; Lethelier, E.; Bortolozzi, F.; Sabourin, R.

    2004-01-01

    This article presents a new segmentation approach applied to unconstrained handwritten digits. The novelty of the proposed algorithm is based on the combination of two types of structural features in order to provide the best segmentation path between connected entities. In this article, we first

  2. Spinal cord grey matter segmentation challenge.

    Science.gov (United States)

    Prados, Ferran; Ashburner, John; Blaiotta, Claudia; Brosch, Tom; Carballido-Gamio, Julio; Cardoso, Manuel Jorge; Conrad, Benjamin N; Datta, Esha; Dávid, Gergely; Leener, Benjamin De; Dupont, Sara M; Freund, Patrick; Wheeler-Kingshott, Claudia A M Gandini; Grussu, Francesco; Henry, Roland; Landman, Bennett A; Ljungberg, Emil; Lyttle, Bailey; Ourselin, Sebastien; Papinutto, Nico; Saporito, Salvatore; Schlaeger, Regina; Smith, Seth A; Summers, Paul; Tam, Roger; Yiannakas, Marios C; Zhu, Alyssa; Cohen-Adad, Julien

    2017-05-15

    An important image processing step in spinal cord magnetic resonance imaging is the ability to reliably and accurately segment grey and white matter for tissue specific analysis. There are several semi- or fully-automated segmentation methods for cervical cord cross-sectional area measurement with an excellent performance close or equal to the manual segmentation. However, grey matter segmentation is still challenging due to small cross-sectional size and shape, and active research is being conducted by several groups around the world in this field. Therefore a grey matter spinal cord segmentation challenge was organised to test different capabilities of various methods using the same multi-centre and multi-vendor dataset acquired with distinct 3D gradient-echo sequences. This challenge aimed to characterize the state-of-the-art in the field as well as identifying new opportunities for future improvements. Six different spinal cord grey matter segmentation methods developed independently by various research groups across the world and their performance were compared to manual segmentation outcomes, the present gold-standard. All algorithms provided good overall results for detecting the grey matter butterfly, albeit with variable performance in certain quality-of-segmentation metrics. The data have been made publicly available and the challenge web site remains open to new submissions. No modifications were introduced to any of the presented methods as a result of this challenge for the purposes of this publication. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  3. Scale selection for supervised image segmentation

    DEFF Research Database (Denmark)

    Li, Yan; Tax, David M J; Loog, Marco

    2012-01-01

    schemes are usually unsupervised, as they do not take into account the actual segmentation problem at hand. In this paper, we consider the problem of selecting scales, which aims at an optimal discrimination between user-defined classes in the segmentation. We show the deficiency of the classical...

  4. Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.

    Science.gov (United States)

    Kidd, Jeffrey M; Gravel, Simon; Byrnes, Jake; Moreno-Estrada, Andres; Musharoff, Shaila; Bryc, Katarzyna; Degenhardt, Jeremiah D; Brisbin, Abra; Sheth, Vrunda; Chen, Rong; McLaughlin, Stephen F; Peckham, Heather E; Omberg, Larsson; Bormann Chung, Christina A; Stanley, Sarah; Pearlstein, Kevin; Levandowsky, Elizabeth; Acevedo-Acevedo, Suehelay; Auton, Adam; Keinan, Alon; Acuña-Alonzo, Victor; Barquera-Lozano, Rodrigo; Canizales-Quinteros, Samuel; Eng, Celeste; Burchard, Esteban G; Russell, Archie; Reynolds, Andy; Clark, Andrew G; Reese, Martin G; Lincoln, Stephen E; Butte, Atul J; De La Vega, Francisco M; Bustamante, Carlos D

    2012-10-05

    Full sequencing of individual human genomes has greatly expanded our understanding of human genetic variation and population history. Here, we present a systematic analysis of 50 human genomes from 11 diverse global populations sequenced at high coverage. Our sample includes 12 individuals who have admixed ancestry and who have varying degrees of recent (within the last 500 years) African, Native American, and European ancestry. We found over 21 million single-nucleotide variants that contribute to a 1.75-fold range in nucleotide heterozygosity across diverse human genomes. This heterozygosity ranged from a high of one heterozygous site per kilobase in west African genomes to a low of 0.57 heterozygous sites per kilobase in segments inferred to have diploid Native American ancestry from the genomes of Mexican and Puerto Rican individuals. We show evidence of all three continental ancestries in the genomes of Mexican, Puerto Rican, and African American populations, and the genome-wide statistics are highly consistent across individuals from a population once ancestry proportions have been accounted for. Using a generalized linear model, we identified subtle variations across populations in the proportion of neutral versus deleterious variation and found that genome-wide statistics vary in admixed populations even once ancestry proportions have been factored in. We further infer that multiple periods of gene flow shaped the diversity of admixed populations in the Americas-70% of the European ancestry in today's African Americans dates back to European gene flow happening only 7-8 generations ago. Copyright © 2012 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  5. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

    DEFF Research Database (Denmark)

    Hellmann, Ines; Mang, Yuan; Gu, Zhiping

    2008-01-01

    We introduce a simple, broadly applicable method for obtaining estimates of nucleotide diversity from genomic shotgun sequencing data. The method takes into account the special nature of these data: random sampling of genomic segments from one or more individuals and a relatively high error rate...... for individual reads. Applying this method to data from the Celera human genome sequencing and SNP discovery project, we obtain estimates of nucleotide diversity in windows spanning the human genome and show that the diversity to divergence ratio is reduced in regions of low recombination. Furthermore, we show...

  6. Improving image segmentation by learning region affinities

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, Lakshman [Los Alamos National Laboratory; Yang, Xingwei [TEMPLE UNIV.; Latecki, Longin J [TEMPLE UNIV.

    2010-11-03

    We utilize the context information of other regions in hierarchical image segmentation to learn new regions affinities. It is well known that a single choice of quantization of an image space is highly unlikely to be a common optimal quantization level for all categories. Each level of quantization has its own benefits. Therefore, we utilize the hierarchical information among different quantizations as well as spatial proximity of their regions. The proposed affinity learning takes into account higher order relations among image regions, both local and long range relations, making it robust to instabilities and errors of the original, pairwise region affinities. Once the learnt affinities are obtained, we use a standard image segmentation algorithm to get the final segmentation. Moreover, the learnt affinities can be naturally unutilized in interactive segmentation. Experimental results on Berkeley Segmentation Dataset and MSRC Object Recognition Dataset are comparable and in some aspects better than the state-of-art methods.

  7. A Hybrid Technique for Medical Image Segmentation

    Directory of Open Access Journals (Sweden)

    Alamgir Nyma

    2012-01-01

    Full Text Available Medical image segmentation is an essential and challenging aspect in computer-aided diagnosis and also in pattern recognition research. This paper proposes a hybrid method for magnetic resonance (MR image segmentation. We first remove impulsive noise inherent in MR images by utilizing a vector median filter. Subsequently, Otsu thresholding is used as an initial coarse segmentation method that finds the homogeneous regions of the input image. Finally, an enhanced suppressed fuzzy c-means is used to partition brain MR images into multiple segments, which employs an optimal suppression factor for the perfect clustering in the given data set. To evaluate the robustness of the proposed approach in noisy environment, we add different types of noise and different amount of noise to T1-weighted brain MR images. Experimental results show that the proposed algorithm outperforms other FCM based algorithms in terms of segmentation accuracy for both noise-free and noise-inserted MR images.

  8. Monitoring fish distributions along electrofishing segments

    Science.gov (United States)

    Miranda, Leandro E.

    2014-01-01

    Electrofishing is widely used to monitor fish species composition and relative abundance in streams and lakes. According to standard protocols, multiple segments are selected in a body of water to monitor population relative abundance as the ratio of total catch to total sampling effort. The standard protocol provides an assessment of fish distribution at a macrohabitat scale among segments, but not within segments. An ancillary protocol was developed for assessing fish distribution at a finer scale within electrofishing segments. The ancillary protocol was used to estimate spacing, dispersion, and association of two species along shore segments in two local reservoirs. The added information provided by the ancillary protocol may be useful for assessing fish distribution relative to fish of the same species, to fish of different species, and to environmental or habitat characteristics.

  9. Aging and the segmentation of narrative film.

    Science.gov (United States)

    Kurby, Christopher A; Asiala, Lillian K E; Mills, Steven R

    2014-01-01

    The perception of event structure in continuous activity is important for everyday comprehension. Although the segmentation of experience into events is a normal concomitant of perceptual processing, previous research has shown age differences in the ability to perceive structure in naturalistic activity, such as a movie of someone washing a car. However, past research has also shown that older adults have a preserved ability to comprehend events in narrative text, which suggests that narrative may improve the event processing of older adults. This study tested whether there are age differences in event segmentation at the intersection of continuous activity and narrative: narrative film. Younger and older adults watched and segmented a narrative film, The Red Balloon, into coarse and fine events. Changes in situational features, such as changes in characters, goals, and objects predicted segmentation. Analyses revealed little age-difference in segmentation behavior. This suggests the possibility that narrative structure supports event understanding for older adults.

  10. The Sequenced Angiosperm Genomes and Genome Databases.

    Science.gov (United States)

    Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

    2018-01-01

    Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

  11. Colour application on mammography image segmentation

    Science.gov (United States)

    Embong, R.; Aziz, N. M. Nik Ab.; Karim, A. H. Abd; Ibrahim, M. R.

    2017-09-01

    The segmentation process is one of the most important steps in image processing and computer vision since it is vital in the initial stage of image analysis. Segmentation of medical images involves complex structures and it requires precise segmentation result which is necessary for clinical diagnosis such as the detection of tumour, oedema, and necrotic tissues. Since mammography images are grayscale, researchers are looking at the effect of colour in the segmentation process of medical images. Colour is known to play a significant role in the perception of object boundaries in non-medical colour images. Processing colour images require handling more data, hence providing a richer description of objects in the scene. Colour images contain ten percent (10%) additional edge information as compared to their grayscale counterparts. Nevertheless, edge detection in colour image is more challenging than grayscale image as colour space is considered as a vector space. In this study, we implemented red, green, yellow, and blue colour maps to grayscale mammography images with the purpose of testing the effect of colours on the segmentation of abnormality regions in the mammography images. We applied the segmentation process using the Fuzzy C-means algorithm and evaluated the percentage of average relative error of area for each colour type. The results showed that all segmentation with the colour map can be done successfully even for blurred and noisy images. Also the size of the area of the abnormality region is reduced when compare to the segmentation area without the colour map. The green colour map segmentation produced the smallest percentage of average relative error (10.009%) while yellow colour map segmentation gave the largest percentage of relative error (11.367%).

  12. SEGMENTATION OF SME PORTFOLIO IN BANKING SYSTEM

    Directory of Open Access Journals (Sweden)

    Namolosu Simona Mihaela

    2013-07-01

    Full Text Available The Small and Medium Enterprises (SMEs represent an important target market for commercial Banks. In this respect, finding the best methods for designing and implementing the optimal marketing strategies (for this target are a continuous concern for the marketing specialists and researchers from the banking system; the purpose is to find the most suitable service model for these companies. SME portfolio of a bank is not homogeneous, different characteristics and behaviours being identified. The current paper reveals empirical evidence about SME portfolio characteristics and segmentation methods used in banking system. Its purpose is to identify if segmentation has an impact in finding the optimal marketing strategies and service model and if this hypothesis might be applicable for any commercial bank, irrespective of country/ region. Some banks are segmenting the SME portfolio by a single criterion: the annual company (official turnover; others are considering also profitability and other financial indicators of the company. In some cases, even the banking behaviour becomes a criterion. For all cases, creating scenarios with different thresholds and estimating the impact in profitability and volumes are two mandatory steps in establishing the final segmentation (criteria matrix. Details about each of these segmentation methods may be found in the paper. Testing the final matrix of criteria is also detailed, with the purpose of making realistic estimations. Example for lending products is provided; the product offer is presented as responding to needs of targeted sub segment and therefore being correlated with the sub segment characteristics. Identifying key issues and trends leads to further action plan proposal. Depending on overall strategy and commercial target of the bank, the focus may shift, one or more sub segments becoming high priority (for acquisition/ activation/ retention/ cross sell/ up sell/ increase profitability etc., while

  13. Efficient assembly of de novo human artificial chromosomes from large genomic loci

    Directory of Open Access Journals (Sweden)

    Stromberg Gregory

    2005-07-01

    Full Text Available Abstract Background Human Artificial Chromosomes (HACs are potentially useful vectors for gene transfer studies and for functional annotation of the genome because of their suitability for cloning, manipulating and transferring large segments of the genome. However, development of HACs for the transfer of large genomic loci into mammalian cells has been limited by difficulties in manipulating high-molecular weight DNA, as well as by the low overall frequencies of de novo HAC formation. Indeed, to date, only a small number of large (>100 kb genomic loci have been reported to be successfully packaged into de novo HACs. Results We have developed novel methodologies to enable efficient assembly of HAC vectors containing any genomic locus of interest. We report here the creation of a novel, bimolecular system based on bacterial artificial chromosomes (BACs for the construction of HACs incorporating any defined genomic region. We have utilized this vector system to rapidly design, construct and validate multiple de novo HACs containing large (100–200 kb genomic loci including therapeutically significant genes for human growth hormone (HGH, polycystic kidney disease (PKD1 and ß-globin. We report significant differences in the ability of different genomic loci to support de novo HAC formation, suggesting possible effects of cis-acting genomic elements. Finally, as a proof of principle, we have observed sustained ß-globin gene expression from HACs incorporating the entire 200 kb ß-globin genomic locus for over 90 days in the absence of selection. Conclusion Taken together, these results are significant for the development of HAC vector technology, as they enable high-throughput assembly and functional validation of HACs containing any large genomic locus. We have evaluated the impact of different genomic loci on the frequency of HAC formation and identified segments of genomic DNA that appear to facilitate de novo HAC formation. These genomic loci

  14. Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

    DEFF Research Database (Denmark)

    Ebert, Grit; Steininger, Anne; Weißmann, Robert

    2014-01-01

    of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation. CONCLUSIONS: Our study suggests a link of nuclear architecture and the propagation of SDs across......BACKGROUND: Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders...... chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome....

  15. Method of manufacturing a large-area segmented photovoltaic module

    Science.gov (United States)

    Lenox, Carl

    2013-11-05

    One embodiment of the invention relates to a segmented photovoltaic (PV) module which is manufactured from laminate segments. The segmented PV module includes rectangular-shaped laminate segments formed from rectangular-shaped PV laminates and further includes non-rectangular-shaped laminate segments formed from rectangular-shaped and approximately-triangular-shaped PV laminates. The laminate segments are mechanically joined and electrically interconnected to form the segmented module. Another embodiment relates to a method of manufacturing a large-area segmented photovoltaic module from laminate segments of various shapes. Other embodiments relate to processes for providing a photovoltaic array for installation at a site. Other embodiments and features are also disclosed.

  16. Study of the morphology exhibited by linear segmented polyurethanes

    International Nuclear Information System (INIS)

    Pereira, I.M.; Orefice, R.L.

    2009-01-01

    Five series of segmented polyurethanes with different hard segment content were prepared by the prepolymer mixing method. The nano-morphology of the obtained polyurethanes and their microphase separation were investigated by infrared spectroscopy, modulated differential scanning calorimetry and small-angle X-ray scattering. Although highly hydrogen bonded hard segments were formed, high hard segment contents promoted phase mixture and decreased the chain mobility, decreasing the hard segment domain precipitation and the soft segments crystallization. The applied techniques were able to show that the hard-segment content and the hard-segment interactions were the two controlling factors for determining the structure of segmented polyurethanes. (author)

  17. Molecular Characterization of a Trisegmented Mycovirus from the Plant Pathogenic Fungus Colletotrichum gloeosporioides

    Directory of Open Access Journals (Sweden)

    Jie Zhong

    2016-09-01

    Full Text Available A novel double-stranded RNA (dsRNA mycovirus, consisting of three dsRNA genome segments and possibly belonging to the family Chrysoviridae, was isolated from the filamentous phytopathogenic fungus Colletotrichum gloeosporioides and designated as Colletotrichum gloeosprioides chrysovirus 1 (CgCV1. The three dsRNAs of the CgCV1 genome with lengths of 3397, 2869, and 2630 bp (dsRNAs1–3 were found to contain a single open reading frame (ORF putatively encoding the RNA-dependent RNA polymerase (RdRp, a capsid protein, and a protease, respectively, all of which exhibited some degree of sequence similarity to the comparable putative proteins encoded by the genus Chrysovirus. The 5′- and 3′-untranslated regions in each dsRNA segment contained similar sequences that were strictly conserved at the termini. Moreover, isometric virus-like particles (VLPs with a diameter of approximately 40 nm were extracted from fungal mycelia. Phylogenetic analysis based on the conserved dsRNA1-encoded RdRp showed that CgCV1 is a new virus belonging to the Chrysoviridae family. BLAST analysis revealed the presence of CgCV1-like sequences in the chromosomes of Medicago truncatula and Solanum tuberosum. Moreover, some sequences in the transcriptome shotgun assembly (TSA library and expressed sequence tag database (ESTdb of other eudicot and monocot plants were also found to be related to CgCV1.

  18. Performance Analysis of Segmentation of Hyperspectral Images Based on Color Image Segmentation

    Directory of Open Access Journals (Sweden)

    Praveen Agarwal

    2017-06-01

    Full Text Available Image segmentation is a fundamental approach in the field of image processing and based on user’s application .This paper propose an original and simple segmentation strategy based on the EM approach that resolves many informatics problems about hyperspectral images which are observed by airborne sensors. In a first step, to simplify the input color textured image into a color image without texture. The final segmentation is simply achieved by a spatially color segmentation using feature vector with the set of color values contained around the pixel to be classified with some mathematical equations. The spatial constraint allows taking into account the inherent spatial relationships of any image and its color. This approach provides effective PSNR for the segmented image. These results have the better performance as the segmented images are compared with Watershed & Region Growing Algorithm and provide effective segmentation for the Spectral Images & Medical Images.

  19. Polyether based segmented copolymers with uniform aramid units

    NARCIS (Netherlands)

    Niesten, M.C.E.J.

    2000-01-01

    Segmented copolymers with short, glassy or crystalline hard segments and long, amorphous soft segments (multi-block copolymers) are thermoplastic elastomers (TPE’s). The hard segments form physical crosslinks for the amorphous (rubbery) soft segments. As a result, this type of materials combines

  20. Cluster Ensemble-Based Image Segmentation

    Directory of Open Access Journals (Sweden)

    Xiaoru Wang

    2013-07-01

    Full Text Available Image segmentation is the foundation of computer vision applications. In this paper, we propose a new cluster ensemble-based image segmentation algorithm, which overcomes several problems of traditional methods. We make two main contributions in this paper. First, we introduce the cluster ensemble concept to fuse the segmentation results from different types of visual features effectively, which can deliver a better final result and achieve a much more stable performance for broad categories of images. Second, we exploit the PageRank idea from Internet applications and apply it to the image segmentation task. This can improve the final segmentation results by combining the spatial information of the image and the semantic similarity of regions. Our experiments on four public image databases validate the superiority of our algorithm over conventional single type of feature or multiple types of features-based algorithms, since our algorithm can fuse multiple types of features effectively for better segmentation results. Moreover, our method is also proved to be very competitive in comparison with other state-of-the-art segmentation algorithms.

  1. An unsupervised strategy for biomedical image segmentation

    Directory of Open Access Journals (Sweden)

    Roberto Rodríguez

    2010-09-01

    Full Text Available Roberto Rodríguez1, Rubén Hernández21Digital Signal Processing Group, Institute of Cybernetics, Mathematics, and Physics, Havana, Cuba; 2Interdisciplinary Professional Unit of Engineering and Advanced Technology, IPN, MexicoAbstract: Many segmentation techniques have been published, and some of them have been widely used in different application problems. Most of these segmentation techniques have been motivated by specific application purposes. Unsupervised methods, which do not assume any prior scene knowledge can be learned to help the segmentation process, and are obviously more challenging than the supervised ones. In this paper, we present an unsupervised strategy for biomedical image segmentation using an algorithm based on recursively applying mean shift filtering, where entropy is used as a stopping criterion. This strategy is proven with many real images, and a comparison is carried out with manual segmentation. With the proposed strategy, errors less than 20% for false positives and 0% for false negatives are obtained.Keywords: segmentation, mean shift, unsupervised segmentation, entropy

  2. Segmentation precedes face categorization under suboptimal conditions

    Directory of Open Access Journals (Sweden)

    Carlijn eVan Den Boomen

    2015-05-01

    Full Text Available Both categorization and segmentation processes play a crucial role in face perception. However, the functional relation between these subprocesses is currently unclear. The present study investigates the temporal relation between segmentation-related and category-selective responses in the brain, using electroencephalography (EEG. Surface segmentation and category content were both manipulated using texture-defined objects, including faces. This allowed us to study brain activity related to segmentation and to categorization. In the main experiment, participants viewed texture-defined objects for a duration of 800 ms. EEG results revealed that segmentation-related responses precede category-selective responses. Three additional experiments revealed that the presence and timing of categorization depends on stimulus properties and presentation duration. Photographic objects were presented for a long and short (92 ms duration and evoked fast category-selective responses in both cases. On the other hand, presentation of texture-defined objects for a short duration only evoked segmentation-related but no category-selective responses. Category-selective responses were much slower when evoked by texture-defined than by photographic objects. We suggest that in case of categorization of objects under suboptimal conditions, such as when low-level stimulus properties are not sufficient for fast object categorization, segmentation facilitates the slower categorization process.

  3. Incorporation of squalene into rod outer segments

    International Nuclear Information System (INIS)

    Keller, R.K.; Fliesler, S.J.

    1990-01-01

    We have reported previously that squalene is the major radiolabeled nonsaponifiable lipid product derived from [ 3 H]acetate in short term incubations of frog retinas. In the present study, we demonstrate that newly synthesized squalene is incorporated into rod outer segments under similar in vitro conditions. We show further that squalene is an endogenous constituent of frog rod outer segment membranes; its concentration is approximately 9.5 nmol/mumol of phospholipid or about 9% of the level of cholesterol. Pulse-chase experiments with radiolabeled precursors revealed no metabolism of outer segment squalene to sterols in up to 20 h of chase. Taken together with our previous absolute rate studies, these results suggest that most, if not all, of the squalene synthesized by the frog retina is transported to rod outer segments. Synthesis of protein is not required for squalene transport since puromycin had no effect on squalene incorporation into outer segments. Conversely, inhibition of isoprenoid synthesis with mevinolin had no effect on the incorporation of opsin into the outer segment. These latter results support the conclusion that the de novo synthesis and subsequent intracellular trafficking of opsin and isoprenoid lipids destined for the outer segment occur via independent mechanisms

  4. A Kalman Filtering Perspective for Multiatlas Segmentation*

    Science.gov (United States)

    Gao, Yi; Zhu, Liangjia; Cates, Joshua; MacLeod, Rob S.; Bouix, Sylvain; Tannenbaum, Allen

    2016-01-01

    In multiatlas segmentation, one typically registers several atlases to the novel image, and their respective segmented label images are transformed and fused to form the final segmentation. In this work, we provide a new dynamical system perspective for multiatlas segmentation, inspired by the following fact: The transformation that aligns the current atlas to the novel image can be not only computed by direct registration but also inferred from the transformation that aligns the previous atlas to the image together with the transformation between the two atlases. This process is similar to the global positioning system on a vehicle, which gets position by inquiring from the satellite and by employing the previous location and velocity—neither answer in isolation being perfect. To solve this problem, a dynamical system scheme is crucial to combine the two pieces of information; for example, a Kalman filtering scheme is used. Accordingly, in this work, a Kalman multiatlas segmentation is proposed to stabilize the global/affine registration step. The contributions of this work are twofold. First, it provides a new dynamical systematic perspective for standard independent multiatlas registrations, and it is solved by Kalman filtering. Second, with very little extra computation, it can be combined with most existing multiatlas segmentation schemes for better registration/segmentation accuracy. PMID:26807162

  5. Segmentation-less Digital Rock Physics

    Science.gov (United States)

    Tisato, N.; Ikeda, K.; Goldfarb, E. J.; Spikes, K. T.

    2017-12-01

    In the last decade, Digital Rock Physics (DRP) has become an avenue to investigate physical and mechanical properties of geomaterials. DRP offers the advantage of simulating laboratory experiments on numerical samples that are obtained from analytical methods. Potentially, DRP could allow sparing part of the time and resources that are allocated to perform complicated laboratory tests. Like classic laboratory tests, the goal of DRP is to estimate accurately physical properties of rocks like hydraulic permeability or elastic moduli. Nevertheless, the physical properties of samples imaged using micro-computed tomography (μCT) are estimated through segmentation of the μCT dataset. Segmentation proves to be a challenging and arbitrary procedure that typically leads to inaccurate estimates of physical properties. Here we present a novel technique to extract physical properties from a μCT dataset without the use of segmentation. We show examples in which we use segmentation-less method to simulate elastic wave propagation and pressure wave diffusion to estimate elastic properties and permeability, respectively. The proposed method takes advantage of effective medium theories and uses the density and the porosity that are measured in the laboratory to constrain the results. We discuss the results and highlight that segmentation-less DRP is more accurate than segmentation based DRP approaches and theoretical modeling for the studied rock. In conclusion, the segmentation-less approach here presented seems to be a promising method to improve accuracy and to ease the overall workflow of DRP.

  6. Segmentation precedes face categorization under suboptimal conditions.

    Science.gov (United States)

    Van Den Boomen, Carlijn; Fahrenfort, Johannes J; Snijders, Tineke M; Kemner, Chantal

    2015-01-01

    Both categorization and segmentation processes play a crucial role in face perception. However, the functional relation between these subprocesses is currently unclear. The present study investigates the temporal relation between segmentation-related and category-selective responses in the brain, using electroencephalography (EEG). Surface segmentation and category content were both manipulated using texture-defined objects, including faces. This allowed us to study brain activity related to segmentation and to categorization. In the main experiment, participants viewed texture-defined objects for a duration of 800 ms. EEG results revealed that segmentation-related responses precede category-selective responses. Three additional experiments revealed that the presence and timing of categorization depends on stimulus properties and presentation duration. Photographic objects were presented for a long and short (92 ms) duration and evoked fast category-selective responses in both cases. On the other hand, presentation of texture-defined objects for a short duration only evoked segmentation-related but no category-selective responses. Category-selective responses were much slower when evoked by texture-defined than by photographic objects. We suggest that in case of categorization of objects under suboptimal conditions, such as when low-level stimulus properties are not sufficient for fast object categorization, segmentation facilitates the slower categorization process.

  7. Bayesian automated cortical segmentation for neonatal MRI

    Science.gov (United States)

    Chou, Zane; Paquette, Natacha; Ganesh, Bhavana; Wang, Yalin; Ceschin, Rafael; Nelson, Marvin D.; Macyszyn, Luke; Gaonkar, Bilwaj; Panigrahy, Ashok; Lepore, Natasha

    2017-11-01

    Several attempts have been made in the past few years to develop and implement an automated segmentation of neonatal brain structural MRI. However, accurate automated MRI segmentation remains challenging in this population because of the low signal-to-noise ratio, large partial volume effects and inter-individual anatomical variability of the neonatal brain. In this paper, we propose a learning method for segmenting the whole brain cortical grey matter on neonatal T2-weighted images. We trained our algorithm using a neonatal dataset composed of 3 fullterm and 4 preterm infants scanned at term equivalent age. Our segmentation pipeline combines the FAST algorithm from the FSL library software and a Bayesian segmentation approach to create a threshold matrix that minimizes the error of mislabeling brain tissue types. Our method shows promising results with our pilot training set. In both preterm and full-term neonates, automated Bayesian segmentation generates a smoother and more consistent parcellation compared to FAST, while successfully removing the subcortical structure and cleaning the edges of the cortical grey matter. This method show promising refinement of the FAST segmentation by considerably reducing manual input and editing required from the user, and further improving reliability and processing time of neonatal MR images. Further improvement will include a larger dataset of training images acquired from different manufacturers.

  8. Deformable segmentation via sparse shape representation.

    Science.gov (United States)

    Zhang, Shaoting; Zhan, Yiqiang; Dewan, Maneesh; Huang, Junzhou; Metaxas, Dimitris N; Zhou, Xiang Sean

    2011-01-01

    Appearance and shape are two key elements exploited in medical image segmentation. However, in some medical image analysis tasks, appearance cues are weak/misleading due to disease/artifacts and often lead to erroneous segmentation. In this paper, a novel deformable model is proposed for robust segmentation in the presence of weak/misleading appearance cues. Owing to the less trustable appearance information, this method focuses on the effective shape modeling with two contributions. First, a shape composition method is designed to incorporate shape prior on-the-fly. Based on two sparsity observations, this method is robust to false appearance information and adaptive to statistically insignificant shape modes. Second, shape priors are modeled and used in a hierarchical fashion. More specifically, by using affinity propagation method, our deformable surface is divided into multiple partitions, on which local shape models are built independently. This scheme facilitates a more compact shape prior modeling and hence a more robust and efficient segmentation. Our deformable model is applied on two very diverse segmentation problems, liver segmentation in PET-CT images and rodent brain segmentation in MR images. Compared to state-of-art methods, our method achieves better performance in both studies.

  9. Identification of pummelo cultivars by using a panel of 25 selected SNPs and 12 DNA segments.

    Directory of Open Access Journals (Sweden)

    Bo Wu

    Full Text Available Pummelo cultivars are usually difficult to identify morphologically, especially when fruits are unavailable. The problem was addressed in this study with the use of two methods: high resolution melting analysis of SNPs and sequencing of DNA segments. In the first method, a set of 25 SNPs with high polymorphic information content were selected from SNPs predicted by analyzing ESTs and sequenced DNA segments. High resolution melting analysis was then used to genotype 260 accessions including 55 from Myanmar, and 178 different genotypes were thus identified. A total of 99 cultivars were assigned to 86 different genotypes since the known somatic mutants were identical to their original genotypes at the analyzed SNP loci. The Myanmar samples were genotypically different from each other and from all other samples, indicating they were derived from sexual propagation. Statistical analysis showed that the set of SNPs was powerful enough for identifying at least 1000 pummelo genotypes, though the discrimination power varied in different pummelo groups and populations. In the second method, 12 genomic DNA segments of 24 representative pummelo accessions were sequenced. Analysis of the sequences revealed the existence of a high haplotype polymorphism in pummelo, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of 1200 pummelo cultivars. The high level of haplotype diversity and an apparent population structure shown by DNA segments and by SNP genotypes, respectively, were discussed in relation to the origin and domestication of the pummelo species.

  10. RNA polymerase of the killer virus of yeast

    International Nuclear Information System (INIS)

    Georgopoulos, D.E.; Leibowitz, M.J.

    1984-01-01

    The L/sub A/ and M double-stranded (ds) RNA segments of the cytoplasmically inherited killer virus of Saccharomyces cerevisiae are encapsidated in virions that contain a DNA-independent transcriptase activity. This enzyme catalyzes the synthesis of full-length (+) stranded copies of the genomic dsRNA segments, denoted l/sub A/ and m. The L/sub A/ dsRNA segment appears to encode the major capsid protein in which both dsRNA molecules are encapsidated, while M dsRNA encodes products responsible for the two killer phenotypes of toxin production and resistance to toxin. Proteins extracted from transcriptionally active virions fail to cross-react with antibody to yeast DNA-dependent RNA polymerases, suggesting that none of the subunits of the host cell polymerases are active in viral transcription. Sequence analysis of the in vitro transcripts reveals neither to be 3'-terminally polyadenylated, although m contains an apparent internal polyA-like tract. In the presence of any three ribonucleoside triphosphates (0.5 mM), the fourth ribonucleoside triphosphate shows an optimal rate of incorporation into transcript at a concentration of 20 μM. However, in a 3-hour reaction, the yield of a product RNA increases with the concentration of the limiting ribonucleotide up to 0.5 mM. Gel electrophoresis of the reaction products reveals that increasing the substrate concentration accelerates the appearance of radioactivity in full-length l/sub A/ and m transcripts

  11. Composition and genomic organization of arthropod Hox clusters.

    Science.gov (United States)

    Pace, Ryan M; Grbić, Miodrag; Nagy, Lisa M

    2016-01-01

    The ancestral arthropod is believed to have had a clustered arrangement of ten Hox genes. Within arthropods, Hox gene mutations result in transformation of segment identities. Despite the fact that variation in segment number/character was common in the diversification of arthropods, few examples of Hox gene gains/losses have been correlated with morphological evolution. Furthermore, a full appreciation of the variation in the genomic arrangement of Hox genes in extant arthropods has not been recognized, as genome sequences from each major arthropod clade have not been reported until recently. Initial genomic analysis of the chelicerate Tetranychus urticae suggested that loss of Hox genes and Hox gene clustering might be more common than previously assumed. To further characterize the genomic evolution of arthropod Hox genes, we compared the genomic arrangement and general characteristics of Hox genes from representative taxa from each arthropod subphylum. In agreement with others, we find arthropods generally contain ten Hox genes arranged in a common orientation in the genome, with an increasing number of sampled species missing either Hox3 or abdominal-A orthologs. The genomic clustering of Hox genes in species we surveyed varies significantly, ranging from 0.3 to 13.6 Mb. In all species sampled, arthropod Hox genes are dispersed in the genome relative to the vertebrate Mus musculus. Differences in Hox cluster size arise from variation in the number of intervening genes, intergenic spacing, and the size of introns and UTRs. In the arthropods surveyed, Hox gene duplications are rare and four microRNAs are, in general, conserved in similar genomic positions relative to the Hox genes. The tightly clustered Hox complexes found in the vertebrates are not evident within arthropods, and differential patterns of Hox gene dispersion are found throughout the arthropods. The comparative genomic data continue to support an ancestral arthropod Hox cluster of ten genes with

  12. Unsupervised Segmentation Methods of TV Contents

    Directory of Open Access Journals (Sweden)

    Elie El-Khoury

    2010-01-01

    Full Text Available We present a generic algorithm to address various temporal segmentation topics of audiovisual contents such as speaker diarization, shot, or program segmentation. Based on a GLR approach, involving the ΔBIC criterion, this algorithm requires the value of only a few parameters to produce segmentation results at a desired scale and on most typical low-level features used in the field of content-based indexing. Results obtained on various corpora are of the same quality level than the ones obtained by other dedicated and state-of-the-art methods.

  13. Contractual Incompleteness, Unemployment, and Labour Market Segmentation

    DEFF Research Database (Denmark)

    Altmann, Steffen; Falk, Armin; Grunewald, Andreas

    2014-01-01

    This article provides evidence that involuntary unemployment, and the segmentation of labour markets into firms offering "good" and "bad" jobs, may both arise as a consequence of contractual incompleteness.We provide a simple model that illustrates how unemployment and market segmentation may...... jointly emerge as part of a market equilibrium in environments where work effort is not third-party verifiable. Using experimental labour markets that differ only in the verifiability of effort, we demonstrate empirically that contractual incompleteness can cause unemployment and segmentation. Our data...

  14. Multi-scale Modelling of Segmentation

    DEFF Research Database (Denmark)

    Hartmann, Martin; Lartillot, Olivier; Toiviainen, Petri

    2016-01-01

    pieces. In a second experiment on non-real-time segmentation, musicians indicated boundaries and their strength for six examples. Kernel density estimation was used to develop multi-scale segmentation models. Contrary to previous research, no relationship was found between boundary strength and boundary......While listening to music, people often unwittingly break down musical pieces into constituent chunks such as verses and choruses. Music segmentation studies have suggested that some consensus regarding boundary perception exists, despite individual differences. However, neither the effects...

  15. Polarimetric Segmentation Using Wishart Test Statistic

    DEFF Research Database (Denmark)

    Skriver, Henning; Schou, Jesper; Nielsen, Allan Aasbjerg

    2002-01-01

    A newly developed test statistic for equality of two complex covariance matrices following the complex Wishart distribution and an associated asymptotic probability for the test statistic has been used in a segmentation algorithm. The segmentation algorithm is based on the MUM (merge using moments......) approach, which is a merging algorithm for single channel SAR images. The polarimetric version described in this paper uses the above-mentioned test statistic for merging. The segmentation algorithm has been applied to polarimetric SAR data from the Danish dual-frequency, airborne polarimetric SAR, EMISAR...

  16. Leisure market segmentation : an integrated preferences/constraints-based approach

    NARCIS (Netherlands)

    Stemerding, M.P.; Oppewal, H.; Beckers, T.A.M.; Timmermans, H.J.P.

    1996-01-01

    Traditional segmentation schemes are often based on a grouping of consumers with similar preference functions. The research steps, ultimately leading to such segmentation schemes, are typically independent. In the present article, a new integrated approach to segmentation is introduced, which

  17. Skin Segmentation Based on Graph Cuts

    Institute of Scientific and Technical Information of China (English)

    HU Zhilan; WANG Guijin; LIN Xinggang; YAN Hong

    2009-01-01

    Skin segmentation is widely used in many computer vision tasks to improve automated visualiza-tion. This paper presents a graph cuts algorithm to segment arbitrary skin regions from images. The detected face is used to determine the foreground skin seeds and the background non-skin seeds with the color probability distributions for the foreground represented by a single Gaussian model and for the background by a Gaussian mixture model. The probability distribution of the image is used for noise suppression to alle-viate the influence of the background regions having skin-like colors. Finally, the skin is segmented by graph cuts, with the regional parameter y optimally selected to adapt to different images. Tests of the algorithm on many real wodd photographs show that the scheme accurately segments skin regions and is robust against illumination variations, individual skin variations, and cluttered backgrounds.

  18. Measurements on a prototype segmented Clover detector

    CERN Document Server

    Shepherd, S L; Cullen, D M; Appelbe, D E; Simpson, J; Gerl, J; Kaspar, M; Kleinböhl, A; Peter, I; Rejmund, M; Schaffner, H; Schlegel, C; France, G D

    1999-01-01

    The performance of a segmented Clover germanium detector has been measured. The segmented Clover detector is a composite germanium detector, consisting of four individual germanium crystals in the configuration of a four-leaf Clover, housed in a single cryostat. Each crystal is electrically segmented on its outer surface into four quadrants, with separate energy read-outs from nine crystal zones. Signals are also taken from the inner contact of each crystal. This effectively produces a detector with 16 active elements. One of the purposes of this segmentation is to improve the overall spectral resolution when detecting gamma radiation emitted following a nuclear reaction, by minimising Doppler broadening caused by the opening angle subtended by each detector element. Results of the tests with sources and in beam will be presented. The improved granularity of the detector also leads to an improved isolated hit probability compared with an unsegmented Clover detector. (author)

  19. Constrained bidirectional propagation and stroke segmentation

    Energy Technology Data Exchange (ETDEWEB)

    Mori, S; Gillespie, W; Suen, C Y

    1983-03-01

    A new method for decomposing a complex figure into its constituent strokes is described. This method, based on constrained bidirectional propagation, is suitable for parallel processing. Examples of its application to the segmentation of Chinese characters are presented. 9 references.

  20. Neural Scene Segmentation by Oscillatory Correlation

    National Research Council Canada - National Science Library

    Wang, DeLiang

    2000-01-01

    The segmentation of a visual scene into a set of coherent patterns (objects) is a fundamental aspect of perception, which underlies a variety of important tasks such as figure/ground segregation, and scene analysis...

  1. Variational mesh segmentation via quadric surface fitting

    KAUST Repository

    Yan, Dongming

    2012-11-01

    We present a new variational method for mesh segmentation by fitting quadric surfaces. Each component of the resulting segmentation is represented by a general quadric surface (including plane as a special case). A novel energy function is defined to evaluate the quality of the segmentation, which combines both L2 and L2 ,1 metrics from a triangle to a quadric surface. The Lloyd iteration is used to minimize the energy function, which repeatedly interleaves between mesh partition and quadric surface fitting. We also integrate feature-based and simplification-based techniques in the segmentation framework, which greatly improve the performance. The advantages of our algorithm are demonstrated by comparing with the state-of-the-art methods. © 2012 Elsevier Ltd. All rights reserved.

  2. Probabilistic segmentation of remotely sensed images

    NARCIS (Netherlands)

    Gorte, B.

    1998-01-01

    For information extraction from image data to create or update geographic information systems, objects are identified and labeled using an integration of segmentation and classification. This yields geometric and thematic information, respectively.

    Bayesian image

  3. Medical image segmentation using genetic algorithms.

    Science.gov (United States)

    Maulik, Ujjwal

    2009-03-01

    Genetic algorithms (GAs) have been found to be effective in the domain of medical image segmentation, since the problem can often be mapped to one of search in a complex and multimodal landscape. The challenges in medical image segmentation arise due to poor image contrast and artifacts that result in missing or diffuse organ/tissue boundaries. The resulting search space is therefore often noisy with a multitude of local optima. Not only does the genetic algorithmic framework prove to be effective in coming out of local optima, it also brings considerable flexibility into the segmentation procedure. In this paper, an attempt has been made to review the major applications of GAs to the domain of medical image segmentation.

  4. Joint shape segmentation with linear programming

    KAUST Repository

    Huang, Qixing; Koltun, Vladlen; Guibas, Leonidas

    2011-01-01

    program is solved via a linear programming relaxation, using a block coordinate descent procedure that makes the optimization feasible for large databases. We evaluate the presented approach on the Princeton segmentation benchmark and show that joint shape

  5. Variational mesh segmentation via quadric surface fitting

    KAUST Repository

    Yan, Dongming; Wang, Wen Ping; Liu, Yang; Yang, Zhouwang

    2012-01-01

    We present a new variational method for mesh segmentation by fitting quadric surfaces. Each component of the resulting segmentation is represented by a general quadric surface (including plane as a special case). A novel energy function is defined to evaluate the quality of the segmentation, which combines both L2 and L2 ,1 metrics from a triangle to a quadric surface. The Lloyd iteration is used to minimize the energy function, which repeatedly interleaves between mesh partition and quadric surface fitting. We also integrate feature-based and simplification-based techniques in the segmentation framework, which greatly improve the performance. The advantages of our algorithm are demonstrated by comparing with the state-of-the-art methods. © 2012 Elsevier Ltd. All rights reserved.

  6. Pitch Synchronous Segmentation of Speech Signals

    Data.gov (United States)

    National Aeronautics and Space Administration — The Pitch Synchronous Segmentation (PSS) that accelerates speech without changing its fundamental frequency method could be applied and evaluated for use at NASA....

  7. Field Sampling from a Segmented Image

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2008-06-01

    Full Text Available This paper presents a statistical method for deriving the optimal prospective field sampling scheme on a remote sensing image to represent different categories in the field. The iterated conditional modes algorithm (ICM) is used for segmentation...

  8. Retina image–based optic disc segmentation

    Directory of Open Access Journals (Sweden)

    Ching-Lin Wang

    2016-05-01

    Full Text Available The change of optic disc can be used to diagnose many eye diseases, such as glaucoma, diabetic retinopathy and macular degeneration. Moreover, retinal blood vessel pattern is unique for human beings even for identical twins. It is a highly stable pattern in biometric identification. Since optic disc is the beginning of the optic nerve and main blood vessels in retina, it can be used as a reference point of identification. Therefore, optic disc segmentation is an important technique for developing a human identity recognition system and eye disease diagnostic system. This article hence presents an optic disc segmentation method to extract the optic disc from a retina image. The experimental results show that the optic disc segmentation method can give impressive results in segmenting the optic disc from a retina image.

  9. Handwriting segmentation of unconstrained Oriya text

    Indian Academy of Sciences (India)

    Segmentation of handwritten text into lines, words and characters .... We now discuss here some terms relating to water reservoirs that will be used in feature ..... is found. Next, based on the touching position, reservoir base-area points, ...

  10. Mixed raster content segmentation, compression, transmission

    CERN Document Server

    Pavlidis, George

    2017-01-01

    This book presents the main concepts in handling digital images of mixed content, traditionally referenced as mixed raster content (MRC), in two main parts. The first includes introductory chapters covering the scientific and technical background aspects, whereas the second presents a set of research and development approaches to tackle key issues in MRC segmentation, compression and transmission. The book starts with a review of color theory and the mechanism of color vision in humans. In turn, the second chapter reviews data coding and compression methods so as to set the background and demonstrate the complexity involved in dealing with MRC. Chapter three addresses the segmentation of images through an extensive literature review, which highlights the various approaches used to tackle MRC segmentation. The second part of the book focuses on the segmentation of color images for optimized compression, including multi-layered decomposition and representation of MRC and the processes that can be employed to op...

  11. Defining functional DNA elements in the human genome

    Science.gov (United States)

    Kellis, Manolis; Wold, Barbara; Snyder, Michael P.; Bernstein, Bradley E.; Kundaje, Anshul; Marinov, Georgi K.; Ward, Lucas D.; Birney, Ewan; Crawford, Gregory E.; Dekker, Job; Dunham, Ian; Elnitski, Laura L.; Farnham, Peggy J.; Feingold, Elise A.; Gerstein, Mark; Giddings, Morgan C.; Gilbert, David M.; Gingeras, Thomas R.; Green, Eric D.; Guigo, Roderic; Hubbard, Tim; Kent, Jim; Lieb, Jason D.; Myers, Richard M.; Pazin, Michael J.; Ren, Bing; Stamatoyannopoulos, John A.; Weng, Zhiping; White, Kevin P.; Hardison, Ross C.

    2014-01-01

    With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease. PMID:24753594

  12. Bioinformatics decoding the genome

    CERN Multimedia

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  13. Genomic research in Eucalyptus.

    Science.gov (United States)

    Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

    2005-09-01

    Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

  14. A competition in unsupervised color image segmentation

    Czech Academy of Sciences Publication Activity Database

    Haindl, Michal; Mikeš, Stanislav

    2016-01-01

    Roč. 57, č. 9 (2016), s. 136-151 ISSN 0031-3203 R&D Projects: GA ČR(CZ) GA14-10911S Institutional support: RVO:67985556 Keywords : Unsupervised image segmentation * Segmentation contest * Texture analysis Subject RIV: BD - Theory of Information Impact factor: 4.582, year: 2016 http://library.utia.cas.cz/separaty/2016/RO/haindl-0459179.pdf

  15. Learning Semantic Segmentation with Diverse Supervision

    OpenAIRE

    Ye, Linwei; Liu, Zhi; Wang, Yang

    2018-01-01

    Models based on deep convolutional neural networks (CNN) have significantly improved the performance of semantic segmentation. However, learning these models requires a large amount of training images with pixel-level labels, which are very costly and time-consuming to collect. In this paper, we propose a method for learning CNN-based semantic segmentation models from images with several types of annotations that are available for various computer vision tasks, including image-level labels fo...

  16. Unfolding Implementation in Industrial Market Segmentation

    DEFF Research Database (Denmark)

    Bøjgaard, John; Ellegaard, Chris

    2011-01-01

    to pave the way towards closing this gap. The extent of implementation coverage is assessed and various notions of implementation are identified. Implementation as the task of converting segmentation plans into action (referred to as execution) is identified as a particularly beneficial focus area...... for marketing management. Three key elements and challenges connected to execution of market segmentation are identified — organization, motivation, and adaptation....

  17. Mounting and Alignment of IXO Mirror Segments

    Science.gov (United States)

    Chan, Kai-Wing; Zhang, William; Evans, Tyler; McClelland, Ryan; Hong, Melinda; Mazzarella, James; Saha, Timo; Jalota, Lalit; Olsen, Lawrence; Byron, Glenn

    2010-01-01

    A suspension-mounting scheme is developed for the IXO (International X-ray Observatory) mirror segments in which the figure of the mirror segment is preserved in each stage of mounting. The mirror, first fixed on a thermally compatible strongback, is subsequently transported, aligned and transferred onto its mirror housing. In this paper, we shall outline the requirement, approaches, and recent progress of the suspension mount processes.

  18. Active Mask Segmentation of Fluorescence Microscope Images

    OpenAIRE

    Srinivasa, Gowri; Fickus, Matthew C.; Guo, Yusong; Linstedt, Adam D.; Kovačević, Jelena

    2009-01-01

    We propose a new active mask algorithm for the segmentation of fluorescence microscope images of punctate patterns. It combines the (a) flexibility offered by active-contour methods, (b) speed offered by multiresolution methods, (c) smoothing offered by multiscale methods, and (d) statistical modeling offered by region-growing methods into a fast and accurate segmentation tool. The framework moves from the idea of the “contour” to that of “inside and outside”, or, masks, allowing for easy mul...

  19. Primary Segmental Volvulus Mimicking Ileal Atresia

    Science.gov (United States)

    Rao, Sadashiva; B Shetty, Kishan

    2013-01-01

    Neonatal intestinal volvulus in the absence of malrotation is a rare occurrence and rarer still is the intestinal volvulus in absence of any other predisposing factors. Primary segmental volvulus in neonates is very rare entity, which can have catastrophic outcome if not intervened at appropriate time. We report two such cases, which were preoperatively diagnosed as ileal atresia and intraoperatively revealed to be primary segmental volvulus of the ileum. PMID:26023426

  20. Genome packaging in viruses

    OpenAIRE

    Sun, Siyang; Rao, Venigalla B.; Rossmann, Michael G.

    2010-01-01

    Genome packaging is a fundamental process in a viral life cycle. Many viruses assemble preformed capsids into which the genomic material is subsequently packaged. These viruses use a packaging motor protein that is driven by the hydrolysis of ATP to condense the nucleic acids into a confined space. How these motor proteins package viral genomes had been poorly understood until recently, when a few X-ray crystal structures and cryo-electron microscopy structures became available. Here we discu...

  1. Osmotic and Heat Stress Effects on Segmentation.

    Directory of Open Access Journals (Sweden)

    Julian Weiss

    Full Text Available During vertebrate embryonic development, early skin, muscle, and bone progenitor populations organize into segments known as somites. Defects in this conserved process of segmentation lead to skeletal and muscular deformities, such as congenital scoliosis, a curvature of the spine caused by vertebral defects. Environmental stresses such as hypoxia or heat shock produce segmentation defects, and significantly increase the penetrance and severity of vertebral defects in genetically susceptible individuals. Here we show that a brief exposure to a high osmolarity solution causes reproducible segmentation defects in developing zebrafish (Danio rerio embryos. Both osmotic shock and heat shock produce border defects in a dose-dependent manner, with an increase in both frequency and severity of defects. We also show that osmotic treatment has a delayed effect on somite development, similar to that observed in heat shocked embryos. Our results establish osmotic shock as an alternate experimental model for stress, affecting segmentation in a manner comparable to other known environmental stressors. The similar effects of these two distinct environmental stressors support a model in which a variety of cellular stresses act through a related response pathway that leads to disturbances in the segmentation process.

  2. SVM Pixel Classification on Colour Image Segmentation

    Science.gov (United States)

    Barui, Subhrajit; Latha, S.; Samiappan, Dhanalakshmi; Muthu, P.

    2018-04-01

    The aim of image segmentation is to simplify the representation of an image with the help of cluster pixels into something meaningful to analyze. Segmentation is typically used to locate boundaries and curves in an image, precisely to label every pixel in an image to give each pixel an independent identity. SVM pixel classification on colour image segmentation is the topic highlighted in this paper. It holds useful application in the field of concept based image retrieval, machine vision, medical imaging and object detection. The process is accomplished step by step. At first we need to recognize the type of colour and the texture used as an input to the SVM classifier. These inputs are extracted via local spatial similarity measure model and Steerable filter also known as Gabon Filter. It is then trained by using FCM (Fuzzy C-Means). Both the pixel level information of the image and the ability of the SVM Classifier undergoes some sophisticated algorithm to form the final image. The method has a well developed segmented image and efficiency with respect to increased quality and faster processing of the segmented image compared with the other segmentation methods proposed earlier. One of the latest application result is the Light L16 camera.

  3. Event segmentation ability uniquely predicts event memory.

    Science.gov (United States)

    Sargent, Jesse Q; Zacks, Jeffrey M; Hambrick, David Z; Zacks, Rose T; Kurby, Christopher A; Bailey, Heather R; Eisenberg, Michelle L; Beck, Taylor M

    2013-11-01

    Memory for everyday events plays a central role in tasks of daily living, autobiographical memory, and planning. Event memory depends in part on segmenting ongoing activity into meaningful units. This study examined the relationship between event segmentation and memory in a lifespan sample to answer the following question: Is the ability to segment activity into meaningful events a unique predictor of subsequent memory, or is the relationship between event perception and memory accounted for by general cognitive abilities? Two hundred and eight adults ranging from 20 to 79years old segmented movies of everyday events and attempted to remember the events afterwards. They also completed psychometric ability tests and tests measuring script knowledge for everyday events. Event segmentation and script knowledge both explained unique variance in event memory above and beyond the psychometric measures, and did so as strongly in older as in younger adults. These results suggest that event segmentation is a basic cognitive mechanism, important for memory across the lifespan. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Process Segmentation Typology in Czech Companies

    Directory of Open Access Journals (Sweden)

    Tucek David

    2016-03-01

    Full Text Available This article describes process segmentation typology during business process management implementation in Czech companies. Process typology is important for a manager’s overview of process orientation as well as for a manager’s general understanding of business process management. This article provides insight into a process-oriented organizational structure. The first part analyzes process segmentation typology itself as well as some original results of quantitative research evaluating process segmentation typology in the specific context of Czech company strategies. Widespread data collection was carried out in 2006 and 2013. The analysis of this data showed that managers have more options regarding process segmentation and its selection. In terms of practicality and ease of use, the most frequently used method of process segmentation (managerial, main, and supportive stems directly from the requirements of ISO 9001. Because of ISO 9001:2015, managers must now apply risk planning in relation to the selection of processes that are subjected to process management activities. It is for this fundamental reason that this article focuses on process segmentation typology.

  5. Between Two Fern Genomes

    Science.gov (United States)

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

  6. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

    2015-01-01

    function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  7. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  8. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  9. Fold distributions at clover, crystal and segment levels for segmented clover detectors

    International Nuclear Information System (INIS)

    Kshetri, R; Bhattacharya, P

    2014-01-01

    Fold distributions at clover, crystal and segment levels have been extracted for an array of segmented clover detectors for various gamma energies. A simple analysis of the results based on a model independant approach has been presented. For the first time, the clover fold distribution of an array and associated array addback factor have been extracted. We have calculated the percentages of the number of crystals and segments that fire for a full energy peak event

  10. Genome mapping and characterization of the Anopheles gambiae heterochromatin

    Directory of Open Access Journals (Sweden)

    Sharakhova Maria V

    2010-08-01

    Full Text Available Abstract Background Heterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles gambiae has not been mapped and characterized. Results To determine the extent of heterochromatin within the An. gambiae genome, genes were physically mapped to the euchromatin-heterochromatin transition zone of polytene chromosomes. The study found that a minimum of 232 genes reside in 16.6 Mb of mapped heterochromatin. Gene ontology analysis revealed that heterochromatin is enriched in genes with DNA-binding and regulatory activities. Immunostaining of the An. gambiae chromosomes with antibodies against Drosophila melanogaster heterochromatin protein 1 (HP1 and the nuclear envelope protein lamin Dm0 identified the major invariable sites of the proteins' localization in all regions of pericentric heterochromatin, diffuse intercalary heterochromatin, and euchromatic region 9C of the 2R arm, but not in the compact intercalary heterochromatin. To better understand the molecular differences among chromatin types, novel Bayesian statistical models were developed to analyze genome features. The study found that heterochromatin and euchromatin differ in gene density and the coverage of retroelements and segmental duplications. The pericentric heterochromatin had the highest coverage of retroelements and tandem repeats, while intercalary heterochromatin was enriched with segmental duplications. We also provide evidence that the diffuse intercalary heterochromatin has a higher coverage of DNA transposable elements, minisatellites, and satellites than does the compact intercalary heterochromatin. The investigation of 42-Mb assembly of unmapped genomic scaffolds showed that it has molecular characteristics similar to cytologically mapped heterochromatin. Conclusions Our results demonstrate that Anopheles polytene chromosomes

  11. Deformable meshes for medical image segmentation accurate automatic segmentation of anatomical structures

    CERN Document Server

    Kainmueller, Dagmar

    2014-01-01

    ? Segmentation of anatomical structures in medical image data is an essential task in clinical practice. Dagmar Kainmueller introduces methods for accurate fully automatic segmentation of anatomical structures in 3D medical image data. The author's core methodological contribution is a novel deformation model that overcomes limitations of state-of-the-art Deformable Surface approaches, hence allowing for accurate segmentation of tip- and ridge-shaped features of anatomical structures. As for practical contributions, she proposes application-specific segmentation pipelines for a range of anatom

  12. CoCoNUT: an efficient system for the comparison and analysis of genomes

    Directory of Open Access Journals (Sweden)

    Kurtz Stefan

    2008-11-01

    Full Text Available Abstract Background Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons. Results Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit that allows solving several different tasks in a unified framework: (1 finding regions of high similarity among multiple genomic sequences and aligning them, (2 comparing two draft or multi-chromosomal genomes, (3 locating large segmental duplications in large genomic sequences, and (4 mapping cDNA/EST to genomic sequences. Conclusion CoCoNUT is competitive with other software tools w.r.t. the quality of the results. The use of state of the art algorithms and data structures allows CoCoNUT to solve comparative genomics tasks more efficiently than previous tools. With the improved user interface (including an interactive visualization component, CoCoNUT provides a unified, versatile, and easy-to-use software tool for large scale studies in comparative genomics.

  13. Universal global imprints of genome growth and evolution--equivalent length and cumulative mutation density.

    Directory of Open Access Journals (Sweden)

    Hong-Da Chen

    Full Text Available BACKGROUND: Segmental duplication is widely held to be an important mode of genome growth and evolution. Yet how this would affect the global structure of genomes has been little discussed. METHODS/PRINCIPAL FINDINGS: Here, we show that equivalent length, or L(e, a quantity determined by the variance of fluctuating part of the distribution of the k-mer frequencies in a genome, characterizes the latter's global structure. We computed the L(es of 865 complete chromosomes and found that they have nearly universal but (k-dependent values. The differences among the L(e of a chromosome and those of its coding and non-coding parts were found to be slight. CONCLUSIONS: We verified that these non-trivial results are natural consequences of a genome growth model characterized by random segmental duplication and random point mutation, but not of any model whose dominant growth mechanism is not segmental duplication. Our study also indicates that genomes have a nearly universal cumulative "point" mutation density of about 0.73 mutations per site that is compatible with the relatively low mutation rates of (1-5 x 10(-3/site/Mya previously determined by sequence comparison for the human and E. coli genomes.

  14. Computational genomics of hyperthermophiles

    NARCIS (Netherlands)

    Werken, van de H.J.G.

    2008-01-01

    With the ever increasing number of completely sequenced prokaryotic genomes and the subsequent use of functional genomics tools, e.g. DNA microarray and proteomics, computational data analysis and the integration of microbial and molecular data is inevitable. This thesis describes the computational

  15. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with D...

  16. Human genome I

    International Nuclear Information System (INIS)

    Anon.

    1989-01-01

    An international conference, Human Genome I, was held Oct. 2-4, 1989 in San Diego, Calif. Selected speakers discussed: Current Status of the Genome Project; Technique Innovations; Interesting regions; Applications; and Organization - Different Views of Current and Future Science and Procedures. Posters, consisting of 119 presentations, were displayed during the sessions. 119 were indexed for inclusion to the Energy Data Base

  17. Single-segment and double-segment INTACS for post-LASIK ectasia.

    Directory of Open Access Journals (Sweden)

    Hassan Hashemi

    2014-09-01

    Full Text Available The objective of the present study was to compare single segment and double segment INTACS rings in the treatment of post-LASIK ectasia. In this interventional study, 26 eyes with post-LASIK ectasia were assessed. Ectasia was defined as progressive myopia regardless of astigmatism, along with topographic evidence of inferior steepening of the cornea after LASIK. We excluded those with a history of intraocular surgery, certain eye conditions, and immune disorders, as well as monocular, pregnant and lactating patients. A total of 11 eyes had double ring and 15 eyes had single ring implantation. Visual and refractive outcomes were compared with preoperative values based on the number of implanted INTACS rings. Pre and postoperative spherical equivalent were -3.92 and -2.29 diopter (P=0.007. The spherical equivalent decreased by 1 ± 3.2 diopter in the single-segment group and 2.56 ± 1.58 diopter in the double-segment group (P=0.165. Mean preoperative astigmatism was 2.38 ± 1.93 diopter which decreased to 2.14 ± 1.1 diopter after surgery (P=0.508; 0.87 ± 1.98 diopter decrease in the single-segment group and 0.67 ± 1.2 diopter increase in the double-segment group (P=0.025. Nineteen patients (75% gained one or two lines, and only three, who were all in the double-segment group, lost one or two lines of best corrected visual acuity. The spherical equivalent and vision significantly decreased in all patients. In these post-LASIK ectasia patients, the spherical equivalent was corrected better with two segments compared to single segment implantation; nonetheless, the level of astigmatism in the single-segment group was significantly better than that in the double-segment group.

  18. Rumen microbial genomics

    International Nuclear Information System (INIS)

    Morrison, M.; Nelson, K.E.

    2005-01-01

    Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

  19. Microbial Genomes Multiply

    Science.gov (United States)

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  20. Musa sebagai Model Genom

    Directory of Open Access Journals (Sweden)

    RITA MEGIA

    2005-12-01

    Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

  1. The genome editing revolution

    DEFF Research Database (Denmark)

    Stella, Stefano; Montoya, Guillermo

    2016-01-01

    -Cas system has become the main tool for genome editing in many laboratories. Currently the targeted genome editing technology has been used in many fields and may be a possible approach for human gene therapy. Furthermore, it can also be used to modifying the genomes of model organisms for studying human......In the last 10 years, we have witnessed a blooming of targeted genome editing systems and applications. The area was revolutionized by the discovery and characterization of the transcription activator-like effector proteins, which are easier to engineer to target new DNA sequences than...... sequence). This ribonucleoprotein complex protects bacteria from invading DNAs, and it was adapted to be used in genome editing. The CRISPR ribonucleic acid (RNA) molecule guides to the specific DNA site the Cas9 nuclease to cleave the DNA target. Two years and more than 1000 publications later, the CRISPR...

  2. SALIENCY BASED SEGMENTATION OF SATELLITE IMAGES

    Directory of Open Access Journals (Sweden)

    A. Sharma

    2015-03-01

    Full Text Available Saliency gives the way as humans see any image and saliency based segmentation can be eventually helpful in Psychovisual image interpretation. Keeping this in view few saliency models are used along with segmentation algorithm and only the salient segments from image have been extracted. The work is carried out for terrestrial images as well as for satellite images. The methodology used in this work extracts those segments from segmented image which are having higher or equal saliency value than a threshold value. Salient and non salient regions of image become foreground and background respectively and thus image gets separated. For carrying out this work a dataset of terrestrial images and Worldview 2 satellite images (sample data are used. Results show that those saliency models which works better for terrestrial images are not good enough for satellite image in terms of foreground and background separation. Foreground and background separation in terrestrial images is based on salient objects visible on the images whereas in satellite images this separation is based on salient area rather than salient objects.

  3. Segmentation in reading and film comprehension.

    Science.gov (United States)

    Zacks, Jeffrey M; Speer, Nicole K; Reynolds, Jeremy R

    2009-05-01

    When reading a story or watching a film, comprehenders construct a series of representations in order to understand the events depicted. Discourse comprehension theories and a recent theory of perceptual event segmentation both suggest that comprehenders monitor situational features such as characters' goals, to update these representations at natural boundaries in activity. However, the converging predictions of these theories had previously not been tested directly. Two studies provided evidence that changes in situational features such as characters, their locations, their interactions with objects, and their goals are related to the segmentation of events in both narrative texts and films. A 3rd study indicated that clauses with event boundaries are read more slowly than are other clauses and that changes in situational features partially mediate this relation. A final study suggested that the predictability of incoming information influences reading rate and possibly event segmentation. Taken together, these results suggest that processing situational changes during comprehension is an important determinant of how one segments ongoing activity into events and that this segmentation is related to the control of processing during reading. (c) 2009 APA, all rights reserved.

  4. Multidimensional Brain MRI segmentation using graph cuts

    International Nuclear Information System (INIS)

    Lecoeur, Jeremy

    2010-01-01

    This thesis deals with the segmentation of multimodal brain MRIs by graph cuts method. First, we propose a method that utilizes three MRI modalities by merging them. The border information given by the spectral gradient is then challenged by a region information, given by the seeds selected by the user, using a graph cut algorithm. Then, we propose three enhancements of this method. The first consists in finding an optimal spectral space because the spectral gradient is based on natural images and then inadequate for multimodal medical images. This results in a learning based segmentation method. We then explore the automation of the graph cut method. Here, the various pieces of information usually given by the user are inferred from a robust expectation-maximization algorithm. We show the performance of these two enhanced versions on multiple sclerosis lesions. Finally, we integrate atlases for the automatic segmentation of deep brain structures. These three new techniques show the adaptability of our method to various problems. Our different segmentation methods are better than most of nowadays techniques, speaking of computation time or segmentation accuracy. (authors)

  5. Experience with mechanical segmentation of reactor internals

    International Nuclear Information System (INIS)

    Carlson, R.; Hedin, G.

    2003-01-01

    Operating experience from BWE:s world-wide has shown that many plants experience initial cracking of the reactor internals after approximately 20 to 25 years of service life. This ''mid-life crisis'', considering a plant design life of 40 years, is now being addressed by many utilities. Successful resolution of these issues should give many more years of trouble-free operation. Replacement of reactor internals could be, in many cases, the most favourable option to achieve this. The proactive strategy of many utilities to replace internals in a planned way is a market-driven effort to minimize the overall costs for power generation, including time spent for handling contingencies and unplanned outages. Based on technical analyses, knowledge about component market prices and in-house costs, a cost-effective, optimized strategy for inspection, mitigation and replacements can be implemented. Also decommissioning of nuclear plants has become a reality for many utilities as numerous plants worldwide are closed due to age and/or other reasons. These facts address a need for safe, fast and cost-effective methods for segmentation of internals. Westinghouse has over the last years developed methods for segmentation of internals and has also carried out successful segmentation projects. Our experience from the segmentation business for Nordic BWR:s is that the most important parameters to consider when choosing a method and equipment for a segmentation project are: - Safety, - Cost-effectiveness, - Cleanliness, - Reliability. (orig.)

  6. Segmentation and Visualisation of Human Brain Structures

    Energy Technology Data Exchange (ETDEWEB)

    Hult, Roger

    2003-10-01

    In this thesis the focus is mainly on the development of segmentation techniques for human brain structures and of the visualisation of such structures. The images of the brain are both anatomical images (magnet resonance imaging (MRI) and autoradiography) and functional images that show blood flow (functional magnetic imaging (fMRI), positron emission tomography (PET), and single photon emission tomography (SPECT)). When working with anatomical images, the structures segmented are visible as different parts of the brain, e.g. the brain cortex, the hippocampus, or the amygdala. In functional images, the activity or the blood flow that be seen. Grey-level morphology methods are used in the segmentations to make tissue types in the images more homogenous and minimise difficulties with connections to outside tissue. A method for automatic histogram thresholding is also used. Furthermore, there are binary operations such as logic operation between masks and binary morphology operations. The visualisation of the segmented structures uses either surface rendering or volume rendering. For the visualisation of thin structures, surface rendering is the better choice since otherwise some voxels might be missed. It is possible to display activation from a functional image on the surface of a segmented cortex. A new method for autoradiographic images has been developed, which integrates registration, background compensation, and automatic thresholding to get faster and more reliable results than the standard techniques give.

  7. Segmentation and Visualisation of Human Brain Structures

    International Nuclear Information System (INIS)

    Hult, Roger

    2003-01-01

    In this thesis the focus is mainly on the development of segmentation techniques for human brain structures and of the visualisation of such structures. The images of the brain are both anatomical images (magnet resonance imaging (MRI) and autoradiography) and functional images that show blood flow (functional magnetic imaging (fMRI), positron emission tomography (PET), and single photon emission tomography (SPECT)). When working with anatomical images, the structures segmented are visible as different parts of the brain, e.g. the brain cortex, the hippocampus, or the amygdala. In functional images, the activity or the blood flow that be seen. Grey-level morphology methods are used in the segmentations to make tissue types in the images more homogenous and minimise difficulties with connections to outside tissue. A method for automatic histogram thresholding is also used. Furthermore, there are binary operations such as logic operation between masks and binary morphology operations. The visualisation of the segmented structures uses either surface rendering or volume rendering. For the visualisation of thin structures, surface rendering is the better choice since otherwise some voxels might be missed. It is possible to display activation from a functional image on the surface of a segmented cortex. A new method for autoradiographic images has been developed, which integrates registration, background compensation, and automatic thresholding to get faster and more reliable results than the standard techniques give

  8. Compound image segmentation of published biomedical figures.

    Science.gov (United States)

    Li, Pengyuan; Jiang, Xiangying; Kambhamettu, Chandra; Shatkay, Hagit

    2018-04-01

    Images convey essential information in biomedical publications. As such, there is a growing interest within the bio-curation and the bio-databases communities, to store images within publications as evidence for biomedical processes and for experimental results. However, many of the images in biomedical publications are compound images consisting of multiple panels, where each individual panel potentially conveys a different type of information. Segmenting such images into constituent panels is an essential first step toward utilizing images. In this article, we develop a new compound image segmentation system, FigSplit, which is based on Connected Component Analysis. To overcome shortcomings typically manifested by existing methods, we develop a quality assessment step for evaluating and modifying segmentations. Two methods are proposed to re-segment the images if the initial segmentation is inaccurate. Experimental results show the effectiveness of our method compared with other methods. The system is publicly available for use at: https://www.eecis.udel.edu/~compbio/FigSplit. The code is available upon request. shatkay@udel.edu. Supplementary data are available online at Bioinformatics.

  9. Infants generalize representations of statistically segmented words

    Directory of Open Access Journals (Sweden)

    Katharine eGraf Estes

    2012-10-01

    Full Text Available The acoustic variation in language presents learners with a substantial challenge. To learn by tracking statistical regularities in speech, infants must recognize words across tokens that differ based on characteristics such as the speaker’s voice, affect, or the sentence context. Previous statistical learning studies have not investigated how these types of surface form variation affect learning. The present experiments used tasks tailored to two distinct developmental levels to investigate the robustness of statistical learning to variation. Experiment 1 examined statistical word segmentation in 11-month-olds and found that infants can recognize statistically segmented words across a change in the speaker’s voice from segmentation to testing. The direction of infants’ preferences suggests that recognizing words across a voice change is more difficult than recognizing them in a consistent voice. Experiment 2 tested whether 17-month-olds can generalize the output of statistical learning across variation to support word learning. The infants were successful in their generalization; they associated referents with statistically defined words despite a change in voice from segmentation to label learning. Infants’ learning patterns also indicate that they formed representations of across-word syllable sequences during segmentation. Thus, low probability sequences can act as object labels in some conditions. The findings of these experiments suggest that the units that emerge during statistical learning are not perceptually constrained, but rather are robust to naturalistic acoustic variation.

  10. Contour tracing for segmentation of mammographic masses

    International Nuclear Information System (INIS)

    Elter, Matthias; Held, Christian; Wittenberg, Thomas

    2010-01-01

    CADx systems have the potential to support radiologists in the difficult task of discriminating benign and malignant mammographic lesions. The segmentation of mammographic masses from the background tissue is an important module of CADx systems designed for the characterization of mass lesions. In this work, a novel approach to this task is presented. The segmentation is performed by automatically tracing the mass' contour in-between manually provided landmark points defined on the mass' margin. The performance of the proposed approach is compared to the performance of implementations of three state-of-the-art approaches based on region growing and dynamic programming. For an unbiased comparison of the different segmentation approaches, optimal parameters are selected for each approach by means of tenfold cross-validation and a genetic algorithm. Furthermore, segmentation performance is evaluated on a dataset of ROI and ground-truth pairs. The proposed method outperforms the three state-of-the-art methods. The benchmark dataset will be made available with publication of this paper and will be the first publicly available benchmark dataset for mass segmentation.

  11. Evolutionary force of AT-rich repeats to trap genomic and episomal DNAs into the rice genome: lessons from endogenous pararetrovirus.

    Science.gov (United States)

    Liu, Ruifang; Koyanagi, Kanako O; Chen, Sunlu; Kishima, Yuji

    2012-12-01

    In plant genomes, the incorporation of DNA segments is not a common method of artificial gene transfer. Nevertheless, various segments of pararetroviruses have been found in plant genomes in recent decades. The rice genome contains a number of segments of endogenous rice tungro bacilliform virus-like sequences (ERTBVs), many of which are present between AT dinucleotide repeats (ATrs). Comparison of genomic sequences between two closely related rice subspecies, japonica and indica, allowed us to verify the preferential insertion of ERTBVs into ATrs. In addition to ERTBVs, the comparative analyses showed that ATrs occasionally incorporate repeat sequences including transposable elements, and a wide range of other sequences. Besides the known genomic sequences, the insertion sequences also represented DNAs of unclear origins together with ERTBVs, suggesting that ATrs have integrated episomal DNAs that would have been suspended in the nucleus. Such insertion DNAs might be trapped by ATrs in the genome in a host-dependent manner. Conversely, other simple mono- and dinucleotide sequence repeats (SSR) were less frequently involved in insertion events relative to ATrs. Therefore, ATrs could be regarded as hot spots of double-strand breaks that induce non-homologous end joining. The insertions within ATrs occasionally generated new gene-related sequences or involved structural modifications of existing genes. Likewise, in a comparison between Arabidopsis thaliana and Arabidopsis lyrata, the insertions preferred ATrs to other SSRs. Therefore ATrs in plant genomes could be considered as genomic dumping sites that have trapped various DNA molecules and may have exerted a powerful evolutionary force. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  12. Poly(ether amide) segmented block copolymers with adipicacid based tetra amide segments

    NARCIS (Netherlands)

    Biemond, G.J.E.; Feijen, Jan; Gaymans, R.J.

    2007-01-01

    Poly(tetramethylene oxide)-based poly(ether ester amide)s with monodisperse tetraamide segments were synthesized. The tetraamide segment was based on adipic acid, terephthalic acid, and hexamethylenediamine. The synthesis method of the copolymers and the influence of the tetraamide concentration,

  13. Market Segmentation in Business Technology Base: The Case of Segmentation of Sparkling

    Directory of Open Access Journals (Sweden)

    Valéria Riscarolli

    2014-08-01

    Full Text Available A common market segmentation premise for products and services rules consumer behavior as the segmentation center piece. Would this be the logic for segmentation used by small technology based companies? In this article we target at determining the principles of market segmentation used by a vitiwinery company, as research object. This company is recognized by its products excellence, either in domestic as well as in the foreign market, among 13 distinct countries. The research method used is a case study, through information from the company’s CEOs and crossed by primary information from observation and formal registries and documents of the company. In this research we look at sparkling wines market segmentation. Main results indicate that the winery studied considers only technological elements as the basis to build a market segment. One may conclude that a market segmentation for this company is based upon technological dominion of sparkling wines production, aligned with a premium-price policy. In the company, directorship believes that as sparkling wines market is still incipient in the country, sparkling wine market segments will form and consolidate after the evolution of consumers tasting preferences, depending on technologies that boost sparkling wines quality. 

  14. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  15. Dynamics in international market segmentation of new product growth

    NARCIS (Netherlands)

    Lemmens, A.; Croux, C.; Stremersch, S.

    2012-01-01

    Prior international segmentation studies have been static in that they have identified segments that remain stable over time. This paper shows that country segments in new product growth are intrinsically dynamic. We propose a semiparametric hidden Markov model to dynamically segment countries based

  16. Analysis tools for the interplay between genome layout and regulation.

    Science.gov (United States)

    Bouyioukos, Costas; Elati, Mohamed; Képès, François

    2016-06-06

    Genome layout and gene regulation appear to be interdependent. Understanding this interdependence is key to exploring the dynamic nature of chromosome conformation and to engineering functional genomes. Evidence for non-random genome layout, defined as the relative positioning of either co-functional or co-regulated genes, stems from two main approaches. Firstly, the analysis of contiguous genome segments across species, has highlighted the conservation of gene arrangement (synteny) along chromosomal regions. Secondly, the study of long-range interactions along a chromosome has emphasised regularities in the positioning of microbial genes that are co-regulated, co-expressed or evolutionarily correlated. While one-dimensional pattern analysis is a mature field, it is often powerless on biological datasets which tend to be incomplete, and partly incorrect. Moreover, there is a lack of comprehensive, user-friendly tools to systematically analyse, visualise, integrate and exploit regularities along genomes. Here we present the Genome REgulatory and Architecture Tools SCAN (GREAT:SCAN) software for the systematic study of the interplay between genome layout and gene expression regulation. SCAN is a collection of related and interconnected applications currently able to perform systematic analyses of genome regularities as well as to improve transcription factor binding sites (TFBS) and gene regulatory network predictions based on gene positional information. We demonstrate the capabilities of these tools by studying on one hand the regular patterns of genome layout in the major regulons of the bacterium Escherichia coli. On the other hand, we demonstrate the capabilities to improve TFBS prediction in microbes. Finally, we highlight, by visualisation of multivariate techniques, the interplay between position and sequence information for effective transcription regulation.

  17. CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species[OPEN

    Science.gov (United States)

    Chen, Hao; Wang, Xiangfeng

    2013-01-01

    In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at http://www.cmbb.arizona.edu/CrusView/. PMID:23898041

  18. Why segmentation matters: experience-driven segmentation errors impair “morpheme” learning

    Science.gov (United States)

    Finn, Amy S.; Hudson Kam, Carla L.

    2015-01-01

    We ask whether an adult learner’s knowledge of their native language impedes statistical learning in a new language beyond just word segmentation (as previously shown). In particular, we examine the impact of native-language word-form phonotactics on learners’ ability to segment words into their component morphemes and learn phonologically triggered variation of morphemes. We find that learning is impaired when words and component morphemes are structured to conflict with a learner’s native-language phonotactic system, but not when native-language phonotactics do not conflict with morpheme boundaries in the artificial language. A learner’s native-language knowledge can therefore have a cascading impact affecting word segmentation and the morphological variation that relies upon proper segmentation. These results show that getting word segmentation right early in learning is deeply important for learning other aspects of language, even those (morphology) that are known to pose a great difficulty for adult language learners. PMID:25730305

  19. Why segmentation matters: Experience-driven segmentation errors impair "morpheme" learning.

    Science.gov (United States)

    Finn, Amy S; Hudson Kam, Carla L

    2015-09-01

    We ask whether an adult learner's knowledge of their native language impedes statistical learning in a new language beyond just word segmentation (as previously shown). In particular, we examine the impact of native-language word-form phonotactics on learners' ability to segment words into their component morphemes and learn phonologically triggered variation of morphemes. We find that learning is impaired when words and component morphemes are structured to conflict with a learner's native-language phonotactic system, but not when native-language phonotactics do not conflict with morpheme boundaries in the artificial language. A learner's native-language knowledge can therefore have a cascading impact affecting word segmentation and the morphological variation that relies upon proper segmentation. These results show that getting word segmentation right early in learning is deeply important for learning other aspects of language, even those (morphology) that are known to pose a great difficulty for adult language learners. (c) 2015 APA, all rights reserved).

  20. Rhythm-based segmentation of Popular Chinese Music

    DEFF Research Database (Denmark)

    Jensen, Karl Kristoffer

    2005-01-01

    We present a new method to segment popular music based on rhythm. By computing a shortest path based on the self-similarity matrix calculated from a model of rhythm, segmenting boundaries are found along the di- agonal of the matrix. The cost of a new segment is opti- mized by matching manual...... and automatic segment boundaries. We compile a small song database of 21 randomly selected popular Chinese songs which come from Chinese Mainland, Taiwan and Hong Kong. The segmenting results on the small corpus show that 78% manual segmentation points are detected and 74% auto- matic segmentation points...

  1. Underwater Object Segmentation Based on Optical Features

    Directory of Open Access Journals (Sweden)

    Zhe Chen

    2018-01-01

    Full Text Available Underwater optical environments are seriously affected by various optical inputs, such as artificial light, sky light, and ambient scattered light. The latter two can block underwater object segmentation tasks, since they inhibit the emergence of objects of interest and distort image information, while artificial light can contribute to segmentation. Artificial light often focuses on the object of interest, and, therefore, we can initially identify the region of target objects if the collimation of artificial light is recognized. Based on this concept, we propose an optical feature extraction, calculation, and decision method to identify the collimated region of artificial light as a candidate object region. Then, the second phase employs a level set method to segment the objects of interest within the candidate region. This two-phase structure largely removes background noise and highlights the outline of underwater objects. We test the performance of the method with diverse underwater datasets, demonstrating that it outperforms previous methods.

  2. Nuclear propulsion apparatus with alternate reactor segments

    International Nuclear Information System (INIS)

    Szekely, T.

    1979-01-01

    Nuclear propulsion apparatus comprising: (a) means for compressing incoming air; (b) nuclear fission reactor means for heating said air; (c) means for expanding a portion of the heated air to drive said compressing means; (d) said nuclear fission reactor means being divided into a plurality of radially extending segments; (e) means for directing a portion of the compressed air for heating through alternate segments of said reactor means and another portion of the compressed air for heating through the remaining segments of said reactor means; and (f) means for further expanding the heated air from said drive means and the remaining heated air from said reactor means through nozzle means to effect reactive thrust on said apparatus. 12 claims

  3. Segmental blood pressure after total hip replacement

    DEFF Research Database (Denmark)

    Gebuhr, Peter Henrik; Soelberg, M; Henriksen, Jens Henrik Sahl

    1992-01-01

    Twenty-nine patients due to have a total hip replacement had their systemic systolic and segmental blood pressures measured prior to operation and 1 and 6 weeks postoperatively. No patients had signs of ischemia. The segmental blood pressure was measured at the ankle and at the toes. A significant...... drop was found in all pressures 1 week postoperatively. The decrease followed the systemic pressure and was restored to normal after 6 weeks. In a group of six patients with preoperatively decreased ankle pressure, a significant transient further decrease in the ankle-toe gradient pressure was found...... on the operated side. None of the patients had symptoms from the lowered pressure. We conclude that in patients without signs of ischemia, the postoperative segmental pressure decrease is reversible and therefore not dangerous....

  4. Active mask segmentation of fluorescence microscope images.

    Science.gov (United States)

    Srinivasa, Gowri; Fickus, Matthew C; Guo, Yusong; Linstedt, Adam D; Kovacević, Jelena

    2009-08-01

    We propose a new active mask algorithm for the segmentation of fluorescence microscope images of punctate patterns. It combines the (a) flexibility offered by active-contour methods, (b) speed offered by multiresolution methods, (c) smoothing offered by multiscale methods, and (d) statistical modeling offered by region-growing methods into a fast and accurate segmentation tool. The framework moves from the idea of the "contour" to that of "inside and outside," or masks, allowing for easy multidimensional segmentation. It adapts to the topology of the image through the use of multiple masks. The algorithm is almost invariant under initialization, allowing for random initialization, and uses a few easily tunable parameters. Experiments show that the active mask algorithm matches the ground truth well and outperforms the algorithm widely used in fluorescence microscopy, seeded watershed, both qualitatively, as well as quantitatively.

  5. Natural color image segmentation using integrated mechanism

    Institute of Scientific and Technical Information of China (English)

    Jie Xu (徐杰); Pengfei Shi (施鹏飞)

    2003-01-01

    A new method for natural color image segmentation using integrated mechanism is proposed in this paper.Edges are first detected in term of the high phase congruency in the gray-level image. K-mean cluster is used to label long edge lines based on the global color information to estimate roughly the distribution of objects in the image, while short ones are merged based on their positions and local color differences to eliminate the negative affection caused by texture or other trivial features in image. Region growing technique is employed to achieve final segmentation results. The proposed method unifies edges, whole and local color distributions, as well as spatial information to solve the natural image segmentation problem.The feasibility and effectiveness of this method have been demonstrated by various experiments.

  6. Continuation of Sets of Constrained Orbit Segments

    DEFF Research Database (Denmark)

    Schilder, Frank; Brøns, Morten; Chamoun, George Chaouki

    Sets of constrained orbit segments of time continuous flows are collections of trajectories that represent a whole or parts of an invariant set. A non-trivial but simple example is a homoclinic orbit. A typical representation of this set consists of an equilibrium point of the flow and a trajectory...... that starts close and returns close to this fixed point within finite time. More complicated examples are hybrid periodic orbits of piecewise smooth systems or quasi-periodic invariant tori. Even though it is possible to define generalised two-point boundary value problems for computing sets of constrained...... orbit segments, this is very disadvantageous in practice. In this talk we will present an algorithm that allows the efficient continuation of sets of constrained orbit segments together with the solution of the full variational problem....

  7. CERES: A new cerebellum lobule segmentation method.

    Science.gov (United States)

    Romero, Jose E; Coupé, Pierrick; Giraud, Rémi; Ta, Vinh-Thong; Fonov, Vladimir; Park, Min Tae M; Chakravarty, M Mallar; Voineskos, Aristotle N; Manjón, Jose V

    2017-02-15

    The human cerebellum is involved in language, motor tasks and cognitive processes such as attention or emotional processing. Therefore, an automatic and accurate segmentation method is highly desirable to measure and understand the cerebellum role in normal and pathological brain development. In this work, we propose a patch-based multi-atlas segmentation tool called CERES (CEREbellum Segmentation) that is able to automatically parcellate the cerebellum lobules. The proposed method works with standard resolution magnetic resonance T1-weighted images and uses the Optimized PatchMatch algorithm to speed up the patch matching process. The proposed method was compared with related recent state-of-the-art methods showing competitive results in both accuracy (average DICE of 0.7729) and execution time (around 5 minutes). Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Video-based noncooperative iris image segmentation.

    Science.gov (United States)

    Du, Yingzi; Arslanturk, Emrah; Zhou, Zhi; Belcher, Craig

    2011-02-01

    In this paper, we propose a video-based noncooperative iris image segmentation scheme that incorporates a quality filter to quickly eliminate images without an eye, employs a coarse-to-fine segmentation scheme to improve the overall efficiency, uses a direct least squares fitting of ellipses method to model the deformed pupil and limbic boundaries, and develops a window gradient-based method to remove noise in the iris region. A remote iris acquisition system is set up to collect noncooperative iris video images. An objective method is used to quantitatively evaluate the accuracy of the segmentation results. The experimental results demonstrate the effectiveness of this method. The proposed method would make noncooperative iris recognition or iris surveillance possible.

  9. Interaction features for prediction of perceptual segmentation

    DEFF Research Database (Denmark)

    Hartmann, Martin; Lartillot, Olivier; Toiviainen, Petri

    2017-01-01

    As music unfolds in time, structure is recognised and understood by listeners, regardless of their level of musical expertise. A number of studies have found spectral and tonal changes to quite successfully model boundaries between structural sections. However, the effects of musical expertise...... and experimental task on computational modelling of structure are not yet well understood. These issues need to be addressed to better understand how listeners perceive the structure of music and to improve automatic segmentation algorithms. In this study, computational prediction of segmentation by listeners...... was investigated for six musical stimuli via a real-time task and an annotation (non real-time) task. The proposed approach involved computation of novelty curve interaction features and a prediction model of perceptual segmentation boundary density. We found that, compared to non-musicians’, musicians...

  10. SIDES - Segment Interconnect Diagnostic Expert System

    International Nuclear Information System (INIS)

    Booth, A.W.; Forster, R.; Gustafsson, L.; Ho, N.

    1989-01-01

    It is well known that the FASTBUS Segment Interconnect (SI) provides a communication path between two otherwise independent, asynchronous bus segments. The SI is probably the most important module in any FASTBUS data acquisition network since it's failure to function can cause whole segments of the network to be inaccessible and sometimes inoperable. This paper describes SIDES, an intelligent program designed to diagnose SI's both in situ as they operate in a data acquisition network, and in the laboratory in an acceptance/repair environment. The paper discusses important issues such as knowledge acquisition; extracting knowledge from human experts and other knowledge sources. SIDES can benefit high energy physics experiments, where SI problems can be diagnosed and solved more quickly. Equipment pool technicians can also benefit from SIDES, first by decreasing the number of SI's erroneously turned in for repair, and secondly as SIDES acts as an intelligent assistant to the technician in the diagnosis and repair process

  11. Quantitative measure of randomness and order for complete genomes

    Science.gov (United States)

    Kong, Sing-Guan; Fan, Wen-Lang; Chen, Hong-Da; Wigger, Jan; Torda, Andrew E.; Lee, H. C.

    2009-06-01

    We propose an order index, ϕ , which gives a quantitative measure of randomness and order of complete genomic sequences. It maps genomes to a number from 0 (random and of infinite length) to 1 (fully ordered) and applies regardless of sequence length. The 786 complete genomic sequences in GenBank were found to have ϕ values in a very narrow range, ϕg=0.031-0.015+0.028 . We show this implies that genomes are halfway toward being completely random, or, at the “edge of chaos.” We further show that artificial “genomes” converted from literary classics have ϕ ’s that almost exactly coincide with ϕg , but sequences of low information content do not. We infer that ϕg represents a high information-capacity “fixed point” in sequence space, and that genomes are driven to it by the dynamics of a robust growth and evolution process. We show that a growth process characterized by random segmental duplication can robustly drive genomes to the fixed point.

  12. Anterior segment developmental anomalies in a 33-week-old fetus with MIDAS syndrome.

    Science.gov (United States)

    Herwig, Martina C; Loeffler, Karin U; Gembruch, Ulrich; Kuchelmeister, Klaus; Müller, Annette M

    2014-01-01

    We report anterior segment abnormalities in both eyes of a 33-week-old fetus endorsing the diagnosis of MIDAS (microphthalmia, dermal aplasia, and sclerocornea) syndrome. After abortion, the fetus was examined by a standard pediatric autopsy that included macroscopic and microscopic examination of both eyes. Postmortem findings included craniofacial stigmata (such as hypertelorism, a flat nose and low-set ears) and an agenesis of the corpus callosum. Array comparative genomic hybridization revealed a deletion of the short arm of the X chromosome (region Xp22.2 to p22.32). Ophthalmopathologic examination of the eyes revealed microphthalmia with anterior segment developmental anomalies, in particular sclerocornea and Peters' anomaly, respectively. General pathology findings plus the ocular findings allowed the diagnosis of MIDAS syndrome. A discussion of differential diagnoses is provided. This case report indicates that ophthalmopathologic investigation of fetal eyes can be of great value for the further classification of syndromes.

  13. Parallel fuzzy connected image segmentation on GPU.

    Science.gov (United States)

    Zhuge, Ying; Cao, Yong; Udupa, Jayaram K; Miller, Robert W

    2011-07-01

    Image segmentation techniques using fuzzy connectedness (FC) principles have shown their effectiveness in segmenting a variety of objects in several large applications. However, one challenge in these algorithms has been their excessive computational requirements when processing large image datasets. Nowadays, commodity graphics hardware provides a highly parallel computing environment. In this paper, the authors present a parallel fuzzy connected image segmentation algorithm implementation on NVIDIA's compute unified device Architecture (CUDA) platform for segmenting medical image data sets. In the FC algorithm, there are two major computational tasks: (i) computing the fuzzy affinity relations and (ii) computing the fuzzy connectedness relations. These two tasks are implemented as CUDA kernels and executed on GPU. A dramatic improvement in speed for both tasks is achieved as a result. Our experiments based on three data sets of small, medium, and large data size demonstrate the efficiency of the parallel algorithm, which achieves a speed-up factor of 24.4x, 18.1x, and 10.3x, correspondingly, for the three data sets on the NVIDIA Tesla C1060 over the implementation of the algorithm on CPU, and takes 0.25, 0.72, and 15.04 s, correspondingly, for the three data sets. The authors developed a parallel algorithm of the widely used fuzzy connected image segmentation method on the NVIDIA GPUs, which are far more cost- and speed-effective than both cluster of workstations and multiprocessing systems. A near-interactive speed of segmentation has been achieved, even for the large data set.

  14. Genetic variation within and among Danish brown trout ( Salmo trutta L) hatchery strains, assessed by PCR-RFLP analysis of mitochondrial DNA segments

    DEFF Research Database (Denmark)

    Hansen, Michael Møller; Mensberg, Karen-Lise Dons; Rasmussen, Gorm

    1997-01-01

    Eleven Danish brown trout hatchery strains were studied by PCR- RFLP analysis of the ND-I and ND-5/6 segments of the mitochondrial genome. For comparison, data from wild trout representing three Danish river systems also were included. Reduced variability in terms of nucleon diversity and number...

  15. Genome-derived vaccines.

    Science.gov (United States)

    De Groot, Anne S; Rappuoli, Rino

    2004-02-01

    Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

  16. The Banana Genome Hub

    Science.gov (United States)

    Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

    2013-01-01

    Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

  17. Genomic instability following irradiation

    International Nuclear Information System (INIS)

    Hacker-Klom, U.B.; Goehde, W.

    2001-01-01

    Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

  18. CT identification of bronchopulmonary segments: 50 normal subjects

    International Nuclear Information System (INIS)

    Osbourne, D.; Vock, P.; Godwin, J.D.; Silverman, P.M.

    1984-01-01

    A systematic evaluation of the fissures, segmental bronchi and arteries, bronchopulmonary segments, and peripheral pulmonary parenchyma was made from computed tomographic (CT) scans of 50 patients with normal chest radiographs. Seventy percent of the segmental bronchi and 76% of the segmental arteries were identified. Arteries could be traced to their sixth- and seventh-order branches; their orientation to the plane of the CT section allowed gross identification and localization of bronchopulmonary segments

  19. Segmentation of Lung Structures in CT

    DEFF Research Database (Denmark)

    Lo, Pechin Chien Pau

    This thesis proposes and evaluates new algorithms for segmenting various lung structures in computed tomography (CT) images, namely the lungs, airway trees and vessel trees. The main objective of these algorithms is to facilitate a better platform for studying Chronic Obstructive Pulmonary Disease......, 200 randomly selected CT scans were manually evaluated by medical experts, and only negligible or minor errors were found in nine scans. The proposed algorithm has been used to study how changes in smoking behavior affect CT based emphysema quantification. The algorithms for segmenting the airway...

  20. Coupled Shape Model Segmentation in Pig Carcasses

    DEFF Research Database (Denmark)

    Hansen, Mads Fogtmann; Larsen, Rasmus; Ersbøll, Bjarne Kjær

    2006-01-01

    levels inside the outline as well as in a narrow band outside the outline. The maximum a posteriori estimate of the outline is found by gradient descent optimization. In order to segment a group of mutually dependent objects we propose 2 procedures, 1) the objects are found sequentially by conditioning...... the initialization of the next search from already found objects; 2) all objects are found simultaneously and a repelling force is introduced in order to avoid overlap between outlines in the solution. The methods are applied to segmentation of cross sections of muscles in slices of CT scans of pig backs for quality...

  1. Self-assembling segmented coiled tubing

    Science.gov (United States)

    Raymond, David W.

    2016-09-27

    Self-assembling segmented coiled tubing is a concept that allows the strength of thick-wall rigid pipe, and the flexibility of thin-wall tubing, to be realized in a single design. The primary use is for a drillstring tubular, but it has potential for other applications requiring transmission of mechanical loads (forces and torques) through an initially coiled tubular. The concept uses a spring-loaded spherical `ball-and-socket` type joint to interconnect two or more short, rigid segments of pipe. Use of an optional snap ring allows the joint to be permanently made, in a `self-assembling` manner.

  2. Segmentation of the Indian photovoltaic market

    International Nuclear Information System (INIS)

    Srinivasan, S.

    2005-01-01

    This paper provides an analytical framework studying the actors, networks and institutions and examines the evolution of the Indian Solar Photovoltaic (PV) Market. Different market segments, along the lines of demand and supply of PV equipment, i.e. on the basis of geography, end-use application, subsidy policy and other financing mechanisms, are detailed. The objective of this effort is to identify segments that require special attention from policy makers, donors and the Ministry of Non-Conventional Energy Sources. The paper also discusses the evolution of the commercial PV market in certain parts of the country and trends in the maturity of the market. (author)

  3. Unsupervised information extraction by text segmentation

    CERN Document Server

    Cortez, Eli

    2013-01-01

    A new unsupervised approach to the problem of Information Extraction by Text Segmentation (IETS) is proposed, implemented and evaluated herein. The authors' approach relies on information available on pre-existing data to learn how to associate segments in the input string with attributes of a given domain relying on a very effective set of content-based features. The effectiveness of the content-based features is also exploited to directly learn from test data structure-based features, with no previous human-driven training, a feature unique to the presented approach. Based on the approach, a

  4. Innovative visualization and segmentation approaches for telemedicine

    Science.gov (United States)

    Nguyen, D.; Roehrig, Hans; Borders, Marisa H.; Fitzpatrick, Kimberly A.; Roveda, Janet

    2014-09-01

    In health care applications, we obtain, manage, store and communicate using high quality, large volume of image data through integrated devices. In this paper we propose several promising methods that can assist physicians in image data process and communication. We design a new semi-automated segmentation approach for radiological images, such as CT and MRI to clearly identify the areas of interest. This approach combines the advantages from both the region-based method and boundary-based methods. It has three key steps compose: coarse segmentation by using fuzzy affinity and homogeneity operator, image division and reclassification using the Voronoi Diagram, and refining boundary lines using the level set model.

  5. Strategies for regular segmented reductions on GPU

    DEFF Research Database (Denmark)

    Larsen, Rasmus Wriedt; Henriksen, Troels

    2017-01-01

    We present and evaluate an implementation technique for regular segmented reductions on GPUs. Existing techniques tend to be either consistent in performance but relatively inefficient in absolute terms, or optimised for specific workloads and thereby exhibiting bad performance for certain input...... is in the context of the Futhark compiler, the implementation technique is applicable to any library or language that has a need for segmented reductions. We evaluate the technique on four microbenchmarks, two of which we also compare to implementations in the CUB library for GPU programming, as well as on two...

  6. Actinic Granuloma with Focal Segmental Glomerulosclerosis

    Directory of Open Access Journals (Sweden)

    Ruedee Phasukthaworn

    2016-02-01

    Full Text Available Actinic granuloma is an uncommon granulomatous disease, characterized by annular erythematous plaque with central clearing predominately located on sun-damaged skin. The pathogenesis is not well understood, ultraviolet radiation is recognized as precipitating factor. We report a case of a 52-year-old woman who presented with asymptomatic annular erythematous plaques on the forehead and both cheeks persisting for 2 years. The clinical presentation and histopathologic findings support the diagnosis of actinic granuloma. During that period of time, she also developed focal segmental glomerulosclerosis. The association between actinic granuloma and focal segmental glomerulosclerosis needs to be clarified by further studies.

  7. Segmentation and informality in Vietnam : a survey of the literature: country case study on labour market segmentation

    OpenAIRE

    Cling, Jean-Pierre; Razafindrakoto, Mireille; Roubaud, François

    2014-01-01

    Labour market segmentation is usually defined as the division of the labour markets into separate sub-markets or segments, distinguished by different characteristics and behavioural rules (incomes, contracts, etc.). The economic debate on the segmentation issue has been focusing in developed countries, and especially in Europe, on contractual segmentation and dualism.

  8. Quantification of expression and methylation of the Igf2r imprinted gene in segmental trisomic mouse model

    Czech Academy of Sciences Publication Activity Database

    Vacík, Tomáš; Forejt, Jiří

    2003-01-01

    Roč. 82, - (2003), s. 261-268 ISSN 0888-7543 R&D Projects: GA MŠk LN00A079; GA ČR GV204/98/K015 Grant - others:HHMI(US) 555000306 Institutional research plan: CEZ:AV0Z5052915 Keywords : Genomic imprinting * dosage-sensitive genes * Ts43H segmental trisomy of chromosome 17 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.488, year: 2003

  9. Traditional medicine and genomics

    Directory of Open Access Journals (Sweden)

    Kalpana Joshi

    2010-01-01

    Full Text Available ′Omics′ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  10. Traditional medicine and genomics.

    Science.gov (United States)

    Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

    2010-01-01

    'Omics' developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics.

  11. Bacillus subtilis genome diversity.

    Science.gov (United States)

    Earl, Ashlee M; Losick, Richard; Kolter, Roberto

    2007-02-01

    Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

  12. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  13. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  14. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  15. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  16. Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway

    Science.gov (United States)

    2012-01-01

    Background Genome-scale RNA-interference (RNAi) screens are becoming ever more common gene discovery tools. However, whilst every screen identifies interacting genes, less attention has been given to how factors such as library design and post-screening bioinformatics may be effecting the data generated. Results Here we present a new genome-wide RNAi screen of the Drosophila JAK/STAT signalling pathway undertaken in the Sheffield RNAi Screening Facility (SRSF). This screen was carried out using a second-generation, computationally optimised dsRNA library and analysed using current methods and bioinformatic tools. To examine advances in RNAi screening technology, we compare this screen to a biologically very similar screen undertaken in 2005 with a first-generation library. Both screens used the same cell line, reporters and experimental design, with the SRSF screen identifying 42 putative regulators of JAK/STAT signalling, 22 of which verified in a secondary screen and 16 verified with an independent probe design. Following reanalysis of the original screen data, comparisons of the two gene lists allows us to make estimates of false discovery rates in the SRSF data and to conduct an assessment of off-target effects (OTEs) associated with both libraries. We discuss the differences and similarities between the resulting data sets and examine the relative improvements in gene discovery protocols. Conclusions Our work represents one of the first direct comparisons between first- and second-generation libraries and shows that modern library designs together with methodological advances have had a significant influence on genome-scale RNAi screens. PMID:23006893

  17. Lung segment geometry study: simulation of largest possible tumours that fit into bronchopulmonary segments.

    Science.gov (United States)

    Welter, S; Stöcker, C; Dicken, V; Kühl, H; Krass, S; Stamatis, G

    2012-03-01

    Segmental resection in stage I non-small cell lung cancer (NSCLC) has been well described and is considered to have similar survival rates as lobectomy but with increased rates of local tumour recurrence due to inadequate parenchymal margins. In consequence, today segmentectomy is only performed when the tumour is smaller than 2 cm. Three-dimensional reconstructions from 11 thin-slice CT scans of bronchopulmonary segments were generated, and virtual spherical tumours were placed over the segments, respecting all segmental borders. As a next step, virtual parenchymal safety margins of 2 cm and 3 cm were subtracted and the size of the remaining tumour calculated. The maximum tumour diameters with a 30-mm parenchymal safety margin ranged from 26.1 mm in right-sided segments 7 + 8 to 59.8 mm in the left apical segments 1-3. Using a three-dimensional reconstruction of lung CT scans, we demonstrated that segmentectomy or resection of segmental groups should be feasible with adequate margins, even for larger tumours in selected cases. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  18. Translocations used to generate chromosome segment duplications ...

    Indian Academy of Sciences (India)

    a duplication (Dp) of the translocated segment and four inviable (white, W) ascospores with .... of this work, namely, the definition of breakpoint junction sequences of 12 ..... then our results would place supercontig 10.9 in distal. LG VIR. A third ...

  19. Optical Character Recognition Using Active Contour Segmentation

    Directory of Open Access Journals (Sweden)

    Nabeel Oudah

    2018-01-01

    Full Text Available Document analysis of images snapped by camera is a growing challenge. These photos are often poor-quality compound images, composed of various objects and text; this makes automatic analysis complicated. OCR is one of the image processing techniques which is used to perform automatic identification of texts. Existing image processing techniques need to manage many parameters in order to clearly recognize the text in such pictures. Segmentation is regarded one of these essential parameters. This paper discusses the accuracy of segmentation process and its effect over the recognition process. According to the proposed method, the images were firstly filtered using the wiener filter then the active contour algorithm could be applied in the segmentation process. The Tesseract OCR Engine was selected in order to evaluate the performance and identification accuracy of the proposed method. The results showed that a more accurate segmentation process shall lead to a more accurate recognition results. The rate of recognition accuracy was 0.95 for the proposed algorithm compared with 0.85 for the Tesseract OCR Engine.

  20. Multichannel shopper segments and their covariates

    NARCIS (Netherlands)

    Konus, U.; Verhoef, P.C.; Neslin, S.A.

    2008-01-01

    The proliferation of channels has created new challenges for research, including understanding how consumers may be segmented with respect to their information search and purchase behavior in multichannel environment. This research considers shopping a dynamic process that consists of search and