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Sample records for preliminary bac-end sequence

  1. Comparative analysis of catfish BAC end sequences with the zebrafish genome

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    Abernathy Jason

    2009-12-01

    Full Text Available Abstract Background Comparative mapping is a powerful tool to transfer genomic information from sequenced genomes to closely related species for which whole genome sequence data are not yet available. However, such an approach is still very limited in catfish, the most important aquaculture species in the United States. This project was initiated to generate additional BAC end sequences and demonstrate their applications in comparative mapping in catfish. Results We reported the generation of 43,000 BAC end sequences and their applications for comparative genome analysis in catfish. Using these and the additional 20,000 existing BAC end sequences as a resource along with linkage mapping and existing physical map, conserved syntenic regions were identified between the catfish and zebrafish genomes. A total of 10,943 catfish BAC end sequences (17.3% had significant BLAST hits to the zebrafish genome (cutoff value ≤ e-5, of which 3,221 were unique gene hits, providing a platform for comparative mapping based on locations of these genes in catfish and zebrafish. Genetic linkage mapping of microsatellites associated with contigs allowed identification of large conserved genomic segments and construction of super scaffolds. Conclusion BAC end sequences and their associated polymorphic markers are great resources for comparative genome analysis in catfish. Highly conserved chromosomal regions were identified to exist between catfish and zebrafish. However, it appears that the level of conservation at local genomic regions are high while a high level of chromosomal shuffling and rearrangements exist between catfish and zebrafish genomes. Orthologous regions established through comparative analysis should facilitate both structural and functional genome analysis in catfish.

  2. A comparative, BAC end sequence enabled map of the genome of the American mink (Neovison vison)

    DEFF Research Database (Denmark)

    Benkel, Bernhard F.; Smith, Amanda; Christensen, Knud

    2012-01-01

    In this report we present the results of the analysis of approximately 2.7 Mb of genomic information for the American mink (Neovison vison) derived through BAC end sequencing. Our study, which encompasses approximately 1/1000th of the mink genome, suggests that simple sequence repeats (SSRs...

  3. An overview of the Phalaenopsis orchid genome through BAC end sequence analysis

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    Hsiao Yu-Yun

    2011-01-01

    Full Text Available Abstract Background Phalaenopsis orchids are popular floral crops, and development of new cultivars is economically important to floricultural industries worldwide. Analysis of orchid genes could facilitate orchid improvement. Bacterial artificial chromosome (BAC end sequences (BESs can provide the first glimpses into the sequence composition of a novel genome and can yield molecular markers for use in genetic mapping and breeding. Results We used two BAC libraries (constructed using the BamHI and HindIII restriction enzymes of Phalaenopsis equestris to generate pair-end sequences from 2,920 BAC clones (71.4% and 28.6% from the BamHI and HindIII libraries, respectively, at a success rate of 95.7%. A total of 5,535 BESs were generated, representing 4.5 Mb, or about 0.3% of the Phalaenopsis genome. The trimmed sequences ranged from 123 to 1,397 base pairs (bp in size, with an average edited read length of 821 bp. When these BESs were subjected to sequence homology searches, it was found that 641 (11.6% were predicted to represent protein-encoding regions, whereas 1,272 (23.0% contained repetitive DNA. Most of the repetitive DNA sequences were gypsy- and copia-like retrotransposons (41.9% and 12.8%, respectively, whereas only 10.8% were DNA transposons. Further, 950 potential simple sequence repeats (SSRs were discovered. Dinucleotides were the most abundant repeat motifs; AT/TA dimer repeats were the most frequent SSRs, representing 253 (26.6% of all identified SSRs. Microsynteny analysis revealed that more BESs mapped to the whole-genome sequences of poplar than to those of grape or Arabidopsis, and even fewer mapped to the rice genome. This work will facilitate analysis of the Phalaenopsis genome, and will help clarify similarities and differences in genome composition between orchids and other plant species. Conclusion Using BES analysis, we obtained an overview of the Phalaenopsis genome in terms of gene abundance, the presence of repetitive

  4. Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.

    Science.gov (United States)

    Biswas, Manosh Kumar; Chai, Lijun; Mayer, Christoph; Xu, Qiang; Guo, Wenwu; Deng, Xiuxin

    2012-05-01

    The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.

  5. Genomic insight into the common carp (Cyprinus carpio genome by sequencing analysis of BAC-end sequences

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    Wang Jintu

    2011-04-01

    Full Text Available Abstract Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio, a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3

  6. Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences

    Science.gov (United States)

    2011-01-01

    Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of

  7. BAC-end sequence-based SNPs and Bin mapping for rapid integration of physical and genetic maps in apple.

    Science.gov (United States)

    Han, Yuepeng; Chagné, David; Gasic, Ksenija; Rikkerink, Erik H A; Beever, Jonathan E; Gardiner, Susan E; Korban, Schuyler S

    2009-03-01

    A genome-wide BAC physical map of the apple, Malus x domestica Borkh., has been recently developed. Here, we report on integrating the physical and genetic maps of the apple using a SNP-based approach in conjunction with bin mapping. Briefly, BAC clones located at ends of BAC contigs were selected, and sequenced at both ends. The BAC end sequences (BESs) were used to identify candidate SNPs. Subsequently, these candidate SNPs were genetically mapped using a bin mapping strategy for the purpose of mapping the physical onto the genetic map. Using this approach, 52 (23%) out of 228 BESs tested were successfully exploited to develop SNPs. These SNPs anchored 51 contigs, spanning approximately 37 Mb in cumulative physical length, onto 14 linkage groups. The reliability of the integration of the physical and genetic maps using this SNP-based strategy is described, and the results confirm the feasibility of this approach to construct an integrated physical and genetic maps for apple.

  8. BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

    Science.gov (United States)

    Zhao, Cui; Zhang, Xiaojun; Liu, Chengzhang; Huan, Pin; Li, Fuhua; Xiang, Jianhai; Huang, Chao

    2012-05-01

    Little is known about the genome of Pacific white shrimp ( Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 pairedends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.

  9. Mapping of Micro-Tom BAC-End Sequences to the Reference Tomato Genome Reveals Possible Genome Rearrangements and Polymorphisms

    Science.gov (United States)

    Asamizu, Erika; Shirasawa, Kenta; Hirakawa, Hideki; Sato, Shusei; Tabata, Satoshi; Yano, Kentaro; Ariizumi, Tohru; Shibata, Daisuke; Ezura, Hiroshi

    2012-01-01

    A total of 93,682 BAC-end sequences (BESs) were generated from a dwarf model tomato, cv. Micro-Tom. After removing repetitive sequences, the BESs were similarity searched against the reference tomato genome of a standard cultivar, “Heinz 1706.” By referring to the “Heinz 1706” physical map and by eliminating redundant or nonsignificant hits, 28,804 “unique pair ends” and 8,263 “unique ends” were selected to construct hypothetical BAC contigs. The total physical length of the BAC contigs was 495, 833, 423 bp, covering 65.3% of the entire genome. The average coverage of euchromatin and heterochromatin was 58.9% and 67.3%, respectively. From this analysis, two possible genome rearrangements were identified: one in chromosome 2 (inversion) and the other in chromosome 3 (inversion and translocation). Polymorphisms (SNPs and Indels) between the two cultivars were identified from the BLAST alignments. As a result, 171,792 polymorphisms were mapped on 12 chromosomes. Among these, 30,930 polymorphisms were found in euchromatin (1 per 3,565 bp) and 140,862 were found in heterochromatin (1 per 2,737 bp). The average polymorphism density in the genome was 1 polymorphism per 2,886 bp. To facilitate the use of these data in Micro-Tom research, the BAC contig and polymorphism information are available in the TOMATOMICS database. PMID:23227037

  10. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L. genome

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    Cloutier Sylvie

    2011-05-01

    Full Text Available Abstract Background Flax (Linum usitatissimum L. is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES from 43,776 clones, providing initial insights into the genome. Results The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb. The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%, followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. Conclusion The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable

  11. Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome.

    Science.gov (United States)

    Ragupathy, Raja; Rathinavelu, Rajkumar; Cloutier, Sylvie

    2011-05-09

    Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome. The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding. The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be

  12. Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly

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    Shultz Jeffry

    2008-07-01

    Full Text Available Abstract Background Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (Glycine max genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS. Here the aim was to use BAC end sequences (BES derived from three minimum tile paths (MTP to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches. Results Results show that when sequence divergence was 1–10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs were single nucleotide polymorphisms (SNPs; 89% and single nucleotide indels (SNIs 10%. Larger indels were rare but present (1%. Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5–10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed. Conclusion The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de

  13. Genome-wide BAC-end sequencing of Musa acuminata DH Pahang reveals further insights into the genome organization of banana

    NARCIS (Netherlands)

    Arnago, R.E.; Togawa, R.C.; Carpentier, S.C.; Lintel Hekkert, te B.; Kema, G.H.J.; Souza, M.T.

    2011-01-01

    Banana and plantain (Musa spp.) are grown in more than 120 countries in tropical and subtropical regions and constitute an important staple food for millions of people. A Musa acuminata ssp. malaccencis DH Pahang bacterial artificial chromosome (BAC) library (MAMB) was submitted for BAC-end

  14. Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome.

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    Santos, Anselmo Azevedo; Penha, Helen Alves; Bellec, Arnaud; Munhoz, Carla de Freitas; Pedrosa-Harand, Andrea; Bergès, Hélène; Vieira, Maria Lucia Carneiro

    2014-09-26

    The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource. The library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n=9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%). We generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome

  15. Chromosome arm-specific BAC end sequences permit comparative analysis of homoeologous chromosomes and genomes of polyploid wheat

    Czech Academy of Sciences Publication Activity Database

    Sehgal, S. K.; Li, W.; Rabinowicz, P. D.; Chan, A.; Šimková, Hana; Doležel, Jaroslav; Gill, B. S.

    2012-01-01

    Roč. 12, č. 64 (2012) ISSN 1471-2229 Grant - others:GA MŠk(CZ) ED0007/01/01 Program:ED Institutional research plan: CEZ:AV0Z50380511 Keywords : BREAD WHEAT * BRACHYPODIUM-DISTACHYON * REPETITIVE ELEMENTS Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.354, year: 2012

  16. End Sequencing and Finger Printing of Human & Mouse BAC Libraries

    Energy Technology Data Exchange (ETDEWEB)

    Fraser, C

    2005-09-27

    This project provided for continued end sequencing of existing and new BAC libraries constructed to support human sequencing as well as to initiate BAC end sequencing from the mouse BAC libraries constructed to support mouse sequencing. The clones, the sequences, and the fingerprints are now an available resource for the community at large. Research and development of new metaodologies for BAC end sequencing have reduced costs and increase throughput.

  17. Preliminary hazard analysis using sequence tree method

    International Nuclear Information System (INIS)

    Huang Huiwen; Shih Chunkuan; Hung Hungchih; Chen Minghuei; Yih Swu; Lin Jiinming

    2007-01-01

    A system level PHA using sequence tree method was developed to perform Safety Related digital I and C system SSA. The conventional PHA is a brainstorming session among experts on various portions of the system to identify hazards through discussions. However, this conventional PHA is not a systematic technique, the analysis results strongly depend on the experts' subjective opinions. The analysis quality cannot be appropriately controlled. Thereby, this research developed a system level sequence tree based PHA, which can clarify the relationship among the major digital I and C systems. Two major phases are included in this sequence tree based technique. The first phase uses a table to analyze each event in SAR Chapter 15 for a specific safety related I and C system, such as RPS. The second phase uses sequence tree to recognize what I and C systems are involved in the event, how the safety related systems work, and how the backup systems can be activated to mitigate the consequence if the primary safety systems fail. In the sequence tree, the defense-in-depth echelons, including Control echelon, Reactor trip echelon, ESFAS echelon, and Indication and display echelon, are arranged to construct the sequence tree structure. All the related I and C systems, include digital system and the analog back-up systems are allocated in their specific echelon. By this system centric sequence tree based analysis, not only preliminary hazard can be identified systematically, the vulnerability of the nuclear power plant can also be recognized. Therefore, an effective simplified D3 evaluation can be performed as well. (author)

  18. Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.)

    Science.gov (United States)

    Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Accordingly molecular markers have low levels of polymorphism and t...

  19. A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

    Czech Academy of Sciences Publication Activity Database

    Bartoš, Jan; Paux, E.; Kofler, R.; Havránková, Miroslava; Kopecký, David; Suchánková, Pavla; Šafář, Jan; Šimková, Hana; Town, C.D.; Lelley, T.; Feuillet, C.; Doležel, Jaroslav

    2008-01-01

    Roč. 8, č. 95 (2008), s. 1-12 ISSN 1471-2229 R&D Projects: GA ČR GP521/06/P412; GA ČR GD521/05/H013; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : BAC libraries * flow-sorted chromosomes Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.030, year: 2008

  20. First fungal genome sequence from Africa: A preliminary analysis

    Directory of Open Access Journals (Sweden)

    Rene Sutherland

    2012-01-01

    Full Text Available Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the ’tsunami‘ of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists

  1. A sequence-based genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa

    NARCIS (Netherlands)

    Choi, H.K.; Kim, D.; Uhm, T.; Limpens, E.H.M.; Lim, H.; Mun, J.H.; Kalo, P.; Penmetsa, R.V.; Seres, A.; Kulikova, O.; Roe, B.A.; Bisseling, T.; Kiss, G.B.; Cook, D.R.

    2004-01-01

    A core genetic map of the legume Medicago truncatula has been established by analyzing the segregation of 288 sequence-characterized genetic markers in an E, population composed of 93 individuals. These molecular markers correspond to 141 ESTs, 80 BAC end sequence tags, and 67 resistance gene

  2. Preliminary study of pseudorandom binary sequence pulsing of ORELA

    International Nuclear Information System (INIS)

    Larson, N.M.; Olsen, D.K.

    1980-03-01

    It has been suggested that pseudorandom binary sequence (PRBS) pulsing might enhance the performance of the Oak Ridge Electron Linear Accelerator (ORELA) for neutron-induced, time-of-flight (TOF) cross-section measurements. In this technical memorandum, equations are developed for expected count rates, statistical variances, and backgrounds for a pulsing scheme in which a PRBS is superimposed on the periodic equalintensity ORELA bursts. Introduction of the PRBS modification permits neutrons of different energies originating from different bursts to reach the detector simultaneously, and the signal corresponding to a unique flight time to be extracted mathematically. Relative advantages and disadvantages of measurements from conventional and PRBS pulsing modes are discussed in terms of counting statistics and backgrounds. Computer models of TOF spectra are generated for both pulsing modes, using as examples a 20-meter 233 U fission-chamber measurement and a 155-meter 238 U sample-in transmission measurement. Detailed comparisons of PRBS vs conventional results are presented. This study indicates that although PRBS pulsing could enhance ORELA performance for selected measurements, for general ORELA operation the disadvantages from PRBS pulsing probably outweigh the advantages

  3. Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing.

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    Margaret Staton

    Full Text Available Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence.

  4. Preliminary consideration on the seismic actions recorded during the 2016 Central Italy seismic sequence

    Science.gov (United States)

    Carlo Ponzo, Felice; Ditommaso, Rocco; Nigro, Antonella; Nigro, Domenico S.; Iacovino, Chiara

    2017-04-01

    After the Mw 6.0 mainshock of August 24, 2016 at 03.36 a.m. (local time), with the epicenter located between the towns of Accumoli (province of Rieti), Amatrice (province of Rieti) and Arquata del Tronto (province of Ascoli Piceno), several activities were started in order to perform some preliminary evaluations on the characteristics of the recent seismic sequence in the areas affected by the earthquake. Ambient vibration acquisitions have been performed using two three-directional velocimetric synchronized stations, with a natural frequency equal to 0.5Hz and a digitizer resolution of equal to 24bit. The activities are continuing after the events of the seismic sequence of October 26 and October 30, 2016. In this paper, in order to compare recorded and code provision values in terms of peak (PGA, PGV and PGD), spectral and integral (Housner Intensity) seismic parameters, several preliminary analyses have been performed on accelerometric time-histories acquired by three near fault station of the RAN (Italian Accelerometric Network): Amatrice station (station code AMT), Norcia station (station code NRC) and Castelsantangelo sul Nera station (station code CNE). Several comparisons between the elastic response spectra derived from accelerometric recordings and the elastic demand spectra provided by the Italian seismic code (NTC 2008) have been performed. Preliminary results retrieved from these analyses highlight several apparent difference between experimental data and conventional code provision. Then, the ongoing seismic sequence appears compatible with the historical seismicity in terms of integral parameters, but not in terms of peak and spectral values. It seems appropriate to reconsider the necessity to revise the simplified design approach based on the conventional spectral values. Acknowledgements This study was partially funded by the Italian Department of Civil Protection within the project DPC-RELUIS 2016 - RS4 ''Seismic observatory of structures and

  5. Preliminary Analysis of Aircraft Loss of Control Accidents: Worst Case Precursor Combinations and Temporal Sequencing

    Science.gov (United States)

    Belcastro, Christine M.; Groff, Loren; Newman, Richard L.; Foster, John V.; Crider, Dennis H.; Klyde, David H.; Huston, A. McCall

    2014-01-01

    Aircraft loss of control (LOC) is a leading cause of fatal accidents across all transport airplane and operational classes, and can result from a wide spectrum of hazards, often occurring in combination. Technologies developed for LOC prevention and recovery must therefore be effective under a wide variety of conditions and uncertainties, including multiple hazards, and their validation must provide a means of assessing system effectiveness and coverage of these hazards. This requires the definition of a comprehensive set of LOC test scenarios based on accident and incident data as well as future risks. This paper defines a comprehensive set of accidents and incidents over a recent 15 year period, and presents preliminary analysis results to identify worst-case combinations of causal and contributing factors (i.e., accident precursors) and how they sequence in time. Such analyses can provide insight in developing effective solutions for LOC, and form the basis for developing test scenarios that can be used in evaluating them. Preliminary findings based on the results of this paper indicate that system failures or malfunctions, crew actions or inactions, vehicle impairment conditions, and vehicle upsets contributed the most to accidents and fatalities, followed by inclement weather or atmospheric disturbances and poor visibility. Follow-on research will include finalizing the analysis through a team consensus process, defining future risks, and developing a comprehensive set of test scenarios with correlation to the accidents, incidents, and future risks. Since enhanced engineering simulations are required for batch and piloted evaluations under realistic LOC precursor conditions, these test scenarios can also serve as a high-level requirement for defining the engineering simulation enhancements needed for generating them.

  6. Detection of illegitimate rearrangement within the immunoglobulin locus on 14q32.3 in B-cell malignancies using end-sequenced probes

    DEFF Research Database (Denmark)

    Silahtaroglu, Asli; Poulsen, Tim; Giselø, Claus

    2001-01-01

    in the literature or at http://www.biologia.uniba.it/rmc/. Validation, orientation, and overlap of these probes were confirmed using interphase-, metaphase-, and fiber-FISH. We have identified seven BAC end-sequenced probes (3087C18, 47P23, 76N15, 12F16, 101G24, 112H5, and 151B17) covering 612 kb of the distal IGHV...

  7. Characterization of new Schistosoma mansoni microsatellite loci in sequences obtained from public DNA databases and microsatellite enriched genomic libraries

    Directory of Open Access Journals (Sweden)

    Rodrigues NB

    2002-01-01

    Full Text Available In the last decade microsatellites have become one of the most useful genetic markers used in a large number of organisms due to their abundance and high level of polymorphism. Microsatellites have been used for individual identification, paternity tests, forensic studies and population genetics. Data on microsatellite abundance comes preferentially from microsatellite enriched libraries and DNA sequence databases. We have conducted a search in GenBank of more than 16,000 Schistosoma mansoni ESTs and 42,000 BAC sequences. In addition, we obtained 300 sequences from CA and AT microsatellite enriched genomic libraries. The sequences were searched for simple repeats using the RepeatMasker software. Of 16,022 ESTs, we detected 481 (3% sequences that contained 622 microsatellites (434 perfect, 164 imperfect and 24 compounds. Of the 481 ESTs, 194 were grouped in 63 clusters containing 2 to 15 ESTs per cluster. Polymorphisms were observed in 16 clusters. The 287 remaining ESTs were orphan sequences. Of the 42,017 BAC end sequences, 1,598 (3.8% contained microsatellites (2,335 perfect, 287 imperfect and 79 compounds. The 1,598 BAC end sequences 80 were grouped into 17 clusters containing 3 to 17 BAC end sequences per cluster. Microsatellites were present in 67 out of 300 sequences from microsatellite enriched libraries (55 perfect, 38 imperfect and 15 compounds. From all of the observed loci 55 were selected for having the longest perfect repeats and flanking regions that allowed the design of primers for PCR amplification. Additionally we describe two new polymorphic microsatellite loci.

  8. Illumina MiSeq Sequencing for Preliminary Analysis of Microbiome Causing Primary Endodontic Infections in Egypt

    Directory of Open Access Journals (Sweden)

    Sally Ali Tawfik

    2018-01-01

    Full Text Available The use of high throughput next generation technologies has allowed more comprehensive analysis than traditional Sanger sequencing. The specific aim of this study was to investigate the microbial diversity of primary endodontic infections using Illumina MiSeq sequencing platform in Egyptian patients. Samples were collected from 19 patients in Suez Canal University Hospital (Endodontic Department using sterile # 15K file and paper points. DNA was extracted using Mo Bio power soil DNA isolation extraction kit followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized on the basis of the V3 and V4 hypervariable region of the 16S rRNA gene by using paired-end sequencing on Illumina MiSeq device. MOTHUR software was used in sequence filtration and analysis of sequenced data. A total of 1858 operational taxonomic units at 97% similarity were assigned to 26 phyla, 245 families, and 705 genera. Four main phyla Firmicutes, Bacteroidetes, Proteobacteria, and Synergistetes were predominant in all samples. At genus level, Prevotella, Bacillus, Porphyromonas, Streptococcus, and Bacteroides were the most abundant. Illumina MiSeq platform sequencing can be used to investigate oral microbiome composition of endodontic infections. Elucidating the ecology of endodontic infections is a necessary step in developing effective intracanal antimicrobials.

  9. Preliminary evaluation of the apparent diffusion coefficient of the kidney with a spiral IVIM sequence

    International Nuclear Information System (INIS)

    Tsuda, Kyo; Murakami, Takamichi; Sakurai, Kousuke

    1997-01-01

    We examined the usefulness of the spiral intravoxel incoherent motion (IVIM) sequence in measuring the apparent diffusion coefficient (ADC) of the kidneys. Five volunteers and five patients with chronic renal failure underwent diffusion-sensitive magnetic resonance imaging of the kidneys with the spiral IVIM sequence. The ADC values in patients with chronic renal failure were significantly lower than those in the renal cortex of volunteers. The mean value of ADC in patients with chronic renal failure was lower than that in volunteers, although there was no statistically significant difference. In volunteers, the ADC of the renal cortex was significantly higher than that of the renal medulla. The phantom study indicated that the accuracy of ADC depended on the signal to noise ratio. A spiral IVIM sequence with a high enough signal to noise ratio may be useful in evaluating renal function, especially that of the cortex. (author)

  10. Preliminary notes on dual relevance of ITS sequences and pigments in Hygrocybe taxonomy .

    NARCIS (Netherlands)

    Babos, M.; Halász, K.; Zagyva, T.; Zöld-Balogh, Á.; Szegö, D.; Bratek, Z.

    2011-01-01

    The relationships based on ITS sequences of 48 Hygrocybe s.l. specimens were studied and compared with previously described taxonomic groups. Our specimens formed two well separated genetic groups. The first one includes the species characterized by vivid yellow and red colours, while species

  11. Magnetic resonance findings in amyotrophic lateral sclerosis using a spin echo magnetization transfer sequence: preliminary report

    Directory of Open Access Journals (Sweden)

    ROCHA ANTÔNIO JOSÉ DA

    1999-01-01

    Full Text Available We present the magnetic resonance (MR findings of five patients with amyotrophic lateral sclerosis (ALS using a spin-echo sequence with an additional magnetization transfer (MT pulse on T1-weighted images (T1 SE/MT. These findings were absent in the control group and consisted of hyperintensity of the corticospinal tract. Moreover we discuss the principles and the use of this fast but simple MR technique in the diagnosis of ALS

  12. 13-colour photometry of pre-main sequence stars: preliminary report and results

    Energy Technology Data Exchange (ETDEWEB)

    Chavarria-K, C; de Lara, E [Universidad Nacional Autonoma de Mexico, Mexico City. Inst. de Astronomia

    1981-01-01

    Broad (UBVRI) and intermediate (13-colour) band photometry of 160 stars selected mainly from the Herbig Rao catalogue are being carried on currently, mainly to complement the published data of these stars in the optical window (for example shortward of the Balmer and longward of the Paschen discontinuities). The 13-colour photometric system and its applications to pre-main sequences stars are briefly discussed. First results are presented.

  13. Preliminary notes on dual relevance of ITS sequences and pigments in Hygrocybe taxonomy.

    Science.gov (United States)

    Babos, M; Halász, K; Zagyva, T; Zöld-Balogh, A; Szegő, D; Bratek, Z

    2011-06-01

    The relationships based on ITS sequences of 48 Hygrocybe s.l. specimens were studied and compared with previously described taxonomic groups. Our specimens formed two well separated genetic groups. The first one includes the species characterized by vivid yellow and red colours, while species belonging to other clades were pallid or pale brown, and in most cases with pink or olive tones. This separation is supported by the presence of muscaflavin pigments among some species referred to Hygrocybe (Bresinsky & Kronawitter 1986). The subgenera distinguished by morphological features can be relatively well recognized on phylogenetic trees, however, the majority of sections were not supported. Variability in the ITS region of Hygrocybe species is unusually high. In some cases sequences differed by more than 25 %, and the lengths of ITS regions also showed large differences. Taxa that were considered as closely related, e.g. the H. conica aggregate, were found to have identical or highly similar sequences. Our results seem to confirm the taxonomic concept of Bresinsky (2008) who proposed the division of the genus Hygrocybe. Hence H. calyptriformis and all examined members of subg. Gliophorus (H. irrigata, H. laeta, H. nitrata, H. psittacina) and subg. Cuphophyllus could be excluded from the genus Hygrocybe s.str. Based on these results further research using DNA markers at the intergeneric level is suggested to revaluate the taxonomy of former Hygrocybe species.

  14. Identification and Mapping of Simple Sequence Repeat Markers from Common Bean (Phaseolus vulgaris L. Bacterial Artificial Chromosome End Sequences for Genome Characterization and Genetic–Physical Map Integration

    Directory of Open Access Journals (Sweden)

    Juana M. Córdoba

    2010-11-01

    Full Text Available Microsatellite markers or simple sequence repeat (SSR loci are useful for diversity characterization and genetic–physical mapping. Different in silico microsatellite search methods have been developed for mining bacterial artificial chromosome (BAC end sequences for SSRs. The overall goal of this study was genome characterization based on SSRs in 89,017 BAC end sequences (BESs from the G19833 common bean ( L. library. Another objective was to identify new SSR taking into account three tandem motif identification programs (Automated Microsatellite Marker Development [AMMD], Tandem Repeats Finder [TRF], and SSRLocator [SSRL]. Among the microsatellite search engines, SSRL identified the highest number of SSRs; however, when primer design was attempted, the number dropped due to poor primer design regions. Automated Microsatellite Marker Development software identified many SSRs with valuable AT/TA or AG/TC motifs, while TRF found fewer SSRs and produced no primers. A subgroup of 323 AT-rich, di-, and trinucleotide SSRs were selected from the AMMD results and used in a parental survey with DOR364 and G19833, of which 75 could be mapped in the corresponding population; these represented 4052 BAC clones. Together with 92 previously mapped BES- and 114 non-BES-derived markers, a total of 280 SSRs were included in the polymerase chain reaction (PCR-based map, integrating a total of 8232 BAC clones in 162 contigs from the physical map.

  15. A Preliminary Neutral Framework for the Accident Sequence Evaluation for a Hydrogen Conversion Reactor

    International Nuclear Information System (INIS)

    Han, Seok Jung; Yang, Joon Eon

    2005-01-01

    A framework for an early stage PSA for a hydrogen conversion reactor has been proposed in this paper. The approach is based on a functional and top-down approach. A main concerning point of this approach is to use a design neutral framework. A design neutral framework of PSA can provide a flexibility to apply to several candidate design concepts or options. This neutral-framework idea was borrowed from a proposed regulatory framework in US NRC. The feasibility of our proposed approach has been assessed to be applied in an accident sequence analysis for a hydrogen conversion reactor

  16. The Preliminary Study of the 4 March 2010 Mw 6.3 Jiasian, Taiwan Earthquake Sequence

    Directory of Open Access Journals (Sweden)

    Hsin-Hua Huang

    2011-01-01

    Full Text Available On 4 March 2010, an inland Mw 6.3 earthquake occurred near the town of Jiasian in Kaohsiung County, Taiwan causing large ground shaking and extensive damage. In this study, we integrate the records from the Central Weather Bureau Seismic Network (CWBSN and Taiwan Strong Motion Instrumentation Program (TSMIP to obtain the relocated earthquake sequence and its first-motion focal mechanisms. This dataset offers us precise and reliable results which suggest a focal depth of 23 km and a possible fault plane of strike 313¢X, dip 41¢X, and rake 42¢X for the Jiasian earthquake. This fault plane significantly differs from the N-S striking Chaochou Fault (CCF as well as the principal trend of Taiwan orogenic belt, and should be an undiscovered fault in southern Taiwan. The relocated Jiasian earthquake sequence initiating from the 23-km-deep mainshock and terminating at around 10 km in depth also indicates it is a blind fault. Peak ground acceleration (PGA and peak ground velocity (PGV recorded by the TSMIP stations reveal a distinct NW-SE-shape pattern from the epicenter area toward the Chiayi region, likely due to the directivity and site effects. Such phenomena should be considered for future regional hazard assessments.

  17. Preliminary Validation of a New Measure of Negative Response Bias: The Temporal Memory Sequence Test.

    Science.gov (United States)

    Hegedish, Omer; Kivilis, Naama; Hoofien, Dan

    2015-01-01

    The Temporal Memory Sequence Test (TMST) is a new measure of negative response bias (NRB) that was developed to enrich the forced-choice paradigm. The TMST does not resemble the common structure of forced-choice tests and is presented as a temporal recall memory test. The validation sample consisted of 81 participants: 21 healthy control participants, 20 coached simulators, and 40 patients with acquired brain injury (ABI). The TMST had high reliability and significantly high positive correlations with the Test of Memory Malingering and Word Memory Test effort scales. Moreover, the TMST effort scales exhibited high negative correlations with the Glasgow Coma Scale, thus validating the previously reported association between probable malingering and mild traumatic brain injury. A suggested cutoff score yielded acceptable classification rates in the ABI group as well as in the simulator and control groups. The TMST appears to be a promising measure of NRB detection, with respectable rates of reliability and construct and criterion validity.

  18. Construction of cDNA library and preliminary analysis of expressed sequence tags from Siberian tiger

    Science.gov (United States)

    Liu, Chang-Qing; Lu, Tao-Feng; Feng, Bao-Gang; Liu, Dan; Guan, Wei-Jun; Ma, Yue-Hui

    2010-01-01

    In this study we successfully constructed a full-length cDNA library from Siberian tiger, Panthera tigris altaica, the most well-known wild Animal. Total RNA was extracted from cultured Siberian tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.30×106 pfu/ml and 1.62×109 pfu/ml respectively. The proportion of recombinants from unamplified library was 90.5% and average length of exogenous inserts was 1.13 kb. A total of 282 individual ESTs with sizes ranging from 328 to 1,142bps were then analyzed the BLASTX score revealed that 53.9% of the sequences were classified as strong match, 38.6% as nominal and 7.4% as weak match. 28.0% of them were found to be related to enzyme/catalytic protein, 20.9% ESTs to metabolism, 13.1% ESTs to transport, 12.1% ESTs to signal transducer/cell communication, 9.9% ESTs to structure protein, 3.9% ESTs to immunity protein/defense metabolism, 3.2% ESTs to cell cycle, and 8.9 ESTs classified as novel genes. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genomic research of Siberian tigers. PMID:20941376

  19. Preliminary results on an innovative plasmonic device for macromolecules analysis and sequencing

    KAUST Repository

    Francardi, Marco; Candeloro, Patrizio; Malara, Natalia Maria; Gentile, Francesco T.; Coluccio, Maria Laura; Perozziello, Gerardo; Gaggero, Aleesandro; De Angelis, Francesco De; Cherubini, Enrico; Di Fabrizio, Enzo M.

    2013-01-01

    In this work we present the fabrication and theoretical simulation for a new device constituted by a on Substrate Plasmonic Antenna (SPA) combined with a bio-functionalized Atomic Force Microscopy (AFM) cantilever. This device could represent a new strategy to sequence and analyze a single protein or DNA. The idea is to use an SPA composed of an innovative "wedding cake"shaped grating (WCG), in order to excite a Surface Plasmon Polariton (SPP) mode, and a 30-tilted Plasmonic Antenna (PA), able to compress adiabatically the SPP until the tip. The Plasmonic device is placed inside an electrical contact that could be used to unfold protein molecules or DNA. A bio-functionalized AFM tip can be used to fish a single biological element and for alignment with the SPA. Then the unfolded element could be scanned close to the PA and a Tip Enhanced Raman Signal (TERS) can be recorded from the biomolecule. The spatial resolution is limited by the size of the radius of curvature of the antenna, which in this work is about 15 nm, while the vertical scanning is controlled by the piezoelectric of the AFM set up. In this work we demonstrate the possibility to fabricate this innovative plasmonic device and we report FDTD simulations of the innovative WCG. The FDTD simulations show the generation of a plasmonic mode that, coupled with the antenna, give rise to an adiabatic compression which produce an increase of the electric field of about 40 times. © 2013 Elsevier B.V. All rights reserved.

  20. Preliminary results on an innovative plasmonic device for macromolecules analysis and sequencing

    KAUST Repository

    Francardi, Marco

    2013-11-01

    In this work we present the fabrication and theoretical simulation for a new device constituted by a on Substrate Plasmonic Antenna (SPA) combined with a bio-functionalized Atomic Force Microscopy (AFM) cantilever. This device could represent a new strategy to sequence and analyze a single protein or DNA. The idea is to use an SPA composed of an innovative "wedding cake"shaped grating (WCG), in order to excite a Surface Plasmon Polariton (SPP) mode, and a 30-tilted Plasmonic Antenna (PA), able to compress adiabatically the SPP until the tip. The Plasmonic device is placed inside an electrical contact that could be used to unfold protein molecules or DNA. A bio-functionalized AFM tip can be used to fish a single biological element and for alignment with the SPA. Then the unfolded element could be scanned close to the PA and a Tip Enhanced Raman Signal (TERS) can be recorded from the biomolecule. The spatial resolution is limited by the size of the radius of curvature of the antenna, which in this work is about 15 nm, while the vertical scanning is controlled by the piezoelectric of the AFM set up. In this work we demonstrate the possibility to fabricate this innovative plasmonic device and we report FDTD simulations of the innovative WCG. The FDTD simulations show the generation of a plasmonic mode that, coupled with the antenna, give rise to an adiabatic compression which produce an increase of the electric field of about 40 times. © 2013 Elsevier B.V. All rights reserved.

  1. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.

    Science.gov (United States)

    Zhang, Tianzhen; Hu, Yan; Jiang, Wenkai; Fang, Lei; Guan, Xueying; Chen, Jiedan; Zhang, Jinbo; Saski, Christopher A; Scheffler, Brian E; Stelly, David M; Hulse-Kemp, Amanda M; Wan, Qun; Liu, Bingliang; Liu, Chunxiao; Wang, Sen; Pan, Mengqiao; Wang, Yangkun; Wang, Dawei; Ye, Wenxue; Chang, Lijing; Zhang, Wenpan; Song, Qingxin; Kirkbride, Ryan C; Chen, Xiaoya; Dennis, Elizabeth; Llewellyn, Danny J; Peterson, Daniel G; Thaxton, Peggy; Jones, Don C; Wang, Qiong; Xu, Xiaoyang; Zhang, Hua; Wu, Huaitong; Zhou, Lei; Mei, Gaofu; Chen, Shuqi; Tian, Yue; Xiang, Dan; Li, Xinghe; Ding, Jian; Zuo, Qiyang; Tao, Linna; Liu, Yunchao; Li, Ji; Lin, Yu; Hui, Yuanyuan; Cao, Zhisheng; Cai, Caiping; Zhu, Xiefei; Jiang, Zhi; Zhou, Baoliang; Guo, Wangzhen; Li, Ruiqiang; Chen, Z Jeffrey

    2015-05-01

    Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.

  2. The OMERACT psoriatic arthritis magnetic resonance imaging scoring system (PsAMRIS): definitions of key pathologies, suggested MRI sequences, and preliminary scoring system for PsA Hands

    DEFF Research Database (Denmark)

    Østergaard, Mikkel; McQueen, Fiona; Wiell, Charlotte

    2009-01-01

    This article describes a preliminary OMERACT psoriatic arthritis magnetic resonance image scoring system (PsAMRIS) for evaluation of inflammatory and destructive changes in PsA hands, which was developed by the international OMERACT MRI in inflammatory arthritis group. MRI definitions of important...... pathologies in peripheral PsA and suggestions concerning appropriate MRI sequences for use in PsA hands are also provided....

  3. Construction of an American mink Bacterial Artificial Chromosome (BAC library and sequencing candidate genes important for the fur industry

    Directory of Open Access Journals (Sweden)

    Christensen Knud

    2011-07-01

    Full Text Available Abstract Background Bacterial artificial chromosome (BAC libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they provide an excellent source of information in genomics projects. Results Here, we report the construction and characterization of the CHORI-231 BAC library constructed from a Danish-farmed, male American mink (Neovison vison. The library contains approximately 165,888 clones with an average insert size of 170 kb, representing approximately 10-fold coverage. High-density filters, each consisting of 18,432 clones spotted in duplicate, have been produced for hybridization screening and are publicly available. Overgo probes derived from expressed sequence tags (ESTs, representing 21 candidate genes for traits important for the mink industry, were used to screen the BAC library. These included candidate genes for coat coloring, hair growth and length, coarseness, and some receptors potentially involved in viral diseases in mink. The extensive screening yielded positive results for 19 of these genes. Thirty-five clones corresponding to 19 genes were sequenced using 454 Roche, and large contigs (184 kb in average were assembled. Knowing the complete sequences of these candidate genes will enable confirmation of the association with a phenotype and the finding of causative mutations for the targeted phenotypes. Additionally, 1577 BAC clones were end sequenced; 2505 BAC end sequences (80% of BACs were obtained. An excess of 2 Mb has been analyzed, thus giving a snapshot of the mink genome. Conclusions The availability of the CHORI-321 American mink BAC library will aid in identification of genes and genomic regions of interest. We have demonstrated how the library can be used to identify specific genes of interest, develop genetic markers, and for BAC end sequencing and deep sequencing of selected clones. To our knowledge, this is the

  4. Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads.

    Directory of Open Access Journals (Sweden)

    Jovan Rebolledo-Mendez

    Full Text Available The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight's half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects' and Twilight's genome or due to errors in the reference. EquCab2 is regarded as "The Twilight Assembly." The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies

  5. Preliminary report on aftershock sequence for earthquake of January 31, 1986, near Painesville, Ohio (time period: 2/1/86-2/10/86)

    Science.gov (United States)

    Borcherdt, R.D.

    1986-01-01

    A ten-station array of broad-band digital instrumentation (GEOS) was deployed by the U. S. Geological Survey with partial support provided by Electric Power Research Institute to record the aftershock sequence of the moderate (mb ~ 4.9) earthquake that occurred on January 31, 1986 (16:46:43 UTC) near Painesville, Ohio. The occurrence of the event has raised questions concerning possible contributory factors to the occurrence of the event and questions concerning the character of earthquake-induced high-frequency ground motions in the area. To aid in the timely resolution of the implications of some of these questions, this preliminary report provides copies of the ground motion time-histories and corresponding spectra for the six identified aftershocks and two events, thought to be quarry blasts, recorded as of February 10, 1986. Recording station locations and epicenter locations based on two preliminary estimates of local seismic velocity structure are provided.

  6. Evaluation of MR cisternography of the cerebellopontine angle using a balanced fast-field-echo sequence: preliminary findings

    Energy Technology Data Exchange (ETDEWEB)

    Tsuchiya, Kazuhiro; Aoki, Chinatsu; Hachiya, Junichi [Department of Radiology, Kyorin University School of Medicine, 6-20-2 Shinkawa, Mitaka, 181-8611, Tokyo (Japan)

    2004-02-01

    We evaluated the feasibility of MR cisternography by the balanced fast-field-echo (bFFE) sequence, comparing with that by a turbo-spin-echo (TSE) sequence, for cerebellopontine angle lesions on a 1.5-T imager (Gyroscan Intera, Philips, Best, The Netherlands). The bFFE MR cisternograms depicted target cranial nerves with less cerebrospinal fluid pulsation artifacts than TSE cisternograms and visualized an acoustic schwannoma in 6 of 44 patients with suspicion and a causative vessel of hemifacial spasm in all of 3 patients in a short scanning time (1 min 53 s). The bFFE sequence can be promising for MR cisternography in the diagnosis of cerebellopontine angle lesions. (orig.)

  7. Antimicrobial susceptibility determined by the E test, Löwenstein-Jensen proportion, and DNA sequencing methods among Mycobacterium tuberculosis isolates discrepancies, preliminary results

    Directory of Open Access Journals (Sweden)

    Maria Inês Moura Freixo

    2004-02-01

    Full Text Available Mycobacterium tuberculosis strains resistant to streptomycin (SM, isoniazid (INH, and/or rifampin (RIF as determined by the conventional Löwenstein-Jensen proportion method (LJPM were compared with the E test, a minimum inhibitory concentration susceptibility method. Discrepant isolates were further evaluated by BACTEC and by DNA sequence analyses for mutations in genes most often associated with resistance to these drugs (rpsL, katG, inhA, and rpoB. Preliminary discordant E test results were seen in 75% of isolates resistant to SM and in 11% to INH. Discordance improved for these two drugs (63% for SM and none for INH when isolates were re-tested but worsened for RIF (30%. Despite good agreement between phenotypic results and sequencing analyses, wild type profiles were detected on resistant strains mainly for SM and INH. It should be aware that susceptible isolates according to molecular methods might contain other mechanisms of resistance. Although reproducibility of the LJPM susceptibility method has been established, variable E test results for some M. tuberculosis isolates poses questions regarding its reproducibility particularly the impact of E test performance which may vary among laboratories despite adherence to recommended protocols. Further studies must be done to enlarge the evaluated samples and looked possible mutations outside of the hot spot sequenced gene among discrepant strains.

  8. Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics.

    Directory of Open Access Journals (Sweden)

    Annika Brinkmann

    2017-11-01

    Full Text Available We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS-based identification of viral hemorrhagic fever (VHF agents and assess the feasibility of this approach in diagnostics.An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients.The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours.Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.

  9. Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics.

    Science.gov (United States)

    Brinkmann, Annika; Ergünay, Koray; Radonić, Aleksandar; Kocak Tufan, Zeliha; Domingo, Cristina; Nitsche, Andreas

    2017-11-01

    We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours. Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.

  10. Preliminary study of a new analytic approach for the design of an automatic device for DNA sequencing

    International Nuclear Information System (INIS)

    Grimm, Bertrand

    1990-01-01

    After having outlined the various drawbacks of conventional methods of DNA sequencing (use of radioactive marking which is to be put aside, use of fluorescent markers with limitations in terms of slowness and of possible evolutions), this research thesis proposes an alternative approach which uses a DNA marking by steady isotopes, a laser ionization of samples, and ion detection by time-of-flight mass spectrometry. The author outlines the numerous benefits of such a combination. He first presents the sequencing process and its different stages, and the currently proposed solutions. Then, he addresses the different chemical aspects of marking, reports the development of various assemblies and methods for the coupling between the separation stage and the envisaged detection means. He reports attempts to make electrophoresis (the only know way to separate samples) more performing in terms of rapidity while maintaining its resolution characteristics [fr

  11. Complete Mitochondrial Genome Sequencing of a Burial from a Romano–Christian Cemetery in the Dakhleh Oasis, Egypt: Preliminary Indications

    Directory of Open Access Journals (Sweden)

    J. Eldon Molto

    2017-10-01

    Full Text Available The curse of ancient Egyptian DNA was lifted by a recent study which sequenced the mitochondrial genomes (mtGenome of 90 ancient Egyptians from the archaeological site of Abusir el-Meleq. Surprisingly, these ancient inhabitants were more closely related to those from the Near East than to contemporary Egyptians. It has been accepted that the timeless highway of the Nile River seeded Egypt with African genetic influence, well before pre-Dynastic times. Here we report on the successful recovery and analysis of the complete mtGenome from a burial recovered from a remote Romano–Christian cemetery, Kellis 2 (K2. K2 serviced the ancient municipality of Kellis, a village located in the Dakhleh Oasis in the southwest desert in Egypt. The data were obtained by high throughput sequencing (HTS performed independently at two ancient DNA facilities (Armed Forces DNA Identification Laboratory, Dover, DE, USA and Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA. These efforts produced concordant haplotypes representing a U1a1a haplogroup lineage. This result indicates that Near Eastern maternal influence previously identified at Abusir el-Meleq was also present further south, in ancient Kellis during the Romano–Christian period.

  12. Fat-Suppressed T2 Sequences for Routine 3.0-Tesla Lumbar Spine Magnetic Resonance Imaging: A Preliminary Report

    Energy Technology Data Exchange (ETDEWEB)

    McKinney, A. M.; Gadani, S.; Palmer, C. S.; Vidarsson, L. (Dept. of Radiology, Hennepin County and Univ. of Minnesota Medical Centers, Minneapolis, MN (United States))

    2008-09-15

    Background: Clear depiction of the ligamentum flavum on routine lumbar magnetic resonance imaging (MRI) is essential in accurately describing the extent of degenerative disease. In routine, noncontrast evaluations, focal fatty deposition or hemangiomas can be difficult to distinguish from malignant foci on fast spin-echo (FSE) T2-weighted images. Purpose: To describe the use of T2 fast field echo (T2FFE) in combination with spectral presaturation inversion recovery (SPIR) fat suppression for noncontrast, routine lumbar spine outpatient MR imaging at 3.0 Tesla (3T). Material and Methods: An axial gradient echo (GE) T2FFE sequence was combined with SPIR fat suppression (T2FFE-SPIR), via a 3T Philips Intera (Philips Medical Systems, Best, The Netherlands) scanner, and added to the routine, noncontrast lumbar MRI examinations, which included sagittal FSE T1-weighted (T1WI), T2-weighted (T2WI), short-tau inversion recovery (STIR), and axial FSE T2WI. The sequence was performed in over 500 patients over a 1-year period, without intravenous contrast, and with slice thickness and planes of section identical to the axial FSE T1WI and T2WI images. The sequence typically lasted about 4.5-6 min. Results: The use of T2FFE-SPIR enabled visualization of the ligamentum flavum in degenerative disease, and the exclusion of focal fatty lesions on FSE T2WI. Other benefits included: the identification of malignant foci, the uncommon detection of hemorrhage, and the elimination of spurious flow voids. Several brief examples are provided to demonstrate the utility of this technique. Conclusion: The addition of T2FFE-SPIR to routine, noncontrast protocols in outpatients could provide further confidence in the visualization of the ligamentum flavum in degenerative disease, and can exclude malignancy in T2-bright areas of focal fatty marrow. Larger studies would be helpful to evaluate the accuracy of this technique versus FSE techniques in depicting degenerative, malignant, or inflammatory

  13. Fat-Suppressed T2* Sequences for Routine 3.0-Tesla Lumbar Spine Magnetic Resonance Imaging: A Preliminary Report

    International Nuclear Information System (INIS)

    McKinney, A. M.; Gadani, S.; Palmer, C. S.; Vidarsson, L.

    2008-01-01

    Background: Clear depiction of the ligamentum flavum on routine lumbar magnetic resonance imaging (MRI) is essential in accurately describing the extent of degenerative disease. In routine, noncontrast evaluations, focal fatty deposition or hemangiomas can be difficult to distinguish from malignant foci on fast spin-echo (FSE) T2-weighted images. Purpose: To describe the use of T2* fast field echo (T2FFE) in combination with spectral presaturation inversion recovery (SPIR) fat suppression for noncontrast, routine lumbar spine outpatient MR imaging at 3.0 Tesla (3T). Material and Methods: An axial gradient echo (GE) T2FFE sequence was combined with SPIR fat suppression (T2FFE-SPIR), via a 3T Philips Intera (Philips Medical Systems, Best, The Netherlands) scanner, and added to the routine, noncontrast lumbar MRI examinations, which included sagittal FSE T1-weighted (T1WI), T2-weighted (T2WI), short-tau inversion recovery (STIR), and axial FSE T2WI. The sequence was performed in over 500 patients over a 1-year period, without intravenous contrast, and with slice thickness and planes of section identical to the axial FSE T1WI and T2WI images. The sequence typically lasted about 4.5-6 min. Results: The use of T2FFE-SPIR enabled visualization of the ligamentum flavum in degenerative disease, and the exclusion of focal fatty lesions on FSE T2WI. Other benefits included: the identification of malignant foci, the uncommon detection of hemorrhage, and the elimination of spurious flow voids. Several brief examples are provided to demonstrate the utility of this technique. Conclusion: The addition of T2FFE-SPIR to routine, noncontrast protocols in outpatients could provide further confidence in the visualization of the ligamentum flavum in degenerative disease, and can exclude malignancy in T2-bright areas of focal fatty marrow. Larger studies would be helpful to evaluate the accuracy of this technique versus FSE techniques in depicting degenerative, malignant, or inflammatory

  14. Construction of a cDNA library and preliminary analysis of expressed sequence tags in Piper hainanense.

    Science.gov (United States)

    Fan, R; Ling, P; Hao, C Y; Li, F P; Huang, L F; Wu, B D; Wu, H S

    2015-10-19

    Black pepper is a perennial climbing vine. It is widely cultivated because its berries can be utilized not only as a spice in food but also for medicinal use. This study aimed to construct a standardized, high-quality cDNA library to facilitated identification of new Piper hainanense transcripts. For this, 262 unigenes were used to generate raw reads. The average length of these 262 unigenes was 774.8 bp. Of these, 94 genes (35.9%) were newly identified, according to the NCBI protein database. Thus, identification of new genes may broaden the molecular knowledge of P. hainanense on the basis of Clusters of Orthologous Groups and Gene Ontology categories. In addition, certain basic genes linked to physiological processes, which can contribute to disease resistance and thereby to the breeding of black pepper. A total of 26 unigenes were found to be SSR markers. Dinucleotide SSR was the main repeat motif, accounting for 61.54%, followed by trinucleotide SSR (23.07%). Eight primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among twenty-one piper germplasm. These results present a novel sequence information of P. hainanense, which can serve as the foundation for further genetic research on this species.

  15. Preliminary steps towards assessing aerosol retention in the break stage of a dry steam generator during severe accident SGTR sequences

    International Nuclear Information System (INIS)

    Herranz, L.E.; Lopez del Pra, C.; Sanchez Velasco, F.J.

    2006-01-01

    Severe accidents SGTR sequences are identified as major contributors to risk of PWRs. Their relevance lies in the potential radioactive release from reactor coolant system to the environment. Lack of knowledge on the source term attenuation capability of the steam generator has avoided its consideration in probabilistic safety studies and severe accident management guidelines. This paper describes a research program presently under way on the aerosol retention in the nearby of the tube breach within the secondary side of the steam generation in the absence of water. Its development has been internationally framed within the EU-SGTR and the ARTIST program. Experimental activities are focused on setting up a reliable database in which the influence of gas mass flow rate, breach configuration and particle nature in the aerosol retention are properly considered. Theoretical activities are aimed at developing a predictive tool (ARISG) capable of assessing source term attenuation in the scenario with reasonable accuracy. Given the major importance of jet aerodynamics, 3D CFD analyses are being conducted to assist both test interpretation and model development. (author)

  16. Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.).

    Science.gov (United States)

    Cloutier, Sylvie; Miranda, Evelyn; Ward, Kerry; Radovanovic, Natasa; Reimer, Elsa; Walichnowski, Andrzej; Datla, Raju; Rowland, Gordon; Duguid, Scott; Ragupathy, Raja

    2012-08-01

    Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax.

  17. Preliminary report for analysis of genome wide mutations from four ciprofloxacin resistant B. anthracis Sterne isolates generated by Illumina, 454 sequencing and microarrays for DHS

    Energy Technology Data Exchange (ETDEWEB)

    Jaing, Crystal [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vergez, Lisa [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hinckley, Aubree [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Thissen, James [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gardner, Shea [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); McLoughlin, Kevin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Jackson, Paul [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ellingson, Sally [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hauser, Loren [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Brettin, Tom [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Fofanov, Viacheslav [Eureka Genomics, Hercules, CA (United States); Koshinsky, Heather [Eureka Genomics, Hercules, CA (United States); Fofanov, Yuriy [Univ. of Houston, TX (United States)

    2011-06-21

    The objective of this project is to provide DHS a comprehensive evaluation of the current genomic technologies including genotyping, Taqman PCR, multiple locus variable tandem repeat analysis (MLVA), microarray and high-throughput DNA sequencing in the analysis of biothreat agents from complex environmental samples. As the result of a different DHS project, we have selected for and isolated a large number of ciprofloxacin resistant B. anthracis Sterne isolates. These isolates vary in the concentrations of ciprofloxacin that they can tolerate, suggesting multiple mutations in the samples. In collaboration with University of Houston, Eureka Genomics and Oak Ridge National Laboratory, we analyzed the ciprofloxacin resistant B. anthracis Sterne isolates by microarray hybridization, Illumina and Roche 454 sequencing to understand the error rates and sensitivity of the different methods. The report provides an assessment of the results and a complete set of all protocols used and all data generated along with information to interpret the protocols and data sets.

  18. The pioneering use of ISSR (Inter Simple Sequence Repeat in Neotropical anurans: preliminary assessment of genetic diversity in populations of Physalaemus cuvieri (Amphibia, Leiuperidae

    Directory of Open Access Journals (Sweden)

    Rafaela M Moresco

    2013-01-01

    Full Text Available The greatest diversity of anurans in the world is in Brazil and one of the major challenges is to reconcile the accelerated economic development with strategies that aim to maintain this diversity in forest fragments, often representing ESUs of some biomes. This study aimed to obtain data that will support conservation projects through the pioneering use of ISSR analysis in Neotropical anurans, estimating the intra- and interpopulation genetic diversity of four populations of P. cuvieri (Paraná and São Paulo regions. Of the 65 loci scored 58 were polymorphic, with 0.797 intrapopulation variation and 0.203 interpopulation variation. The index of interpopulation genetic differentiation (Fst proved to be high among the population of Marmeleiro-PR and the three populations of SP (Fst > 0.288; genetic dissimilarity was related to the geographical distance. The ISSR proved to be efficient and useful molecular markers in comparison with other markers most widely used for preliminary diagnosis of genetic diversity in populations of amphibians, and could be applied as a tool for future conservation projects, since they could identify potential ESUs and influence decisions on the preservation of fragments.

  19. Distortion-free diffusion MRI using an MRI-guided Tri-Cobalt 60 radiotherapy system: Sequence verification and preliminary clinical experience.

    Science.gov (United States)

    Gao, Yu; Han, Fei; Zhou, Ziwu; Cao, Minsong; Kaprealian, Tania; Kamrava, Mitchell; Wang, Chenyang; Neylon, John; Low, Daniel A; Yang, Yingli; Hu, Peng

    2017-10-01

    Monitoring tumor response during the course of treatment and adaptively modifying treatment plan based on tumor biological feedback may represent a new paradigm for radiotherapy. Diffusion MRI has shown great promises in assessing and predicting tumor response to radiotherapy. However, the conventional diffusion-weighted single-shot echo-planar-imaging (DW-ssEPI) technique suffers from limited resolution, severe distortion, and possibly inaccurate ADC at low field strength. The purpose of this work was to develop a reliable, accurate and distortion-free diffusion MRI technique that is practicable for longitudinal tumor response evaluation and adaptive radiotherapy on a 0.35 T MRI-guided radiotherapy system. A diffusion-prepared turbo spin echo readout (DP-TSE) sequence was developed and compared with the conventional diffusion-weighted single-shot echo-planar-imaging sequence on a 0.35 T MRI-guided radiotherapy system (ViewRay). A spatial integrity phantom was used to quantitate and compare the geometric accuracy of the two diffusion sequences for three orthogonal orientations. The apparent diffusion coefficient (ADC) accuracy was evaluated on a diffusion phantom under both 0 °C and room temperature to cover a diffusivity range between 0.40 × 10 -3 and 2.10 × 10 -3 mm 2 /s. Ten room temperature measurements repeated on five different days were conducted to assess the ADC reproducibility of DP-TSE. Two glioblastoma (GBM) and six sarcoma patients were included to examine the in vivo feasibility. The target registration error (TRE) was calculated to quantitate the geometric accuracy where structural CT or MR images were co-registered to the diffusion images as references. ADC maps from DP-TSE and DW-ssEPI were calculated and compared. A tube phantom was placed next to patients not treated on ViewRay, and ADCs of this reference tube were also compared. The proposed DP-TSE passed the spatial integrity test (< 1 mm within 100 mm radius and < 2 mm within 175 mm radius

  20. Construction of a Full-Length Enriched cDNA Library and Preliminary Analysis of Expressed Sequence Tags from Bengal Tiger Panthera tigris tigris

    Science.gov (United States)

    Liu, Changqing; Liu, Dan; Guo, Yu; Lu, Taofeng; Li, Xiangchen; Zhang, Minghai; Ma, Jianzhang; Ma, Yuehui; Guan, Weijun

    2013-01-01

    In this study, a full-length enriched cDNA library was successfully constructed from Bengal tiger, Panthera tigris tigris, the most well-known wild Animal. Total RNA was extracted from cultured Bengal tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.28 × 106 pfu/mL and 1.56 × 109 pfu/mL respectively. The percentage of recombinants from unamplified library was 90.2% and average length of exogenous inserts was 0.98 kb. A total of 212 individual ESTs with sizes ranging from 356 to 1108 bps were then analyzed. The BLASTX score revealed that 48.1% of the sequences were classified as a strong match, 45.3% as nominal and 6.6% as a weak match. Among the ESTs with known putative function, 26.4% ESTs were found to be related to all kinds of metabolisms, 19.3% ESTs to information storage and processing, 11.3% ESTs to posttranslational modification, protein turnover, chaperones, 11.3% ESTs to transport, 9.9% ESTs to signal transducer/cell communication, 9.0% ESTs to structure protein, 3.8% ESTs to cell cycle, and only 6.6% ESTs classified as novel genes. By EST sequencing, a full-length gene coding ferritin was identified and characterized. The recombinant plasmid pET32a-TAT-Ferritin was constructed, coded for the TAT-Ferritin fusion protein with two 6× His-tags in N and C-terminal. After BCA assay, the concentration of soluble Trx-TAT-Ferritin recombinant protein was 2.32 ± 0.12 mg/mL. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genome and transcriptome research of Bengal tigers. PMID:23708105

  1. Construction of a Full-Length Enriched cDNA Library and Preliminary Analysis of Expressed Sequence Tags from Bengal Tiger Panthera tigris tigris

    Directory of Open Access Journals (Sweden)

    Changqing Liu

    2013-05-01

    Full Text Available In this study, a full-length enriched cDNA library was successfully constructed from Bengal tiger, Panthera tigris tigris, the most well-known wild Animal. Total RNA was extracted from cultured Bengal tiger fibroblasts in vitro. The titers of primary and amplified libraries were 1.28 × 106 pfu/mL and 1.56 × 109 pfu/mL respectively. The percentage of recombinants from unamplified library was 90.2% and average length of exogenous inserts was 0.98 kb. A total of 212 individual ESTs with sizes ranging from 356 to 1108 bps were then analyzed. The BLASTX score revealed that 48.1% of the sequences were classified as a strong match, 45.3% as nominal and 6.6% as a weak match. Among the ESTs with known putative function, 26.4% ESTs were found to be related to all kinds of metabolisms, 19.3% ESTs to information storage and processing, 11.3% ESTs to posttranslational modification, protein turnover, chaperones, 11.3% ESTs to transport, 9.9% ESTs to signal transducer/cell communication, 9.0% ESTs to structure protein, 3.8% ESTs to cell cycle, and only 6.6% ESTs classified as novel genes. By EST sequencing, a full-length gene coding ferritin was identified and characterized. The recombinant plasmid pET32a-TAT-Ferritin was constructed, coded for the TAT-Ferritin fusion protein with two 6× His-tags in N and C-terminal. After BCA assay, the concentration of soluble Trx-TAT-Ferritin recombinant protein was 2.32 ± 0.12 mg/mL. These results demonstrated that the reliability and representativeness of the cDNA library attained to the requirements of a standard cDNA library. This library provided a useful platform for the functional genome and transcriptome research of Bengal tigers.

  2. Purification, crystallization and preliminary X-ray crystallographic analysis of the ETS domain of human Ergp55 in complex with the cfos promoter DNA sequence

    International Nuclear Information System (INIS)

    Gangwar, Shanti P.; Meena, Sita R.; Saxena, Ajay K.

    2012-01-01

    The ETS domain of human Ergp55 was purified and crystallized in native, complexes with E74, and cfos promoter DNA sequences. The X-ray intensity data set was collected on ETS–cfos promoter DNA complex crystal at 3.1 Å resolution to analyze the structure by molecular replacement technique. The Ergp55 protein belongs to the Ets family of transciption factors. The Ets transcription factors are involved in various developmental processes and the regulation of cancer metabolism. They contain a highly similar DNA-binding domain known as the ETS domain and have diverse functions in oncogenesis and physiology. The Ets transcription factors differ in their DNA-binding preference at the ETS site and the mechanisms by which they target genes are not clearly understood. To understand its DNA-binding mechanism, the ETS domain of Ergp55 was expressed and purified. The ETS domain was crystallized in the native form and in complex forms with DNA sequences from the E74 and cfos promoters. An X-ray diffraction data set was collected from an ETS–cfos DNA complex crystal at a wavelength of 0.9725 Å on the BM14 synchrotron beamline at the ESRF, France. The ETS–cfos DNA complex crystal belonged to space group C222 1 , with four molecules in the asymmetric unit. For structure analysis, initial phases for the ETS–cfos DNA complex were obtained by the molecular-replacement technique with Phaser in the CCP4 suite using the coordinates of Fli-1 protein and cfos DNA as search models. Structure analysis of the ETS–cfos DNA complex may possibly explain the DNA-binding specificity and its mechanism of interaction with the ETS domain of Ergp55

  3. Effects of UVA1 Phototherapy on Expression of Human Endogenous Retroviral Sequence (HERV)-K10 gag in Morphea: A Preliminary Study.

    Science.gov (United States)

    Kowalczyk, Michał Jacek; Teresiak-Mikołajczak, Ewa; Dańczak-Pazdrowska, Aleksandra; Żaba, Ryszard; Adamski, Zygmunt; Osmola-Mańkowska, Agnieszka

    2017-01-28

    BACKGROUND Morphea, also known as localized scleroderma, is a rare autoimmune connective tissue disease characterized by skin fibrosis. UVA1 phototherapy is an important asset in the reduction of clinical manifestations in morphea. There are studies claiming that UV light modulates the expression of some human endogenous retroviral sequences. The aim of this study was to determine if the expression of HERV-K10 gag element is lowered by UVA1 phototherapy in morphea, a disease in which such irradiation has a soothing effect. MATERIAL AND METHODS The expression levels of the HERV-K10 gag were assessed by real-time PCR (polymerase chain reaction) in peripheral blood mononuclear cells (PBMC) and skin-punch biopsies of healthy volunteers and 9 morphea patients before and after phototherapy. Additionally, correlations between the HERV-K10 gag expression and age, disease duration, the Localized Scleroderma Skin Severity Index (LoSSI), and antinuclear antibody (ANA) titers were assessed. RESULTS In PBMC, HERV-K10 gag mRNA was significantly elevated after UVA1 phototherapy compared to healthy controls. Most of the patients responded with an increased expression level of this sequence. However, we found no statistical evidence at this point that phototherapy indeed has an effect on the HERV-K10 gag expression (there were no statistical differences in PBMC of morphea patients before and after phototherapy). Similarly, there was no statistically relevant effect of the UVA1 on the expression of HERV-K10 gag in skin. CONCLUSIONS At this point, the effect of UVA1 phototherapy on the expression of HERV-K10 gag cannot be statistically confirmed.

  4. Complete amino-acid sequence, crystallization and preliminary X-ray diffraction studies of leucurolysin-a, a nonhaemorrhagic metalloproteinase from Bothrops leucurus snake venom

    International Nuclear Information System (INIS)

    Ferreira, Rodrigo Novaes; Rates, Breno; Richardson, Michael; Guimarães, Beatriz Gomes; Sanchez, Eládio Oswaldo Flores; Castro Pimenta, Adriano Monteiro de; Nagem, Ronaldo Alves Pinto

    2009-01-01

    Leucurolysin-a, a nonhaemorrhagic metalloproteinase from B. leucurus snake venom, has been crystallized in a free form and in a complexed form. Leucurolysin-a (leuc-a) is a class P-I snake-venom metalloproteinase isolated from the venom of the South American snake Bothrops leucurus (white-tailed jararaca). The mature protein is composed of 202 amino-acid residues in a single polypeptide chain. It contains a blocked N-terminus and is not glycosylated. In vitro studies revealed that leuc-a dissolves clots made either from purified fibrinogen or from whole blood. Unlike some other venom fibrinolytic metalloproteinases, leuc-a has no haemorrhagic activity. Leuc-a was sequenced and was crystallized using the hanging-drop vapour-diffusion technique. Crystals were obtained using PEG 6000 or PEG 1500. Diffraction data to 1.80 and 1.60 Å resolution were collected from two crystals (free enzyme and the endogenous ligand–protein complex, respectively). They both belonged to space group P2 1 2 1 2 1 , with very similar unit-cell parameters (a = 44.0, b = 56.2, c = 76.3 Å for the free-enzyme crystal)

  5. The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

    Directory of Open Access Journals (Sweden)

    Volckaert Filip AM

    2010-01-01

    Full Text Available Abstract Background Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model. Results End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690 were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome. Conclusions The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.

  6. Draft Sequencing of the Heterozygous Diploid Genome of Satsuma (Citrus unshiu Marc. Using a Hybrid Assembly Approach

    Directory of Open Access Journals (Sweden)

    Tokurou Shimizu

    2017-12-01

    Full Text Available Satsuma (Citrus unshiu Marc. is one of the most abundantly produced mandarin varieties of citrus, known for its seedless fruit production and as a breeding parent of citrus. De novo assembly of the heterozygous diploid genome of Satsuma (“Miyagawa Wase” was conducted by a hybrid assembly approach using short-read sequences, three mate-pair libraries, and a long-read sequence of PacBio by the PLATANUS assembler. The assembled sequence, with a total size of 359.7 Mb at the N50 length of 386,404 bp, consisted of 20,876 scaffolds. Pseudomolecules of Satsuma constructed by aligning the scaffolds to three genetic maps showed genome-wide synteny to the genomes of Clementine, pummelo, and sweet orange. Gene prediction by modeling with MAKER-P proposed 29,024 genes and 37,970 mRNA; additionally, gene prediction analysis found candidates for novel genes in several biosynthesis pathways for gibberellin and violaxanthin catabolism. BUSCO scores for the assembled scaffold and predicted transcripts, and another analysis by BAC end sequence mapping indicated the assembled genome consistency was close to those of the haploid Clementine, pummel, and sweet orange genomes. The number of repeat elements and long terminal repeat retrotransposon were comparable to those of the seven citrus genomes; this suggested no significant failure in the assembly at the repeat region. A resequencing application using the assembled sequence confirmed that both kunenbo-A and Satsuma are offsprings of Kishu, and Satsuma is a back-crossed offspring of Kishu. These results illustrated the performance of the hybrid assembly approach and its ability to construct an accurate heterozygous diploid genome.

  7. Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers

    Science.gov (United States)

    Kamphuis, Lars G; Hane, James K; Nelson, Matthew N; Gao, Lingling; Atkins, Craig A; Singh, Karam B

    2015-01-01

    Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is an important grain legume crop that is valuable for sustainable farming and is becoming recognized as a human health food. NLL breeding is directed at improving grain production, disease resistance, drought tolerance and health benefits. However, genetic and genomic studies have been hindered by a lack of extensive genomic resources for the species. Here, the generation, de novo assembly and annotation of transcriptome datasets derived from five different NLL tissue types of the reference accession cv. Tanjil are described. The Tanjil transcriptome was compared to transcriptomes of an early domesticated cv. Unicrop, a wild accession P27255, as well as accession 83A:476, together being the founding parents of two recombinant inbred line (RIL) populations. In silico predictions for transcriptome-derived gene-based length and SNP polymorphic markers were conducted and corroborated using a survey assembly sequence for NLL cv. Tanjil. This yielded extensive indel and SNP polymorphic markers for the two RIL populations. A total of 335 transcriptome-derived markers and 66 BAC-end sequence-derived markers were evaluated, and 275 polymorphic markers were selected to genotype the reference NLL 83A:476 × P27255 RIL population. This significantly improved the completeness, marker density and quality of the reference NLL genetic map. PMID:25060816

  8. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

    Directory of Open Access Journals (Sweden)

    King Graham J

    2010-10-01

    Full Text Available Abstract Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola. Results In this study, we identified over 23,000 simple sequence repeats (SSRs from 536 sequenced BACs. 890 SSR markers (designated as BrGMS were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH. Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs, 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species.

  9. Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey.

    Science.gov (United States)

    Luo, Meizhong; Kim, Hyeran; Kudrna, Dave; Sisneros, Nicholas B; Lee, So-Jeong; Mueller, Christopher; Collura, Kristi; Zuccolo, Andrea; Buckingham, E Bryan; Grim, Suzanne M; Yanagiya, Kazuyo; Inoko, Hidetoshi; Shiina, Takashi; Flajnik, Martin F; Wing, Rod A; Ohta, Yuko

    2006-05-03

    Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 x 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6-28 primary positive clones per probe of which 50-90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

  10. Construction of a nurse shark (Ginglymostoma cirratum bacterial artificial chromosome (BAC library and a preliminary genome survey

    Directory of Open Access Journals (Sweden)

    Inoko Hidetoshi

    2006-05-01

    Full Text Available Abstract Background Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. Aims In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC library for the nurse shark, Ginglymostoma cirratum. Results The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 × 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6–28 primary positive clones per probe of which 50–90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. Conclusion We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.

  11. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  12. 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...

  13. Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes

    Czech Academy of Sciences Publication Activity Database

    Garbus, I.; Romero, J.R.; Valárik, Miroslav; Vanžurová, Hana; Karafiátová, Miroslava; Doležel, Jaroslav; Tranquilli, G.; Helguera, M.; Echenique, V.

    2015-01-01

    Roč. 16, MAY 12 (2015) ISSN 1471-2164 Institutional support: RVO:61389030 Keywords : VIRTUAL GENE ORDER * BAC END SEQUENCES * NEXT-GENERATION Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.867, year: 2015

  14. Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

    Science.gov (United States)

    2011-01-01

    Background Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecular genetic manipulations and lines of research. The generation of genomic resources for these microbes is leading to novel insights into biology such as interactions with the hosts and guiding directions for breakthrough research in plant pathology. Results To support gene discovery and gene model verification in the genome of the wheat leaf rust fungus, Puccinia triticina (Pt), we have generated Expressed Sequence Tags (ESTs) by sampling several life cycle stages. We focused on several spore stages and isolated haustorial structures from infected wheat, generating 17,684 ESTs. We produced sequences from both the sexual (pycniospores, aeciospores and teliospores) and asexual (germinated urediniospores) stages of the life cycle. From pycniospores and aeciospores, produced by infecting the alternate host, meadow rue (Thalictrum speciosissimum), 4,869 and 1,292 reads were generated, respectively. We generated 3,703 ESTs from teliospores produced on the senescent primary wheat host. Finally, we generated 6,817 reads from haustoria isolated from infected wheat as well as 1,003 sequences from germinated urediniospores. Along with 25,558 previously generated ESTs, we compiled a database of 13,328 non-redundant sequences (4,506 singlets and 8,822 contigs). Fungal genes were predicted using the EST version of the self-training GeneMarkS algorithm. To refine the EST database, we compared EST sequences by BLASTN to a set of 454 pyrosequencing-generated contigs and Sanger BAC-end sequences derived both from the Pt genome, and to ESTs and genome reads from wheat. A collection of 6,308 fungal genes was identified and compared to sequences of the cereal rusts, Puccinia graminis f. sp. tritici (Pgt) and stripe rust, P. striiformis f. sp. tritici (Pst), and poplar

  15. Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

    Directory of Open Access Journals (Sweden)

    Wynhoven Brian

    2011-03-01

    Full Text Available Abstract Background Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecular genetic manipulations and lines of research. The generation of genomic resources for these microbes is leading to novel insights into biology such as interactions with the hosts and guiding directions for breakthrough research in plant pathology. Results To support gene discovery and gene model verification in the genome of the wheat leaf rust fungus, Puccinia triticina (Pt, we have generated Expressed Sequence Tags (ESTs by sampling several life cycle stages. We focused on several spore stages and isolated haustorial structures from infected wheat, generating 17,684 ESTs. We produced sequences from both the sexual (pycniospores, aeciospores and teliospores and asexual (germinated urediniospores stages of the life cycle. From pycniospores and aeciospores, produced by infecting the alternate host, meadow rue (Thalictrum speciosissimum, 4,869 and 1,292 reads were generated, respectively. We generated 3,703 ESTs from teliospores produced on the senescent primary wheat host. Finally, we generated 6,817 reads from haustoria isolated from infected wheat as well as 1,003 sequences from germinated urediniospores. Along with 25,558 previously generated ESTs, we compiled a database of 13,328 non-redundant sequences (4,506 singlets and 8,822 contigs. Fungal genes were predicted using the EST version of the self-training GeneMarkS algorithm. To refine the EST database, we compared EST sequences by BLASTN to a set of 454 pyrosequencing-generated contigs and Sanger BAC-end sequences derived both from the Pt genome, and to ESTs and genome reads from wheat. A collection of 6,308 fungal genes was identified and compared to sequences of the cereal rusts, Puccinia graminis f. sp. tritici (Pgt and stripe rust, P. striiformis f. sp

  16. Preliminary Monthly Climatological Summaries

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Preliminary Local Climatological Data, recorded since 1970 on Weather Burean Form 1030 and then National Weather Service Form F-6. The preliminary climate data pages...

  17. Infinite matrices and sequence spaces

    CERN Document Server

    Cooke, Richard G

    2014-01-01

    This clear and correct summation of basic results from a specialized field focuses on the behavior of infinite matrices in general, rather than on properties of special matrices. Three introductory chapters guide students to the manipulation of infinite matrices, covering definitions and preliminary ideas, reciprocals of infinite matrices, and linear equations involving infinite matrices.From the fourth chapter onward, the author treats the application of infinite matrices to the summability of divergent sequences and series from various points of view. Topics include consistency, mutual consi

  18. Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence.

    Science.gov (United States)

    Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E

    2016-01-01

    It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

  19. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  20. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Sequence Read Archive (SRA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  2. Severe accident sequence assessment for boiling water reactors: program overview

    International Nuclear Information System (INIS)

    Fontana, M.H.

    1980-10-01

    The Severe Accident Sequence Assessment (SASA) Program was started at the Oak Ridge National Laboratory (ORNL) in June 1980. This report documents the initial planning, specification of objectives, potential uses of the results, plan of attack, and preliminary results. ORNL was assigned the Brown's Ferry Unit 1 Plant with the station blackout being the initial sequence set to be addressed. This set includes: (1) loss of offsite and onsite ac power with no coolant injection; and (2) loss of offsite and onsite ac power with high pressure coolant injection (HPCI) and reactor core isolation cooling (RCIC) as long as dc power supply lasts. This report includes representative preliminary results for the former case

  3. Psychrophilic anaerobic digestion of swine manure slurry in sequencing batch reactors

    Energy Technology Data Exchange (ETDEWEB)

    Masse, D.I. [Agriculture Canada, Ottawa, ON (Canada). Food Research Branch; Droste, R.L. [Ottawa Univ., ON (Canada). Dept. of Civil Engineering

    1993-12-31

    This work presents preliminary results of an ongoing laboratory study to evaluate the feasibility of psychrophilic anaerobic digestion in sequencing batch reactors (SBR) for stabilizing, deodorizing and adding value to swine manure. Preliminary results show that the process is feasible. (author). 14 refs., 7 tabs.

  4. Psychrophilic anaerobic digestion of swine manure slurry in sequencing batch reactors

    Energy Technology Data Exchange (ETDEWEB)

    Masse, D I [Agriculture Canada, Ottawa, ON (Canada). Food Research Branch; Droste, R L [Ottawa Univ., ON (Canada). Dept. of Civil Engineering

    1994-12-31

    This work presents preliminary results of an ongoing laboratory study to evaluate the feasibility of psychrophilic anaerobic digestion in sequencing batch reactors (SBR) for stabilizing, deodorizing and adding value to swine manure. Preliminary results show that the process is feasible. (author). 14 refs., 7 tabs.

  5. Nonparametric combinatorial sequence models.

    Science.gov (United States)

    Wauthier, Fabian L; Jordan, Michael I; Jojic, Nebojsa

    2011-11-01

    This work considers biological sequences that exhibit combinatorial structures in their composition: groups of positions of the aligned sequences are "linked" and covary as one unit across sequences. If multiple such groups exist, complex interactions can emerge between them. Sequences of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This article presents a nonparametric prior on sequences which allows combinatorial structures to emerge and which induces a posterior distribution over factorized sequence representations. We carry out experiments on three biological sequence families which indicate that combinatorial structures are indeed present and that combinatorial sequence models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution over sequence representations induced by the prior. By integrating out the posterior, our method compares favorably to leading binding predictors.

  6. A Blumeria graminis f.sp. hordei BAC library - contig building and microsynteny studies

    DEFF Research Database (Denmark)

    Pedersen, C.; Wu, B.; Giese, H.

    2002-01-01

    A bacterial artificial chromosome (BAC) library of Blumeria graminis f.sp. hordei, containing 12,000 clones with an average insert size of 41 kb, was constructed. The library represents about three genome equivalents and BAC-end sequencing showed a high content of repetitive sequences, making...... contigs, at or close to avirulence loci, were constructed. Single nucleotide polymorphism (SNP) markers were developed from BAC-end sequences to link the contigs to the genetic maps. Two other BAC contigs were used to study microsynteny between B. graminis and two other ascomycetes, Neurospora crassa...

  7. Draft genome sequence of Therminicola potens strain JR

    Energy Technology Data Exchange (ETDEWEB)

    Byrne-Bailey, K.G.; Wrighton, K.C.; Melnyk, R.A.; Agbo, P.; Hazen, T.C.; Coates, J.D.

    2010-07-01

    'Thermincola potens' strain JR is one of the first Gram-positive dissimilatory metal-reducing bacteria (DMRB) for which there is a complete genome sequence. Consistent with the physiology of this organism, preliminary annotation revealed an abundance of multiheme c-type cytochromes that are putatively associated with the periplasm and cell surface in a Gram-positive bacterium. Here we report the complete genome sequence of strain JR.

  8. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  9. UVISS preliminary visibility analysis

    DEFF Research Database (Denmark)

    Betto, Maurizio

    1998-01-01

    The goal of this work is to obtain a preliminary assessment of the sky visibility for anastronomical telescope located on the express pallet of the International SpaceStation (ISS)} taking into account the major constraints imposed on the instrument by the ISSattitude and structure. Part of the w......The goal of this work is to obtain a preliminary assessment of the sky visibility for anastronomical telescope located on the express pallet of the International SpaceStation (ISS)} taking into account the major constraints imposed on the instrument by the ISSattitude and structure. Part...... of the work is also to setup the kernel of a software tool for the visibility analysis thatshould be easily expandable to consider more complex strucures for future activities.This analysis is part of the UVISS assessment study and it is meant to provide elementsfor the definition and the selection...

  10. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  11. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  12. Anomaly Detection in Sequences

    Data.gov (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  13. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)

    1991-06-19

    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  14. sequenceMiner algorithm

    Data.gov (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  15. Antares: preliminary demonstrator results

    International Nuclear Information System (INIS)

    Kouchner, A.

    2000-05-01

    The ANTARES collaboration is building an undersea neutrino telescope off Toulon (Mediterranean sea) with effective area ∼ 0.1 km 2 . An extensive study of the site properties has been achieved together with software analysis in order to optimize the performance of the detector. Results are summarized here. An instrumented line, linked to shore for first time via an electro-optical cable, has been immersed late 1999. The preliminary results of this demonstrator line are reported. (author)

  16. Environmental Survey preliminary report

    Energy Technology Data Exchange (ETDEWEB)

    1988-04-01

    This report presents the preliminary findings from the first phase of the Environmental Survey of the United States Department of Energy (DOE) Sandia National Laboratories conducted August 17 through September 4, 1987. The objective of the Survey is to identify environmental problems and areas of environmental risk associated with Sandia National Laboratories-Albuquerque (SNLA). The Survey covers all environmental media and all areas of environmental regulation. It is being performed in accordance with the DOE Environmental Survey Manual. This phase of the Survey involves the review of existing site environmental data, observations of the operations carried on at SNLA, and interviews with site personnel. 85 refs., 49 figs., 48 tabs.

  17. Ruiz Volcano: Preliminary report

    Science.gov (United States)

    Ruiz Volcano, Colombia (4.88°N, 75.32°W). All times are local (= GMT -5 hours).An explosive eruption on November 13, 1985, melted ice and snow in the summit area, generating lahars that flowed tens of kilometers down flank river valleys, killing more than 20,000 people. This is history's fourth largest single-eruption death toll, behind only Tambora in 1815 (92,000), Krakatau in 1883 (36,000), and Mount Pelée in May 1902 (28,000). The following briefly summarizes the very preliminary and inevitably conflicting information that had been received by press time.

  18. OMEGA Upgrade preliminary design

    International Nuclear Information System (INIS)

    Craxton, R.S.

    1989-10-01

    The OMEGA laser system at the Laboratory for Laser Energetics of the University of Rochester is the only major facility in the United States capable of conducting fully diagnosed, direct-drive, spherical implosion experiments. As such, it serves as the national Laser Users Facility, benefiting scientists throughout the country. The University's participation in the National Inertial Confinement Fusion (ICF) program underwent review by a group of experts under the auspices of the National Academy of Sciences (the Happer Committee) in 1985. The Happer Committee recommended that the OMEGA laser be upgraded in energy to 30 kJ. To this end, Congress appropriated $4,000,000 for the preliminary design of the OMEGA Upgrade, spread across FY88 and FY89. This document describes the preliminary design of the OMEGA Upgrade. The proposed enhancements to the existing OMEGA facility will result in a 30-kHJ, 351-nm, 60-beam direct-drive system, with a versatile pulse-shaping facility and a 1%--2% uniformity of target drive. The Upgrade will allow scientists to explore the ignition-scaling regime, and to study target behavior that is hydrodynamically equivalent to that of targets appropriate for a laboratory microfusion facility (LMF). In addition, it will be possible to perform critical interaction experiments with large-scale-length uniformly irradiated plasmas

  19. The convergence of the order sequence and the solution function sequence on fractional partial differential equation

    Science.gov (United States)

    Rusyaman, E.; Parmikanti, K.; Chaerani, D.; Asefan; Irianingsih, I.

    2018-03-01

    One of the application of fractional ordinary differential equation is related to the viscoelasticity, i.e., a correlation between the viscosity of fluids and the elasticity of solids. If the solution function develops into function with two or more variables, then its differential equation must be changed into fractional partial differential equation. As the preliminary study for two variables viscoelasticity problem, this paper discusses about convergence analysis of function sequence which is the solution of the homogenous fractional partial differential equation. The method used to solve the problem is Homotopy Analysis Method. The results show that if given two real number sequences (αn) and (βn) which converge to α and β respectively, then the solution function sequences of fractional partial differential equation with order (αn, βn) will also converge to the solution function of fractional partial differential equation with order (α, β).

  20. TREE STEM RECONSTRUCTION USING VERTICAL FISHEYE IMAGES: A PRELIMINARY STUDY

    Directory of Open Access Journals (Sweden)

    A. Berveglieri

    2016-06-01

    Full Text Available A preliminary study was conducted to assess a tree stem reconstruction technique with panoramic images taken with fisheye lenses. The concept is similar to the Structure from Motion (SfM technique, but the acquisition and data preparation rely on fisheye cameras to generate a vertical image sequence with height variations of the camera station. Each vertical image is rectified to four vertical planes, producing horizontal lateral views. The stems in the lateral view are rectified to the same scale in the image sequence to facilitate image matching. Using bundle adjustment, the stems are reconstructed, enabling later measurement and extraction of several attributes. The 3D reconstruction was performed with the proposed technique and compared with SfM. The preliminary results showed that the stems were correctly reconstructed by using the lateral virtual images generated from the vertical fisheye images and with the advantage of using fewer images and taken from one single station.

  1. A set of BAC clones spanning the human genome.

    NARCIS (Netherlands)

    Krzywinski, M.; Bosdet, I.; Smailus, D.; Chiu, R.; Mathewson, C.; Wye, N.; Barber, S.; Brown-John, M.; Chan, S.; Chand, S.; Cloutier, A.; Girn, N.; Lee, D.; Masson, A.; Mayo, M.; Olson, T.; Pandoh, P.; Prabhu, A.L.; Schoenmakers, E.F.P.M.; Tsai, M.Y.; Albertson, D.; Lam, W.W.; Choy, C.O.; Osoegawa, K.; Zhao, S.; Jong, P.J. de; Schein, J.; Jones, S.; Marra, M.A.

    2004-01-01

    Using the human bacterial artificial chromosome (BAC) fingerprint-based physical map, genome sequence assembly and BAC end sequences, we have generated a fingerprint-validated set of 32 855 BAC clones spanning the human genome. The clone set provides coverage for at least 98% of the human

  2. Sequences for Student Investigation

    Science.gov (United States)

    Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette

    2004-01-01

    We describe two classes of sequences that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first sequence is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…

  3. Preliminary rail access study

    International Nuclear Information System (INIS)

    1990-01-01

    The Yucca Mountain site, located on the southwestern edge of the Nevada Test Site, is an undeveloped area under investigation as a potential site for nuclear waste disposal by the US Department of Energy. The site currently lacks rail service and an existing rail right-of-way. If the site is suitable and selected for development as a disposal site, rail service is desirable to the Office of Civilian Radioactive Waste Management Program because of the potential of rail to reduce number of shipments and costs relative to highway transportation. This preliminary report is a summary of progress to date for activities to identify and evaluate potential rail options from major rail carriers in the region to the Yucca Mountain site. It is currently anticipated that the rail spur will be operational after the year 2000. 9 refs., 13 figs., 2 tabs

  4. Sequence History Update Tool

    Science.gov (United States)

    Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris

    2008-01-01

    The Sequence History Update Tool performs Web-based sequence statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of sequencing conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The Sequence History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the sequence commanding for MRO.

  5. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-10-05

    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  6. Mapping sequences by parts

    Directory of Open Access Journals (Sweden)

    Guziolowski Carito

    2007-09-01

    Full Text Available Abstract Background: We present the N-map method, a pairwise and asymmetrical approach which allows us to compare sequences by taking into account evolutionary events that produce shuffled, reversed or repeated elements. Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores. Results: We introduce an algorithm computing an optimal N-map with time complexity O (|s| × |t| × N using O (|s| × |t| × N memory space. Among all the numbers of parts taken in a reasonable range, we select the value N for which the optimal N-map has the most significant score. To evaluate this significance, we study the empirical distributions of the scores of optimal N-maps and show that they can be approximated by normal distributions with a reasonable accuracy. We test the functionality of the approach over random sequences on which we apply artificial evolutionary events. Practical Application: The method is illustrated with four case studies of pairs of sequences involving non-standard evolutionary events.

  7. The Colliding Beams Sequencer

    International Nuclear Information System (INIS)

    Johnson, D.E.; Johnson, R.P.

    1989-01-01

    The Colliding Beam Sequencer (CBS) is a computer program used to operate the pbar-p Collider by synchronizing the applications programs and simulating the activities of the accelerator operators during filling and storage. The Sequencer acts as a meta-program, running otherwise stand alone applications programs, to do the set-up, beam transfers, acceleration, low beta turn on, and diagnostics for the transfers and storage. The Sequencer and its operational performance will be described along with its special features which include a periodic scheduler and command logger. 14 refs., 3 figs

  8. Phylogenetic Trees From Sequences

    Science.gov (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  9. Transcriptome sequencing of the Microarray Quality Control (MAQC RNA reference samples using next generation sequencing

    Directory of Open Access Journals (Sweden)

    Thierry-Mieg Danielle

    2009-06-01

    Full Text Available Abstract Background Transcriptome sequencing using next-generation sequencing platforms will soon be competing with DNA microarray technologies for global gene expression analysis. As a preliminary evaluation of these promising technologies, we performed deep sequencing of cDNA synthesized from the Microarray Quality Control (MAQC reference RNA samples using Roche's 454 Genome Sequencer FLX. Results We generated more that 3.6 million sequence reads of average length 250 bp for the MAQC A and B samples and introduced a data analysis pipeline for translating cDNA read counts into gene expression levels. Using BLAST, 90% of the reads mapped to the human genome and 64% of the reads mapped to the RefSeq database of well annotated genes with e-values ≤ 10-20. We measured gene expression levels in the A and B samples by counting the numbers of reads that mapped to individual RefSeq genes in multiple sequencing runs to evaluate the MAQC quality metrics for reproducibility, sensitivity, specificity, and accuracy and compared the results with DNA microarrays and Quantitative RT-PCR (QRTPCR from the MAQC studies. In addition, 88% of the reads were successfully aligned directly to the human genome using the AceView alignment programs with an average 90% sequence similarity to identify 137,899 unique exon junctions, including 22,193 new exon junctions not yet contained in the RefSeq database. Conclusion Using the MAQC metrics for evaluating the performance of gene expression platforms, the ExpressSeq results for gene expression levels showed excellent reproducibility, sensitivity, and specificity that improved systematically with increasing shotgun sequencing depth, and quantitative accuracy that was comparable to DNA microarrays and QRTPCR. In addition, a careful mapping of the reads to the genome using the AceView alignment programs shed new light on the complexity of the human transcriptome including the discovery of thousands of new splice variants.

  10. Gomphid DNA sequence data

    Data.gov (United States)

    U.S. Environmental Protection Agency — DNA sequence data for several genetic loci. This dataset is not publicly accessible because: It's already publicly available on GenBank. It can be accessed through...

  11. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  12. Dynamic Sequence Assignment.

    Science.gov (United States)

    1983-12-01

    D-136 548 DYNAMIIC SEQUENCE ASSIGNMENT(U) ADVANCED INFORMATION AND 1/2 DECISION SYSTEMS MOUNTAIN YIELW CA C A 0 REILLY ET AL. UNCLSSIIED DEC 83 AI/DS...I ADVANCED INFORMATION & DECISION SYSTEMS Mountain View. CA 94040 84 u ,53 V,..’. Unclassified _____ SCURITY CLASSIFICATION OF THIS PAGE REPORT...reviews some important heuristic algorithms developed for fas- ter solution of the sequence assignment problem. 3.1. DINAMIC MOGRAMUNIG FORMULATION FOR

  13. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2010-12-31

    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.

  14. General LTE Sequence

    OpenAIRE

    Billal, Masum

    2015-01-01

    In this paper,we have characterized sequences which maintain the same property described in Lifting the Exponent Lemma. Lifting the Exponent Lemma is a very powerful tool in olympiad number theory and recently it has become very popular. We generalize it to all sequences that maintain a property like it i.e. if p^{\\alpha}||a_k and p^\\b{eta}||n, then p^{{\\alpha}+\\b{eta}}||a_{nk}.

  15. A PRELIMINARY JUPITER MODEL

    International Nuclear Information System (INIS)

    Hubbard, W. B.; Militzer, B.

    2016-01-01

    In anticipation of new observational results for Jupiter's axial moment of inertia and gravitational zonal harmonic coefficients from the forthcoming Juno orbiter, we present a number of preliminary Jupiter interior models. We combine results from ab initio computer simulations of hydrogen–helium mixtures, including immiscibility calculations, with a new nonperturbative calculation of Jupiter's zonal harmonic coefficients, to derive a self-consistent model for the planet's external gravity and moment of inertia. We assume helium rain modified the interior temperature and composition profiles. Our calculation predicts zonal harmonic values to which measurements can be compared. Although some models fit the observed (pre-Juno) second- and fourth-order zonal harmonics to within their error bars, our preferred reference model predicts a fourth-order zonal harmonic whose absolute value lies above the pre-Juno error bars. This model has a dense core of about 12 Earth masses and a hydrogen–helium-rich envelope with approximately three times solar metallicity

  16. A PRELIMINARY JUPITER MODEL

    Energy Technology Data Exchange (ETDEWEB)

    Hubbard, W. B. [Lunar and Planetary Laboratory, The University of Arizona, Tucson, AZ 85721 (United States); Militzer, B. [Department of Earth and Planetary Science, Department of Astronomy, University of California, Berkeley, CA 94720 (United States)

    2016-03-20

    In anticipation of new observational results for Jupiter's axial moment of inertia and gravitational zonal harmonic coefficients from the forthcoming Juno orbiter, we present a number of preliminary Jupiter interior models. We combine results from ab initio computer simulations of hydrogen–helium mixtures, including immiscibility calculations, with a new nonperturbative calculation of Jupiter's zonal harmonic coefficients, to derive a self-consistent model for the planet's external gravity and moment of inertia. We assume helium rain modified the interior temperature and composition profiles. Our calculation predicts zonal harmonic values to which measurements can be compared. Although some models fit the observed (pre-Juno) second- and fourth-order zonal harmonics to within their error bars, our preferred reference model predicts a fourth-order zonal harmonic whose absolute value lies above the pre-Juno error bars. This model has a dense core of about 12 Earth masses and a hydrogen–helium-rich envelope with approximately three times solar metallicity.

  17. Pairwise Sequence Alignment Library

    Energy Technology Data Exchange (ETDEWEB)

    2015-05-20

    Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

  18. Pickering safeguards: a preliminary analysis

    International Nuclear Information System (INIS)

    Todd, J.L.; Hodgkinson, J.G.

    1977-05-01

    A summary is presented of thoughts relative to a systems approach for implementing international safeguards. Included is a preliminary analysis of the Pickering Generating Station followed by a suggested safeguards system for the facility

  19. Cell emulation and preliminary results.

    Science.gov (United States)

    2016-07-01

    This report details preliminary results of the testing plan implemented by the Hawaii Natural Energy Institute to evaluate Electric Vehicle (EV) battery durability and reliability under electric utility grid operations. Commercial EV battery cells ar...

  20. Laser mass spectrometry for DNA sequencing, disease diagnosis, and fingerprinting

    Energy Technology Data Exchange (ETDEWEB)

    Winston Chen, C.H.; Taranenko, N.I.; Zhu, Y.F.; Chung, C.N.; Allman, S.L.

    1997-03-01

    Since laser mass spectrometry has the potential for achieving very fast DNA analysis, the authors recently applied it to DNA sequencing, DNA typing for fingerprinting, and DNA screening for disease diagnosis. Two different approaches for sequencing DNA have been successfully demonstrated. One is to sequence DNA with DNA ladders produced from Snager`s enzymatic method. The other is to do direct sequencing without DNA ladders. The need for quick DNA typing for identification purposes is critical for forensic application. The preliminary results indicate laser mass spectrometry can possibly be used for rapid DNA fingerprinting applications at a much lower cost than gel electrophoresis. Population screening for certain genetic disease can be a very efficient step to reducing medical costs through prevention. Since laser mass spectrometry can provide very fast DNA analysis, the authors applied laser mass spectrometry to disease diagnosis. Clinical samples with both base deletion and point mutation have been tested with complete success.

  1. PRELIMINARY SELECTION OF MGR DESIGN BASIS EVENTS

    International Nuclear Information System (INIS)

    Kappes, J.A.

    1999-01-01

    The purpose of this analysis is to identify the preliminary design basis events (DBEs) for consideration in the design of the Monitored Geologic Repository (MGR). For external events and natural phenomena (e.g., earthquake), the objective is to identify those initiating events that the MGR will be designed to withstand. Design criteria will ensure that radiological release scenarios resulting from these initiating events are beyond design basis (i.e., have a scenario frequency less than once per million years). For internal (i.e., human-induced and random equipment failures) events, the objective is to identify credible event sequences that result in bounding radiological releases. These sequences will be used to establish the design basis criteria for MGR structures, systems, and components (SSCs) design basis criteria in order to prevent or mitigate radiological releases. The safety strategy presented in this analysis for preventing or mitigating DBEs is based on the preclosure safety strategy outlined in ''Strategy to Mitigate Preclosure Offsite Exposure'' (CRWMS M andO 1998f). DBE analysis is necessary to provide feedback and requirements to the design process, and also to demonstrate compliance with proposed 10 CFR 63 (Dyer 1999b) requirements. DBE analysis is also required to identify and classify the SSCs that are important to safety (ITS)

  2. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.; Bonny, Talal; Salama, Khaled N.

    2012-01-01

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  3. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed A.

    2012-01-26

    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  4. Main sequence mass loss

    International Nuclear Information System (INIS)

    Brunish, W.M.; Guzik, J.A.; Willson, L.A.; Bowen, G.

    1987-01-01

    It has been hypothesized that variable stars may experience mass loss, driven, at least in part, by oscillations. The class of stars we are discussing here are the δ Scuti variables. These are variable stars with masses between about 1.2 and 2.25 M/sub θ/, lying on or very near the main sequence. According to this theory, high rotation rates enhance the rate of mass loss, so main sequence stars born in this mass range would have a range of mass loss rates, depending on their initial rotation velocity and the amplitude of the oscillations. The stars would evolve rapidly down the main sequence until (at about 1.25 M/sub θ/) a surface convection zone began to form. The presence of this convective region would slow the rotation, perhaps allowing magnetic braking to occur, and thus sharply reduce the mass loss rate. 7 refs

  5. Functional features of a single chromosome arm in wheat (1AL) determined from its structure

    Czech Academy of Sciences Publication Activity Database

    Lucas, S. J.; Šimková, Hana; Šafář, Jan; Jurman, I.; Cattonaro, F.; Vautrin, S.; Bellec, A.; Berges, H.; Doležel, Jaroslav; Budak, H.

    2012-01-01

    Roč. 12, č. 1 (2012), s. 173-182 ISSN 1438-793X Institutional research plan: CEZ:AV0Z50380511 Keywords : Wheat * A genome * BAC end sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.292, year: 2012

  6. A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome

    Czech Academy of Sciences Publication Activity Database

    Parlange, Z.; Oberhaensli, S.; Breen, J.; Platzer, M.; Taudien, S.; Šimková, Hana; Wicker, T.; Doležel, Jaroslav; Keller, B.

    2011-01-01

    Roč. 11, č. 4 (2011), s. 671-677 ISSN 1438-793X R&D Projects: GA MŠk ED0007/01/01 Institutional research plan: CEZ:AV0Z50380511 Keywords : Blumeria graminis * BAC library * BAC-end sequences Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.842, year: 2011

  7. Electricity sequence control

    International Nuclear Information System (INIS)

    Shin, Heung Ryeol

    2010-03-01

    The contents of the book are introduction of control system, like classification and control signal, introduction of electricity power switch, such as push-button and detection switch sensor for induction type and capacitance type machinery for control, solenoid valve, expression of sequence and type of electricity circuit about using diagram, time chart, marking and term, logic circuit like Yes, No, and, or and equivalence logic, basic electricity circuit, electricity sequence control, added condition, special program control about choice and jump of program, motor control, extra circuit on repeat circuit, pause circuit in a conveyer, safety regulations and rule about classification of electricity disaster and protective device for insulation.

  8. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    , Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  9. ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS

    Directory of Open Access Journals (Sweden)

    Alves-Ferreira Marcelo

    2008-09-01

    Full Text Available Abstract Background Genome survey sequences (GSS offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation of the nature, quantity and variability of repetitive sequences very early in a genome sequencing project is of considerable importance, as such data strongly influence the estimation of genome coverage, library quality and progress in scaffold construction. Also, the elimination of repetitive sequences from the initial assembly process is important to avoid errors and unnecessary complexity. Repetitive sequences are also of interest in a variety of other studies, for instance as molecular markers. Results We designed and implemented a straightforward pipeline called ReRep, which combines bioinformatics tools for identifying repetitive structures in a GSS dataset. In a case study, we first applied the pipeline to a set of 970 GSSs, sequenced in our laboratory from the human pathogen Leishmania braziliensis, the causative agent of leishmaniosis, an important public health problem in Brazil. We also verified the applicability of ReRep to new sequencing technologies using a set of 454-reads of an Escheria coli. The behaviour of several parameters in the algorithm is evaluated and suggestions are made for tuning of the analysis. Conclusion The ReRep approach for identification of repetitive elements in GSS datasets proved to be straightforward and efficient. Several potential repetitive sequences were found in a L. braziliensis GSS dataset generated in our laboratory, and further validated by the analysis of a more complete genomic dataset from the EMBL and Sanger Centre databases. ReRep also identified most of the E. coli K12 repeats prior to assembly in an example dataset obtained by automated sequencing using 454 technology. The parameters controlling the algorithm behaved consistently and may be tuned to the properties

  10. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene...

  11. THE RHIC SEQUENCER

    International Nuclear Information System (INIS)

    VAN ZEIJTS, J.; DOTTAVIO, T.; FRAK, B.; MICHNOFF, R.

    2001-01-01

    The Relativistic Heavy Ion Collider (RHIC) has a high level asynchronous time-line driven by a controlling program called the ''Sequencer''. Most high-level magnet and beam related issues are orchestrated by this system. The system also plays an important task in coordinated data acquisition and saving. We present the program, operator interface, operational impact and experience

  12. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke

    2014-01-01

    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak

  13. simple sequence repeat (SSR)

    African Journals Online (AJOL)

    In the present study, 78 mapped simple sequence repeat (SSR) markers representing 11 linkage groups of adzuki bean were evaluated for transferability to mungbean and related Vigna spp. 41 markers amplified characteristic bands in at least one Vigna species. The transferability percentage across the genotypes ranged ...

  14. A preliminary assessment of the true morels (Morchella) in Newfoundland and Labrador

    Science.gov (United States)

    A preliminary assessment of true morels (Morchella) from Newfoundland and Labrador (NL) was obtained by using DNA sequence data from portions of three genes to identify 20 collections from Newfoundland and one from a remote location in Labrador. To place this work in a broader context, data on 25 co...

  15. A Snapshot of the Emerging Tomato Genome Sequence

    Directory of Open Access Journals (Sweden)

    Lukas A. Mueller

    2009-03-01

    Full Text Available The genome of tomato ( L. is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy, and the United States as part of the larger “International Solanaceae Genome Project (SOL: Systems Approach to Diversity and Adaptation” initiative. The tomato genome sequencing project uses an ordered bacterial artificial chromosome (BAC approach to generate a high-quality tomato euchromatic genome sequence for use as a reference genome for the Solanaceae and euasterids. Sequence is deposited at GenBank and at the SOL Genomics Network (SGN. Currently, there are around 1000 BACs finished or in progress, representing more than a third of the projected euchromatic portion of the genome. An annotation effort is also underway by the International Tomato Annotation Group. The expected number of genes in the euchromatin is ∼40,000, based on an estimate from a preliminary annotation of 11% of finished sequence. Here, we present this first snapshot of the emerging tomato genome and its annotation, a short comparison with potato ( L. sequence data, and the tools available for the researchers to exploit this new resource are also presented. In the future, whole-genome shotgun techniques will be combined with the BAC-by-BAC approach to cover the entire tomato genome. The high-quality reference euchromatic tomato sequence is expected to be near completion by 2010.

  16. Targeted sequencing of plant genomes

    Science.gov (United States)

    Mark D. Huynh

    2014-01-01

    Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, wholegenome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-...

  17. Almost convergence of triple sequences

    OpenAIRE

    Ayhan Esi; M.Necdet Catalbas

    2013-01-01

    In this paper we introduce and study the concepts of almost convergence and almost Cauchy for triple sequences. Weshow that the set of almost convergent triple sequences of 0's and 1's is of the first category and also almost everytriple sequence of 0's and 1's is not almost convergent.Keywords: almost convergence, P-convergent, triple sequence.

  18. A few Smarandache Integer Sequences

    OpenAIRE

    Ibstedt, Henry

    2010-01-01

    This paper deals with the analysis of a few Smarandache Integer Sequences which first appeared in Properties or the Numbers, F. Smarandache, University or Craiova Archives, 1975. The first four sequences are recurrence generated sequences while the last three are concatenation sequences.

  19. Preliminary design county plan Zeeland

    International Nuclear Information System (INIS)

    1987-01-01

    The preliminary design 'Streekplan Zeeland' (Country plan Zeeland, with regard to the location of additional nuclear power plants in Zeeland, the Netherlands) has passed through a consultation and participation round. Thereupon 132 reactions have been received. These have been incorporated and answered in two notes. This proposal deals with the principal points of the preliminary design and treats also the remarks of the committees Environmental (town and country) Planning (RO), Provincial (town and country) Planning Committee (PPC) and Association of Communities of Zeeland (VZG), on the reply notes. The preliminary design with the modifications, collected in appendix 3, is proposed to be the starting point in the drawing-up of the design-country-plan. This design subsequently will pass the formal country-plan procedure. (author). 1 fig

  20. Whole genome sequence analysis of Mycobacterium suricattae

    KAUST Repository

    Dippenaar, Anzaan; Parsons, Sven David Charles; Sampson, Samantha Leigh; Van Der Merwe, Ruben Gerhard; Drewe, Julian Ashley; Abdallah, Abdallah; Siame, Kabengele Keith; Gey Van Pittius, Nicolaas Claudius; Van Helden, Paul David; Pain, Arnab; Warren, Robin Mark

    2015-01-01

    Tuberculosis occurs in various mammalian hosts and is caused by a range of different lineages of the Mycobacterium tuberculosis complex (MTBC). A recently described member, Mycobacterium suricattae, causes tuberculosis in meerkats (Suricata suricatta) in Southern Africa and preliminary genetic analysis showed this organism to be closely related to an MTBC pathogen of rock hyraxes (Procavia capensis), the dassie bacillus. Here we make use of whole genome sequencing to describe the evolution of the genome of M. suricattae, including known and novel regions of difference, SNPs and IS6110 insertion sites. We used genome-wide phylogenetic analysis to show that M. suricattae clusters with the chimpanzee bacillus, previously isolated from a chimpanzee (Pan troglodytes) in West Africa. We propose an evolutionary scenario for the Mycobacterium africanum lineage 6 complex, showing the evolutionary relationship of M. africanum and chimpanzee bacillus, and the closely related members M. suricattae, dassie bacillus and Mycobacterium mungi.

  1. Whole genome sequence analysis of Mycobacterium suricattae

    KAUST Repository

    Dippenaar, Anzaan

    2015-10-21

    Tuberculosis occurs in various mammalian hosts and is caused by a range of different lineages of the Mycobacterium tuberculosis complex (MTBC). A recently described member, Mycobacterium suricattae, causes tuberculosis in meerkats (Suricata suricatta) in Southern Africa and preliminary genetic analysis showed this organism to be closely related to an MTBC pathogen of rock hyraxes (Procavia capensis), the dassie bacillus. Here we make use of whole genome sequencing to describe the evolution of the genome of M. suricattae, including known and novel regions of difference, SNPs and IS6110 insertion sites. We used genome-wide phylogenetic analysis to show that M. suricattae clusters with the chimpanzee bacillus, previously isolated from a chimpanzee (Pan troglodytes) in West Africa. We propose an evolutionary scenario for the Mycobacterium africanum lineage 6 complex, showing the evolutionary relationship of M. africanum and chimpanzee bacillus, and the closely related members M. suricattae, dassie bacillus and Mycobacterium mungi.

  2. Space reactor preliminary mechanical design

    International Nuclear Information System (INIS)

    Meier, K.L.

    1983-01-01

    An analysis was performed on the SABRE reactor space power system to determine the effect of the number and size of heat pipes on the design parameters of the nuclear subsystem. Small numbers of thin walled heat pipes were found to give a lower subsystem mass, but excessive fuel swelling resulted. The SP-100 preliminary design uses 120 heat pipes because of acceptable fuel swelling and a minimum nuclear subsystem mass of 1875 kg. Salient features of the reactor preliminary design are: individual fuel modules, ZrO 2 block core mounts, bolted collar fuel module restraints, and a BeO central plug

  3. Technetium removal: preliminary flowsheet options

    International Nuclear Information System (INIS)

    Eager, K.M.

    1995-01-01

    This document presents the results of a preliminary investigation into options for preliminary flowsheets for 99Tc removal from Hanford Site tank waste. A model is created to show the path of 99Tc through pretreatment to disposal. The Tank Waste Remediation (TWRS) flowsheet (Orme 1995) is used as a baseline. Ranges of important inputs to the model are developed, such as 99Tc inventory in the tanks and important splits through the TWRS flowsheet. Several technetium removal options are discussed along with sensitivities of the removal schemes to important model parameters

  4. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

    Byrne, Stephen; Farrell, Jacqueline Danielle; Asp, Torben

    2013-01-01

    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information....

  5. Multilocus Sequence Typing

    OpenAIRE

    Belén, Ana; Pavón, Ibarz; Maiden, Martin C.J.

    2009-01-01

    Multilocus sequence typing (MLST) was first proposed in 1998 as a typing approach that enables the unambiguous characterization of bacterial isolates in a standardized, reproducible, and portable manner using the human pathogen Neisseria meningitidis as the exemplar organism. Since then, the approach has been applied to a large and growing number of organisms by public health laboratories and research institutions. MLST data, shared by investigators over the world via the Internet, have been ...

  6. Achalasia Carcinoma Sequence

    OpenAIRE

    Makmun, Dadang

    2001-01-01

    We report a case of carcinoma of the esophagus in a 58 years old woman with achalasia, who has been diagnosed since 30 years ago, which initiated by surgical treatment (myotomy) and the symptoms recurred since 3 years ago. According to the progress of the disease, Malignancy was strongly suspected due to prolonged stasis and mucosal irritation caused by achalasia (achalasia carcinoma sequence). Because of these contributing factors for the development of serious complications such as Malignan...

  7. Sequencing BPS spectra

    Energy Technology Data Exchange (ETDEWEB)

    Gukov, Sergei [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Max-Planck-Institut für Mathematik,Vivatsgasse 7, D-53111 Bonn (Germany); Nawata, Satoshi [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Centre for Quantum Geometry of Moduli Spaces, University of Aarhus,Nordre Ringgade 1, DK-8000 (Denmark); Saberi, Ingmar [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Stošić, Marko [CAMGSD, Departamento de Matemática, Instituto Superior Técnico,Av. Rovisco Pais, 1049-001 Lisbon (Portugal); Mathematical Institute SANU,Knez Mihajlova 36, 11000 Belgrade (Serbia); Sułkowski, Piotr [Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena, CA 91125 (United States); Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland)

    2016-03-02

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  8. Sequencing BPS spectra

    International Nuclear Information System (INIS)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr

    2016-01-01

    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel “sliding” property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d N=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  9. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  10. Preliminary HECTOR analysis by Dragon

    Energy Technology Data Exchange (ETDEWEB)

    Presser, W; Woloch, F

    1972-06-02

    From the different cores measured in HECTOR, only ACH 4/B-B was selected for the Dragon analysis, since it presented the largest amount of uniform fuel loading in the central test region and is therefore nearest to an infinite lattice. Preliminary results are discussed.

  11. Machine-Checked Sequencer for Critical Embedded Code Generator

    Science.gov (United States)

    Izerrouken, Nassima; Pantel, Marc; Thirioux, Xavier

    This paper presents the development of a correct-by-construction block sequencer for GeneAuto a qualifiable (according to DO178B/ED12B recommendation) automatic code generator. It transforms Simulink models to MISRA C code for safety critical systems. Our approach which combines classical development process and formal specification and verification using proof-assistants, led to preliminary fruitful exchanges with certification authorities. We present parts of the classical user and tools requirements and derived formal specifications, implementation and verification for the correctness and termination of the block sequencer. This sequencer has been successfully applied to real-size industrial use cases from various transportation domain partners and led to requirement errors detection and a correct-by-construction implementation.

  12. BIPS-FS preliminary design, miscellaneous notes

    International Nuclear Information System (INIS)

    1976-01-01

    A compendium of flight system preliminary design internal memos and progress report extracts for the Brayton Isotope Power System Preliminary Design Review to be held July 20, 21, and 22, 1975 is presented. The purpose is to bring together those published items which relate only to the preliminary design of the Flight System, Task 2 of Phase I. This preliminary design effort was required to ensure that the Ground Demonstration System will represent the Flight System as closely as possible

  13. Foundations of Sequence-to-Sequence Modeling for Time Series

    OpenAIRE

    Kuznetsov, Vitaly; Mariet, Zelda

    2018-01-01

    The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forecasting framework. We include a comparison of sequence-to-sequence modeling to classical time series models, and as such our theory can serve as a quantitative guide for practiti...

  14. 45 CFR 150.217 - Preliminary determination.

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 1 2010-10-01 2010-10-01 false Preliminary determination. 150.217 Section 150.217... Are Failing To Substantially Enforce HIPAA Requirements § 150.217 Preliminary determination. If, at... designees). (b) Notifies the State of CMS's preliminary determination that the State has failed to...

  15. Novel expressed sequence tag- simple sequence repeats (EST ...

    African Journals Online (AJOL)

    Using different bioinformatic criteria, the SUCEST database was used to mine for simple sequence repeat (SSR) markers. Among 42,189 clusters, 1,425 expressed sequence tag- simple sequence repeats (EST-SSRs) were identified in silico. Trinucleotide repeats were the most abundant SSRs detected. Of 212 primer pairs ...

  16. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad

    1956-01-01

    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  17. Preliminary shielding analysis of VHTR reactors

    International Nuclear Information System (INIS)

    Flaspoehler, Timothy M.; Petrovic, Bojan

    2011-01-01

    Over the last 20 years a number of methods have been established for automated variance reduction in Monte Carlo shielding simulations. Hybrid methods rely on deterministic adjoint and/or forward calculations to generate these parameters. In the present study, we use the FWCADIS method implemented in MAVRIC sequence of the SCALE6 package to perform preliminary shielding analyses of a VHTR reactor. MAVRIC has been successfully used by a number of researchers for a range of shielding applications, including modeling of LWRs, spent fuel storage, radiation field throughout a nuclear power plant, study of irradiation facilities, and others. However, experience in using MAVRIC for shielding studies of VHTRs is more limited. Thus, the objective of this work is to contribute toward validating MAVRIC for such applications, and identify areas for potential improvement. A simplified model of a prismatic VHTR has been devised, based on general features of the 600 MWt reactor considered as one of the NGNP options. Fuel elements have been homogenized, and the core region is represented as an annulus. However, the overall mix of materials and the relatively large dimensions of the spatial domain challenging the shielding simulations have been preserved. Simulations are performed to evaluate fast neutron fluence, dpa, and other parameters of interest at relevant positions. The paper will investigate and discuss both the effectiveness of the automated variance reduction, as well as applicability of physics model from the standpoint of specific VHTR features. (author)

  18. Preliminary High-Throughput Metagenome Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Dusheyko, Serge; Furman, Craig; Pangilinan, Jasmyn; Shapiro, Harris; Tu, Hank

    2007-03-26

    Metagenome data sets present a qualitatively different assembly problem than traditional single-organism whole-genome shotgun (WGS) assembly. The unique aspects of such projects include the presence of a potentially large number of distinct organisms and their representation in the data set at widely different fractions. In addition, multiple closely related strains could be present, which would be difficult to assemble separately. Failure to take these issues into account can result in poor assemblies that either jumble together different strains or which fail to yield useful results. The DOE Joint Genome Institute has sequenced a number of metagenomic projects and plans to considerably increase this number in the coming year. As a result, the JGI has a need for high-throughput tools and techniques for handling metagenome projects. We present the techniques developed to handle metagenome assemblies in a high-throughput environment. This includes a streamlined assembly wrapper, based on the JGI?s in-house WGS assembler, Jazz. It also includes the selection of sensible defaults targeted for metagenome data sets, as well as quality control automation for cleaning up the raw results. While analysis is ongoing, we will discuss preliminary assessments of the quality of the assembly results (http://fames.jgi-psf.org).

  19. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    fast alignment algorithm, called 'Alignment By Scanning' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the 'GAP' (which is heuristic) and the 'Needleman

  20. Next-Generation Sequencing Platforms

    Science.gov (United States)

    Mardis, Elaine R.

    2013-06-01

    Automated DNA sequencing instruments embody an elegant interplay among chemistry, engineering, software, and molecular biology and have built upon Sanger's founding discovery of dideoxynucleotide sequencing to perform once-unfathomable tasks. Combined with innovative physical mapping approaches that helped to establish long-range relationships between cloned stretches of genomic DNA, fluorescent DNA sequencers produced reference genome sequences for model organisms and for the reference human genome. New types of sequencing instruments that permit amazing acceleration of data-collection rates for DNA sequencing have been developed. The ability to generate genome-scale data sets is now transforming the nature of biological inquiry. Here, I provide an historical perspective of the field, focusing on the fundamental developments that predated the advent of next-generation sequencing instruments and providing information about how these instruments work, their application to biological research, and the newest types of sequencers that can extract data from single DNA molecules.

  1. Draft Genome Sequence of the Efficient Bioflocculant-Producing Bacterium Paenibacillus sp. Strain A9

    Science.gov (United States)

    Liu, Jin-liang; Hu, Xiao-min

    2013-01-01

    Paenibacillus sp. strain A9 is an important bioflocculant-producing bacterium, isolated from a soil sample, and is pale pink-pigmented, aerobic, and Gram-positive. Here, we report the draft genome sequence and the initial findings from a preliminary analysis of strain A9, which is a novel species of Paenibacillus. PMID:23618713

  2. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  3. The advantages of SMRT sequencing

    OpenAIRE

    Roberts, Richard J; Carneiro, Mauricio O; Schatz, Michael C

    2013-01-01

    Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes.

  4. Putting instruction sequences into effect

    NARCIS (Netherlands)

    Bergstra, J.A.

    2011-01-01

    An attempt is made to define the concept of execution of an instruction sequence. It is found to be a special case of directly putting into effect of an instruction sequence. Directly putting into effect of an instruction sequences comprises interpretation as well as execution. Directly putting into

  5. 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

  6. Space Elevators Preliminary Architectural View

    Science.gov (United States)

    Pullum, L.; Swan, P. A.

    Space Systems Architecture has been expanded into a process by the US Department of Defense for their large scale systems of systems development programs. This paper uses the steps in the process to establishes a framework for Space Elevator systems to be developed and provides a methodology to manage complexity. This new approach to developing a family of systems is based upon three architectural views: Operational View OV), Systems View (SV), and Technical Standards View (TV). The top level view of the process establishes the stages for the development of the first Space Elevator and is called Architectural View - 1, Overview and Summary. This paper will show the guidelines and steps of the process while focusing upon components of the Space Elevator Preliminary Architecture View. This Preliminary Architecture View is presented as a draft starting point for the Space Elevator Project.

  7. Radioactive waste shredding: Preliminary evaluation

    International Nuclear Information System (INIS)

    Soelberg, N.R.; Reimann, G.A.

    1994-07-01

    The critical constraints for sizing solid radioactive and mixed wastes for subsequent thermal treatment were identified via a literature review and a survey of shredding equipment vendors. The types and amounts of DOE radioactive wastes that will require treatment to reduce the waste volume, destroy hazardous organics, or immobilize radionuclides and/or hazardous metals were considered. The preliminary steps of waste receipt, inspection, and separation were included because many potential waste treatment technologies have limits on feedstream chemical content, physical composition, and particle size. Most treatment processes and shredding operations require at least some degree of feed material characterization. Preliminary cost estimates show that pretreatment costs per unit of waste can be high and can vary significantly, depending on the processing rate and desired output particle size

  8. Exploratory shaft facility preliminary designs - Permian Basin

    International Nuclear Information System (INIS)

    1983-09-01

    The purpose of the Preliminary Design Report, Permian Basin, is to provide a description of the preliminary design for an Exploratory Shaft Facility in the Permian Basin, Texas. This issue of the report describes the preliminary design for constructing the exploratory shaft using the Large Hole Drilling method of construction and outlines the preliminary design and estimates of probable construction cost. The Preliminary Design Report is prepared to complement and summarize other documents that comprise the design at the preliminary stage of completion, December 1982. Other design documents include drawings, cost estimates and schedules. The preliminary design drawing package, which includes the construction schedule drawing, depicts the descriptions in this report. For reference, a list of the drawing titles and corresponding numbers are included in the Appendix. The report is divided into three principal sections: Design Basis, Facility Description, and Construction Cost Estimate. 30 references, 13 tables

  9. Log-balanced combinatorial sequences

    Directory of Open Access Journals (Sweden)

    Tomislav Došlic

    2005-01-01

    Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

  10. New MR pulse sequence

    International Nuclear Information System (INIS)

    Harms, S.E.; Flamig, D.P.; Griffey, R.H.

    1990-01-01

    This paper describes a method for fat suppression for three-dimensional MR imaging. The FATS (fat-suppressed acquisition with echo time shortened) sequence employs a pair of opposing adiabatic half-passage RF pulses tuned on fat resonance. The imaging parameters are as follows: TR, 20 msec; TE, 21.7-3.2 msec; 1,024 x 128 x 128 acquired matrix; imaging time, approximately 11 minutes. A series of 54 examinations were performed. Excellent fat suppression with water excitation is achieved in all cases. The orbital images demonstrate superior resolution of small orbital lesions. The high signal-to-noise ratio (SNR) in cranial studies demonstrates excellent petrous bone and internal auditory canal anatomy

  11. Quantum-Sequencing: Fast electronic single DNA molecule sequencing

    Science.gov (United States)

    Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

    2014-03-01

    A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

  12. Supervised Learning for Detection of Duplicates in Genomic Sequence Databases.

    Directory of Open Access Journals (Sweden)

    Qingyu Chen

    Full Text Available First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and existing automatic systems cannot detect duplicates as precisely as can experts. Supervised learning has the potential to address such problems by building automatic systems that learn from expert curation to detect duplicates precisely and efficiently. While machine learning is a mature approach in other duplicate detection contexts, it has seen only preliminary application in genomic sequence databases.We developed and evaluated a supervised duplicate detection method based on an expert curated dataset of duplicates, containing over one million pairs across five organisms derived from genomic sequence databases. We selected 22 features to represent distinct attributes of the database records, and developed a binary model and a multi-class model. Both models achieve promising performance; under cross-validation, the binary model had over 90% accuracy in each of the five organisms, while the multi-class model maintains high accuracy and is more robust in generalisation. We performed an ablation study to quantify the impact of different sequence record features, finding that features derived from meta-data, sequence identity, and alignment quality impact performance most strongly. The study demonstrates machine learning can be an effective additional tool for de-duplication of genomic sequence databases. All Data are available as described in the supplementary material.

  13. Supervised Learning for Detection of Duplicates in Genomic Sequence Databases.

    Science.gov (United States)

    Chen, Qingyu; Zobel, Justin; Zhang, Xiuzhen; Verspoor, Karin

    2016-01-01

    First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and existing automatic systems cannot detect duplicates as precisely as can experts. Supervised learning has the potential to address such problems by building automatic systems that learn from expert curation to detect duplicates precisely and efficiently. While machine learning is a mature approach in other duplicate detection contexts, it has seen only preliminary application in genomic sequence databases. We developed and evaluated a supervised duplicate detection method based on an expert curated dataset of duplicates, containing over one million pairs across five organisms derived from genomic sequence databases. We selected 22 features to represent distinct attributes of the database records, and developed a binary model and a multi-class model. Both models achieve promising performance; under cross-validation, the binary model had over 90% accuracy in each of the five organisms, while the multi-class model maintains high accuracy and is more robust in generalisation. We performed an ablation study to quantify the impact of different sequence record features, finding that features derived from meta-data, sequence identity, and alignment quality impact performance most strongly. The study demonstrates machine learning can be an effective additional tool for de-duplication of genomic sequence databases. All Data are available as described in the supplementary material.

  14. Universal sequence map (USM of arbitrary discrete sequences

    Directory of Open Access Journals (Sweden)

    Almeida Jonas S

    2002-02-01

    Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

  15. The canine sarcoglycan delta gene: BAC clone contig assembly, chromosome assignment and interrogation as a candidate gene for dilated cardiomyopathy in Dobermann dogs.

    Science.gov (United States)

    Stabej, P; Leegwater, P A J; Imholz, S; Versteeg, S A; Zijlstra, C; Stokhof, A A; Domanjko-Petriè, A; van Oost, B A

    2005-01-01

    Dilated cardiomyopathy (DCM) is a common disease of the myocardium recognized in human, dog and experimental animals. Genetic factors are responsible for a large proportion of cases in humans, and 17 genes with DCM causing mutations have been identified. The genetic origin of DCM in the Dobermann dogs has been suggested, but no disease genes have been identified to date. In this paper, we describe the characterization and evaluation of the canine sarcoglycan delta (SGCD), a gene implicated in DCM in human and hamster. Bacterial artificial chromosomes (BACs) containing the canine SGCD gene were isolated with probes for exon 3 and exons 4-8 and were characterized by Southern blot analysis. BAC end sequences were obtained for four BACs. Three of the BACs overlapped and could be ordered relative to each other and the end sequences of all four BACs could be anchored on the preliminary assembly of the dog genome sequence (www. ensembl.org). One of the BACs of the partial contig was localized by fluorescent in situ hybridization to canine chromosome 4q22, in agreement with the dog genome sequence. Two highly informative polymorphic microsatellite markers in intron 7 of the SGCD gene were identified. In 25 DCM-affected and 13 non DCM-affected dogs seven different haplotypes could be distinguished. However, no association between any of the SGCD variants and the disease locus was apparent.

  16. Preliminaries

    Directory of Open Access Journals (Sweden)

    Desde el jardín de Freud

    2014-10-01

    Full Text Available Desde el Jardín de Freud se encuentra indexada en el IBN-Publindex (Colciencias, en categoría C, y en Latindex. También se encuentra en las siguientes bases de datos y catálogos: ebsco, Dialnet, Rebiun, Doaj y e-Revistas.

  17. Preliminary

    Directory of Open Access Journals (Sweden)

    Desde el Jardín de Freud

    2017-01-01

    Full Text Available Desde el Jardín de Freud is indexed in the IBN-Publindex (Colciencias in category C, and the following databases and catalogs: EBSCO, ProQuest, Google Scholar, CLASE, Latindex, Dialnet, Rebiun, Doaj, e-revistas and Library Luis Angel Arango virtual.

  18. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  19. Preliminary considerations concerning actinide solubilities

    International Nuclear Information System (INIS)

    Newton, T.W.; Bayhurst, B.P.; Daniels, W.R.; Erdal, B.R.; Ogard, A.E.

    1980-01-01

    Work at the Los Alamos Scientific Laboratory on the fundamental solution chemistry of the actinides has thus far been confined to preliminary considerations of the problems involved in developing an understanding of the precipitation and dissolution behavior of actinide compounds under environmental conditions. Attempts have been made to calculate solubility as a function of Eh and pH using the appropriate thermodynamic data; results have been presented in terms of contour maps showing lines of constant solubility as a function of Eh and pH. Possible methods of control of the redox potential of rock-groundwater systems by the use of Eh buffers (redox couples) is presented

  20. TCA High Lift Preliminary Assessment

    Science.gov (United States)

    Wyatt, G. H.; Polito, R. C.; Yeh, D. T.; Elzey, M. E.; Tran, J. T.; Meredith, Paul T.

    1999-01-01

    This paper presents a TCA (Technology Concept Airplane) High lift Preliminary Assessment. The topics discussed are: 1) Model Description; 2) Data Repeatability; 3) Effect of Inboard L.E. (Leading Edge) Flap Span; 4) Comparison of 14'x22' TCA-1 With NTF (National Transonic Facility) Modified Ref. H; 5) Comparison of 14'x22' and NTF Ref. H Results; 6) Effect of Outboard Sealed Slat on TCA; 7) TCA Full Scale Build-ups; 8) Full Scale L/D Comparisons; 9) TCA Full Scale; and 10) Touchdown Lift Curves. This paper is in viewgraph form.

  1. Preliminary ECLSS waste water model

    Science.gov (United States)

    Carter, Donald L.; Holder, Donald W., Jr.; Alexander, Kevin; Shaw, R. G.; Hayase, John K.

    1991-01-01

    A preliminary waste water model for input to the Space Station Freedom (SSF) Environmental Control and Life Support System (ECLSS) Water Processor (WP) has been generated for design purposes. Data have been compiled from various ECLSS tests and flight sample analyses. A discussion of the characterization of the waste streams comprising the model is presented, along with a discussion of the waste water model and the rationale for the inclusion of contaminants in their respective concentrations. The major objective is to establish a methodology for the development of a waste water model and to present the current state of that model.

  2. Versator divertor experiment: preliminary designs

    International Nuclear Information System (INIS)

    Wan, A.S.; Yang, T.F.

    1984-08-01

    The emergence of magnetic divertors as an impurity control and ash removal mechanism for future tokamak reactors bring on the need for further experimental verification of the divertor merits and their ability to operate at reactor relevant conditions, such as with auxiliary heating. This paper presents preliminary designs of a bundle and a poloidal divertor for Versator II, which can operate in conjunction with the existing 150 kW of LHRF heating or LH current drive. The bundle divertor option also features a new divertor configuration which should improve the engineering and physics results of the DITE experiment. Further design optimization in both physics and engineering designs are currently under way

  3. Preliminary ATWS analysis for the IRIS PRA

    International Nuclear Information System (INIS)

    Maddalena Barra; Marco S Ghisu; David J Finnicum; Luca Oriani

    2005-01-01

    Full text of publication follows: The pressurized light water cooled, medium power (1000 MWt) IRIS (International Reactor Innovative and Secure) has been under development for four years by an international consortium of over 21 organizations from ten countries. The plant conceptual design was completed in 2001 and the preliminary design is nearing completion. The pre-application licensing process with NRC started in October, 2002. IRIS has been primarily focused on establishing a design with innovative safety characteristics. The first line of defense in IRIS is to eliminate event initiators that could potentially lead to core damage. In IRIS, this concept is implemented through the 'safety by design' approach, which allows to minimize the number and complexity of the safety systems and required operator actions. The end result is a design with significantly reduced complexity and improved operability, and extensive plant simplifications to enhance construction. To support the optimization of the plant design and confirm the effectiveness of the safety by design approach in mitigating or eliminating events and thus providing a significant reduction in the probability of severe accidents, the PRA is being used as an integral part of the design process. A preliminary but extensive Level 1 PRA model has been developed to support the pre-application licensing of the IRIS design. As a result of the Preliminary IRIS PRA, an optimization of the design from a reliability point of view was completed, and an extremely low (about 1.2 E -8 ) core damage frequency (CDF) was assessed to confirm the impact of the safety by design approach. This first assessment is a result of a PRA model including internal initiating events. During this assessment, several assumptions were necessary to complete the CDF evaluation. In particular Anticipated Transients Without Scram (ATWS) were not included in this initial assessment, because their contribution to core damage frequency was assumed

  4. Genomic sequencing in clinical trials

    OpenAIRE

    Mestan, Karen K; Ilkhanoff, Leonard; Mouli, Samdeep; Lin, Simon

    2011-01-01

    Abstract Human genome sequencing is the process by which the exact order of nucleic acid base pairs in the 24 human chromosomes is determined. Since the completion of the Human Genome Project in 2003, genomic sequencing is rapidly becoming a major part of our translational research efforts to understand and improve human health and disease. This article reviews the current and future directions of clinical research with respect to genomic sequencing, a technology that is just beginning to fin...

  5. Biosensors for DNA sequence detection

    Science.gov (United States)

    Vercoutere, Wenonah; Akeson, Mark

    2002-01-01

    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  6. On Preliminary Test Estimator for Median

    OpenAIRE

    Okazaki, Takeo; 岡崎, 威生

    1990-01-01

    The purpose of the present paper is to discuss about estimation of median with a preliminary test. Two procedures are presented, one uses Median test and the other uses Wilcoxon two-sample test for the preliminary test. Sections 3 and 4 give mathematical formulations of such properties, including mean square errors with one specified case. Section 5 discusses their optimal significance levels of the preliminary test and proposes their numerical values by Monte Carlo method. In addition to mea...

  7. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal

    2011-08-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  8. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal; Salama, Khaled N.

    2011-01-01

    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the 'Needleman-Wunsch' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  9. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  10. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon

    2012-01-01

    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS...

  11. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  12. How do providers discuss the results of pediatric exome sequencing with families?

    Science.gov (United States)

    Walser, Sarah A; Werner-Lin, Allison; Mueller, Rebecca; Miller, Victoria A; Biswas, Sawona; Bernhardt, Barbara A

    2017-09-01

    This study provides preliminary data on the process and content of returning results from exome sequencing offered to children through one of the Clinical Sequencing Exploratory Research (CSER) projects. We recorded 25 sessions where providers returned diagnostic and secondary sequencing results to families. Data interpretation utilized inductive thematic analysis. Typically, providers followed a results report and discussed diagnostic findings using technical genomic and sequencing concepts. We identified four provider processes for returning results: teaching genetic concepts; assessing family response; personalizing findings; and strengthening patient-provider relationships. Sessions should reflect family interest in medical management and next steps, and minimize detailed genomic concepts. As the scope and complexity of sequencing increase, the traditional information-laden counseling model requires revision.

  13. SVX Sequencer Board

    International Nuclear Information System (INIS)

    Utes, M.

    1997-01-01

    The SVX Sequencer boards are 9U by 280mm circuit boards that reside in slots 2 through 21 of each of eight Eurocard crates in the D0 Detector Platform. The basic purpose is to control the SVX chips for data acquisition and when a trigger occurs, to gather the SVX data and relay the data to the VRB boards in the Movable Counting House. Functions and features are as follows: (1) Initialization of eight SVX chip strings using the MIL-STD-1553 data bus; (2) Real time manipulation of the SVX control lines to effect data acquisition, digitization, and readout based on the NRZ/Clock signals from the Controller; (3) Conversion of 8-bit electrical SVX readout data to an optical signal operating at 1.062 Gbit/sec, sent to the VRB. Eight HDIs will be serviced per board; (4) Built-in logic analyzer which can record the most important control and data lines during a data acquisition cycle and put this recorded information onto the 1553 bus; (5) Identification header and end of data trailer tacked onto data stream; (6) 1553 register which can read the current values of the control and data lines; (7) 1553 register which can test the optical link; (8) 1553 registers for crossing pulse width, calibration pulse voltage, and calibration pipeline select; (9) 1553 register for reading the optical drivers status link; (10) 1553 register for power control of SVX chips and ignoring bad SVX strings; (11) Front panel displays and LEDs show the board status at a glance; (12) In-system programmable EPLDs are programmed via 1553 or Altera's 'Bitblaster'; (13) Automatic readout abort after 45us; (14) Supplies BUSY signal back to Trigger Framework; (15) Supports a heartbeat system to prevent excessive SVX current draw; and (16) Supports a SVX power trip feature if heartbeat failure occurs.

  14. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    International Nuclear Information System (INIS)

    Rauzy, Antoine B.

    2011-01-01

    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  15. Fukushima. A preliminary assessment in July 2011; Fukushima. Eine vorlaeufige Bilanz im Juli 2011

    Energy Technology Data Exchange (ETDEWEB)

    Michel, Rolf

    2011-07-01

    Four months after the reactor accidents in Fukushima Daiichi a preliminary assessment of the accident sequence vents is performed based on the available incomplete information. The following topics are discussed: initiating events and accident sequences, radioactive materials release and dispersion, fundamentals on radiation exposure following the accident in the nuclear power plant Fukushima Daiichi, contamination of food stuff, fission product release into the Pacific Ocean, source tern and external radiation exposure in the first year, preliminary radiological assessment, radiological situation throughout the different accident phases (radioactive cloud and fallout, late phase), estimation of radiation exposure in the first year due to decay of short-lived radionuclides based on the state end of July 2011, comparison of the reactor accidents in Chernobyl and Fukushima Daiichi.

  16. Polymerase chain reaction in the diagnosis of tuberculous meningitis: preliminary report

    Directory of Open Access Journals (Sweden)

    L.R. Machado

    1994-09-01

    Full Text Available In this preliminary report the results of PCR for detection of DNA sequences (65 KDa antigen of Mycobacterium tuberculosis in CSF samples from 20 patients are registered. In 10 patients there were clinical and laboratory findings suggesting the diagnosis of tuberculous meningitis (test group. In the other 10 patients, clinical and laboratory findings suggested meningitis or meningo-encephalitis from other etiologies (control group. In 7 patients from the test group antigenic DNA sequences of Mycobacterium tuberculosis were found in CSF by PCR; positive results were not registered in the control group.

  17. Marker discovery in Trypanosoma vivax through GSS and comparative analysis. Preliminary data and perspectives

    International Nuclear Information System (INIS)

    Davila, A.M.R.; Guerreiro, L.T.A.; Souza, S.S.

    2005-01-01

    Trypanosoma vivax is a haemoparasite affecting the livestock industry in South America and Africa. Despite the high economic relevance of the disease caused by T. vivax, little work has been done on its molecular characterization, in contrast with human trypanosomes, such as T. brucei and T. cruzi. The present study reports the construction of a semi-normalized genomic library and the sequencing of 160 Genome Sequence Survey (GSS) ends of T. vivax. The analyses of this preliminary data show that this simple and rapid approach worked well to generate some potential new markers for this species. (author)

  18. Chameleon sequences in neurodegenerative diseases

    International Nuclear Information System (INIS)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-01-01

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  19. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  20. Chameleon sequences in neurodegenerative diseases.

    Science.gov (United States)

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Farey sequences and resistor networks

    Indian Academy of Sciences (India)

    Green's function, while the perturbation of a network is investigated in [3]. ... In Theorem 1 below, we employ the Farey sequence to establish a strict .... We next show that the Farey sequence method is applicable for circuits with n or fewer.

  2. DNA Sequencing by Capillary Electrophoresis

    Science.gov (United States)

    Karger, Barry L.; Guttman, Andras

    2009-01-01

    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA sequencing methods have evolved from the labor intensive slab gel electrophoresis, through automated multicapillary electrophoresis systems using fluorophore labeling with multispectral imaging, to the “next generation” technologies of cyclic array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes was only possible by the advent of modern sequencing technologies that was a result of step by step advances with a contribution of academics, medical personnel and instrument companies. While next generation sequencing is moving ahead at break-neck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of capillary electrophoresis in DNA sequencing based in part of several of our articles in this journal. PMID:19517496

  3. Graphene nanodevices for DNA sequencing

    NARCIS (Netherlands)

    Heerema, S.J.; Dekker, C.

    2016-01-01

    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with

  4. Chameleon sequences in neurodegenerative diseases

    Energy Technology Data Exchange (ETDEWEB)

    Bahramali, Golnaz [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Goliaei, Bahram, E-mail: goliaei@ut.ac.ir [Institute of Biochemistry and Biophysics, University of Tehran, Tehran (Iran, Islamic Republic of); Minuchehr, Zarrin, E-mail: minuchehr@nigeb.ac.ir [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of); Salari, Ali [Department of Systems Biotechnology, National Institute of Genetic Engineering and Biotechnology, (NIGEB), Tehran (Iran, Islamic Republic of)

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to “helix to strand (HE)”, “helix to coil (HC)” and “strand to coil (CE)” alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  5. Commercial Art: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a commercial art vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  6. Rapid Diagnostics of Onboard Sequences

    Science.gov (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

    2012-01-01

    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  7. Sludge Treatment Project Engineered Container Retrieval And Transfer System Preliminary Design Hazard Analysis Supplement 1

    International Nuclear Information System (INIS)

    Franz, G.R.; Meichle, R.H.

    2011-01-01

    This 'What/If' Hazards Analysis addresses hazards affecting the Sludge Treatment Project Engineered Container Retrieval and Transfer System (ECRTS) NPH and external events at the preliminary design stage. In addition, the hazards of the operation sequence steps for the mechanical handling operations in preparation of Sludge Transport and Storage Container (STSC), disconnect STSC and prepare STSC and Sludge Transport System (STS) for shipping are addressed.

  8. Accident sequence quantification with KIRAP

    International Nuclear Information System (INIS)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

  9. Accident sequence quantification with KIRAP

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong

    1997-01-01

    The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP`s cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs.

  10. Repeated DNA sequences in fungi

    Energy Technology Data Exchange (ETDEWEB)

    Dutta, S K

    1974-11-01

    Several fungal species, representatives of all broad groups like basidiomycetes, ascomycetes and phycomycetes, were examined for the nature of repeated DNA sequences by DNA:DNA reassociation studies using hydroxyapatite chromatography. All of the fungal species tested contained 10 to 20 percent repeated DNA sequences. There are approximately 100 to 110 copies of repeated DNA sequences of approximately 4 x 10/sup 7/ daltons piece size of each. Repeated DNA sequence homoduplexes showed on average 5/sup 0/C difference of T/sub e/50 (temperature at which 50 percent duplexes dissociate) values from the corresponding homoduplexes of unfractionated whole DNA. It is suggested that a part of repetitive sequences in fungi constitutes mitochondrial DNA and a part of it constitutes nuclear DNA. (auth)

  11. [Complete genome sequencing and sequence analysis of BCG Tice].

    Science.gov (United States)

    Wang, Zhiming; Pan, Yuanlong; Wu, Jun; Zhu, Baoli

    2012-10-04

    The objective of this study is to obtain the complete genome sequence of Bacillus Calmette-Guerin Tice (BCG Tice), in order to provide more information about the molecular biology of BCG Tice and design more reasonable vaccines to prevent tuberculosis. We assembled the data from high-throughput sequencing with SOAPdenovo software, with many contigs and scaffolds obtained. There are many sequence gaps and physical gaps remained as a result of regional low coverage and low quality. We designed primers at the end of contigs and performed PCR amplification in order to link these contigs and scaffolds. With various enzymes to perform PCR amplification, adjustment of PCR reaction conditions, and combined with clone construction to sequence, all the gaps were finished. We obtained the complete genome sequence of BCG Tice and submitted it to GenBank of National Center for Biotechnology Information (NCBI). The genome of BCG Tice is 4334064 base pairs in length, with GC content 65.65%. The problems and strategies during the finishing step of BCG Tice sequencing are illuminated here, with the hope of affording some experience to those who are involved in the finishing step of genome sequencing. The microarray data were verified by our results.

  12. Preliminary Context Analysis of Community Informatics Social ...

    African Journals Online (AJOL)

    Preliminary context analysis is always part of the feasibility study phase in the development of information system for Community Development (CD) purposes. In this paper, a context model and a preliminary context analysis are presented for Social Network Web Application (SNWA) for CD in the Niger Delta region of ...

  13. 23 CFR 645.109 - Preliminary engineering.

    Science.gov (United States)

    2010-04-01

    ... 23 Highways 1 2010-04-01 2010-04-01 false Preliminary engineering. 645.109 Section 645.109 Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION ENGINEERING AND TRAFFIC OPERATIONS UTILITIES Utility Relocations, Adjustments, and Reimbursement § 645.109 Preliminary engineering. (a) As...

  14. Plutonium Immobilization Can Loading Preliminary Specifications

    Energy Technology Data Exchange (ETDEWEB)

    Kriikku, E.

    1998-11-25

    This report discusses the Plutonium Immobilization can loading preliminary equipment specifications and includes a process block diagram, process description, equipment list, preliminary equipment specifications, plan and elevation sketches, and some commercial catalogs. This report identifies loading pucks into cans and backfilling cans with helium as the top priority can loading development areas.

  15. Strategic Cognitive Sequencing: A Computational Cognitive Neuroscience Approach

    Directory of Open Access Journals (Sweden)

    Seth A. Herd

    2013-01-01

    Full Text Available We address strategic cognitive sequencing, the “outer loop” of human cognition: how the brain decides what cognitive process to apply at a given moment to solve complex, multistep cognitive tasks. We argue that this topic has been neglected relative to its importance for systematic reasons but that recent work on how individual brain systems accomplish their computations has set the stage for productively addressing how brain regions coordinate over time to accomplish our most impressive thinking. We present four preliminary neural network models. The first addresses how the prefrontal cortex (PFC and basal ganglia (BG cooperate to perform trial-and-error learning of short sequences; the next, how several areas of PFC learn to make predictions of likely reward, and how this contributes to the BG making decisions at the level of strategies. The third models address how PFC, BG, parietal cortex, and hippocampus can work together to memorize sequences of cognitive actions from instruction (or “self-instruction”. The last shows how a constraint satisfaction process can find useful plans. The PFC maintains current and goal states and associates from both of these to find a “bridging” state, an abstract plan. We discuss how these processes could work together to produce strategic cognitive sequencing and discuss future directions in this area.

  16. KALIMER preliminary conceptual design report

    Energy Technology Data Exchange (ETDEWEB)

    Hahn, Do Hee; Kim, Y. J.; Kim, Y. G. and others

    2000-08-01

    This report, which summarizes the result of preliminary conceptual design activities during Phase 1, follows the format of safety analysis report. The purpose of publishing this report is to gather all of the design information developed so far in a systematic way so that KALIMER designers have a common source of the consistent design information necessary for their future design activities. This report will be revised and updated as design changes occur and more detailed design specification is developed during Phase 2. Chapter 1 describes the KALIMER Project. Chapter 2 includes the top level design requirements of KALIMER and general plant description. Chapter 3 summarizes the design of structures, components, equipment and systems. Specific systems and safety analysis results are described in the remaining chapters. Appendix on the HCDA evaluation is attached at the end of this report.

  17. Psychohistory and Slavery: Preliminary Issues.

    Science.gov (United States)

    Adams, Kenneth Alan

    2015-01-01

    "Psychohistory and Slavery: Preliminary Issues," begins an examination of slavery in the antebellum South. The paper suggests that how slavery and the group-fantasy of white male supremacy were perpetuated among slaveholders is a question of fundamental importance for psychohistorians. The family and childrearing are the focus of attention. Given the ferocity of slavery, it is argued that the psychological and emotional consequences of this barbarism were not limited to the slaves themselves, but had significant impact on the slaveholders as well-their parenting, their children, and their children's parenting of the next generation. In each generation the trauma of slavery was injected into slaveholder children and became a fundamental component of elite Southern personality.

  18. KALIMER preliminary conceptual design report

    International Nuclear Information System (INIS)

    Hahn, Do Hee; Kim, Y. J.; Kim, Y. G. and others

    2000-08-01

    This report, which summarizes the result of preliminary conceptual design activities during Phase 1, follows the format of safety analysis report. The purpose of publishing this report is to gather all of the design information developed so far in a systematic way so that KALIMER designers have a common source of the consistent design information necessary for their future design activities. This report will be revised and updated as design changes occur and more detailed design specification is developed during Phase 2. Chapter 1 describes the KALIMER Project. Chapter 2 includes the top level design requirements of KALIMER and general plant description. Chapter 3 summarizes the design of structures, components, equipment and systems. Specific systems and safety analysis results are described in the remaining chapters. Appendix on the HCDA evaluation is attached at the end of this report

  19. Preliminary hazards analysis -- vitrification process

    International Nuclear Information System (INIS)

    Coordes, D.; Ruggieri, M.; Russell, J.; TenBrook, W.; Yimbo, P.

    1994-06-01

    This paper presents a Preliminary Hazards Analysis (PHA) for mixed waste vitrification by joule heating. The purpose of performing a PHA is to establish an initial hazard categorization for a DOE nuclear facility and to identify those processes and structures which may have an impact on or be important to safety. The PHA is typically performed during and provides input to project conceptual design. The PHA is then followed by a Preliminary Safety Analysis Report (PSAR) performed during Title 1 and 2 design. The PSAR then leads to performance of the Final Safety Analysis Report performed during the facility's construction and testing. It should be completed before routine operation of the facility commences. This PHA addresses the first four chapters of the safety analysis process, in accordance with the requirements of DOE Safety Guidelines in SG 830.110. The hazards associated with vitrification processes are evaluated using standard safety analysis methods which include: identification of credible potential hazardous energy sources; identification of preventative features of the facility or system; identification of mitigative features; and analyses of credible hazards. Maximal facility inventories of radioactive and hazardous materials are postulated to evaluate worst case accident consequences. These inventories were based on DOE-STD-1027-92 guidance and the surrogate waste streams defined by Mayberry, et al. Radiological assessments indicate that a facility, depending on the radioactive material inventory, may be an exempt, Category 3, or Category 2 facility. The calculated impacts would result in no significant impact to offsite personnel or the environment. Hazardous materials assessment indicates that a Mixed Waste Vitrification facility will be a Low Hazard facility having minimal impacts to offsite personnel and the environment

  20. Preliminary hazards analysis -- vitrification process

    Energy Technology Data Exchange (ETDEWEB)

    Coordes, D.; Ruggieri, M.; Russell, J.; TenBrook, W.; Yimbo, P. [Science Applications International Corp., Pleasanton, CA (United States)

    1994-06-01

    This paper presents a Preliminary Hazards Analysis (PHA) for mixed waste vitrification by joule heating. The purpose of performing a PHA is to establish an initial hazard categorization for a DOE nuclear facility and to identify those processes and structures which may have an impact on or be important to safety. The PHA is typically performed during and provides input to project conceptual design. The PHA is then followed by a Preliminary Safety Analysis Report (PSAR) performed during Title 1 and 2 design. The PSAR then leads to performance of the Final Safety Analysis Report performed during the facility`s construction and testing. It should be completed before routine operation of the facility commences. This PHA addresses the first four chapters of the safety analysis process, in accordance with the requirements of DOE Safety Guidelines in SG 830.110. The hazards associated with vitrification processes are evaluated using standard safety analysis methods which include: identification of credible potential hazardous energy sources; identification of preventative features of the facility or system; identification of mitigative features; and analyses of credible hazards. Maximal facility inventories of radioactive and hazardous materials are postulated to evaluate worst case accident consequences. These inventories were based on DOE-STD-1027-92 guidance and the surrogate waste streams defined by Mayberry, et al. Radiological assessments indicate that a facility, depending on the radioactive material inventory, may be an exempt, Category 3, or Category 2 facility. The calculated impacts would result in no significant impact to offsite personnel or the environment. Hazardous materials assessment indicates that a Mixed Waste Vitrification facility will be a Low Hazard facility having minimal impacts to offsite personnel and the environment.

  1. GROUPING WEB ACCESS SEQUENCES uSING SEQUENCE ALIGNMENT METHOD

    OpenAIRE

    BHUPENDRA S CHORDIA; KRISHNAKANT P ADHIYA

    2011-01-01

    In web usage mining grouping of web access sequences can be used to determine the behavior or intent of a set of users. Grouping websessions is how to measure the similarity between web sessions. There are many shortcomings in traditional measurement methods. The taskof grouping web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-groupsimilarity is done using sequence alignment method. This paper introduces a new method to group we...

  2. LPTAU, Quasi Random Sequence Generator

    International Nuclear Information System (INIS)

    Sobol, Ilya M.

    1993-01-01

    1 - Description of program or function: LPTAU generates quasi random sequences. These are uniformly distributed sets of L=M N points in the N-dimensional unit cube: I N =[0,1]x...x[0,1]. These sequences are used as nodes for multidimensional integration; as searching points in global optimization; as trial points in multi-criteria decision making; as quasi-random points for quasi Monte Carlo algorithms. 2 - Method of solution: Uses LP-TAU sequence generation (see references). 3 - Restrictions on the complexity of the problem: The number of points that can be generated is L 30 . The dimension of the space cannot exceed 51

  3. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)

    2006-05-19

    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  4. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

    OpenAIRE

    Zuccolo, Andrea; Bowers, John E; Estill, James C; Xiong, Zhiyong; Luo, Meizhong; Sebastian, Aswathy; Goicoechea, Jos? Luis; Collura, Kristi; Yu, Yeisoo; Jiao, Yuannian; Duarte, Jill; Tang, Haibao; Ayyampalayam, Saravanaraj; Rounsley, Steve; Kudrna, Dave

    2011-01-01

    Background Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome....

  5. Preliminary sequence stratigraphy and tectonic evolution of the Tokar Delta, (Southern Sudanese Red Sea)

    OpenAIRE

    Yagoub, Abbas Musa

    2007-01-01

    The study area comprises about 2500sq.Kms. From the seismic data acquired by the Oil Companies (Chevron 1975-76 Total 1980 and IPC 1992), thirty two seismic lines were selected Fig (2). Also synthetic seismograms of Suakin-1, Bashayer-1 A and Bashayer-2A wells are used. The stratigraphy and sedimentation of the Sudanese Red Sea can be placed into four major tectonic phases, Pre-rifting stratigraphy, Syn-Rift Pre-Salt Stratigarphy, Salt Phase and Syn-Rift Post Salt Stratigraphy. Basic conce...

  6. A preliminary molecular phylogeny of planthoppers (Hemiptera: Fulgoroidea based on nuclear and mitochondrial DNA sequences.

    Directory of Open Access Journals (Sweden)

    Nan Song

    Full Text Available The planthopper superfamily Fulgoroidea (Insecta: Hemiptera is one of the most dominant groups of phytophagous insects. It comprises about 20 families, containing a total of 9000 species worldwide. Despite several recent studies, the phylogeny of Fulgoroidea is not yet satisfactorily resolved and the phylogenetic positions of several key families, especially Cixiidae, Delphacidae, Tettigometridae, Nogodinidae, Acanaloniidae and Issidae, are contentious. Here, we expand upon recent phylogenetic work using additional nuclear (18S and 28S and novel mitochondrial (16S and cytb markers. Maximum likelihood and Bayesian analyses yielded robust phylogenetic trees. In these topologies, a group containing Cixiidae and Delphacidae is recovered as the sister group to the remaining taxa. Tettigometridae is placed in a more nested position and is grouped with Caliscelidae. Sister relationships are found between Flatidae and Ricaniidae, and between Dictyopharidae and Fulgoridae. Nogodinidae and Issidae are confirmed to be non-monophyletic families. For major nodes of interest, divergence date estimates are generally older than those from the fossil record.

  7. Waste Feed Delivery System Phase 1 Preliminary RAM Analysis

    International Nuclear Information System (INIS)

    DYKES, A.A.

    2000-01-01

    This report presents the updated results of the preliminary reliability, availability, and maintainability (RAM) analysis of selected waste feed delivery (WFD) operations to be performed by the Tank Farm Contractor (TFC) during Phase I activities in support of the Waste Treatment and Immobilization Plant (WTP). For planning purposes, waste feed tanks are being divided into five classes in accordance with the type of waste in each tank and the activities required to retrieve, qualify, and transfer waste feed. This report reflects the baseline design and operating concept, as of the beginning of Fiscal Year 2000, for the delivery of feed from three of these classes, represented by source tanks 241-AN-102, 241-AZ-101 and 241-AN-105. The preliminary RAM analysis quantifies the potential schedule delay associated with operations and maintenance (OBM) field activities needed to accomplish these operations. The RAM analysis is preliminary because the system design, process definition, and activity planning are in a state of evolution. The results are being used to support the continuing development of an O and M Concept tailored to the unique requirements of the WFD Program, which is being documented in various volumes of the Waste Feed Delivery Technical Basis (Carlson. 1999, Rasmussen 1999, and Orme 2000). The waste feed provided to the WTP must: (1) meet limits for chemical and radioactive constituents based on pre-established compositional envelopes (i.e., feed quality); (2) be in acceptable quantities within a prescribed sequence to meet feed quantities; and (3) meet schedule requirements (i.e., feed timing). In the absence of new criteria related to acceptable schedule performance due to the termination of the TWRS Privatization Contract, the original criteria from the Tank Waste Remediation System (77443s) Privatization Contract (DOE 1998) will continue to be used for this analysis

  8. Preliminary analysis of accident in SST-1 current feeder system

    International Nuclear Information System (INIS)

    Roy, Swati; Kanabar, Deven; Garg, Atul; Singh, Amit; Tanna, Vipul; Prasad, Upendra; Srinivasan, R.

    2017-01-01

    Steady-state Tokamak-1 (SST-1) has 16 superconducting Toroidal field (TF) and 9 superconducting poloidal field (PF) coils rated for 10kA DC. All the TF are connected in series and are operated in DC condition whereas PF coils are individually operated in pulse mode during SST-1 campaigns. SST-1 current feeder system (CFS) houses 9 pairs of PF current leads and 1 pair of TF current leads. During past SST-1 campaign, there were arcing incidents within SST-1 CFS chamber which caused significant damage to PF superconducting current leads as well as its Helium cooling lines of the current leads. This paper brings out the preliminary analysis of the mentioned arcing incident, possible reasons and its investigation thereby laying out the sequence of events. From this analysis and observations, various measures to avoid such arcing incidents have also been proposed. (author)

  9. Preliminary Economics for Hydrocarbon Fuel Production from Cellulosic Sugars

    Energy Technology Data Exchange (ETDEWEB)

    Collett, James R.; Meyer, Pimphan A.; Jones, Susanne B.

    2014-05-18

    Biorefinery process and economic models built in CHEMCAD and a preliminary, genome-scale metabolic model for the oleaginous yeast Lipomyces starkeyi were used to simulate the bioconversion of corn stover to lipids, and the upgrading of these hydrocarbon precursors to diesel and jet fuel. The metabolic model was based on the recently released genome sequence for L. starkeyi and on metabolic pathway information from the literature. The process model was based on bioconversion, lipid extraction, and lipid oil upgrading data found in literature, on new laboratory experimental data, and on yield predictions from the preliminary L. starkeyi metabolic model. The current plant gate production cost for a distillate-range hydrocarbon fuel was estimated by the process model Base Case to be $9.5/gallon ($9.0 /gallon of gasoline equivalent) with assumptions of 2011$, 10% internal return on investment, and 2205 ton/day dry feed rate. Opportunities for reducing the cost to below $5.0/gallon, such as improving bioconversion lipid yield and hydrogenation catalyst selectivity, are presented in a Target Case. The process and economic models developed for this work will be updated in 2014 with new experimental data and predictions from a refined metabolic network model for L. starkeyi. Attaining a production cost of $3.0/gallon will require finding higher value uses for lignin other than power generation, such as conversion to additional fuel or to a co-product.

  10. Sedimentation on the Valencia Continental Shelf: Preliminary results

    Science.gov (United States)

    Maldonado, Andres; Swift, Donald J. P.; Young, Robert A.; Han, Gregory; Nittrouer, Charles A.; DeMaster, David J.; Rey, Jorge; Palomo, Carlos; Acosta, Juan; Ballester, A.; Castellvi, J.

    1983-10-01

    Preliminary analysis of data collected during the course of a cooperative Spanish-United States investigation of the Valencia Shelf (western Mediterranean) reveals a storm-dominated, mud-accumulating sedimentary regime. Calcareous mud is accumulating seaward of a narrow band of shoreface sand and gravel. On the outer shelf the mud is enriched by a pelagic calcareous component. Preliminary 210Pb data from vertical profiles of box cores yield nominal accumulation rates from 2.6 mm y -1 near the Ebro Delta to 1.3 mm y -1 on the southern portion of the Valencia Shelf. Storm-current winnowing has resulted in the development of a biogenic lag sand over the mid-shelf mud in the northern part of the study area. Piston cores reveal a basal Holocene sand and gravel facies similar to that presently seen on the inner shelf. Upward-fining sequences on the central and outer shelf are inferred to result from the landward shift of lithotopes during the course of the Holocene transgression. These sequences are locally repeated, perhaps as the consequence of brief, local interludes of coastal progradation. Application of a diagnostic circulation model suggests that intense, downwelling coastal flows occur during winter northeastern storms. Storm activity has induced erosional shoreface retreat during the course of the Holocene transgression and has generated by this means the basal coarse facies observed in the piston cores. In the central part of the study area seaward of the Albufera Lagoon, the mud blanket thins to a layer several centimeters thick which is draped over a thickened (10 m) basal sand. The basal sand is molded into northwest trending ridges. The data are not sufficient to determine whether these are overstepped barriers, or submarine sand ridges formed by storm flows during the shoreface retreat process.

  11. Sequence analysis of Leukemia DNA

    Science.gov (United States)

    Nacong, Nasria; Lusiyanti, Desy; Irawan, Muhammad. Isa

    2018-03-01

    Cancer is a very deadly disease, one of which is leukemia disease or better known as blood cancer. The cancer cell can be detected by taking DNA in laboratory test. This study focused on local alignment of leukemia and non leukemia data resulting from NCBI in the form of DNA sequences by using Smith-Waterman algorithm. SmithWaterman algorithm was invented by TF Smith and MS Waterman in 1981. These algorithms try to find as much as possible similarity of a pair of sequences, by giving a negative value to the unequal base pair (mismatch), and positive values on the same base pair (match). So that will obtain the maximum positive value as the end of the alignment, and the minimum value as the initial alignment. This study will use sequences of leukemia and 3 sequences of non leukemia.

  12. Binning sequences using very sparse labels within a metagenome

    Directory of Open Access Journals (Sweden)

    Halgamuge Saman K

    2008-04-01

    Full Text Available Abstract Background In metagenomic studies, a process called binning is necessary to assign contigs that belong to multiple species to their respective phylogenetic groups. Most of the current methods of binning, such as BLAST, k-mer and PhyloPythia, involve assigning sequence fragments by comparing sequence similarity or sequence composition with already-sequenced genomes that are still far from comprehensive. We propose a semi-supervised seeding method for binning that does not depend on knowledge of completed genomes. Instead, it extracts the flanking sequences of highly conserved 16S rRNA from the metagenome and uses them as seeds (labels to assign other reads based on their compositional similarity. Results The proposed seeding method is implemented on an unsupervised Growing Self-Organising Map (GSOM, and called Seeded GSOM (S-GSOM. We compared it with four well-known semi-supervised learning methods in a preliminary test, separating random-length prokaryotic sequence fragments sampled from the NCBI genome database. We identified the flanking sequences of the highly conserved 16S rRNA as suitable seeds that could be used to group the sequence fragments according to their species. S-GSOM showed superior performance compared to the semi-supervised methods tested. Additionally, S-GSOM may also be used to visually identify some species that do not have seeds. The proposed method was then applied to simulated metagenomic datasets using two different confidence threshold settings and compared with PhyloPythia, k-mer and BLAST. At the reference taxonomic level Order, S-GSOM outperformed all k-mer and BLAST results and showed comparable results with PhyloPythia for each of the corresponding confidence settings, where S-GSOM performed better than PhyloPythia in the ≥ 10 reads datasets and comparable in the ≥ 8 kb benchmark tests. Conclusion In the task of binning using semi-supervised learning methods, results indicate S-GSOM to be the best of

  13. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  14. Optimization of sequence alignment for simple sequence repeat regions

    Directory of Open Access Journals (Sweden)

    Ogbonnaya Francis C

    2011-07-01

    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs. SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic

  15. ADDRESS SEQUENCES FOR MULTI RUN RAM TESTING

    Directory of Open Access Journals (Sweden)

    V. N. Yarmolik

    2014-01-01

    Full Text Available A universal approach for generation of address sequences with specified properties is proposed and analyzed. A modified version of the Antonov and Saleev algorithm for Sobol sequences genera-tion is chosen as a mathematical description of the proposed method. Within the framework of the proposed universal approach, the Sobol sequences form a subset of the address sequences. Other sub-sets are also formed, which are Gray sequences, anti-Gray sequences, counter sequences and sequenc-es with specified properties.

  16. Fast and secure retrieval of DNA sequences

    NARCIS (Netherlands)

    2014-01-01

    Sequence models are retrieved from a sequences index. The sequence models model DNA or RNA sequences stored in a database, and each comprises a finite memory tree source model and parameters for the finite memory tree source model. One or more DNA or RNA sequences stored in the database are

  17. Decidability of uniform recurrence of morphic sequences

    OpenAIRE

    Durand , Fabien

    2012-01-01

    We prove that the uniform recurrence of morphic sequences is decidable. For this we show that the number of derived sequences of uniformly recurrent morphic sequences is bounded. As a corollary we obtain that uniformly recurrent morphic sequences are primitive substitutive sequences.

  18. Preliminary nuclear decommissioning cost study

    International Nuclear Information System (INIS)

    Sissingh, R.A.P.

    1981-04-01

    The decommissioning of a nuclear power plant may involve one or more of three possible options: storage with surveillance (SWS), restricted site release (RSR), and unrestricted site use(USU). This preliminary study concentrates on the logistical, technical and cost aspects of decommissioning a multi-unit CANDU generating station using Pickering GS as the reference design. The procedure chosen for evaluation is: i) removal of the fuel and heavy water followed by decontamination prior to placing the station in SWS for thiry years; ii) complete dismantlement to achieve a USU state. The combination of SWS and USU with an interim period of surveillance allows for radioactive decay and hence less occupational exposure in achieving USU. The study excludes the conventional side of the station, assumes waste disposal repositories are available 1600 km away from the station, and uses only presently available technologies. The dismantlement of all systems except the reactor core can be accomplished using Ontario Hydro's current operating, maintenance and construction procedures. The total decommissioning period is spread out over approximately 40 years, with major activities concentrated in the first and last five years. The estimated dose would be approximately 1800 rem. Overall Pickering GS A costs would be $162,000,000 (1980 Canadian dollars)

  19. Preliminary Iron Distribution on Vesta

    Science.gov (United States)

    Mittlefehldt, David W.; Mittlefehldt, David W.

    2013-01-01

    The distribution of iron on the surface of the asteroid Vesta was investigated using Dawn's Gamma Ray and Neutron Detector (GRaND) [1,2]. Iron varies predictably with rock type for the howardite, eucrite, and diogenite (HED) meteorites, thought to be representative of Vesta. The abundance of Fe in howardites ranges from about 12 to 15 wt.%. Basaltic eucrites have the highest abundance, whereas, lower crustal and upper mantle materials (cumulate eucrites and diogenites) have the lowest, and howardites are intermediate [3]. We have completed a mapping study of 7.6 MeV gamma rays produced by neutron capture by Fe as measured by the bismuth germanate (BGO) detector of GRaND [1]. The procedures to determine Fe counting rates are presented in detail here, along with a preliminary distribution map, constituting the necessary initial step to quantification of Fe abundances. We find that the global distribution of Fe counting rates is generally consistent with independent mineralogical and compositional inferences obtained by other instruments on Dawn such as measurements of pyroxene absorption bands by the Visual and Infrared Spectrometer (VIR) [4] and Framing Camera (FC) [5] and neutron absorption measurements by GRaND [6].

  20. Stardust Interstellar Preliminary Examination (ISPE)

    Science.gov (United States)

    Westphal, A. J.; Allen, C.; Bajt, S.; Basset, R.; Bastien, R.; Bechtel, H.; Bleuet, P.; Borg, J.; Brenker F.; Bridges, J.

    2009-01-01

    In January 2006 the Stardust sample return capsule returned to Earth bearing the first solid samples from a primitive solar system body, C omet 81P/Wild2, and a collector dedicated to the capture and return o f contemporary interstellar dust. Both collectors were approximately 0.1m(exp 2) in area and were composed of aerogel tiles (85% of the co llecting area) and aluminum foils. The Stardust Interstellar Dust Col lector (SIDC) was exposed to the interstellar dust stream for a total exposure factor of 20 m(exp 2-) day during two periods before the co metary encounter. The Stardust Interstellar Preliminary Examination ( ISPE) is a three-year effort to characterize the collection using no ndestructive techniques. The ISPE consists of six interdependent proj ects: (1) Candidate identification through automated digital microsco py and a massively distributed, calibrated search (2) Candidate extr action and photodocumentation (3) Characterization of candidates thro ugh synchrotronbased FourierTranform Infrared Spectroscopy (FTIR), S canning XRay Fluoresence Microscopy (SXRF), and Scanning Transmission Xray Microscopy (STXM) (4) Search for and analysis of craters in f oils through FESEM scanning, Auger Spectroscopy and synchrotronbased Photoemission Electron Microscopy (PEEM) (5) Modeling of interstell ar dust transport in the solar system (6) Laboratory simulations of h ypervelocity dust impacts into the collecting media

  1. Preliminary design of smart fuel

    International Nuclear Information System (INIS)

    Kim, Y.; Ha, D.; Park, S.; Nahm, K.; Lee, K.; Kim, J.

    2007-01-01

    SMART (System-integrated Modular Advanced Reactor) is a novel light water rector with a modular, integral primary system configuration. This concept has been developing a 660 MWt by Korean Nuclear Power Industry Group with KAERI. SMART is being developed for use as an energy source for small-scale power generation and seawater desalination. Although the design of SMART is based on the current pressurized water reactor technology, new technologies such as enhanced safety, and passive safety have been applied, and system simplification and modularization, innovations in manufacturing and installation technologies have been implemented culminating in a design that has enhanced safety and economy, and is environment -friendly. In this paper described the preliminary design of the nuclear Fuel for this SMART, the design concept and the characteristics of SMART Fuel. In specially this paper describe the optimization of grid span adjustment to improve the thermal performance of the SMART Fuel as well as to improve the seismic resistance performance of the SMART Fuel, it is not easy to improve the both performance simultaneously because of design parameter of each performance inversely proportional. SMART Fuel enable to extra-long extended fuel cycle length and resistance of proliferation, enhanced safety, improved economics and reduced nuclear waste

  2. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  3. Preliminary design study of the TMT Telescope structure system: overview

    Science.gov (United States)

    Usuda, Tomonori; Ezaki, Yutaka; Kawaguchi, Noboru; Nagae, Kazuhiro; Kato, Atsushi; Takaki, Junji; Hirano, Masaki; Hattori, Tomoya; Tabata, Masaki; Horiuchi, Yasushi; Saruta, Yusuke; Sofuku, Satoru; Itoh, Noboru; Oshima, Takeharu; Takanezawa, Takashi; Endo, Makoto; Inatani, Junji; Iye, Masanori; Sadjadpour, Amir; Sirota, Mark; Roberts, Scott; Stepp, Larry

    2014-07-01

    We present an overview of the preliminary design of the Telescope Structure System (STR) of Thirty Meter Telescope (TMT). NAOJ was given responsibility for the TMT STR in early 2012 and engaged Mitsubishi Electric Corporation (MELCO) to take over the preliminary design work. MELCO performed a comprehensive preliminary design study in 2012 and 2013 and the design successfully passed its Preliminary Design Review (PDR) in November 2013 and April 2014. Design optimizations were pursued to better meet the design requirements and improvements were made in the designs of many of the telescope subsystems as follows: 1. 6-legged Top End configuration to support secondary mirror (M2) in order to reduce deformation of the Top End and to keep the same 4% blockage of the full aperture as the previous STR design. 2. "Double Lower Tube" of the elevation (EL) structure to reduce the required stroke of the primary mirror (M1) actuators to compensate the primary mirror cell (M1 Cell) deformation caused during the EL angle change in accordance with the requirements. 3. M1 Segment Handling System (SHS) to be able to make removing and installing 10 Mirror Segment Assemblies per day safely and with ease over M1 area where access of personnel is extremely difficult. This requires semi-automatic sequence operation and a robotic Segment Lifting Fixture (SLF) designed based on the Compliance Control System, developed for controlling industrial robots, with a mechanism to enable precise control within the six degrees of freedom of position control. 4. CO2 snow cleaning system to clean M1 every few weeks that is similar to the mechanical system that has been used at Subaru Telescope. 5. Seismic isolation and restraint systems with respect to safety; the maximum acceleration allowed for M1, M2, tertiary mirror (M3), LGSF, and science instruments in 1,000 year return period earthquakes are defined in the requirements. The Seismic requirements apply to any EL angle, regardless of the

  4. Discovery of a trachyte ignimbrite sequence at Hualālai, Hawaii

    OpenAIRE

    Shea, Thomas; Owen, Jacqueline

    2016-01-01

    Ignimbrites are common in many intraplate ocean islands but have been missing from the known geological record in Hawaii. During a recent field campaign, the remnants of a trachytic ignimbrite sequence have been discovered at Hualālai volcano, fortuitously preserved from subsequent basaltic lava flow cover. We provide a preliminary description of these deposits, as well as bulk and glass chemical analyses to determine their potential relationship with other nearby trachytes from Pu’u Wa’awa’a...

  5. Modelling of blackout sequence at Atucha-1 using the MARCH3 code

    International Nuclear Information System (INIS)

    Baron, J.; Bastianelli, B.

    1997-01-01

    This paper presents the modelling of a complete blackout at the Atucha-1 NPP as preliminary phase for a Level II safety probabilistic analysis. The MARCH3 code of the STCP (Source Term Code Package) is used, based on a plant model made in accordance with particularities of the plant design. The analysis covers all the severe accident phases. The results allow to view the time sequence of the events, and provide the basis for source term studies. (author). 6 refs., 2 figs

  6. Authentication by Keystroke Timing: Some Preliminary Results

    National Research Council Canada - National Science Library

    Gaines, R. S; Lisowski, William; Press, S. J; Shapiro, Norman

    1980-01-01

    ... of an individual seeking access to the computer. This report summarizes preliminary efforts to establish whether an individual can be identified by the statistical characteristics of his or her typing...

  7. Preliminary Phytochemical and Physicochemical Characterization of ...

    African Journals Online (AJOL)

    Purpose: To carry out phytochemical and physicochemical studies on the leaves of Gynura segetum. Methods: Preliminary phytochemical and physicochemical studies using chromatographic techniques,were carried out, Parameters evaluated include ash value, loss on drying and extractive value, amongst others.

  8. Original Article PRELIMINARY BIOAUTOGRAPHIC ANALYSIS OF ...

    African Journals Online (AJOL)

    PRELIMINARY BIOAUTOGRAPHIC ANALYSIS OF THE SEEDS OF GLYPHAEA BREVIS. (SPRENG) MONACHINO FOR ANTIOXIDANT AND ANTIBACTERIAL PRINCIPLES. Michael Lahai1, Tiwalade Adewale Olugbade2. 1Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, College of Medicine ...

  9. Preliminary engineering cost trends for highway projects.

    Science.gov (United States)

    2011-10-21

    Preliminary engineering (PE) for a highway project encompasses two efforts: planning to minimize the physical, social, and human environmental impacts of projects and engineering design to deliver the best alternative. PE efforts begin years in advan...

  10. Preliminary Analysis of Reinforced Concrete Waffle Walls

    National Research Council Canada - National Science Library

    Shugar, Theodore

    1997-01-01

    A preliminary analytical method based upon modified plate bending theory is offered for structural analysis of a promising new construction method for walls of small buildings and residential housing...

  11. Preliminary design data package. Appendix C

    Energy Technology Data Exchange (ETDEWEB)

    1979-07-25

    The design requirements, design philosophy, method and assumptions, and preliminary computer-aided design of the Near-Term Hybrid Vehicle including its electric and heat power units, control equipment, transmission system, body, and overall vehicle characteristics are presented. (LCL)

  12. Renewable Energy Park - Preliminary Feasibility & Engineering Report

    Energy Technology Data Exchange (ETDEWEB)

    Ariwite, Roderick [Fallon Paiute Shoshone Tribe, NV (United States)

    2015-07-31

    This "Renewable Energy Park - Preliminary Feasibility & Engineering Report" seeks to provide an overall assessment and review of renewable energy development opportunities on the Fallon Indian Reservation and Colony Lands.

  13. Decentralised wastewater treatment effluent fertigation: preliminary ...

    African Journals Online (AJOL)

    Decentralised wastewater treatment effluent fertigation: preliminary technical assessment. ... living in informal settlements with the effluent produced being used on agricultural land. ... Banana and taro required 3 514 mm of irrigation effluent.

  14. Analysis of Pteridium ribosomal RNA sequences by rapid direct sequencing.

    Science.gov (United States)

    Tan, M K

    1991-08-01

    A total of 864 bases from 5 regions interspersed in the 18S and 26S rRNA molecules from various clones of Pteridium covering the general geographical distribution of the genus was analysed using a rapid rRNA sequencing technique. No base difference has been detected amongst the three major lineages, two of which apparently separated before the breakup of the ancient supercontinent, Pangaea. These regions of the rRNA sequences have thus been conserved for at least 160 million years and are here compared with other eukaryotic, especially plant rRNAs.

  15. Sirius PSB: a generic system for analysis of biological sequences.

    Science.gov (United States)

    Koh, Chuan Hock; Lin, Sharene; Jedd, Gregory; Wong, Limsoon

    2009-12-01

    Computational tools are essential components of modern biological research. For example, BLAST searches can be used to identify related proteins based on sequence homology, or when a new genome is sequenced, prediction models can be used to annotate functional sites such as transcription start sites, translation initiation sites and polyadenylation sites and to predict protein localization. Here we present Sirius Prediction Systems Builder (PSB), a new computational tool for sequence analysis, classification and searching. Sirius PSB has four main operations: (1) Building a classifier, (2) Deploying a classifier, (3) Search for proteins similar to query proteins, (4) Preliminary and post-prediction analysis. Sirius PSB supports all these operations via a simple and interactive graphical user interface. Besides being a convenient tool, Sirius PSB has also introduced two novelties in sequence analysis. Firstly, genetic algorithm is used to identify interesting features in the feature space. Secondly, instead of the conventional method of searching for similar proteins via sequence similarity, we introduced searching via features' similarity. To demonstrate the capabilities of Sirius PSB, we have built two prediction models - one for the recognition of Arabidopsis polyadenylation sites and another for the subcellular localization of proteins. Both systems are competitive against current state-of-the-art models based on evaluation of public datasets. More notably, the time and effort required to build each model is greatly reduced with the assistance of Sirius PSB. Furthermore, we show that under certain conditions when BLAST is unable to find related proteins, Sirius PSB can identify functionally related proteins based on their biophysical similarities. Sirius PSB and its related supplements are available at: http://compbio.ddns.comp.nus.edu.sg/~sirius.

  16. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

    2018-01-01

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  17. Genome Sequences of Oryza Species

    KAUST Repository

    Kumagai, Masahiko

    2018-02-14

    This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

  18. Transformed composite sequences for improved qubit addressing

    Science.gov (United States)

    Merrill, J. True; Doret, S. Charles; Vittorini, Grahame; Addison, J. P.; Brown, Kenneth R.

    2014-10-01

    Selective laser addressing of a single atom or atomic ion qubit can be improved using narrow-band composite pulse sequences. We describe a Lie-algebraic technique to generalize known narrow-band sequences and introduce sequences related by dilation and rotation of sequence generators. Our method improves known narrow-band sequences by decreasing both the pulse time and the residual error. Finally, we experimentally demonstrate these composite sequences using 40Ca+ ions trapped in a surface-electrode ion trap.

  19. Survey of transposable elements in sugarcane expressed sequence tags (ESTs

    Directory of Open Access Journals (Sweden)

    Rossi Magdalena

    2001-01-01

    Full Text Available The sugarcane expressed sequence tag (SUCEST project has produced a large number of cDNA sequences from several plant tissues submitted or not to different conditions of stress. In this paper we report the result of a search for transposable elements (TEs revealing a surprising amount of expressed TEs homologues. Of the 260,781 sequences grouped in 81,223 fragment assembly program (Phrap clusters, a total of 276 clones showed homology to previously reported TEs using a stringent cut-off value of e-50 or better. Homologous clones to Copia/Ty1 and Gypsy/Ty3 groups of long terminal repeat (LTR retrotransposons were found but no non-LTR retroelements were identified. All major transposon families were represented in sugarcane including Activator (Ac, Mutator (MuDR, Suppressor-mutator (En/Spm and Mariner. In order to compare the TE diversity in grasses genomes, we carried out a search for TEs described in sugarcane related species O.sativa, Z. mays and S. bicolor. We also present preliminary results showing the potential use of TEs insertion pattern polymorphism as molecular markers for cultivar identification.

  20. TECHNOLOGY FOR INSTALLATION OF REINFORCED CONCRETE FLOOR SLABS LIGHTENED BY CORE DRIVERS WITH PRELIMINARY REINFORCEMENT STRESS

    Directory of Open Access Journals (Sweden)

    S. N. Leonovich

    2015-01-01

    Full Text Available The paper presents technology for installation of floor slabs lightened by plastic core drivers which are preliminary stressed under construction conditions.  Efficiency of such constructive solution is justified by the action of preliminary concrete compression in the tensile zone while reducing structure dead weight due to void arrangement.  The paper provides classification of systems for preliminary stress and contains recommendations on selection of the system depending on peculiariar features of the designed construction.  Main products and materials required for execution of works , requirements to stressed wire rope reinforcement, its main characteristics have been considered in the paper.Principal diagram of the lightened preliminary stressed slab stipulates arrangement of so called  dummy caisson. Strands of reinforcement ropes are located within the framework of bars passing over supporting structures (over vertical bearing structures of  the framework and voids are formed in the cells between bars by laying hollow plastic items joined together by a cage. The paper presents technological sequence of operations required for arrangement of the lightened preliminary stressed slab, schemes for equipment arrangement and characteristics of the applied devices and units (pushing device for reinforcement ropes, hydraulic jack with delivery hydraulic pump, mixing station, injection pump and others.  Recommendations have been given for execution of works in cold weather. The paper considers problems pertaining to control quality of the materials and items which are supplied to a construction site and directly execution of works on preliminary stress of a cellular slab.The executed analysis of technology permits to conclude that it is characterized by high level of applicability for import substitution. It is necessary to consider the possibility to apply the technology at objects of various application while comparing it with other

  1. Sequences, groups, and number theory

    CERN Document Server

    Rigo, Michel

    2018-01-01

    This collaborative book presents recent trends on the study of sequences, including combinatorics on words and symbolic dynamics, and new interdisciplinary links to group theory and number theory. Other chapters branch out from those areas into subfields of theoretical computer science, such as complexity theory and theory of automata. The book is built around four general themes: number theory and sequences, word combinatorics, normal numbers, and group theory. Those topics are rounded out by investigations into automatic and regular sequences, tilings and theory of computation, discrete dynamical systems, ergodic theory, numeration systems, automaton semigroups, and amenable groups.  This volume is intended for use by graduate students or research mathematicians, as well as computer scientists who are working in automata theory and formal language theory. With its organization around unified themes, it would also be appropriate as a supplemental text for graduate level courses.

  2. Explaining the harmonic sequence paradox.

    Science.gov (United States)

    Schmidt, Ulrich; Zimper, Alexander

    2012-05-01

    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced. ©2011 The British Psychological Society.

  3. Dissociation - a preliminary contextual model

    Directory of Open Access Journals (Sweden)

    C Krüger

    2007-02-01

    Full Text Available Background. The Diagnostic and Statistical Manual of Mental Disorders (DSM system has certain limitations when applied to two South African examples of dissociation, because it is descriptive (non-explanatory and focuses on intrapsychic (non-communal processes. Even the existing Western explanatory models of dissociation fail to accommodate fully the communal aspects of dissociation in our South African context. Objectives and methods. The aim was to explore an expanded perspective on dissociation that does not limit it to an intrapsychic phenomenon, but that accounts for the interrelatedness of individuals within their social context. Auto-ethnography was used. In this article a collective, socially orientated, contextual hermeneutic was applied to two local examples of dissociation. Three existing Western models were expanded along multicontextual, collective lines, for them to be more useful in the pluralistic South African context. Results. This preliminary contextual model of dissociation includes a person’s interpersonal, socio-cultural, and spiritual contexts, in addition to the intrapsychic context. Dissociation is considered to be a normal information-processing tool that maintains balanced, coherent selves-in-society, i.e. individuals connected to each other. In the South African context dissociation appears mostly as a normal phenomenon and seldom as a sign of mental illness. Dissociation is pivotal for the normal construction of individual and communal identities in the face of conflicting sets of information from various contexts. Dissociation may help individuals or communities to survive in a world of conflicting messages, where conflict is often interpersonal/cultural/societal in nature, rather than primarily intrapsychic. Conclusions. This model should be developed and evaluated further. Such evaluation would require suitable new local terminology.

  4. Project Rulison: A preliminary report

    Energy Technology Data Exchange (ETDEWEB)

    Reynolds, Miles Jr [Austral Oil Company Incorporated, Houston, TX (United States); Bray, Bruce G; Mann, Robert L [CER Geonuclear Corporation, Las Vegas, NV (United States)

    1970-05-01

    Project Rulison was designed to use underground nuclear technology to determine the potential of this technique for commercial development of the deep, thick, lenticular, low permeability, Mesaverde Formation of the Rulison Field in Garfield County, Colorado. Since discovery in 1952, this reservoir has been tested by nine widely-spaced conventionally completed wells. A method of stimulation, far greater in magnitude and efficiency than conventional hydraulic fracturing, is needed to recover this gas at economic rates. A feasibility study completed in July 1966 indicated that nuclear explosives were a potentially economic method of stimulating recovery of natural gas from the reservoir. The gas-in-place, estimated to be between 90-125 billion cubic feet per 640 acres from earlier wells, was confirmed from information obtained on two conventional wells completed in 1966. The Project Rulison exploratory well, R-EX, was completed in May 1968. Detailed testing of this well provided data on geology, hydrology and reservoir characteristics. The data obtained from the testing have been used to determine the flow capacity of the Mesaverde reservoir. The reservoir characteristics were then used as input data to make predictions of post-shot reservoir performance in the nuclear stimulated well, using a radial, unsteady state gas flow computer model. A nuclear explosive with a design yield of 40 kilotons was emplaced in a 10-3/4 inch hole at a depth of 8426 feet below ground surface and detonated on September 10, 1969. A preliminary appraisal of the data taken at shot time indicate that the explosive behaved as predicted. The explosion was completely contained underground as predicted and no major seismic damage occurred. The post-shot drilling program, to reenter the chimney, will congruence in March 1970, approximately six months after detonation. A test program will be initiated at that time to determine the degree of reservoir stimulation achieved. (author)

  5. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  6. Matrix transformations and sequence spaces

    International Nuclear Information System (INIS)

    Nanda, S.

    1983-06-01

    In most cases the most general linear operator from one sequence space into another is actually given by an infinite matrix and therefore the theory of matrix transformations has always been of great interest in the study of sequence spaces. The study of general theory of matrix transformations was motivated by the special results in summability theory. This paper is a review article which gives almost all known results on matrix transformations. This also suggests a number of open problems for further study and will be very useful for research workers. (author)

  7. Green's theorem and Gorenstein sequences

    OpenAIRE

    Ahn, Jeaman; Migliore, Juan C.; Shin, Yong-Su

    2016-01-01

    We study consequences, for a standard graded algebra, of extremal behavior in Green's Hyperplane Restriction Theorem. First, we extend his Theorem 4 from the case of a plane curve to the case of a hypersurface in a linear space. Second, assuming a certain Lefschetz condition, we give a connection to extremal behavior in Macaulay's theorem. We apply these results to show that $(1,19,17,19,1)$ is not a Gorenstein sequence, and as a result we classify the sequences of the form $(1,a,a-2,a,1)$ th...

  8. Generalized min-max bound-based MRI pulse sequence design framework for wide-range T1 relaxometry: A case study on the tissue specific imaging sequence.

    Directory of Open Access Journals (Sweden)

    Yang Liu

    Full Text Available This paper proposes a new design strategy for optimizing MRI pulse sequences for T1 relaxometry. The design strategy optimizes the pulse sequence parameters to minimize the maximum variance of unbiased T1 estimates over a range of T1 values using the Cramér-Rao bound. In contrast to prior sequences optimized for a single nominal T1 value, the optimized sequence using our bound-based strategy achieves improved precision and accuracy for a broad range of T1 estimates within a clinically feasible scan time. The optimization combines the downhill simplex method with a simulated annealing process. To show the effectiveness of the proposed strategy, we optimize the tissue specific imaging (TSI sequence. Preliminary Monte Carlo simulations demonstrate that the optimized TSI sequence yields improved precision and accuracy over the popular driven-equilibrium single-pulse observation of T1 (DESPOT1 approach for normal brain tissues (estimated T1 700-2000 ms at 3.0T. The relative mean estimation error (MSE for T1 estimation is less than 1.7% using the optimized TSI sequence, as opposed to less than 7.0% using DESPOT1 for normal brain tissues. The optimized TSI sequence achieves good stability by keeping the MSE under 7.0% over larger T1 values corresponding to different lesion tissues and the cerebrospinal fluid (up to 5000 ms. The T1 estimation accuracy using the new pulse sequence also shows improvement, which is more pronounced in low SNR scenarios.

  9. Sequences in language and text

    CERN Document Server

    Mikros, George K

    2015-01-01

    The aim of this volume is to present the diverse but highly interesting area of the quantitative analysis of the sequence of various linguistic structures. The collected articles present a wide spectrum of quantitative analyses of linguistic syntagmatic structures and explore novel sequential linguistic entities. This volume will be interesting to all researchers studying linguistics using quantitative methods.

  10. Probabilistic studies of accident sequences

    International Nuclear Information System (INIS)

    Villemeur, A.; Berger, J.P.

    1986-01-01

    For several years, Electricite de France has carried out probabilistic assessment of accident sequences for nuclear power plants. In the framework of this program many methods were developed. As the interest in these studies was increasing and as adapted methods were developed, Electricite de France has undertaken a probabilistic safety assessment of a nuclear power plant [fr

  11. MRI sequences and their parameters

    International Nuclear Information System (INIS)

    Teissier, J.M.

    1993-01-01

    Listing basic sequences and their present variants makes a synthetic classification of the various acquisition modes possible. The knowledge of the advantages of each of them, as well as of their disadvantages and restraints, seems to be an essential prerequisite to an optimal utilization of each magnetic resonance imaging system. (author)

  12. Degree sequence in message transfer

    Science.gov (United States)

    Yamuna, M.

    2017-11-01

    Message encryption is always an issue in current communication scenario. Methods are being devised using various domains. Graphs satisfy numerous unique properties which can be used for message transfer. In this paper, I propose a message encryption method based on degree sequence of graphs.

  13. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)

    2002-01-01

    Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

  14. On primes in Lucas sequences

    Czech Academy of Sciences Publication Activity Database

    Křížek, Michal; Somer, L.

    2015-01-01

    Roč. 53, č. 1 (2015), s. 2-23 ISSN 0015-0517 R&D Projects: GA ČR GA14-02067S Institutional support: RVO:67985840 Keywords : Lucas sequence * primes Subject RIV: BA - General Mathematics http://www.fq.math.ca/Abstracts/53-1/somer.pdf

  15. Births: preliminary data for 2005.

    Science.gov (United States)

    Hamilton, Brady E; Martin, Joyce A; Ventura, Stephanie J

    2006-12-28

    This report presents preliminary data for 2005 on births in the United States. U.S. data on births are shown by age, live-birth order, race, and Hispanic origin of mother. Data on marital status, cesarean delivery, preterm births, and low birthweight (LBW) are also presented. Data in this report are based on 99.2 percent of births for 2005. The records are weighted to independent control counts of all births received in state vital statistics offices in 2005. Comparisons are made with 2004 data. The crude birth rate in 2005 was 14.0 births per 1,000 total population, unchanged from 2004. The general fertility rate, however, rose to 66.7 births per 1,000 women aged 15-44 years in 2005, the highest level since 1993. The birth rate for teenagers declined by 2 percent in 2005, falling to 40.4 births per 1,000 women aged 15-19 years, the lowest ever recorded in the 65 years for which a consistent series of rates are available. The rate declined for teenagers 15-17 years to 21.4 births per 1,000, but was essentially stable for older teenagers 18-19 years. The birth rate for women aged 20-24 years rose in 2005, whereas the rate for women aged 25-29 years was essentially unchanged. The birth rates for women aged 30 years and over rose to levels not seen in almost 40 years. Childbearing by unmarried women increased to record levels for the Nation in 2005. The birth rate rose 3 percent to 47.6 births per 1,000 unmarried women aged 15-44 years; the proportion of all births to unmarried women increased to 36.8 percent. The cesarean delivery rate rose by 4 percent in 2005 to 30.2 percent of all births, another record high for the Nation. The preterm birth rate continued to rise (to 12.7 percent in 2005) as did the rate for LBW births (8.2 percent).

  16. Births: preliminary data for 2000.

    Science.gov (United States)

    Martin, J A; Hamilton, B E; Ventura, S J

    2001-07-24

    This report presents preliminary data for 2000 on births in the United States. U.S. data on births are shown by age, race, and Hispanic origin of mother. Data on marital status, prenatal care, cesarean delivery, and low birthweight are also presented. Data in this report are based on more than 96 percent of births for 2000. The records are weighted to independent control counts of births received in State vital statistics offices in 2000. Comparisons are made with 1999 final data. The number of births rose 3 percent between 1999 and 2000. The crude birth rate increased to 14.8 per 1,000 population in 2000, 2 percent higher than the 1999 rate. The fertility rate rose 3 percent to 67.6 per 1,000 women aged 15-44 years between 1999 and 2000. The birth rate for teenagers, which has been falling since 1991, declined 2 percent in 2000 to 48.7 births per 1,000 females aged 15-19 years, another historic low. The rate for teenagers 15-17 years fell 4 percent, and the rate for 18-19 year olds was down 1 percent. Since 1991, rates have fallen 29 percent for teenagers 15-17 years and 16 percent for teenagers 18-19 years. Birth rates for all of the older age groups increased for 1999-2000: 1 percent among women aged 20-24 years, 3 percent for women aged 25-29 years, and 5 percent for women in their thirties. Rates for women aged 40-54 years were also up for 2000. The birth rate for unmarried women increased 2 percent to 45.2 births per 1,000 unmarried women aged 15-44 years in 2000, but was still lower than the peak reached in 1994. The number of births to unmarried women was up 3 percent, the highest number ever reported in the United States. However, the number of births to unmarried teenagers declined. The proportion of women who began prenatal care in the first trimester of pregnancy (83.2 percent) did not improve for 2000, nor did the rate of low birthweight (7.6 percent). The total cesarean rate rose for the fourth consecutive year to 22.9 percent, the result of both a

  17. Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

    Science.gov (United States)

    Deroost, Natacha; Coomans, Daphné

    2018-02-01

    We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

  18. Microbiological profile of chicken carcasses: A comparative analysis using shotgun metagenomic sequencing

    Directory of Open Access Journals (Sweden)

    Alessandra De Cesare

    2018-04-01

    Full Text Available In the last few years metagenomic and 16S rRNA sequencing have completly changed the microbiological investigations of food products. In this preliminary study, the microbiological profile of chicken carcasses collected from animals fed with different diets were tested by using shotgun metagenomic sequencing. A total of 15 carcasses have been collected at the slaughetrhouse at the end of the refrigeration tunnel from chickens reared for 35 days and fed with a control diet (n=5, a diet supplemented with 1500 FTU/kg of commercial phytase (n=5 and a diet supplemented with 1500 FTU/kg of commercial phytase and 3g/kg of inositol (n=5. Ten grams of neck and breast skin were obtained from each carcass and submited to total DNA extraction by using the DNeasy Blood & Tissue Kit (Qiagen. Sequencing libraries have been prepared by using the Nextera XT DNA Library Preparation Kit (Illumina and sequenced in a HiScanSQ (Illumina at 100 bp in paired ends. A number of sequences ranging between 5 and 9 million was obtained for each sample. Sequence analysis showed that Proteobacteria and Firmicutes represented more than 98% of whole bacterial populations associated to carcass skin in all groups but their abundances were different between groups. Moraxellaceae and other degradative bacteria showed a significantly higher abundance in the control compared to the treated groups. Furthermore, Clostridium perfringens showed a relative frequency of abundance significantly higher in the group fed with phytase and Salmonella enterica in the group fed with phytase plus inositol. The results of this preliminary study showed that metagenome sequencing is suitable to investigate and monitor carcass microbiota in order to detect specific pathogenic and/or degradative populations.

  19. Teaching Task Sequencing via Verbal Mediation.

    Science.gov (United States)

    Rusch, Frank R.; And Others

    1987-01-01

    Verbal sequence training was used to teach a moderately mentally retarded woman to sequence job-related tasks. Learning to say the tasks in the proper sequence resulted in the employee performing her tasks in that sequence, and the employee was capable of mediating her own work behavior when scheduled changes occurred. (Author/JDD)

  20. Repdigits in k-Lucas sequences

    Indian Academy of Sciences (India)

    57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence ( L n ( 2 ) ) n . In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences ...

  1. Orbital motion in pre-main sequence binaries

    Energy Technology Data Exchange (ETDEWEB)

    Schaefer, G. H. [The CHARA Array of Georgia State University, Mount Wilson Observatory, Mount Wilson, CA 91023 (United States); Prato, L. [Lowell Observatory, 1400 West Mars Hill Road, Flagstaff, AZ 86001 (United States); Simon, M. [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794 (United States); Patience, J., E-mail: schaefer@chara-array.org [Astrophysics Group, School of Physics, University of Exeter, Exeter, EX4 4QL (United Kingdom)

    2014-06-01

    We present results from our ongoing program to map the visual orbits of pre-main sequence (PMS) binaries in the Taurus star forming region using adaptive optics imaging at the Keck Observatory. We combine our results with measurements reported in the literature to analyze the orbital motion for each binary. We present preliminary orbits for DF Tau, T Tau S, ZZ Tau, and the Pleiades binary HBC 351. Seven additional binaries show curvature in their relative motion. Currently, we can place lower limits on the orbital periods for these systems; full solutions will be possible with more orbital coverage. Five other binaries show motion that is indistinguishable from linear motion. We suspect that these systems are bound and might show curvature with additional measurements in the future. The observations reported herein lay critical groundwork toward the goal of measuring precise masses for low-mass PMS stars.

  2. Crystallization and preliminary crystallographic characterization of the PAS domains of EAG and ELK potassium channels

    International Nuclear Information System (INIS)

    Adaixo, Ricardo; Morais-Cabral, João Henrique

    2010-01-01

    The N-terminal PAS domains from the eukaryotic EAG potassium channels are thought to have a regulatory function. Here the expression, purification, crystallization and preliminary crystallographic characterization of two of these domains are described. Per–Arnt–Sim (PAS) domains are ubiquitous in nature; they are ∼130-amino-acid protein domains that adopt a fairly conserved three-dimensional structure despite their low degree of sequence homology. These domains constitute the N-terminus or, less frequently, the C-terminus of a number of proteins, where they exert regulatory functions. PAS-containing proteins generally display two or more copies of this motif. In this work, the crystallization and preliminary analysis of the PAS domains of two eukaryotic potassium channels from the ether-à-go-go (EAG) family are reported

  3. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying

    2012-02-01

    This article proposes a nonparametric method for estimating the period and values of a periodic sequence when the data are evenly spaced in time. The period is estimated by a "leave-out-one-cycle" version of cross-validation (CV) and complements the periodogram, a widely used tool for period estimation. The CV method is computationally simple and implicitly penalizes multiples of the smallest period, leading to a "virtually" consistent estimator of integer periods. This estimator is investigated both theoretically and by simulation.We also propose a nonparametric test of the null hypothesis that the data have constantmean against the alternative that the sequence of means is periodic. Finally, our methodology is demonstrated on three well-known time series: the sunspots and lynx trapping data, and the El Niño series of sea surface temperatures. © 2012 American Statistical Association and the American Society for Quality.

  4. Multi-qubit compensation sequences

    International Nuclear Information System (INIS)

    Tomita, Y; Merrill, J T; Brown, K R

    2010-01-01

    The Hamiltonian control of n qubits requires precision control of both the strength and timing of interactions. Compensation pulses relax the precision requirements by reducing unknown but systematic errors. Using composite pulse techniques designed for single qubits, we show that systematic errors for n-qubit systems can be corrected to arbitrary accuracy given either two non-commuting control Hamiltonians with identical systematic errors or one error-free control Hamiltonian. We also examine composite pulses in the context of quantum computers controlled by two-qubit interactions. For quantum computers based on the XY interaction, single-qubit composite pulse sequences naturally correct systematic errors. For quantum computers based on the Heisenberg or exchange interaction, the composite pulse sequences reduce the logical single-qubit gate errors but increase the errors for logical two-qubit gates.

  5. Cassini Mission Sequence Subsystem (MSS)

    Science.gov (United States)

    Alland, Robert

    2011-01-01

    This paper describes my work with the Cassini Mission Sequence Subsystem (MSS) team during the summer of 2011. It gives some background on the motivation for this project and describes the expected benefit to the Cassini program. It then introduces the two tasks that I worked on - an automatic system auditing tool and a series of corrections to the Cassini Sequence Generator (SEQ_GEN) - and the specific objectives these tasks were to accomplish. Next, it details the approach I took to meet these objectives and the results of this approach, followed by a discussion of how the outcome of the project compares with my initial expectations. The paper concludes with a summary of my experience working on this project, lists what the next steps are, and acknowledges the help of my Cassini colleagues.

  6. Post-contrast T1-weighted sequences in pediatric abdominal imaging: comparative analysis of three different sequences and imaging approach

    Energy Technology Data Exchange (ETDEWEB)

    Roque, Andreia; Ramalho, Miguel; AlObaidy, Mamdoh; Heredia, Vasco; Burke, Lauren M.; De Campos, Rafael O.P.; Semelka, Richard C. [University of North Carolina at Chapel Hill, Department of Radiology, Chapel Hill, NC (United States)

    2014-10-15

    Post-contrast T1-weighted imaging is an essential component of a comprehensive pediatric abdominopelvic MR examination. However, consistent good image quality is challenging, as respiratory motion in sedated children can substantially degrade the image quality. To compare the image quality of three different post-contrast T1-weighted imaging techniques - standard three-dimensional gradient-echo (3-D-GRE), magnetization-prepared gradient-recall echo (MP-GRE) and 3-D-GRE with radial data sampling (radial 3-D-GRE) - acquired in pediatric patients younger than 5 years of age. Sixty consecutive exams performed in 51 patients (23 females, 28 males; mean age 2.5 ± 1.4 years) constituted the final study population. Thirty-nine scans were performed at 3 T and 21 scans were performed at 1.5 T. Two different reviewers independently and blindly qualitatively evaluated all sequences to determine image quality and extent of artifacts. MP-GRE and radial 3-D-GRE sequences had the least respiratory motion (P < 0.0001). Standard 3-D-GRE sequences displayed the lowest average score ratings in hepatic and pancreatic edge definition, hepatic vessel clarity and overall image quality. Radial 3-D-GRE sequences showed the highest scores ratings in overall image quality. Our preliminary results support the preference of fat-suppressed radial 3-D-GRE as the best post-contrast T1-weighted imaging approach for patients under the age of 5 years, when dynamic imaging is not essential. (orig.)

  7. Dinoflagellate phylogeny as inferred from heat shock protein 90 and ribosomal gene sequences.

    Directory of Open Access Journals (Sweden)

    Mona Hoppenrath

    2010-10-01

    Full Text Available Interrelationships among dinoflagellates in molecular phylogenies are largely unresolved, especially in the deepest branches. Ribosomal DNA (rDNA sequences provide phylogenetic signals only at the tips of the dinoflagellate tree. Two reasons for the poor resolution of deep dinoflagellate relationships using rDNA sequences are (1 most sites are relatively conserved and (2 there are different evolutionary rates among sites in different lineages. Therefore, alternative molecular markers are required to address the deeper phylogenetic relationships among dinoflagellates. Preliminary evidence indicates that the heat shock protein 90 gene (Hsp90 will provide an informative marker, mainly because this gene is relatively long and appears to have relatively uniform rates of evolution in different lineages.We more than doubled the previous dataset of Hsp90 sequences from dinoflagellates by generating additional sequences from 17 different species, representing seven different orders. In order to concatenate the Hsp90 data with rDNA sequences, we supplemented the Hsp90 sequences with three new SSU rDNA sequences and five new LSU rDNA sequences. The new Hsp90 sequences were generated, in part, from four additional heterotrophic dinoflagellates and the type species for six different genera. Molecular phylogenetic analyses resulted in a paraphyletic assemblage near the base of the dinoflagellate tree consisting of only athecate species. However, Noctiluca was never part of this assemblage and branched in a position that was nested within other lineages of dinokaryotes. The phylogenetic trees inferred from Hsp90 sequences were consistent with trees inferred from rDNA sequences in that the backbone of the dinoflagellate clade was largely unresolved.The sequence conservation in both Hsp90 and rDNA sequences and the poor resolution of the deepest nodes suggests that dinoflagellates reflect an explosive radiation in morphological diversity in their recent

  8. Hydrothermal Liquefaction Treatment Preliminary Hazard Analysis Report

    Energy Technology Data Exchange (ETDEWEB)

    Lowry, Peter P.; Wagner, Katie A.

    2015-08-31

    A preliminary hazard assessment was completed during February 2015 to evaluate the conceptual design of the modular hydrothermal liquefaction treatment system. The hazard assessment was performed in 2 stages. An initial assessment utilizing Hazard Identification and Preliminary Hazards Analysis (PHA) techniques identified areas with significant or unique hazards (process safety-related hazards) that fall outside of the normal operating envelope of PNNL and warranted additional analysis. The subsequent assessment was based on a qualitative What-If analysis. This analysis was augmented, as necessary, by additional quantitative analysis for scenarios involving a release of hazardous material or energy with the potential for affecting the public.

  9. Preliminary I&C Design for LORELEI

    International Nuclear Information System (INIS)

    Korotkin, S.; Kaufman, Y.; Guttmann, E. B.; Levy, S.; Amidan, D.; Gdalyho, B.; Cahana, T.; Ellenbogen, A.; Arad, M.; Weiss, Y.; Sasson, A.; Ferry, L.; Bourrelly, F.; Cohen, Y.

    2014-01-01

    This document summarizes the preliminary I&C design for LORELEI experiment The preliminary design deals with considerations regarding appropriate safety and service instrumentation. The determined closed loop control rules for temperature and position will be implemented in the detailed design. The Computer Aided Operator Decisions System (CAODS) will be used for prediction of hot spot temperature and thickness of oxidation layer using Baker-Just correlation. The proposed hybrid simulation system comprising of both virtual and real hardware will be in-cooperated for LORELEI verification. It will perform both integration cold tests for a partial hardware loop and virtual tests for the final I&C design

  10. Sequence complexity and work extraction

    International Nuclear Information System (INIS)

    Merhav, Neri

    2015-01-01

    We consider a simplified version of a solvable model by Mandal and Jarzynski, which constructively demonstrates the interplay between work extraction and the increase of the Shannon entropy of an information reservoir which is in contact with a physical system. We extend Mandal and Jarzynski’s main findings in several directions: first, we allow sequences of correlated bits rather than just independent bits. Secondly, at least for the case of binary information, we show that, in fact, the Shannon entropy is only one measure of complexity of the information that must increase in order for work to be extracted. The extracted work can also be upper bounded in terms of the increase in other quantities that measure complexity, like the predictability of future bits from past ones. Third, we provide an extension to the case of non-binary information (i.e. a larger alphabet), and finally, we extend the scope to the case where the incoming bits (before the interaction) form an individual sequence, rather than a random one. In this case, the entropy before the interaction can be replaced by the Lempel–Ziv (LZ) complexity of the incoming sequence, a fact that gives rise to an entropic meaning of the LZ complexity, not only in information theory, but also in physics. (paper)

  11. Entropic fluctuations in DNA sequences

    Science.gov (United States)

    Thanos, Dimitrios; Li, Wentian; Provata, Astero

    2018-03-01

    The Local Shannon Entropy (LSE) in blocks is used as a complexity measure to study the information fluctuations along DNA sequences. The LSE of a DNA block maps the local base arrangement information to a single numerical value. It is shown that despite this reduction of information, LSE allows to extract meaningful information related to the detection of repetitive sequences in whole chromosomes and is useful in finding evolutionary differences between organisms. More specifically, large regions of tandem repeats, such as centromeres, can be detected based on their low LSE fluctuations along the chromosome. Furthermore, an empirical investigation of the appropriate block sizes is provided and the relationship of LSE properties with the structure of the underlying repetitive units is revealed by using both computational and mathematical methods. Sequence similarity between the genomic DNA of closely related species also leads to similar LSE values at the orthologous regions. As an application, the LSE covariance function is used to measure the evolutionary distance between several primate genomes.

  12. Blackout sequence modeling for Atucha-I with MARCH3 code

    International Nuclear Information System (INIS)

    Baron, J.; Bastianelli, B.

    1997-01-01

    The modeling of a blackout sequence in Atucha I nuclear power plant is presented in this paper, as a preliminary phase for a level II probabilistic safety assessment. Such sequence is analyzed with the code MARCH3 from STCP (Source Term Code Package), based on a specific model developed for Atucha, that takes into accounts it peculiarities. The analysis includes all the severe accident phases, from the initial transient (loss of heat sink), loss of coolant through the safety valves, core uncovered, heatup, metal-water reaction, melting and relocation, heatup and failure of the pressure vessel, core-concrete interaction in the reactor cavity, heatup and failure of the containment building (multi-compartmented) due to quasi-static overpressurization. The results obtained permit to visualize the time sequence of these events, as well as provide the basis for source term studies. (author) [es

  13. Monte Carlo simulation of a statistical mechanical model of multiple protein sequence alignment.

    Science.gov (United States)

    Kinjo, Akira R

    2017-01-01

    A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are used for both parameter optimization of the model and production runs to explore the sequence subspace around a given protein family. In this Note, I describe the details of the MC algorithm as well as some preliminary results of MC simulations with various temperatures and chemical potentials, and compare them with the mean-field approximation. The existence of a two-state transition in the sequence space is suggested for the SH3 domain family, and inappropriateness of the mean-field approximation for the LGM is demonstrated.

  14. Method and apparatus for biological sequence comparison

    Science.gov (United States)

    Marr, T.G.; Chang, W.I.

    1997-12-23

    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  15. Memory and learning with rapid audiovisual sequences

    Science.gov (United States)

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  16. Memory and learning with rapid audiovisual sequences.

    Science.gov (United States)

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

  17. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto

    2013-06-01

    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  18. The mimivirus R355 gene product: preliminary crystallographic analysis of a putative ubiquitin-like protein-specific protease

    International Nuclear Information System (INIS)

    Jeudy, Sandra; Lartigue, Audrey; Mansuelle, Pascal; Ogata, Yuki; Abergel, Chantal

    2010-01-01

    The genome sequence of mimivirus, the largest known double-stranded DNA virus, encodes a putative protease: the R355 gene product. Its expression in E. coli, its crystallization and the preliminary phasing of a MAD data set using the selenium signal present in a crystal of recombinant selenomethionine-substituted protein are reported. The complete genome sequence of the largest known double-stranded DNA virus, mimivirus, reveals the presence of a gene (denoted R355) that potentially encodes a cysteine protease that is expressed late (after 6 h) in the infectious cycle of the virus. In order to verify a sequence-based functional prediction and understand its role during the infectious process, the R355 protein was produced to assay its proteolytic activity and solve its three-dimensional structure. Here, the preliminary crystallographic analysis of the recombinant viral protein is reported. The crystals belonged to the orthorhombic space group P2 1 2 1 2 1 , with a monomer in the asymmetric unit. A MAD data set was used for preliminary phasing using the selenium signal from a selenomethionine-substituted protein crystal

  19. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

  20. Experimental-demonstrative system for energy conversion using hydrogen fuel cell - preliminary results

    International Nuclear Information System (INIS)

    Stoenescu, D.; Stefanescu, I.; Patularu, I.; Culcer, M.; Lazar, R.E.; Carcadea, E.; Mirica, D. . E-mail address of corresponding author: daniela@icsi.ro; Stoenescu, D.)

    2005-01-01

    It is well known that hydrogen is the most promising solution of future energy, both for long and medium term strategies. Hydrogen can be produced using many primary sources (natural gas, methane, biomass, etc.), it can be burned or chemically react having a high yield of energy conversion, being a non-polluted fuel. This paper presents the preliminary results obtained by ICSI Rm. Valcea in an experimental-demonstrative conversion energy system made by a sequence of hydrogen purification units and a CO removing reactors until a CO level lower than 10ppm, that finally feeds a hydrogen fuel stack. (author)

  1. Preliminary Validation of Composite Material Constitutive Characterization

    Science.gov (United States)

    John G. Michopoulos; Athanasios lliopoulos; John C. Hermanson; Adrian C. Orifici; Rodney S. Thomson

    2012-01-01

    This paper is describing the preliminary results of an effort to validate a methodology developed for composite material constitutive characterization. This methodology involves using massive amounts of data produced from multiaxially tested coupons via a 6-DoF robotic system called NRL66.3 developed at the Naval Research Laboratory. The testing is followed by...

  2. Phytochemical Screening and Preliminary Evaluation of Analgesic ...

    African Journals Online (AJOL)

    In this study, the methanolic root extract of Cissus polyantha was subjected to preliminary phytochemical screening, analgesic and anti-inflammatory studies. Phytochemical studies was carried out using standard phytochemical protocol while the analgesic studies was carried out using acetic acid-induced writhing tests in ...

  3. French 900 MWe PWR PSA preliminary results

    International Nuclear Information System (INIS)

    Lanore, J.M.; Brisbois, J.

    1988-10-01

    A PSA is performed by the Safety Assessment Department of CEA for a 900 MWe standardized plant. The paper presents the objectives, the scope of the study and the relative preliminary results. Some general insights are drawn, especially the benefit related to the implementation of emergency procedures

  4. Original Article PRELIMINARY BIOAUTOGRAPHIC ANALYSIS OF ...

    African Journals Online (AJOL)

    Sierra Leone 2Department of Pharmaceutical Chemistry, Faculty of Pharmacy, ... the seeds are used in the treatment of skin infections. ... Screening with DPPH showed prominent antioxidant spots on silica at Rf 0.8, 0.5, 0.4 .... underpins conditions like rheumatoid arthritis, ..... As a follow-up to the preliminary TLC studies.

  5. Preliminary radiation shielding design for BOOMERANG

    International Nuclear Information System (INIS)

    Donahue, Richard J.

    2002-01-01

    Preliminary radiation shielding specifications are presented here for the 3 GeV BOOMERANG Australian synchrotron light source project. At this time the bulk shield walls for the storage ring and injection system (100 MeV Linac and 3 GeV Booster) are considered for siting purposes

  6. Resumption Of Sexual Relationship After Childbirth: Preliminary ...

    African Journals Online (AJOL)

    Resumption Of Sexual Relationship After Childbirth: Preliminary Observations On Husband\\'s Attitude. ... An open-ended questionnaire developed by the authors was used to elicit information on relevant aspects of husbands' reproductive behaviour. We found that husbands' preferred time of resumption of sexual ...

  7. Preliminary failure mode and effect analysis

    International Nuclear Information System (INIS)

    Addison, J.V.

    1972-01-01

    A preliminary Failure Mode and Effect Analysis (FMEA) was made on the overall 5 Kwe system. A general discussion of the system and failure effect is given in addition to the tabulated FMEA and a primary block diagram of the system. (U.S.)

  8. The Adaptation Gap Report - a Preliminary Assessment

    DEFF Research Database (Denmark)

    Alverson, Keith; Olhoff, Anne; Noble, Ian

    This first Adaptation Gap report provides an equally sobering assessment of the gap between adaptation needs and reality, based on preliminary thinking on how baselines, future goals or targets, and gaps between them might be defined for climate change adaptation. The report focuses on gaps...... in developing countries in three important areas: finance, technology and knowledge....

  9. Preliminary Findings on Rural Homelessness in Ohio.

    Science.gov (United States)

    First, Richard J.; And Others

    This report is designed to present preliminary findings from the first comprehensive study of rural homelessness in the United States. The study was conducted during the first 6 months of 1990, and data were collected from interviews with 921 homeless adults in 21 randomly selected rural counties in Ohio. The sample counties represent 26% of the…

  10. Preliminary safety analysis report for the TFTR

    International Nuclear Information System (INIS)

    Lind, K.E.; Levine, J.D.; Howe, H.J.

    A Preliminary Safety Analysis Report has been prepared for the Tokamak Fusion Test Reactor. No accident scenarios have been identified which would result in exposures to on-site personnel or the general public in excess of the guidelines defined for the project by DOE

  11. HTGR gas turbine power plant preliminary design

    International Nuclear Information System (INIS)

    Koutz, S.L.; Krase, J.M.; Meyer, L.

    1973-01-01

    The preliminary reference design of the HTGR gas turbine power plant is presented. Economic and practical problems and incentives related to the development and introduction of this type of power plant are evaluated. The plant features and major components are described, and a discussion of its performance, economics, development, safety, control, and maintenance is presented. 4 references

  12. Preliminary tests of the electrostatic plasma accelerator

    Science.gov (United States)

    Aston, G.; Acker, T.

    1990-01-01

    This report describes the results of a program to verify an electrostatic plasma acceleration concept and to identify those parameters most important in optimizing an Electrostatic Plasma Accelerator (EPA) thruster based upon this thrust mechanism. Preliminary performance measurements of thrust, specific impulse and efficiency were obtained using a unique plasma exhaust momentum probe. Reliable EPA thruster operation was achieved using one power supply.

  13. Preliminary characterization of slow growing rhizobial strains ...

    African Journals Online (AJOL)

    In this paper, we did some preliminary characterization of six slow growing rhizobial strains, isolated from Retama monosperma (L.) Boiss. root nodules sampled from 3 sites along the coast of Oran (CapeFalcon, Bousfer and MersElHadjadj) in Northwestern Algeria. Results of this study showed that all strains had a very ...

  14. Preliminary bathymetry; approaches to Unakwik Inlet, Alaska

    Science.gov (United States)

    Post, Austin

    1980-01-01

    A map, scale 1:20,000, shows water depths, rocks, and hazards to navigation. These data are noted on track lines run by the Research Vessel Growler in Alaskan waters, where data on navigation shown on published charts are nonexistant, preliminary, or out dated. (USGS)

  15. Blind sequence-length estimation of low-SNR cyclostationary sequences

    CSIR Research Space (South Africa)

    Vlok, JD

    2014-06-01

    Full Text Available Several existing direct-sequence spread spectrum (DSSS) detection and estimation algorithms assume prior knowledge of the symbol period or sequence length, although very few sequence-length estimation techniques are available in the literature...

  16. Preliminary designs: passive solar manufactured housing. Technical status report

    Energy Technology Data Exchange (ETDEWEB)

    1980-05-12

    The criteria established to guide the development of the preliminary designs are listed. Three preliminary designs incorporating direct gain and/or sunspace are presented. Costs, drawings, and supporting calculations are included. (MHR)

  17. Unique Trichomonas vaginalis gene sequences identified in multinational regions of Northwest China.

    Science.gov (United States)

    Liu, Jun; Feng, Meng; Wang, Xiaolan; Fu, Yongfeng; Ma, Cailing; Cheng, Xunjia

    2017-07-24

    Trichomonas vaginalis (T. vaginalis) is a flagellated protozoan parasite that infects humans worldwide. This study determined the sequence of the 18S ribosomal RNA gene of T. vaginalis infecting both females and males in Xinjiang, China. Samples from 73 females and 28 males were collected and confirmed for infection with T. vaginalis, a total of 110 sequences were identified when the T. vaginalis 18S ribosomal RNA gene was sequenced. These sequences were used to prepare a phylogenetic network. The rooted network comprised three large clades and several independent branches. Most of the Xinjiang sequences were in one group. Preliminary results suggest that Xinjiang T. vaginalis isolates might be genetically unique, as indicated by the sequence of their 18S ribosomal RNA gene. Low migration rate of local people in this province may contribute to a genetic conservativeness of T. vaginalis. The unique genetic feature of our isolates may suggest a different clinical presentation of trichomoniasis, including metronidazole susceptibility, T. vaginalis virus or Mycoplasma co-infection characteristics. The transmission and evolution of Xinjiang T. vaginalis is of interest and should be studied further. More attention should be given to T. vaginalis infection in both females and males in Xinjiang.

  18. The impact of simulation sequencing on perceived clinical decision making.

    Science.gov (United States)

    Woda, Aimee; Hansen, Jamie; Paquette, Mary; Topp, Robert

    2017-09-01

    An emerging nursing education trend is to utilize simulated learning experiences as a means to optimize competency and decision making skills. The purpose of this study was to examine differences in students' perception of clinical decision making and clinical decision making-related self-confidence and anxiety based on the sequence (order) in which they participated in a block of simulated versus hospital-based learning experiences. A quasi-experimental crossover design was used. Between and within group differences were found relative to self-confidence with the decision making process. When comparing groups, at baseline the simulation followed by hospital group had significantly higher self-confidence scores, however, at 14-weeks both groups were not significantly different. Significant within group differences were found in the simulation followed by hospital group only, demonstrating a significant decrease in clinical decision making related anxiety across the semester. Finally, there were no significant difference in; perceived clinical decision making within or between the groups at the two measurement points. Preliminary findings suggest that simulated learning experiences can be offered with alternating sequences without impacting the process, anxiety or confidence with clinical decision making. This study provides beginning evidence to guide curriculum development and allow flexibility based on student needs and available resources. Copyright © 2017. Published by Elsevier Ltd.

  19. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed; Mansour, Essam; Kalnis, Panos

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern

  20. Computational analysis of sequence selection mechanisms.

    Science.gov (United States)

    Meyerguz, Leonid; Grasso, Catherine; Kleinberg, Jon; Elber, Ron

    2004-04-01

    Mechanisms leading to gene variations are responsible for the diversity of species and are important components of the theory of evolution. One constraint on gene evolution is that of protein foldability; the three-dimensional shapes of proteins must be thermodynamically stable. We explore the impact of this constraint and calculate properties of foldable sequences using 3660 structures from the Protein Data Bank. We seek a selection function that receives sequences as input, and outputs survival probability based on sequence fitness to structure. We compute the number of sequences that match a particular protein structure with energy lower than the native sequence, the density of the number of sequences, the entropy, and the "selection" temperature. The mechanism of structure selection for sequences longer than 200 amino acids is approximately universal. For shorter sequences, it is not. We speculate on concrete evolutionary mechanisms that show this behavior.

  1. The recurrence sequences via Sylvester matrices

    Science.gov (United States)

    Karaduman, Erdal; Deveci, Ömür

    2017-07-01

    In this work, we define the Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by using the Slyvester matrices which are obtained from the characteristic polynomials of the Pell and Jacobsthal sequences and then, we study the sequences defined modulo m. Also, we obtain the cyclic groups and the semigroups from the generating matrices of these sequences when read modulo m and then, we derive the relationships among the orders of the cyclic groups and the periods of the sequences. Furthermore, we redefine Pell-Jacobsthal-Slyvester sequence and the Jacobsthal-Pell-Slyvester sequence by means of the elements of the groups and then, we examine them in the finite groups.

  2. ON SOME RECURRENCE TYPE SMARANDACHE SEQUENCES

    OpenAIRE

    MAJUMDAR, A.A.K.; GUNARTO, H.

    2000-01-01

    In this paper, we study some properties of ten recurrence type Smarandache sequences, namely, the Smarandache odd, even, prime product, square product, higher-power product, permutation, consecutive, reverse, symmetric, and pierced chain sequences.

  3. "First generation" automated DNA sequencing technology.

    Science.gov (United States)

    Slatko, Barton E; Kieleczawa, Jan; Ju, Jingyue; Gardner, Andrew F; Hendrickson, Cynthia L; Ausubel, Frederick M

    2011-10-01

    Beginning in the 1980s, automation of DNA sequencing has greatly increased throughput, reduced costs, and enabled large projects to be completed more easily. The development of automation technology paralleled the development of other aspects of DNA sequencing: better enzymes and chemistry, separation and imaging technology, sequencing protocols, robotics, and computational advancements (including base-calling algorithms with quality scores, database developments, and sequence analysis programs). Despite the emergence of high-throughput sequencing platforms, automated Sanger sequencing technology remains useful for many applications. This unit provides background and a description of the "First-Generation" automated DNA sequencing technology. It also includes protocols for using the current Applied Biosystems (ABI) automated DNA sequencing machines. © 2011 by John Wiley & Sons, Inc.

  4. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...... diseases in Europe. As part of the EURL proficiency test for fish diseases it is required to sequence any RANA virus isolates found in any of the samples. It is also highly recommended to sequence the ISA virus to determine whether it be HPRΔ or HPR0. Furthermore, it is recommended that any VHSV and IHNV...... isolates be genotyped. As part of the evaluation of the proficiency results it was decided this year to look into the quality and similarity of the sequence results for selected viruses. Ampoule III in the proficiency test 2013 contained an EHNV isolate. The EURL received 43 sequences from 41 laboratories...

  5. 32 CFR 644.30 - Preliminary real estate work.

    Science.gov (United States)

    2010-07-01

    ... 32 National Defense 4 2010-07-01 2010-07-01 true Preliminary real estate work. 644.30 Section 644... PROPERTY REAL ESTATE HANDBOOK Project Planning Military (army and Air Force) and Other Federal Agencies § 644.30 Preliminary real estate work. (a) Preliminary real estate work is defined as that action taken...

  6. 28 CFR 2.48 - Revocation: Preliminary interview.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Revocation: Preliminary interview. 2.48....48 Revocation: Preliminary interview. (a) Interviewing officer. A parolee who is retaken on a warrant issued by a Commissioner shall be given a preliminary interview by an official designated by the Regional...

  7. Perfect sequences over the real quaternions

    OpenAIRE

    Kuznetsov, Oleg

    2017-01-01

    In this Thesis, perfect sequences over the real quaternions are first considered. Definitions for the right and left periodic autocorrelation functions are given, and right and left perfect sequences introduced. It is shown that the right (left) perfection of any sequence implies the left (right) perfection, so concepts of right and left perfect sequences over the real quaternions are equivalent. Unitary transformations of the quaternion space ℍ are then considered. Using the equivalence of t...

  8. Information decomposition method to analyze symbolical sequences

    International Nuclear Information System (INIS)

    Korotkov, E.V.; Korotkova, M.A.; Kudryashov, N.A.

    2003-01-01

    The information decomposition (ID) method to analyze symbolical sequences is presented. This method allows us to reveal a latent periodicity of any symbolical sequence. The ID method is shown to have advantages in comparison with application of the Fourier transformation, the wavelet transform and the dynamic programming method to look for latent periodicity. Examples of the latent periods for poetic texts, DNA sequences and amino acids are presented. Possible origin of a latent periodicity for different symbolical sequences is discussed

  9. A Three-Dimensional Approach and Open Source Structure for the Design and Experimentation of Teaching-Learning Sequences: The Case of Friction

    Science.gov (United States)

    Besson, Ugo; Borghi, Lidia; De Ambrosis, Anna; Mascheretti, Paolo

    2010-01-01

    We have developed a teaching-learning sequence (TLS) on friction based on a preliminary study involving three dimensions: an analysis of didactic research on the topic, an overview of usual approaches, and a critical analysis of the subject, considered also in its historical development. We found that mostly the usual presentations do not take…

  10. Purification, identification and preliminary crystallographic studies of a 2S albumin seed protein from Lens culinaris

    International Nuclear Information System (INIS)

    Gupta, Pankaj; Gaur, Vineet; Salunke, Dinakar M.

    2008-01-01

    A 2S albumin from L. culinaris was purified and crystallized and preliminary crystallographic studies were carried out. Lens culinaris (lentil) is a widely consumed high-protein-content leguminous crop. A 2S albumin protein (26.5 kDa) has been identified using NH 2 -terminal sequencing from a 90% ammonium sulfate saturation fraction of total L. culinaris seed protein extract. The NH 2 -terminal sequence shows very high homology to PA2, an allergy-related protein from Pisum sativum. The 2S albumin protein was purified using a combination of size-exclusion and ion-exchange chromatography. Crystals of the 2S seed albumin obtained using the hanging-drop vapour-diffusion method diffracted to 2.5 Å resolution and were indexed in space group P4 1 (or P4 3 ), with unit-cell parameters a = b = 78.6, c = 135.2 Å

  11. Parallel sequencing lives, or what makes large sequencing projects successful.

    Science.gov (United States)

    Quilez, Javier; Vidal, Enrique; Dily, François Le; Serra, François; Cuartero, Yasmina; Stadhouders, Ralph; Graf, Thomas; Marti-Renom, Marc A; Beato, Miguel; Filion, Guillaume

    2017-11-01

    T47D_rep2 and b1913e6c1_51720e9cf were 2 Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, and Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high-throughput sequencing data. © The Author 2017. Published by Oxford University Press.

  12. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole

    1999-01-01

    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...

  13. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.

    2008-01-01

    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  14. DNA sequence modeling based on context trees

    NARCIS (Netherlands)

    Kusters, C.J.; Ignatenko, T.; Roland, J.; Horlin, F.

    2015-01-01

    Genomic sequences contain instructions for protein and cell production. Therefore understanding and identification of biologically and functionally meaningful patterns in DNA sequences is of paramount importance. Modeling of DNA sequences in its turn can help to better understand and identify such

  15. Compact flow diagrams for state sequences

    NARCIS (Netherlands)

    Buchin, K.A.; Buchin, M.E.; Gudmundsson, J.; Horton, M.J.; Sijben, S.

    2016-01-01

    We introduce the concept of compactly representing a large number of state sequences, e.g., sequences of activities, as a flow diagram. We argue that the flow diagram representation gives an intuitive summary that allows the user to detect patterns among large sets of state sequences. Simplified,

  16. Blazar Sequence in Fermi Era Liang Chen

    Indian Academy of Sciences (India)

    Abstract. In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power- high-synchrotron-peaked and ...

  17. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Science.gov (United States)

    Tedersoo, Leho; Abarenkov, Kessy; Nilsson, R Henrik; Schüssler, Arthur; Grelet, Gwen-Aëlle; Kohout, Petr; Oja, Jane; Bonito, Gregory M; Veldre, Vilmar; Jairus, Teele; Ryberg, Martin; Larsson, Karl-Henrik; Kõljalg, Urmas

    2011-01-01

    Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  18. Preliminary Analysis For Wolsong Par Effects Using ISACC Calculations

    International Nuclear Information System (INIS)

    Song, Yong Mann; Kim, Dong Ha

    2012-01-01

    In the paper, hydrogen control effects using PARs only are analyzed for severe SBO station blackout (SBO) sequences beyond the design basis accidents in WS-1 which are of CANDU6 type reactor. As a computational tool, the latest version of ISAAC4.3 (Integrated Severe Accident Analysis Code for CANDU), which is a fully integrated and lumped severe accident computer code, is used to simulate hydrogen generation and transport inside the reactor building (R/B) before its failure. For the performance of hydrogen removal, the depletion rate equation of K-PAR developed in Korea is applied. In a CANDU reactor, three areas are identified as sources of hydrogen under severe accidents: fuel-coolant interactions in intact channels, suspended fuel or debris interactions in-calandria tank and debris interactions in-calandria vault. The first two origins provide source for the late ('late' terminology is used because it takes more than one day before calandria tank failure) potential hydrogen combustion before calandria tank failure and all the three origins would provide source for the very late potential hydrogen combustion occurring at or after calaria tank failure. If the hydrogen mitigation system fails, the AICC (adiabatic isochoric complete combustion) burning of highly flammable hydrogen may cause Wolsong R/B failure. So hydrogen induced failure possibility is evaluated, using preliminary ISAAC calculations, under several SBO conditions with and without PAR for both late and very late accident periods

  19. Preliminary test conditions for KNGR SBLOCA DVI ECCS performance test

    International Nuclear Information System (INIS)

    Bae, Kyoo Whan; Song, Jin Ho; Chung, Young Jong; Sim, Suk Ku; Park, Jong Kyun

    1999-03-01

    The Korean Next Generation Reactor (KNGR) adopts 4-train Direct Vessel Injection (DVI) configuration and injects the safety injection water directly into the downcomer through the 8.5'' DVI nozzle. Thus, the thermal hydraulic phenomena such as ECCS mixing and bypass are expected to be different from those observed in the cold leg injection. In order to investigate the realistic injection phenomena and modify the analysis code developed in the basis of cold leg injection, thermal hydraulic test with the performance evaluation is required. Preliminarily, the sequence of events and major thermal hydraulic phenomena during the small break LOCA for KNGR are identified from the analysis results calculated by the CEFLASH-4AS/REM. It is shown from the analysis results that the major transient behaviors including the core mixture level are largely affected by the downcomer modeling. Therefore, to investigate the proper thermal hydraulic phenomena occurring in the downcomer with limited budget and time, the separate effects test focusing on this region is considered to be effective and the conceptual test facility based on this recommended. For this test facility the test initial and boundary conditions are developed using the CEFLASH-4AS/REM analysis results that will be used as input for the preliminary test requirements. The final test requirements will be developed through the further discussions with the test performance group. (Author). 10 refs., 18 tabs., 4 figs

  20. MR evaluation of renal function. A preliminary study

    Energy Technology Data Exchange (ETDEWEB)

    Beomonte Zobel, B; Giammarile, F; Matarese, A; Gallucci, M; Mascicchi, C; Passariello, R; Di Renzi, P; Splendiani, G; Casciani, C U

    1988-01-01

    The amount of functioning renal parenchyma can be estimated by MRI by considering the ratio between the mean intensities of cortical and medullar zones of the kidney. Fifty-six patients and 5 healthy volunteers were studied by MRI in our department. Scanning was performed with a superconductive magnet system operating at 0.5 Tesla. Pulse sequence was Spin-Echo with TR 300/TE 30 ms. The cortimedullary ratio (CMR) and differentiation (CMD) were standardized and related with creatine blood levels. CMR data ranged from 1.05 to 3.00, while CMD data ranged from 0.04 to 0.50. High values (good cortico-medullary contrast) were observed in subjects with normal renal function. Patients with renal diseases had low CMR and CMD, proportionally to the degree of renal failure, as proved by laboratory findings. Our preliminary study seems to demonstrate that MRI is an useful technique in the follow-up of patients with chronic renal disease. 19 refs.

  1. Cloning, expression, and preliminary structural characterization of RTN-1C

    International Nuclear Information System (INIS)

    Fazi, Barbara; Melino, Sonia; Sano, Federica Di; Cicero, Daniel O.; Piacentini, Mauro; Paci, Maurizio

    2006-01-01

    Reticulons (RTNs) are endoplasmic reticulum-associated proteins widely distributed in plants, yeast, and animals. They are characterized by unique N-terminal parts and a common 200 amino acid C-terminal domain containing two long hydrophobic sequences. Despite their implication in many cellular processes, their molecular structure and function are still largely unknown. In this study, the reticulon family member RTN-1C has been expressed and purified in Escherichia coli and its molecular structure has been analysed by fluorescence and CD spectroscopy in different detergents in order to obtain a good solubility and a relative stability. The isotopically enriched protein has been also produced to perform structural studies by NMR spectroscopy. The preliminary results obtained showed that RTN-1C protein possesses helical transmembrane segments when a membrane-like environment is produced by detergents. Moreover, fluorescence experiments indicated the exposure of tryptophan side chains as predicted by structure prediction programs. We also produced the isotopically labelled protein and the procedure adopted allowed us to plan future NMR studies to investigate the biochemical behaviour of reticulon-1C and of its peptides spanning out from the membrane

  2. Permutation Entropy for Random Binary Sequences

    Directory of Open Access Journals (Sweden)

    Lingfeng Liu

    2015-12-01

    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  3. The 2016 Kumamoto earthquake sequence.

    Science.gov (United States)

    Kato, Aitaro; Nakamura, Kouji; Hiyama, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An M j 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an M j 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest.

  4. Data selector group sequencer interface

    International Nuclear Information System (INIS)

    Zizka, G.; Turko, B.

    1984-01-01

    A CAMAC-based module for high rate data selection and transfer to Tracor Northern TN-1700 multichannel analysis system is described. The module can select any group of 4096 consecutive addresses of events, in the range of 24 bits. This module solves the problem of connecting a number of time digitizing systems to the memory of a multichannel analyzer. Continuous processing rate up to 200,000 events per second along with the live display make the testing of the above systems very efficient and relatively inexpensive. The module also can be programmed for storing the preset group of addresses into more than one section of the memory. The events are analyzed in each section of the memory during the preset time. Multiple spectra can thus be taken automatically in a sequence

  5. A main sequence for quasars

    Science.gov (United States)

    Marziani, Paola; Dultzin, Deborah; Sulentic, Jack W.; Del Olmo, Ascensión; Negrete, C. A.; Martínez-Aldama, Mary L.; D'Onofrio, Mauro; Bon, Edi; Bon, Natasa; Stirpe, Giovanna M.

    2018-03-01

    The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  6. The 2016 Kumamoto earthquake sequence

    Science.gov (United States)

    KATO, Aitaro; NAKAMURA, Kouji; HIYAMA, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An Mj 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an Mj 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest. PMID:27725474

  7. A Main Sequence for Quasars

    Directory of Open Access Journals (Sweden)

    Paola Marziani

    2018-03-01

    Full Text Available The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

  8. RANDNA: a random DNA sequence generator.

    Science.gov (United States)

    Piva, Francesco; Principato, Giovanni

    2006-01-01

    Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo-random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed. We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.

  9. Genome Sequence of the 1,4-Dioxane-Degrading Pseudonocardia dioxanivoransStrain CB1190▿

    Science.gov (United States)

    Sales, Christopher M.; Mahendra, Shaily; Grostern, Ariel; Parales, Rebecca E.; Goodwin, Lynne A.; Woyke, Tanja; Nolan, Matt; Lapidus, Alla; Chertkov, Olga; Ovchinnikova, Galina; Sczyrba, Alexander; Alvarez-Cohen, Lisa

    2011-01-01

    Pseudonocardia dioxanivoransCB1190 is the first bacterium reported to be capable of growth on the environmental contaminant 1,4-dioxane and the first member of the genus Pseudonocardiafor which there is an annotated genome sequence. Preliminary analysis of the genome (chromosome and three plasmids) indicates that strain CB1190 possesses several multicomponent monooxygenases that could be involved in the aerobic degradation of 1,4-dioxane and other environmental contaminants. PMID:21725009

  10. Locomotor sequence learning in visually guided walking

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 years, N = 20) could learn a specific sequence...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...... to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence non-specific learning during...

  11. Preliminary study of mercury target structure

    Energy Technology Data Exchange (ETDEWEB)

    Kaminaga, Masanori; Haga, Katsuhiro; Hino, Ryutaro [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Kumasaka, Katsuyuki; Uchida, Shoji; Nakagawa, Toshi; Mori, Seiji; Nishikawa, Akira

    1997-11-01

    Development of a proton accelerator based neutron source (1.5 GeV, 5.3 mA (for neutron source 3.3 mA), thermal power 8 MW) is currently conducted by the Special Task Force for Neutron Science Initiative, JAERI. Preliminary design studies and related R and D of a solid metal target for the first stage (1.5 GeV, 1 mA) and a liquid metal target for both the first and second stages (1.5 GeV, 3.3 mA) are conducted by the Target Group to develop both solid and liquid metal target systems. A few kinds of target structures have been investigated in FY 1996 and the preliminary results for the target structures are described in this paper. Investigation results of alternative materials for the target container are also described in this paper. (author)

  12. Preliminary results from NOAMP deep drifting floats

    International Nuclear Information System (INIS)

    Ollitrault, M.

    1989-01-01

    This paper is a very brief and preliminary outline of first results obtained with deep SOFAR floats in the NOAMP area. The work is now going toward more precise statistical estimations of mean and variable currents, together with better tracking to resolve submesoscales and estimate diffusivities due to mesoscale and smaller scale motions. However the preliminary results confirm that the NOAMP region (and surroundings) has a deep mesoscale eddy field that is considerably more energetic that the mean field (r.m.s. velocities are of order 5 cm s -1 ), although both values are diminished compared to the western basin. A data report containing trajectories and statistics is scheduled to be published by IFREMER in the near future. The project main task is to especially study the dispersion of radioactive substances

  13. Preliminary waste acceptance requirements - Konrad repository project

    International Nuclear Information System (INIS)

    Brennecke, P.W.; Warnecke, E.H.

    1991-01-01

    In Germany, the planned Konrad repository is proposed for the disposal of all types of radioactive wastes whose thermal influence upon the host rock is negligible. The Bundesamt fuer Strahlenschutz has established Preliminary Waste Acceptance Requirements (as of April 1990) for this facility. The respective requirements were developed on the basis of the results of site-specific safety assessments. They include general requirements on the waste packages to be disposed of as well as more specific requirements on the waste forms, the packaging and the radionuclide inventory per waste package. In addition, the delivery of waste packages was regulated. An outline of the structure and the elements of the Preliminary Waste Acceptance Requirements of April 1990 is given including comments on their legal status. (Author)

  14. Licensing Support System: Preliminary data scope analysis

    International Nuclear Information System (INIS)

    1989-01-01

    The purpose of this analysis is to determine the content and scope of the Licensing Support System (LSS) data base. Both user needs and currently available data bases that, at least in part, address those needs have been analyzed. This analysis, together with the Preliminary Needs Analysis (DOE, 1988d) is a first effort under the LSS Design and Implementation Contract toward developing a sound requirements foundation for subsequent design work. These reports are preliminary. Further refinements must be made before requirements can be specified in sufficient detail to provide a basis for suitably specific system specifications. This document provides a baseline for what is known at this time. Additional analyses, currently being conducted, will provide more precise information on the content and scope of the LSS data base. 23 refs., 4 figs., 8 tabs

  15. Safety performance of preliminary KALIMER conceptual design

    Energy Technology Data Exchange (ETDEWEB)

    Hahn Dohee; Kim Kyoungdoo; Kwon Youngmin; Chang Wonpyo; Suk Soodong [Korea atomic Energy Resarch Inst., Taejon (Korea)

    1999-07-01

    The Korea Atomic Energy Research Institute (KAERI) is developing KALIMER (Korea Advanced Liquid Metal Reactor), which is a sodium cooled, 150 MWe pool-type reactor. The safety design of KALIMER emphasizes accident prevention by using passive processes, which can be accomplished by the safety design objectives including the utilization of inherent safety features. In order to assess the effectiveness of the inherent safety features in achieving the safety design objectives, a preliminary evaluation of ATWS performance for the KALIMER design has been performed with SSC-K code, which is a modified version of SSC-L code. KAERI's modification of the code includes development of reactivity feedback models for the core and a pool model for KALIMER reactor vessel. This paper describes the models for control rod driveline expansion, gas expansion module and the thermal hydraulic model for reactor pool and the results of preliminary analyses for unprotected loss of flow and loss o heat sink. (author)

  16. Safety performance of preliminary KALIMER conceptual design

    International Nuclear Information System (INIS)

    Hahn Dohee; Kim Kyoungdoo; Kwon Youngmin; Chang Wonpyo; Suk Soodong

    1999-01-01

    The Korea Atomic Energy Research Institute (KAERI) is developing KALIMER (Korea Advanced Liquid Metal Reactor), which is a sodium cooled, 150 MWe pool-type reactor. The safety design of KALIMER emphasizes accident prevention by using passive processes, which can be accomplished by the safety design objectives including the utilization of inherent safety features. In order to assess the effectiveness of the inherent safety features in achieving the safety design objectives, a preliminary evaluation of ATWS performance for the KALIMER design has been performed with SSC-K code, which is a modified version of SSC-L code. KAERI's modification of the code includes development of reactivity feedback models for the core and a pool model for KALIMER reactor vessel. This paper describes the models for control rod driveline expansion, gas expansion module and the thermal hydraulic model for reactor pool and the results of preliminary analyses for unprotected loss of flow and loss o heat sink. (author)

  17. Exploratory shaft facility preliminary designs - Gulf Interior Region salt domes

    International Nuclear Information System (INIS)

    1983-09-01

    The purpose of the Preliminary Design Report, Gulf Interior Region, is to provide a description of the preliminary design for an Exploratory Shaft Facility on the Richton Dome, Mississippi. This issue of the report describes the preliminary design for constructing the exploratory shaft using the Large Hole Drilling method of construction and outlines the preliminary design and estimates of probable construction cost. The Preliminary Design Report is prepared to complement and summarize other documents that comprise the design at the preliminary stage of completion, December 1982. Other design documents include drawings, cost estimates and schedules. The preliminary design drawing package, which includes the construction schedule drawing, depicts the descriptions in this report. For reference, a list of the drawing titles and corresponding numbers are included in the Appendix. The report is divided into three principal sections: Design Basis, Facility Description and Construction Cost Estimate

  18. Exploratory shaft facility preliminary designs - Paradox Basin. Technical report

    International Nuclear Information System (INIS)

    1983-09-01

    The purpose of the Preliminary Design Report, Paradox Basin, is to provide a description of the preliminary design for an Exploratory Shaft Facility in the Paradox Basin, Utah. This issue of the report describes the preliminary design for constructing the exploratory shaft using the Large Hole Drilling Method of construction and outlines the preliminary design and estimates of probable construction cost. The Preliminary Design Report is prepared to complement and summarize other documents that comprise the design at the preliminary stage of completion, December 1982. Other design documents include drawings, cost estimates and schedules. The preliminary design drawing package, which includes the construction schedule drawing, depicts the descriptions in this report. For reference, a list of the drawing titles and corresponding numbers is included in the Appendix. The report is divided into three principal sections: Design Basis, Facility Description, and Construction Cost Estimate. 30 references

  19. The RNA world, automatic sequences and oncogenetics

    Energy Technology Data Exchange (ETDEWEB)

    Tahir Shah, K

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. (1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. (2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or ``accept`` other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs.

  20. The RNA world, automatic sequences and oncogenetics

    International Nuclear Information System (INIS)

    Tahir Shah, K.

    1993-04-01

    We construct a model of the RNA world in terms of naturally evolving nucleotide sequences assuming only Crick-Watson base pairing and self-cleaving/splicing capability. These sequences have the following properties. 1) They are recognizable by an automation (or automata). That is, to each k-sequence, there exist a k-automation which accepts, recognizes or generates the k-sequence. These are known as automatic sequences. Fibonacci and Morse-Thue sequences are the most natural outcome of pre-biotic chemical conditions. 2) Infinite (resp. large) sequences are self-similar (resp. nearly self-similar) under certain rewrite rules and consequently give rise to fractal (resp.fractal-like) structures. Computationally, such sequences can also be generated by their corresponding deterministic parallel re-write system, known as a DOL system. The self-similar sequences are fixed points of their respective rewrite rules. Some of these automatic sequences have the capability that they can read or 'accept' other sequences while others can detect errors and trigger error-correcting mechanisms. They can be enlarged and have block and/or palindrome structure. Linear recurring sequences such as Fibonacci sequence are simply Feed-back Shift Registers, a well know model of information processing machines. We show that a mutation of any rewrite rule can cause a combinatorial explosion of error and relates this to oncogenetical behavior. On the other hand, a mutation of sequences that are not rewrite rules, leads to normal evolutionary change. Known experimental results support our hypothesis. (author). Refs

  1. Preliminary list of plant invaders in Montenegro

    OpenAIRE

    Stešević, D.; Petrović, D.

    2010-01-01

    Due to the fact that Invasive alien species (IAS) are considered to be the second cause of global biodiversity loss after direct habitat destruction and have adverse environmental, economic and social impacts from the local level upwards, in last decades investigations of alien flora of Montenegro are intensified. In this paper we are presenting a preliminary list of IAS, with the aim to provide a basic data on IAS in Montenegro, to enable future monitoring and to draw attention o...

  2. Life cycle analysis in preliminary design stages

    OpenAIRE

    Agudelo , Lina-Maria; Mejía-Gutiérrez , Ricardo; Nadeau , Jean-Pierre; PAILHES , Jérôme

    2014-01-01

    International audience; In a design process the product is decomposed into systems along the disciplinary lines. Each stage has its own goals and constraints that must be satisfied and has control over a subset of design variables that describe the overall system. When using different tools to initiate a product life cycle, including the environment and impacts, its noticeable that there is a gap in tools that linked the stages of preliminary design and the stages of materialization. Differen...

  3. Preliminary safety assessment of the WIPP facility

    International Nuclear Information System (INIS)

    Balestri, R.J.; Torres, B.W.; Pahwa, S.B.; Brannen, J.P.

    1979-01-01

    This paper summarizes the efforts to perform a safety assessment of the Waste Isolation Pilot Plant (WIPP) facility being proposed for southeastern New Mexico. This preliminary safety assessment is limited to a consequence assessment in terms of the dose to a maximally exposed individual as a result of introducing the radionuclides into the biosphere. The extremely low doses to the organs as a result of the liquid breach scenarios are contrasted with the background radiation

  4. Preliminary results from the hierarchical glitch pipeline

    International Nuclear Information System (INIS)

    Mukherjee, Soma

    2007-01-01

    This paper reports on the preliminary results obtained from the hierarchical glitch classification pipeline on LIGO data. The pipeline that has been under construction for the past year is now complete and end-to-end tested. It is ready to generate analysis results on a daily basis. The details of the pipeline, the classification algorithms employed and the results obtained with one days analysis on the gravitational wave and several auxiliary and environmental channels from all three LIGO detectors are discussed

  5. Preliminary safety analysis methodology for the SMART

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Kyoo Hwan; Chung, Y. J.; Kim, H. C.; Sim, S. K.; Lee, W. J.; Chung, B. D.; Song, J. H. [Korea Atomic Energy Research Institute, Taejeon (Korea)

    2000-03-01

    This technical report was prepared for a preliminary safety analysis methodology of the 330MWt SMART (System-integrated Modular Advanced ReacTor) which has been developed by Korea Atomic Energy Research Institute (KAERI) and funded by the Ministry of Science and Technology (MOST) since July 1996. This preliminary safety analysis methodology has been used to identify an envelope for the safety of the SMART conceptual design. As the SMART design evolves, further validated final safety analysis methodology will be developed. Current licensing safety analysis methodology of the Westinghouse and KSNPP PWRs operating and under development in Korea as well as the Russian licensing safety analysis methodology for the integral reactors have been reviewed and compared to develop the preliminary SMART safety analysis methodology. SMART design characteristics and safety systems have been reviewed against licensing practices of the PWRs operating or KNGR (Korean Next Generation Reactor) under construction in Korea. Detailed safety analysis methodology has been developed for the potential SMART limiting events of main steam line break, main feedwater pipe break, loss of reactor coolant flow, CEA withdrawal, primary to secondary pipe break and the small break loss of coolant accident. SMART preliminary safety analysis methodology will be further developed and validated in parallel with the safety analysis codes as the SMART design further evolves. Validated safety analysis methodology will be submitted to MOST as a Topical Report for a review of the SMART licensing safety analysis methodology. Thus, it is recommended for the nuclear regulatory authority to establish regulatory guides and criteria for the integral reactor. 22 refs., 18 figs., 16 tabs. (Author)

  6. PLANT COMMUNITIES OF ALBANIA - A PRELIMINARY OVERVIEW

    Directory of Open Access Journals (Sweden)

    J. DRING

    2002-04-01

    Full Text Available The phytosociological analysis of Albania was initiated by F. Markgraf in the 30ies, but still remains incomplete. This is a preliminary list of the plant communities resulting from the literature and from field research carried out during the last years and may represent a first contribution for further research. Many communities are described only by dominant species, other are quoted as nomina nuda. Some further syntaxa. probably present in the study area, are added.

  7. Preliminary Data on Eutrophication of Carstic Lakes

    OpenAIRE

    , B. Hoxha; , F. Cane; , M. Avdolli; , A. Dauti

    2016-01-01

    Nutrients play an important role in the health and functioning of aquatic ecosystems. However, an excess of nutrients, particularly phosphorous and nitrogen compounds, can lead to adverse effects on both ecology and uses of receiving waters. This process accelerated by human activities is termed cultural eutrophication, and is recognized as a significant environmental problem. The purpose of this paper is to represent some preliminary data on eutrophication of water bodies from a chemical poi...

  8. Preliminary Analysis of Google+'s Privacy

    OpenAIRE

    Mahmood, Shah; Desmedt, Yvo

    2011-01-01

    In this paper we provide a preliminary analysis of Google+ privacy. We identified that Google+ shares photo metadata with users who can access the photograph and discuss its potential impact on privacy. We also identified that Google+ encourages the provision of other names including maiden name, which may help criminals performing identity theft. We show that Facebook lists are a superset of Google+ circles, both functionally and logically, even though Google+ provides a better user interfac...

  9. Preliminary model for core/concrete interactions

    International Nuclear Information System (INIS)

    Murfin, W.B.

    1977-08-01

    A preliminary model is described for computing the rate of penetration of concrete by a molten LWR core. Among the phenomena included are convective stirring of the melt by evolved gases, admixture of concrete decomposition products to the melt, chemical reactions, radiative heat loss, and variation of heat transfer coefficients with local pressure. The model is most applicable to a two-phase melt (metallic plus oxidic) having a fairly high metallic content

  10. Preliminary rock mechanics laboratory: Investigation plan

    International Nuclear Information System (INIS)

    Oschman, K.P.; Hummeldorf, R.G.; Hume, H.R.; Karakouzian, M.; Vakili, J.E.

    1987-01-01

    This document presents the rationale for rock mechanics laboratory testing (including the supporting analysis and numerical modeling) planned for the site characterization of a nuclear waste repository in salt. This plan first identifies what information is required for regulatory and design purposes, and then presents the rationale for the testing that satisfies the required information needs. A preliminary estimate of the minimum sampling requirements for rock laboratory testing during site characterization is also presented. Periodic revision of this document is planned

  11. Preliminary results from film boiling destabilisation experiments

    International Nuclear Information System (INIS)

    Naylor, P.

    1984-05-01

    A series of experiments to investigate the triggered destabilisation of film boiling has been undertaken. Film boiling was established on a polished brass rod immersed in water and the effects of various triggers were investigated. Preliminary results are presented and two thresholds have been observed: an impulse threshold below which triggered destabilisation will not occur and a thermal threshold above which film boiling will re-establish following triggered destabilisation. (author)

  12. Preliminary plan for treating mixed waste

    International Nuclear Information System (INIS)

    Vandegrift, G.F.; Conner, C.; Hutter, J.C.; Leonard, R.A.; Nunez, L.; Sedlet, J.; Wygmans, D.G.

    1993-06-01

    A preliminary waste treatment plan was developed for disposing of radioactive inorganic liquid wastes that contain hazardous metals and/or hazardous acid concentrations at Argonne National Laboratory. This plan, which involves neutralization and sulfide precipitation followed by filtration, reduces the concentration of hazardous metals and the acidity so that the filtrate liquid is simply a low-level radioactive waste that can be fed to a low-level waste evaporator

  13. Preliminary risk assessments of the small HTGR

    International Nuclear Information System (INIS)

    Everline, C.J.; Bellis, E.A.

    1985-05-01

    Preliminary investment and safety risk assessments were performed for a preconceptual design of a four-module 250-MW(t) side-by-side steel-vessel pebble bed HTGR plant. Broad event spectra were analyzed involving component damage resulting in unscheduled plant outages and fission product releases resulting in offsite doses. The preliminary assessment indicates at this stage of the design that two categories of events govern the investment risk envelope: primary coolant leaks which release some circulating and plate-out activity that contaminates the confinement and turbogenerator damage which involves extensive turbine blade failure. Primary coolant leaks are important contributors because associated cleanup and decontamination requirements result in longer outages that arise from other events with comparable frequencies. Turbogenerator damage is the salient low-frequency investment risk accident due to the relatively long outages being experienced in the industry. Thermal transients are unimportant investment risk contributors because pressurized core heatups cause little damage, and depressurized core heatups occur at negligible frequencies relative to the forced outage goal. These preliminary results demonstrate investment and safety risk goal compliance at this stage in the design process. Studies are continuing in order to provide valuable insights into risk-significant events to assure a balanced approach to meeting user and regulatory requirements

  14. Sequences of 12 monoclonal anti-dinitrophenyl spin-label antibodies for NMR studies

    International Nuclear Information System (INIS)

    Leahy, D.J.; Rule, G.S.; Whittaker, M.M.; McConnell, H.M.

    1988-01-01

    Eleven monoclonal antibodies specific for a spin-labeled dinitrophenyl hapten (DNP-SL) have been produces for use in NMR studies. They have been named AN01 and ANO3-AN12. The stability constants for the association of these antibodies with DNP-SL and related haptens were measured by fluorescence quenching. cDNA clones coding for the heavy and light chains of each antibody and of an additional anti-DNP-SL monoclonal antibody, ANO2, have been isolated. The nucleic acid sequence of the 5' end of each clone has been determined, and the amino acid sequence of the variable regions of each antibody has been deduced from the cDNA sequence. The sequences are relatively heterogeneous, but both the heavy and the light chains of ANO1 and ANO3 are derived from the same variable-region gene families as those of the ANO2 antibody. ANO7 has a heavy chain that is related to that of ANO2, and ANO9 has a related light chain. ANO5 and ANO6 are unrelated to ANO2 but share virtually identical heavy and light chains. Preliminary NMR difference spectra comparing related antibodies show that sequence-specific assignment of resonances is possible. Such spectra also provide a measure of structural relatedness

  15. Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer.

    Science.gov (United States)

    Liu, Mingshan; Liu, Yang; Di, Jiabo; Su, Zhe; Yang, Hong; Jiang, Beihai; Wang, Zaozao; Zhuang, Meng; Bai, Fan; Su, Xiangqian

    2017-11-23

    Colorectal cancer is a heterogeneous group of malignancies with complex molecular subtypes. While colon cancer has been widely investigated, studies on rectal cancer are very limited. Here, we performed multi-region whole-exome sequencing and single-cell whole-genome sequencing to examine the genomic intratumor heterogeneity (ITH) of rectal tumors. We sequenced nine tumor regions and 88 single cells from two rectal cancer patients with tumors of the same molecular classification and characterized their mutation profiles and somatic copy number alterations (SCNAs) at the multi-region and the single-cell levels. A variable extent of genomic heterogeneity was observed between the two patients, and the degree of ITH increased when analyzed on the single-cell level. We found that major SCNAs were early events in cancer development and inherited steadily. Single-cell sequencing revealed mutations and SCNAs which were hidden in bulk sequencing. In summary, we studied the ITH of rectal cancer at regional and single-cell resolution and demonstrated that variable heterogeneity existed in two patients. The mutational scenarios and SCNA profiles of two patients with treatment naïve from the same molecular subtype are quite different. Our results suggest each tumor possesses its own architecture, which may result in different diagnosis, prognosis, and drug responses. Remarkable ITH exists in the two patients we have studied, providing a preliminary impression of ITH in rectal cancer.

  16. Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

    Science.gov (United States)

    Church, Philip C; Goscinski, Andrzej; Holt, Kathryn; Inouye, Michael; Ghoting, Amol; Makarychev, Konstantin; Reumann, Matthias

    2011-01-01

    The challenge of comparing two or more genomes that have undergone recombination and substantial amounts of segmental loss and gain has recently been addressed for small numbers of genomes. However, datasets of hundreds of genomes are now common and their sizes will only increase in the future. Multiple sequence alignment of hundreds of genomes remains an intractable problem due to quadratic increases in compute time and memory footprint. To date, most alignment algorithms are designed for commodity clusters without parallelism. Hence, we propose the design of a multiple sequence alignment algorithm on massively parallel, distributed memory supercomputers to enable research into comparative genomics on large data sets. Following the methodology of the sequential progressiveMauve algorithm, we design data structures including sequences and sorted k-mer lists on the IBM Blue Gene/P supercomputer (BG/P). Preliminary results show that we can reduce the memory footprint so that we can potentially align over 250 bacterial genomes on a single BG/P compute node. We verify our results on a dataset of E.coli, Shigella and S.pneumoniae genomes. Our implementation returns results matching those of the original algorithm but in 1/2 the time and with 1/4 the memory footprint for scaffold building. In this study, we have laid the basis for multiple sequence alignment of large-scale datasets on a massively parallel, distributed memory supercomputer, thus enabling comparison of hundreds instead of a few genome sequences within reasonable time.

  17. Interactive Block Games for Assessing Children's Cognitive Skills: Design and Preliminary Evaluation

    Directory of Open Access Journals (Sweden)

    Kiju Lee

    2018-05-01

    Full Text Available Background: This paper presents design and results from preliminary evaluation of Tangible Geometric Games (TAG-Games for cognitive assessment in young children. The TAG-Games technology employs a set of sensor-integrated cube blocks, called SIG-Blocks, and graphical user interfaces for test administration and real-time performance monitoring. TAG-Games were administered to children from 4 to 8 years of age for evaluating preliminary efficacy of this new technology-based approach.Methods: Five different sets of SIG-Blocks comprised of geometric shapes, segmented human faces, segmented animal faces, emoticons, and colors, were used for three types of TAG-Games, including Assembly, Shape Matching, and Sequence Memory. Computational task difficulty measures were defined for each game and used to generate items with varying difficulty. For preliminary evaluation, TAG-Games were tested on 40 children. To explore the clinical utility of the information assessed by TAG-Games, three subtests of the age-appropriate Wechsler tests (i.e., Block Design, Matrix Reasoning, and Picture Concept were also administered.Results: Internal consistency of TAG-Games was evaluated by the split-half reliability test. Weak to moderate correlations between Assembly and Block Design, Shape Matching and Matrix Reasoning, and Sequence Memory and Picture Concept were found. The computational measure of task complexity for each TAG-Game showed a significant correlation with participants' performance. In addition, age-correlations on TAG-Game scores were found, implying its potential use for assessing children's cognitive skills autonomously.

  18. Targeted assembly of short sequence reads.

    Directory of Open Access Journals (Sweden)

    René L Warren

    Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

  19. Artificial Intelligence In Processing A Sequence Of Time-Varying Images

    Science.gov (United States)

    Siler, W.; Tucker, D.; Buckley, J.; Hess, R. G.; Powell, V. G.

    1985-04-01

    A computer system is described for unsupervised analysis of five sets of ultrasound images of the heart. Each set consists of 24 frames taken at 33 millisecond intervals. The images are acquired in real time with computer control of the ultrasound apparatus. After acquisition the images are segmented by a sequence of image-processing programs; features are extracted and stored in a version of the Carnegie- Mellon Blackboard. Region classification is accomplished by a fuzzy logic expert system FLOPS based on OPS5. Preliminary results are given.

  20. Preliminary characterisation of tumor necrosis factor alpha and interleukin-10 responses to Chlamydia pecorum infection in the koala (Phascolarctos cinereus.

    Directory of Open Access Journals (Sweden)

    Marina Mathew

    Full Text Available Debilitating infectious diseases caused by Chlamydia are major contributors to the decline of Australia's iconic native marsupial species, the koala (Phascolarctos cinereus. An understanding of koala chlamydial disease pathogenesis and the development of effective strategies to control infections continue to be hindered by an almost complete lack of species-specific immunological reagents. The cell-mediated immune response has been shown to play an influential role in the response to chlamydial infection in other hosts. The objective of this study, hence, was to provide preliminary data on the role of two key cytokines, pro-inflammatory tumour necrosis factor alpha (TNFα and anti-inflammatory interleukin 10 (IL10, in the koala Chlamydia pecorum response. Utilising sequence homology between the cytokine sequences obtained from several recently sequenced marsupial genomes, this report describes the first mRNA sequences of any koala cytokine and the development of koala specific TNFα and IL10 real-time PCR assays to measure the expression of these genes from koala samples. In preliminary studies comparing wild koalas with overt chlamydial disease, previous evidence of C. pecorum infection or no signs of C. pecorum infection, we revealed strong but variable expression of TNFα and IL10 in wild koalas with current signs of chlamydiosis. The description of these assays and the preliminary data on the cell-mediated immune response of koalas to chlamydial infection paves the way for future studies characterising the koala immune response to a range of its pathogens while providing reagents to assist with measuring the efficacy of ongoing attempts to develop a koala chlamydial vaccine.

  1. Preliminary characterisation of tumor necrosis factor alpha and interleukin-10 responses to Chlamydia pecorum infection in the koala (Phascolarctos cinereus).

    Science.gov (United States)

    Mathew, Marina; Beagley, Kenneth W; Timms, Peter; Polkinghorne, Adam

    2013-01-01

    Debilitating infectious diseases caused by Chlamydia are major contributors to the decline of Australia's iconic native marsupial species, the koala (Phascolarctos cinereus). An understanding of koala chlamydial disease pathogenesis and the development of effective strategies to control infections continue to be hindered by an almost complete lack of species-specific immunological reagents. The cell-mediated immune response has been shown to play an influential role in the response to chlamydial infection in other hosts. The objective of this study, hence, was to provide preliminary data on the role of two key cytokines, pro-inflammatory tumour necrosis factor alpha (TNFα) and anti-inflammatory interleukin 10 (IL10), in the koala Chlamydia pecorum response. Utilising sequence homology between the cytokine sequences obtained from several recently sequenced marsupial genomes, this report describes the first mRNA sequences of any koala cytokine and the development of koala specific TNFα and IL10 real-time PCR assays to measure the expression of these genes from koala samples. In preliminary studies comparing wild koalas with overt chlamydial disease, previous evidence of C. pecorum infection or no signs of C. pecorum infection, we revealed strong but variable expression of TNFα and IL10 in wild koalas with current signs of chlamydiosis. The description of these assays and the preliminary data on the cell-mediated immune response of koalas to chlamydial infection paves the way for future studies characterising the koala immune response to a range of its pathogens while providing reagents to assist with measuring the efficacy of ongoing attempts to develop a koala chlamydial vaccine.

  2. Pareto optimal pairwise sequence alignment.

    Science.gov (United States)

    DeRonne, Kevin W; Karypis, George

    2013-01-01

    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  3. Hierarchically nested river landform sequences

    Science.gov (United States)

    Pasternack, G. B.; Weber, M. D.; Brown, R. A.; Baig, D.

    2017-12-01

    River corridors exhibit landforms nested within landforms repeatedly down spatial scales. In this study we developed, tested, and implemented a new way to create river classifications by mapping domains of fluvial processes with respect to the hierarchical organization of topographic complexity that drives fluvial dynamism. We tested this approach on flow convergence routing, a morphodynamic mechanism with different states depending on the structure of nondimensional topographic variability. Five nondimensional landform types with unique functionality (nozzle, wide bar, normal channel, constricted pool, and oversized) represent this process at any flow. When this typology is nested at base flow, bankfull, and floodprone scales it creates a system with up to 125 functional types. This shows how a single mechanism produces complex dynamism via nesting. Given the classification, we answered nine specific scientific questions to investigate the abundance, sequencing, and hierarchical nesting of these new landform types using a 35-km gravel/cobble river segment of the Yuba River in California. The nested structure of flow convergence routing landforms found in this study revealed that bankfull landforms are nested within specific floodprone valley landform types, and these types control bankfull morphodynamics during moderate to large floods. As a result, this study calls into question the prevailing theory that the bankfull channel of a gravel/cobble river is controlled by in-channel, bankfull, and/or small flood flows. Such flows are too small to initiate widespread sediment transport in a gravel/cobble river with topographic complexity.

  4. Sequencing intractable DNA to close microbial genomes.

    Directory of Open Access Journals (Sweden)

    Richard A Hurt

    Full Text Available Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled "intractable" resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such problematic regions in the "non-contiguous finished" Desulfovibrio desulfuricans ND132 genome (6 intractable gaps and the Desulfovibrio africanus genome (1 intractable gap. The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. The developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  5. Sequencing Intractable DNA to Close Microbial Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Hurt, Jr., Richard Ashley [ORNL; Brown, Steven D [ORNL; Podar, Mircea [ORNL; Palumbo, Anthony Vito [ORNL; Elias, Dwayne A [ORNL

    2012-01-01

    Advancement in high throughput DNA sequencing technologies has supported a rapid proliferation of microbial genome sequencing projects, providing the genetic blueprint for for in-depth studies. Oftentimes, difficult to sequence regions in microbial genomes are ruled intractable resulting in a growing number of genomes with sequence gaps deposited in databases. A procedure was developed to sequence such difficult regions in the non-contiguous finished Desulfovibrio desulfuricans ND132 genome (6 intractable gaps) and the Desulfovibrio africanus genome (1 intractable gap). The polynucleotides surrounding each gap formed GC rich secondary structures making the regions refractory to amplification and sequencing. Strand-displacing DNA polymerases used in concert with a novel ramped PCR extension cycle supported amplification and closure of all gap regions in both genomes. These developed procedures support accurate gene annotation, and provide a step-wise method that reduces the effort required for genome finishing.

  6. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    Science.gov (United States)

    de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

  7. cis sequence effects on gene expression

    Directory of Open Access Journals (Sweden)

    Jacobs Kevin

    2007-08-01

    Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.

  8. Multiple tag labeling method for DNA sequencing

    Science.gov (United States)

    Mathies, R.A.; Huang, X.C.; Quesada, M.A.

    1995-07-25

    A DNA sequencing method is described which uses single lane or channel electrophoresis. Sequencing fragments are separated in the lane and detected using a laser-excited, confocal fluorescence scanner. Each set of DNA sequencing fragments is separated in the same lane and then distinguished using a binary coding scheme employing only two different fluorescent labels. Also described is a method of using radioisotope labels. 5 figs.

  9. Exome sequencing and genetic testing for MODY.

    Directory of Open Access Journals (Sweden)

    Stefan Johansson

    Full Text Available Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive.The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results.We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism.On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes.Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

  10. Identifying driver mutations in sequenced cancer genomes

    DEFF Research Database (Denmark)

    Raphael, Benjamin J; Dobson, Jason R; Oesper, Layla

    2014-01-01

    High-throughput DNA sequencing is revolutionizing the study of cancer and enabling the measurement of the somatic mutations that drive cancer development. However, the resulting sequencing datasets are large and complex, obscuring the clinically important mutations in a background of errors, nois...... patterns of mutual exclusivity. These techniques, coupled with advances in high-throughput DNA sequencing, are enabling precision medicine approaches to the diagnosis and treatment of cancer....

  11. EGNAS: an exhaustive DNA sequence design algorithm

    Directory of Open Access Journals (Sweden)

    Kick Alfred

    2012-06-01

    Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

  12. Genome Sequencing and Analysis Conference IV

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

    J. Craig Venter and C. Thomas Caskey co-chaired Genome Sequencing and Analysis Conference IV held at Hilton Head, South Carolina from September 26--30, 1992. Venter opened the conference by noting that approximately 400 researchers from 16 nations were present four times as many participants as at Genome Sequencing Conference I in 1989. Venter also introduced the Data Fair, a new component of the conference allowing exchange and on-site computer analysis of unpublished sequence data.

  13. FRESCO: Referential compression of highly similar sequences.

    Science.gov (United States)

    Wandelt, Sebastian; Leser, Ulf

    2013-01-01

    In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

  14. Robustness analysis of chiller sequencing control

    International Nuclear Information System (INIS)

    Liao, Yundan; Sun, Yongjun; Huang, Gongsheng

    2015-01-01

    Highlights: • Uncertainties with chiller sequencing control were systematically quantified. • Robustness of chiller sequencing control was systematically analyzed. • Different sequencing control strategies were sensitive to different uncertainties. • A numerical method was developed for easy selection of chiller sequencing control. - Abstract: Multiple-chiller plant is commonly employed in the heating, ventilating and air-conditioning system to increase operational feasibility and energy-efficiency under part load condition. In a multiple-chiller plant, chiller sequencing control plays a key role in achieving overall energy efficiency while not sacrifices the cooling sufficiency for indoor thermal comfort. Various sequencing control strategies have been developed and implemented in practice. Based on the observation that (i) uncertainty, which cannot be avoided in chiller sequencing control, has a significant impact on the control performance and may cause the control fail to achieve the expected control and/or energy performance; and (ii) in current literature few studies have systematically addressed this issue, this paper therefore presents a study on robustness analysis of chiller sequencing control in order to understand the robustness of various chiller sequencing control strategies under different types of uncertainty. Based on the robustness analysis, a simple and applicable method is developed to select the most robust control strategy for a given chiller plant in the presence of uncertainties, which will be verified using case studies

  15. Multiplexed microsatellite recovery using massively parallel sequencing

    Science.gov (United States)

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  16. Digital Recovery Sequencer - Advanced Concept Ejection Seats

    National Research Council Canada - National Science Library

    Ross, David A; Cotter, Lee; Culhane, David; Press, Matthew J

    2005-01-01

    .... Continued usage of the Analog Sequencer is undesirable due to limitations with respect to its installed life, electronic component obsolescence, flexibility to accommodate seat safety improvements...

  17. Quantitative phenotyping via deep barcode sequencing.

    Science.gov (United States)

    Smith, Andrew M; Heisler, Lawrence E; Mellor, Joseph; Kaper, Fiona; Thompson, Michael J; Chee, Mark; Roth, Frederick P; Giaever, Guri; Nislow, Corey

    2009-10-01

    Next-generation DNA sequencing technologies have revolutionized diverse genomics applications, including de novo genome sequencing, SNP detection, chromatin immunoprecipitation, and transcriptome analysis. Here we apply deep sequencing to genome-scale fitness profiling to evaluate yeast strain collections in parallel. This method, Barcode analysis by Sequencing, or "Bar-seq," outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex chemogenomic assay, Bar-seq quantitatively identifies drug targets, with performance superior to the benchmark microarray assay. We also show that Bar-seq is well-suited for a multiplex format. We completely re-sequenced and re-annotated the yeast deletion collection using deep sequencing, found that approximately 20% of the barcodes and common priming sequences varied from expectation, and used this revised list of barcode sequences to improve data quality. Together, this new assay and analysis routine provide a deep-sequencing-based toolkit for identifying gene-environment interactions on a genome-wide scale.

  18. Hardware Accelerated Sequence Alignment with Traceback

    Directory of Open Access Journals (Sweden)

    Scott Lloyd

    2009-01-01

    in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop computer is demonstrated on sequence lengths of 16000. For greater performance, the architecture is scalable to more processing elements.

  19. Multipliers on Generalized Mixed Norm Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Oscar Blasco

    2014-01-01

    Full Text Available Given 1≤p,q≤∞ and sequences of integers (nkk and (nk′k such that nk≤nk′≤nk+1, the generalized mixed norm space ℓℐ(p,q is defined as those sequences (ajj such that ((∑j∈Ik‍|aj|p1/pk∈ℓq where Ik={j∈ℕ0 s.t. nk≤jsequence λ=(λjj to belong to the space of multipliers (ℓℐ(r,s,ℓ(u,v, for different sequences ℐ and of intervals in ℕ0, are determined.

  20. Recursive sequences in first-year calculus

    Science.gov (United States)

    Krainer, Thomas

    2016-02-01

    This article provides ready-to-use supplementary material on recursive sequences for a second-semester calculus class. It equips first-year calculus students with a basic methodical procedure based on which they can conduct a rigorous convergence or divergence analysis of many simple recursive sequences on their own without the need to invoke inductive arguments as is typically required in calculus textbooks. The sequences that are accessible to this kind of analysis are predominantly (eventually) monotonic, but also certain recursive sequences that alternate around their limit point as they converge can be considered.

  1. A measurement of disorder in binary sequences

    Science.gov (United States)

    Gong, Longyan; Wang, Haihong; Cheng, Weiwen; Zhao, Shengmei

    2015-03-01

    We propose a complex quantity, AL, to characterize the degree of disorder of L-length binary symbolic sequences. As examples, we respectively apply it to typical random and deterministic sequences. One kind of random sequences is generated from a periodic binary sequence and the other is generated from the logistic map. The deterministic sequences are the Fibonacci and Thue-Morse sequences. In these analyzed sequences, we find that the modulus of AL, denoted by |AL | , is a (statistically) equivalent quantity to the Boltzmann entropy, the metric entropy, the conditional block entropy and/or other quantities, so it is a useful quantitative measure of disorder. It can be as a fruitful index to discern which sequence is more disordered. Moreover, there is one and only one value of |AL | for the overall disorder characteristics. It needs extremely low computational costs. It can be easily experimentally realized. From all these mentioned, we believe that the proposed measure of disorder is a valuable complement to existing ones in symbolic sequences.

  2. Polynomial sequences generated by infinite Hessenberg matrices

    Directory of Open Access Journals (Sweden)

    Verde-Star Luis

    2017-01-01

    Full Text Available We show that an infinite lower Hessenberg matrix generates polynomial sequences that correspond to the rows of infinite lower triangular invertible matrices. Orthogonal polynomial sequences are obtained when the Hessenberg matrix is tridiagonal. We study properties of the polynomial sequences and their corresponding matrices which are related to recurrence relations, companion matrices, matrix similarity, construction algorithms, and generating functions. When the Hessenberg matrix is also Toeplitz the polynomial sequences turn out to be of interpolatory type and we obtain additional results. For example, we show that every nonderogative finite square matrix is similar to a unique Toeplitz-Hessenberg matrix.

  3. Genomic sequencing of Pleistocene cave bears

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Hofreiter, Michael; Smith, Doug; Priest, JamesR.; Rohland, Nadin; Rabeder, Gernot; Krause, Johannes; Detter, J. Chris; Paabo, Svante; Rubin, Edward M.

    2005-04-01

    Despite the information content of genomic DNA, ancient DNA studies to date have largely been limited to amplification of mitochondrial DNA due to technical hurdles such as contamination and degradation of ancient DNAs. In this study, we describe two metagenomic libraries constructed using unamplified DNA extracted from the bones of two 40,000-year-old extinct cave bears. Analysis of {approx}1 Mb of sequence from each library showed that, despite significant microbial contamination, 5.8 percent and 1.1 percent of clones in the libraries contain cave bear inserts, yielding 26,861 bp of cave bear genome sequence. Alignment of this sequence to the dog genome, the closest sequenced genome to cave bear in terms of evolutionary distance, revealed roughly the expected ratio of cave bear exons, repeats and conserved noncoding sequences. Only 0.04 percent of all clones sequenced were derived from contamination with modern human DNA. Comparison of cave bear with orthologous sequences from several modern bear species revealed the evolutionary relationship of these lineages. Using the metagenomic approach described here, we have recovered substantial quantities of mammalian genomic sequence more than twice as old as any previously reported, establishing the feasibility of ancient DNA genomic sequencing programs.

  4. BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data

    Science.gov (United States)

    Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Pareja, Eduardo; Tobes, Raquel

    2012-01-01

    BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version – which is developed in Java, takes advantage of Amazon Web Services (AWS) cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future. PMID:23185310

  5. Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens.

    Directory of Open Access Journals (Sweden)

    Bonnie B Blaimer

    Full Text Available Obtaining sequence data from historical museum specimens has been a growing research interest, invigorated by next-generation sequencing methods that allow inputs of highly degraded DNA. We applied a target enrichment and next-generation sequencing protocol to generate ultraconserved elements (UCEs from 51 large carpenter bee specimens (genus Xylocopa, representing 25 species with specimen ages ranging from 2-121 years. We measured the correlation between specimen age and DNA yield (pre- and post-library preparation DNA concentration and several UCE sequence capture statistics (raw read count, UCE reads on target, UCE mean contig length and UCE locus count with linear regression models. We performed piecewise regression to test for specific breakpoints in the relationship of specimen age and DNA yield and sequence capture variables. Additionally, we compared UCE data from newer and older specimens of the same species and reconstructed their phylogeny in order to confirm the validity of our data. We recovered 6-972 UCE loci from samples with pre-library DNA concentrations ranging from 0.06-9.8 ng/μL. All investigated DNA yield and sequence capture variables were significantly but only moderately negatively correlated with specimen age. Specimens of age 20 years or less had significantly higher pre- and post-library concentrations, UCE contig lengths, and locus counts compared to specimens older than 20 years. We found breakpoints in our data indicating a decrease of the initial detrimental effect of specimen age on pre- and post-library DNA concentration and UCE contig length starting around 21-39 years after preservation. Our phylogenetic results confirmed the integrity of our data, giving preliminary insights into relationships within Xylocopa. We consider the effect of additional factors not measured in this study on our age-related sequence capture results, such as DNA fragmentation and preservation method, and discuss the promise of the UCE

  6. BG7: a new approach for bacterial genome annotation designed for next generation sequencing data.

    Directory of Open Access Journals (Sweden)

    Pablo Pareja-Tobes

    Full Text Available BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version - which is developed in Java, takes advantage of Amazon Web Services (AWS cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future.

  7. Design of Long Period Pseudo-Random Sequences from the Addition of -Sequences over

    Directory of Open Access Journals (Sweden)

    Ren Jian

    2004-01-01

    Full Text Available Pseudo-random sequence with good correlation property and large linear span is widely used in code division multiple access (CDMA communication systems and cryptology for reliable and secure information transmission. In this paper, sequences with long period, large complexity, balance statistics, and low cross-correlation property are constructed from the addition of -sequences with pairwise-prime linear spans (AMPLS. Using -sequences as building blocks, the proposed method proved to be an efficient and flexible approach to construct long period pseudo-random sequences with desirable properties from short period sequences. Applying the proposed method to , a signal set is constructed.

  8. DNA Data Bank of Japan at work on genome sequence data.

    Science.gov (United States)

    Tateno, Y; Fukami-Kobayashi, K; Miyazaki, S; Sugawara, H; Gojobori, T

    1998-01-01

    We at the DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) have recently begun receiving, processing and releasing EST and genome sequence data submitted by various Japanese genome projects. The data include those for human, Arabidopsis thaliana, rice, nematode, Synechocystis sp. and Escherichia coli. Since the quantity of data is very large, we organized teams to conduct preliminary discussions with project teams about data submission and handling for release to the public. We also developed a mass submission tool to cope with a large quantity of data. In addition, to provide genome data on WWW, we developed a genome information system using Java. This system (http://mol.genes.nig.ac.jp/ecoli/) can in theory be used for any genome sequence data. These activities will facilitate processing of large quantities of EST and genome data.

  9. A Preliminary Fire PSA on PGSFR

    International Nuclear Information System (INIS)

    Kim, Kilyoo; Han, Sanghoon; Lee, KwiLim

    2017-01-01

    A Prototype Generation IV Sodium Fast Reactor (PGSFR) is under design with defense in depth concept with active, passive, and inherent safety features to acquire a design approval for PGSFR from Korean regulatory authority by around 2017. A preliminary fire PSA on PGSFR is done in 2016 and a final fire PSA of PGSFR will be done in 2017. The characteristics of the preliminary fire PSA on PGSFR are described in this paper. Since PGSFR is very safe reactor, it is not bad approach to use a conservative assumption in the preliminary PSA. In addition, several drawings including cable routing are not yet issued, a conservative calculation for CDF is performed. As shown in Table 2, the CDF caused by the fire in the control room takes 89% portion of total CDF. Thus, a detailed fire modeling for control room is necessary for the final fire PSA on PGSFR. Also, the increased ignition frequency due to sodium leak would be derived by considering the sodium piping complexity in the final fire PSA on PGSFR. The 4th column of Table 2 is derived the 3rd column by multiplying the factor (592/1177). The 5th column is the ignition frequency caused by the sodium leak. The 6th column is derived by summing the 4th column and the 5th column. The 7th column is the CDF portion of each fire area. The control room (fire area F-A404A) is the most important area since the control room fire takes 89% portion of total CDF.

  10. Preliminary design of a coffee harvester

    Directory of Open Access Journals (Sweden)

    Raphael Magalhães Gomes Moreira

    2016-10-01

    Full Text Available Design of an agricultural machine is a highly complex process due to interactions between the operator, machine, and environment. Mountain coffee plantations constitute an economic sector that requires huge investments for the development of agricultural machinery to improve the harvesting and post-harvesting processes and to overcome the scarcity of work forces in the fields. The aim of this study was to develop a preliminary design for a virtual prototype of a coffee fruit harvester. In this study, a project methodology was applied and adapted for the development of the following steps: project planning, informational design, conceptual design, and preliminary design. The construction of a morphological matrix made it possible to obtain a list of different mechanisms with specific functions. The union between these mechanisms resulted in variants, which were weighed to attribute scores for each selected criterion. From each designated proposal, two variants with the best scores were selected and this permitted the preparation of the preliminary design of both variants. The archetype was divided in two parts, namely the hydraulically articulated arms and the harvesting system that consisted of the vibration mechanism and the detachment mechanism. The proposed innovation involves the use of parallel rods, which were fixed in a plane and rectangular metal sheet. In this step, dimensions including a maximum length of 4.7 m, a minimum length of 3.3 m, and a total height of 2.15 m were identified based on the functioning of the harvester in relation to the coupling point of the tractor.

  11. Preliminary list of plant invaders in Montenegro

    Directory of Open Access Journals (Sweden)

    Stešević, D.

    2010-12-01

    Full Text Available Due to the fact that Invasive alien species (IAS are considered to be the second cause of global biodiversity loss after direct habitat destruction and have adverse environmental, economic and social impacts from the local level upwards, in last decades investigations of alien flora of Montenegro are intensified. In this paper we are presenting a preliminary list of IAS, with the aim to provide a basic data on IAS in Montenegro, to enable future monitoring and to draw attention on the problems which expansion of IAS is bringing with itself. The list consists of 50 plant taxa species and supspecies level.

  12. Preliminary summary of the ETF conceptual studies

    Science.gov (United States)

    Seikel, G. R.; Bercaw, R. W.; Pearson, C. V.; Owens, W. R.

    1978-01-01

    Power plant studies have shown the attractiveness of MHD topped steam power plants for baseload utility applications. To realize these advantages, a three-phase development program was initiated. In the first phase, the engineering data and experience were developed for the design and construction of a pilot plant, the Engineering Test Facility (ETF). Results of the ETF studies are reviewed. These three parallel independent studies were conducted by industrial teams led by the AVCO Everett Research Laboratory, the General Electric Corporation, and the Westinghouse Corporation. A preliminary analysis and the status of the critical evaluation of these results are presented.

  13. Preliminary economic evaluation of the Alkox process

    International Nuclear Information System (INIS)

    Silva, L.J.; Lilga, M.A.; Camaioni, D.M.; Snowden, L.J.

    1991-09-01

    A new chemical process has been invented at Battelle Pacific Northwest Laboratories for converting alkanes to alcohols. This new chemistry has been named the ''Alkox Process.'' Pacific Northwest Laboratory prepared a preliminary economic analysis for converting cyclohexane to cyclohexanol, which may be one of the most attractive applications of the Alkox process. A process flow scheme and a material balance were prepared to support rough equipment sizing and costing. The results from the economic analysis are presented in the non-proprietary section of this report. The process details, including the flow diagram and material balance, are contained in separate section of this report that is proprietary to Battelle. 7 refs., 4 tabs

  14. Vasectomy: preliminary report on 25 cases.

    Science.gov (United States)

    Lema, V M; Makokha, A E

    1989-05-01

    Preliminary data on 25 men who underwent vasectomy for contraception between June 1986 and May 1988 at the Marie Stopes Clinic--Nairobi is presented. The majority (76.0%) of the subjects were aged between 25 and 39 years. 68.0% had 4 living children or less. Professionals including lecturers, lawyers, teachers, engineers etc, formed 88.0% of the total. Three clients(12.0%) had documented complications; one had aseptic wound, one had haematoma and the last one had a failed vasectomy. All were treated successfully. Complications of vasectomy and the need for follow-up of vasectomised men are discussed.

  15. Danish Anaesthesia Allergy Centre - preliminary results

    DEFF Research Database (Denmark)

    Garvey, L H; Roed-Petersen, J; Menné, T

    2001-01-01

    BACKGROUND: Anaphylactoid reactions in anaesthesia are rare and should ideally be investigated in specialist centres. At Gentofte University Hospital, we established such a centre in 1998 as a joint venture between the Departments of Anaesthesiology and Dermatology. We present the methodology...... for chlorhexidine. Only one patient has tested positive to a neuromuscular blocking drug (NMBD) so far. DISCUSSION: Our preliminary results appear to differ in two ways from results usually found in this field. Firstly, only one patient has tested positive for a NMBD and secondly, we have had four patients...

  16. Preliminary investigations of piezoelectric based LED luminary

    DEFF Research Database (Denmark)

    Nielsen, Dennis; Andersen, Michael A. E.; Meyer, Kaspar Sinding

    2011-01-01

    , modulation schemes, LEDs and LED driving conditions are analyzed. A prototype radial mode PT optimized for ZVS (Zero Voltage Switching) is designed. FEM (Final Element Method) and measurements validates the PT design. A prototype PT based AC/DC converter operating from european mains is proposed......This paper presents a preliminary study of PT (Piezoelectric Transformer) based SMPS’s (Switch Mode Power Supplies) for LED luminary. The unique properties of PTs (efficiency, power density and EMI) make them highly suitable for this application. Power stage topologies, rectifiers circuits...

  17. Preliminary study on AC superconducting machines

    International Nuclear Information System (INIS)

    Yamamoto, M.; Ishigohka, T.; Shimohka, T.; Mizukami, N.; Yamaguchi, M.

    1988-01-01

    This paper describes the issues involved in developing AC superconducting machines. In the first phase, as a preliminary experiment, a 4kVa AC superconducting coil which employs 100A class 50/60Hz superconductors is made and tested. And, in the second phase, as an extension of the 4kVa coil, a model superconducting transformer is made and examined. The transformer has a novel quench protection system with an auxiliary coil only in the low voltage side. The behavior of the overcurrent protection system is confirmed

  18. Ecological economics - a special perspective? Preliminary reflections

    DEFF Research Database (Denmark)

    Røpke, Inge

    2002-01-01

    This paper reports on some preliminary reflections from a research project concerning ecological economics as a special perspective. As Clive Spash noted in a presentation at the ESEE conference in Cambridge, July 2001, ecological economics has reached the age of puberty, looks into the glass...... and searches its own identity. The identity seeking processes are visible in the large number of publications discussing the characteristics of ecological economics as well as the similarities to and differences from environmental economics. The present paper is a part of this stream. The paper is work...

  19. Preliminary cost estimating for the nuclear industry

    International Nuclear Information System (INIS)

    Klumpar, I.V.; Soltz, K.M.

    1985-01-01

    The nuclear industry has higher costs for personnel, equipment, construction, and engineering than conventional industry, which means that cost estimation procedures may need adjustment. The authors account for the special technical and labor requirements of the nuclear industry in making adjustments to equipment and installation cost estimations. Using illustrative examples, they show that conventional methods of preliminary cost estimation are flexible enough for application to emerging industries if their cost structure is similar to that of the process industries. If not, modifications can provide enough engineering and cost data for a statistical analysis. 9 references, 14 figures, 4 tables

  20. Preliminary simulation study of doppler reflectometry

    International Nuclear Information System (INIS)

    Ishii, Yuta; Hojo, Hitoshi; Yoshikawa, Masashi; Ichimura, Makoto; Haraguchi, Yusuke; Imai, Tsuyoshi; Mase, Atsushi

    2010-01-01

    A preliminary simulation study of Doppler reflectometry is performed. The simulations solve Maxwell's equations by a finite difference time domain (FDTD) code method in two dimensions. A moving corrugated metal target is used as a plasma cutoff layer to study the basic features of Doppler reflectometry. We examined the effects of the full width at half maximum (FWHM) of the electromagnetic waves and the corrugation depth of the metal target. Furthermore, the effect of a nonuniform plasma is studied using this FDTD analysis. The Doppler shift and velocity are compared with those obtained from FDTD analysis of a uniform plasma. (author)

  1. Isotope angiocardiography. Method and preliminary own studies

    Energy Technology Data Exchange (ETDEWEB)

    Stepinska, J; Ruzyllo, W; Konieczny, W [Centrum Medyczne Ksztalcenia Podyplomowego, Warsaw (Poland)

    1979-01-01

    Method of technetium isotope 99 m pass through the heart recording with the aid of radioisotope scanner connected with seriograph and computer is being presented. Preliminary tests were carried out in 26 patients with coronary disease without or with previous myocardial infarction, cardiomyopathy, ventricular septal defect and in patients with artificial mitral and aortic valves. The obtained scans were evaluated qualitatively and compared with performed later contrast X-rays of the heart. Size of the right ventricle, volume and rate of left atrial evacuation, size and contractability of left ventricle were evaluated. Similarity of direct and isotope angiocardiographs, non-invasional character and repeatability of isotope angiocardiography advocate its usefulness.

  2. Preliminary Cost Model for Space Telescopes

    Science.gov (United States)

    Stahl, H. Philip; Prince, F. Andrew; Smart, Christian; Stephens, Kyle; Henrichs, Todd

    2009-01-01

    Parametric cost models are routinely used to plan missions, compare concepts and justify technology investments. However, great care is required. Some space telescope cost models, such as those based only on mass, lack sufficient detail to support such analysis and may lead to inaccurate conclusions. Similarly, using ground based telescope models which include the dome cost will also lead to inaccurate conclusions. This paper reviews current and historical models. Then, based on data from 22 different NASA space telescopes, this paper tests those models and presents preliminary analysis of single and multi-variable space telescope cost models.

  3. Preliminary recommendations of the Noise Working Group

    International Nuclear Information System (INIS)

    Legerton, M.L.

    1995-01-01

    In 1993 the DTI set up a Working Group largely consisting of independent experts on wind turbine noise. The main objectives of the Working Group were to define a framework which can be used to measure and rate the noise from wind turbines and to provide indicative noise levels thought to offer a reasonable degree of protection to wind farm neighbours and encourage best practice in turbine design and wind farm siting and layout. This paper presents the preliminary recommendations of the Working Group. (Author)

  4. Preliminary biogeochemical assessment of EPICA LGM and Holocene ice samples

    Science.gov (United States)

    Bulat, S.; Alekhina, I.; Marie, D.; Wagenbach, D.; Raynaud, D.; Petit, J. R.

    2009-04-01

    We are investigating the biological content (biomass and microbial diversity of Aeolian origin) of EPICA ice core within the frame of EPICA Microbiology consortium*. Two ice core sections were selected from EPICA Dome C and Droning Maud Land, both from LGM and Holocene. Preliminary measurements of DOC (dissolved organic content) and microbial cell concentrations have been performed. Both analyses showed the very low biomass and ultra low DOC content. Trace DNA analyses are in a progress. The ice sections were decontaminated in LGGE cold and clean room facilities benefiting the protocol developed for Vostok ice core studies. The melt water was then shared between two party laboratories for a complementary approach in studying microbial content. Prior to biology the melt water was tested for chemical contaminant ions and organic acids, DOC and dust contents. The biological methods included all the spectra of appropriate molecular techniques (gDNA extraction, PCR, clone libraries and sequencing). As preliminary results, both LGM (well identified by dust fallout) and Holocene ice samples (EDC99 and EDML) proved to be extremely clear (i.e. pristine) in terms of biomass (less then 4 cells per ml) and DOC contents (less then 5 ppbC). There was no obvious difference between LGM and Holocene in cell counts, while LGM showed a bit high organic carbon content. The latter in terms of biology means ultra-oligotrophic conditions (i.e., no possibility for heterotrophic life style). In fact no metabolizing microbial cells or propagating populations are expected at these depths at temperature -38oC and lower (limiting life temperature threshold is -20°C). Nevertheless some life seeds brought in Antarctica with precipitation could be well preserved because the age is rather young (21 kyr and less). Trying to identify these aliens and document their distribution during last climate cycle the meltwater was concentrated about 1000 times down. The genomic DNA was extracted and very

  5. Compressing DNA sequence databases with coil

    Directory of Open Access Journals (Sweden)

    Hendy Michael D

    2008-05-01

    Full Text Available Abstract Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

  6. Direct chloroplast sequencing: comparison of sequencing platforms and analysis tools for whole chloroplast barcoding.

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

    Full Text Available Direct sequencing of total plant DNA using next generation sequencing technologies generates a whole chloroplast genome sequence that has the potential to provide a barcode for use in plant and food identification. Advances in DNA sequencing platforms may make this an attractive approach for routine plant identification. The HiSeq (Illumina and Ion Torrent (Life Technology sequencing platforms were used to sequence total DNA from rice to identify polymorphisms in the whole chloroplast genome sequence of a wild rice plant relative to cultivated rice (cv. Nipponbare. Consensus chloroplast sequences were produced by mapping sequence reads to the reference rice chloroplast genome or by de novo assembly and mapping of the resulting contigs to the reference sequence. A total of 122 polymorphisms (SNPs and indels between the wild and cultivated rice chloroplasts were predicted by these different sequencing and analysis methods. Of these, a total of 102 polymorphisms including 90 SNPs were predicted by both platforms. Indels were more variable with different sequencing methods, with almost all discrepancies found in homopolymers. The Ion Torrent platform gave no apparent false SNP but was less reliable for indels. The methods should be suitable for routine barcoding using appropriate combinations of sequencing platform and data analysis.

  7. Temporal correlation of fluvial and alluvial sequences in the Makran Range, SE-Iran

    Science.gov (United States)

    Kober, F.; Zeilinger, G.; Ivy-Ochs, S.; Dolati, A.; Smit, J.; Burg, J.-P.; Bahroudi, A.; Kubik, P. W.; Baur, H.; Wieler, R.; Haghipour, N.

    2009-04-01

    The Makran region of southeastern Iran is an active accretionary wedge with a partially subaerial component. New investigations have revealed a rather complex geodynamic evolution of the Makran active accretionary wedge that is not yet fully understood in its entity. Ongoing convergence between the Arabian and Eurasian plates and tectonic activity since the late Mesozoic has extended all trough the Quaternary. We focus here on fluvial and alluvial sequences in tectonically separated basins that have been deposited probably in the Pliocene/Quaternary, based on stratigraphic classification in official geological maps, in order to understand the climatic and tectonic forces occurring during the ongoing accretionary wegde formation. Specifically, we investigate the influence of Quaternary climate variations (Pleistocene cold period, monsoonal variations) on erosional and depositional processes in the (semi)arid Makran as well as local and regional tectonic forces in the Coastal and Central Makran Range region. Necessary for such an analysis is a temporal calibration of alluvial and fluvial terrace sequences that will allow an inter-basin correlation. We utilize the exposure age dating method using terrestrial cosmogenic nuclides (TCN) due to the lack of otherwise datatable material in the arid Makran region. Limited radiocarbon data are only available for marine terraces (wave-cut platforms). Our preliminary 21Ne and 10Be TCN-ages of amalgamated clast samples from (un)deformed terrace and alluvial sequences range from ~250 ky to present day (modern wash). These ages agree in relative terms with sequences previously assigned by other investigations through correlation of Quaternary sequences from Central and Western Iran regions. However, our minimum ages suggest that all age sequences are of middle to late Pleistocene age, compared to Pliocene age estimates previously assigned for the oldest units. Although often suggested, a genetical relation and connection of those

  8. Preliminary clinical applications of DTI in human cervical spinal cord

    International Nuclear Information System (INIS)

    Song Ting; Mai Weiwen; Liang Biling; Shen Jun; Huang Suiqiao; Hu Chunhong

    2007-01-01

    Objective: To condcut preliminary study of the value of DTI(diffusion tensor imaging) in human cervical spinal cord. Methods: Twenty-one patients suffering from cervical spondylotic myelopathy and twenty volunteers without any clinical symptoms underwent routine MRI and DTI examination. DTI was performed in six non-collinear directions with single-shot fast spin echo echo, planar imaging sequence(b value = 400 s·mm -2 ). ADC(apparent diffusion coefficient) and FA(fractional anisotropy)values were measured by ROIs(regions of interest) in 4 different level segment spinal cord (C 2/3 , C 3/4 , C 4/5 , C 5/6 ) in normal volunteers, in lesions and normal segmental spinal cord in clinical cases respectively. DTI original images were automatically processed by using IDL (Version 5.6) soft- ware to produce color tensor images. SPSS11.0 software for windows was used for t-test and one-way ANOVA analysis. The difference was considered statistically significant if P 2/3 , C 3/4 , C 4/5 , C 5/6 , were analyzed and it was found that FA value between them had a significant difference by ANOVA, F=159.24, P 2/3 level. However, ADC value between 4 segments had no significant difference(F=2.191, P>0.05). (2)In patients of cervical spondylotic myelopathy, routine MRI T2WI showed abnormal signal in 9 cases, and showed no abnormal signal in 12 dases. In sixteen cases it was found that abnormal patchy green signal on colorized tensor maps appeared on the normal blue spinal cord. Also, in patients of cervical spondylotic myelopathy, there was significant difference in ADC and FA value between lesions and normal spinal cord (paired t test, for ADC, t=2.88, P 2/3 level segment spinal cord in normal volunteers (0.85 ± 0.03) is the highest among other segments. FA value decreases gradually along cervical spinal cord towards the caudal direction. However, the difference of ADC values amongst 4 segments is not significant. DTI colorized tensor maps can show more lesions than routine MRI

  9. Step out - Step in Sequencing Games

    NARCIS (Netherlands)

    Musegaas, M.; Borm, P.E.M.; Quant, M.

    2014-01-01

    In this paper a new class of relaxed sequencing games is introduced: the class of Step out - Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order.

  10. Step out-step in sequencing games

    NARCIS (Netherlands)

    Musegaas, Marieke; Borm, Peter; Quant, Marieke

    2015-01-01

    In this paper a new class of relaxed sequencing games is introduced: the class of Step out–Step in sequencing games. In this relaxation any player within a coalition is allowed to step out from his position in the processing order and to step in at any position later in the processing order. First,

  11. Enhanced throughput for infrared automated DNA sequencing

    Science.gov (United States)

    Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

    1995-04-01

    Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

  12. Thread extraction for polyadic instruction sequences

    NARCIS (Netherlands)

    Bergstra, J.; Middelburg, C.

    2011-01-01

    In this paper, we study the phenomenon that instruction sequences are split into fragments which somehow produce a joint behaviour. In order to bring this phenomenon better into the picture, we formalize a simple mechanism by which several instruction sequence fragments can produce a joint

  13. Genome sequence of Lactobacillus rhamnosus ATCC 8530.

    Science.gov (United States)

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R; Ziola, Barry

    2012-02-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

  14. Genome Sequence of Lactobacillus rhamnosus ATCC 8530

    OpenAIRE

    Pittet, Vanessa; Ewen, Emily; Bushell, Barry R.; Ziola, Barry

    2012-01-01

    Lactobacillus rhamnosus is found in the human gastrointestinal tract and is important for probiotics. We became interested in L. rhamnosus isolate ATCC 8530 in relation to beer spoilage and hops resistance. We report here the genome sequence of this isolate, along with a brief comparison to other available L. rhamnosus genome sequences.

  15. Question-answer sequences in survey interviews

    NARCIS (Netherlands)

    Dijkstra, W.; Ongena, Y.P.

    2006-01-01

    Interaction analysis was used to analyze a total of 14,265 question-answer sequences of (Q-A Sequences) 80 questions that originated from two face-to-face and three telephone surveys. The analysis was directed towards the causes and effects of particular interactional problems. Our results showed

  16. Trace maps for arbitrary substitution sequences

    International Nuclear Information System (INIS)

    Avishai, Y.

    1993-01-01

    The discovery of quasi-crystals and their 1-dimensional modeling have led to a deep mathematical study of Schroedinger operators with an arbitrary deterministic potential sequence. In this work we address this problem and find trace maps for an arbitrary substitution sequence. our trace maps have lower dimensionality than those of Kolar and Nori, which make them quite attractive for actual applications. (authors)

  17. Stochastic modelling of daily rainfall sequences

    NARCIS (Netherlands)

    Buishand, T.A.

    1977-01-01

    Rainfall series of different climatic regions were analysed with the aim of generating daily rainfall sequences. A survey of the data is given in I, 1. When analysing daily rainfall sequences one must be aware of the following points:
    a. Seasonality. Because of seasonal variation

  18. Learning of Sensory Sequences in Cerebellar Patients

    Science.gov (United States)

    Frings, Markus; Boenisch, Raoul; Gerwig, Marcus; Diener, Hans-Christoph; Timmann, Dagmar

    2004-01-01

    A possible role of the cerebellum in detecting and recognizing event sequences has been proposed. The present study sought to determine whether patients with cerebellar lesions are impaired in the acquisition and discrimination of sequences of sensory stimuli of different modalities. A group of 26 cerebellar patients and 26 controls matched for…

  19. On peculiar Šindel sequences

    Czech Academy of Sciences Publication Activity Database

    Křížek, Michal; Somer, L.

    2010-01-01

    Roč. 17, č. 2 (2010), s. 129-140 ISSN 0972-5555 R&D Projects: GA AV ČR(CZ) IAA100190803 Institutional research plan: CEZ:AV0Z10190503 Keywords : quadratic residue * Chinese remainder theorem * primitive Šindel sequences * Prague clock sequence Subject RIV: BA - General Mathematics http://www.pphmj.com/abstract/5095.htm

  20. Protecting genomic sequence anonymity with generalization lattices.

    Science.gov (United States)

    Malin, B A

    2005-01-01

    Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

  1. Occupational Sequences: Auto Engines 1. AT 121.

    Science.gov (United States)

    Korb, A. W.; And Others

    In an attempt to individualize an automotive course, the Vocational-Technical Division of Northern Montana College has developed Occupational Sequences for an engine rebuilding course. Occupational Sequences, a learning or teaching aid, is an analysis of numbered operations involved in engine rebuilding. Job sheets, included in the book, provide a…

  2. Sequencing Events: Exploring Art and Art Jobs.

    Science.gov (United States)

    Stephens, Pamela Geiger; Shaddix, Robin K.

    2000-01-01

    Presents an activity for upper-elementary students that correlates the actions of archaeologists, patrons, and artists with the sequencing of events in a logical order. Features ancient Egyptian art images. Discusses the preparation of materials, motivation, a pre-writing activity, and writing a story in sequence. (CMK)

  3. Wijsman Orlicz Asymptotically Ideal -Statistical Equivalent Sequences

    Directory of Open Access Journals (Sweden)

    Bipan Hazarika

    2013-01-01

    in Wijsman sense and present some definitions which are the natural combination of the definition of asymptotic equivalence, statistical equivalent, -statistical equivalent sequences in Wijsman sense. Finally, we introduce the notion of Cesaro Orlicz asymptotically -equivalent sequences in Wijsman sense and establish their relationship with other classes.

  4. Nitrogen chronology of massive main sequence stars

    NARCIS (Netherlands)

    Köhler, K.; Borzyszkowski, M.; Brott, I.; Langer, N.; de Koter, A.

    2012-01-01

    Context. Rotational mixing in massive main sequence stars is predicted to monotonically increase their surface nitrogen abundance with time. Aims. We use this effect to design a method for constraining the age and the inclination angle of massive main sequence stars, given their observed luminosity,

  5. Massively parallel sequencing of forensic STRs

    DEFF Research Database (Denmark)

    Parson, Walther; Ballard, David; Budowle, Bruce

    2016-01-01

    The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that...

  6. Novel algorithms for protein sequence analysis

    NARCIS (Netherlands)

    Ye, Kai

    2008-01-01

    Each protein is characterized by its unique sequential order of amino acids, the so-called protein sequence. Biology”s paradigm is that this order of amino acids determines the protein”s architecture and function. In this thesis, we introduce novel algorithms to analyze protein sequences. Chapter 1

  7. Cyprinus carpio Genome sequencing and assembly

    NARCIS (Netherlands)

    Kolder, I.C.R.M.; Plas-Duivesteijn, van der Suzanne J.; Tan, G.; Wiegertjes, G.; Forlenza, M.; Guler, A.T.; Travin, D.Y.; Nakao, M.; Moritomo, T.; Irnazarow, I.; Jansen, H.J.

    2013-01-01

    Sequencing of the common carp (Cyprinus carpio carpio Linnaeus, 1758) genome, with the objective of establishing carp as a model organism to supplement the closely related zebrafish (Danio rerio). The sequenced individual is a homozygous female (by gynogenesis) of R3 x R8 carp, the heterozygous

  8. Sequence Comparison: Close and Open problems

    NARCIS (Netherlands)

    Lenzini, Gabriele; Cerrai, P.; Freguglia, P.

    Comparing sequences is a very important activity both in computer science and in a many other areas as well. For example thank to text editors, everyone knows the particular instance of a sequence comparison problem knonw as ``string mathcing problem''. It consists in searching a given work

  9. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol

    2010-01-01

    preferentially selected for sequencing. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement the data have been released into public sequence repositories (Genbank/EMBL, NCBI/Ensembl trace repositories) in a timely manner and in advance of publication. CONCLUSIONS...

  10. Swab-to-Sequence: Real-time Data Analysis Platform for the Biomolecule Sequencer

    Data.gov (United States)

    National Aeronautics and Space Administration — DNA was successfully sequenced on the ISS in 2016, but the DNA sequenced was prepared on the ground. With FY’16 IRAD funds, the same team developed a...

  11. From Sequence to Morphology - Long-Range Correlations in Complete Sequenced Genomes

    NARCIS (Netherlands)

    T.A. Knoch (Tobias)

    2004-01-01

    textabstractThe largely unresolved sequential organization, i.e. the relations within DNA sequences, and its connection to the three-dimensional organization of genomes was investigated by correlation analyses of completely sequenced chromosomes from Viroids, Archaea, Bacteria, Arabidopsis

  12. Expression, purification, crystallization and preliminary diffraction studies of the mammalian DAG kinase homologue YegS from Escherichia coli

    International Nuclear Information System (INIS)

    Bakali H, M. Amin; Nordlund, Pär; Hallberg, B. Martin

    2006-01-01

    The overexpression, crystallization and preliminary diffraction analysis of E. coli YegS are reported. yegS is a gene encoding a 32 kDa cytosolic protein with unknown function but with strong sequence homology to a family of structurally uncharacterized eukaryotic non-protein kinases: diacylglycerol kinases, sphingosine kinases and ceramide kinases. Here, the overexpression, crystallization and preliminary diffraction analysis of Escherichia coli YegS are reported. The crystals belong to space group P2 1 , with unit-cell parameters a = 42.4, b = 166.1, c = 48.5 Å, β = 96.97°. The presence of a dimer in the asymmetric unit was estimated to give a Matthews coefficient (V M ) of 2.5 Å 3 Da −1 and a solvent content of 50.8%(v/v). Single-wavelength diffraction data were collected to a resolution of 1.9 Å using synchrotron radiation

  13. Preliminary impression techniques for microstomia patients

    Directory of Open Access Journals (Sweden)

    K Aswini Kumar

    2016-01-01

    Full Text Available The Prosthetic rehabilitation of microstomia patients presents difficulties at all the stages. The difficulty starts with the preliminary impression making. This is due to the tongue rigidity and the decreased oral opening. A maximum oral opening which is smaller than the size of the tray can make prosthetic treatment challenging. Due to the restricted mouth opening, insertion and removal of the impression trays is extremely cumbersome and various modifications of the trays have been used in the past. Among these are the flexible trays and the sectional trays used with different modes of reassembling the segments extra orally after the impression is made. This article reviews the literature published from 1971 to 2015 concerning preliminary impression techniques used in making impressions for patients with microstomia based on various tray designs. An electronic search was performed across three databases (PubMed, Science Direct and Google Scolar for relevant citations. The keywords/combinations used for the search were microstomia, limited/constricted/restricted mouth opening/oral access, trismus, sectional trays, impressions and prosthetic/prosthodontic rehabilitation. The search was limited to papers written in English which resulted in a total of 45 related articles of which 17 articles were included for discussion of this review.

  14. Preliminary Hazards Analysis Plasma Hearth Process

    International Nuclear Information System (INIS)

    Aycock, M.; Coordes, D.; Russell, J.; TenBrook, W.; Yimbo, P.

    1993-11-01

    This Preliminary Hazards Analysis (PHA) for the Plasma Hearth Process (PHP) follows the requirements of United States Department of Energy (DOE) Order 5480.23 (DOE, 1992a), DOE Order 5480.21 (DOE, 1991d), DOE Order 5480.22 (DOE, 1992c), DOE Order 5481.1B (DOE, 1986), and the guidance provided in DOE Standards DOE-STD-1027-92 (DOE, 1992b). Consideration is given to ft proposed regulations published as 10 CFR 830 (DOE, 1993) and DOE Safety Guide SG 830.110 (DOE, 1992b). The purpose of performing a PRA is to establish an initial hazard categorization for a DOE nuclear facility and to identify those processes and structures which may have an impact on or be important to safety. The PHA is typically performed during and provides input to project conceptual design. The PRA then is followed by a Preliminary Safety Analysis Report (PSAR) performed during Title I and II design. This PSAR then leads to performance of the Final Safety Analysis Report performed during construction, testing, and acceptance and completed before routine operation. Radiological assessments indicate that a PHP facility, depending on the radioactive material inventory, may be an exempt, Category 3, or Category 2 facility. The calculated impacts would result in no significant impact to offsite personnel or the environment. Hazardous material assessments indicate that a PHP facility will be a Low Hazard facility having no significant impacts either onsite or offsite to personnel and the environment

  15. Business System Planning Project, Preliminary System Design

    International Nuclear Information System (INIS)

    EVOSEVICH, S.

    2000-01-01

    CH2M HILL Hanford Group, Inc. (CHG) is currently performing many core business functions including, but not limited to, work control, planning, scheduling, cost estimating, procurement, training, and human resources. Other core business functions are managed by or dependent on Project Hanford Management Contractors including, but not limited to, payroll, benefits and pension administration, inventory control, accounts payable, and records management. In addition, CHG has business relationships with its parent company CH2M HILL, U.S. Department of Energy, Office of River Protection and other River Protection Project contractors, government agencies, and vendors. The Business Systems Planning (BSP) Project, under the sponsorship of the CH2M HILL Hanford Group, Inc. Chief Information Officer (CIO), have recommended information system solutions that will support CHG business areas. The Preliminary System Design was developed using the recommendations from the Alternatives Analysis, RPP-6499, Rev 0 and will become the design base for any follow-on implementation projects. The Preliminary System Design will present a high-level system design, providing a high-level overview of the Commercial-Off-The-Shelf (COTS) modules and identify internal and external relationships. This document will not define data structures, user interface components (screens, reports, menus, etc.), business rules or processes. These in-depth activities will be accomplished at implementation planning time

  16. A preliminary neutron crystallographic study of thaumatin

    Energy Technology Data Exchange (ETDEWEB)

    Teixeira, Susana C. M. [ILL-EMBL Deuteration Laboratory, Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble (France); Institut Laue Langevin, 6 Rue Jules Horowitz, 38042 Grenoble (France); EPSAM and ISTM, Keele University, Staffordshire ST5 5BG (United Kingdom); Blakeley, Matthew P. [Institut Laue Langevin, 6 Rue Jules Horowitz, 38042 Grenoble (France); Leal, Ricardo M. F. [ILL-EMBL Deuteration Laboratory, Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble (France); Institut Laue Langevin, 6 Rue Jules Horowitz, 38042 Grenoble (France); EPSAM and ISTM, Keele University, Staffordshire ST5 5BG (United Kingdom); ESRF, 6 Rue Jules Horowitz, BP-220, 38043 Grenoble (France); Mitchell, Edward P. [EPSAM and ISTM, Keele University, Staffordshire ST5 5BG (United Kingdom); ESRF, 6 Rue Jules Horowitz, BP-220, 38043 Grenoble (France); Forsyth, V. Trevor, E-mail: tforsyth@ill.fr [ILL-EMBL Deuteration Laboratory, Partnership for Structural Biology, 6 Rue Jules Horowitz, 38042 Grenoble (France); Institut Laue Langevin, 6 Rue Jules Horowitz, 38042 Grenoble (France); EPSAM and ISTM, Keele University, Staffordshire ST5 5BG (United Kingdom)

    2008-05-01

    Preliminary neutron crystallographic data from the sweet protein thaumatin have been recorded using the LADI-III diffractometer at the Institut Laue Langevin (ILL). The results illustrate the feasibility of a full neutron structural analysis aimed at further understanding the molecular basis of the perception of sweet taste. Such an analysis will exploit the use of perdeuterated thaumatin. A preliminary neutron crystallographic study of the sweet protein thaumatin is presented. Large hydrogenated crystals were prepared in deuterated crystallization buffer using the gel-acupuncture method. Data were collected to a resolution of 2 Å on the LADI-III diffractometer at the Institut Laue Langevin (ILL). The results demonstrate the feasibility of a full neutron crystallographic analysis of this structure aimed at providing relevant information on the location of H atoms, the distribution of charge on the protein surface and localized water in the structure. This information will be of interest for understanding the specificity of thaumatin–receptor interactions and will contribute to further understanding of the molecular mechanisms underlying the perception of taste.

  17. Defining resilience: A preliminary integrative literature review

    Science.gov (United States)

    Wilt, Bonnie; Long, Suzanna K.; Shoberg, Thomas G.

    2016-01-01

    The term “resilience” is ubiquitous in technical literature; it appears in numerous forms, such as resilience, resiliency, or resilient, and each use may have a different definition depending on the interpretation of the writer. This creates difficulties in understanding what is meant by ‘resilience’ in any given use case, especially in discussions of interdisciplinary research. To better understand this problem, this research constructs a preliminary integrative literature review to map different definitions, applications and calculation methods of resilience invoked within critical infrastructure applications. The preliminary review uses a State-of-the-Art Matrix (SAM) analysis to characterize differences in definition across disciplines and between regions. Qualifying the various usages of resilience will produce a greater precision in the literature and a deeper insight into types of data required for its evaluation, particularly with respect to critical infrastructure calculations and how such data may be analyzed. Results from this SAM analysis will create a framework of key concepts as part of the most common applications for “resilient critical infrastructure” modeling.

  18. Ship design methodologies of preliminary design

    CERN Document Server

    Papanikolaou, Apostolos

    2014-01-01

    This book deals with ship design and in particular with methodologies of the preliminary design of ships. The book is complemented by a basic bibliography and five appendices with useful updated charts for the selection of the main dimensions and other basic characteristics of different types of ships (Appendix A), the determination of hull form  from the data of systematic hull form series (Appendix B), the detailed description of the relational method for the preliminary estimation of ship weights (Appendix C), a brief review of the historical evolution of shipbuilding science and technology from the prehistoric era to date (Appendix D) and finally a historical review of regulatory developments of ship's damage stability to date (Appendix E).  The book can be used as textbook for ship design courses or as additional reading for university or college students of naval architecture courses and related disciplines; it may also serve as a reference book for naval architects, practicing engineers of rel...

  19. Preliminary design for a maglev development facility

    Energy Technology Data Exchange (ETDEWEB)

    Coffey, H.T.; He, J.L.; Chang, S.L.; Bouillard, J.X.; Chen, S.S.; Cai, Y.; Hoppie, L.O.; Lottes, S.A.; Rote, D.M. (Argonne National Lab., IL (United States)); Zhang, Z.Y. (Polytechnic Univ., Brooklyn, NY (United States)); Myers, G.; Cvercko, A. (Sterling Engineering, Westchester, IL (United States)); Williams, J.R. (Alfred Benesch and Co., Chicago, IL (United States))

    1992-04-01

    A preliminary design was made of a national user facility for evaluating magnetic-levitation (maglev) technologies in sizes intermediate between laboratory experiments and full-scale systems. A technical advisory committee was established and a conference was held to obtain advice on the potential requirements of operational systems and how the facility might best be configured to test these requirements. The effort included studies of multiple concepts for levitating, guiding, and propelling maglev vehicles, as well as the controls, communications, and data-acquisition and -reduction equipment that would be required in operating the facility. Preliminary designs for versatile, dual 2-MVA power supplies capable of powering attractive or repulsive systems were developed. Facility site requirements were identified. Test vehicles would be about 7.4 m (25 ft) long, would weigh form 3 to 7 metric tons, and would operate at speeds up to 67 m/s (150 mph) on a 3.3-km (2.05-mi) elevated guideway. The facility would utilize modular vehicles and guideways, permitting the substitution of levitation, propulsion, and guideway components of different designs and materials for evaluation. The vehicle would provide a test cell in which individual suspension or propulsion components or subsystems could be tested under realistic conditions. The system would allow economical evaluation of integrated systems under varying weather conditions and in realistic geometries.

  20. KALIMER fuel system preliminary design description

    International Nuclear Information System (INIS)

    Hwang, Woan; Lee, B.O.; Nam, C.; Paek, S.K.

    1998-10-01

    This document provides general design concepts, design basis, preliminary design specification and design technologies which are needed for designing the fuel/non-fuel rods and assembly ducts of the KALIMER fuel system. The core of LMFBR consists of driver fuel assembly, blanket assembly, reflector assembly, shielding assembly, control assembly and GEM (Gas Expansion Module) as well as USS, dummy assembly, detector assembly. These core components must be designed to withstand the high temperature, high flux for a long irradiation exposure time. Due to the high temperature and high flux, irradiation creep and swelling as well as thermal-mechanical deformation are occurred at the fuel/non-fuel system and cause the deformations of materials and the geometric deflections at fuel/non-fuel rods, assembly ducts and components. In order to overcome these intricate phenomena through the engineering design, the design basis including theoretical analysis methodologies and design considerations, material characteristics of fuel system, and the specifications and drawings of fuel/non-fuel rods and assembly ducts, respectively, are presented. This document is preliminary design description which is produced in the conceptual design stage, and does not present the detailed and finalized design data which can be for the manufacturing. (author). 22 refs

  1. Fabrication of preliminary fuel rods for SFR

    International Nuclear Information System (INIS)

    Kim, Sun Ki; Oh, Seok Jin; Ko, Young Mo; Woo, Youn Myung; Kim, Ki Hwan

    2012-01-01

    Metal fuels was selected for fueling many of the first reactors in the US, including the Experimental Breeder Reactor-I (EBR-I) and the Experimental Breeder Reactor-II (EBR-II) in Idaho, the FERMI-I reactor, and the Dounreay Fast Reactor (DFR) in the UK. Metallic U.Pu.Zr alloys were the reference fuel for the US Integral Fast Reactor (IFR) program. Metallic fuel has advantages such as simple fabrication procedures, good neutron economy, high thermal conductivity, excellent compatibility with a Na coolant and inherent passive safety. U-Zr-Pu alloy fuels have been used for SFR (sodium-cooled fast reactor) related to the closed fuel cycle for managing minor actinides and reducing a high radioactivity levels since the 1980s. Fabrication technology of metallic fuel for SFR has been in development in Korea as a national nuclear R and D program since 2007. For the final goal of SFR fuel rod fabrication with good performance, recently, three preliminary fuel rods were fabricated. In this paper, the preliminary fuel rods were fabricated, and then the inspection for QC(quality control) of the fuel rods was performed

  2. Preliminary remediation goals for ecological endpoints

    International Nuclear Information System (INIS)

    Efroymson, R.A.; Suter, G.W. II; Sample, B.E.; Jones, D.S.

    1996-07-01

    Preliminary remediation goals (PRGs) are useful for risk assessment and decision making at Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) sites. PRGs are upper concentration limits for specific chemicals in specific environmental media that are anticipated to protect human health or the environment. They can be used for multiple remedial investigations at multiple facilities. In addition to media and chemicals of potential concern, the development of PRGs generally requires some knowledge or anticipation of future land use. In Preliminary Remediation Goals for Use at the U.S. Department of Energy Oak Ridge Operations Office (Energy Systems 1995), PRGs intended to protect human health were developed with guidance from Risk Assessment Guidance for Superfund: Volume I - Human Health Evaluation Manual, Part B (RAGS) (EPA 1991). However, no guidance was given for PRGs based on ecological risk. The numbers that appear in this volume have, for the most part, been extracted from toxicological benchmarks documents for Oak Ridge National Laboratory (ORNL) and have previously been developed by ORNL. The sources of the quantities, and many of the uncertainties associated with their derivation, are described in this technical memorandum

  3. Preliminary remediation goals for ecological endpoints

    International Nuclear Information System (INIS)

    Efroymson, R.A.; Suter, G.W. II.

    1995-09-01

    Preliminary remediation goals (PRGs) are useful for risk assessment and decision making at Comprehensive Environmental Response, compensation, and Liability Act (CERCLA) sites. PRGs are upper concentration limits for specific chemicals in specific environmental media that are anticipated to protect human health or the environment. They can be used for multiple remedial investigations at multiple facilities. In addition to media and chemicals of potential concern, the development of PRGs generally requires some knowledge or anticipation of future land use. In Preliminary Remediation Goals for Use at the US Department of Energy Oak Ridge Operations Office (Energy Systems 1995), PRGs intended to protect human health were developed with guidance from Risk Assessment Guidance for Superfund: Volume I-Human Health Evaluation Manual, Part B (RAGS) (EPA 1991). However, no guidance was given for PRGs based on ecological risk. The numbers that appear in this volume have, for the most part, been extracted from toxicological benchmarks documents for Oak Ridge National Laboratory (ORNL) and have previously been developed by ORNL. The sources of the quantities, and many of the uncertainties associated with their derivation, are described in this technical memorandum

  4. Nucleotide sequence preservation of human mitochondrial DNA

    International Nuclear Information System (INIS)

    Monnat, R.J. Jr.; Loeb, L.A.

    1985-01-01

    Recombinant DNA techniques have been used to quantitate the amount of nucleotide sequence divergence in the mitochondrial DNA population of individual normal humans. Mitochondrial DNA was isolated from the peripheral blood lymphocytes of five normal humans and cloned in M13 mp11; 49 kilobases of nucleotide sequence information was obtained from 248 independently isolated clones from the five normal donors. Both between- and within-individual differences were identified. Between-individual differences were identified in approximately = to 1/200 nucleotides. In contrast, only one within-individual difference was identified in 49 kilobases of nucleotide sequence information. This high degree of mitochondrial nucleotide sequence homogeneity in human somatic cells is in marked contrast to the rapid evolutionary divergence of human mitochondrial DNA and suggests the existence of mechanisms for the concerted preservation of mammalian mitochondrial DNA sequences in single organisms

  5. Snake Genome Sequencing: Results and Future Prospects.

    Science.gov (United States)

    Kerkkamp, Harald M I; Kini, R Manjunatha; Pospelov, Alexey S; Vonk, Freek J; Henkel, Christiaan V; Richardson, Michael K

    2016-12-01

    Snake genome sequencing is in its infancy-very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  6. Sequencing Cyclic Peptides by Multistage Mass Spectrometry

    Science.gov (United States)

    Mohimani, Hosein; Yang, Yu-Liang; Liu, Wei-Ting; Hsieh, Pei-Wen; Dorrestein, Pieter C.; Pevzner, Pavel A.

    2012-01-01

    Some of the most effective antibiotics (e.g., Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. While hundreds of biomedically important cyclic peptides have been sequenced, the computational techniques for sequencing cyclic peptides are still in their infancy. Previous methods for sequencing peptide antibiotics and other cyclic peptides are based on Nuclear Magnetic Resonance spectroscopy, and require large amount (miligrams) of purified materials that, for most compounds, are not possible to obtain. Recently, development of mass spectrometry based methods has provided some hope for accurate sequencing of cyclic peptides using picograms of materials. In this paper we develop a method for sequencing of cyclic peptides by multistage mass spectrometry, and show its advantages over single stage mass spectrometry. The method is tested on known and new cyclic peptides from Bacillus brevis, Dianthus superbus and Streptomyces griseus, as well as a new family of cyclic peptides produced by marine bacteria. PMID:21751357

  7. Snake Genome Sequencing: Results and Future Prospects

    Directory of Open Access Journals (Sweden)

    Harald M. I. Kerkkamp

    2016-12-01

    Full Text Available Snake genome sequencing is in its infancy—very much behind the progress made in sequencing the genomes of humans, model organisms and pathogens relevant to biomedical research, and agricultural species. We provide here an overview of some of the snake genome projects in progress, and discuss the biological findings, with special emphasis on toxinology, from the small number of draft snake genomes already published. We discuss the future of snake genomics, pointing out that new sequencing technologies will help overcome the problem of repetitive sequences in assembling snake genomes. Genome sequences are also likely to be valuable in examining the clustering of toxin genes on the chromosomes, in designing recombinant antivenoms and in studying the epigenetic regulation of toxin gene expression.

  8. Sequencing and comparing whole mitochondrial genomes ofanimals

    Energy Technology Data Exchange (ETDEWEB)

    Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

    2005-04-22

    Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based on our experiences to date with determining and comparing complete mtDNA sequences.

  9. Divide and conquer: enriching environmental sequencing data.

    Directory of Open Access Journals (Sweden)

    Anne Bergeron

    2007-09-01

    Full Text Available In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species.Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities.Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort.

  10. Sequence Matters but How Exactly? A Method for Evaluating Activity Sequences from Data

    Science.gov (United States)

    Doroudi, Shayan; Holstein, Kenneth; Aleven, Vincent; Brunskill, Emma

    2016-01-01

    How should a wide variety of educational activities be sequenced to maximize student learning? Although some experimental studies have addressed this question, educational data mining methods may be able to evaluate a wider range of possibilities and better handle many simultaneous sequencing constraints. We introduce Sequencing Constraint…

  11. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

    DEFF Research Database (Denmark)

    de Souza, S J; Camargo, A A; Briones, M R

    2000-01-01

    Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central ...

  12. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area.

    Science.gov (United States)

    Nakano, Kazuma; Shiroma, Akino; Shimoji, Makiko; Tamotsu, Hinako; Ashimine, Noriko; Ohki, Shun; Shinzato, Misuzu; Minami, Maiko; Nakanishi, Tetsuhiro; Teruya, Kuniko; Satou, Kazuhito; Hirano, Takashi

    2017-07-01

    PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

  13. [Clone, construct, expression and verification of lactoferricin B gene and several sequence mutations in yeast].

    Science.gov (United States)

    Feng, Yong-qian; Zha, Xiao-jun; Zhai, Chao-yang

    2007-07-01

    To construct the eucaryotic recombinant plasmid of pYES2/LactoferricinB expressing in yeast of S. cerevisiae, of which the expressed protein antibacterial activity was verified in preliminary. By self-template PCR method, the gene of Lactoferricin B and its several sequence mutations were amplified with the parts of the pre-synthesized single chains. And then Lactoferricin B gene and its mutants were cloned into the vector of pYES2 to construct the recombined expression plasmid pYES2/Lactoferricin B etc. extracted and used to transform the yeast S. cerevisiae. The expressions of proteins were determined after induced by galactose. The expression proteins were collected and purified by hydronium-exchange column, and the bacterial inhibited test was applied to identify the protein antibacterial activities. The PCR amplifying and DNA sequencing tests indicated that the purpose plasmid contained the Lactoferricin B gene and several mutations. The induced target proteins were confirmed by SDS-PAGE electrophoresis and mass spectrum test. The protein antibacterial activities of mutations were verified in preliminary. The recombined plasmid pYES2/Lactoferricin B etc. are successfully constructed and induced to express in yeast cell of S. cerevisiae; the obtained recombined protein of Lactoferricin B provides a basis for further research work on the biological function and antibacterial activity.

  14. A comparative evaluation of sequence classification programs

    Directory of Open Access Journals (Sweden)

    Bazinet Adam L

    2012-05-01

    Full Text Available Abstract Background A fundamental problem in modern genomics is to taxonomically or functionally classify DNA sequence fragments derived from environmental sampling (i.e., metagenomics. Several different methods have been proposed for doing this effectively and efficiently, and many have been implemented in software. In addition to varying their basic algorithmic approach to classification, some methods screen sequence reads for ’barcoding genes’ like 16S rRNA, or various types of protein-coding genes. Due to the sheer number and complexity of methods, it can be difficult for a researcher to choose one that is well-suited for a particular analysis. Results We divided the very large number of programs that have been released in recent years for solving the sequence classification problem into three main categories based on the general algorithm they use to compare a query sequence against a database of sequences. We also evaluated the performance of the leading programs in each category on data sets whose taxonomic and functional composition is known. Conclusions We found significant variability in classification accuracy, precision, and resource consumption of sequence classification programs when used to analyze various metagenomics data sets. However, we observe some general trends and patterns that will be useful to researchers who use sequence classification programs.

  15. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    Energy Technology Data Exchange (ETDEWEB)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-04-14

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis.

  16. Exploration of noncoding sequences in metagenomes.

    Directory of Open Access Journals (Sweden)

    Fabián Tobar-Tosse

    Full Text Available Environment-dependent genomic features have been defined for different metagenomes, whose genes and their associated processes are related to specific environments. Identification of ORFs and their functional categories are the most common methods for association between functional and environmental features. However, this analysis based on finding ORFs misses noncoding sequences and, therefore, some metagenome regulatory or structural information could be discarded. In this work we analyzed 23 whole metagenomes, including coding and noncoding sequences using the following sequence patterns: (G+C content, Codon Usage (Cd, Trinucleotide Usage (Tn, and functional assignments for ORF prediction. Herein, we present evidence of a high proportion of noncoding sequences discarded in common similarity-based methods in metagenomics, and the kind of relevant information present in those. We found a high density of trinucleotide repeat sequences (TRS in noncoding sequences, with a regulatory and adaptive function for metagenome communities. We present associations between trinucleotide values and gene function, where metagenome clustering correlate with microorganism adaptations and kinds of metagenomes. We propose here that noncoding sequences have relevant information to describe metagenomes that could be considered in a whole metagenome analysis in order to improve their organization, classification protocols, and their relation with the environment.

  17. CATEGORIZATION OF EVENT SEQUENCES FOR LICENSE APPLICATION

    International Nuclear Information System (INIS)

    G.E. Ragan; P. Mecheret; D. Dexheimer

    2005-01-01

    The purposes of this analysis are: (1) Categorize (as Category 1, Category 2, or Beyond Category 2) internal event sequences that may occur before permanent closure of the repository at Yucca Mountain. (2) Categorize external event sequences that may occur before permanent closure of the repository at Yucca Mountain. This includes examining DBGM-1 seismic classifications and upgrading to DBGM-2, if appropriate, to ensure Beyond Category 2 categorization. (3) State the design and operational requirements that are invoked to make the categorization assignments valid. (4) Indicate the amount of material put at risk by Category 1 and Category 2 event sequences. (5) Estimate frequencies of Category 1 event sequences at the maximum capacity and receipt rate of the repository. (6) Distinguish occurrences associated with normal operations from event sequences. It is beyond the scope of the analysis to propose design requirements that may be required to control radiological exposure associated with normal operations. (7) Provide a convenient compilation of the results of the analysis in tabular form. The results of this analysis are used as inputs to the consequence analyses in an iterative design process that is depicted in Figure 1. Categorization of event sequences for permanent retrieval of waste from the repository is beyond the scope of this analysis. Cleanup activities that take place after an event sequence and other responses to abnormal events are also beyond the scope of the analysis

  18. On site DNA barcoding by nanopore sequencing.

    Directory of Open Access Journals (Sweden)

    Michele Menegon

    Full Text Available Biodiversity research is becoming increasingly dependent on genomics, which allows the unprecedented digitization and understanding of the planet's biological heritage. The use of genetic markers i.e. DNA barcoding, has proved to be a powerful tool in species identification. However, full exploitation of this approach is hampered by the high sequencing costs and the absence of equipped facilities in biodiversity-rich countries. In the present work, we developed a portable sequencing laboratory based on the portable DNA sequencer from Oxford Nanopore Technologies, the MinION. Complementary laboratory equipment and reagents were selected to be used in remote and tough environmental conditions. The performance of the MinION sequencer and the portable laboratory was tested for DNA barcoding in a mimicking tropical environment, as well as in a remote rainforest of Tanzania lacking electricity. Despite the relatively high sequencing error-rate of the MinION, the development of a suitable pipeline for data analysis allowed the accurate identification of different species of vertebrates including amphibians, reptiles and mammals. In situ sequencing of a wild frog allowed us to rapidly identify the species captured, thus confirming that effective DNA barcoding in the field is possible. These results open new perspectives for real-time-on-site DNA sequencing thus potentially increasing opportunities for the understanding of biodiversity in areas lacking conventional laboratory facilities.

  19. Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk

    2013-01-01

    to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D......Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms...

  20. System-level hazard analysis using the sequence-tree method

    International Nuclear Information System (INIS)

    Huang, H.-W.; Shih Chunkuan; Yih Swu; Chen, M.-H.

    2008-01-01

    A system-level PHA using the sequence-tree method is presented to perform safety-related digital I and C system SSA. The conventional PHA involves brainstorming among experts on various portions of the system to identify hazards through discussions. However, since the conventional PHA is not a systematic technique, the analysis results depend strongly on the experts' subjective opinions. The quality of analysis cannot be appropriately controlled. Therefore, this study presents a system-level sequence tree based PHA, which can clarify the relationship among the major digital I and C systems. This sequence-tree-based technique has two major phases. The first phase adopts a table to analyze each event in SAR Chapter 15 for a specific safety-related I and C system, such as RPS. The second phase adopts a sequence tree to recognize the I and C systems involved in the event, the working of the safety-related systems and how the backup systems can be activated to mitigate the consequence if the primary safety systems fail. The defense-in-depth echelons, namely the Control echelon, Reactor trip echelon, ESFAS echelon and Monitoring and indicator echelon, are arranged to build the sequence-tree structure. All the related I and C systems, including the digital systems and the analog back-up systems, are allocated in their specific echelons. This system-centric sequence-tree analysis not only systematically identifies preliminary hazards, but also vulnerabilities in a nuclear power plant. Hence, an effective simplified D3 evaluation can also be conducted

  1. New paleomagnetic and paleointensity results from late pliocene volcanic sequences from southern Georgia (Caucasus)

    Energy Technology Data Exchange (ETDEWEB)

    Calvo-Rathert, Manuel; Bogalo, Maria-Felicidad; Carrancho, Angel; Villalain, Juan Jose [Universidad de Burgos, Burgos (Spain). Departamento de Fisica, EPS; Goguichaichvili, Avto [Universidad Nacional Autonoma de Mexico, Morelia (Mexico). Laboratorio de Magnetismo Natural, Instituto de Geofisica; Vegas-Tubia, Nestor [Universidad del Pais Vasco, Bilbao (Spain). Departamento de Geodinamica; Sologashvili, Jemal [Ivane Javakhishvili State University of Tbilisi, Tbilisi (Georgia). Department of Geophysics

    2009-07-01

    Complete text of publication follows. Paleomagnetic and rock-magnetic experiments were carried out on 21 basaltic lava flows belonging to four different sequences of late Pliocene age from southern Georgia (Caucasus): Dmanisi (11 flows), Diliska (5 flows), Kvemo Orozmani (5 flows), and Zemo Karabulaki (3 flows). Paleomagnetic analysis generally showed the presence of a single component (mainly in the Dmanisi sequence) but also two more or less superimposed components in several other cases. All sites except one clearly displayed a normal-polarity characteristic component. Rock-magnetic experiments included measurement of thermomagnetic curves and hysteresis parameters. Susceptibility-versus-temperature curves measured in argon atmosphere on whole-rock powdered samples yielded low-Ti titanomagnetite as main carrier of remanence, although a lower T{sub C}-component was also observed in several cases. Both reversible and non-reversible k-T curves were measured. A pilot paleointensity study was performed with the Coe (1967) method on two samples of each of those sites considered suitable after interpretation of rock-magnetic and paleomagnetic data from all sites. The pilot study showed that reliable paleointensity results were mainly obtained from sites of the Dmanisi sequence. This thick sequence of basaltic lava flows records the upper end of the normal-polarity Olduvai subchron, a fact confirmed by {sup 40}Ar/{sup 39}Ar dating of the uppermost lava flow and overlying volcanogenic ashes, which yields ages of 1.8 to 1.85 My. A second paleointensity experiment was carried out only on samples belonging to the Dmanisi sequence. Preliminary results show that paleointensities often are low, their values lying between 10 and 20 muT in many cases. For comparison, present day field is 47 muT. The Dmanisi sequence of lava flows directly underlies the Dmanisi paleoanthropologic site, in which the end of the Olduvai subchron is recorded.

  2. 45 CFR 671.15 - Publication of preliminary determination

    Science.gov (United States)

    2010-10-01

    ... 45 Public Welfare 3 2010-10-01 2010-10-01 false Publication of preliminary determination 671.15... Publication of preliminary determination Prior to any designation or redesignation of substances pursuant to... Environmental Protection Agency and other federal agencies, within 30 days after the date of publication of...

  3. 37 CFR 1.480 - Demand for international preliminary examination.

    Science.gov (United States)

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Demand for international... Provisions International Preliminary Examination § 1.480 Demand for international preliminary examination. (a) On the filing of a proper Demand in an application for which the United States International...

  4. 46 CFR 176.635 - Preliminary examination requirements.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Preliminary examination requirements. 176.635 Section... (UNDER 100 GROSS TONS) INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 176.635 Preliminary examination requirements. (a) If you exclusively use divers to examine the underwater hull plating, you must...

  5. Standing the Test of Time: Reference for a Preliminary Ruling

    DEFF Research Database (Denmark)

    Butler, Graham

    2017-01-01

    It is often too easy to forget just how important the preliminary reference procedure is for the functionality of European Union law. For the Court of Justice, there are both formal and informal means of judicial dialogue. This article focuses on the formal means of dialogue through the preliminary...

  6. Researches on Preliminary Chemical Reactions in Spark-Ignition Engines

    Science.gov (United States)

    1943-06-01

    compression type, without ignition, the resulting preliminary reactions being detectable and meas- urable thermometrically . Contents I. Influence of Preliminary...thoroughly insulated be- tween the carburettor and the engine, by aluminium foil and asbestos. -I -I " I" I ’I il i~ " !, I I 1𔃻I I’ ) To enable the

  7. Preliminary Opto-Mechanical Design for the X2000 Transceiver

    Science.gov (United States)

    Hemmati, H.; Page, N. A.

    2000-01-01

    Preliminary optical design and mechanical conceptual design for a 30 cm aperture transceiver are described. A common aperture is used for both transmit and receive. Special attention was given to off-axis and scattered light rejection and isolation of the receive channel from the transmit channel. Requirements, details of the design and preliminary performance analysis of the transceiver are provided.

  8. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  9. Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

    Science.gov (United States)

    Wang, Ji; Ke, Yue Hua; Zhang, Yong; Huang, Ke Qiang; Wang, Lei; Shen, Xin Xin; Dong, Xiao Ping; Xu, Wen Bo; Ma, Xue Jun

    2017-10-01

    Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequencer is increasingly used to sequence various viral pathogens in many clinical situations because of its long reads, portability, real-time accessibility of sequenced data, and very low initial costs. However, information is lacking on MinION sequencing of enterovirus genomes. In this proof-of-concept study using Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) strains as examples, we established an amplicon-based whole genome sequencing method using MinION. We explored the accuracy, minimum sequencing time, discrimination and high-throughput sequencing ability of MinION, and compared its performance with Sanger sequencing. Within the first minute (min) of sequencing, the accuracy of MinION was 98.5% for the single EV71 strain and 94.12%-97.33% for 10 genetically-related CA16 strains. In as little as 14 min, 99% identity was reached for the single EV71 strain, and in 17 min (on average), 99% identity was achieved for 10 CA16 strains in a single run. MinION is suitable for whole genome sequencing of enteroviruses with sufficient accuracy and fine discrimination and has the potential as a fast, reliable and convenient method for routine use. Copyright © 2017 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  10. Computer simulation of replacement sequences in copper

    International Nuclear Information System (INIS)

    Schiffgens, J.O.; Schwartz, D.W.; Ariyasu, R.G.; Cascadden, S.E.

    1978-01-01

    Results of computer simulations of , , and replacement sequences in copper are presented, including displacement thresholds, focusing energies, energy losses per replacement, and replacement sequence lengths. These parameters are tabulated for six interatomic potentials and shown to vary in a systematic way with potential stiffness and range. Comparisons of results from calculations made with ADDES, a quasi-dynamical code, and COMENT, a dynamical code, show excellent agreement, demonstrating that the former can be calibrated and used satisfactorily in the analysis of low energy displacement cascades. Upper limits on , , and replacement sequences were found to be approximately 10, approximately 30, and approximately 14 replacements, respectively. (author)

  11. Whole-genome sequencing of veterinary pathogens

    DEFF Research Database (Denmark)

    Ronco, Troels

    -electrophoresis and single-locus sequencing has been widely used to characterize such types of veterinary pathogens. However, DNA sequencing techniques have become fast and cost effective in recent years and whole-genome sequencing data provide a much higher discriminative power and reproducibility than any...... genetic background. This indicates that dairy cows can be natural carriers of S. aureus subtypes that in certain cases lead to CM. A group of isolates that mostly belonged to ST151 carried three pathogenicity islands that were primarily found in this group. The prevalence of resistance genes was generally...

  12. Spreadsheet macros for coloring sequence alignments.

    Science.gov (United States)

    Haygood, M G

    1993-12-01

    This article describes a set of Microsoft Excel macros designed to color amino acid and nucleotide sequence alignments for review and preparation of visual aids. The colored alignments can then be modified to emphasize features of interest. Procedures for importing and coloring sequences are described. The macro file adds a new menu to the menu bar containing sequence-related commands to enable users unfamiliar with Excel to use the macros more readily. The macros were designed for use with Macintosh computers but will also run with the DOS version of Excel.

  13. Tensor products of higher almost split sequences

    OpenAIRE

    Pasquali, Andrea

    2015-01-01

    We investigate how the higher almost split sequences over a tensor product of algebras are related to those over each factor. Herschend and Iyama gave a precise criterion for when the tensor product of an $n$-representation finite algebra and an $m$-representation finite algebra is $(n+m)$-representation finite. In this case we give a complete description of the higher almost split sequences over the tensor product by expressing every higher almost split sequence as the mapping cone of a suit...

  14. Arbitrarily accurate twin composite π -pulse sequences

    Science.gov (United States)

    Torosov, Boyan T.; Vitanov, Nikolay V.

    2018-04-01

    We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .

  15. Modeling of Prepregs during Automated Draping Sequences

    DEFF Research Database (Denmark)

    Krogh, Christian; Glud, Jens Ammitzbøll; Jakobsen, Johnny

    2017-01-01

    algorithm used to generate target points on the mold which are used as input to a draping sequence planner. The draping sequence planner prescribes the displacement history for each gripper in the drape tool and these displacements are then applied to each gripper in a transient model of the draping...... sequence. The model is based on a transient finite element analysis with the material’s constitutive behavior currently being approximated as linear elastic orthotropic. In-plane tensile and bias-extension tests as well as bending tests are conducted and used as input for the model. The virtual draping...

  16. Deep-sequencing protocols influence the results obtained in small-RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Joern Toedling

    Full Text Available Second-generation sequencing is a powerful method for identifying and quantifying small-RNA components of cells. However, little attention has been paid to the effects of the choice of sequencing platform and library preparation protocol on the results obtained. We present a thorough comparison of small-RNA sequencing libraries generated from the same embryonic stem cell lines, using different sequencing platforms, which represent the three major second-generation sequencing technologies, and protocols. We have analysed and compared the expression of microRNAs, as well as populations of small RNAs derived from repetitive elements. Despite the fact that different libraries display a good correlation between sequencing platforms, qualitative and quantitative variations in the results were found, depending on the protocol used. Thus, when comparing libraries from different biological samples, it is strongly recommended to use the same sequencing platform and protocol in order to ensure the biological relevance of the comparisons.

  17. Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

    Directory of Open Access Journals (Sweden)

    Shan Wei

    2018-05-01

    Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

  18. Repository Subsurface Preliminary Fire Hazard Analysis

    International Nuclear Information System (INIS)

    Logan, Richard C.

    2001-01-01

    This fire hazard analysis identifies preliminary design and operations features, fire, and explosion hazards, and provides a reasonable basis to establish the design requirements of fire protection systems during development and emplacement phases of the subsurface repository. This document follows the Technical Work Plan (TWP) (CRWMS M and O 2001c) which was prepared in accordance with AP-2.21Q, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities''; Attachment 4 of AP-ESH-008, ''Hazards Analysis System''; and AP-3.11Q, ''Technical Reports''. The objective of this report is to establish the requirements that provide for facility nuclear safety and a proper level of personnel safety and property protection from the effects of fire and the adverse effects of fire-extinguishing agents

  19. Plasma brake model for preliminary mission analysis

    Science.gov (United States)

    Orsini, Leonardo; Niccolai, Lorenzo; Mengali, Giovanni; Quarta, Alessandro A.

    2018-03-01

    Plasma brake is an innovative propellantless propulsion system concept that exploits the Coulomb collisions between a charged tether and the ions in the surrounding environment (typically, the ionosphere) to generate an electrostatic force orthogonal to the tether direction. Previous studies on the plasma brake effect have emphasized the existence of a number of different parameters necessary to obtain an accurate description of the propulsive acceleration from a physical viewpoint. The aim of this work is to discuss an analytical model capable of estimating, with the accuracy required by a preliminary mission analysis, the performance of a spacecraft equipped with a plasma brake in a (near-circular) low Earth orbit. The simplified mathematical model is first validated through numerical simulations, and is then used to evaluate the plasma brake performance in some typical mission scenarios, in order to quantify the influence of the system parameters on the mission performance index.

  20. Preliminary study of radium-contaminated soils

    Energy Technology Data Exchange (ETDEWEB)

    Healy, J.W.; Rodgers, J.C.

    1978-10-01

    A preliminary study was made of the potential radiation exposures to people from radium-226 contamination in the soil in order to provide guidance on limits to be applied in decontaminating land. Pathways included were inhalation of radium from resuspension; ingestion of radium with foods; external gamma radiation from radium daughters; inhalation of radon and daughter, both in the open air and in houses; and the intake of /sup 210/Pb and /sup 210/Po from both inhalation and ingestion. The depth of the contaminated layer is of importance for external exposure and especially for radon emanation. The most limiting pathway was found to be emanation of the radon into buildings with limiting values comparable to those found naturally in many areas.