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Sample records for preliminary bac-end sequencing

  1. Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus.

    Science.gov (United States)

    Ollitrault, Frédérique; Terol, Javier; Pina, Jose Antonio; Navarro, Luis; Talon, Manuel; Ollitrault, Patrick

    2010-11-01

    Microsatellite primers were developed from bacterial artificial chromosome (BAC) end sequences of Citrus clementina and their transferability and polymorphism tested in the genus Citrus for future anchorage of physical and genetic maps and comparative interspecific genetic mapping. • Using PAGE and DNA silver staining, 79 primer pairs were selected for their transferability and polymorphism among 526 microsatellites mined in BES. A preliminary diversity study in Citrus was conducted with 18 of them, in C. reticulata, C. maxima, C. medica, C. sinensis, C. aurantium, C. paradisi, C. lemon, C. aurantifolia, and some papedas (wild citrus), using a capillary electrophoresis fragment analyzer. Intra- and interspecific polymorphism was observed, and heterozygous markers were identified for the different genotypes to be used for genetic mapping. • These results indicate the utility of the developed primers for comparative mapping studies and the integration of physical and genetic maps.

  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. 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.

  4. Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries

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    Puigdomènech Pere

    2010-11-01

    Full Text Available Abstract Background Although melon (Cucumis melo L. is an economically important fruit crop, no genome-wide sequence information is openly available at the current time. We therefore sequenced BAC-ends representing a total of 33,024 clones, half of them from a previously described melon BAC library generated with restriction endonucleases and the remainder from a new random-shear BAC library. Results We generated a total of 47,140 high-quality BAC-end sequences (BES, 91.7% of which were paired-BES. Both libraries were assembled independently and then cross-assembled to obtain a final set of 33,372 non-redundant, high-quality sequences. These were grouped into 6,411 contigs (4.5 Mb and 26,961 non-assembled BES (14.4 Mb, representing ~4.2% of the melon genome. The sequences were used to screen genomic databases, identifying 7,198 simple sequence repeats (corresponding to one microsatellite every 2.6 kb and 2,484 additional repeats of which 95.9% represented transposable elements. The sequences were also used to screen expressed sequence tag (EST databases, revealing 11,372 BES that were homologous to ESTs. This suggests that ~30% of the melon genome consists of coding DNA. We observed regions of microsynteny between melon paired-BES and six other dicotyledonous plant genomes. Conclusion The analysis of nearly 50,000 BES from two complementary genomic libraries covered ~4.2% of the melon genome, providing insight into properties such as microsatellite and transposable element distribution, and the percentage of coding DNA. The observed synteny between melon paired-BES and six other plant genomes showed that useful comparative genomic data can be derived through large scale BAC-end sequencing by anchoring a small proportion of the melon genome to other sequenced genomes.

  5. Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus

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    Lindblad-Toh Kerstin

    2010-11-01

    Full Text Available Abstract Background The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species. Results We obtained sequence from one or both ends of 106,259 tilapia BACs. BLAST analysis against the genome assemblies of stickleback, medaka and pufferfish allowed identification of homologies for approximately 25,000 BACs for each species. We calculate that rearrangement breakpoints between tilapia and these species occur about every 3 Mb across the genome. Analysis of 35,000 clones previously assembled into contigs by restriction fingerprints allowed identification of longer-range syntenies. Conclusions Our data suggest that chromosomal evolution in recent teleosts is dominated by alternate loss of gene duplicates, and by intra-chromosomal rearrangements (~one per million years. These physical maps are a useful resource for comparative positional cloning of traits in cichlid fishes. The paired BAC end sequences from these clones will be an important resource for scaffolding forthcoming shotgun sequence assemblies of the tilapia genome.

  6. BAC-end sequence-based SNP mining in Allotetraploid Cotton (Gossypium) utilizing re-sequencing data, phylogenetic inferences and perspectives for genetic mapping

    Science.gov (United States)

    A bacterial artificial chromosome (BAC) library and BAC-end sequences for Gossypium hirsutum L. have recently been developed. Here we report on genomic-based genome-wide SNP mining utilizing re-sequencing data with a BAC-end sequence reference for twelve G. hirsutum L. lines, one G. barbadense L. li...

  7. 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

  8. Analysis of BAC end sequences in oak, a keystone forest tree species, providing insight into the composition of its genome

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    Le Provost Grégoire

    2011-06-01

    Full Text Available Abstract Background One of the key goals of oak genomics research is to identify genes of adaptive significance. This information may help to improve the conservation of adaptive genetic variation and the management of forests to increase their health and productivity. Deep-coverage large-insert genomic libraries are a crucial tool for attaining this objective. We report herein the construction of a BAC library for Quercus robur, its characterization and an analysis of BAC end sequences. Results The EcoRI library generated consisted of 92,160 clones, 7% of which had no insert. Levels of chloroplast and mitochondrial contamination were below 3% and 1%, respectively. Mean clone insert size was estimated at 135 kb. The library represents 12 haploid genome equivalents and, the likelihood of finding a particular oak sequence of interest is greater than 99%. Genome coverage was confirmed by PCR screening of the library with 60 unique genetic loci sampled from the genetic linkage map. In total, about 20,000 high-quality BAC end sequences (BESs were generated by sequencing 15,000 clones. Roughly 5.88% of the combined BAC end sequence length corresponded to known retroelements while ab initio repeat detection methods identified 41 additional repeats. Collectively, characterized and novel repeats account for roughly 8.94% of the genome. Further analysis of the BESs revealed 1,823 putative genes suggesting at least 29,340 genes in the oak genome. BESs were aligned with the genome sequences of Arabidopsis thaliana, Vitis vinifera and Populus trichocarpa. One putative collinear microsyntenic region encoding an alcohol acyl transferase protein was observed between oak and chromosome 2 of V. vinifera. Conclusions This BAC library provides a new resource for genomic studies, including SSR marker development, physical mapping, comparative genomics and genome sequencing. BES analysis provided insight into the structure of the oak genome. These sequences will be

  9. Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing

    Science.gov (United States)

    2011-01-01

    Background Lupinus angustifolius L, also known as narrow-leafed lupin (NLL), is becoming an important grain legume crop that is valuable for sustainable farming and is becoming recognised as a potential human health food. Recent interest is being directed at NLL to improve grain production, disease and pest management and health benefits of the grain. However, studies have been hindered by a lack of extensive genomic resources for the species. Results A NLL BAC library was constructed consisting of 111,360 clones with an average insert size of 99.7 Kbp from cv Tanjil. The library has approximately 12 × genome coverage. Both ends of 9600 randomly selected BAC clones were sequenced to generate 13985 BAC end-sequences (BESs), covering approximately 1% of the NLL genome. These BESs permitted a preliminary characterisation of the NLL genome such as organisation and composition, with the BESs having approximately 39% G:C content, 16.6% repetitive DNA and 5.4% putative gene-encoding regions. From the BESs 9966 simple sequence repeat (SSR) motifs were identified and some of these are shown to be potential markers. Conclusions The NLL BAC library and BAC-end sequences are powerful resources for genetic and genomic research on lupin. These resources will provide a robust platform for future high-resolution mapping, map-based cloning, comparative genomics and assembly of whole-genome sequencing data for the species. PMID:22014081

  10. 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.

  11. BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution

    OpenAIRE

    Dereeper, Alexis; Guyot, Romain; Dubreuil Tranchant, Christine; Anthony, François; Argout, X.; Bellis, F; Combes, Marie-Christine; Gavory, F.; De Kochko, Alexandre; Kudrna, D.; Leroy, T.; Poulain, J.; Rondeau, M.; Song, X; Wing, R

    2013-01-01

    Coffee is one of the world's most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,41...

  12. Construction of an integrated pepper map using RFLP, SSR, CAPS, AFLP, WRKY, rRAMP, and BAC end sequences.

    Science.gov (United States)

    Lee, Heung-Ryul; Bae, Ik-Hyun; Park, Soung-Woo; Kim, Hyoun-Joung; Min, Woong-Ki; Han, Jung-Heon; Kim, Ki-Taek; Kim, Byung-Dong

    2009-01-31

    Map-based cloning to find genes of interest, markerassisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.

  13. 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

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

    Institute of Scientific and Technical Information of China (English)

    ZHAO Cui; ZHANG Xiaojun; LIU Chengzhang; HUAN Pin; LI Fuhua; XIANG Jianhai; HUANG Chao

    2012-01-01

    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 abtmdant 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.

  15. 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.

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

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    Sehgal Sunish K

    2012-05-01

    Full Text Available Abstract Background Bread wheat, one of the world’s staple food crops, has the largest, highly repetitive and polyploid genome among the cereal crops. The wheat genome holds the key to crop genetic improvement against challenges such as climate change, environmental degradation, and water scarcity. To unravel the complex wheat genome, the International Wheat Genome Sequencing Consortium (IWGSC is pursuing a chromosome- and chromosome arm-based approach to physical mapping and sequencing. Here we report on the use of a BAC library made from flow-sorted telosomic chromosome 3A short arm (t3AS for marker development and analysis of sequence composition and comparative evolution of homoeologous genomes of hexaploid wheat. Results The end-sequencing of 9,984 random BACs from a chromosome arm 3AS-specific library (TaaCsp3AShA generated 11,014,359 bp of high quality sequence from 17,591 BAC-ends with an average length of 626 bp. The sequence represents 3.2% of t3AS with an average DNA sequence read every 19 kb. Overall, 79% of the sequence consisted of repetitive elements, 1.38% as coding regions (estimated 2,850 genes and another 19% of unknown origin. Comparative sequence analysis suggested that 70-77% of the genes present in both 3A and 3B were syntenic with model species. Among the transposable elements, gypsy/sabrina (12.4% was the most abundant repeat and was significantly more frequent in 3A compared to homoeologous chromosome 3B. Twenty novel repetitive sequences were also identified using de novo repeat identification. BESs were screened to identify simple sequence repeats (SSR and transposable element junctions. A total of 1,057 SSRs were identified with a density of one per 10.4 kb, and 7,928 junctions between transposable elements (TE and other sequences were identified with a density of one per 1.39 kb. With the objective of enhancing the marker density of chromosome 3AS, oligonucleotide primers were successfully designed from

  17. 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

  18. Development of genomic resources for Citrus clementina: Characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences

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    Talon Manuel

    2008-09-01

    Full Text Available Abstract Background Citrus species constitute one of the major tree fruit crops of the subtropical regions with great economic importance. However, their peculiar reproductive characteristics, low genetic diversity and the long-term nature of tree breeding mostly impair citrus variety improvement. In woody plants, genomic science holds promise of improvements and in the Citrus genera the development of genomic tools may be crucial for further crop improvements. In this work we report the characterization of three BAC libraries from Clementine (Citrus clementina, one of the most relevant citrus fresh fruit market cultivars, and the analyses of 46.000 BAC end sequences. Clementine is a diploid plant with an estimated haploid genome size of 367 Mb and 2n = 18 chromosomes, which makes feasible the use of genomics tools to boost genetic improvement. Results Three genomic BAC libraries of Citrus clementina were constructed through EcoRI, MboI and HindIII digestions and 56,000 clones, representing an estimated genomic coverage of 19.5 haploid genome-equivalents, were picked. BAC end sequencing (BES of 28,000 clones produced 28.1 Mb of genomic sequence that allowed the identification of the repetitive fraction (12.5% of the genome and estimation of gene content (31,000 genes of this species. BES analyses identified 3,800 SSRs and 6,617 putative SNPs. Comparative genomic studies showed that citrus gene homology and microsyntheny with Populus trichocarpa was rather higher than with Arabidopsis thaliana, a species phylogenetically closer to citrus. Conclusion In this work, we report the characterization of three BAC libraries from C. clementina, and a new set of genomic resources that may be useful for isolation of genes underlying economically important traits, physical mapping and eventually crop improvement in Citrus species. In addition, BAC end sequencing has provided a first insight on the basic structure and organization of the citrus genome and has

  19. A genome-wide BAC end-sequence survey of sugarcane elucidates genome composition, and identifies BACs covering much of the euchromatin.

    Science.gov (United States)

    Kim, Changsoo; Lee, Tae-Ho; Compton, Rosana O; Robertson, Jon S; Pierce, Gary J; Paterson, Andrew H

    2013-01-01

    BAC-end sequences (BESs) of hybrid sugarcane cultivar R570 are presented. A total of 66,990 informative BESs were obtained from 43,874 BAC clones. Similarity search using a variety of public databases revealed that 13.5 and 42.8 % of BESs match known gene-coding and repeat regions, respectively. That 11.7 % of BESs are still unmatched to any nucleotide sequences in the current public databases despite the fact that a close relative, sorghum, is fully sequenced, indicates that there may be many sugarcane-specific or lineage-specific sequences. We found 1,742 simple sequence repeat motifs in 1,585 BESs, spanning 27,383 bp in length. As simple sequence repeat markers derived from BESs have some advantages over randomly generated markers, these may be particularly useful for comparing BAC-based physical maps with genetic maps. BES and overgo hybridization information was used for anchoring sugarcane BAC clones to the sorghum genome sequence. While sorghum and sugarcane have extensive similarity in terms of genomic structure, only 2,789 BACs (6.4 %) could be confidently anchored to the sorghum genome at the stringent threshold of having both-end information (BESs or overgos) within 300 Kb. This relatively low rate of anchoring may have been caused in part by small- or large-scale genomic rearrangements in the Saccharum genus after two rounds of whole genome duplication since its divergence from the sorghum lineage about 7.8 million years ago. Limiting consideration to only low-copy matches, 1,245 BACs were placed to 1,503 locations, covering ~198 Mb of the sorghum genome or about 78 % of the estimated 252 Mb of euchromatin. BESs and their analyses presented here may provide an early profile of the sugarcane genome as well as a basis for BAC-by-BAC sequencing of much of the basic gene set of sugarcane.

  20. Exploring the genome of the salt-marsh Spartina maritima (Poaceae, Chloridoideae) through BAC end sequence analysis.

    Science.gov (United States)

    Ferreira de Carvalho, J; Chelaifa, H; Boutte, J; Poulain, J; Couloux, A; Wincker, P; Bellec, A; Fourment, J; Bergès, H; Salmon, A; Ainouche, M

    2013-12-01

    Spartina species play an important ecological role on salt marshes. Spartina maritima is an Old-World species distributed along the European and North-African Atlantic coasts. This hexaploid species (2n = 6x = 60, 2C = 3,700 Mb) hybridized with different Spartina species introduced from the American coasts, which resulted in the formation of new invasive hybrids and allopolyploids. Thus, S. maritima raises evolutionary and ecological interests. However, genomic information is dramatically lacking in this genus. In an effort to develop genomic resources, we analysed 40,641 high-quality bacterial artificial chromosome-end sequences (BESs), representing 26.7 Mb of the S. maritima genome. BESs were searched for sequence homology against known databases. A fraction of 16.91% of the BESs represents known repeats including a majority of long terminal repeat (LTR) retrotransposons (13.67%). Non-LTR retrotransposons represent 0.75%, DNA transposons 0.99%, whereas small RNA, simple repeats and low-complexity sequences account for 1.38% of the analysed BESs. In addition, 4,285 simple sequence repeats were detected. Using the coding sequence database of Sorghum bicolor, 6,809 BESs found homology accounting for 17.1% of all BESs. Comparative genomics with related genera reveals that the microsynteny is better conserved with S. bicolor compared to other sequenced Poaceae, where 37.6% of the paired matching BESs are correctly orientated on the chromosomes. We did not observe large macrosyntenic rearrangements using the mapping strategy employed. However, some regions appeared to have experienced rearrangements when comparing Spartina to Sorghum and to Oryza. This work represents the first overview of S. maritima genome regarding the respective coding and repetitive components. The syntenic relationships with other grass genomes examined here help clarifying evolution in Poaceae, S. maritima being a part of the poorly-known Chloridoideae sub-family.

  1. A BAC end view of the Musa acuminata genome

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    Town Christopher D

    2007-06-01

    Full Text Available Abstract Background Musa species contain the fourth most important crop in developing countries. Here, we report the analysis of 6,252 BAC end-sequences, in order to view the sequence composition of the Musa acuminata genome in a cost effective and efficient manner. Results BAC end sequencing generated 6,252 reads representing 4,420,944 bp, including 2,979 clone pairs with an average read length after cleaning and filtering of 707 bp. All sequences have been submitted to GenBank, with the accession numbers DX451975 – DX458350. The BAC end-sequences, were searched against several databases and significant homology was found to mitochondria and chloroplast (2.6%, transposons and repetitive sequences (36% and proteins (11%. Functional interpretation of the protein matches was carried out by Gene Ontology assignments from matches to Arabidopsis and was shown to cover a broad range of categories. From protein matching regions of Musa BAC end-sequences, it was determined that the GC content of coding regions was 47%. Where protein matches encompassed a start codon, GC content as a function of position (5' to 3' across 129 bp sliding windows generates a "rice-like" gradient. A total of 352 potential SSR markers were discovered. The most abundant simple sequence repeats in four size categories were AT-rich. After filtering mitochondria and chloroplast matches, thousands of BAC end-sequences had a significant BLASTN match to the Oryza sativa and Arabidopsis genome sequence. Of these, a small number of BAC end-sequence pairs were shown to map to neighboring regions of the Oryza sativa genome representing regions of potential microsynteny. Conclusion Database searches with the BAC end-sequences and ab initio analysis identified those reads likely to contain transposons, repeat sequences, proteins and simple sequence repeats. Approximately 600 BAC end-sequences contained protein sequences that were not found in the existing available Musa expressed

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

    Directory of Open Access Journals (Sweden)

    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

  3. Genome evolution in Reptilia: in silico chicken mapping of 12,000 BAC-end sequences from two reptiles and a basal bird

    Directory of Open Access Journals (Sweden)

    Edwards Scott V

    2009-07-01

    Full Text Available Abstract Background With the publication of the draft chicken genome and the recent production of several BAC clone libraries from non-avian reptiles and birds, it is now possible to undertake more detailed comparative genomic studies in Reptilia. Of interest in particular are the genomic events that transformed the large, repeat-rich genomes of mammals and non-avian reptiles into the minimalist chicken genome. We have used paired BAC end sequences (BESs from the American alligator (Alligator mississippiensis, painted turtle (Chrysemys picta and emu (Dromaius novaehollandiae to investigate patterns of sequence divergence, gene and retroelement content, and microsynteny between these species and chicken. Results From a total of 11,967 curated BESs, we successfully mapped 725, 773 and 2597 sequences in alligator, turtle, and emu, respectively, to sites in the draft chicken genome using a stringent BLAST protocol. Most commonly, sequences mapped to a single site in the chicken genome. Of 1675, 1828 and 2936 paired BESs obtained for alligator, turtle, and emu, respectively, a total of 34 (alligator, 2%, 24 (turtle, 1.3% and 479 (emu, 16.3% pairs were found to map with high confidence and in the correct orientation and with BAC-sized intermarker distances to single chicken chromosomes, including 25 such paired hits in emu mapping to the chicken Z chromosome. By determining the insert sizes of a subset of BAC clones from these three species, we also found a significant correlation between the intermarker distance in alligator and turtle and in chicken, with slopes as expected on the basis of the ratio of the genome sizes. Conclusion Our results suggest that a large number of small-scale chromosomal rearrangements and deletions in the lineage leading to chicken have drastically reduced the number of detected syntenies observed between the chicken and alligator, turtle, and emu genomes and imply that small deletions occurring widely throughout the

  4. Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L..

    Directory of Open Access Journals (Sweden)

    Mahendar Thudi

    Full Text Available Chickpea (Cicer arietinum L. is the third most important cool season food legume, cultivated in arid and semi-arid regions of the world. The goal of this study was to develop novel molecular markers such as microsatellite or simple sequence repeat (SSR markers from bacterial artificial chromosome (BAC-end sequences (BESs and diversity arrays technology (DArT markers, and to construct a high-density genetic map based on recombinant inbred line (RIL population ICC 4958 (C. arietinum×PI 489777 (C. reticulatum. A BAC-library comprising 55,680 clones was constructed and 46,270 BESs were generated. Mining of these BESs provided 6,845 SSRs, and primer pairs were designed for 1,344 SSRs. In parallel, DArT arrays with ca. 15,000 clones were developed, and 5,397 clones were found polymorphic among 94 genotypes tested. Screening of newly developed BES-SSR markers and DArT arrays on the parental genotypes of the RIL mapping population showed polymorphism with 253 BES-SSR markers and 675 DArT markers. Segregation data obtained for these polymorphic markers and 494 markers data compiled from published reports or collaborators were used for constructing the genetic map. As a result, a comprehensive genetic map comprising 1,291 markers on eight linkage groups (LGs spanning a total of 845.56 cM distance was developed (http://cmap.icrisat.ac.in/cmap/sm/cp/thudi/. The number of markers per linkage group ranged from 68 (LG 8 to 218 (LG 3 with an average inter-marker distance of 0.65 cM. While the developed resource of molecular markers will be useful for genetic diversity, genetic mapping and molecular breeding applications, the comprehensive genetic map with integrated BES-SSR markers will facilitate its anchoring to the physical map (under construction to accelerate map-based cloning of genes in chickpea and comparative genome evolution studies in legumes.

  5. SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae, phylogenetic inferences and perspectives for genetic mapping

    Directory of Open Access Journals (Sweden)

    Ollitrault Patrick

    2012-01-01

    Full Text Available Abstract Background With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i to estimate the transferability within the genus Citrus of SNPs discovered from Clementine BACend sequencing (BES, (ii to estimate bias associated with the very narrow discovery panel, and (iii to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated Citrus species. Results Fifty-four accessions covering the main Citrus species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within C. maxima, C. medica, C. reticulata and C. micrantha. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in C. medica, C. maxima and wild Citrus species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the C. reticulata diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping. Conclusions A set of 622 SNP markers providing consistent results was selected. Of the

  6. SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping.

    Science.gov (United States)

    Ollitrault, Patrick; Terol, Javier; Garcia-Lor, Andres; Bérard, Aurélie; Chauveau, Aurélie; Froelicher, Yann; Belzile, Caroline; Morillon, Raphaël; Navarro, Luis; Brunel, Dominique; Talon, Manuel

    2012-01-10

    With the increasing availability of EST databases and whole genome sequences, SNPs have become the most abundant and powerful polymorphic markers. However, SNP chip data generally suffers from ascertainment biases caused by the SNP discovery and selection process in which a small number of individuals are used as discovery panels. The ongoing International Citrus Genome Consortium sequencing project of the highly heterozygous Clementine and sweet orange genomes will soon result in the release of several hundred thousand SNPs. The primary goals of this study were: (i) to estimate the transferability within the genus Citrus of SNPs discovered from Clementine BACend sequencing (BES), (ii) to estimate bias associated with the very narrow discovery panel, and (iii) to evaluate the usefulness of the Clementine-derived SNP markers for diversity analysis and comparative mapping studies between the different cultivated Citrus species. Fifty-four accessions covering the main Citrus species and 52 interspecific hybrids between pummelo and Clementine were genotyped on a GoldenGate array platform using 1,457 SNPs mined from Clementine BES and 37 SNPs identified between and within C. maxima, C. medica, C. reticulata and C. micrantha. Consistent results were obtained from 622 SNP loci. Of these markers, 116 displayed incomplete transferability primarily in C. medica, C. maxima and wild Citrus species. The two primary biases associated with the SNP mining in Clementine were an overestimation of the C. reticulata diversity and an underestimation of the interspecific differentiation. However, the genetic stratification of the gene pool was high, with very frequent significant linkage disequilibrium. Furthermore, the shared intraspecific polymorphism and accession heterozygosity were generally enough to perform interspecific comparative genetic mapping. A set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully

  7. Development of SSR Markers from Citrus BAC End Sequences and Their Integration into Linkage Map%柑桔BES-SSR标记开发及连锁图延伸和加密

    Institute of Scientific and Technical Information of China (English)

    马喜军; 龚桂芝; 彭祝春; 韩学智; 洪棋斌

    2012-01-01

    Simple Sequence Repeats (SSR) were surveyed in citrus BAC-End sequence (BES) for the development of new SSR markers to extend and saturate existing genetic map. 22 403 SSRs with 1~6 bp motif were identified in 46 339 citrus BESs retrieved from NCBI. The estimated frequency of SSRs was approximately 1/1. 25 kb, nearly twice the frequency found in Citrus Expressed Sequence Tags. 323 primers were selected in the present mapping study,of which 40 were mono-nucleotide repeats, 184 di-nucleotide repeats, 99 tri-nucleotide or above repeats. Polymorphism tests showed that 316 primer-pairs (98%) could be amplified successfully and 173 pairs (55%) were polymorphic. Among the polymorphic primers, 15 pairs were of mono-nucleotide repeats, 100 pairs of di-nucleotide repeats,58 pairs of tri-nucleotide or above repeats. A new linkage map was produced by combining the segregating data of new markers and markers in the previous map. When compared with the published map, the new map integrated 334 SSR markers, 9 linkage groups and covered 844. 2 cM of citrus genome with an average genetic distance standing at 2. 53 cM. The results demonstrated that citrus BES was good for SSR marker development and the developed markers were useful in extending and saturating the citrus genetic maps. So this will provide a reference for development of other species SSR markers and lay a good foundation for citrus gene mapping,map-based cloning and marker-assisted breeding.%为了系统性地开发和拓展柑桔SSR标记,通过对公布的柑桔BAC文库末端序列(BAC-End sequence,BES)进行SSR分析,选择1500个SSR位点设计合成并检测323对引物.结果表明:(1)从总长度为28.1 Mb的46 339条序列中共检测出22403个SSR位点,约每2条序列就会出现一个SSR位点,发生频率为48%,相当于平均1.25 kb的序列中就会出现1个SSR,频率约为柑桔EST的2倍,且不同核心重复序列的SSR发生特点与EST也不同.(2)所合成的323对引物中,有效扩增316

  8. Library Resources for Bac End Sequencing. Final Technical Report

    Energy Technology Data Exchange (ETDEWEB)

    Pieter J. de Jong

    2000-10-01

    Studies directed towards the specific aims outlined for this research award are summarized. The RPCI II Human Bac Library has been expanded by the addition of 6.9-fold genomic coverage. This segment has been generated from a MBOI partial digest of the same anonymous donor DNA used for the rest of the library. A new cloning vector, pTARBAC1, has been constructed and used in the construction of RPCI-II segment 5. This new cloning vector provides a new strategy in identifying targeted genomic regions and will greatly facilitate a large-scale analysis for positional cloning. A new maleCS7BC/6J mouse BAC library has been constructed. RPCI-23 contain 576 plates (approx 210,000 clones) and represents approximately 11-fold coverage of the mouse genome.

  9. BAC-end microsatellites from intra and inter-genic regions of the common bean genome and their correlation with cytogenetic features.

    Directory of Open Access Journals (Sweden)

    Matthew Wohlgemuth Blair

    Full Text Available Highly polymorphic markers such as simple sequence repeats (SSRs or microsatellites are very useful for genetic mapping. In this study novel SSRs were identified in BAC-end sequences (BES from non-contigged, non-overlapping bacterial artificial clones (BACs in common bean (Phaseolus vulgaris L.. These so called "singleton" BACs were from the G19833 Andean gene pool physical map and the new BES-SSR markers were used for the saturation of the inter-gene pool, DOR364×G19833 genetic map. A total of 899 SSR loci were found among the singleton BES, but only 346 loci corresponded to the single di- or tri-nucleotide motifs that were likely to be polymorphic (ATT or AG motifs, principally and useful for primer design and individual marker mapping. When these novel SSR markers were evaluated in the DOR364×G19833 population parents, 136 markers revealed polymorphism and 106 were mapped. Genetic mapping resulted in a map length of 2291 cM with an average distance between markers of 5.2 cM. The new genetic map was compared to the most recent cytogenetic analysis of common bean chromosomes. We found that the new singleton BES-SSR were helpful in filling peri-centromeric spaces on the cytogenetic map. Short genetic distances between some new singleton-derived BES-SSR markers was common showing suppressed recombination in these regions compared to other parts of the genome. The correlation of singleton-derived SSR marker distribution with other cytogenetic features of the bean genome is discussed.

  10. 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.

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

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    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

  12. 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 analog

  13. Integration of chicken genomic resources to enable whole-genome sequencing

    NARCIS (Netherlands)

    Aerts, J.A.; Crooijmans, R.P.M.A.; Cornelissen, S.J.B.; Hemmatian, K.; Veenendaal, A.; Jaader, A.; Poel, van der J.J.; Fillon, V.; Vignal, I.; Groenen, M.A.M.

    2003-01-01

    Different genomic resources in chicken were integrated through the Wageningen chicken BAC library. First, a BAC anchor map was created by screening this library with two sets of markers: microsatellite markers from the consensus linkage map and markers created from BAC end sequencing in chromosome w

  14. Preliminary macroseismic survey of the 2016 Amatrice seismic sequence

    Directory of Open Access Journals (Sweden)

    Mariano Angelo Zanini

    2016-11-01

    Full Text Available After the recent destructive L’Aquila 2009 and Emilia-Romagna 2012 earthquakes, a sudden Mw 6.0 seismic event hit Central Italy on August 24, 2016. A low population density characterizes the area but, due to its nighttime occurrence, about 300 victims were registered. This work presents the first preliminary results of a macroseismic survey conducted by two teams of the University of Padova in the territories that suffered major damages. Macroseismic intensities were assessed according to the European Macroseismic Scale (EMS98 for 180 sites.

  15. Repetitive Genomic Elements in a European Corn Borer, Ostrinia nubilalis, BAC Library were Indicated by BAC End Sequencing and Development of Sequence Tag Site Markers: Implications for Lepidopteran Genomic Research

    Science.gov (United States)

    The European corn borer, Ostrinia nubilalis, is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia, and a model system for insect olfaction and speciation. A bacterial artificial chromosome (BAC) library constructed for O. nubilalis contains 36,864 clones with estim...

  16. 瘤胃微生物基因组文库中BAC末端序列分析%Analysis of bacterial artificial chromosome (BAC) end sequences from microbial metagenomic library of rumen

    Institute of Scientific and Technical Information of China (English)

    赵圣国; 王加启; 李发弟; 刘开朗; 卜登攀; 李旦; 于萍

    2010-01-01

    基于前期从瘤胃微生物基因组文库中筛选的功能酶克隆菌,利用T7和pIBRP引物,测定功能酶克隆菌的BAC末端序列,并利用NCBI Blast系统对BAC末端序列进行分析.结果表明:共得到26条BAC末端序列,经Blast比对分析,与已知编码基因的匹配度低,而大部分BAC末端序列与阪崎肠杆菌和环境中的微生物匹配度高,说明瘤胃中的微生物与其它环境中的微生物具有一定的相似性,进一步丰富了对瘤胃微生物的认识.

  17. A Bac Library and Paired-PCR Approach to Mapping and Completing the Genome Sequence of Sulfolobus Solfataricus P2

    DEFF Research Database (Denmark)

    She, Qunxin; Confalonieri, F.; Zivanovic, Y.;

    2000-01-01

    -productive because there was a high sequence bias in the cosmid and lambda libraries. Therefore, a new approach was devised for linking the sequenced regions which may be generally applicable. BAC libraries were constructed and terminal sequences of the clones were determined and used for both end mapping and PCR...... screening. The PCR approaches included a novel chromosome walking method termed “paired-PCR”. 21 gaps were filled by BAC end sequence analyses and 6 gaps were filled by PCR including three large ones by paired-PCR. The complete map revealed that 0.9 Mb remained to be sequenced and 34 BAC clones were...... selected for walking over small gaps and preparing template libraries for larger ones. It is concluded that an optimal strategy for sequencing microorganism genomes involves construction of a high-resolution physical map by BAC end analyses, PCR screening and paired-PCR chromosome walking after about half...

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

    Directory of Open Access Journals (Sweden)

    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.

  19. Association and in silico assignment of sequences from turkey BACs.

    Science.gov (United States)

    Reed, Kent M; Faile, Gretchen M; Kreuth, Stacy B; Chaves, Lee D; Sullivan, Laura M

    2008-01-01

    Bacterial artificial chromosomes (BACs) provide an important resource in genetic mapping. An initial set of BACs corresponding to microsatellite markers in the turkey (Meleagris gallopavo) was isolated from the CHORI-260 turkey BAC library. The selected markers were distributed on both macro- and microchromosomes and included a genetically unlinked marker. End sequences were obtained for a subset of the recovered BACs and compared to the chicken whole genome sequence. Close association of the turkey BAC-end sequences and original marker sequences was generally conserved in the chicken genome. Gene content of the turkey BACs is predicted from the comparative sequence alignments.

  20. Preliminary data on Trachurus picturatus (Bowdich 1825 phylogeography inferred from mitochondrial DNA sequence data

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    Cláudia Filipa Moreira

    2015-11-01

    Full Text Available The populations of marine pelagic fishes, in particular the migratory ones as the Trachurus picturatus (Bowdich 1825, may be erroneously considered an homogenous population unit because they show broad geographic distributions, large population sizes and high migratory movements. The blue jack mackerel, T. picturatus is widely distributed in the NE Atlantic and also found in the Mediterranean and Black Seas. It is an economically important resource in the Macaronesian islands of Azores, Madeira and Canaries, but despite its fishery value and ecological importance, fluctuations in the landings are difficult to explain since studies regarding the population dynamics, stocks structure, fish movements and habitat connectivity are inexistent. Moreover, genetic methods that can act as a complementary tool for stock identification and population dynamics have never been applied to this species. The blue jack mackerel was sampled by artisanal fleets in the Islands of Azores, Madeira and Canaries, and at the Portuguese mainland - Matosinhos, Peniche and Portimão -during the spring-summer of 2013. A tissue sample was taken from each individual and stored in 96% ethanol for molecular analysis. Total DNA was successfully extracted, followed by a Polymerase Chain Reaction amplification of part of the cytochrome b gene (Cyt b. Amplifications and sequencing of the Cyt b gene were carried out using published primers used for the Carangidae family (Cárdenas et al. 2005. Sequences from Greece and Turkey, available on GenBank, were added to our sequences and all analysed together. In total 46 sequences were analysed, including the closely related outgroup (Trachurus Trachurus. Preliminary results show that there are sequences in the GenBank that are incorrectly assigned to this species. In addition, within the samples collected one was proven to be T. Trachurus. Preliminary phylogeographic analyses revealed a very shallow phylogenetic tree and a star

  1. Whole genome sequencing of M.tuberculosis in Kazakhstan: preliminary data

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    Ulykbek Kairov

    2014-03-01

    Full Text Available Background: Tuberculosis is a major public health problem which infects one third of the world’s population, resulting in more than two million deaths every year. The emergence of whole genome sequencing (WGS technologies as a primary research tool has allowed for the detection of genetic diversity in Mycobacterium tuberculosis (MTB with unprecedented resolution. WGS has been used to address a broad range of topics, including the dynamics of evolution, transmission, and treatment. To our knowledge, studies involving WGS of Kazakhstani strains of M. tuberculosis have not yet been performed. Aim: To perform whole genome sequencing of M. tuberculosis strains isolated in Kazakhstan and analyze sequence data (first experience and preliminary data. Results: In the present report, we announce the whole-genome sequences of the two clinical isolates of Mycobacterium tuberculosis, MTB-489 and MTB-476, isolated from the Almaty region. These strains were part of a repository that was created during our project “Creating prerequisites of personalized approach in the diagnosis and treatment of tuberculosis, based on whole genome-sequencing of M. tuberculosis”. Two strains were isolated from sputum samples of patients P1 and P2. Phenotypically, two isolates were drug-susceptible M. tuberculosis. Sequence data was compared with the publicly available data on M. tuberculosis laboratory strain H37Rv and others. The sequencing of the strains was performed on a Roche 454 GS FLX+ next-generation sequencing platform using a standard protocol for a shotgun genome library. The whole genome sequencing was performed for two M.tuberculosis isolates MTB-476 and MTB-489. 96 M bp with an average read length of 520 bp, approximately 21.8X coverage and 104.2 M bp with an average read length of 589 bp and approximately 23.7X coverage were generated for the MTB-476 and MTB-489, respectively. The genome of MTB-476 consists of 257 contigs, 4204 CDS, 46 tRNAs and 3 rRNAs. MTB

  2. 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

  3. Assessing soil-structure interaction during the 2016 central Italy seismic sequence (Italy: preliminary results

    Directory of Open Access Journals (Sweden)

    Arrigo Caserta

    2016-12-01

    Full Text Available We used the moderate-magnitude aftershocks succeeding to the 2016 August 24th, Mw = 6.0, Amatrice (Italy mainshok to asses, specially during an ongoing seismic sequence, the soil-structure interaction where cultural Heritage is involved. We have chosen as case study the San Giovanni Battista church (A.D. 1039  in Acquasanta Terme town, about 20 Km northeast of Amatrice. First of all we studied the soil shaking features in order to characterize the input to the monument. Then, using the recordings in the church, we tried to figure out  how the input seismic energy is distributed over the different monument parts. Some preliminary results are shown and discussed.

  4. Substitute CT generation from a single ultra short time echo MRI sequence: preliminary study

    Science.gov (United States)

    Ghose, Soumya; Dowling, Jason A.; Rai, Robba; Liney, Gary P.

    2017-04-01

    In MR guided radiation therapy planning both MR and CT images for a patient are acquired and co-registered to obtain a tissue specific HU map. Generation of the HU map directly from the MRI would eliminate the CT acquisition and may improve radiation therapy planning. In this preliminary study of substitute CT (sCT) generation, two porcine leg phantoms were scanned using a 3D ultrashort echo time (PETRA) sequence and co-registered to corresponding CT images to build tissue specific regression models. The model was created from one co-registered CT-PETRA pair to generate the sCT for the other PETRA image. An expectation maximization based clustering was performed on the co-registered PETRA image to identify the soft tissues, dense bone and air class membership probabilities. A tissue specific non linear regression model was built from one registered CT-PETRA pair dataset to predict the sCT of the second PETRA image in a two-fold cross validation schema. A complete substitute CT is generated in 3 min. The mean absolute HU error for air was 0.3 HU, bone was 95 HU, fat was 30 HU and for muscle it was 10 HU. The mean surface reconstruction error for the bone was 1.3 mm. The PETRA sequence enabled a low mean absolute surface distance for the bone and a low HU error for other classes. The sCT generated from a single PETRA sequence shows promise for the generation of fast sCT for MRI based radiation therapy planning.

  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. Preliminary results of high resolution magneto-biostratigraphy of continental sequences in Chapala Basin, Southwestern Mexico

    Science.gov (United States)

    Mendez Cardenas, D. L.; Benammi, M.

    2007-05-01

    Chapala Lake is south from Guadalajara, Jalisco State (Southwestern Mexico). Belongs to a series of Pliocenic lakes along the Mexican Volcanic Belt. It is localized in the Chapala rift, and the entire area is controlled by the tectonic setting of the Colima, Tepic and Chapala rifts, constituting the triple junction rift-rift-rift. The deposits studied belong to volcanosedimentary sequences, composed by lacustrine and fluvial associations alternated with units of ash and pumice. The faunistic component reported consists at least of 27 mammals species, and the sediments were there're in have to work with special attention for seek rodents by handpicking. Probably these rodents will be the clue to determine the deposits correlation. Core demagnetization shows that they are low-coercivity magnetic minerals like magnetite or Ti-magnetite. It was verified that the characteristic magnetization corresponds to MNRp and the inversion test resulted good. Rodents are represented by Geomynae, Sigmondontinae and Sciurinae. The Geomynae family is the most common, and the faunistic association indicates Blancan age. This also allows a correlation with the polarity pattern in the GSS between 3,6 and 2,6 Ma. Actually, is known that this kind of studies in continental sequences supported with paleontological record of vertebrates could give us a more precised calibration of the age of such deposits. Allowing better understanding of the evolution of these mammals and their path trough geological record. This work shows the preliminary results of rodents palaeontology and high resolution magneto-stratigraphy in the units from to Chapala Basin.

  7. Radiometric dating of the Earlier Stone Age sequence in excavation I at Wonderwerk Cave, South Africa: preliminary results.

    Science.gov (United States)

    Chazan, Michael; Ron, Hagai; Matmon, Ari; Porat, Naomi; Goldberg, Paul; Yates, Royden; Avery, Margaret; Sumner, Alexandra; Horwitz, Liora Kolska

    2008-07-01

    We present here the results of 44 paleomagnetic measurements, and single cosmogenic burial and optically stimulated luminescence ages for the Earlier Stone Age deposits from Wonderwerk Cave, Northern Cape, South Africa. The resulting paleomagnetic sequence: N>R>N>R>N constrains the Earlier Stone Age strata in this part of the site to between approximately 0.78-1.96 Ma. A single cosmogenic date of approximately 2.0 Ma from the base of the section offers some corroboration for the paleomagnetic sequence. Preliminary results indicate that the small lithic assemblage from the basal stratum may contain an Oldowan facies. This is overlain by several strata containing Acheulean industries. The preliminary radiometric dates reported here place the onset of the Acheulean at this site to approximately 1.6 Ma, which is roughly contemporaneous with that of East Africa.

  8. 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...

  9. 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.

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

    Science.gov (United States)

    Rodrigues, N B; Loverde, P T; Romanha, A J; Oliveira, G

    2002-01-01

    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.

  11. Purification, in vitro reassembly, and preliminary sequence analysis of epiplasmins, the major constituent of the membrane skeleton of Paramecium.

    Science.gov (United States)

    Coffe, G; Le Caer, J P; Lima, O; Adoutte, A

    1996-01-01

    The epiplasmic layer, a continuous rigid granulo-fibrillar sheet directly subtending the surface membranes of Paramecium, is one of the outermost of the various cytoskeletal networks that compose it cortex. We have previously shown that the epiplasm consists of a set of 30 to 50 protein bands on SDS-PAGE in the range 50 to 33 kDa, the epiplasmins. We report a purification procedure for the set of epiplasmic proteins, a description of their physicochemical and reassembly properties, and a preliminary characterization of their sequence. The conditions for solubilization of the epiplasm and for in vitro reassembly of its purified constituents ar described. Reassembly of the entire set of proteins and of some (but not all) subsets are shown to yield filamentous aggregates. Microsequences of two purified bands of epiplasmins reveal a striking amino acid sequence consisting of heptad repeats of only three main amino acids, P, V, and Q. These repeats were confirmed by DNA sequencing of polymerase chain reaction products. The motif is QPVQ-h, in which h is a hydrophobic residue. This may constitute the core of the epiplasmin sequence and, in view of the tendency of such a sequence to form a coiled-coil, may account for the remarkable self-aggregation properties of epiplasmins.

  12. Inference of Global HIV-1 Sequence Patterns and Preliminary Feature Analysis

    Institute of Scientific and Technical Information of China (English)

    Yan Wang; Reda Rawi; Daniel Hoffmann; Binlian Sun; Rongge Yang

    2013-01-01

    The epidemiology of HIV-1 varies in different areas of the world,and it is possible that this complexity may leave unique footprints in the viral genome.Thus,we attempted to find significant patterns in global HIV-1 genome sequences.By applying the rule inference algorithm RIPPER (Repeated Incremental Pruning to Produce Error Reduction) to multiple sequence alignments of Env sequences from four classes of compiled datasets,we generated four sets of signature patterns.We found that these patterns were able to distinguish southeastern Asian from nonsoutheastern Asian sequences with 97.5% accuracy,Chinese from non-Chinese sequences with 98.3% accuracy,African from non-African sequences with 88.4% accuracy,and southern African from non-southern African sequences with 91.2% accuracy.These patterns showed different associations with subtypes and with amino acid positions.In addition,some signature patterns were characteristic of the geographic area from which the sample was taken.Amino acid features corresponding to the phylogenetic clustering of HIV-1 sequences were consistent with some of the deduced patterns.Using a combination of patterns inferred from subtypes B,C,and all subtypes chimeric with CRF01_AE worldwide,we found that signature patterns of subtype C were extremely common in some sampled countries (for example,Zambia in southern Africa),which may hint at the origin of this HIV-1 subtype and the need to pay special attention to this area of Africa.Signature patterns of subtype B sequences were associated with different countries.Even more,there are distinct patterns at single position 21 with glycine,leucine and isoleucine corresponding to subtype C,B and all possible recombination forms chimeric with CRF01_AE,which also indicate distinct geographic features.Our method widens the scope of inference of signature from geographic,genetic,and genomic viewpoints.These findings may provide a valuable reference for epidemiological research or vaccine design.

  13. Preliminary study on mitochondrial 16S rRNA gene sequences and phylogeny of flatfishes (Pleuronectiformes)

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A 605 bp section of mitochondrial 16S rRNA gene from Paralichthys olivaceus, Pseudorhombus cinnamomeus, Psetta maxima and Kareius bicoloratus, which represent 3 families of Order Pleuronectiformes was amplified by PCR and sequenced to show the molecular systematics of Pleuronectiformes for comparison with related gene sequences of other 6 flatfish downloaded from GenBank. Phylogenetic analysis based on genetic distance from related gene sequences of 10 flatfish showed that this method was ideal to explore the relationship between species, genera and families. Phylogenetic trees set-up is based on neighbor-joining, maximum parsimony and maximum likelihood methods that accords to the general rule of Pleuronectiformes evolution. But they also resulted in some confusion. Unlike data from morphological characters, P. olivaceus clustered with K.bicoloratus, but P. cinnamomeus did not cluster with P. olivaceus, which is worth further studying.

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

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Hallers, Boudewijn ten; Nefedov, Michael

    2011-01-01

    of genes of interest in small genomics projects. The BAC end sequences described in this paper have been deposited in the GenBank data library [HN339419-HN341884, HN604664-HN604702]. The 454 produced contigs derived from selected clones are deposited with reference numbers [GenBank: JF288166-JF288183 &JF......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...

  15. Preliminary earthquake focal mechanism forecasts for the Amatrice sequence (central Italy

    Directory of Open Access Journals (Sweden)

    Pamela Roselli

    2016-12-01

    Full Text Available We place the Amatrice (central Italy seismic sequence and the related epicentral area in a contest of Probabilistic Seismic Hazard Analysis (PSHA. We apply a procedure to compute the probability to observe in the future a normal, reverse or strike-slip event and the average distribution of the P, T and N axes. This is a fundamental step to reduce the uncertainty connected to the Ground Motion Prediction Equation models, part of PSHA. For this purpose we use a significant focal mechanism catalogue and the latest present-day stress field data release for Italy to produce forecasted information that we compare with the equivalent data observed during the sequence.

  16. 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

  17. Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences

    Directory of Open Access Journals (Sweden)

    Ganko Eric W

    2004-03-01

    Full Text Available Abstract Background LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants. Results To explore the evolutionary history of long terminal repeat (LTR retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10. Conclusions Gypsy-like elements were found to be >4 × more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (

  18. 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.

  19. 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.

  20. Preliminary Evaluation of the Effect of Investigational Ebola Virus Disease Treatments on Viral Genome Sequences.

    Science.gov (United States)

    Whitmer, Shannon L M; Albariño, César; Shepard, Samuel S; Dudas, Gytis; Sheth, Mili; Brown, Shelley C; Cannon, Deborah; Erickson, Bobbie R; Gibbons, Aridth; Schuh, Amy; Sealy, Tara; Ervin, Elizabeth; Frace, Mike; Uyeki, Timothy M; Nichol, Stuart T; Ströher, Ute

    2016-10-15

     Several patients with Ebola virus disease (EVD) managed in the United States have received ZMapp monoclonal antibodies, TKM-Ebola small interfering RNA, brincidofovir, and/or convalescent plasma as investigational therapeutics.  To investigate whether treatment selected for Ebola virus (EBOV) mutations conferring resistance, viral sequencing was performed on RNA extracted from clinical blood specimens from patients with EVD following treatment, and putative viral targets were analyzed.  We observed no major or minor EBOV mutations within regions targeted by therapeutics.  This small subset of patients and clinical specimens suggests that evolution of resistance is not a direct consequence of antiviral treatment. As EVD antiviral treatments are introduced into wider use, it is essential that continuous viral full-genome surveillance is performed, to monitor for the emergence of escape mutations. Published by Oxford University Press for the Infectious Diseases Society of America 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  1. 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.

  2. Mitochondrial DNA sequence diversity in three ethnic populations from the South-west Iran: a preliminary study

    Institute of Scientific and Technical Information of China (English)

    Elham DAVOUDI-DEHAGHANI; Ali Mohammad FOROUGHMAND; Babak SAFFARI; Massoud HOUSHMAND; Hamid GALEHDARI; Mehdi SHAFA SHARIAT PANAHI; Majid YAVARIAN; Mohammad Hossein SANATI; Somayeh TORFI

    2011-01-01

    To investigate the genetic structure of human populations in the South-west region of Iran,mitochondrial first hypervariable DNA sequences were obtained from 50 individuals representing three different ethnic groups from Khuzestan Province.Studied groups were Shushtari Persians and Chahar Lang Bakhtiyaries from Indo-Europeanspeaking populations and Bani Torof Arabs from Semitic-speaking linguistic families.Genetic analysis of mtDNA data showed high similarity of Chahar Lang Bakhtiyaries with other Iranian Indo-European-speaking populations while Shushtaries and Bani Torofs had a closer affinity with Semitic-speaking groups rather than to other Iranian populations.The relationship of Chahar Lang Bakhtiyaries and Bani Torof Arabs with their neighbor populations can be explained by linguistic and geographic proximity.Whereas,the greater similarity of Shushtari Persians with West Asian Arabs is probably according to high gene flow between them.This article represents a preliminary study of three major ethnic groups of South-west Iran which investigates the potential genetic substructure of the region.

  3. Renewal and preliminary study of expressed sequence tags database on human fetal liver aged 22 wk of gestation

    Institute of Scientific and Technical Information of China (English)

    CHEN TingGui; WU SongFeng; ZHOU GangQiao; ZHU YunPing; HE FuChu

    2008-01-01

    With the developments of international human transcriptome data and our ESTs of human fetal liver aged 22 weeks (wk) of gestation (HFL22w), the former research must be renewed. In this work, the EST data were firstly clustered by blasting against the ESTs of HFL22w, UniGene, DOTS, MGC and Twin-scan-predicted human transcriptome. Then, after EST assembly and gene identification, the known genes were classified by GO (gene ontology), and the unknown genes were predicted by Pfam and ScanProsite to clarify their functions. In the end, the relations of 5 tissues including fetal liver, adult liver, bone marrow, thymus and lymph node that possess hemopoiesis or can indicate fetal liver char-acteristics were analyzed by hierarchical clustering. The results show that: (i) By comparing the 5 newest human transcriptome databases, we can largely reduce the probability that the ESTS belonging to unconnected parts of one gene were probably divided into different clusters, so it is recommended to blast against the newest databases when clustering EST data; (ii) some previous unknown ESTs had been identified as function-known genes, and 1379 genes were identified as fully new sequences pos-sessed in our lab; (iii) through GO classification, we got a rough understanding of HFL22w, and ob-tained 6 cell migration genes and 6 hemopoiesis genes; (iv) prediction of gene function had enabled us to obtain 277 profiles, among them, there are 5 categories distributed in more than 10 genes; (v) five tissue relations analyzed by hierarchical clustering are related to their functions; (vi) We have built the world's largest EST database on HFL22w. Renewal and preliminary analysis of EST database on HFL22w will help to understand hemopoiesis and cell migration mechanism, and promote future re-search on human fetal liver.

  4. A sequence based synteny map between soybean and Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Lightfoot David A

    2007-01-01

    Full Text Available Abstract Background Soybean (Glycine max, L. Merr. is one of the world's most important crops, however, its complete genomic sequence has yet to be determined. Nonetheless, a large body of sequence information exists, particularly in the form of expressed sequence tags (ESTs. Herein, we report the use of the model organism Arabidopsis thaliana (thale cress for which the entire genomic sequence is available as a framework to align thousands of short soybean sequences. Results A series of JAVA-based programs were created that processed and compared 341,619 soybean DNA sequences against A. thaliana chromosomal DNA. A. thaliana DNA was probed for short, exact matches (15 bp to each soybean sequence, and then checked for the number of additional 7 bp matches in the adjacent 400 bp region. The position of these matches was used to order soybean sequences in relation to the A. thaliana genome. Conclusion Reported associations between soybean sequences and A. thaliana were within a 95% confidence interval of e-30 – e-100. In addition, the clustering of soybean expressed sequence tags (ESTs based on A. thaliana sequence was accurate enough to identify potential single nucleotide polymorphisms (SNPs within the soybean sequence clusters. An EST, bacterial artificial chromosome (BAC end sequence and marker amplicon sequence synteny map of soybean and A. thaliana is presented. In addition, all JAVA programs used to create this map are available upon request and on the WEB.

  5. 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

  6. A preliminary phylogenetic analysis of the Capsalidae (Platyhelminthes: Monogenea: Monopisthocotylea) inferred from large subunit rDNA sequences.

    Science.gov (United States)

    Whittington, I D; Deveney, M R; Morgan, J A T; Chisholm, L A; Adlard, R D

    2004-05-01

    Phylogenetic relationships within the Capsalidae (Monogenea) were examined using large subunit ribosomal DNA sequences from 17 capsalid species (representing 7 genera, 5 subfamilies), 2 outgroup taxa (Monocotylidae) plus Udonella caligorum (Udonellidae). Trees were constructed using maximum likelihood, minimum evolution and maximum parsimony algorithms. An initial tree, generated from sequences 315 bases long, suggests that Capsalinae, Encotyllabinae, Entobdellinae and Trochopodinae are monophyletic, but that Benedeniinae is paraphyletic. Analyses indicate that Neobenedenia, currently in the Benedeniinae, should perhaps be placed in a separate subfamily. An additional analysis was made which omitted 3 capsalid taxa (for which only short sequences were available) and all outgroup taxa because of alignment difficulties. Sequence length increased to 693 bases and good branch support was achieved. The Benedeniinae was again paraphyletic. Higher-level classification of the Capsalidae, evolution of the Entobdellinae and issues of species identity in Neobenedenia are discussed.

  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. Preliminary Study of Phylogenetic Relationship of Rice Field Chironomidae (Diptera Inferred From DNA Sequences of Mitochondrial Cytochrome Oxidase Subunit I

    Directory of Open Access Journals (Sweden)

    Salman A. Al-Shami

    2009-01-01

    Full Text Available Problem statement: Chironomidae have been recorded in rice fields throughout the world including in many countries such as India, Australia and the USA. Although some studies provide the key to genera level and note the difficulty of identifying the larvae to species level. Chironomid researches have been hindered because of difficulties in specimen preparation, identification, morphology and literature. Systematics, phylogenetics and taxonomic studies of insects developed quickly with emergence of molecular techniques. These techniques provide an effective tool toward more accurate identification of ambiguous chironomid species. Approach: Samples of chironomids larvae were collected from rice plots at Bukit Merah Agricultural Experimental Station (BMAES, Penang, Malaysia. A 710 bp fragment of mitochondrial gene Cytochrome Oxidase subunit I (COI was amplified and sequenced. Results: Five species of Chironomidae; three species of subfamily Chironominae, Chironomus kiiensis, Polypedilum trigonus, Tanytarsus formosanus, two species of subfamily Tanypodinae, Clinotanypus sp and Tanypus punctipennis were morphologically identified. The phylogenetic relationship among these species was been investigated. High sequence divergence was observed between two individuals of the presumed C. kiiensis and it is suggested that more than one species may be present. However the intraspecific sequence divergence was lower between the other species of Tanypodinae subfamily. Interestingly, Tanytarsus formosanus showed close phylogenetic relationship to Tanypodinae species and this presumably reflect co-evolutionary traits of different subfamilies. Conclusion: The sequence of the mtDNA cytochrome oxidase subunit I gene has proven useful to investigate the phylogenetic relationship among the ambiguous species of chironomids.

  9. Mandible traction with wires for the treatment of upper airway obstruction caused by Pierre Robin sequence in Chinese infants: preliminary findings.

    Science.gov (United States)

    Dong, Chen-Bin; Zheng, Shan; Shen, Chun; Li, Hao

    2014-10-01

    Pierre Robin sequence (PRS) is a congenital abnormality that may cause upper airway obstruction requiring surgical intervention. This preliminary study aimed to examine the feasibility and effectiveness of mandible traction with wires for the treatment of upper airway obstruction caused by PRS in Chinese infants. Measures of interest included transcutaneous oxygen saturation before and after surgery, duration of surgery and traction, complications, and CT findings. Seven infants were included in the study (mean birth weight: 2485 g, range: 2405-2570 g); four were born preterm and three were born full term. Mean age at surgery was 13.7 days (range: 2-28 days), mean duration of surgery was 16.6 min (range: 13-25 min) and mean duration of traction was 26.6 days (range: 21-35 days). Mean follow-up was 6.2 months (range: 1-11 months). No infant experienced severe complications. All infants experienced increases in transcutaneous oxygen saturation after surgery. Mean transcutaneous oxygen saturation was 82% before surgery and 98% after surgery. Follow-up morphology of the mandible was excellent. There was no upper airway obstruction, and short-term growth and development were satisfactory. These preliminary findings suggest that mandibular traction with wires may be an effective treatment for upper airway obstruction caused by PRS in Chinese infants.

  10. Characterization of genome-wide microsatellites of Saccharina japonica based on a preliminary assembly of Illumina sequencing reads

    Science.gov (United States)

    Zhang, Linan; Peng, Jie; Li, Xiaojie; Cui, Cuiju; Sun, Juan; Yang, Guanpin

    2016-06-01

    Microsatellites or simple sequence repeats (SSR) function widely and locate dependently in genome. However, their characteristics are often ignored due to the lack of genomic sequences of most species. Kelp ( Saccharina japonica), a brown macroalga, is extensively cultured in China. In this study, the genome of S. japonica was surveyed using an Illumina sequencing platform, and its microsatellites were characterized. The preliminarily assembled genome was 469.4 Mb in size, with a scaffold N50 of 20529 bp. Among the 128370 identified microsatellites, 90671, 25726 and 11973 were found in intergenic regions, introns and exons, averaging 339.3, 178.8 and 205.4 microsatellites per Mb, respectively. These microsatellites distributed unevenly in S. japonica genome. Mononucleotide motifs were the most abundant in the genome, while trinucleotide ones were the most prevalent in exons. The microsatellite abundance decreased significantly with the increase of motif repeat numbers, and the microsatellites with a small number of repeats accounted for a higher proportion of the exons than those of the intergenic regions and introns. C/G-rich motifs were more common in exons than in intergenic regions and introns. These characteristics of microsatellites in S. japonica genome may associate with their functions, and ultimately their adaptation and evolution. Among the 120140 pairs of designed microsatellite primers, approximately 75% were predicted to be able to amplify S. japonica DNA. These microsatellite markers will be extremely useful for the genetic breeding and population evolution studies of kelp.

  11. Generation of Physical Map Contig-Specific Sequences Useful for Whole Genome Sequence Scaffolding

    Science.gov (United States)

    Jiang, Yanliang; Ninwichian, Parichart; Liu, Shikai; Zhang, Jiaren; Kucuktas, Huseyin; Sun, Fanyue; Kaltenboeck, Ludmilla; Sun, Luyang; Bao, Lisui; Liu, Zhanjiang

    2013-01-01

    Along with the rapid advances of the nextgen sequencing technologies, more and more species are added to the list of organisms whose whole genomes are sequenced. However, the assembled draft genome of many organisms consists of numerous small contigs, due to the short length of the reads generated by nextgen sequencing platforms. In order to improve the assembly and bring the genome contigs together, more genome resources are needed. In this study, we developed a strategy to generate a valuable genome resource, physical map contig-specific sequences, which are randomly distributed genome sequences in each physical contig. Two-dimensional tagging method was used to create specific tags for 1,824 physical contigs, in which the cost was dramatically reduced. A total of 94,111,841 100-bp reads and 315,277 assembled contigs are identified containing physical map contig-specific tags. The physical map contig-specific sequences along with the currently available BAC end sequences were then used to anchor the catfish draft genome contigs. A total of 156,457 genome contigs (~79% of whole genome sequencing assembly) were anchored and grouped into 1,824 pools, in which 16,680 unique genes were annotated. The physical map contig-specific sequences are valuable resources to link physical map, genetic linkage map and draft whole genome sequences, consequently have the capability to improve the whole genome sequences assembly and scaffolding, and improve the genome-wide comparative analysis as well. The strategy developed in this study could also be adopted in other species whose whole genome assembly is still facing a challenge. PMID:24205335

  12. Generation of physical map contig-specific sequences useful for whole genome sequence scaffolding.

    Directory of Open Access Journals (Sweden)

    Yanliang Jiang

    Full Text Available Along with the rapid advances of the nextgen sequencing technologies, more and more species are added to the list of organisms whose whole genomes are sequenced. However, the assembled draft genome of many organisms consists of numerous small contigs, due to the short length of the reads generated by nextgen sequencing platforms. In order to improve the assembly and bring the genome contigs together, more genome resources are needed. In this study, we developed a strategy to generate a valuable genome resource, physical map contig-specific sequences, which are randomly distributed genome sequences in each physical contig. Two-dimensional tagging method was used to create specific tags for 1,824 physical contigs, in which the cost was dramatically reduced. A total of 94,111,841 100-bp reads and 315,277 assembled contigs are identified containing physical map contig-specific tags. The physical map contig-specific sequences along with the currently available BAC end sequences were then used to anchor the catfish draft genome contigs. A total of 156,457 genome contigs (~79% of whole genome sequencing assembly were anchored and grouped into 1,824 pools, in which 16,680 unique genes were annotated. The physical map contig-specific sequences are valuable resources to link physical map, genetic linkage map and draft whole genome sequences, consequently have the capability to improve the whole genome sequences assembly and scaffolding, and improve the genome-wide comparative analysis as well. The strategy developed in this study could also be adopted in other species whose whole genome assembly is still facing a challenge.

  13. Preliminary functional characterization, cloning and primary sequence of Fastuosain, a cysteine peptidase isolated from fruits of Bromelia fastuosa.

    Science.gov (United States)

    Cabral, Hamilton; Leopoldino, Andréia M; Tajara, Eloiza H; Greene, Lewis J; Faça, Vitor M; Mateus, Rogério P; Ceron, Carlos R; de Souza Judice, Wagner A; Julianod, Luiz; Bonilla-Rodriguez, Gustavo O

    2006-01-01

    The present work reports the characterization of Fastuosain, a novel cysteine protease of 25kDa, purified from the unripe fruits of Bromelia fastuosa, a wild South American Bromeliaceae. Proteolytic activity, measured using casein and synthetic substrates, was dependent on the presence of thiol reagents, having maximum activity at pH 7.0. The present work reports cDNA cloning of Fastuosain; cDNA was amplified by PCR using specific primers. The product was 1096pb long. Mature fastuosain has 217 residues, and with the proregion has a total length of 324 residues. Its primary sequence showed high homology with ananain(74%), stem bromelain (66%) and papain (44%).

  14. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes

    Directory of Open Access Journals (Sweden)

    Anderson Olin D

    2008-07-01

    Full Text Available Abstract Background Wheat, barley, and rye, of tribe Triticeae in the Poaceae, are among the most important crops worldwide but they present many challenges to genomics-aided crop improvement. Brachypodium distachyon, a close relative of those cereals has recently emerged as a model for grass functional genomics. Sequencing of the nuclear and organelle genomes of Brachypodium is one of the first steps towards making this species available as a tool for researchers interested in cereals biology. Findings The chloroplast genome of Brachypodium distachyon was sequenced by a combinational approach using BAC end and shotgun sequences derived from a selected BAC containing the entire chloroplast genome. Comparative analysis indicated that the chloroplast genome is conserved in gene number and organization with respect to those of other cereals. However, several Brachypodium genes evolve at a faster rate than those in other grasses. Sequence analysis reveals that rice and wheat have a ~2.1 kb deletion in their plastid genomes and this deletion must have occurred independently in both species. Conclusion We demonstrate that BAC libraries can be used to sequence plastid, and likely other organellar, genomes. As expected, the Brachypodium chloroplast genome is very similar to those of other sequenced grasses. The phylogenetic analyses and the pattern of insertions and deletions in the chloroplast genome confirmed that Brachypodium is a close relative of the tribe Triticeae. Nevertheless, we show that some large indels can arise multiple times and may confound phylogenetic reconstruction.

  15. 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

  16. Preliminary investigation of sequence-independent DNA binding proteins in rat skeletal muscle sarcoplasmic reticulum and their function

    Institute of Scientific and Technical Information of China (English)

    赵文; 姜志胜; 倪菊华; 陈光慧; 刘乃奎; 汤健; 贾弘褆; 唐朝枢

    2000-01-01

    To observe the binding of plasmid DNA to non-nuclear DNA binding proteins in sar-coplasmic reticulum (SR) and the effects of this binding on SR function, sarcoplasmic reticulum proteins in rat skeletal muscle were isolated by differential centrifuge and sucrose density-gradient centrifuge. The results showed that there are two sequence-independent DNA binding proteins in SR proteins, the molecular weights of which are 83 and 58 ku, respectively. Ca2+ uptake and release of SR were remarkably promoted by the binding of plasmid DNA to DNA binding proteins in SR, the mechanism is probably through increasing of Ca2+-ATPase activity in SR and changing of character of Ca2+ release channel ryanodine receptors induced by the binding. These results suggest that there exist DNA binding proteins in SR and its binding to DNA may affect Ca2+ transport of SR.

  17. Preliminary investigation of sequence-independent DNA binding proteins in rat skeletal muscle sarcoplasmic reticulum and their function

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    To observe the binding of plasmid DNA to non-nuclear DNA binding proteins in sarcoplasmic reticulum (SR) and the effects of this binding on SR function, sarcoplasmic reticulum proteins in rat skeletal muscle were isolated by differential centrifuge and sucrose density-gradient centrifuge. The results showed that there are two sequence-independent DNA binding proteins in SR proteins, the molecular weights of which are 83 and 58 ku, respectively. Ca2+ uptake and release of SR were remarkably promoted by the binding of plasmid DNA to DNA binding proteins in SR, the mechanism is probably through increasing of Ca2+-ATPase activity in SR and changing of character of Ca2+ release channel ryanodine receptors induced by the binding. These results suggest that there exist DNA binding proteins in SR and its binding to DNA may affect Ca2+ transport of SR.

  18. 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.

  19. 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

    Translocation involving the immunoglobulin heavy chain (IGH) locus is a recurring event in B-cell oncogenesis. The aim of this study was to characterize clones from bacterial artificial chromosome (BAC) libraries and/or bacteriophage P1 artificial chromosome libraries spanning the IGH locus...... for detection of illegitimate rearrangement within the region by fluorescence in situ hybridization (FISH). In silico analysis of the IGH variable (IGHV) DNA sequence (NT_001716.v1) was performed to identify BAC probes located within the IGHV cluster. Clones of the constant (IGHC) cluster were found...... 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...

  20. Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome.

    Science.gov (United States)

    Krzywinski, Martin; Wallis, John; Gösele, Claudia; Bosdet, Ian; Chiu, Readman; Graves, Tina; Hummel, Oliver; Layman, Dan; Mathewson, Carrie; Wye, Natasja; Zhu, Baoli; Albracht, Derek; Asano, Jennifer; Barber, Sarah; Brown-John, Mabel; Chan, Susanna; Chand, Steve; Cloutier, Alison; Davito, Jonathon; Fjell, Chris; Gaige, Tony; Ganten, Detlev; Girn, Noreen; Guggenheimer, Kurtis; Himmelbauer, Heinz; Kreitler, Thomas; Leach, Stephen; Lee, Darlene; Lehrach, Hans; Mayo, Michael; Mead, Kelly; Olson, Teika; Pandoh, Pawan; Prabhu, Anna-Liisa; Shin, Heesun; Tänzer, Simone; Thompson, Jason; Tsai, Miranda; Walker, Jason; Yang, George; Sekhon, Mandeep; Hillier, LaDeana; Zimdahl, Heike; Marziali, Andre; Osoegawa, Kazutoyo; Zhao, Shaying; Siddiqui, Asim; de Jong, Pieter J; Warren, Wes; Mardis, Elaine; McPherson, John D; Wilson, Richard; Hübner, Norbert; Jones, Steven; Marra, Marco; Schein, Jacqueline

    2004-04-01

    As part of the effort to sequence the genome of Rattus norvegicus, we constructed a physical map comprised of fingerprinted bacterial artificial chromosome (BAC) clones from the CHORI-230 BAC library. These BAC clones provide approximately 13-fold redundant coverage of the genome and have been assembled into 376 fingerprint contigs. A yeast artificial chromosome (YAC) map was also constructed and aligned with the BAC map via fingerprinted BAC and P1 artificial chromosome clones (PACs) sharing interspersed repetitive sequence markers with the YAC-based physical map. We have annotated 95% of the fingerprint map clones in contigs with coordinates on the version 3.1 rat genome sequence assembly, using BAC-end sequences and in silico mapping methods. These coordinates have allowed anchoring 358 of the 376 fingerprint map contigs onto the sequence assembly. Of these, 324 contigs are anchored to rat genome sequences localized to chromosomes, and 34 contigs are anchored to unlocalized portions of the rat sequence assembly. The remaining 18 contigs, containing 54 clones, still require placement. The fingerprint map is a high-resolution integrative data resource that provides genome-ordered associations among BAC, YAC, and PAC clones and the assembled sequence of the rat genome.

  1. 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...

  2. Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species

    Directory of Open Access Journals (Sweden)

    Zhao Shaying

    2009-06-01

    Full Text Available Abstract Background Manduca sexta, Heliothis virescens, and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critical resources for many molecular studies, including physical mapping and genome sequencing, but not available to date. Results We report the construction and characterization of six large-insert BAC libraries for the three species and sampling sequence analysis of the genomes. The six BAC libraries were constructed with two restriction enzymes, two libraries for each species, and each has an average clone insert size ranging from 152–175 kb. We estimated that the genome coverage of each library ranged from 6–9 ×, with the two combined libraries of each species being equivalent to 13.0–16.3 × haploid genomes. The genome coverage, quality and utility of the libraries were further confirmed by library screening using 6~8 putative single-copy probes. To provide a first glimpse into these genomes, we sequenced and analyzed the BAC ends of ~200 clones randomly selected from the libraries of each species. The data revealed that the genomes are AT-rich, contain relatively small fractions of repeat elements with a majority belonging to the category of low complexity repeats, and are more abundant in retro-elements than DNA transposons. Among the species, the H. erato genome is somewhat more abundant in repeat elements and simple repeats than those of M. sexta and H. virescens. The BLAST analysis of the BAC end sequences suggested that the evolution of the three genomes is widely varied, with the genome of H. virescens being the most conserved as a typical lepidopteran, whereas both genomes of H. erato and M. sexta appear to have evolved significantly, resulting in a higher level of species- or evolutionary lineage-specific sequences. Conclusion The high-quality and large-insert BAC libraries of the insects, together

  3. Preliminary Results of De Novo Whole Genome Sequencing of the Siberian Larch (Larix sibirica Ledeb. and the Siberian Stone Pine (Pinus sibirica Du Tour

    Directory of Open Access Journals (Sweden)

    K. V. Krutovsky

    2014-08-01

    Full Text Available The Illumina HiSeq2000 DNA sequencing generated 2 906 977 265 high quality paired-end nucleotide sequences (reads and 576 Gbp for Siberian larch (Larix sibirica Ledeb. that corresponds to 48X coverage of the larch genome (12.03 Gbp, and 3 427 566 813 reads and 679 Gbp for Siberian stone pine (Pinus sibirica Du Tour that corresponds to 29X coverage of its genome (23.6 Gbp. These data are not enough to assemble and annotate whole genomes, but the obtained nucleotide sequences have allowed us to discover and develop effective highly polymorphic molecular genetic markers, such as microsatellite loci that are required for population genetic studies and identification of the timber origin. Sequence data can be used also to discover single nucleotide polymorphisms (SNPs. Genomic studies of Russian boreal forests and major phytopathogens associated with them will also allow us to identify biomarkers that can be used for solving important scientific and economic problems related to the conservation of forest genetic resources and breeding more resilient and fast growing trees with improved timber and resistance to diseases and adverse environmental factors.

  4. 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.

  5. Preliminary results on a promising long paleoclimatic archive for the Near East: the lacustrine sequence of Acigöl (Anatolia, Turkey).

    Science.gov (United States)

    Demory, François; Perrin, Mireille; Cihat Alçiçek, Mehmet; Lebatard, Anne-Elizabeth; Nomade, Sébastien; Andrieu-Ponel, Valérie; Djamali, Morteza; Rochette, Pierre; Helvaci, Cahit

    2016-04-01

    A 601 m long core was drilled in Lake Acigöl located in an extensional basin in SW Anatolia (Turkey). The alternation of carbonates relatively rich in evaporites, siliciclastic particles and fossils (ostracods, gastropods and bivalves) gives to the sequence a high potential for palaeoclimatic record. The Acigöl sequence is younger than 3.4 Ma, the oldest age determination recorded for lacustrine successions elsewhere in SW Anatolia (van den Hoek Ostende, 2015). The first paleomagnetic investigations show numerous reverse polarities implying that two third of the sequence is older than 0.78 Ma (Brunhes/Matuyama transition) with a base dating back to 1.7 Ma or more. Indeed, although Jaramillo subchron (from 0.9 to 1.06 Ma) is well recorded, uncertainty remains for the Odulvaï subchron (from 1.78 to 2 Ma) which is not yet robustly identified. The age model will be soon completed by radiometric dating of a tephra found in the sequence and by authigenic 10Be/9Be dating. Detrital proxies (such as magnetic susceptibility) versus biological proxies will allow discrimination between tectonic and climatic signals and may reveal the response of terrestrial ecosystems to the mid-Pleistocene climatic transition. This research is supported by a two-year bilateral cooperation between CNRS-INSU and TUBITAK (grant number 114Y723). Reference: van den Hoek Ostende L.W. Gardner J.D. van Bennekom L. Alçiçek M.C. Murray A.M. Wesselingh F.P. Alçiçek H. Tesakov A.S. 2015. Ericek, a new Pliocene vertebrate locality from the Çameli Basin (SW Anatolia, Turkey). Palaeobiodiversity and Palaeoenvironments 95, 305-320

  6. Development and preliminary evaluation of an online educational video about whole-genome sequencing for research participants, patients, and the general public.

    Science.gov (United States)

    Sanderson, Saskia C; Suckiel, Sabrina A; Zweig, Micol; Bottinger, Erwin P; Jabs, Ethylin Wang; Richardson, Lynne D

    2016-05-01

    As whole-genome sequencing (WGS) increases in availability, WGS educational aids are needed for research participants, patients, and the general public. Our aim was therefore to develop an accessible and scalable WGS educational aid. We engaged multiple stakeholders in an iterative process over a 1-year period culminating in the production of a novel 10-minute WGS educational animated video, "Whole Genome Sequencing and You" (https://goo.gl/HV8ezJ). We then presented the animated video to 281 online-survey respondents (the video-information group). There were also two comparison groups: a written-information group (n = 281) and a no-information group (n = 300). In the video-information group, 79% reported the video was easy to understand, satisfaction scores were high (mean 4.00 on 1-5 scale, where 5 = high satisfaction), and knowledge increased significantly. There were significant differences in knowledge compared with the no-information group but few differences compared with the written-information group. Intention to receive personal results from WGS and decisional conflict in response to a hypothetical scenario did not differ between the three groups. The educational animated video, "Whole Genome Sequencing and You," was well received by this sample of online-survey respondents. Further work is needed to evaluate its utility as an aid to informed decision making about WGS in other populations.Genet Med 18 5, 501-512.

  7. Preliminary validation of a novel high-resolution melt-based typing method based on the multilocus sequence typing scheme of Streptococcus pyogenes.

    Science.gov (United States)

    Richardson, L J; Tong, S Y C; Towers, R J; Huygens, F; McGregor, K; Fagan, P K; Currie, B J; Carapetis, J R; Giffard, P M

    2011-09-01

    The major limitation of current typing methods for Streptococcus pyogenes, such as emm sequence typing and T typing, is that these are based on regions subject to considerable selective pressure. Multilocus sequence typing (MLST) is a better indicator of the genetic backbone of a strain but is not widely used due to high costs. The objective of this study was to develop a robust and cost-effective alternative to S. pyogenes MLST. A 10-member single nucleotide polymorphism (SNP) set that provides a Simpson's Index of Diversity (D) of 0.99 with respect to the S. pyogenes MLST database was derived. A typing format involving high-resolution melting (HRM) analysis of small fragments nucleated by each of the resolution-optimized SNPs was developed. The fragments were 59-119 bp in size and, based on differences in G+C content, were predicted to generate three to six resolvable HRM curves. The combination of curves across each of the 10 fragments can be used to generate a melt type (MelT) for each sequence type (ST). The 525 STs currently in the S. pyogenes MLST database are predicted to resolve into 298 distinct MelTs and the method is calculated to provide a D of 0.996 against the MLST database. The MelTs are concordant with the S. pyogenes population structure. To validate the method we examined clinical isolates of S. pyogenes of 70 STs. Curves were generated as predicted by G+C content discriminating the 70 STs into 65 distinct MelTs.

  8. 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

    2013-05-24

    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.

  9. Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey

    Directory of Open Access Journals (Sweden)

    den Dunnen Johan T

    2009-10-01

    Full Text Available Abstract Background The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs in species lacking a sequenced reference genome, we set-up an analysis pipeline based on a short read de novo sequence assembler and a program designed to identify variation within short reads. To illustrate the potential of this technique, we present the results obtained with a randomly sheared, enzymatically generated, 2-3 kbp genome fraction of six pooled Meleagris gallopavo (turkey individuals. Results A total of 100 million 36 bp reads were generated, representing approximately 5-6% (~62 Mbp of the turkey genome, with an estimated sequence depth of 58. Reads consisting of bases called with less than 1% error probability were selected and assembled into contigs. Subsequently, high throughput discovery of nucleotide variation was performed using sequences with more than 90% reliability by using the assembled contigs that were 50 bp or longer as the reference sequence. We identified more than 7,500 SNPs with a high probability of representing true nucleotide variation in turkeys. Increasing the reference genome by adding publicly available turkey BAC-end sequences increased the number of SNPs to over 11,000. A comparison with the sequenced chicken genome indicated that the assembled turkey contigs were distributed uniformly across the turkey genome. Genotyping of a representative sample of 340 SNPs resulted in a SNP conversion rate of 95%. The correlation of the minor allele count (MAC and observed minor allele frequency (MAF for the validated SNPs was 0.69. Conclusion We provide an efficient and cost-effective approach for the identification of thousands of high quality SNPs in species currently lacking a sequenced genome and applied this to turkey. The methodology addresses a random fraction of the genome, resulting in an even

  10. Preliminary experience with MRA in evaluating the degree of carotid stenosis and plaque morphology using high-resolution sequences after gadofosveset trisodium (Vasovist) administration: comparison with CTA and DSA.

    Science.gov (United States)

    Anzidei, M; Napoli, A; Geiger, D; Cavallo Marincola, B; Zini, C; Zaccagna, F; Di Paolo, P; Catalano, C; Passariello, R

    2010-06-01

    The authors performed a preliminary study with blood-pool contrast-enhanced magnetic resonance angiography (MRA) in evaluating the degree of carotid artery stenosis and plaque morphology, comparing the diagnostic performance of first-pass (FP) and steady-state (SS) acquisitions with 64-slice computed tomography angiography (CTA) and using digital subtraction angiography (DSA) as the reference standard. Twenty patients with >or=50% carotid artery stenosis at Doppler sonography underwent blood-pool contrast-enhanced MRA, CTA and DSA. Two independent radiologists evaluated MRA and CTA examinations to assess the degree of stenosis and characterise plaque morphology. Accuracy, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated for FP, SS and CTA. The McNemar and Wilcoxon tests were used to determine significant differences (p0.05). Blood-pool contrast-enhanced MRA with SS sequences allow improved diagnostic evaluation of the degree of carotid stenosis and plaque morphology compared with FP and is substantially equal to CTA and DSA.

  11. Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.).

    Science.gov (United States)

    Ha, Jungmin; Abernathy, Brian; Nelson, William; Grant, David; Wu, Xiaolei; Nguyen, Henry T; Stacey, Gary; Yu, Yeisoo; Wing, Rod A; Shoemaker, Randy C; Jackson, Scott A

    2012-03-01

    Soybean is a model for the legume research community because of its importance as a crop, densely populated genetic maps, and the availability of a genome sequence. Even though a whole-genome shotgun sequence and bacterial artificial chromosome (BAC) libraries are available, a high-resolution, chromosome-based physical map linked to the sequence assemblies is still needed for whole-genome alignments and to facilitate map-based gene cloning. Three independent G. max BAC libraries combined with genetic and gene-based markers were used to construct a minimum tiling path (MTP) of BAC clones. A total of 107,214 clones were assembled into 1355 FPC (FingerPrinted Contigs) contigs, incorporating 4628 markers and aligned to the G. max reference genome sequence using BAC end-sequence information. Four different MTPs were made for G. max that covered from 92.6% to 95.0% of the soybean draft genome sequence (gmax1.01). Because our purpose was to pick the most reliable and complete MTP, and not the MTP with the minimal number of clones, the FPC map and draft sequence were integrated and clones with unpaired BES were added to build a high-quality physical map with the fewest gaps possible (http://soybase.org). A physical map was also constructed for the undomesticated ancestor (G. soja) of soybean to explore genome variation between G. max and G. soja. 66,028 G. soja clones were assembled into 1053 FPC contigs covering approximately 547 Mbp of the G. max genome sequence. These physical maps for G. max and its undomesticated ancestor, G. soja, will serve as a framework for ordering sequence fragments, comparative genomics, cloning genes, and evolutionary analyses of legume genomes.

  12. A Comprehensive Transcriptome Assembly of Pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing Platforms

    Science.gov (United States)

    Kudapa, Himabindu; Bharti, Arvind K.; Cannon, Steven B.; Farmer, Andrew D.; Mulaosmanovic, Benjamin; Kramer, Robin; Bohra, Abhishek; Weeks, Nathan T.; Crow, John A.; Tuteja, Reetu; Shah, Trushar; Dutta, Sutapa; Gupta, Deepak K.; Singh, Archana; Gaikwad, Kishor; Sharma, Tilak R.; May, Gregory D.; Singh, Nagendra K.; Varshney, Rajeev K.

    2012-01-01

    A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript assembly contigs (TACs) with an N50 of 1510 bp, the largest one being ∼8 kb. Of the 21 434 TACs, 16 622 (77.5%) could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions (ISRs). By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping positions at the chromosome level were predicted for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of eight genotypes. While 116 markers were validated, 70 markers showed one to three alleles, with an average of 0.16 polymorphism information content (PIC) value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea. PMID:22241453

  13. A Comprehensive Transcriptome Assembly of Pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing Platforms

    Institute of Scientific and Technical Information of China (English)

    Himabindu Kudapa; Reetu Tuteja; Trushar Shah; Sutapa Dutta; Deepak K.Gupta; Archana Singh; Kishor Gaikwad; Tilak R.Sharma; Gregory D.May; Nagendra K.Singh; Rajeev K.Varshney; Arvind K.Bharti; Steven B.Cannon; Andrew D.Farmer; Benjamin Mulaosmanovic; Robin Kramer; Abhishek Bohra; Nathan T.Weeks; John A.Crow

    2012-01-01

    A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA Ⅱx single end reads,2.19 million single end FLX/454 reads,and 18353 Sanger expressed sequenced tags from more than 16 genotypes.The resultant transcriptome assembly,referred to as CcTA v2,comprised 21434 transcript assembly contigs (TACs) with an N50 of 1510 bp,the largest one being ~8 kb.Of the 21434 TACs,16622 (77.5%) could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters.Based on knowledge of intron junctions,10009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions (ISRs).By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference,putative mapping positions at the chromosome level were predicted for 6284 ISR markers,covering all 11 pigeonpea chromosomes.A subset of 128 ISR markers were analyzed on a set of eight genotypes.While 116 markers were validated,70 markers showed one to three alleles,with an average of 0.16 polymorphism information content (PIC) value.In summary,the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.

  14. 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

  15. 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.

  16. 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.

  17. SEQUENCE ANALYSIS AND PRELIMINARY IDENTIFICATION OF MOLECULES WITH EF-HAND DOMAIN OF SCHISTOSOMA JAPONICUM%日本血吸虫含EF手性结构域分子序列的分析和初步鉴定

    Institute of Scientific and Technical Information of China (English)

    张艳丽; 贾侃; 李莹; 苑纯秀; 杨健美; 林矫矫; 冯新港

    2011-01-01

    为分离鉴定日本血吸虫含EF手性结构域分子及分析其序列结构特征,首先找到含有EF—hand结构域的分子,按照序列一级结构进行分类,之后进行生物信息学分析。然后用PCR方法以虫卵和成虫cDNA文库为模板扩增分类后的分子,构建重组质粒,诱导蛋白表达并纯化,选取14个纯化蛋白用Western blot进行初步免疫原性鉴定。结果269个原始含EF-hand结构域分子按照序列一级结构分为70个;成功表达和纯化了49个含EF手性分子,进化树分析将其分为9类;Western blot显示,14个纯化蛋白均可被日本血吸虫感染小鼠阳性血清识别。本研究结果为下一步采用这类分子进行动物保护性效果评价以及保护性免疫机制的研究奠定了基础。%To isolate and identify the molecules with EF-hand domain of Schistosoma japonicum and analyse the sequence structural characteristics of them, the molecules with EF-hand domain were firstly found and classified according to the primary structure, and then analyzed by bioinformatics. PCR was used to amplify the classified molecules with the S.japonicum adult and egg cDNA library. The recombinant plasmids were constructed and the protein with EF-hand domain were expressed and purified. Western blot was used to identify the preliminary immunogenicity of 14 purified proteins. Two hundred and sixty nine original molecules with EF-hand domain were divided into 70 molecules. Forty nine molecules with EF-hand domain were expressed and divided into 9 categories by phylogenetic tree. Western blot analysis showed that 14 purified proteins were specifically recognized by the positive serum from mice infected with S.japonicum. The study provided the basis for further study of immune protection of the molecules.

  18. 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.

  19. 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.

  20. A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing.

    Science.gov (United States)

    Khorasani, Maryam Zadeh; Hennig, Steffen; Imre, Gabriele; Asakawa, Shuichi; Palczewski, Stefanie; Berger, Anja; Hori, Hiroshi; Naruse, Kiyoshi; Mitani, Hiroshi; Shima, Akihiro; Lehrach, Hans; Wittbrodt, Jochen; Kondoh, Hisato; Shimizu, Nobuyoshi; Himmelbauer, Heinz

    2004-07-01

    In order to realize the full potential of the medaka as a model system for developmental biology and genetics, characterized genomic resources need to be established, culminating in the sequence of the medaka genome. To facilitate the map-based cloning of genes underlying induced mutations and to provide templates for clone-based genomic sequencing, we have created a first-generation physical map of the medaka genome in bacterial artificial chromosome (BAC) clones. In particular, we exploited the synteny to the closely related genome of the pufferfish, Takifugu rubripes, by marker content mapping. As a first step, we clustered 103,144 public medaka EST sequences to obtain a set of 21,121 non-redundant sequence entities. Avoiding oversampling of gene-dense regions, 11,254 of EST clusters were successfully matched against the draft sequence of the fugu genome, and 2363 genes were selected for the BAC map project. We designed 35mer oligonucleotide probes from the selected genes and hybridized them against 64,500 BAC clones of strains Cab and Hd-rR, representing 14-fold coverage of the medaka genome. Our data set is further supplemented with 437 results generated from PCR-amplified inserts of medaka cDNA clones and BAC end-fragment markers. Our current, edited, first generation medaka BAC map consists of 902 map segments that cover about 74% of the medaka genome. The map contains 2721 markers. Of these, 2534 are from expressed sequences, equivalent to a non-redundant set of 2328 loci. The 934 markers (724 different) are anchored to the medaka genetic map. Thus, genetic map assignments provide immediate access to underlying clones and contigs, simplifying molecular access to candidate gene regions and their characterization.

  1. Using the Amatrice (Italy) seismic sequence we asses the soil-structure in the case of San Giovanni Battista church (A.D. 1039) in Acquasanta Terme town. We tried to figure out how the input seismic energy is distributed over the different monument parts. Some preliminary results are shown and discussed.

    Science.gov (United States)

    Caserta, A.; Doumaz, F.; Costanzo, A.; Buongiorno, M. F.

    2016-12-01

    We used the moderate-magnitude aftershocks succeeding to the 2016 August 24th, Mw = 6.0, Amatrice (Italy) mainshok to asses, specially during an ongoing seismic sequence, the soil-structure interaction where cultural Heritage is involved. We have chosen as case study the San Giovanni Battista church (A.D. 1039) in Acquasanta Terme town, about 20 Km northeast of Amatrice. First of all we studied the soil shaking features in order to characterize the input to the monument. Then, using the recordings in the church, we tried to figure out how the input seismic energy is distributed over the different monument parts. Some preliminary results are shown and discussed.

  2. Complexity of genome evolution by segmental rearrangement in Brassica rapa revealed by sequence-level analysis

    Directory of Open Access Journals (Sweden)

    Paterson Andrew H

    2009-11-01

    Full Text Available Abstract Background The Brassica species, related to Arabidopsis thaliana, include an important group of crops and represent an excellent system for studying the evolutionary consequences of polyploidy. Previous studies have led to a proposed structure for an ancestral karyotype and models for the evolution of the B. rapa genome by triplication and segmental rearrangement, but these have not been validated at the sequence level. Results We developed computational tools to analyse the public collection of B. rapa BAC end sequence, in order to identify candidates for representing collinearity discontinuities between the genomes of B. rapa and A. thaliana. For each putative discontinuity, one of the BACs was sequenced and analysed for collinearity with the genome of A. thaliana. Additional BAC clones were identified and sequenced as part of ongoing efforts to sequence four chromosomes of B. rapa. Strikingly few of the 19 inter-chromosomal rearrangements corresponded to the set of collinearity discontinuities anticipated on the basis of previous studies. Our analyses revealed numerous instances of newly detected collinearity blocks. For B. rapa linkage group A8, we were able to develop a model for the derivation of the chromosome from the ancestral karyotype. We were also able to identify a rearrangement event in the ancestor of B. rapa that was not shared with the ancestor of A. thaliana, and is represented in triplicate in the B. rapa genome. In addition to inter-chromosomal rearrangements, we identified and analysed 32 BACs containing the end points of segmental inversion events. Conclusion Our results show that previous studies of segmental collinearity between the A. thaliana, Brassica and ancestral karyotype genomes, although very useful, represent over-simplifications of their true relationships. The presence of numerous cryptic collinear genome segments and the frequent occurrence of segmental inversions mean that inference of the positions

  3. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  4. 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...

  5. Modified Genetic Algorithm for DNA Sequence Assembly by Shotgun and Hybridization Sequencing Techniques

    Directory of Open Access Journals (Sweden)

    Prof.Narayan Kumar Sahu

    2012-09-01

    Full Text Available Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion of pair wise fragment overlap. While shotgun sequencing infers a DNA sequence given the sequences of overlapping fragments, a recent and complementary method, called sequencing by hybridization (SBH, infers a DNA sequence given the set of oligomers that represents all sub words of some fixed length, k. In this paper, we propose a new computer algorithm for DNA sequence assembly that combines in a novel way the techniques of both shotgun and SBH methods. Based on our preliminary investigations, the algorithm promises- to be very fast and practical for DNA sequence assembly [1].

  6. 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...

  7. Sequencing of 6.7 Mb of the melon genome using a BAC pooling strategy

    Directory of Open Access Journals (Sweden)

    Garcia-Mas Jordi

    2010-11-01

    allowed us to gain further insight into characteristics of the melon genome such as gene density, average protein length, or microsatellite and transposon content. The annotation of the BAC sequences revealed a high degree of collinearity and protein sequence identity between melon and its close relative Cucumis sativus (cucumber. Transposon content analysis of the syntenic regions suggests that transposition activity after the split of both cucurbit species has been low in cucumber but very high in melon. Conclusions The results presented here show that the strategy followed, which combines shotgun and BAC-end sequencing together with anchored marker information, is an excellent method for sequencing specific genomic regions, especially from relatively compact genomes such as that of melon. However, in agreement with other results, this map-based, BAC approach is confirmed to be an expensive way of sequencing a whole plant genome. Our results also provide a partial description of the melon genome's structure. Namely, our analysis shows that the melon genome is highly collinear with the smaller one of cucumber, the size difference being mainly due to the expansion of intergenic regions and proliferation of transposable elements.

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

    Science.gov (United States)

    Poulsen, T S; Silahtaroglu, A N; Gisselø, C G; Gaarsdal, E; Rasmussen, T; Tommerup, N; Johnsen, H E

    2001-11-01

    Translocation involving the immunoglobulin heavy chain (IGH) locus is a recurring event in B-cell oncogenesis. The aim of this study was to characterize clones from bacterial artificial chromosome (BAC) libraries and/or bacteriophage P1 artificial chromosome libraries spanning the IGH locus for detection of illegitimate rearrangement within the region by fluorescence in situ hybridization (FISH). In silico analysis of the IGH variable (IGHV) DNA sequence (NT_001716.v1) was performed to identify BAC probes located within the IGHV cluster. Clones of the constant (IGHC) cluster were found 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 cluster, which, together with probes covering the IGHC cluster (11771 and 998D24), could be used in interphase nuclei and metaphase chromosome analysis. A visual split of the IGHV and IGHC clusters indicating a translocation was analyzed by dual-color FISH in a series of 21 cell lines of different origins. Translocations were found, as expected, in eight of eight myelomas, four of four lymphomas, none of five leukemias, and none of four Epstein-Barr virus-transformed B-lymphoblastoid cell lines. To summarize, we have established a set of IGHV and IGHC probes that can be used for universal screening of illegitimate rearrangement within the IGH locus in B-cell malignancies. These probes allow for routine FISH analysis to detect this early central oncogenic event. Copyright 2001 Wiley-Liss, Inc.

  9. Probabilistic motor sequence yields greater offline and less online learning than fixed sequence

    Directory of Open Access Journals (Sweden)

    Yue eDu

    2016-03-01

    Full Text Available 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 of the presence of a sequence. The sequence and instruction types were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge or declarative (fixed sequence; with preliminary knowledge memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a two-minute 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 preliminary knowledge 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 preliminary knowledge, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of preliminary knowledge, 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

  10. Maternal inheritance of mitochondrial DNA (mtDNA) in the Pacific oyster (Crassostrea gigas): a preliminary study using mtDNA sequence analysis with evidence of random distribution of MitoTracker-stained sperm mitochondria in fertilized eggs.

    Science.gov (United States)

    Obata, Mayu; Shimizu, Michiyo; Sano, Natsumi; Komaru, Akira

    2008-03-01

    In many bivalve species, paternal and maternal mitochondrial DNA (mtDNA) from sperm and eggs is transmitted to the offspring. This phenomenon is known as doubly uniparental inheritance (DUI). In these species, sperm mtDNA (M type) is inherited by the male gonad of the offspring. Egg mtDNA (F type) is inherited by both male and female somatic cells and female gonadal cells. In Mytilidae, sperm mitochondria are distributed in the cytoplasm of differentiating male germ cells because they are transmitted to the male gonad. In the present study, we investigated maternal inheritance of mtDNA in the Pacific oyster, Crassostrea gigas. Sequence analysis of two mitochondrial non-coding regions revealed an identical sequence pattern in the gametes and adductor muscle samples taken from six males and five females. To observe whether sperm mitochondria were specifically located in the cytoplasm of differentiating germ cells, their distribution was recorded in C. gigas fertilized eggs by vital staining with MitoTracker Green. Although the 1D blastomere was identified in the cytoplasm of differentiating germ cells, sperm mitochondria were located at the 1D blastomere in only 32% of eggs during the 8-cell stage. Thus, in C. gigas, sperm mitochondria do not specifically locate in the germ cell region at the 1D blastomere. We suggest that the distribution of sperm mitochondria is not associated with germ cell formation in C. gigas. Furthermore, as evidenced by the mtDNA sequences of two non-coding regions, we conclude that mitochondrial DNA is maternally inherited in this species.

  11. 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...

  12. 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

  13. Identification of Potential Key Long Non-Coding RNAs and Target Genes Associated with Pneumonia Using Long Non-Coding RNA Sequencing (lncRNA-Seq): A Preliminary Study

    Science.gov (United States)

    Huang, Sai; Feng, Cong; Chen, Li; Huang, Zhi; Zhou, Xuan; Li, Bei; Wang, Li-li; Chen, Wei; Lv, Fa-qin; Li, Tan-shi

    2016-01-01

    Background This study aimed to identify the potential key long non-coding RNAs (lncRNAs) and target genes associated with pneumonia using lncRNA sequencing (lncRNA-seq). Material/Methods A total of 9 peripheral blood samples from patients with mild pneumonia (n=3) and severe pneumonia (n=3), as well as volunteers without pneumonia (n=3), were received for lncRNA-seq. Based on the sequencing data, differentially expressed lncRNAs (DE-lncRNAs) were identified by the limma package. After the functional enrichment analysis, target genes of DE-lncRNAs were predicted, and the regulatory network was constructed. Results In total, 99 DE-lncRNAs (14 upregulated and 85 downregulated ones) were identified in the mild pneumonia group and 85 (72 upregulated and 13 downregulated ones) in the severe pneumonia group, compared with the control group. Among these DE-lncRNAs, 9 lncRNAs were upregulated in both the mild and severe pneumonia groups. A set of 868 genes were predicted to be targeted by these 9 DE-lncRNAs. In the network, RP11-248E9.5 and RP11-456D7.1 targeted the majority of genes. RP11-248E9.5 regulated several genes together with CTD-2300H10.2, such as QRFP and EPS8. Both upregulated RP11-456D7.1 and RP11-96C23.9 regulated several genes, such as PDK2. RP11-456D7.1 also positively regulated CCL21. Conclusions These novel lncRNAs and their target genes may be closely associated with the progression of pneumonia. PMID:27663962

  14. Dna Sequencing

    Science.gov (United States)

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  15. ISSR-PCR技术在对虾中的应用初步研究%Preliminary study on the application of inter-simple sequence repeats (ISSR)-PCR technique in Chinese shrimp (Fenneropenaeus chinensis)

    Institute of Scientific and Technical Information of China (English)

    王伟继; 孔杰

    2002-01-01

    采用ISSR(Inter Simple Sequence Repeats)技术对中国对虾(Penaeus chinensis)进行了PCR扩增.优化了PCR反应体系和反应参数,对PCR产物进行聚丙烯酰胺凝胶电泳和银染检测.从100条ISSR引物中筛选了40条有清晰产物的引物,每条引物检测到的位点数从1到19不等,平均每条引物可检测到位点数为7.7个.实验发现:中国对虾简单重复序列区主要由两碱基循环组成.通过分析ISSR-PCR技术本身的原理,探讨了该技术相对于同工酶检测和RAPD技术在遗传多样性分析中的优势所在,以及该技术用于遗传标识的确认和遗传图谱构建方面的前景.

  16. 2016 TRI Preliminary Dataset

    Science.gov (United States)

    The TRI preliminary dataset includes the most current TRI data available and reflects toxic chemical releases and pollution prevention activities that occurred at TRI facilities during the 2016 calendar year.

  17. Lesion detection value of Cine sequence in the small intestinal Crohn’s disease:a preliminary study%MR 电影成像对小肠克罗恩病变的检出价值

    Institute of Scientific and Technical Information of China (English)

    徐慧新; 刘伟; 刘希胜; 俞同福; 唐立钧; 徐青

    2015-01-01

    Objective To evaluate the detection rate of lesions of patients with Crohn’s Disease(CD)tusing combining the con-ventional MR and Cine MRE(MR enterography).Methods MRI images of twenty-nine patients with CD confirmed by clinic were analyzed retrospectively.Scan sequences include coronal Cine MRE,and standard MR protocol (FIESTA,SS-FSE,LAVA C+). Two radiologists analyzed the images with double blind method to explored whether there were significant differences existing be-tween having or having not Cine MRE on lesion detection rate (wall thickness,stenosis,comb sign,adhesions,fistulas).Results The number of lesions detected by standard MR combined with Cine MRE compared with standard MR alone were 82/80 (P =0.1 6) for wall thickening,52/43 (P =0.03)for stenosis,6/7 (P =0.36)for the comb sign,5/7(P =0.66)for adhesions,2/2for fistulas re-spectivily.Conclusion It is meaningless to combine Cine MRE with standard MR in lesions detection in patients with CD,Cine ima-ges can accurately determine diseased bowel stenosis,and show the adhesive location.On the basis of standard MR,Cine MRE can be added in patients with CD when necessary.%目的:评价常规小肠 MR 结合 MR 电影动态成像(Cine MRE)能否提高小肠克罗恩病(CD)相关病变的检出率。方法回顾性分析29例经临床证实的 CD 患者的 MRI 资料,扫描序列包括 FIESTA、SS-FSE、LAVA C+等常规静态小肠 MR 序列以及Cine MRE 序列。由2名影像科医生对图像进行双盲法分析,对比有或无 Cine MRE 对于 CD 相关病变(包括肠壁增厚、肠腔狭窄、梳状征、粘连及瘘管)的检出数量有无显著差别。结果单独常规 MR 及增加 Cine MRE 后的病变检出数量分别为:肠壁增厚节段82/80,无统计学差异(P >0.05);肠腔狭窄52/43,有统计学差异(P 0.05);粘连5/7,无统计学差异(P >0.05);瘘管2/2。结论Cine MRE 对于 CD 相关肠壁增厚、梳状征、粘连及瘘管诊断的意义不大,但其能较准确判断病

  18. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_seq...uence_db.fasta.zip kome_ine_full_sequence_db.zip kome_ine_full_sequence_db ...

  19. 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...

  20. 16 CFR 1610.7 - Test sequence and classification criteria.

    Science.gov (United States)

    2010-01-01

    ... REGULATIONS STANDARD FOR THE FLAMMABILITY OF CLOTHING TEXTILES The Standard § 1610.7 Test sequence and... classification. (b) Test sequence and classification criteria. (1) Step 1, Plain Surface Textile Fabrics in the... Textile Fabrics after refurbishing in accordance with § 1610.6(b)(1). (i) Conduct preliminary tests...

  1. 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

  2. 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...

  3. On Preliminary Breakdown

    Science.gov (United States)

    Beasley, W. H.; Petersen, D.

    2013-12-01

    The preliminary breakdown phase of a negative cloud-to-ground lightning flash was observed in detail. Observations were made with a Photron SA1.1 high-speed video camera operating at 9,000 frames per second, fast optical sensors, a flat-plate electric field antenna covering the SLF to MF band, and VHF and UHF radio receivers with bandwidths of 20 MHz. Bright stepwise extensions of a negative leader were observed at an altitude of 8 km during the first few milliseconds of the flash, and were coincident with bipolar electric field pulses called 'characteristic pulses'. The 2-D step lengths of the preliminary processes were in excess of 100 meters, with some 2-D step lengths in excess of 200 meters. Smaller and shorter unipolar electric field pulses were superposed onto the bipolar electric field pulses, and were coincident with VHF and UHF radio pulses. After a few milliseconds, the emerging negative stepped leader system showed a marked decrease in luminosity, step length, and propagation velocity. Details of these events will be discussed, including the possibility that the preliminary breakdown phase consists not of a single developing lightning leader system, but of multiple smaller lightning leader systems that eventually join together into a single system.

  4. 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.

  5. 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.

  6. 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.

  7. Classifying Genomic Sequences by Sequence Feature Analysis

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hua Liu; Dian Jiao; Xiao Sun

    2005-01-01

    Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream,exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.

  8. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_seq...uence_amino_db.fasta.zip kome_ine_full_sequence_amino_db.zip kome_ine_full_sequence_amino_db ...

  9. 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.

  10. 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...

  11. A Preliminary Jupiter Model

    CERN Document Server

    Hubbard, W 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...

  12. A Preliminary Jupiter Model

    Science.gov (United States)

    Hubbard, W. B.; Militzer, B.

    2016-03-01

    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.

  13. Tree STEM Reconstruction Using Vertical Fisheye Images: a Preliminary Study

    Science.gov (United States)

    Berveglieri, A.; Tommaselli, A. M. G.

    2016-06-01

    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.

  14. 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.

  15. Thermal energy storage in aquifiers: preliminary information

    Energy Technology Data Exchange (ETDEWEB)

    Allen, R.D.

    1979-12-01

    Topics discussed include: conceptual designs; numerical modelling; field experiments; relevant technical information; feasibility studies; preliminary aquifer selection considerations; and preliminary design and operating considerations. (TFD)

  16. 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...

  17. 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.

  18. Coordinate cytokine regulatory sequences

    Science.gov (United States)

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  19. 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.

  20. The Preliminaries of a Reference

    DEFF Research Database (Denmark)

    Butler, Graham; Sadl, Urska

    2017-01-01

    by the reasons why the Court after an oral hearing held in the presence of the parties and eight intervening Member States, and after hearing the Advocate General did not deliver one. The comment examines the legal framework, as well as the detailed procedural rules and guidelines that govern the cooperation...... of national courts in the preliminary reference procedure. It highlights the fact that preliminary references can only work when the preliminaries of a reference – the culture of sincere cooperation and litigation, efficient communication and flexible procedural rules – are in place....

  1. 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.

  2. Preliminary reference Earth model

    Science.gov (United States)

    Dziewonski, Adam M.; Anderson, Don L.

    1981-06-01

    A large data set consisting of about 1000 normal mode periods, 500 summary travel time observations, 100 normal mode Q values, mass and moment of inertia have been inverted to obtain the radial distribution of elastic properties, Q values and density in the Earth's interior. The data set was supplemented with a special study of 12 years of ISC phase data which yielded an additional 1.75 × 10 6 travel time observations for P and S waves. In order to obtain satisfactory agreement with the entire data set we were required to take into account anelastic dispersion. The introduction of transverse isotropy into the outer 220 km of the mantle was required in order to satisfy the shorter period fundamental toroidal and spheroidal modes. This anisotropy also improved the fit of the larger data set. The horizontal and vertical velocities in the upper mantle differ by 2-4%, both for P and S waves. The mantle below 220 km is not required to be anisotropic. Mantle Rayleigh waves are surprisingly sensitive to compressional velocity in the upper mantle. High S n velocities, low P n velocities and a pronounced low-velocity zone are features of most global inversion models that are suppressed when anisotropy is allowed for in the inversion. The Preliminary Reference Earth Model, PREM, and auxiliary tables showing fits to the data are presented.

  3. Arapahoe NWR diversion reconstruction : Preliminary

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is a preliminary plan for a diversion reconstruction for Hubbard #2. Oklahoma #1, Dryer, Hill and Crowder sites on the Arapahoe National Wildlife Refuge.

  4. Genome-scale validation of deep-sequencing libraries.

    Directory of Open Access Journals (Sweden)

    Dominic Schmidt

    Full Text Available Chromatin immunoprecipitation followed by high-throughput (HTP sequencing (ChIP-seq is a powerful tool to establish protein-DNA interactions genome-wide. The primary limitation of its broad application at present is the often-limited access to sequencers. Here we report a protocol, Mab-seq, that generates genome-scale quality evaluations for nucleic acid libraries intended for deep-sequencing. We show how commercially available genomic microarrays can be used to maximize the efficiency of library creation and quickly generate reliable preliminary data on a chromosomal scale in advance of deep sequencing. We also exploit this technique to compare enriched regions identified using microarrays with those identified by sequencing, demonstrating that they agree on a core set of clearly identified enriched regions, while characterizing the additional enriched regions identifiable using HTP sequencing.

  5. 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.

  6. PRELIMINARY SELECTION OF MGR DESIGN BASIS EVENTS

    Energy Technology Data Exchange (ETDEWEB)

    J.A. Kappes

    1999-09-16

    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&O 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).

  7. Contamination of sequence databases with adaptor sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D. [National Institute of Mental Health, Bethesda, MD (United States)

    1997-02-01

    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  8. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.

    1999-04-25

    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  9. 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...

  10. 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.

  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. 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.

  13. 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....

  14. Enhanced virome sequencing using targeted sequence capture.

    Science.gov (United States)

    Wylie, Todd N; Wylie, Kristine M; Herter, Brandi N; Storch, Gregory A

    2015-12-01

    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

  15. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.

    1987-10-27

    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  16. Low autocorrelation binary sequences

    Science.gov (United States)

    Packebusch, Tom; Mertens, Stephan

    2016-04-01

    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  17. Repdigits in -Lucas Sequences

    Indian Academy of Sciences (India)

    Jhon J J Bravo; Florian Luca

    2014-05-01

    For an integer ≥ 2, let $(L_n^{(k)})_n$ be the -Lucas sequence which starts with $0,\\ldots,0,2,1$ ( terms) and each term afterwards is the sum of the preceding terms. In 2000, Luca (Port. Math. 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 and occur in formulae simultaneously with the latter.

  18. On Maximal Green Sequences

    CERN Document Server

    Brüstle, Thomas; Pérotin, Matthieu

    2012-01-01

    Maximal green sequences are particular sequences of quiver mutations which were introduced by Keller in the context of quantum dilogarithm identities and independently by Cecotti-Cordova-Vafa in the context of supersymmetric gauge theory. Our aim is to initiate a systematic study of these sequences from a combinatorial point of view. Interpreting maximal green sequences as paths in various natural posets arising in representation theory, we prove the finiteness of the number of maximal green sequences for cluster finite quivers, affine quivers and acyclic quivers with at most three vertices. We also give results concerning the possible numbers and lengths of these maximal green sequences. Finally we describe an algorithm for computing maximal green sequences for arbitrary valued quivers which we used to obtain numerous explicit examples that we present.

  19. THE EFFECTS OF PRELIMINARY RULINGS

    Directory of Open Access Journals (Sweden)

    Iuliana-Mădălina LARION

    2015-07-01

    Full Text Available The study analyses the effects of the preliminary rulings rendered by the Court of Justice for the judicial body that made the reference and for other bodies dealing with similar cases, for the member states, for the European Union’ s institutions and for EU legal order. Starting from the binding effect of the preliminary judgment for national judicial bodies, which requires them to follow the ruling or make a new reference, to the lack of precedent doctrine in EU law, continuing with the possibility to indirectly verify the compatibility of national law of the member states with EU law and ending with the administrative or legislative measures that can or must be taken by the member states, the study intends to highlight the limits, nuances and consequences of the binding effect. It mentions the contribution of the national courts and of the Court of Justice of the European Union to the development of EU law, such as clarifying autonomous notions and it emphasizes the preliminary procedure's attributes of being a form of judicial protection of individual rights, as well as a means to review the legality of acts of EU institutions. The paper is meant to be a useful instrument for practitioners. Therefor, it also deals with the possibility and limits of asking new questions, in order to obtain reconsideration or a refinement of the legal issue and with the problem of judicial control over the interpretation and application of the preliminary ruling by the lower court.

  20. 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...

  1. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    the feasibility of predicting the fetal KEL1 phenotype using next-generation sequencing (NGS) technology. STUDY DESIGN AND METHODS: The KEL1/2 single-nucleotide polymorphism was polymerase chain reaction (PCR) amplified with one adjoining base, and the PCR product was sequenced using a genome analyzer (GAIIx......, 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...

  2. Processing Aftershock Sequences Using Waveform Correlation

    Science.gov (United States)

    Resor, M. E.; Procopio, M. J.; Young, C. J.; Carr, D. B.

    2008-12-01

    months following the mainshock, and only 265 events during the same period for the previous year, so this sequence represents a formidable challenge for any automatic processing system. Preliminary results suggest that a waveform correlation-based system can detect on the order of 10% or more of the aftershocks for this event. Results published in the recent literature suggest that significantly larger proportions may be achievable for other aftershock sequences with smaller fault ruptures; we investigate and report encouraging results from one such sequence. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under Contract DE-AC04- 94AL85000.

  3. PRELIMINARY ANALYSIS OF ESTS (EXPRESSED SEQUENCE TAGS) FROM LIVE AND KINEY OF HALIOTIS DISCUS HANNAI AND CLONING OF NPY(NEUROPEPTIDE Y) RECEPTOR GENE%皱纹盘鲍肝、肾表达序列标签及神经肽Y(NPY)受体基因的克隆与分析

    Institute of Scientific and Technical Information of China (English)

    郑明刚; 毕元兑; 王玲; 孙修勤; 刘峰; 王波

    2011-01-01

    通过构建皱纹盘鲍(Haliotis discus Hannai)cDNA文库并进行大规模测序,获得了1282条高质量的ESTs序列,对这些序列进行拼接,获得了包括650条序列在内的244组片段重叠群(Contigs)和632个单一序列(Singletons).使用BlastX软件对876个Unigenes(Unigerie为Coiltig和Singleton的总和)进行同源性对比,有393个获得了功能提示,占总基因数的45%.根据EST信息,采用RACE方法.首次得到皱纹盘鲍神经肤Y(neuropeptide Y,NPY)受体基因,并对其结构进行了分析.结果表明,该受体基因cDNA由1534个核苷酸组成,编码区1050bp,可以编码350个氨基酸;该多肤的分子量为39.56kda,等电点为9.57,具有7个明显的跨膜螺旋且TM7区有NPXXY模体.%A cDNA library was constructed from liver and kidney of abalone (Haliotis discus Hannai) and 1445 clones were selected for sequencing. One thousand and two hundred eighty two high qualitative ESTs were obtained through bioinformatics analyses. Splicing of these sequences, 244 contigs (consisting of 650 sequences) and 632 singletons were obtained. Using BlastX program for the Homologous comparison, 393 unigenes shared signifi cant homology with known sequences in protein database of NCBI accounted for 45 % of the number of unigenes. Among that, 63 (16%) were immune-related. The full length of the NPY (neuropeptide Y) receptor cDNA was cloned through the 5'-RACE with the specific primers based on the sequence of the EST. The full length of NPY receptor cDNA from Haliotis discus hannai was 1534bp and encoded 350 amino acid. BLAST analysis revealed that the NPY receptor gene from Haliotis discus hannai shared high identity with the NPY receptor genes from other organisms in amino acid. This NPY receptor have a predicted molecular of 39.56 kDa and theoretical isoelectric point of 9.57, receptively.

  4. Hardware bitstream sequence recognizer

    OpenAIRE

    Karpin, Oleksandr; Sokil, Volodymyr

    2009-01-01

    This paper describes how to implement in hardware a bistream sequence recognizer using the PSoC Pseudo Random Sequence Generator (PRS) User Module. The PRS can be used in digital communication systems with the serial data interface for automatic preamble detection and extraction, control words selection, etc.

  5. Cosmetology: Scope and Sequence.

    Science.gov (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology 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. DNA sequencing by CE.

    Science.gov (United States)

    Karger, Barry L; Guttman, András

    2009-06-01

    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 multiCE 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 were only possible with the advent of modern sequencing technologies that were 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 breakneck 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 CE in DNA sequencing based in part of several of our articles in this journal.

  7. 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.

  8. 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).

  9. Sequencing the maize genome.

    Science.gov (United States)

    Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard

    2004-04-01

    Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.

  10. Dicty_cDB: Contig-U05675-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 799158 ) PPTI537TF Solanum tuberosum RHPOTKEY BAC ends Sol... 50 0.070 1 ( CU603906 ) Theobroma cacao, mRNA ...um berghei strain ANKA cDNA clone:MG01826... 44 4.3 1 ( CU595687 ) Theobroma cacao, mRNA sequence (KZ0AAF10Y

  11. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    OpenAIRE

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; AKIYAMA, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto seque...

  12. Cancer Genome Sequencing and Its Implications for Personalized Cancer Vaccines

    Energy Technology Data Exchange (ETDEWEB)

    Li, Lijin [Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110 (United States); Goedegebuure, Peter [Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110 (United States); The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO 63110 (United States); Mardis, Elaine R. [The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO 63110 (United States); The Genome Institute at Washington University School of Medicine, St. Louis, MO 63108 (United States); Ellis, Matthew J.C. [The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO 63110 (United States); Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 (United States); Zhang, Xiuli; Herndon, John M. [Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110 (United States); Fleming, Timothy P. [Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110 (United States); The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO 63110 (United States); Carreno, Beatriz M. [The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO 63110 (United States); Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 (United States); Hansen, Ted H. [The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO 63110 (United States); Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110 (United States); Gillanders, William E., E-mail: gillandersw@wudosis.wustl.edu [Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110 (United States); The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO 63110 (United States)

    2011-11-25

    New DNA sequencing platforms have revolutionized human genome sequencing. The dramatic advances in genome sequencing technologies predict that the $1,000 genome will become a reality within the next few years. Applied to cancer, the availability of cancer genome sequences permits real-time decision-making with the potential to affect diagnosis, prognosis, and treatment, and has opened the door towards personalized medicine. A promising strategy is the identification of mutated tumor antigens, and the design of personalized cancer vaccines. Supporting this notion are preliminary analyses of the epitope landscape in breast cancer suggesting that individual tumors express significant numbers of novel antigens to the immune system that can be specifically targeted through cancer vaccines.

  13. Cancer Genome Sequencing and Its Implications for Personalized Cancer Vaccines

    Directory of Open Access Journals (Sweden)

    William E. Gillanders

    2011-11-01

    Full Text Available New DNA sequencing platforms have revolutionized human genome sequencing. The dramatic advances in genome sequencing technologies predict that the $1,000 genome will become a reality within the next few years. Applied to cancer, the availability of cancer genome sequences permits real-time decision-making with the potential to affect diagnosis, prognosis, and treatment, and has opened the door towards personalized medicine. A promising strategy is the identification of mutated tumor antigens, and the design of personalized cancer vaccines. Supporting this notion are preliminary analyses of the epitope landscape in breast cancer suggesting that individual tumors express significant numbers of novel antigens to the immune system that can be specifically targeted through cancer vaccines.

  14. 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.

  15. 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.

  16. 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.

  17. 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...

  18. Scope and Sequence.

    Science.gov (United States)

    Callison, Daniel

    2002-01-01

    Discusses scope and sequence plans for curriculum coordination in elementary and secondary education related to school libraries. Highlights include library skills; levels of learning objectives; technology skills; media literacy skills; and information inquiry skills across disciplines by grade level. (LRW)

  19. Evolution of DNA sequencing

    National Research Council Canada - National Science Library

    Tipu, Hamid Nawaz; Shabbir, Ambreen

    2015-01-01

    Sanger and coworkers introduced DNA sequencing in 1970s for the first time. It principally relied on termination of growing nucleotide chain when a dideoxythymidine triphosphate (ddTTP) was inserted...

  20. Pierre Robin sequence

    Science.gov (United States)

    Pierre Robin syndrome; Pierre Robin complex; Pierre Robin anomaly ... The exact causes of Pierre Robin sequence are unknown. It may be part of many genetic syndromes. The lower jaw develops slowly before birth, but may grow ...

  1. In Favor of Sequencing?

    NARCIS (Netherlands)

    van der Borgh, G.J.C.

    2014-01-01

    This short article is a contribution to an online discussion about political sequencing and stability. It argues that despite all the risks of democratization in fragile states,a more gradual approach should be preferred.

  2. 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...

  3. Text Mining: (Asynchronous Sequences

    Directory of Open Access Journals (Sweden)

    Sheema Khan

    2014-12-01

    Full Text Available In this paper we tried to correlate text sequences those provides common topics for semantic clues. We propose a two step method for asynchronous text mining. Step one check for the common topics in the sequences and isolates these with their timestamps. Step two takes the topic and tries to give the timestamp of the text document. After multiple repetitions of step two, we could give optimum result.

  4. Malaria Genome Sequencing Project

    Science.gov (United States)

    2004-01-01

    million cases and up to 2.7 million A whole chromosome shotgun sequencing strategy was used to deaths from malaria each year. The mortality levels are...deaths from malaria each year. The mortality levels are greatest in determine the genome sequence of P. falciparum clone 3D7. This sub-Saharan Africa...aminolevulinic acid dehydratase. Cura . Genet. 40, 391-398 (2002). 15. Lasonder, E. et al Analysis of the Plasmodium falciparum proteome by high-accuracy mass

  5. 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......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...

  6. Genome sequencing conference II

    Energy Technology Data Exchange (ETDEWEB)

    1990-01-01

    Genome Sequencing Conference 2 was held September 30 to October 30, 1990. 26 speaker abstracts and 33 poster presentations were included in the program report. New and improved methods for DNA sequencing and genetic mapping were presented. Many of the papers were concerned with accuracy and speed of acquisition of data with computers and automation playing an increasing role. Individual papers have been processed separately for inclusion on the database.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Preliminary considerations concerning actinide solubilities

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. A Preliminary Screening and Characteristic Analysis of Microsatellite Markers from Transcriptome Sequences in Mugilogobius chulae%诸氏鲻虾虎鱼转录组序列中微卫星标记的初步筛选及特征分析

    Institute of Scientific and Technical Information of China (English)

    蔡磊; 余露军; 陈小曲; 叶惠欣; 陈琳; 李建军

    2015-01-01

    旨在为大规模开发诸氏鲻虾虎鱼微卫星标记,采用高通量测序技术,对诸氏鲻虾虎鱼肝脏转录组进行了测序。结果共获得47979条Unigenes,利用微卫星查找程序在47979条Unigenes中共获得6225个微卫星位点(12.97%),平均每7.02 kb就出现1个微卫星位点。6225个微卫星位点由226种重复基序组成,主要分布在三、四和五碱基重复类型中。在数量上,单碱基重复类型微卫星位点最多,占42.49%,二碱基和三碱基重复类型所占比例相似,分别为25.22%和26.27%,四、五、六重复类型较少,合计占6.03%。单碱基重复序列中最多的类型为A/T,二碱基重复序列中以AG/CT重复单元为主,三碱基重复序列中以AGC/TCG为优势类型。挑选部分二、三和四单元重复类型微卫星序列,共设计76对引物,可稳定扩增出目的条带的有55对,其中32对具有多态性。结果表明,利用诸氏鲻虾虎鱼转录组数据可快速大量开发微卫星标记。%In order to explore microsatellite markers in large-scale, the liver transcriptome of Mugilogobius chulae was sequenced by high-throughput sequencing technology. A total of 6 225(12.97%)microsatellite markers were screened from 47 979 Unigenes by microsatellite software, averagely 1 microsatellite marker in every 7.02 kb. The 6 225 microsatellite markers consisted of 226 repeat motifs, which mainly distributed in tri-nucleotide, quad-nucleotide and penta-nucleotide repeats. The mono-nucleotide repeats were of the most by number, accounting for 42.49% of all the microsatellite markers, the di-nucleotide repeats and tri-nucleotide repeats had the similar proportion(25.22% and 26.27%of all the markers, respectively), the rest were the quad-nucleotide, penta-nucleotide and hexa-nucleotide repeats, together accounting for 6.03%. A/T, AG/CT and AGC/TCG were the most frequent motifs in mono-nucleotide, di-nucleotide and tri-nucleotide repeats

  13. PCR-based Screening BAC Library and Direct End Sequencing of BAC Clones%PCR筛选BAC文库和直接BAC末端测序方法的建立

    Institute of Scientific and Technical Information of China (English)

    何聪芬; 小松田隆夫

    2004-01-01

    A PCR based strategy was developed which required four steps to identify positive BAC clones from barley BAC(bacterial artificial chromosome)library.In the protocol,two levels of BAC DNA pools(super-pool and pool)were prepared for analysis.One pool is made of one plate DNAs and one super-pool is made of mixing ten consecutive 1/100 diluted pool DNAs(1~10,11~20 ect).First,super-pool DNAs were analysed and then 10 pool DNAs contained in every positive super-pool were analysed.Once positive BAC plates were identified,the bacterial cultures were dipped into PCR mixtures and reaction is made to identify positive BAC clones.The BAC clones identified by each marker were grouped into contigs.BAC-end sequence was obtained from BACs within each contig and primers were designed for the next step chromosome walking.In case of the BAC ends belong to repetitive sequence,the primers were designed based on the subcloned unique band in the contig(identified by Hind III digestion pattern).This method allows us to construct the BAC contig without the costly and time-consuming efforts,and no radioactivity harmful to the body.%建立了一种用PCR方法筛选富含高度重复序列的大麦BAC DNA 文库和直接对 BAC DNA进行末端测序的方法.用PCR技术进行大麦BAC DNA 文库(含816个平板,每个平板含384个克隆)的筛选分4步进行.在实验中,建立了两个水平的BAC DNA池(一级池和二级池).一个二级池由一个平板(含有384个克隆)的DNA 组成,一个一级池由连续10个稀释100倍的二级池的DNA混合而成(如1~10,11~20等),共82个一级池.BAC DNA 文库筛选的第一步是对82个一级池的筛选.得到阳性一级池后(如2号一级池),对其所含的10个二级池(从11~20)进行第二步筛选.得到阳性二级池后,培养相应的阳性平板的所有克隆(384个),从头开始(左上侧),每相邻的4个克隆为一组,在96孔板上(4 X 96=384) 进行第三轮PCR反应;之后对筛选结果为阳性的4

  14. Preliminary Investigation of a Paraglider

    Science.gov (United States)

    Rogallo, Francis M.; Lowry, John G.; Croom, Delwin R.; Taylor, Robert T.

    1960-01-01

    A preliminary investigation of the aerodynamic and control characteristics of a flexible glider similar to a parachute in construction has been made at the Langley Research Center to evaluate its capabilities as a reentry glider. Preliminary weight estimates of the proposed vehicle indicate that such a structure can be made with extremely low wing loading. Maximum temperatures during the reentry maneuver might be held as low as about 1,500 F. The results of wind-tunnel and free-glide tests show that the glider when constructed of nonporous material performed extremely well at subsonic speeds and could be flown at angles of attack from about 200 to 900. At supersonic speeds the wing showed none of the unfavorable tendencies exhibited by conventional parachutes at these speeds, such as squidding and breathing. Several methods of packing and deploying the glider have been successfully demonstrated. The results of this study indicate that this flexible-lifting-surface concept may provide a lightweight controllable paraglider for manned space vehicles.

  15. Topaz II preliminary safety assessment

    Science.gov (United States)

    Marshall, Albert C.; Standley, Vaughn; Voss, Susan S.; Haskin, Eric

    1993-01-01

    The Strategic Defense Initiative Organization (SDIO) decided to investigate the possibility of launching a Russian Topaz II space nuclear power system. A preliminary safety assessment was conducted to determine whether or not a space mission could be conducted safely and within budget constraints. As part of this assessment, a safety policy and safety functional requirements were developed to guide both the safety assessment and future Topaz II activities. A review of the Russian flight safety program was conducted and documented. Our preliminary safety assessment included a top level event tree, neutronic analysis of normal and accident configurations, an evaluation of temperature coefficients of reactivity, a reentry and disposal analysis, and analysis of postulated launch abort impact accidents, and an analysis of postulated propellant fire and explosion accidents. Based on the assessment, it appears that it will be possible to safely launch the Topaz II system in the U.S. with some possible system modifications. The principal system modifications will probably include design changes to preclude water flooded criticality and to assure intact reentry.

  16. 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.

  17. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan

    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.

  18. Controlled processing during sequencing.

    Science.gov (United States)

    Thothathiri, Malathi; Rattinger, Michelle

    2015-01-01

    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region's activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  19. Controlled processing during sequencing

    Directory of Open Access Journals (Sweden)

    Malathi eThothathiri

    2015-10-01

    Full Text Available Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6 in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex (ACC. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  20. 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

  1. Program Synthesizes UML Sequence Diagrams

    Science.gov (United States)

    Barry, Matthew R.; Osborne, Richard N.

    2006-01-01

    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  2. 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.

  3. The Nature of Red-Sequence Cluster Spiral Galaxies

    Science.gov (United States)

    Kashur, Lane; Barkhouse, Wayne; Sultanova, Madina; Kalawila Vithanage, Sandanuwa; Archer, Haylee; Foote, Gregory; Mathew, Elijah; Rude, Cody; Lopez-Cruz, Omar

    2017-01-01

    Preliminary analysis of the red-sequence galaxy population from a sample of 57 low-redshift galaxy clusters observed using the KPNO 0.9m telescope and 74 clusters from the WINGS dataset, indicates that a small fraction of red-sequence galaxies have a morphology consistent with spiral systems. For spiral galaxies to acquire the color of elliptical/S0s at a similar luminosity, they must either have been stripped of their star-forming gas at an earlier epoch, or contain a larger than normal fraction of dust. To test these ideas we have compiled a sample of red-sequence spiral galaxies and examined their infrared properties as measured by 2MASS, WISE, Spitzer, and Herschel. These IR data allows us to estimate the amount of dust in each of our red-sequence spiral galaxies. We compare the estimated dust mass in each of these red-sequence late-type galaxies with spiral galaxies located in the same cluster field but having colors inconsistent with the red-sequence. We thus provide a statistical measure to discriminate between purely passive spiral galaxy evolution and dusty spirals to explain the presence of these late-type systems in cluster red-sequences.

  4. Sequencing BPS Spectra

    CERN Document Server

    Gukov, Sergei; Saberi, Ingmar; Stosic, Marko; Sulkowski, Piotr

    2015-01-01

    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 Poincar\\'e 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 identifi...

  5. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars

    2013-01-01

    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......, 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...

  6. 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...

  7. 33 CFR 116.10 - Preliminary review.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Preliminary review. 116.10... ALTERATION OF UNREASONABLY OBSTRUCTIVE BRIDGES § 116.10 Preliminary review. (a) Upon receipt of a written complaint, the District Commander will review the complaint to determine if, in the District...

  8. 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.

  9. 18 CFR 1b.6 - Preliminary investigations.

    Science.gov (United States)

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Preliminary investigations. 1b.6 Section 1b.6 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY GENERAL RULES RULES RELATING TO INVESTIGATIONS § 1b.6 Preliminary investigations....

  10. 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.

  11. 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.

  12. Family Sequencing and Cooperation

    NARCIS (Netherlands)

    Grundel, S.; Ciftci, B.B.; Borm, P.E.M.; Hamers, H.J.M.

    2012-01-01

    To analyze the allocation problem of the maximal cost savings of the whole group of jobs, we define and analyze a so-called corresponding cooperative family sequencing game which explicitly takes into account the maximal cost savings for any coalition of jobs. Using nonstandard techniques we prove t

  13. 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 Syst

  14. 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

  15. 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...

  16. 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.

  17. SLUDGE TREATMENT PROJECT ENGINEERED CONTAINER RETRIEVAL AND TRANSFER SYSTEM PRELIMINARY DESIGN HAZARD ANALYSIS SUPPLEMENT 1

    Energy Technology Data Exchange (ETDEWEB)

    FRANZ GR; MEICHLE RH

    2011-07-18

    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.

  18. Genetic Variation A mong European Lophodermium piceae Populations - Preliminary Results

    Directory of Open Access Journals (Sweden)

    MÜLLER, Michael M.

    2007-01-01

    Full Text Available Lophodermium piceae is a common needle endophyte of Norway spruce (Picea abies. The aim of the present study was to examine the degree of differentiation within and among European populations separated by various distances and geographical obstacles. For this purpose, populations (including > 10 isolates/subpopulation were collected along a north-south transect stretching from the northern timberline in Finnish Lapland to the southern border of the distribution area of Norway spruce in northern Italy. Differentiation between L. piceae populations was determined from DNA sequences of three genetic markers. One of the markers was the internal transcribed spacer (ITS of the ribosomal DNA and the other two (LP1 and LP2 were based on sequence characterized amplified regions (SCAR designed for L. piceae. Preliminary results including sequences of Finnish, Swiss and Italian isolates show low differentiation among populations. According to analysis of molecular variance the among population variation was 1%, 5% and 0% in ITS, LP1 and LP2 markers, respectively.

  19. 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.

  20. 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....

  1. Complete mitochondrial sequences from Mesolithic Sardinia

    Science.gov (United States)

    Modi, Alessandra; Tassi, Francesca; Susca, Roberta Rosa; Vai, Stefania; Rizzi, Ermanno; Bellis, Gianluca De; Lugliè, Carlo; Gonzalez Fortes, Gloria; Lari, Martina; Barbujani, Guido; Caramelli, David; Ghirotto, Silvia

    2017-01-01

    Little is known about the genetic prehistory of Sardinia because of the scarcity of pre-Neolithic human remains. From a genetic perspective, modern Sardinians are known as genetic outliers in Europe, showing unusually high levels of internal diversity and a close relationship to early European Neolithic farmers. However, how far this peculiar genetic structure extends and how it originated was to date impossible to test. Here we present the first and oldest complete mitochondrial sequences from Sardinia, dated back to 10,000 yBP. These two individuals, while confirming a Mesolithic occupation of the island, belong to rare mtDNA lineages, which have never been found before in Mesolithic samples and that are currently present at low frequencies not only in Sardinia, but in the whole Europe. Preliminary Approximate Bayesian Computations, restricted by biased reference samples for Mesolithic Sardinia (the two typed samples) and Neolithic Europe (limited to central and north European sequences), suggest that the first inhabitants of the island have had a small or negligible contribution to the present-day Sardinian population, which mainly derives its genetic diversity from continental migration into the island by Neolithic times. PMID:28256601

  2. Rapid-Sequence Intubation

    Directory of Open Access Journals (Sweden)

    Evangelina Dávila Cabo de Villa

    2015-09-01

    Full Text Available In medical practice there are several situations that require immediate intervention of the airway in some patients, in order to ensure proper entrance and exit of gases into and out of the lungs and prevent aspiration. Rapid-sequence intubation has been considered as the administration of a hypnotic agent and a neuromuscular relaxant consecutively (virtually simultaneously to facilitate orotracheal intubation in critically ill patients and minimize the risk of aspiration. This paper aims to collect elements that promote a successful medical management according to the situation presented, since there is no single way of proceeding in case of rapid-sequence intubation. The elements to consider include: knowing the anatomy of the upper respiratory tract, having a group of drugs to choose from, receiving adequate training and having an alternative plan for the difficulties that may arise.

  3. Sequence Classification: 885394 [

    Lifescience Database Archive (English)

    Full Text Available 703); The expression pattern of this gene is described in PMID:12000842; possible frameshift detected when compared...Non-TMB TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|23619146|ref|NP_705108.1| Slight di...fference exist when compared to the published sequence of EBL-1 from Dd2 strain of P. falciparum (PMID:10613

  4. Sequencing of aromatase inhibitors

    OpenAIRE

    2005-01-01

    Since the development of the third-generation aromatase inhibitors (AIs), anastrozole, letrozole and exemestane, these agents have been the subject of intensive research to determine their optimal use in advanced breast cancer. Not only have they replaced progestins in second-line therapy and challenged the role of tamoxifen in first-line, but there is also evidence for a lack of cross-resistance between the steroidal and nonsteroidal AIs, meaning that they may be used in sequence to obtain p...

  5. Properties of Semijoin Sequences

    Institute of Scientific and Technical Information of China (English)

    BengC.Ooi; B.Srinivasan

    1989-01-01

    The problem of finding optimum semijoin sequ4ence of an arbitrary query under linear cost function for the transmission cost is NP.hard.Hence heuristic algorithms with desirable properties are explored.In this paper four properties of semijoin programs for distributed query processing are identified,The use of these properties in constructing semijoin sequence is justified.An existing algorithm is modified incorporating these properties.Empirical comparison with existing algorithms shows the superiority of the proposed algorithm.

  6. Learning Sequence Neighbourhood Metrics

    CERN Document Server

    Bayer, Justin; van der Smagt, Patrick

    2011-01-01

    Recurrent neural networks (RNNs) in combination with a pooling operator and the neighbourhood components analysis (NCA) objective function are able to detect the characterizing dynamics of sequences and embed them into a fixed-length vector space of arbitrary dimensionality. Subsequently, the resulting features are meaningful and can be used for visualization or nearest neighbour classification in linear time. This kind of metric learning for sequential data enables the use of algorithms tailored towards fixed length vector spaces such as R^n.

  7. Sequencing BPS spectra

    Science.gov (United States)

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

    2016-03-01

    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.

  8. 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 ...

  9. The Galaxy End Sequence

    Science.gov (United States)

    Eales, Stephen; de Vis, Pieter; Smith, Matthew W. L.; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2017-03-01

    A common assumption is that galaxies fall in two distinct regions of a plot of specific star formation rate (SSFR) versus galaxy stellar mass: a star-forming galaxy main sequence (GMS) and a separate region of 'passive' or 'red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus representing the end-point of ≃12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the 'red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather than implying a distinct population of galaxies. Herschel observations, which show at least half of early-type galaxies contain a cool interstellar medium, also imply continuity between early-type and late-type galaxies. This picture of a unitary population of galaxies requires more gradual evolutionary processes than the rapid quenching process needed to explain two distinct populations. We challenge theorists to predict quantitatively the properties of this 'Galaxy End Sequence'.

  10. 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.

  11. Births: preliminary data for 2012.

    Science.gov (United States)

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

    2013-09-01

    Objectives-This report presents preliminary data for 2012 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 are also presented. Methods-Data in this report are based on 99.96% of 2012 births.Records for the few states with less than 100% of records received are weighted to independent control counts of all births received in state vital statistics offices in 2012. Comparisons are made with final 2011 data. Results-The preliminary number of births for the United States in 2012 was 3,952,937, essentially unchanged (not statistically significant) from 2011; the general fertility rate was 63.0 births per 1,000 women aged 15-44, down only slightly from 2011, after declining nearly 3% a year from 2007 through 2010. The number of births and fertility rate either declined or were unchanged for most race and Hispanic origin groups from 2011 to 2012; however, both the number of births and the fertility rate for Asian or Pacific Islander women rose in 2012 (7% and 4%, respectively). The birth rate for teenagers aged 15-19 was down 6% in 2012 (29.4 births per 1,000 teenagers aged 15-19), yet another historic low for the United States, with rates declining for younger and older teenagers and for nearly all race and Hispanic origin groups. The birth rate for women in their early 20s also declined in 2012, to a new record low of 83.1 births per 1,000 women. Birth rates for women in their 30s rose in 2012, as did the birth rate for women in their early 40s. The birth rate for women in their late 40s was unchanged. The nonmarital birth rate declined in 2012 (to 45.3 birth per 1,000 unmarried women aged 15-44), whereas the number of births to unmarried women rose 1% and the percentage of births to unmarried women was unchanged (at 40.7%). The cesarean delivery rate for the United States was unchanged in 2012 at 32.8%. The preterm

  12. 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.

  13. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David

    2012-01-01

    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  14. 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].

  15. EUPORIAS: plans and preliminary results

    Science.gov (United States)

    Buontempo, C.

    2013-12-01

    Recent advances in our understanding and ability to forecast climate variability have meant that skilful predictions are beginning to be routinely made on seasonal to decadal (s2d) timescales. Such forecasts have the potential to be of great value to a wide range of decision-making, where outcomes are strongly influenced by variations in the climate. In 2012 the European Commission funded EUPORIAS, a four year long project to develop prototype end-to-end climate impact prediction services operating on a seasonal to decadal timescale, and assess their value in informing decision-making. EUPORIAS commenced on 1 November 2012, coordinated by the UK Met Office leading a consortium of 24 organisations representing world-class European climate research and climate service centres, expertise in impacts assessments and seasonal predictions, two United Nations agencies, specialists in new media, and commercial companies in climate-vulnerable sectors such as energy, water and tourism. The poster describes the setup of the project, its main outcome and some of the very preliminary results.

  16. Preliminary results of ANAIS-25

    CERN Document Server

    Amaré, J; Cuesta, C; García, E; Ginestra, C; Martínez, M; Oliván, M A; Ortigoza, Y; de Solórzano, A Ortiz; Pobes, C; Puimedón, J; Sarsa, M L; Villar, P; Villar, J A

    2013-01-01

    The ANAIS (Annual Modulation with NaI(Tl) Scintillators) experiment aims at the confirmation of the DAMA/LIBRA signal using the same target and technique at the Canfranc Underground Laboratory. 250 kg of ultrapure NaI(Tl) crystals will be used as a target, divided into 20 modules, each coupled to two photomultipliers. Two NaI(Tl) crystals of 12.5 kg each, grown by Alpha Spectra from a powder having a potassium level under the limit of our analytical techniques, form the ANAIS-25 set-up. The background contributions are being carefully studied and preliminary results are presented: their natural potassium content in the bulk has been quantified, as well as the uranium and thorium radioactive chains presence in the bulk through the discrimination of the corresponding alpha events by PSA, and due to the fast commissioning, the contribution from cosmogenic activated isotopes is clearly identified and their decay observed along the first months of data taking. Following the procedures established with ANAIS-0 and ...

  17. 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

  18. Preliminary investigation into the possible endocrine disrupting ...

    African Journals Online (AJOL)

    JTEkanem

    In this study, we quantified the effect of Bonny- light crude oil contaminated diet ... This preliminary result suggest that Bonny-Light crude oil may have the potential .... different components. Its exploration ... organisms found in crude oil polluted.

  19. 42 CFR 457.925 - Preliminary investigation.

    Science.gov (United States)

    2010-10-01

    ... (CONTINUED) STATE CHILDREN'S HEALTH INSURANCE PROGRAMS (SCHIPs) ALLOTMENTS AND GRANTS TO STATES Program Integrity § 457.925 Preliminary investigation. If the State agency receives a complaint of fraud or abuse...

  20. 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)

  1. Preliminary project proposal : Missouri chutes, NE & IA

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This proposal is for the Missouri Chutes National Wildlife Refuge that would be in Nebraska and Iowa on the Missouri River. This preliminary project proposal focuses...

  2. Preliminary Survey of Ectoparasites Infesting Chickens (Gallus ...

    African Journals Online (AJOL)

    Preliminary Survey of Ectoparasites Infesting Chickens (Gallus domesticus) in. Four Areas of ... were identified with the following prevalences: the shaft louse, Menopon gallinae (8.1%), the chicken ..... Canis lupus familiaris in Mueang district ...

  3. 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.

  4. Preliminary Determination of Epicenters (PDE) Bulletin

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The NEIC global earthquake bulletin is called the Preliminary Determination of Epicenters or PDE, and is one of many discrete products in the ANSS Comprehensive...

  5. Alaska gold rush trails study: Preliminary draft

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Preliminary study draft, with maps, of seven gold rush trails in Alaska, to determine suitability for inclusion in the National Scenic Trails system and their...

  6. A vision for ubiquitous sequencing.

    Science.gov (United States)

    Erlich, Yaniv

    2015-10-01

    Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors--miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors.

  7. Psychoacoustic Properties of Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    J. Sokoll

    2008-01-01

    Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses. 

  8. Preliminary organizational culture scale focused on artifacts.

    Science.gov (United States)

    Bonavia, Tomas

    2006-12-01

    In this preliminary study, an Organizational Culture Scale was developed to assess cultural artifacts according to Schein's typology (1985). It includes a set of cultural artifacts to measure the extent to which an organization is more or less traditional. A total of 249 managers from a range of different companies responded to the items. Preliminary analysis yielded a one-dimensional scale with 14 items with high internal consistency and homogeneity.

  9. Preliminary organizational culture scale focused on artifacts

    OpenAIRE

    Bonavia, Tomas

    2006-01-01

    In this preliminary study, an organizational culture scale was developed to assess cultural artifacts according to Schein´s typology (1985). It includes a set of cultural artifacts to measure the extent to which an organization is more or less traditional. A total of 249 managers from a range of different companies responded to the items. Preliminary analysis yielded a one-dimensional scale with 14 items with high internal consistency and homogeneity.

  10. 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

  11. 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

  12. 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.

  13. Spaces of Ideal Convergent Sequences

    Directory of Open Access Journals (Sweden)

    M. Mursaleen

    2014-01-01

    Full Text Available In the present paper, we introduce some sequence spaces using ideal convergence and Musielak-Orlicz function ℳ=Mk. We also examine some topological properties of the resulting sequence spaces.

  14. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard

    2006-01-01

    The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl...

  15. The Galaxy End Sequence

    CERN Document Server

    Eales, Stephen; Smith, Matthew; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon

    2016-01-01

    A common assumption is that galaxies fall in two distinct regions on a plot of specific star-formation rate (SSFR) versus galaxy stellar mass: a star-forming Galaxy Main Sequence (GMS) and a separate region of `passive' or `red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus being a fair representation of the Universe at the end of 12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the `red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather t...

  16. 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.

  17. Novel sequences propel familiar folds.

    Science.gov (United States)

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  18. 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...... the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56...... MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types...

  19. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer

    Science.gov (United States)

    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; Akiyama, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin; Hazama, Makoto; Nishine, Tsutomu; Harada, Akira; Yamamoto, Rintaro; Matsumoto, Hiroyuki; Sakaguchi, Sumito; Ikegami, Takashi; Kashiwagi, Katsuya; Fujiwake, Syuji; Inoue, Kouji; Togawa, Yoshiyuki; Izawa, Masaki; Ohara, Eiji; Watahiki, Masanori; Yoneda, Yuko; Ishikawa, Tomokazu; Ozawa, Kaori; Tanaka, Takumi; Matsuura, Shuji; Kawai, Jun; Okazaki, Yasushi; Muramatsu, Masami; Inoue, Yorinao; Kira, Akira; Hayashizaki, Yoshihide

    2000-01-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3′ end and 5′ end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can

  20. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer.

    Science.gov (United States)

    Shibata, K; Itoh, M; Aizawa, K; Nagaoka, S; Sasaki, N; Carninci, P; Konno, H; Akiyama, J; Nishi, K; Kitsunai, T; Tashiro, H; Itoh, M; Sumi, N; Ishii, Y; Nakamura, S; Hazama, M; Nishine, T; Harada, A; Yamamoto, R; Matsumoto, H; Sakaguchi, S; Ikegami, T; Kashiwagi, K; Fujiwake, S; Inoue, K; Togawa, Y

    2000-11-01

    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be

  1. Musical Sequences in Comics

    Directory of Open Access Journals (Sweden)

    Kieron Michael Brown

    2013-11-01

    Full Text Available Critical attention paid to the media of music and comics has historically focused on parallels between the temporal rhythm and pacing of music and the implied rhythm and temporality of comics (Eisner 2008, Godek 2007. Recent attention has begun to focus on both comics’ potential to represent the character of music (Whitted 2011 and the effects of musical images and themes on comics’ narratology (Peters 2013.    I suggest that analyses of comics that combine the traditional interplay of image and word with the use of elements of musical notation are able to shed further light on each of these areas, via the connotations and conventions of symbols pulled exclusively from the realms of music, and their integration with the other elements of the page in sequence.

  2. Auditory stream segregation with cochlear implants: A preliminary report.

    Science.gov (United States)

    Chatterjee, Monita; Sarampalis, Anastasios; Oba, Sandra I

    2006-12-01

    Auditory stream segregation was measured in cochlear implant (CI) listeners using a subjective "Yes-No" task in which listeners indicated whether a sequence of stimuli was perceived as two separate streams or not. Stimuli were brief, 50-ms pulse trains A and B, presented in an A_B_A_A_B_A... sequence, with 50 ms in between consecutive stimuli. All stimuli were carefully loudness-balanced prior to the experiments. The cochlear electrode location of A was fixed, while the location of B was varied systematically. Measures of electrode discrimination and subjective perceptual difference were also included for comparison. There was strong intersubject variation in the pattern of results. One of the participants participated in a second series of experiments, the results of which indicated that he was able to perceptually segregate stimuli that were different in cochlear electrode location, as well as stimuli that were different in temporal envelope. Although preliminary, these results suggest that it is possible for some cochlear implant listeners to perceptually segregate stimuli based on differences in cochlear location as well as temporal envelope.

  3. ERIS: preliminary design phase overview

    Science.gov (United States)

    Kuntschner, Harald; Jochum, Lieselotte; Amico, Paola; Dekker, Johannes K.; Kerber, Florian; Marchetti, Enrico; Accardo, Matteo; Brast, Roland; Brinkmann, Martin; Conzelmann, Ralf D.; Delabre, Bernard A.; Duchateau, Michel; Fedrigo, Enrico; Finger, Gert; Frank, Christoph; Rodriguez, Fernando G.; Klein, Barbara; Knudstrup, Jens; Le Louarn, Miska; Lundin, Lars; Modigliani, Andrea; Müller, Michael; Neeser, Mark; Tordo, Sebastien; Valenti, Elena; Eisenhauer, Frank; Sturm, Eckhard; Feuchtgruber, Helmut; George, Elisabeth M.; Hartl, Michael; Hofmann, Reiner; Huber, Heinrich; Plattner, Markus P.; Schubert, Josef; Tarantik, Karl; Wiezorrek, Erich; Meyer, Michael R.; Quanz, Sascha P.; Glauser, Adrian M.; Weisz, Harald; Esposito, Simone; Xompero, Marco; Agapito, Guido; Antichi, Jacopo; Biliotti, Valdemaro; Bonaglia, Marco; Briguglio, Runa; Carbonaro, Luca; Cresci, Giovanni; Fini, Luca; Pinna, Enrico; Puglisi, Alfio T.; Quirós-Pacheco, Fernando; Riccardi, Armando; Di Rico, Gianluca; Arcidiacono, Carmelo; Dolci, Mauro

    2014-07-01

    The Enhanced Resolution Imager and Spectrograph (ERIS) is the next-generation adaptive optics near-IR imager and spectrograph for the Cassegrain focus of the Very Large Telescope (VLT) Unit Telescope 4, which will soon make full use of the Adaptive Optics Facility (AOF). It is a high-Strehl AO-assisted instrument that will use the Deformable Secondary Mirror (DSM) and the new Laser Guide Star Facility (4LGSF). The project has been approved for construction and has entered its preliminary design phase. ERIS will be constructed in a collaboration including the Max- Planck Institut für Extraterrestrische Physik, the Eidgenössische Technische Hochschule Zürich and the Osservatorio Astrofisico di Arcetri and will offer 1 - 5 μm imaging and 1 - 2.5 μm integral field spectroscopic capabilities with a high Strehl performance. Wavefront sensing can be carried out with an optical high-order NGS Pyramid wavefront sensor, or with a single laser in either an optical low-order NGS mode, or with a near-IR low-order mode sensor. Due to its highly sensitive visible wavefront sensor, and separate near-IR low-order mode, ERIS provides a large sky coverage with its 1' patrol field radius that can even include AO stars embedded in dust-enshrouded environments. As such it will replace, with a much improved single conjugated AO correction, the most scientifically important imaging modes offered by NACO (diffraction limited imaging in the J to M bands, Sparse Aperture Masking and Apodizing Phase Plate (APP) coronagraphy) and the integral field spectroscopy modes of SINFONI, whose instrumental module, SPIFFI, will be upgraded and re-used in ERIS. As part of the SPIFFI upgrade a new higher resolution grating and a science detector replacement are envisaged, as well as PLC driven motors. To accommodate ERIS at the Cassegrain focus, an extension of the telescope back focal length is required, with modifications of the guider arm assembly. In this paper we report on the status of the

  4. The Amatrice 2016 seismic sequence: a preliminary look at the mainshock and aftershocks distribution

    Directory of Open Access Journals (Sweden)

    Maddalena Michele

    2016-11-01

    Full Text Available We relocated the aftershocks of the MW 6.0 Amatrice 2016 mainshock by inverting with a non-linear probabilitstic method P- and S-arrival time readings produced and released in near realtime by the analyst seismologists of IGNV on duty in the seismic monitoring room. Earthquakes distribution shows the activation of a normal fault system with a main SW-dipping fault extending from Amatrice to NW of Accumoli village for a total length of 40 km. On the northern portion of the main fault hanging-wall volume, the structure become more complex activating an antithetic fault below the Norcia basin. It is worth nothing that below 8-9 km of depth, the whole fault system has an almost continuous sub-horizontal layer interested by an intense seismic activity, about 2 km thick.

  5. 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.

  6. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles (Del Mar, CA); Koster, Hubert (La Jolla, CA)

    2010-09-28

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  7. Fast, Sequence Adaptive Parcellation of Brain MR Using Parametric Models

    DEFF Research Database (Denmark)

    Puonti, Oula; Iglesias, Juan Eugenio; Van Leemput, Koen

    2013-01-01

    -of-the-art segmentation performance in both cortical and subcortical structures, while retaining all the benefits of generative parametric models, including high computational speed, automatic adaptiveness to changes in image contrast when different scanner platforms and pulse sequences are used, and the ability......In this paper we propose a method for whole brain parcellation using the type of generative parametric models typically used in tissue classification. Compared to the non-parametric, multi-atlas segmentation techniques that have become popular in recent years, our method obtains state...... to handle multi-contrast (vector-valued intensities) MR data. We have validated our method by comparing its segmentations to manual delineations both within and across scanner platforms and pulse sequences, and show preliminary results on multi-contrast test-retest scans, demonstrating the feasibility...

  8. Spectral Envelopes - A Preliminary Report

    CERN Document Server

    Lawton, Wayne

    2012-01-01

    The spectral envelope S(F) of a subset of integers is the set of probability measures on the circle group that are weak star limits of squared moduli of trigonometric polynomials with frequencies in F. Fourier transforms of these measures are positive and supported in F - F but the converse generally fails. The characteristic function chiF of F is a binary sequence whose orbit closure gives a symbolic dynamical system O(F). Analytic properties of S(F) are related to dynamical properties of chiF. The Riemann-Lebesque lemma implies that if chiF is minimal, then S(F) is convex and hence S(F) is the closure of the convex hull of its extreme points Se(F). In this paper we (i) review the relationship between these concepts and the special case of the still open 1959 Kadison-Singer problem called Feichtinger's conjecture for exponential functions, (ii) partially characterize of elements in Se(F), for minimal chiF, in terms of ergodic properties of (O(F),lambda) where lambda is a shift invariant probability measure w...

  9. Live sequence charts to model medical information

    Directory of Open Access Journals (Sweden)

    Aslakson Eric

    2012-06-01

    Full Text Available Abstract Background Medical records accumulate data concerning patient health and the natural history of disease progression. However, methods to mine information systematically in a form other than an electronic health record are not yet available. The purpose of this study was to develop an object modeling technique as a first step towards a formal database of medical records. Method Live Sequence Charts (LSC were used to formalize the narrative text obtained during a patient interview. LSCs utilize a visual scenario-based programming language to build object models. LSC extends the classical language of UML message sequence charts (MSC, predominantly through addition of modalities and providing executable semantics. Inter-object scenarios were defined to specify natural history event interactions and different scenarios in the narrative text. Result A simulated medical record was specified into LSC formalism by translating the text into an object model that comprised a set of entities and events. The entities described the participating components (i.e., doctor, patient and record and the events described the interactions between elements. A conceptual model is presented to illustrate the approach. An object model was generated from data extracted from an actual new patient interview, where the individual was eventually diagnosed as suffering from Chronic Fatigue Syndrome (CFS. This yielded a preliminary formal designated vocabulary for CFS development that provided a basis for future formalism of these records. Conclusions Translation of medical records into object models created the basis for a formal database of the patient narrative that temporally depicts the events preceding disease, the diagnosis and treatment approach. The LSCs object model of the medical narrative provided an intuitive, visual representation of the natural history of the patient’s disease.

  10. 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.

  11. Solid phase sequencing of biopolymers

    Science.gov (United States)

    Cantor, Charles R.; Hubert, Koster

    2014-06-24

    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  12. Graphene nanodevices for DNA sequencing

    Science.gov (United States)

    Heerema, Stephanie J.; Dekker, Cees

    2016-02-01

    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 nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  13. 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

  14. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  15. 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.

  16. Preliminary analysis of the use of smartwatches for longitudinal health monitoring.

    Science.gov (United States)

    Jovanov, Emil

    2015-08-01

    New generations of smartwatches feature continuous measurement of physiological parameters, such as heart rate, galvanic skin resistance (GSR), and temperature. In this paper we present the results of preliminary analysis of the use of Basis Peak smartwatch for longitudinal health monitoring during a 4 month period. Physiological measurements during sleep are validated using Zephyr Bioharness 3 monitor and SOMNOscreen+ polysomnographic monitoring system from SOMNOmedics. Average duration of sequences with no missed data was 49.9 minutes, with maximum length of 17 hours, and they represent 88.88% of recording time. Average duration of the charging event was 221.9 min, and average time between charges was 54 hours, with maximum duration of the charging event of 16.3 hours. Preliminary results indicate that the physiological monitoring performance of existing smartwatches provides sufficient performance for longitudinal monitoring of health status and analysis of health and wellness trends.

  17. Expression, purification and preliminary crystallographic characterization of FlhF from Bacillus subtilis

    Energy Technology Data Exchange (ETDEWEB)

    Bange, Gert; Petzold, Georg; Wild, Klemens; Sinning, Irmgard, E-mail: irmi.sinning@bzh.uni-heidelberg.de [Heidelberg University Biochemistry Centre (BZH), INF 328, 69120 Heidelberg (Germany)

    2007-05-01

    Preliminary crystallographic data are reported for the third SRP GTPase FlhF from Bacillus subtilis. The Gram-positive bacterium Bacillus subtilis contains three proteins belonging to the signal recognition particle (SRP) type GTPase family. The well characterized signal sequence-binding protein SRP54 and the SRP receptor protein FtsY are universally conserved components of the SRP system of protein transport. The third member, FlhF, has been implicated in the placement and assembly of polar flagella. This article describes the overexpression and preliminary X-ray crystallographic analysis of an FlhF fragment that corresponds to the well characterized GTPase domains in SRP54 and FtsY. Three crystal forms are reported with either GDP or GMPPNP and diffract to a resolution of about 3 Å.

  18. Blazar Sequence in Fermi Era

    Indian Academy of Sciences (India)

    Liang Chen

    2014-09-01

    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 low-power-low-sychrotron-peaked blazars. Because most blazars have similar size of emission region, theoretical blazar sequence implies that the break of Spectral Energy Distribution (SED) is a cooling break in nature.

  19. 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.

  20. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

    Latombe, J.C. [Stanford Univ., CA (United States). Robotics Lab.; Wilson, R.H. [Sandia National Labs., Albuquerque, NM (United States). Intelligent Systems and Robotics Center

    1995-02-21

    The goal of assembly sequencing is to plan a feasible series of operations to construct a product from its individual parts. Previous research has thoroughly investigated assembly sequencing under the assumption that parts have nominal geometry. This paper considers the case where parts have toleranced geometry. Its main contribution is an efficient procedure that decides if a product admits an assembly sequence with infinite translations that is feasible for all possible instances of the components within the specified tolerances. If the product admits one such sequence, the procedure can also generate it. For the cases where there exists no such assembly sequence, another procedure is proposed which generates assembly sequences that are feasible only for some values of the toleranced dimensions. If this procedure produces no such sequence, then no instance of the product is assemblable. Finally, this paper analyzes the relation between assembly and disassembly sequences in the presence of toleranced parts. This work assumes a simple, but non-trivial tolerance language that falls short of capturing all imperfections of a manufacturing process. Hence, it is only one step toward assembly sequencing with toleranced parts.

  1. SNMR pulse sequence phase cycling

    Science.gov (United States)

    Walsh, David O; Grunewald, Elliot D

    2013-11-12

    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  2. The ontology of biological sequences

    Directory of Open Access Journals (Sweden)

    Kelso Janet

    2009-11-01

    Full Text Available Abstract Background Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most basic question about sequences remains unanswered: what kind of entity is a biological sequence? An answer to this question benefits formal ontologies that use the notion of biological sequences and analyses in computational biology alike. Results We provide both an ontological analysis of biological sequences and a formal representation that can be used in knowledge-based applications and other ontologies. We distinguish three distinct kinds of entities that can be referred to as "biological sequence": chains of molecules, syntactic representations such as those in biological databases, and the abstract information-bearing entities. For use in knowledge-based applications and inclusion in biomedical ontologies, we implemented the developed axiom system for use in automated theorem proving. Conclusion Axioms are necessary to achieve the main goal of ontologies: to formally specify the meaning of terms used within a domain. The axiom system for the ontology of biological sequences is the first elaborate axiom system for an OBO Foundry ontology and can serve as starting point for the development of more formal ontologies and ultimately of knowledge-based applications.

  3. 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.

  4. High-Quality Draft Whole-Genome Sequences of Three Strains of Enterobacter Isolated from Jamaican Dioscorea cayenensis (Yellow Yam)

    OpenAIRE

    Gan, Han Ming; Triassi, Alexander J.; Wheatley, Matthew S.; Savka, Michael A.; Hudson, André O.

    2014-01-01

    Here we report the whole-genome sequences of three endophytic bacteria, Enterobacter sp. strain DC1, Enterobacter sp. strain DC3, and Enterobacter sp. strain DC4, from root tubers of the yellow yam plant, Dioscorea cayenensis. Preliminary analyses suggest that the genomes of the three bacteria contain genes involved in acetoin and indole-3-acetic acid metabolism.

  5. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rauzy, Antoine B., E-mail: Antoine.Rauzy@lix.polytechnique.f [LIX-CNRS, Computer Science, Ecole Polytechnique, 91128 Palaiseau Cedex (France)

    2011-07-15

    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.

  7. 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)

  8. Preliminary design package for Sunair SEC-601 solar collector

    Science.gov (United States)

    1978-01-01

    The preliminary design of the Owens-Illinois model Sunair SEC-601 tubular air solar collector is presented. Information in this package includes the subsystem design and development approaches, hazard analysis, and detailed drawings available as the preliminary design review.

  9. Three-Distance Sequences with Three Symbols

    OpenAIRE

    SAKAMOTO, Kuniko

    2003-01-01

    We will show that every $3$ dimensional cutting sequence is a three-distance sequence, and there are uncountable many periodic or aperiodic three-distance sequences (with $3$-symbols) which are not $3$ dimensional cutting sequences.

  10. NSIT: novel sequence identification tool.

    Directory of Open Access Journals (Sweden)

    Benjarath Pupacdi

    Full Text Available Novel sequences are DNA sequences present in an individual's genome but absent in the human reference assembly. They are predicted to be biologically important, both individual and population specific, and consistent with the known human migration paths. Recent works have shown that an average person harbors 2-5 Mb of such sequences and estimated that the human pan-genome contains as high as 19-40 Mb of novel sequences. To identify them in a de novo genome assembly, some existing sequence aligners have been used but no computational method has been specifically proposed for this task. In this work, we developed NSIT (Novel Sequence Identification Tool, a software that can accurately and efficiently identify novel sequences in an individual's de novo whole genome assembly. We identified and characterized 1.1 Mb, 1.2 Mb, and 1.0 Mb of novel sequences in NA18507 (African, YH (Asian, and NA12878 (European de novo genome assemblies, respectively. Our results show very high concordance with the previous work using the respective reference assembly. In addition, our results using the latest human reference assembly suggest that the amount of novel sequences per individual may not be as high as previously reported. We additionally developed a graphical viewer for comparisons of novel sequence contents. The viewer also helped in identifying sequence contamination; we found 130 kb of Epstein-Barr virus sequence in the previously published NA18507 novel sequences as well as 287 kb of zebrafish repeats in NA12878 de novo assembly. NSIT requires [Formula: see text]2GB of RAM and 1.5-2 hrs on a commodity desktop. The program is applicable to input assemblies with varying contig/scaffold sizes, ranging from 100 bp to as high as 50 Mb. It works in both 32-bit and 64-bit systems and outperforms, by large margins, other fast sequence aligners previously applied to this task. To our knowledge, NSIT is the first software designed specifically for novel sequence

  11. 19 CFR 4.8 - Preliminary entry.

    Science.gov (United States)

    2010-04-01

    ... electronic equivalent of a complete Customs Form 1302 (Cargo Declaration), in the manner provided in § 4.7(b... 19 Customs Duties 1 2010-04-01 2010-04-01 false Preliminary entry. 4.8 Section 4.8 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE...

  12. 40 CFR 1042.210 - Preliminary approval.

    Science.gov (United States)

    2010-07-01

    ... specific provisions that apply for deterioration factors. Decisions made under this section are considered... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Preliminary approval. 1042.210 Section 1042.210 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION...

  13. Preliminary aerothermodynamic design method for hypersonic vehicles

    Science.gov (United States)

    Harloff, G. J.; Petrie, S. L.

    1987-01-01

    Preliminary design methods are presented for vehicle aerothermodynamics. Predictions are made for Shuttle orbiter, a Mach 6 transport vehicle and a high-speed missile configuration. Rapid and accurate methods are discussed for obtaining aerodynamic coefficients and heat transfer rates for laminar and turbulent flows for vehicles at high angles of attack and hypersonic Mach numbers.

  14. 25 CFR 11.1005 - Preliminary inquiry.

    Science.gov (United States)

    2010-04-01

    ... ORDER CODE Juvenile Offender Procedure § 11.1005 Preliminary inquiry. (a) If a minor is placed in... purpose of determining: (1) Whether probable cause exist to believe the minor committed the alleged.... (b) If a minor has been released to the parents, guardian or custodian, the children's court shall...

  15. Preliminary aspects of a qualitative research projection

    Directory of Open Access Journals (Sweden)

    Simona Haidau

    2012-12-01

    Full Text Available In this paper are presented preliminary aspects on the design of of qualitative research achieved by nongovernmental organizations in the North-East of Romȃnia. The research aims to identify attitudes, opinions and behaviors to nongovernmental organizations to implement public relations programs and campaigns.

  16. 15 CFR 270.101 - Preliminary reconnaissance.

    Science.gov (United States)

    2010-01-01

    ... establishment of a Team, the leader of the initial assessment will report his/her findings to the Director in a... the extent the Director deems it appropriate, the Director may conduct a preliminary reconnaissance at the site of a building failure. The Director may establish and deploy a Team to conduct the...

  17. Preliminary investigations of piezoelectric based LED luminary

    DEFF Research Database (Denmark)

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

    2011-01-01

    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, modul...

  18. Preliminary Results on Charmed Meson Spectroscopy

    CERN Document Server

    Sarwar, S; Paolone, V S; Reyes, M; Anjos, J C; Yager, P M; Bediaga, I; Göbel, C; Magnin, J; De Miranda, J M; Pepe, I M; Dos Reis, A C; Simão, F R A; Carrillo, S; Casimiro, E; Méndez, H; Sánchez-Hernández, A; Uribe, C; Vásquez, F; Cinquini, L; Cumalat, J P; Ramírez, J E; O'Reilly, B; Vaandering, E W; Butler, J N; Cheung, H W K; Gaines, I; Garbincius, P H; Garren, L A; Gottschalk, E E; Gourlay, S A; Kasper, P H; Kreymer, A E; Kutschke, R; Bianco, S; Fabbri, Franco Luigi; Sarwar, S; Cawlfield, C; Kim, D Y; Park, K S; Rahimi, A; Gardner, R; Chung, Y S; Kang, J S; Ko, B R; Kwak, J W; Lee, K B; Myung, S S; Alimonti, G; Boschini, M; Brambilla, D; Caccianiga, B; Calandrino, A; D'Angelo, P; Di Corato, M; Dini, P; Giammarchi, M G; Inzani, P; Leveraro, F; Malvezzi, S; Menasce, D; Mezzadri, M; Milazzo, L; Moroni, L; Pedrini, D; Prelz, F; Rovere, M; Sala, A; Sala, S; Arena, V; Boca, G; Bonomi, G; Gianini, G; Liguori, G; Merlo, M; Pantea, D; Ratti, S P; Riccardi, C; Torre, P; Viola, L; Vitulo, P; Hernández, Pilar; López, A M; Méndez, L; Mirles, M A; Montiel, E; Olaya, D; Quinones, J; Rivera, C; Zhang-Mayaguez, Y; Copty, N K; Purohit, M; Cho, K; Handler, T; Engh, D; Johns, W E; Hosack, M; Nehring, M S; Sales, M; Sheldon, P D; Stenson, K; Webster, M S; Sheaff, M; Kwon, Y; Sarwar, Shahzad

    2001-01-01

    We report the preliminary measurement by the FOCUS Collaboration (E831 at Fermilab) of masses and widths of the L=1 charm mesons $D_2^{*0}$ and $D_2^{*+}$. The fit of the invariant mass distribution requires an additional term to account for a broad structure over background.

  19. Preliminary Study on Airlift Membran—Bioreactor

    Institute of Scientific and Technical Information of China (English)

    XUNong; XINGWeihong; 等

    2002-01-01

    A new type of membrane bioreactor named “airlift membrane-bioreactor”is discussed.For municipal wastewater reclamation,the preliminary study on airlift membrane-bioreactor shows its good performance such as high flux and lower energy consumption.The airlift membrane-bioreactor is potentially applicable in bioengineering and environmental protection fields.

  20. A DESCRIPTIVE INDONESIAN GRAMMAR--PRELIMINARY EDITION.

    Science.gov (United States)

    DYEN, ISIDORE

    THIS PRELIMINARY EDITION COMPRISES A DESCRIPTIVE GRAMMAR OF INDONESIAN (BAHASA INDONESIA), THE OFFICIAL LANGUAGE OF THE REPUBLIC OF INDONESIA. THE THREE SECTIONS--PHONOLOGY, SYNTAX, AND MORPHOLOGY--PRESENT A COMPREHENSIVE LINGUISTIC ANALYSIS OF INDONESIAN, WITH OCCASIONAL CONTRASTIVE REFERENCE TO MALAY, JAVANESE, SUNDANESE, AND SUMATRAN. THIS…

  1. 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 de...... in developing countries in three important areas: finance, technology and knowledge....

  2. The show starts here: viewers’ interactions with recent television serials’ main title sequences

    Directory of Open Access Journals (Sweden)

    Annette Davison

    2013-12-01

    Full Text Available Recent title sequences for high production value television serials are generally one of two kinds: either extremely minimal, appearing part way through the episode with credits dispersed through the show, or as an extended format of c. ninety seconds’ duration, at or near the start of the show. In a previous book chapter I presented analyses of examples of the latter, arguing that the sequences form an efficient part of the brand image for both the show and commissioning channel. In order to explore the extent to which such sequences are watched or skipped by viewers, and how such decisions are made I organised a series of preliminary focus groups in February 2012 with participants who identified themselves as regular viewers of television serials, the findings of which are presented here. Two forms of stimuli were used: a main title sequence and an end credit sequence from a serial where different music is selected for this sequence for each episode. Analysis of the discussions indicates that the decision to view these sequences is dependent on a variety of factors. While for some the titles are required viewing, the participants in the groups are more likely to persistently view an end credit sequence where the music changes with the episode than an unchanging main title sequence. Perhaps most surprising, given the increase in opportunities for mobile viewing, is that for the participants of these groups television serials continue to be associated with social viewing in a domestic setting.

  3. Main-Sequence Binary Stars in the Core of NGC 6397

    Science.gov (United States)

    Bolton, A. S.; Cool, A. M.; Anderson, J.

    1999-12-01

    Using HST WFPC2 data, we isolate main-sequence binary candidates in the central region of the globular cluster NGC 6397 based on their locations in an I vs. V - I color--magnitude diagram. We have largely eliminated field stars from the sample beforehand based on proper motions determined from two sets of position data separated by approximately three years. Binary candidates are fit to models based on the empirically derived main-sequence ridge line for the cluster, and component masses are determined using theoretical mass--luminosity relations appropriate to the cluster. Preliminary results suggest an upper limit of 3% on the binary fraction for stars in the apparent magnitude range 17.0 mass ratios greater than approximately 0.45. We also present preliminary results for the distribution of binaries as a function of primary mass and mass ratio, as well as a comparison of these results to previously published findings for field stars.

  4. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    XuChengqian; ZhaoXiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP)is proposed .A new class of block design-Difference Family Pair (DFP)is also proposed .The relationship between PCSP and DFP,the properties and exising conditions of PCSP and the recursive constructions for PCSP are given.

  5. PERIODIC COMPLEMENTARY BINARY SEQUENCE PAIRS

    Institute of Scientific and Technical Information of China (English)

    Xu Chengqian; Zhao Xiaoqun

    2002-01-01

    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP) is proposed. A new class of block design-Difference Family Pair (DFP) is also proposed.The relationship between PCSP and DFP, the properties and existing conditions of PCSP and the recursive constructions for PCSP are given.

  6. DNA Sequencing Sensors: An Overview

    Directory of Open Access Journals (Sweden)

    Jose Antonio Garrido-Cardenas

    2017-03-01

    Full Text Available The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.

  7. Gambling strategies for random sequences

    OpenAIRE

    George Davie

    2010-01-01

    There is a general consensus that it is not possible to gamble successfully against a random se-quence. This consensus is based on results from probability theory that all gambling systems arein some sense futile and the idea that at any stage of the sequence, the next outcome is entirelyunpredictable.

  8. Sequence conserved for subcellular localization

    Science.gov (United States)

    Nair, Rajesh; Rost, Burkhard

    2002-01-01

    The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. The precise thresholds used in automated genome annotations depend on the particular aspect of protein function transferred by homology. Here, we presented the first large-scale analysis of the relation between sequence similarity and identity in subcellular localization. Three results stood out: (1) The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs like nuclear localization signals can alter the native compartment; (2) the sequence conservation of localization is similar between different compartments; and (3) it is similar to the conservation of structure and enzymatic activity. In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. In fact, BLAST expectation values outperformed the HSSP distance only for alignments in the subtwilight zone. We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes. PMID:12441382

  9. Bayesian analysis of binary sequences

    Science.gov (United States)

    Torney, David C.

    2005-03-01

    This manuscript details Bayesian methodology for "learning by example", with binary n-sequences encoding the objects under consideration. Priors prove influential; conformable priors are described. Laplace approximation of Bayes integrals yields posterior likelihoods for all n-sequences. This involves the optimization of a definite function over a convex domain--efficiently effectuated by the sequential application of the quadratic program.

  10. 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.

  11. 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

  12. 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...

  13. 29 CFR 1601.23 - Preliminary or temporary relief.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 4 2010-07-01 2010-07-01 false Preliminary or temporary relief. 1601.23 Section 1601.23... Employment Practices § 1601.23 Preliminary or temporary relief. (a) In the interest of the expeditious... subdivision, any recommendation for preliminary or temporary relief shall be transmitted directly to the...

  14. Investigation of the protein osteocalcin of Camelops hesternus: Sequence, structure and phylogenetic implications

    Science.gov (United States)

    Humpula, James F.; Ostrom, Peggy H.; Gandhi, Hasand; Strahler, John R.; Walker, Angela K.; Stafford, Thomas W.; Smith, James J.; Voorhies, Michael R.; George Corner, R.; Andrews, Phillip C.

    2007-12-01

    Ancient DNA sequences offer an extraordinary opportunity to unravel the evolutionary history of ancient organisms. Protein sequences offer another reservoir of genetic information that has recently become tractable through the application of mass spectrometric techniques. The extent to which ancient protein sequences resolve phylogenetic relationships, however, has not been explored. We determined the osteocalcin amino acid sequence from the bone of an extinct Camelid (21 ka, Camelops hesternus) excavated from Isleta Cave, New Mexico and three bones of extant camelids: bactrian camel ( Camelus bactrianus); dromedary camel ( Camelus dromedarius) and guanaco ( Llama guanacoe) for a diagenetic and phylogenetic assessment. There was no difference in sequence among the four taxa. Structural attributes observed in both modern and ancient osteocalcin include a post-translation modification, Hyp 9, deamidation of Gln 35 and Gln 39, and oxidation of Met 36. Carbamylation of the N-terminus in ancient osteocalcin may result in blockage and explain previous difficulties in sequencing ancient proteins via Edman degradation. A phylogenetic analysis using osteocalcin sequences of 25 vertebrate taxa was conducted to explore osteocalcin protein evolution and the utility of osteocalcin sequences for delineating phylogenetic relationships. The maximum likelihood tree closely reflected generally recognized taxonomic relationships. For example, maximum likelihood analysis recovered rodents, birds and, within hominins, the Homo-Pan-Gorilla trichotomy. Within Artiodactyla, character state analysis showed that a substitution of Pro 4 for His 4 defines the Capra-Ovis clade within Artiodactyla. Homoplasy in our analysis indicated that osteocalcin evolution is not a perfect indicator of species evolution. Limited sequence availability prevented assigning functional significance to sequence changes. Our preliminary analysis of osteocalcin evolution represents an initial step towards a

  15. Spatiotemporal correlations of aftershock sequences

    CERN Document Server

    Peixoto, Tiago P; Davidsen, Jörn

    2010-01-01

    Aftershock sequences are of particular interest in seismic research since they may condition seismic activity in a given region over long time spans. While they are typically identified with periods of enhanced seismic activity after a large earthquake as characterized by the Omori law, our knowledge of the spatiotemporal correlations between events in an aftershock sequence is limited. Here, we study the spatiotemporal correlations of two aftershock sequences form California (Parkfield and Hector Mine) using the recently introduced concept of "recurrent" events. We find that both sequences have very similar properties and that most of them are captured by the space-time epidemic-type aftershock sequence (ETAS) model if one takes into account catalog incompleteness. However, the stochastic model does not capture the spatiotemporal correlations leading to the observed structure of seismicity on small spatial scales.

  16. Quantum Exchangeable Sequences of Algebras

    CERN Document Server

    Curran, Stephen

    2008-01-01

    We extend the notion of quantum exchangeability, introduced by K\\"ostler and Speicher in arXiv:0807.0677, to sequences (\\rho_1,\\rho_2,...c) of homomorphisms from an algebra C into a noncommutative probability space (A,\\phi), and prove a free de Finetti theorem: an infinite quantum exchangeable sequence (\\rho_1,\\rho_2,...c) is freely independent and identically distributed with respect to a conditional expectation. As a corollary we obtain a free analogue of the Hewitt Savage zero-one law. As in the classical case, the theorem fails for finite sequences. We give a characterization of finite quantum exchangeable sequences, which can be viewed as a noncommutative analogue of sampling without replacement. We then give an approximation to how far a finite quantum exchangeable sequence is from being freely independent with amalgamation.

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

    Science.gov (United States)

    Zuccolo, Andrea; Bowers, John E; Estill, James C; Xiong, Zhiyong; Luo, Meizhong; Sebastian, Aswathy; Goicoechea, José Luis; Collura, Kristi; Yu, Yeisoo; Jiao, Yuannian; Duarte, Jill; Tang, Haibao; Ayyampalayam, Saravanaraj; Rounsley, Steve; Kudrna, Dave; Paterson, Andrew H; Pires, J Chris; Chanderbali, Andre; Soltis, Douglas E; Chamala, Srikar; Barbazuk, Brad; Soltis, Pamela S; Albert, Victor A; Ma, Hong; Mandoli, Dina; Banks, Jody; Carlson, John E; Tomkins, Jeffrey; dePamphilis, Claude W; Wing, Rod A; Leebens-Mack, Jim

    2011-01-01

    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. Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella. When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.

  18. Draft genome sequence of a marine actinobacteria Sciscionella strain SE31.

    Science.gov (United States)

    Teo, Wee Fei Aaron; Wee, Wei Yee; Choo, Siew Woh; Tan, Geok Yuan Annie

    2015-04-01

    The bacterium strain SE31, a member of the genus Sciscionella, was isolated from intertidal sediments collected from Cape Rachado, Malaysia. The high quality draft genome sequence of Sciscionella strain SE31 with a genome size of approximately 7.4 Mbp is reported. Preliminary analysis revealed 46 putative gene clusters involved in the biosynthesis of secondary metabolites and 113 putative genes that are associated with bacterial virulence, disease and defense. Availability of the genome sequence of Sciscionella SE31 will contribute to a better understanding of the genus Sciscionella. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. 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

  20. Toxoplasma gondii: a rapid method for the isolation of pure tachyzoites: preliminary characterization of its genome

    Directory of Open Access Journals (Sweden)

    Juan Carlos Garberi

    1990-12-01

    Full Text Available A rapid and simple technique for the purification of Toxoplasma gondii tachyzoites was developed. Highly purified parasites were obtained from the peritoneal exudates of infected mice by means of two consecutive discontinous sucrose gradients run at low speed (10,000xg, 30 min. Parasites obtained by this method conserved its biological activity. Hybridizations tudies with DNA from healthy mice and from purified tachyzoites preparations demonstrated that Toxoplasma gondii tachyzoites DNA could be obtained with better than 90 per cents purity. Preliminary studies with DNA endonucleases showed the presence in the tachyzoites genome of highly repetitives sequences.

  1. Efficient newly designed primers for the amplification and sequencing of bird mitochondrial genomes.

    Science.gov (United States)

    Amer, Sayed A M; Ahmed, Mohamed Mohamed; Shobrak, Mohammed

    2013-01-01

    In the present study, 27 mitochondrial genomes of diverse avian supra-orders were collected from the Genbank database and their genes were aligned separately. From the alignments, the conserved sequences were selected to design novel conserved primers for amplification and sequencing of the different mitochondrial genes. The reproducibility of these primers was tested in the amplification and sequencing of diverse avian supra-order mitochondrial genomes and was confirmed. This method helped in designing a new set of primers to accelerate both the amplification and the sequencing of bird mitogenomes. It also aids in building mitogenome markers in studying the genetic framework of endemic birds as a preliminary strategy for conservation management of them.

  2. Ossification sequence heterochrony among amphibians.

    Science.gov (United States)

    Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A

    2013-01-01

    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans.

  3. A Criterion for Regular Sequences

    Indian Academy of Sciences (India)

    D P Patil; U Storch; J Stückrad

    2004-05-01

    Let be a commutative noetherian ring and $f_1,\\ldots,f_r \\in R$. In this article we give (cf. the Theorem in $\\mathcal{x}$2) a criterion for $f_1,\\ldots,f_r$ to be regular sequence for a finitely generated module over which strengthens and generalises a result in [2]. As an immediate consequence we deduce that if $V(g_1,\\ldots,g_r) \\subseteq V(f_1,\\ldots,f_r)$ in Spec and if $f_1,\\ldots,f_r$ is a regular sequence in , then $g_1,\\ldots,g_r$ is also a regular sequence in .

  4. 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)

  5. Correcting sequencing errors in DNA coding regions using a dynamic programming approach.

    Science.gov (United States)

    Xu, Y; Mural, R J; Uberbacher, E C

    1995-04-01

    This paper presents an algorithm for detecting and 'correcting' sequencing errors that occur in DNA coding regions. The types of sequencing errors addressed are insertions and deletions (indels) of DNA bases. The goal is to provide a capability which makes single-pass or low-redundancy sequence data more informative, reducing the need for high-redundancy sequencing for gene identification and characterization purposes. This would permit improved sequencing efficiency and reduce genome sequencing costs. The algorithm detects sequencing errors by discovering changes in the statistically preferred reading frame within a putative coding region and then inserts a number of 'neutral' bases at a perceived reading frame transition point to make the putative exon candidate frame consistent. We have implemented the algorithm as a front-end subsystem of the GRAIL DNA sequence analysis system to construct a version which is very error tolerant and also intend to use this as a testbed for further development of sequencing error-correction technology. Preliminary test results have shown the usefulness of this algorithm and also exhibited some of its weakness, providing possible directions for further improvement. On a test set consisting of 68 human DNA sequences with 1% randomly generated indels in coding regions, the algorithm detected and corrected 76% of the indels. The average distance between the position of an indel and the predicted one was 9.4 bases. With this subsystem in place, GRAIL correctly predicted 89% of the coding messages with 10% false message on the 'corrected' sequences, compared to 69% correctly predicted coding messages and 11% falsely predicted messages on the 'corrupted' sequences using standard GRAIL II method (version 1.2).(ABSTRACT TRUNCATED AT 250 WORDS)

  6. A draft sequence of the rice(Oryza sativa ssp. indica) genome

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development, and evolution, as well as information on many beneficial phenotypes of economic significance. Using a "whole genome shotgun" approach, we have produced a draft rice genome sequence of Oryza sativa ssp. indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over 4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb from an indica variant cultivar 93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEM- BLER, a custom-designed software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences from both indica and japanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0% of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities to facilitate genomic and genetic studies on rice biology.

  7. Preliminary results in surgery of Parkinson's disease.

    Science.gov (United States)

    Nasser, J A; Confort, C I; Ferraz, A; Bouza, A A

    1998-09-01

    The authors present the preliminary results of 20 patients selected to be operated on between January 1996 and April 1997. These patients presented one of the present indications for stereotactic posteroventral pallidotomy (PVP), such as: rigidity, akinesia/bradykinesia, gait dysfunction, drug induced dyskinesias and tremor. Every patient of this protocol was evaluated by: UPDRS score, Schwab and England scale, Hoehn and Yahr Staging Scale before and after surgery. The results in 3 months showed a remarkable improvement after PVP (P < 0.01) in all functional assessments, except for facial expression, speech and posture. The morbidity was 5%. 5 patients (25%) who were in Hoehn and Yahr 5 underwent a bilateral simultaneous PVP. In 5 patients (25%), who had tremor, during the PVP, VIM thalamotomy was added. These preliminary results, suggest that PVP is highly effective for PD symptoms.

  8. Rare earth optogalvanic spectroscopy: preliminary results

    Energy Technology Data Exchange (ETDEWEB)

    Destro, Marcelo G.; Neri, Jose W.; Rodrigues, Nicolau A.S.; Silveira, Carlos A.B.; Riva, Rudimar [Instituto de Estudos Avancados (IEAv/EFO), Sao Jose dos Campos, SP (Brazil). Div. de Fotonica]. E-mail: destro@ieav.cta.br; Victor, Alessandro R. [Instituto Tecnologico de Aeronautica (ITA), Sao Jose dos Campos, SP (Brazil)

    2008-07-01

    The IEAv has special interest in the studies of rare earth isotope applications in laser medium and integrated optics as well as aerospace research. We are starting to work with Ytterbium, Erbium, Dysprosium and Neodymium laser selective photoionization research. This paper describes the preliminary results of emission and optogalvanic spectroscopy obtained from a Neodymium hollow cathode lamps. Furthermore these results were used to setup our laser systems to work to leads a Nd isotopes selective laser photoionization. (author)

  9. Institutional Repositories in India: A preliminary study

    OpenAIRE

    2011-01-01

    This preliminary study investigates various aspects of institutional repositories (IR’s) developed in India. The present study has identified the existence of 16 functional IRs some of which were not registered in any of the directories such as ROAR, Open DOAR. The study explores the timeline involved in planning, pilot testing, to system implementation of IR, exploratory activities conducted before implementing IR, its anticipated benefits.

  10. A Toolbox for Rotorcraft Preliminary Design

    OpenAIRE

    Lier, Max; Krenik, Alex; Kunze, Philipp; Kohlgrüber, Dieter; Schwinn, Dominik; Lützenberger, Marius

    2015-01-01

    The German Aerospace Center (DLR) developed a toolbox, which is able to reflect the conceptual and preliminary design process of rotorcraft configuration. Such a toolbox is a valuable aid for the design engineer and can be used for the assessment of new technologies with regard to the overall configuration. This toolbox is currently extended to model novel rotorcraft configurations. Automated optimization procedures will be added in the future as well. This paper describes the too...

  11. Preliminary rock mechanics laboratory: Investigation plan

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. 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)

  13. 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.

  14. PLANT COMMUNITIES OF ALBANIA - A PRELIMINARY OVERVIEW

    Directory of Open Access Journals (Sweden)

    J, RODWELL

    2002-01-01

    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.

  15. [Tonsillectomy with a laser dissector. Preliminary report].

    Science.gov (United States)

    Lenz, H

    1984-11-01

    A so called laser-dissector with a flexible beam guide system for tonsillectomy is described. With this instrument the tissue is irradiated for a very short time resulting in a coagulation of the peritonsillar tissue with closure of the small vessels even before mechanical dissection is performed. A preliminary report of 10 patients is given. The main advantage is that the procedure could be performed without or with much less bleeding as in tonsillectomy without using vasoconstrictors.

  16. Preliminary Analysis of Google+'s Privacy

    OpenAIRE

    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...

  17. Preliminary Design and Evaluation of Portable Electronic Flight Progress Strips

    Science.gov (United States)

    Doble, Nathan A.; Hansman, R. John

    2002-01-01

    There has been growing interest in using electronic alternatives to the paper Flight Progress Strip (FPS) for air traffic control. However, most research has been centered on radar-based control environments, and has not considered the unique operational needs of the airport air traffic control tower. Based on an analysis of the human factors issues for control tower Decision Support Tool (DST) interfaces, a requirement has been identified for an interaction mechanism which replicates the advantages of the paper FPS (e.g., head-up operation, portability) but also enables input and output with DSTs. An approach has been developed which uses a Portable Electronic FPS that has attributes of both a paper strip and an electronic strip. The prototype flight strip system uses Personal Digital Assistants (PDAs) to replace individual paper strips in addition to a central management interface which is displayed on a desktop computer. Each PDA is connected to the management interface via a wireless local area network. The Portable Electronic FPSs replicate the core functionality of paper flight strips and have additional features which provide a heads-up interface to a DST. A departure DST is used as a motivating example. The central management interface is used for aircraft scheduling and sequencing and provides an overview of airport departure operations. This paper will present the design of the Portable Electronic FPS system as well as preliminary evaluation results.

  18. Preliminary Safety Evaluation of a New Bacteroides xylanisolvens Isolate

    Science.gov (United States)

    Toutounian, Kawe; Schmidt, Jens; Karsten, Uwe; Goletz, Steffen

    2012-01-01

    Besides conferring some health benefit to the host, a bacterial strain must present an unambiguous safety status to be considered a probiotic. We here present the preliminary safety evaluation of a new Bacteroides xylanisolvens strain (DSM 23964) isolated from human feces. First results suggest that it may be able to provide probiotic health benefits. Its identity was confirmed by biochemical analysis, by sequencing of its 16S rRNA genes, and by DNA-DNA hybridization. Virulence determinants known to occur in the genus Bacteroides, such the bft enterotoxin and other enzymatic activities involved in the degradation of the extracellular matrix and the capsular polysaccharide PS A, were absent in this strain. The investigation of the antibiotic susceptibility indicated that strain DSM 23964 was sensitive to metronidazole, meropenem agents, and clindamycin. Resistance to penicillin and ampicillin was identified to be conferred by the β-lactamase cepA gene and could therefore be restored by adding β-lactamase inhibitors. The localization of the cepA gene in the genome of strain DSM 23964 and the absence of detectable plasmids further suggest that a transfer of β-lactamase activity or the acquisition of other antibiotic resistances are highly improbable. Taken together, the presented data indicate that the strain B. xylanisolvens DSM 23964 has no virulence potential. Since it also resists the action of gastric enzymes and low-pH conditions, this strain is an interesting candidate for further investigation of its safety and potential health-promoting properties. PMID:22101046

  19. Magnetic resonance imaging urodynamics: technique development and preliminary results

    Directory of Open Access Journals (Sweden)

    Gustavo Borghesi

    2006-06-01

    Full Text Available OBJECTIVES: In this preliminary study we report the development of the video urodynamic technique using magnetic resonance imaging (MRI. MATERIALS AND METHODS: We studied 6 women with genuine stress urinary incontinence, diagnosed by history and physical examination. Urodynamic examination was performed on multichannel equipment with the patient in the supine position. Coughing and Valsalva maneuvers were performed at volumes of 150, 250 and 350 mL. Simultaneously, MRI was carried out by using 1.5 T GE Signa CV/i high-speed scanner with real time fluoroscopic imaging possibilities. Fluoroscopic imaging was accomplished in the corresponding planes with T2-weighted single shot fast spin echo sequences at a speed of about 1 frame per second. Both studies were recorded and synchronized, resulting in a single video urodynamic examination. RESULTS: Dynamic MRI with cine-loop reconstruction of 1 image per second demonstrated the movement of all compartment of the relaxed pelvis during straining with the concomitant registration of abdominal and intravesical pressures. In 5 patients, urinary leakage was demonstrated during straining and the Valsalva leak point pressure (VLPP was determined as the vesical pressure at leak subtracted from baseline bladder pressure. Mean VLPP was 72.6 cm H2O (ranging from 43 to 122 cm H2O. CONCLUSIONS: The concept of MRI video urodynamics is feasible. In a clinical perspective, practical aspects represent a barrier to daily use and it should be recommended for research purposes.

  20. ISIS Individualized Support In Sequencing

    NARCIS (Netherlands)

    Drachsler, Hendrik; Hummel, Hans

    2007-01-01

    Drachsler, H., & Hummel, H. G. K. (2007). ISIS Individualized Support In Sequencing. Presentation given during the PIP meeting on March 22, 2007. Open University of the Netherlands: Heerlen, The Netherlands.

  1. Molecular beacon sequence design algorithm.

    Science.gov (United States)

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  2. Classification of Base Sequences (+1,

    Directory of Open Access Journals (Sweden)

    Dragomir Ž. Ðoković

    2010-01-01

    Full Text Available Base sequences BS(+1, are quadruples of {±1}-sequences (;;;, with A and B of length +1 and C and D of length n, such that the sum of their nonperiodic autocor-relation functions is a -function. The base sequence conjecture, asserting that BS(+1, exist for all n, is stronger than the famous Hadamard matrix conjecture. We introduce a new definition of equivalence for base sequences BS(+1, and construct a canonical form. By using this canonical form, we have enumerated the equivalence classes of BS(+1, for ≤30. As the number of equivalence classes grows rapidly (but not monotonically with n, the tables in the paper cover only the cases ≤13.

  3. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  4. Pythagorean Triples from Harmonic Sequences.

    Science.gov (United States)

    DiDomenico, Angelo S.; Tanner, Randy J.

    2001-01-01

    Shows how all primitive Pythagorean triples can be generated from harmonic sequences. Use inductive and deductive reasoning to explore how Pythagorean triples are connected with another area of mathematics. (KHR)

  5. Nanopore Sequencing: Electrical Measurements of the Code of Life.

    Science.gov (United States)

    Timp, Winston; Mirsaidov, Utkur M; Wang, Deqiang; Comer, Jeff; Aksimentiev, Aleksei; Timp, Gregory

    2010-05-01

    Sequencing a single molecule of deoxyribonucleic acid (DNA) using a nanopore is a revolutionary concept because it combines the potential for long read lengths (>5 kbp) with high speed (1 bp/10 ns), while obviating the need for costly amplification procedures due to the exquisite single molecule sensitivity. The prospects for implementing this concept seem bright. The cost savings from the removal of required reagents, coupled with the speed of nanopore sequencing places the $1000 genome within grasp. However, challenges remain: high fidelity reads demand stringent control over both the molecular configuration in the pore and the translocation kinetics. The molecular configuration determines how the ions passing through the pore come into contact with the nucleotides, while the translocation kinetics affect the time interval in which the same nucleotides are held in the constriction as the data is acquired. Proteins like α-hemolysin and its mutants offer exquisitely precise self-assembled nanopores and have demonstrated the facility for discriminating individual nucleotides, but it is currently difficult to design protein structure ab initio, which frustrates tailoring a pore for sequencing genomic DNA. Nanopores in solid-state membranes have been proposed as an alternative because of the flexibility in fabrication and ease of integration into a sequencing platform. Preliminary results have shown that with careful control of the dimensions of the pore and the shape of the electric field, control of DNA translocation through the pore is possible. Furthermore, discrimination between different base pairs of DNA may be feasible. Thus, a nanopore promises inexpensive, reliable, high-throughput sequencing, which could thrust genomic science into personal medicine.

  6. Overview of Sequence Data Formats.

    Science.gov (United States)

    Zhang, Hongen

    2016-01-01

    Next-generation sequencing experiment can generate billions of short reads for each sample and processing of the raw reads will add more information. Various file formats have been introduced/developed in order to store and manipulate this information. This chapter presents an overview of the file formats including FASTQ, FASTA, SAM/BAM, GFF/GTF, BED, and VCF that are commonly used in analysis of next-generation sequencing data.

  7. Structural Complexity of DNA Sequence

    Directory of Open Access Journals (Sweden)

    Cheng-Yuan Liou

    2013-01-01

    Full Text Available In modern bioinformatics, finding an efficient way to allocate sequence fragments with biological functions is an important issue. This paper presents a structural approach based on context-free grammars extracted from original DNA or protein sequences. This approach is radically different from all those statistical methods. Furthermore, this approach is compared with a topological entropy-based method for consistency and difference of the complexity results.

  8. Nanogrid rolling circle DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Church, George M.; Porreca, Gregory J.; Shendure, Jay; Rosenbaum, Abraham Meir

    2017-04-18

    The present invention relates to methods for sequencing a polynucleotide immobilized on an array having a plurality of specific regions each having a defined diameter size, including synthesizing a concatemer of a polynucleotide by rolling circle amplification, wherein the concatemer has a cross-sectional diameter greater than the diameter of a specific region, immobilizing the concatemer to the specific region to make an immobilized concatemer, and sequencing the immobilized concatemer.

  9. 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.

  10. Pig genome sequence - analysis and publication strategy

    NARCIS (Netherlands)

    Archibald, A.L.; Bolund, L.; Churcher, C.; Fredholm, M.; Groenen, M.A.M.; Harlizius, B.

    2010-01-01

    Background - The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. Results - Assemblies of the B

  11. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.

    2016-10-18

    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  12. Sequencing and comparative analysis of the gorilla MHC genomic sequence.

    Science.gov (United States)

    Wilming, Laurens G; Hart, Elizabeth A; Coggill, Penny C; Horton, Roger; Gilbert, James G R; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L

    2013-01-01

    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.

  13. The Alignment of Red-Sequence Dwarf Galaxies

    Science.gov (United States)

    Archer, Haylee; Barkhouse, Wayne; Burgad, Jaford; Foote, Gregory; Rude, Cody; Lopez-Cruz, Omar

    2015-01-01

    The alignment of cluster galaxies has been used to determine the impact of the high-density environment on the evolution of galaxies. We have undertaken a study to measure the alignment of cluster dwarf galaxies based on a sample of 57 low-redshift Abell clusters imaged at KPNO using the 0.9-meter telescope. To supplement our KPNO sample, we have included an additional 64 low-redshift clusters from the WINGS dataset. From the combined cluster sample (121 clusters), we have selected cluster dwarf galaxies based on their position relative to the cluster red-sequence. We present our preliminary results based on the alignment of the dwarf galaxies with: 1) the major axis of the brightest cluster galaxy, 2) the major axis of the cluster defined by position of the cluster members, and 3) a radius vector pointing from the cluster center to the dwarf galaxy.

  14. ARC Code TI: sequenceMiner

    Data.gov (United States)

    National Aeronautics and Space Administration — The sequenceMiner was developed to address the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. sequenceMiner works...

  15. Sequencing Needs for Viral Diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S N; Lam, M; Mulakken, N J; Torres, C L; Smith, J R; Slezak, T

    2004-01-26

    We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.

  16. Sequence-dependent nucleosome positioning.

    Science.gov (United States)

    Chung, Ho-Ryun; Vingron, Martin

    2009-03-13

    Eukaryotic DNA is organized into a macromolecular structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of two copies of each of the four core histones and DNA. The nucleosomal organization and the positions of nucleosomes have profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is therefore of general interest. Among the many determinants of nucleosome positioning, the DNA sequence has been proposed to have a major role. Here, we analyzed more than 860,000 nucleosomal DNA sequences to identify sequence features that guide the formation of nucleosomes in vivo. We found that both a periodic enrichment of AT base pairs and an out-of-phase oscillating enrichment of GC base pairs as well as the overall preference for GC base pairs are determinants of nucleosome positioning. The preference for GC pairs can be related to a lower energetic cost required for deformation of the DNA to wrap around the histones. In line with this idea, we found that only incorporation of both signal components into a sequence model for nucleosome formation results in maximal predictive performance on a genome-wide scale. In this manner, one achieves greater predictive power than published approaches. Our results confirm the hypothesis that the DNA sequence has a major role in nucleosome positioning in vivo.

  17. Mitochondrial genome sequences of Nematocera (lower Diptera): evidence of rearrangement following a complete genome duplication in a winter crane fly.

    Science.gov (United States)

    Beckenbach, Andrew T

    2012-01-01

    The complete mitochondrial DNA sequences of eight representatives of lower Diptera, suborder Nematocera, along with nearly complete sequences from two other species, are presented. These taxa represent eight families not previously represented by complete mitochondrial DNA sequences. Most of the sequences retain the ancestral dipteran mitochondrial gene arrangement, while one sequence, that of the midge Arachnocampa flava (family Keroplatidae), has an inversion of the trnE gene. The most unusual result is the extensive rearrangement of the mitochondrial genome of a winter crane fly, Paracladura trichoptera (family Trichocera). The pattern of rearrangement indicates that the mechanism of rearrangement involved a tandem duplication of the entire mitochondrial genome, followed by random and nonrandom loss of one copy of each gene. Another winter crane fly retains the ancestral diperan gene arrangement. A preliminary mitochondrial phylogeny of the Diptera is also presented.

  18. 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.

  19. Transgressive Surface as Sequence Boundary

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Analysis of the four cases of the sequence boundary (SB)-transgressive surface (TS) relation in nature shows that applying transgressive surfaces as sequence boundaries has the following merits: it improves the methodology of stratigraphic subdivision; the position of transgressive surface in a sea level curve is relatively fixed; the transgressive surface is a transforming surface of the stratal structure; in platforms or ramps, the transgressive surface is the only choice for determining the sequence boundary; the transgressive surface is a readily recognized physical surface reflected by seismic records in seismostratigraphy. The paper reaches a conclusion that to delineate a SB in terms of the TS is theoretically and practically better than to delineate it between highstand and lowstand sediments as has been done traditionally.

  20. On the base sequence conjecture

    CERN Document Server

    Djokovic, Dragomir Z

    2010-01-01

    Let BS(m,n) denote the set of base sequences (A;B;C;D), with A and B of length m and C and D of length n. The base sequence conjecture (BSC) asserts that BS(n+1,n) exist (i.e., are non-empty) for all n. This is known to be true for n <= 36 and when n is a Golay number. We show that it is also true for n=37 and n=38. It is worth pointing out that BSC is stronger than the famous Hadamard matrix conjecture. In order to demonstrate the abundance of base sequences, we have previously attached to BS(n+1,n) a graph Gamma_n and computed the Gamma_n for n <= 27. We now extend these computations and determine the Gamma_n for n=28,...,35. We also propose a conjecture describing these graphs in general.

  1. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    . All but one sequence mapped to the MCP gene while the last sequence mapped to the Neurofilament gene. Approx. half of the sequences contained no errors while the rest differed with 88-99 percent similarity with most having 99% similarity. One sequence, when BLASTed, showed most similarity to European...... 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...

  2. Sequence Patterns of Identity Authentication Protocols

    Institute of Scientific and Technical Information of China (English)

    Tao Hongcai; He Dake

    2006-01-01

    From the viewpoint of protocol sequence, analyses are made of the sequence patterns of possible identity authentication protocol under two cases: with or without the trusted third party (TTP). Ten feasible sequence patterns of authentication protocol with TTP and 5 sequence patterns without TTP are gained. These gained sequence patterns meet the requirements for identity authentication,and basically cover almost all the authentication protocols with TTP and without TTP at present. All of the sequence patterns gained are classified into unilateral or bilateral authentication. Then , according to the sequence symmetry, several good sequence patterns with TTP are evaluated. The accompolished results can provide a reference to design of new identity authentication protocols.

  3. Seismic sequences, swarms, and large earthquakes in Italy

    Science.gov (United States)

    Amato, Alessandro; Piana Agostinetti, Nicola; Selvaggi, Giulio; Mele, Franco

    2016-04-01

    In recent years, particularly after the L'Aquila 2009 earthquake and the 2012 Emilia sequence, the issue of earthquake predictability has been at the center of the discussion in Italy, not only within the scientific community but also in the courtrooms and in the media. Among the noxious effects of the L'Aquila trial there was an increase of scaremongering and false alerts during earthquake sequences and swarms, culminated in a groundless one-night evacuation in northern Tuscany in 2013. We have analyzed the Italian seismicity of the last decades in order to determine the rate of seismic sequences and investigate some of their characters, including frequencies, min/max durations, maximum magnitudes, main shock timing, etc. Selecting only sequences with an equivalent magnitude of 3.5 or above, we find an average of 30 sequences/year. Although there is an extreme variability in the examined parameters, we could set some boundaries, useful to obtain some quantitative estimates of the ongoing activity. In addition, the historical catalogue is rich of complex sequences in which one main shock is followed, seconds, days or months later, by another event with similar or higher magnitude We also analysed the Italian CPT11 catalogue (Rovida et al., 2011) between 1950 and 2006 to highlight the foreshock-mainshock event couples that were suggested in previous studies to exist (e.g. six couples, Marzocchi and Zhuang, 2011). Moreover, to investigate the probability of having random foreshock-mainshock couples over the investigated period, we produced 1000 synthetic catalogues, randomly distributing in time the events occured in such period. Preliminary results indicate that: (1) all but one of the the so-called foreshock-mainshock pairs found in Marzocchi and Zhuang (2011) fall inside previously well-known and studied seismic sequences (Belice, Friuli and Umbria-Marche), meaning that suggested foreshocks are also aftershocks; and (2) due to the high-rate of the italian

  4. Applied Sequence Stratigraphy in Nonmarine Basin of China

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper presents a preliminary summary of the applied sequence stratigraphy in nonmarine basins in China. The geological and geophysical data show that the nonmarine sequences mainly resulted from both allocyclic and autocyclic processes where the most important factors were isolated tectonics and climate. However, the environmental factor should have been crucial. The depositionai base level served as the sea level in the marine environment, while the water table, lake level and fluvial equilibrium were profiled in a terrigenous environment. This accommodation varied periodically with the base level, resulting in the formation of a series of depositional sequences in terms of genesis and space. Basically, the base level of the inner continent was not affected by the changes in the relative sea level. But there would have been some relations between the changes in the relative sea level and that in the continental base level during eustacy flooding. However, a small time lag existed between the changes in the marine basin and the inner continent basin, The lake basin is smaller than the marine basin,but its velocity of sediment supply is greater than that of the marine basin. Therefore, the number of nonmarine sequences is greater than that of marine ones in the same period. It is important to recognize the system tracts for the study of high-precision or high-resolution sequence stratigraphy, especially to analyze the Iow-stand systems tract with its depositional system. The sequence boundary is genetically characterized by subaerial exposure, stratigraphic truncation and subaqueous erosion. The deposition analysis of Zhanhua depression reveals 5 sequence architectures: alluvial-fluvial/lacustrine architecture,transitional architecture formed between haline (mesohaline) lake and fresh lake, marine duration-deep lacustrine architecture, half deep lacustrine-ramp architecture and fluvial-alluvial plain architecture.During the major development of the nonmarine

  5. KERNEL WORDS AND GAP SEQUENCE OF THE TRIBONACCI SEQUENCE

    Institute of Scientific and Technical Information of China (English)

    Yuke HUANG; Zhiying WEN

    2016-01-01

    In this paper, we investigate the factor properties and gap sequence of the Tri-bonacci sequence, the fixed point of the substitution σ(a, b, c) = (ab, ac, a). Let ωp be the p-th occurrence of ω and Gp(ω) be the gap between ωp and ωp+1. We introduce a notion of kernel for each factor ω, and then give the decomposition of the factor ω with respect to its kernel. Using the kernel and the decomposition, we prove the main result of this paper:for each factorω, the gap sequence{Gp(ω)}p≥1 is the Tribonacci sequence over the alphabet{G1(ω), G2(ω), G4(ω)}, and the expressions of gaps are determined completely. As an appli-cation, for each factorω and p∈N, we determine the position ofωp. Finally we introduce a notion of spectrum for studying some typical combinatorial properties, such as power, overlap and separate of factors.

  6. Sequences and series involving the sequence of composite numbers

    Directory of Open Access Journals (Sweden)

    Panayiotis Vlamos

    2002-01-01

    Full Text Available Denoting by pn and cn the nth prime number and the nth composite number, respectively, we prove that both the sequence (xnn≥1, defined by xn=∑k=1n (ck+1−ck / k−pn / n, and the series ∑n=1∞ (pcn−cpn / npn are convergent.

  7. 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.

  8. 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

  9. Network motifs in music sequences

    CERN Document Server

    Zanette, Damian H

    2010-01-01

    In this note, I summarize ongoing research on motif distribution in networks built up out of symbolic sequences of Western musical origin. Their motif significance profiles exhibit remarkable consistency over different styles and periods, and define a class that cannot be identified with any of the four "superfamilies" to which most real networks seem to belong. Networks from music sequences possess an unusual abundance of bidirectional connections, due to the inherent reversibility of short musical note patterns. This property contributes to motif significance from both local and large-scale features of musical structure.

  10. Convergence of Fuzzy Set Sequences

    Institute of Scientific and Technical Information of China (English)

    FENG Yu-hu

    2002-01-01

    There are more than one mode of convergence with respect to the fuzzy set sequences. In this paper,common six modes of convergence and their relationships are discussed. These six modes are convergence in uniform metric D, convergence in separable metric Dp or D*p, 1 ≤ p <∞, convergence in level set, strong convergence in level set and weak convergence. Suitable counterexamples are given. The necessary and sufficient conditions of convergence in uniform metric D are described. Some comme nts on the convergence of LRfuzzy number sequences are represented.

  11. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger

    2011-05-09

    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  12. Preliminary investigations of piezoelectric based LED luminary

    DEFF Research Database (Denmark)

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

    2011-01-01

    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......, 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...

  13. PRELIMINARY PROGRAMMED WHOLE—BODY COUNTER

    Institute of Scientific and Technical Information of China (English)

    张少东; 郑文忠; 等

    1995-01-01

    It is capable of giving the initial intakes of radionuclides and the assessment quantitites used in radiation protection according to its measured results of radionuclides in vivo.It is accomplished by providing the software of controlling,interface and internal dose estimation programs to the original iron cabin shielding whole-body counter.The preliminary application shows that its data processing is rapid and correct,and can meet the requirement of rapid internal radioactive contamination monitoring and diagnosing in case of lots of internal contamination subjects happened in nuclear accident.

  14. Underwater Munitions Expert System: Preliminary Design Report

    Science.gov (United States)

    2015-08-21

    coral   reefs ,  can  be  added  to  future  versions  of  UnMES.     For  this  preliminary  UnMES...administer  areas   polluted  by  discarded  munitions.    Towards  this  end,  SERDP  is   sponsoring   the   development...estimating   seawater   pollution   from   dissolved   chemical   components  of  munitions.    

  15. Preliminary results from a new spin spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Tobin, J.G.; Bedrossian, P.J. [Lawrence Livermore National Lab., CA (United States); Cummins, T.R. [Univ. of Missouri, Rolla, MO (United States). Dept. of Physics] [and others

    1998-12-31

    The first preliminary results from a novel spectrometer for elementally-specific measurements of magnetic surfaces and ultrathin films are presented here. The key measurements are based upon spin-resolving and photon-dichroic photoelectron spectroscopy. True spin-resolution is achieved by the use of a Mini-Mott detection scheme. The photon-dichroic measurements include the variant magnetic x-ray linear dichroism (MXLD). Both a multi-channel, energy dispersive collection scheme as well as the spin-detecting Mini-Mott apparatus are used in data collection. The Spin Spectrometer is based at the Spectromicroscopy Facility (Beamline 7) at the Advanced Light Source.

  16. preliminary study of American legal culture

    Institute of Scientific and Technical Information of China (English)

    周杨

    2016-01-01

    This thesis is a preliminary study of American legal culture. Nowadays more and more scholars see the importance of legal culture and do studies on it. The author selects a number of American legal TV plays and movies; analyzes their topics, main characters, and plots; then finds out why United States adopt the legal system; what kind of legal culture it has; and how the legal culture is reflected in those movies and TV plays. The author hopes this thesis can work not only as an insight into the American legal culture, but also a source of reference for china to improve its legal system.

  17. 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...

  18. Preliminary results on nonparametric facial occlusion detection

    Directory of Open Access Journals (Sweden)

    Daniel LÓPEZ SÁNCHEZ

    2016-10-01

    Full Text Available The problem of face recognition has been extensively studied in the available literature, however, some aspects of this field require further research. The design and implementation of face recognition systems that can efficiently handle unconstrained conditions (e.g. pose variations, illumination, partial occlusion... is still an area under active research. This work focuses on the design of a new nonparametric occlusion detection technique. In addition, we present some preliminary results that indicate that the proposed technique might be useful to face recognition systems, allowing them to dynamically discard occluded face parts.

  19. 33 CFR 127.315 - Preliminary transfer inspection.

    Science.gov (United States)

    2010-07-01

    ... (CONTINUED) WATERFRONT FACILITIES WATERFRONT FACILITIES HANDLING LIQUEFIED NATURAL GAS AND LIQUEFIED HAZARDOUS GAS Waterfront Facilities Handling Liquefied Natural Gas Operations § 127.315 Preliminary...

  20. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Toon Rosseel

    Full Text Available Sequence Independent Single Primer Amplification is one of the most widely used random amplification approaches in virology for sequencing template preparation. This technique relies on oligonucleotides consisting of a 3' random part used to prime complementary DNA synthesis and a 5' defined tag sequence for subsequent amplification. Recently, this amplification method was combined with next generation sequencing to obtain viral sequences. However, these studies showed a biased distribution of the resulting sequence reads over the analyzed genomes. The aim of this study was to elucidate the mechanisms that lead to biased sequence depth when using random amplification. Avian paramyxovirus type 8 was used as a model RNA virus to investigate these mechanisms. We showed, based on in silico analysis of the sequence depth in relation to GC-content, predicted RNA secondary structure and sequence complementarity to the 3' part of the tag sequence, that the tag sequence has the main contribution to the observed bias in sequence depth. We confirmed this finding experimentally using both fragmented and non-fragmented viral RNAs as well as primers differing in random oligomer length (6 or 12 nucleotides and in the sequence of the amplification tag. The observed oligonucleotide annealing bias can be reduced by extending the random oligomer sequence and by in silico combining sequence data from SISPA experiments using different 5' defined tag sequences. These findings contribute to the optimization of random nucleic acid amplification protocols that are currently required for downstream applications such as viral metagenomics and microarray analysis.

  1. 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.

  2. 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. PMID:23527290

  3. 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

  4. 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.

  5. Instruction Sequences for Computer Science

    NARCIS (Netherlands)

    Bergstra, J.A.; Middelburg, C.A.

    2012-01-01

    This book demonstrates that the concept of an instruction sequence offers a novel and useful viewpoint on issues relating to diverse subjects in computer science. Selected issues relating to well-known subjects from the theory of computation and the area of computer architecture are rigorously

  6. Single-primer fluorescent sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Ruth, J.L.; Morgan, C.A.; Middendorf, L.R.; Grone, D.L.; Brumbaugh, J.A.

    1987-05-01

    Modified linker arm oligonucleotides complementary to standard M13 priming sites were synthesized, labelled with either one, two, or three fluoresceins, and purified by reverse-phase HPLC. When used as primers in standard dideoxy M13 sequencing with /sup 32/P-dNTPs, normal autoradiographic patterns were obtained. To eliminate the radioactivity, direct on-line fluorescence detection was achieved by the use of a scanning 10 mW Argon laser emitting 488 nm light. Fluorescent bands were detected directly in standard 0.2 or 0.35 mm thick polyacrylamide gels at a distance of 24 cm from the loading wells by a photomultiplier tube filtered at 520 nm. Horizontal and temporal location of each band was displayed by computer as a band in real time, providing visual appearance similar to normal 4-lane autoradiograms. Using a single primer labelled with two fluoresceins, sequences of between 500 and 600 bases have been read in a single loading with better than 98% accuracy; up to 400 bases can be read reproducibly with no errors. More than 50 sequences have been determined by this method. This approach requires only 1-2 ug of cloned template, and produces continuous sequence data at about one band per minute.

  7. Multifractal analyses of music sequences

    Science.gov (United States)

    Su, Zhi-Yuan; Wu, Tzuyin

    2006-09-01

    Multifractal analysis is applied to study the fractal property of music. In this paper, a method is proposed to transform both the melody and rhythm of a music piece into individual sets of distributed points along a one-dimensional line. The structure of the musical composition is thus manifested and characterized by the local clustering pattern of these sequences of points. Specifically, the local Hölder exponent and the multifractal spectrum are calculated for the transformed music sequences according to the multifractal formalism. The observed fluctuations of the Hölder exponent along the music sequences confirm the non-uniformity feature in the structures of melodic and rhythmic motions of music. Our present result suggests that the shape and opening width of the multifractal spectrum plot can be used to distinguish different styles of music. In addition, a characteristic curve is constructed by mapping the point sequences converted from the melody and rhythm of a musical work into a two-dimensional graph. Each different pieces of music has its own unique characteristic curve. This characteristic curve, which also exhibits a fractal trait, unveils the intrinsic structure of music.

  8. 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.

  9. Farey Sequences and Resistor Networks

    Indian Academy of Sciences (India)

    Sameen Ahmed Khan

    2012-05-01

    In this article, we employ the Farey sequence and Fibonacci numbers to establish strict upper and lower bounds for the order of the set of equivalent resistances for a circuit constructed from equal resistors combined in series and in parallel. The method is applicable for networks involving bridge and non-planar circuits.

  10. Complete genomic sequence and an infectious BAC clone of feline herpesvirus-1 (FHV-1).

    Science.gov (United States)

    Tai, S H Sheldon; Niikura, Masahiro; Cheng, Hans H; Kruger, John M; Wise, Annabel G; Maes, Roger K

    2010-06-05

    Infection with feline herpesvirus-1 (FHV-1) is a major cause of upper respiratory and ocular diseases in Felidae. We report the first complete genomic sequence of FHV-1, as well as the construction and characterization of a bacterial artificial chromosome (BAC) clone of FHV-1, which contains the entire FHV-1 genome and has the BAC vector inserted at the left end of U(L). Complete genomic sequences were derived from both the FHV-1 BAC clone and purified virion DNA. The FHV-1 genome is 135,797bp in size with an overall G+C content of 45%. A total of 78 open reading frames were predicted, encoding 74 distinct proteins. The gene arrangement is collinear with that of most sequenced varicelloviruses. The virus regenerated from the BAC was very similar to the parental C-27 strain in vitro in terms of plaque morphology and growth characteristics and highly virulent in cats in a preliminary in vivo study.

  11. Preliminary Results of Field Emission Cathode Tests

    Science.gov (United States)

    Sovey, James S.; Kovaleski, Scott D.

    2001-01-01

    Preliminary screening tests of field emission cathodes such as chemical vapor deposited (CVD) diamond, textured pyrolytic graphite, and textured copper were conducted at background pressures typical of electric thruster test facilities to assess cathode performance and stability. Very low power electric thrusters which provide tens to hundreds micronewtons of thrust may need field emission neutralizers that have a capability of tens to hundreds of microamperes. From current voltage characteristics, it was found that the CVD diamond and textured metals cathodes clearly satisfied the Fowler-Nordheim emission relation. The CVD diamond and a textured copper cathode had average current densities of 270 and 380 mA/sq cm, respectively, at the beginning-of-life. After a few hours of operation the cathode emission currents degraded by 40 to 75% at background pressures in the 10(exp -5) Pa to 10(exp -4) Pa range. The textured pyrolytic graphite had a modest current density at beginning-of-life of 84 mA/sq cm, but this cathode was the most stable of all. Extended testing of the most promising cathodes is warranted to determine if current degradation is a burn-in effect or whether it is a long-term degradation process. Preliminary experiments with ferroelectric emission cathodes, which are ceramics with spontaneous electric polarization, were conducted. Peak current densities of 30 to 120 mA/sq cm were obtained for pulse durations of about 500 ns in the 10(exp -4) Pa pressure range.

  12. 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.

  13. Preliminary impression techniques for microstomia patients.

    Science.gov (United States)

    Kumar, K Aswini; Bhat, Vinaya; Nair, K Chandrasekheran; Suresh, Reshma

    2016-01-01

    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. Fabrication of preliminary fuel rods for SFR

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sun Ki; Oh, Seok Jin; Ko, Young Mo; Woo, Youn Myung; Kim, Ki Hwan [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2012-05-15

    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

  15. 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...

  16. 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.

  17. 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.

  18. 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.

  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. Preliminary Hazards Analysis Plasma Hearth Process

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

  1. Preliminary design for a MAGLEV development facility

    Science.gov (United States)

    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.; Zhang, Z. Y.

    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 from 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.

  2. Preliminary results of ground-motion characteristics

    Directory of Open Access Journals (Sweden)

    Francesca Bozzoni

    2012-10-01

    Full Text Available The preliminary results are presented herein for the engineering applications of the characteristics of the ground motion induced by the May 20, 2012, Emilia earthquake. Shake maps are computed to provide estimates of the spatial distribution of the induced ground motion. The signals recorded at the Mirandola (MRN station, the closest to the epicenter, have been processed to obtain acceleration, velocity and displacement response spectra. Ground-motion parameters from the MRN recordings are compared with the corresponding estimates from recent ground-motion prediction equations, and with the spectra prescribed by the current Italian Building Code for different return periods. The records from the MRN station are used to plot the particle orbit (hodogram described by the waveform. The availability of results from geotechnical field tests that were performed at a few sites in the Municipality of Mirandola prior to this earthquake of May 2012 has allowed preliminary assessment of the ground response. The amplification effects at Mirandola are estimated using fully stochastic site-response analyses. The seismic input comprises seven actual records that are compatible with the Italian code-based spectrum that refers to a 475-year return period. The computed acceleration response spectrum and the associated dispersion are compared to the spectra calculated from the recordings of the MRN station. Good agreement is obtained for periods up to 1 s, especially for the peak ground acceleration. For the other periods, the spectral acceleration of the MRN recordings exceeds that of the computed spectra.

  3. ISSA/TSS power preliminary design

    Science.gov (United States)

    Main, John A.

    1996-01-01

    A projected power shortfall during the initial utilization flights of the International Space Station Alpha (ISSA) has prompted an inquiry into the use of the Tethered Satellite System (TSS) to provide station power. The preliminary design of the combined ISSA/TSS system is currently underway in the Preliminary Design Office at the Marshall Space Flight Center. This document focuses on the justification for using a tether system on space station, the physical principles behind such a system, and how it might be operated to best utilize its capabilities. The basic components of a simple DC generator are a magnet of some type and a conductive wire. Moving the wire through the magnetic field causes forces to be applied to the electric charges in the conductor, and thus current is induced to flow. This simple concept is the idea behind generating power with space-borne tether systems. The function of the magnet is performed by the earth's magnetic field, and orbiting a conductive tether about the earth effectively moves the tether through the field.

  4. 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.)

  5. 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…

  6. The Toothpick Sequence and Other Sequences from Cellular Automata

    CERN Document Server

    Applegate, David; Sloane, N J A

    2010-01-01

    A two-dimensional arrangement of toothpicks is constructed by the following iterative procedure. At stage 1, place a single toothpick of length 1 on a square grid, aligned with the y-axis. At each subsequent stage, for every exposed toothpick end, place an orthogonal toothpick centered at that end. The resulting structure has a fractal-like appearance. We will analyze the toothpick sequence, which gives the total number of toothpicks after n steps. We also study several related sequences that arise from enumerating active cells in cellular automata. Some unusual recurrences appear: a typical example is that instead of the Fibonacci recurrence, which we may write as a(2+i) = a(i) + a(i+1), we set n = 2^k+i (0 = 0} (1+x^{2^k-1}+2x^{2^k}) and variations thereof.

  7. Algebraic divisibility sequences over function fields

    CERN Document Server

    Ingram, Patrick; Silverman, Joseph H; Stange, Katherine E; Streng, Marco

    2011-01-01

    We study the existence of primes and of primitive divisors in classical divisibility sequences defined over function fields. Under various hypotheses, we prove that Lucas sequences and elliptic divisibility sequences over function fields defined over number fields contain infinitely many irreducible elements. We also prove that an elliptic divisibility sequence over a function field has only finitely many terms lacking a primitive divisor.

  8. Stream cipher based on GSS sequences

    Institute of Scientific and Technical Information of China (English)

    HU Yupu; XIAO Guozhen

    2004-01-01

    Generalized self-shrinking sequences, simply named the GSS sequences,are novel periodic sequences that have many advantages in cryptography. In this paper,we give several results about GSS sequence's application to cryptography. First, we give a simple method for selecting those GSS sequences whose least periods reach the maximum. Second, we give a method for describing and computing the auto-correlation coefficients of GSS sequences. Finally, we point out that some GSS sequences, when used as stream ciphers, have a security weakness.

  9. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol;

    2010-01-01

    BACKGROUND: The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. RESULTS: Assemblies......) is under construction and will incorporate whole genome shotgun sequence (WGS) data providing > 30x genome coverage. The WGS sequence, most of which comprise short Illumina/Solexa reads, were generated from DNA from the same single Duroc sow as the source of the BAC library from which clones were...

  10. Sequence-structure relations of biopolymers

    CERN Document Server

    Barrett, Christopher; Reidys, Christian M

    2015-01-01

    Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as structural semantics of sequence data that allows for a different interpretation than conventional sequence alignment. Structural semantics could enable us to identify more general embedded "patterns" in DNA and RNA sequences. Results: We compute the partition function of sequences with respect to a fixed structure and connect this computation to the mutual information of a sequence-structure pair for RNA secondary structures. We present a Boltzmann sampler and obtain the a priori probability of specific sequence patterns. We present a detailed analysis for the three PDB-structures, 2JXV (hairpin), 2N3R (3-branch multi-loop) and 1EHZ (tRNA). We localize specific sequence patterns, contrast the energy spectrum of the Boltzmann sampled sequences versus those sequences that refold ...

  11. Expressing stochastic filters via number sequences

    OpenAIRE

    Capponi, A.; Farina, A; Pilotto, C.

    2010-01-01

    We generalize the results presented in [1] regarding the relation between the Kalman filter and the Fibonacci sequence. We consider more general filtering models and relate the finite dimensional Kalman and Benes filters to the Fibonacci sequence and to the Golden Section. We also prove that Fibonacci numbers may be expressed as the convolution of the Fibonacci and Padovan sequence, thus extending the connection between stochastic filtering and Fibonacci sequence to the Padovan sequence.

  12. Preliminary criteria for the very early diagnosis of systemic sclerosis

    DEFF Research Database (Denmark)

    Avouac, J; Fransen, Julie Munk; Walker, U A

    2011-01-01

    To identify a core set of preliminary items considered as important for the very early diagnosis of systemic sclerosis (SSc).......To identify a core set of preliminary items considered as important for the very early diagnosis of systemic sclerosis (SSc)....

  13. 40 CFR 8.6 - Preliminary environmental review.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Preliminary environmental review. 8.6 Section 8.6 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY GENERAL ENVIRONMENTAL IMPACT ASSESSMENT OF NONGOVERNMENTAL ACTIVITIES IN ANTARCTICA § 8.6 Preliminary environmental review. (a) Unless an...

  14. Preliminary design of pseudo satellites: Basic methods and feasibility criteria

    Science.gov (United States)

    Klimenko, N. N.

    2016-12-01

    Analytical models of weight and energy balances, aerodynamic models, and solar irradiance models to perform pseudo-satellite preliminary design are presented. Feasibility criteria are determined in accordance with the aim of preliminary design dependent on mission scenario and type of payload.

  15. 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... violated his parole as charged, and if so, whether a revocation hearing should be conducted. The...

  16. 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...

  17. 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.

  18. Preliminary design package for Sunair SEC-601 solar collector

    Energy Technology Data Exchange (ETDEWEB)

    1978-12-01

    This report presents the preliminary design of the Owens-Illinois mode Sunair SEC-601 tubular air solar collector. Information in this package includes the Subsystem Design and Development Approaches, hazard analysis, and detailed drawings available as the Preliminary Design Review.

  19. Cold Gas in Blue-Sequence E/S0s: Galaxies in Transition

    CERN Document Server

    Wei, Lisa H; Vogel, Stuart N; Baker, Andrew J

    2009-01-01

    We examine the HI+H_2 content of blue-sequence E/S0s -- a recently identified population of galaxies that are morphologically early type, but reside alongside spiral galaxies in color vs. stellar mass space. We test the idea that the majority of low-to-intermediate mass blue-sequence E/S0s may be settled products of past mergers evolving toward later-type morphology via disk regrowth. We find that blue-sequence E/S0s with stellar masses 1.0, comparable to those of spiral galaxies. Preliminary CO(1-0) maps reveal disk-like rotation of molecular gas in the inner regions of several of our blue-sequence E/S0s, which suggests that they may have gas disks suitable for stellar disk regrowth. At the current rate of star formation, many of our blue-sequence E/S0s will exhaust their atomic gas reservoirs in <~ 3 Gyr. Over the same time period, most of these galaxies are capable of substantial growth in the stellar component. Star formation in blue-sequence E/S0s appears to be bursty, and likely involves inflow trig...

  20. 76 FR 39399 - Chlorpyrifos Registration Review; Preliminary Human Health Risk Assessment; Notice of Availability

    Science.gov (United States)

    2011-07-06

    ... AGENCY Chlorpyrifos Registration Review; Preliminary Human Health Risk Assessment; Notice of Availability... availability of EPA's preliminary human health risk assessment for the registration review of chlorpyrifos and... comprehensive preliminary human health risk assessment for all chlorpyrifos uses. After reviewing comments...

  1. 76 FR 52945 - Chlorpyrifos Registration Review; Preliminary Human Health Risk Assessment; Extension of Comment...

    Science.gov (United States)

    2011-08-24

    ... AGENCY Chlorpyrifos Registration Review; Preliminary Human Health Risk Assessment; Extension of Comment... availability of the chlorpyrifos registration review; preliminary human health risk assessment. This document... for the chlorpyrifos reregistration review, preliminary human health risk assessment, established in...

  2. 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.

  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. Genome Sequence of Mycobacteriophage Momo.

    Science.gov (United States)

    Pope, Welkin H; Bina, Elizabeth A; Brahme, Indraneel S; Hill, Amy B; Himmelstein, Philip H; Hunsicker, Sara M; Ish, Amanda R; Le, Tinh S; Martin, Mary M; Moscinski, Catherine N; Shetty, Sameer A; Swierzewski, Tomasz; Iyengar, Varun B; Kim, Hannah; Schafer, Claire E; Grubb, Sarah R; Warner, Marcie H; Bowman, Charles A; Russell, Daniel A; Hatfull, Graham F

    2015-06-18

    Momo is a newly discovered phage of Mycobacterium smegmatis mc(2)155. Momo has a double-stranded DNA genome 154,553 bp in length, with 233 predicted protein-encoding genes, 34 tRNA genes, and one transfer-messenger RNA (tmRNA) gene. Momo has a myoviral morphology and shares extensive nucleotide sequence similarity with subcluster C1 mycobacteriophages. Copyright © 2015 Pope et al.

  5. Multiplicative LSTM for sequence modelling

    OpenAIRE

    Krause, Ben; Lu, Liang; Murray, Iain; Renals, Steve

    2016-01-01

    This paper introduces multiplicative LSTM, a novel hybrid recurrent neural network architecture for sequence modelling that combines the long short-term memory (LSTM) and multiplicative recurrent neural network architectures. Multiplicative LSTM is motivated by its flexibility to have very different recurrent transition functions for each possible input, which we argue helps make it more expressive in autoregressive density estimation. We show empirically that multiplicative LSTM outperforms ...

  6. Preliminary Model of Porphyry Copper Deposits

    Science.gov (United States)

    Berger, Byron R.; Ayuso, Robert A.; Wynn, Jeffrey C.; Seal, Robert R., II

    2008-01-01

    The U.S. Geological Survey (USGS) Mineral Resources Program develops mineral-deposit models for application in USGS mineral-resource assessments and other mineral resource-related activities within the USGS as well as for nongovernmental applications. Periodic updates of models are published in order to incorporate new concepts and findings on the occurrence, nature, and origin of specific mineral deposit types. This update is a preliminary model of porphyry copper deposits that begins an update process of porphyry copper models published in USGS Bulletin 1693 in 1986. This update includes a greater variety of deposit attributes than were included in the 1986 model as well as more information about each attribute. It also includes an expanded discussion of geophysical and remote sensing attributes and tools useful in resource evaluations, a summary of current theoretical concepts of porphyry copper deposit genesis, and a summary of the environmental attributes of unmined and mined deposits.

  7. Repository Subsurface Preliminary Fire Hazard Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Richard C. Logan

    2001-07-30

    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&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.

  8. 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.

  9. The Preliminaries of a Reference: Chain

    DEFF Research Database (Denmark)

    Butler, Graham; Sadl, Urska

    2016-01-01

    No decisive ruling was delivered by the Court of Justice of the European Union (hereafter: the Court) in Case C-189/14, Bogdan Chain v Atlanco Ltd. There is usually no case note worth writing without a judgment. However, the case in question came close to being concluded with a judgment, and the ......No decisive ruling was delivered by the Court of Justice of the European Union (hereafter: the Court) in Case C-189/14, Bogdan Chain v Atlanco Ltd. There is usually no case note worth writing without a judgment. However, the case in question came close to being concluded with a judgment......, and the reasons why no conclusive ruling was delivered is precisely what makes this case worth writing about. A preliminary reference was issued by a national court in Nicosia (Cyprus) following which at the Court, a reporting Judge and Advocate General were appointed. An oral hearing in the presence...

  10. CTF3 Design Report Preliminary Phase

    CERN Document Server

    Allard, D; Bernard, M; Bertuzzi, J P; Bienvenu, G; Bonzano, R; Bossart, Rudolf; Braun, H; Bravin, Enrico; Borburgh, J; Buttkus, J; Chazarenc, E; Chaput, R; Chohan, V; Cloye, J J; Corsini, R; Coudert, G; Damiani, M; Deghaye, S; Delahaye, J P; Di Maio, F; Dobers, T; Dubief, P; Dupuy, B; Durieu, L; Ferrari, A; Garvey, Terence; Geschonke, Günther; Hansen, J; Hellgren, H; Hourican, M; Lamidon, M; Le Duff, J; Lefèvre, T; Lewis, J H; Lindroos, J; Mahner, E; McMonagle, G; Monteiro, J; Mourier, J; Mouton, B; Odier, P; Otto, T; Pearce, P; Pittin, R; Poehler, M; Potier, J P; Raich, U; Rettig, M; Rinolfi, Louis; Risselada, Thys; Riva, R; Rossat, G; Royer, P; Sermeus, L; Setas, K; Simonet, G; Sladen, Jonathan P H; Søby, L; Tanner, L; Tecker, F A; Thomi, J C; Wilson, Ian H; Yvon, G

    2001-01-01

    The design of CLIC is based on a two-beam scheme, where the short pulses of high power 30 GHz RF are extracted from a drive beam running parallel to the main beam. The 3rd generation CLIC Test Facility (CTF3) will demonstrate the generation of the drive beam with the appropriate time structure, the extraction of 30 GHz RF power from this beam, as well as acceleration of a probe beam with 30 GHz RF cavities. The project makes maximum use of existing equipment and infrastructure of the LPI complex, which became available after the closure of LEP. In the first stage of the project, the "Preliminary Phase", the existing LIL linac and the EPA ring, both modified to suit the new requirements, are used to investigate the technique of frequency multiplication by means of interleaving bunches from subsequent trains. This report describes the design of this phase.

  11. Laryngeal electromyography in movement disorders: preliminary data

    Directory of Open Access Journals (Sweden)

    Kimaid Paulo A.T.

    2004-01-01

    Full Text Available This study describes preliminary laryngeal electromyography (LEMG data and botulinum toxin treatment in patients with dysphonia due to movement disorders. Twenty-five patients who had been clinically selected for botulinum toxin administration were examined, 19 with suspected laryngeal dystonia or spasmodic dysphonia (SD, 5 with vocal tremor, and 1 with Gilles de la Tourette syndrome (GTS. LEMG evaluations were performed before botulinum toxin administration using monopolar electrodes. Electromyography was consistent with dystonia in 14 patients and normal in 5, and differences in frequency suggesting essential tremor in 3 and Parkinson tremors in 2. The different LEMG patterns and significant improvement in our patients from botulinum toxin therapy has led us to perform laryngeal electromyography as a routine in UNICAMP movement disorders ambulatory.

  12. Lockheed Martin T-Rex: Preliminary report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-07-31

    T-Rex is a robot which may be used in toxic or flammable environments. The assessment of the T-Rex conducted at the Lockheed Martin facility was limited in its scope. The scope of the assessment was directed by the type of equipment being used and the amount of accessibility to the equipment. Due to severe time constraints--the assessment was conducted in one day--human factors interface activities were limited. This should be considered a preliminary assessment. This report covers aspects of the technology that were available to the assessment team. Recommendations for future evaluation of this technology are also included. The contents are as follows: Electrical Considerations; General Electrical Consideration; Trailing Cables; Grounding; Surface High Voltage Distribution; Low and Medium Voltage Alternating Current Circuits; Potential for Harmful Human Factor Incidents and Enterprise Disablement; Exclusion Zone Emergency Maintenance; and Recommendations.

  13. Preliminary Design of a Femtosecond Oscilloscope

    CERN Document Server

    Gazazyan, Edmond D; Kalantaryan, Davit K; Laziev, Edouard; Margaryan, Amour

    2005-01-01

    The calculations on motion of electrons in a finite length electromagnetic field of linearly and circularly polarized laser beams have shown that one can use the transversal deflection of electrons on a screen at a certain distance after the interaction region for the measurement of the length and longitudinal particle distribution of femtosecond bunches. In this work the construction and preliminary parameters of various parts of a device that may be called femtosecond oscilloscope are considered. The influence of various factors, such as the energy spread and size of the electron bunches, are taken into account. For CO2 laser intensity 1016 W/cm2 and field free drift length 1m the deflection is 5.3 and 0.06 cm, while the few centimeters long interaction length between 2 mirrors requires assembling accuracy 6 mm and 1.3 micron for 20 MeV to 50 keV, respectively.

  14. Helminthiases in Montes Claros. Preliminary survey

    Directory of Open Access Journals (Sweden)

    Rina Girard Kaminsky

    1976-04-01

    Full Text Available A preliminary survey was conducted for the presence of helminths in the city of Montes Claros, M. G., Brazil. Three groups of persons were examined by the direct smear, Kato thick film and MIFC techniques; one group by direct smear and Kato only. General findings were: a high prevalence of hookworm, followed by ascariasis, S. mansoni, S. stercoralis and very light infections with T. trichiurá. E. vermicularis and H. nana were ranking parasites at an orphanage, with some hookworm and S. mansoni infections as well. At a pig slaughter house, the dominant parasites were hookworm and S. mansoni. Pig cysticercosis was an incidental finding worth mentioning for the health hazard it represents for humans as well as an economic loss. From the comparative results between the Kato and the MIF the former proved itself again as a more sensitive and reliable concentration method for helminth eggs, of low cost and easy performance.

  15. North Korean refugee doctors' preliminary examination scores

    Directory of Open Access Journals (Sweden)

    Sung Uk Chae

    2016-12-01

    Full Text Available Purpose Although there have been studies emphasizing the re-education of North Korean (NK doctors for post-unification of the Korean Peninsula, study on the content and scope of such re-education has yet to be conducted. Researchers intended to set the content and scope of re-education by a comparative analysis for the scores of the preliminary examination, which is comparable to the Korean Medical Licensing Examination (KMLE. Methods The scores of the first and second preliminary exams were analyzed by subject using the Wilcoxon signed rank test. The passing status of the group of NK doctors for KMLE in recent 3 years were investigated. The multiple-choice-question (MCQ items of which difficulty indexes of NK doctors were lower than those of South Korean (SK medical students by two times of the standard deviation of the scores of SK medical students were selected to investigate the relevant reasons. Results The average scores of nearly all subjects were improved in the second exam compared with the first exam. The passing rate of the group of NK doctors was 75%. The number of MCQ items of which difficulty indexes of NK doctors were lower than those of SK medical students was 51 (6.38%. NK doctors’ lack of understandings for Diagnostic Techniques and Procedures, Therapeutics, Prenatal Care, and Managed Care Programs was suggested as the possible reason. Conclusion The education of integrated courses focusing on Diagnostic Techniques and Procedures and Therapeutics, and apprenticeship-style training for clinical practice of core subjects are needed. Special lectures on the Preventive Medicine are likely to be required also.

  16. Preliminary dose assessment of the Chernobyl accident

    Energy Technology Data Exchange (ETDEWEB)

    Hull, A.P.

    1987-01-01

    From the major accident at Unit 4 of the Chernobyl nuclear power station, a plume of airborne radioactive fission products was initially carried northwesterly toward Poland, thence toward Scandinavia and into Central Europe. Reports of the levels of radioactivity in a variety of media and of external radiation levels were collected in the Department of Energy's Emergency Operations Center and compiled into a data bank. Portions of these and other data which were obtained directly from published and official reports were utilized to make a preliminary assessment of the extent and magnitude of the external dose to individuals downwind from Chernobyl. Radioactive /sup 131/I was the predominant fission product. The time of arrival of the plume and the maximum concentrations of /sup 131/I in air, vegetation and milk and the maximum reported depositions and external radiation levels have been tabulated country by country. A large amount of the total activity in the release was apparently carried to a significant elevation. The data suggest that in areas where rainfall occurred, deposition levels were from ten to one-hundred times those observed in nearby ''dry'' locations. Sufficient spectral data were obtained to establish average release fractions and to establish a reference spectra of the other nuclides in the release. Preliminary calculations indicated that the collective dose equivalent to the population in Scandinavia and Central Europe during the first year after the Chernobyl accident would be about 8 x 10/sup 6/ person-rem. From the Soviet report, it appears that a first year population dose of about 2 x 10/sup 7/ person-rem (2 x 10/sup 5/ Sv) will be received by the population who were downwind of Chernobyl within the U.S.S.R. during the accident and its subsequent releases over the following week. 32 refs., 14 figs., 20 tabs.

  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. 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.

  19. Preliminary correlations of lithology and seismic reflectors in prograding Neogene carbonate of Great Bahama Bank

    Energy Technology Data Exchange (ETDEWEB)

    Eberli, G.P. (Geological Inst., Zurich (Switzerland)); Ginsburg, R.N.; Swart, P.K.; McNeill, D.F.; Kenter, J.A.M. (Univ. of Miami, FL (United States))

    1991-03-01

    Excellent overall recovery of 80% in two continuous core borings provides the data on lithology necessary to calibrate prograding late Cenozoic sequences and their seismic signatures. Hole UNDA, 10 km inside the modern platform edge of Great Bahama Bank (GBB), penetrated onlapping and topset reflectors and a buried platform rim. The 500 m core revealed two platform sequences alternating with fine grainstone units with internal hardground surfaces. At hole CLINO, 5.5 km farther basinward, 657 m of core document the progradation of GBB with 150 m of shallow platform deposits and reefal sequences over mostly fine-grained, foraminifera-rich periplatform slope sediments with intercalations of coarser beds, some of which contain platform lithoclasts. Within these slope deposits, there is significant variation in the degree of cementation; friable, porous limestones alternate with well cemented beds. Preliminary correlations between lithofacies and seismic signatures suggest a strong influence of both the sedimentologic and diagenetic facies on the seismic signal. Major lithologic changes, such as from mudstone to coral-bearing packstone or from skeletal sand to reefal limestone, produce strong reflectors. These latter transitions also coincide with seismic sequence boundaries. Within the more homogeneous slope sections, where seismic reflection horizons are not characterized by a facies change, differential cementation seems to be responsible for the seismic signal. Nevertheless, three reflectors identified as sequence boundaries are overlain by units containing coarse-grained beds with platform lithoclasts and blackened grains, indicating that these deposits were shed during low sea level and represent parts of the lowstand systems tract.

  20. Cloning and sequencing of the trpE gene from Arthrobacter globiformis ATCC 8010 and several related subsurface Arthrobacter isolates

    Energy Technology Data Exchange (ETDEWEB)

    Chernova, T.; Viswanathan, V.K.; Austria, N.; Nichols, B.P.

    1998-09-01

    Tryptophan dependent mutants of Arthrobacter globiformis ATCC 8010 were isolated and trp genes were cloned by complementation and marker rescue of the auxotrophic strains. Rescue studies and preliminary sequence analysis reveal that at least the genes trpE, trpC, and trpB are clustered together in this organism. In addition, sequence analysis of the entire trpE gene, which encodes component I of anthranilate synthase, is described. Segments of the trpE gene from 17 subsurface isolates of Arthrobacter sp. were amplified by PCR and sequenced. The partial trpE sequences from the various strains were aligned and subjected to phylogenetic analysis. The data suggest that in addition to single base changes, recombination and genetic exchange play a major role in the evolution of the Arthrobacter genome.

  1. 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...

  2. On Inclusion Relations between Some Sequence Spaces

    Directory of Open Access Journals (Sweden)

    R. Çolak

    2016-01-01

    Full Text Available We determine the relations between the classes S^λ of almost λ-statistically convergent sequences and the relations between the classes V^,λ of strongly almost V,λ-summable sequences for various sequences λ, μ in the class Λ. Furthermore we also give the relations between the classes S^λ of almost λ-statistically convergent sequences and the classes V^,λ of strongly almost V,λ-summable sequences for various sequences λ,μ∈Λ.

  3. Bernoulli measure of complex admissible kneading sequences

    CERN Document Server

    Bruin, Henk

    2012-01-01

    Iterated quadratic polynomials give rise to a rich collection of different dynamical systems that are parametrized by a simple complex parameter $c$. The different dynamical features are encoded by the \\emph{kneading sequence} which is an infinite sequence over $\\{0,\\1\\}$. Not every such sequence actually occurs in complex dynamics. The set of admissible kneading sequences was described by Milnor and Thurston for real quadratic polynomials, and by the authors in the complex case. We prove that the set of admissible kneading sequences has positive Bernoulli measure within the set of sequences over $\\{0,\\1\\}$.

  4. Thirty Meter Telescope: observatory software requirements, architecture, and preliminary implementation strategies

    Science.gov (United States)

    Silva, David R.; Angeli, George; Boyer, Corinne; Sirota, Mark; Trinh, Thang

    2008-07-01

    The Thirty Meter Telescope (TMT) will be a ground-based, 30-m optical-IR alt-az telescope with a highly segmented primary mirror located in a remote location. Efficient science operations require the asynchronous coordination of many different sub-systems including telescope mount, three independent active optics sub-systems, adaptive optics, laser guide stars, and user-configured science instrument. An important high-level requirement is target acquisition and observatory system configuration must be completed in less than 5 minutes (or 10 minutes if moving to a new instrument). To meet this coordination challenge and target acquisition time requirement, a distributed software architecture is envisioned consisting of software components linked by a service-based software communications backbone. A master sequencer coordinates the activities of mid-layer sequencers for the telescope, adaptive optics, and selected instrument. In turn, these mid-layer sequencers coordinate the activities of groups of sub-systems. In this paper, TMT observatory requirements are presented in more detail, followed by a description of the design reference software architecture and a discussion of preliminary implementation strategies.

  5. Preliminary investigation of flow dynamics during the start-up of a bulb turbine model

    Science.gov (United States)

    Coulaud, M.; Fraser, R.; Lemay, J.; Duquesne, P.; Aeschlimann, V.; Deschênes, C.

    2016-11-01

    Nowadays, the electricity network undergoes more perturbations due to the market demand. Additionally, an increase of the production from alternative resources such as wind or solar also induces important variations on the grid. Hydraulic power plants are used to respond quickly to these variations to stabilize the network. Hydraulic turbines have to face more frequent start-up and stop sequences that might shorten significantly their life time. In this context, an experimental analysis of start-up sequences has been conducted on the bulb turbine model of the BulbT project at the Hydraulic Machines Laboratory (LAMH) of Laval University. Maintaining a constant head, guide vanes are opened from 0 ° to 30 °. Three guide vanes opening speed have been chosen from 5 °/s to 20 °/s. Several repetitions were done for each guide vanes opening speed. During these sequences, synchronous time resolved measurements have been performed. Pressure signals were recorded at the runner inlet and outlet and along the draft tube. Also, 25 pressure measurements and strain measurements were obtained on the runner blades. Time resolved particle image velocimetry were used to evaluate flowrate during start-up for some repetitions. Torque fluctuations at shaft were also monitored. This paper presents the experimental set-up and start-up conditions chosen to simulate a prototype start-up. Transient flowrate methodology is explained and validation measurements are detailed. The preliminary results of global performances and runner pressure measurements are presented.

  6. 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...

  7. Biomolecule Sequencer: Nanopore Sequencing Technology for In-Situ Environmental Monitoring and Astrobiology

    Science.gov (United States)

    John, K. K.; Botkin, D. J.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lupisella, M. L.; Mason, C. E.; Rubins, K. H.; Smith, D. J.; Stahl, S.; Switzer, C.

    2016-10-01

    Biomolecule Sequencer will demonstrate, for the first time, that DNA sequencing is feasible as a tool for in-situ environmental monitoring and astrobiology. A space-based sequencer could identify microbes, diseases, and help detect DNA-based life.

  8. Integration of retinal image sequences

    Science.gov (United States)

    Ballerini, Lucia

    1998-10-01

    In this paper a method for noise reduction in ocular fundus image sequences is described. The eye is the only part of the human body where the capillary network can be observed along with the arterial and venous circulation using a non invasive technique. The study of the retinal vessels is very important both for the study of the local pathology (retinal disease) and for the large amount of information it offers on systematic haemodynamics, such as hypertension, arteriosclerosis, and diabetes. In this paper a method for image integration of ocular fundus image sequences is described. The procedure can be divided in two step: registration and fusion. First we describe an automatic alignment algorithm for registration of ocular fundus images. In order to enhance vessel structures, we used a spatially oriented bank of filters designed to match the properties of the objects of interest. To evaluate interframe misalignment we adopted a fast cross-correlation algorithm. The performances of the alignment method have been estimated by simulating shifts between image pairs and by using a cross-validation approach. Then we propose a temporal integration technique of image sequences so as to compute enhanced pictures of the overall capillary network. Image registration is combined with image enhancement by fusing subsequent frames of a same region. To evaluate the attainable results, the signal-to-noise ratio was estimated before and after integration. Experimental results on synthetic images of vessel-like structures with different kind of Gaussian additive noise as well as on real fundus images are reported.

  9. NSLS-II Preliminary Design Report

    Energy Technology Data Exchange (ETDEWEB)

    Dierker, S.

    2007-11-01

    Following the CD0 approval of the National Synchrotron Light Source II (NSLS-II) during August 2005, Brookhaven National Laboratory prepared a conceptual design for a worldclass user facility for scientific research using synchrotron radiation. DOE SC review of the preliminary baseline in December 2006 led to the subsequent CD1 approval (approval of alternative selection and cost range). This report is the documentation of the preliminary design work for the NSLS-II facility. The preliminary design of the Accelerator Systems (Part 1) was developed mostly based of the Conceptual Design Report, except for the Booster design, which was changed from in-storage-ring tunnel configuration to in external- tunnel configuration. The design of beamlines (Part 2) is based on designs developed by engineering firms in accordance with the specification provided by the Project. The conventional facility design (Part 3) is the Title 1 preliminary design by the AE firm that met the NSLS-II requirements. Last and very important, Part 4 documents the ES&H design and considerations related to this preliminary design. The NSLS-II performance goals are motivated by the recognition that major advances in many important technology problems will require scientific breakthroughs in developing new materials with advanced properties. Achieving this will require the development of new tools that will enable the characterization of the atomic and electronic structure, chemical composition, and magnetic properties of materials, at nanoscale resolution. These tools must be nondestructive, to image and characterize buried structures and interfaces, and they must operate in a wide range of temperatures and harsh environments. The NSLS-II facility will provide ultra high brightness and flux and exceptional beam stability. It will also provide advanced insertion devices, optics, detectors, and robotics, and a suite of scientific instruments designed to maximize the scientific output of the facility

  10. NSLS-II Preliminary Design Report

    Energy Technology Data Exchange (ETDEWEB)

    Dierker, S.

    2007-11-01

    Following the CD0 approval of the National Synchrotron Light Source II (NSLS-II) during August 2005, Brookhaven National Laboratory prepared a conceptual design for a worldclass user facility for scientific research using synchrotron radiation. DOE SC review of the preliminary baseline in December 2006 led to the subsequent CD1 approval (approval of alternative selection and cost range). This report is the documentation of the preliminary design work for the NSLS-II facility. The preliminary design of the Accelerator Systems (Part 1) was developed mostly based of the Conceptual Design Report, except for the Booster design, which was changed from in-storage-ring tunnel configuration to in external- tunnel configuration. The design of beamlines (Part 2) is based on designs developed by engineering firms in accordance with the specification provided by the Project. The conventional facility design (Part 3) is the Title 1 preliminary design by the AE firm that met the NSLS-II requirements. Last and very important, Part 4 documents the ES&H design and considerations related to this preliminary design. The NSLS-II performance goals are motivated by the recognition that major advances in many important technology problems will require scientific breakthroughs in developing new materials with advanced properties. Achieving this will require the development of new tools that will enable the characterization of the atomic and electronic structure, chemical composition, and magnetic properties of materials, at nanoscale resolution. These tools must be nondestructive, to image and characterize buried structures and interfaces, and they must operate in a wide range of temperatures and harsh environments. The NSLS-II facility will provide ultra high brightness and flux and exceptional beam stability. It will also provide advanced insertion devices, optics, detectors, and robotics, and a suite of scientific instruments designed to maximize the scientific output of the facility

  11. Discrete low-discrepancy sequences

    CERN Document Server

    Angel, Omer; Martin, James B; Propp, James

    2009-01-01

    Holroyd and Propp used Hall's marriage theorem to show that, given a probability distribution pi on a finite set S, there exists an infinite sequence s_1,s_2,... in S such that for all integers k >= 1 and all s in S, the number of i in [1,k] with s_i = s differs from k pi(s) by at most 1. We prove a generalization of this result using a simple explicit algorithm. A special case of this algorithm yields an extension of Holroyd and Propp's result to the case of discrete probability distributions on infinite sets.

  12. Differential correlation for sequencing data.

    Science.gov (United States)

    Siska, Charlotte; Kechris, Katerina

    2017-01-19

    Several methods have been developed to identify differential correlation (DC) between pairs of molecular features from -omics studies. Most DC methods have only been tested with microarrays and other platforms producing continuous and Gaussian-like data. Sequencing data is in the form of counts, often modeled with a negative binomial distribution making it difficult to apply standard correlation metrics. We have developed an R package for identifying DC called Discordant which uses mixture models for correlations between features and the Expectation Maximization (EM) algorithm for fitting parameters of the mixture model. Several correlation metrics for sequencing data are provided and tested using simulations. Other extensions in the Discordant package include additional modeling for different types of differential correlation, and faster implementation, using a subsampling routine to reduce run-time and address the assumption of independence between molecular feature pairs. With simulations and breast cancer miRNA-Seq and RNA-Seq data, we find that Spearman's correlation has the best performance among the tested correlation methods for identifying differential correlation. Application of Spearman's correlation in the Discordant method demonstrated the most power in ROC curves and sensitivity/specificity plots, and improved ability to identify experimentally validated breast cancer miRNA. We also considered including additional types of differential correlation, which showed a slight reduction in power due to the additional parameters that need to be estimated, but more versatility in applications. Finally, subsampling within the EM algorithm considerably decreased run-time with negligible effect on performance. A new method and R package called Discordant is presented for identifying differential correlation with sequencing data. Based on comparisons with different correlation metrics, this study suggests Spearman's correlation is appropriate for sequencing data

  13. Asymptotics of Lagged Fibonacci Sequences

    CERN Document Server

    Mertens, Stephan

    2009-01-01

    Consider "lagged" Fibonacci sequences $a(n) = a(n-1)+a(\\lfloor n/k\\rfloor)$ for $k > 1$. We show that $\\lim_{n\\to\\infty} a(kn)/a(n)\\cdot\\ln n/n = k\\ln k$ and we demonstrate the slow numerical convergence to this limit and how to deal with this slow convergence. We also discuss the connection between two classical results of N.G. de Bruijn and K. Mahler on the asymptotics of $a(n)$.

  14. Waste Feed Delivery System Phase 1 Preliminary RAM Analysis [SEC 1 and 2

    Energy Technology Data Exchange (ETDEWEB)

    DYKES, A.A.

    2000-10-11

    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&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.

  15. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm

    Science.gov (United States)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra

    2013-04-01

    In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a time gain of (70-90)% for highly similar nucleotide sequences (> 80% similarity), and (54-70)% for sequences having (30-80)% similarity. For other sequences, it terminates with an approximate score. For protein sequences, the average time gain is between (25-40)%. Compared to three heuristic global alignment methods, the quality of alignment is improved by about 23%-53%. FOGSAA is, in general, suitable for aligning any two sequences defined over a finite alphabet set, where the quality of the global alignment is of supreme importance.

  16. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿

    OpenAIRE

    Brown, Pamela J.B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V

    2011-01-01

    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.

  17. Genome sequences of eight morphologically diverse Alphaproteobacteria.

    Science.gov (United States)

    Brown, Pamela J B; Kysela, David T; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V

    2011-09-01

    The Alphaproteobacteria comprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.

  18. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿

    Science.gov (United States)

    Brown, Pamela J. B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V.

    2011-01-01

    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium. PMID:21705585

  19. The Art of Gymnastics: Creating Sequences.

    Science.gov (United States)

    Rovegno, Inez

    1988-01-01

    Offering students opportunities for creating movement sequences in gymnastics allows them to understand the essence of gymnastics, have creative experiences, and learn about themselves. The process of creating sequences is described. (MT)

  20. CONSONANT SEQUENCE REDUCTION IN CHILD PHONOLOGY

    African Journals Online (AJOL)

    Dr Kola ADENIYI

    in children's developmental difficulties, it is apparent that their vocal tracts are not ... proper articulation of certain complex sounds or sound sequences. ...... the nasal-oral consonant sequence is even limited in Yoruba, it means the frequency of.

  1. On topological spaces possessing uniformly distributed sequences

    CERN Document Server

    Bogachev, V I

    2007-01-01

    Two classes of topological spaces are introduced on which every probability Radon measure possesses a uniformly distributed sequence or a uniformly tight uniformly distributed sequence. It is shown that these classes are stable under multiplication by completely regular Souslin spaces

  2. On General Fibonacci Sequences in Groups

    OpenAIRE

    Özkan, Engin

    2003-01-01

    In this paper, we have constituted 3-step general Fibonacci sequences in a nilpotent group with exponent p (p is a prime number) and nilpotency class 4 and given formulas to find the a term of the sequence.

  3. On Paranorm Zweier -Convergent Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Vakeel A. Khan

    2013-01-01

    Full Text Available In this paper, we introduce the paranorm Zweier -convergent sequence spaces , , and , a sequence of positive real numbers. We study some topological properties, prove the decomposition theorem, and study some inclusion relations on these spaces.

  4. Preliminary results of steel containment vessel model test

    Energy Technology Data Exchange (ETDEWEB)

    Luk, V.K.; Hessheimer, M.F. [Sandia National Labs., Albuquerque, NM (United States); Matsumoto, T.; Komine, K.; Arai, S. [Nuclear Power Engineering Corp., Tokyo (Japan); Costello, J.F. [Nuclear Regulatory Commission, Washington, DC (United States)

    1998-04-01

    A high pressure test of a mixed-scaled model (1:10 in geometry and 1:4 in shell thickness) of a steel containment vessel (SCV), representing an improved boiling water reactor (BWR) Mark II containment, was conducted on December 11--12, 1996 at Sandia National Laboratories. This paper describes the preliminary results of the high pressure test. In addition, the preliminary post-test measurement data and the preliminary comparison of test data with pretest analysis predictions are also presented.

  5. Preliminary Framework for Human-Automation Collaboration

    Energy Technology Data Exchange (ETDEWEB)

    Oxstrand, Johanna Helene [Idaho National Lab. (INL), Idaho Falls, ID (United States); Le Blanc, Katya Lee [Idaho National Lab. (INL), Idaho Falls, ID (United States); Spielman, Zachary Alexander [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-09-01

    The Department of Energy’s Advanced Reactor Technologies Program sponsors research, development and deployment activities through its Next Generation Nuclear Plant, Advanced Reactor Concepts, and Advanced Small Modular Reactor (aSMR) Programs to promote safety, technical, economical, and environmental advancements of innovative Generation IV nuclear energy technologies. The Human Automation Collaboration (HAC) Research Project is located under the aSMR Program, which identifies developing advanced instrumentation and controls and human-machine interfaces as one of four key research areas. It is expected that the new nuclear power plant designs will employ technology significantly more advanced than the analog systems in the existing reactor fleet as well as utilizing automation to a greater extent. Moving towards more advanced technology and more automation does not necessary imply more efficient and safer operation of the plant. Instead, a number of concerns about how these technologies will affect human performance and the overall safety of the plant need to be addressed. More specifically, it is important to investigate how the operator and the automation work as a team to ensure effective and safe plant operation, also known as the human-automation collaboration (HAC). The focus of the HAC research is to understand how various characteristics of automation (such as its reliability, processes, and modes) effect an operator’s use and awareness of plant conditions. In other words, the research team investigates how to best design the collaboration between the operators and the automated systems in a manner that has the greatest positive impact on overall plant performance and reliability. This report addresses the Department of Energy milestone M4AT-15IN2302054, Complete Preliminary Framework for Human-Automation Collaboration, by discussing the two phased development of a preliminary HAC framework. The framework developed in the first phase was used as the

  6. Astor Pass Seismic Surveys Preliminary Report

    Energy Technology Data Exchange (ETDEWEB)

    Louie, John [UNR; Pullammanappallil, Satish [Optim; Faulds, James; Eisses, Amy; Kell, Annie; Frary, Roxanna; Kent, Graham

    2011-08-05

    In collaboration with the Pyramid Lake Paiute Tribe (PLPT), the University of Nevada, Reno (UNR) and Optim re-processed, or collected and processed, over 24 miles of 2d seismic-reflection data near the northwest corner of Pyramid Lake, Nevada. The network of 2d land surveys achieved a near-3d density at the Astor Pass geothermal prospect that the PLPT drilled during Nov. 2010 to Feb. 2011. The Bureau of Indian Affairs funded additional seismic work around the Lake, and an extensive, detailed single-channel marine survey producing more than 300 miles of section, imaging more than 120 ft below the Lake bottom. Optim’s land data collection utilized multiple heavy vibrators and recorded over 200 channels live, providing a state-of-the-art reflection-refraction data set. After advanced seismic analysis including first-arrival velocity optimization and prestack depth migration, the 2d sections show clear fault-plane reflections, in some areas as deep as 4000 ft, tying to distinct terminations of the mostly volcanic stratigraphy. Some lines achieved velocity control to 3000 ft depth; all lines show reflections and terminations to 5000 ft depth. Three separate sets of normal faults appear in an initial interpretation of fault reflections and stratigraphic terminations, after loading the data into the OpendTect 3d seismic visualization system. Each preliminary fault set includes a continuous trace more than 3000 ft long, and a swarm of short fault strands. The three preliminary normal-fault sets strike northerly with westward dip, northwesterly with northeast dip, and easterly with north dip. An intersection of all three fault systems documented in the seismic sections at the end of Phase I helped to locate the APS-2 and APS-3 slimholes. The seismic sections do not show the faults connected to the Astor Pass tufa spire, suggesting that we have imaged mostly Tertiary-aged faults. We hypothesize that the Recent, active faults that produced the tufa through hotspring

  7. Strong sequences and independent sets

    Directory of Open Access Journals (Sweden)

    Joanna Jureczko

    2016-05-01

    Full Text Available A family $\\mathcal{S} \\in \\mathcal{P}(\\omega$ is \\textit{an independent family} if for each pair $\\mathcal{A, B}$ of disjoint finite subsets of $\\mathcal{S}$ the set $\\bigcap \\mathcal{A} \\cap (\\omega \\setminus \\bigcup \\mathcal{B}$ is nonempty. The fact that there is an independent family on $\\omega$ of size continuum was proved by Fichtenholz and Kantorowicz in \\cite{FK}. If we substitute $\\mathcal{P}(\\omega$ by a set $(X, r$ with arbitrary relation \\textit{r} it is natural question about existence and length of an independent set on $(X, r$. In this paper special assumptions of such existence will be considered. On the other hand in 60s' of the last century the strong sequences method was introduced by Efimov. He used it for proving some famous theorems in dyadic spaces like: Marczewski theorem on cellularity, Shanin theorem on a calibre, Esenin-Volpin theorem and others. In this paper there will be considered: length of strong sequences, the length of independent sets and other well known cardinal invariants and there will be examined inequalities among them.

  8. Sequence Analysis in Demographic Research

    Directory of Open Access Journals (Sweden)

    Billari, Francesco C.

    2001-01-01

    Full Text Available EnglishThis paper examines the salient features of sequence analysis in demogrpahicresearch. The new approach allows a holistic perspective on life course analysis and is based on arepresentation of lives as sequences of states. Some of the methods for analyzing such data aresketched, from complex description to optimal matching ot monoethetic divisive algorithms. Afer ashort ilustration of a demographically-relevant example, the needs in terms of data collection and theopportunities of applying the same aproach to synthetic data are discussed.FrenchOn examine ici les principaux éléments de l’analyse par séquence endémographie. Cette nouvelle technique permet une perspective unifiée del’analyse du cours de la vie, en représentant la vie comme une série d’états.Certaines des méthodes pour de telles analyses sont décrites, en commençant parla description complexe, pour considérer ensuite les alignements optimales, etles algorithmes de division. Après un court exemple en démographie, onconsidère les besoins en données et les possibilités d’application aux donnéessynthétique.

  9. Information Analysis of DNA Sequences

    CERN Document Server

    Mohammed, Riyazuddin

    2010-01-01

    The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they do not seem to participate in the process of transcription of amino-acids, they have been termed "junk DNA." Although it is believed that the non-coding regions in genomes have no role in cell growth and evolution, demonstration that these regions carry useful information would tend to falsify this belief. In this paper, we consider entropy as a measure of information by modifying the entropy expression to take into account the varying length of these sequences. Exons are usually much shorter in length than introns; therefore the comparison of the entropy values needs to be normalized. A length correction strategy was employed using randomly generated nucleonic base strings built out of the alphabet of the same size as the exons under question. Our analysis shows that intron...

  10. Movement sequencing in Huntington disease.

    Science.gov (United States)

    Georgiou-Karistianis, Nellie; Long, Jeffrey D; Lourens, Spencer G; Stout, Julie C; Mills, James A; Paulsen, Jane S

    2014-08-01

    To examine longitudinal changes in movement sequencing in prodromal Huntington's disease (HD) participants (795 prodromal HD; 225 controls) from the PREDICT-HD study. Prodromal HD participants were tested over seven annual visits and were stratified into three groups (low, medium, high) based on their CAG-Age Product (CAP) score, which indicates likely increasing proximity to diagnosis. A cued movement sequence task assessed the impact of advance cueing on response initiation and execution via three levels of advance information. Compared to controls, all CAP groups showed longer initiation and movement times across all conditions at baseline, demonstrating a disease gradient for the majority of outcomes. Across all conditions, the high CAP group had the highest mean for baseline testing, but also demonstrated an increase in movement time across the study. For initiation time, the high CAP group showed the highest mean baseline time across all conditions, but also faster decreasing rates of change over time. With progress to diagnosis, participants may increasingly use compensatory strategies, as evidenced by faster initiation. However, this occurred in conjunction with slowed execution times, suggesting a decline in effectively accessing control processes required to translate movement into effective execution.

  11. Effects of Sequence Partitioning on Compression Rate

    CERN Document Server

    Alagoz, B Baykant

    2010-01-01

    In the paper, a theoretical work is done for investigating effects of splitting data sequence into packs of data set. We proved that a partitioning of data sequence is possible to find such that the entropy rate at each subsequence is lower than entropy rate of the source. Effects of sequence partitioning on overall compression rate are argued on the bases of partitioning statistics, and then, an optimization problem for an optimal partition is defined to improve overall compression rate of a sequence.

  12. Cross-correlation properties of cyclotomic sequences

    CERN Document Server

    Cai, Kai; Zheng, Zhiming

    2009-01-01

    Sequences with good correlation properties are widely used in engineering applications, especially in the area of communications. Among the known sequences, cyclotomic families have the optimal autocorrelation property. In this paper, we decide the cross-correlation function of the known cyclotomic sequences completely. Moreover, to get our results, the relations between the multiplier group and the decimations of the characteristic sequence are also established for an arbitrary difference set.

  13. [The use of MLVA for Corynebacterium diphtheriae genotyping--preliminary studies].

    Science.gov (United States)

    Zasada, Aleksandra A; Jagielski, Marek; Rzeczkowska, Magdalena; Januszkiewicz, Aleksandra

    2011-01-01

    The complete genome sequence of strain NCTC 13129 C. diphtheriae were investigated in order to identify tandem repeats (VNTR). From 75 VNTR loci identified in the genome 14 were selected. Primers were designed and PCR conditions were optimized for amplification of the selected VNTR markers. Preliminary studies of usefulness of selected VNTR markers were conducted using a group of 28 C. diphtheriae strains. From 14 markers 8 were regarded as potentially useful. The diversity of individual markers ranged from 1 to 6 alleles (Simpson index from 0 to 0,746). No diversity were observed for 3 VNTR markers but it could be a results of too small group of strains analyzed in the tests. Simpson diversity index calculated for all the markers tested on 28 strains was 0,87. Results of the preliminary studies showed usefulness of MLVA for C. diphtheriae genotyping. Nevertheless, confirmation of reliability of the method should be done using a large group of strains. Moreover, the method should be compared with other genotyping methods.

  14. Family Histories of Anxiety in Overweight Men and Women with Binge Eating Disorder: A Preliminary Investigation

    Science.gov (United States)

    Blomquist, Kerstin K.; Grilo, Carlos M.

    2015-01-01

    Objective A preliminary examination of the significance of family histories of anxiety in the expression of binge eating disorder (BED) and associated functioning. Methods Participants were 166 overweight patients with BED assessed using diagnostic interviews. Participants were administered a structured psychiatric history interview about their first-degree relatives (parents, siblings, children) (N=897) to determine lifetime diagnoses of DSM-IV anxiety disorders and completed a battery of questionnaires assessing current and historical eating and weight variables and associated psychological functioning (depression). Results BED patients with a family history of anxiety disorder were significantly more likely than BED patients without a family history of anxiety disorder to have lifetime diagnoses of anxiety disorders and mood disorders but not substance use disorders. A family history of anxiety was not significantly associated with timing or sequencing of age at onset of anxiety disorder, binge eating, dieting, or obesity, or with variability in current levels of binge eating, eating disorder psychopathology, or psychological functioning. Conclusions Although replication with direct interview method is needed, our preliminary findings suggest that a family history of anxiety confers greater risk for comorbid anxiety and mood disorders but is largely unrelated to the development of binge eating, dieting, or obesity and unrelated to variability in eating disorder psychopathology or psychological functioning in overweight patients with BED. PMID:26343481

  15. Purification, identification and preliminary crystallographic studies of Pru du amandin, an allergenic protein from Prunus dulcis

    Energy Technology Data Exchange (ETDEWEB)

    Gaur, Vineet; Sethi, Dhruv K.; Salunke, Dinakar M., E-mail: dinakar@nii.res.in [National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067 (India)

    2008-01-01

    The purification, identification, crystallization and preliminary crystallographic studies of an allergy-related protein, Pru du amandin, from P. dulcis nuts are reported. Food allergies appear to be one of the foremost causes of hypersensitivity reactions. Nut allergies account for most food allergies and are often permanent. The 360 kDa hexameric protein Pru du amandin, a known allergen, was purified from almonds (Prunus dulcis) by ammonium sulfate fractionation and ion-exchange chromatography. The protein was identified by a BLAST homology search against the nonredundant sequence database. Pru du amandin belongs to the 11S legumin family of seed storage proteins characterized by the presence of a cupin motif. Crystals were obtained by the hanging-drop vapour-diffusion method. The crystals belong to space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 150.7, c = 164.9 Å.

  16. Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase.

    Science.gov (United States)

    Jeudy, Sandra; Coutard, Bruno; Lebrun, Régine; Abergel, Chantal

    2005-06-01

    The complete sequence of the largest known double-stranded DNA virus, Acanthamoeba polyphaga mimivirus, has recently been determined [Raoult et al. (2004), Science, 306, 1344-1350] and revealed numerous genes not expected to be found in a virus. A comprehensive structural and functional study of these gene products was initiated [Abergel et al. (2005), Acta Cryst. F61, 212-215] both to better understand their role in the virus physiology and to obtain some clues to the origin of DNA viruses. Here, the preliminary crystallographic analysis of the viral nucleoside diphosphate kinase protein is reported. The crystal belongs to the cubic space group P2(1)3, with unit-cell parameter 99.425 A. The self-rotation function confirms that there are two monomers per asymmetric unit related by a twofold non-crystallographic axis and that the unit cell thus contains four biological entities.

  17. Crystallization and preliminary X-ray analysis of Leishmania major glyoxalase I

    Energy Technology Data Exchange (ETDEWEB)

    Ariza, Antonio; Vickers, Tim J.; Greig, Neil; Fairlamb, Alan H.; Bond, Charles S., E-mail: c.s.bond@dundee.ac.uk [Division of Biological Chemistry and Molecular Microbiology, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee DD1 5EH,Scotland (United Kingdom)

    2005-08-01

    The detoxification enzyme glyoxalase I from L. major has been crystallized. Preliminary molecular-replacement calculations indicate the presence of three glyoxalase I dimers in the asymmetric unit. Glyoxalase I (GLO1) is a putative drug target for trypanosomatids, which are pathogenic protozoa that include the causative agents of leishmaniasis. Significant sequence and functional differences between Leishmania major and human GLO1 suggest that it may make a suitable template for rational inhibitor design. L. major GLO1 was crystallized in two forms: the first is extremely disordered and does not diffract, while the second, an orthorhombic form, produces diffraction to 2.0 Å. Molecular-replacement calculations indicate that there are three GLO1 dimers in the asymmetric unit, which take up a helical arrangement with their molecular dyads arranged approximately perpendicular to the c axis. Further analysis of these data are under way.

  18. Preliminary Work for Examining the Scalability of Reinforcement Learning

    Science.gov (United States)

    Clouse, Jeff

    1998-01-01

    Researchers began studying automated agents that learn to perform multiple-step tasks early in the history of artificial intelligence (Samuel, 1963; Samuel, 1967; Waterman, 1970; Fikes, Hart & Nilsonn, 1972). Multiple-step tasks are tasks that can only be solved via a sequence of decisions, such as control problems, robotics problems, classic problem-solving, and game-playing. The objective of agents attempting to learn such tasks is to use the resources they have available in order to become more proficient at the tasks. In particular, each agent attempts to develop a good policy, a mapping from states to actions, that allows it to select actions that optimize a measure of its performance on the task; for example, reducing the number of steps necessary to complete the task successfully. Our study focuses on reinforcement learning, a set of learning techniques where the learner performs trial-and-error experiments in the task and adapts its policy based on the outcome of those experiments. Much of the work in reinforcement learning has focused on a particular, simple representation, where every problem state is represented explicitly in a table, and associated with each state are the actions that can be chosen in that state. A major advantage of this table lookup representation is that one can prove that certain reinforcement learning techniques will develop an optimal policy for the current task. The drawback is that the representation limits the application of reinforcement learning to multiple-step tasks with relatively small state-spaces. There has been a little theoretical work that proves that convergence to optimal solutions can be obtained when using generalization structures, but the structures are quite simple. The theory says little about complex structures, such as multi-layer, feedforward artificial neural networks (Rumelhart & McClelland, 1986), but empirical results indicate that the use of reinforcement learning with such structures is promising

  19. 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...

  20. Incidental Sequence Learning across the Lifespan

    Science.gov (United States)

    Weiermann, Brigitte; Meier, Beat

    2012-01-01

    The purpose of the present study was to investigate incidental sequence learning across the lifespan. We tested 50 children (aged 7-16), 50 young adults (aged 20-30), and 50 older adults (aged >65) with a sequence learning paradigm that involved both a task and a response sequence. After several blocks of practice, all age groups slowed down…

  1. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    NARCIS (Netherlands)

    Hasan, L.

    2011-01-01

    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of pr

  2. Disease gene identification strategies for exome sequencing

    NARCIS (Netherlands)

    Gilissen, C.; Hoischen, A.; Brunner, H.G.; Veltman, J.A.

    2012-01-01

    Next generation sequencing can be used to search for Mendelian disease genes in an unbiased manner by sequencing the entire protein-coding sequence, known as the exome, or even the entire human genome. Identifying the pathogenic mutation amongst thousands to millions of genomic variants is a major c

  3. PacBio Sequencing and Its Applications

    Institute of Scientific and Technical Information of China (English)

    Anthony Rhoads; Kin Fai Au

    2015-01-01

    Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read lengths than the second-generation sequencing (SGS) technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research. The highly-contiguous de novo assemblies using PacBio sequencing can close gaps in current reference assemblies and characterize structural variation (SV) in personal genomes. With longer reads, we can sequence through extended repetitive regions and detect mutations, many of which are associated with dis-eases. Moreover, PacBio transcriptome sequencing is advantageous for the identification of gene isoforms and facilitates reliable discoveries of novel genes and novel isoforms of annotated genes, due to its ability to sequence full-length transcripts or fragments with significant lengths. Addition-ally, PacBio’s sequencing technique provides information that is useful for the direct detection of base modifications, such as methylation. In addition to using PacBio sequencing alone, many hybrid sequencing strategies have been developed to make use of more accurate short reads in conjunction with PacBio long reads. In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using PacBio Sequencing alone. The advent of PacBio sequencing has made available much information that could not be obtained via SGS alone.

  4. Joint Sequence Analysis: Association and Clustering

    Science.gov (United States)

    Piccarreta, Raffaella

    2017-01-01

    In its standard formulation, sequence analysis aims at finding typical patterns in a set of life courses represented as sequences. Recently, some proposals have been introduced to jointly analyze sequences defined on different domains (e.g., work career, partnership, and parental histories). We introduce measures to evaluate whether a set of…

  5. RNAome sequencing delineates the complete RNA landscape

    NARCIS (Netherlands)

    K.W.J. Derks (Kasper); J. Pothof (Joris)

    2015-01-01

    textabstractStandard RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species. For example, small and large RNAs from the same sample cannot be sequenced in a single sequence run. We designed RNAome sequencing, which is a strand-specif

  6. The recurrence sequence via the Fibonacci groups

    Science.gov (United States)

    Aküzüm, Yeşim; Deveci, Ömür

    2016-04-01

    This work develops properties of the recurrence sequence defined by the aid of the relation matrix of the Fibonacci groups. The study of this sequence modulo m yields cyclic groups and semigroups from generating matrix. Finally, we extend the sequence defined to groups and then, we obtain its period in the Fibonacci groups.

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

    Directory of Open Access Journals (Sweden)

    Leho Tedersoo

    Full Text Available 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.

  8. Galaxy Zoo Hubble: First results of the redshift evolution of disk fraction in the red sequence

    Science.gov (United States)

    Galloway, Melanie; Willett, Kyle; Fortson, Lucy; Scarlata, Claudia; Beck, Melanie; Masters, Karen; Melvin, Tom

    2016-01-01

    The transition of galaxies from the blue cloud to the red sequence is commonly linked to a morphological transformation from disk to elliptical structure. However, the correlation between color and morphology is not one-to-one, as evidenced by the existence of a significant population of red disks. As this stage in a galaxy's evolution is likely to be transitory, the mechanism by which red disks are formed offers insight to the processes that trigger quenching of star formation and the galaxy's position on the star-forming sequence. To study the population of disk galaxies in the red sequence as a function of cosmic time, we utilize data from the Galaxy Zoo: Hubble project, which uses crowdsourced visual classifications of images of galaxies selected from the AEGIS, COSMOS, GEMS, and GOODS surveys. We construct a large sample of over 10,000 disk galaxies spanning a wide (0 < z < 1.0) redshift range. We use this sample to examine the change in the fraction of disks in the red sequence with respect to all disks from z˜1 to the present day. Preliminary results confirm that the fraction of disks in the red sequence decreases as the Universe evolves. We discuss the quenching processes which may explain this trend, and which morphological transformations are most affected by it.

  9. 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.

  10. Preliminary conceptual design about the CEPC calorimeters

    Science.gov (United States)

    Yang, Haijun

    2016-11-01

    The Circular Electron Positron Collider (CEPC) as a Higgs factory was proposed in September 2013. The preliminary conceptual design report was completed in 2015.1 The CEPC detector design was using International Linear Collider Detector — ILD2 as an initial baseline. The CEPC calorimeters, including the high granularity electromagnetic calorimeter (ECAL) and the hadron calorimeter (HCAL), are designed for precise energy measurements of electrons, photons, taus and hadronic jets. The basic resolution requirements for the ECAL and HCAL are about 16%E (GeV) and 50%E (GeV), respectively. To fully exploit the physics potential of the Higgs, W, Z and related Standard Model processes, the jet energy resolution is required to reach 3%-4%, or 30%/E (GeV) at energies below about 100 GeV. To achieve the required performance, a Particle Flow Algorithm (PFA) — oriented calorimetry system is being considered as the baseline design. The CEPC ECAL detector options include silicon-tungsten or scintillator-tungsten structures with analog readout, while the HCAL detector options have scintillator or gaseous detector as the active sensor and iron as the absorber. Some latest R&D studies about ECAL and HCAL within the CEPC working group is also presented.

  11. Overweight and urban pollution: preliminary results.

    Science.gov (United States)

    Ponticiello, Barnaba Giuseppina; Capozzella, Assunta; Di Giorgio, Valeria; Casale, Teodorico; Giubilati, Roberto; Tomei, Gianfranco; Tomei, Francesco; Rosati, Maria Valeria; Sancini, Angela

    2015-06-15

    The aim of this study is to determine whether in workers exposed to urban pollution the risk of developing overweight and obesity is higher in workers exposed to urban pollution compared to a control group. The study was conducted on 150 volunteers, 75 workers exposed to urban pollution (50 women and 25 men) and 75 indoor workers (50 women and 25 men). Once measured the weight and height and calculated body mass index (BMI) for each worker, the research was based on the comparison, between the two groups, of the mean values of the measurements and of the frequency of workers with BMI index higher than the cut-off of normality. The only statistically significant difference found was for the mean value of weight in women, which was higher among outdoor workers compared to indoor workers. The mean values of BMI and the frequency of workers with BMI higher than normal was higher among outdoor workers compared to indoor workers in both sexes, but not statistically significant. The data suggest that outdoor workers may be subject to an additional risk of developing obesity as a result of exposure to urban air pollution (which, like obesity, is a source of oxidative stress). So, our preliminary study encourages to continue this line of research by implementing the sample and considering all the confounding factors. Furthermore, the results highlight the necessity to take account of gender differences in the context of health surveillance of workers.

  12. Preliminary test results for the SVX4

    Energy Technology Data Exchange (ETDEWEB)

    Christofek, L.; Hanagaki, K.; Rapidis, P.; Utes, M.; /Fermilab

    2005-06-01

    We present and summarize the preliminary test results for SVX4 chip testing. There are presently two versions of the SVX4. Version 2 has on-chip bypassing and Version 1 does not. The on-chip bypassing is a layer of transistors under the front-end analog pipeline that acts as a bypassing capacitor for the voltage supply. Its size is about a microfarad. We aggressively choose to test Version 2 because of this feature. The feature is advantageous for hybrid design because it eliminates the need for an additional passive component on the hybrid itself by placing it on the actual SVX4 die. Also, the SVX4 was designed to operate in two modes: D. and CDF. One can set which mode the chip will operate by placing a jumper in the proper position on the SVX4 chip carrier. In either mode, the chip can either use the operating parameters from the shift register or the shadow register. Similarly, this is selected by placing a jumper on the SVX4 chip carrier. This chip has this feature because it was unknown whether the new design of the shadow register would be operable. The shadow register is also call the SEU register or Single Event Upset register. An introduction into the functionality of the chip and an explanation on the difference between D. and CDF mode can be found in the SVX4 User's Manual [1].

  13. Preliminary experiments on quantification of skin condition

    Science.gov (United States)

    Kitajima, Kenzo; Iyatomi, Hitoshi

    2014-03-01

    In this study, we investigated a preliminary assessment method for skin conditions such as a moisturizing property and its fineness of the skin with an image analysis only. We captured a facial images from volunteer subjects aged between 30s and 60s by Pocket Micro (R) device (Scalar Co., Japan). This device has two image capturing modes; the normal mode and the non-reflection mode with the aid of the equipped polarization filter. We captured skin images from a total of 68 spots from subjects' face using both modes (i.e. total of 136 skin images). The moisture-retaining property of the skin and subjective evaluation score of the skin fineness in 5-point scale for each case were also obtained in advance as a gold standard (their mean and SD were 35.15 +/- 3.22 (μS) and 3.45 +/- 1.17, respectively). We extracted a total of 107 image features from each image and built linear regression models for estimating abovementioned criteria with a stepwise feature selection. The developed model for estimating the skin moisture achieved the MSE of 1.92 (μS) with 6 selected parameters, while the model for skin fineness achieved that of 0.51 scales with 7 parameters under the leave-one-out cross validation. We confirmed the developed models predicted the moisture-retaining property and fineness of the skin appropriately with only captured image.

  14. The deuteron accelerator preliminary design for BISOL

    Energy Technology Data Exchange (ETDEWEB)

    Peng, S.X., E-mail: sxpeng@pku.edu.cn; Zhu, F.; Wang, Z.; Gao, Y.; Guo, Z.Y.

    2016-06-01

    BISOL, which was named as Beijing-ISOL before (Cui et al., 2013), is the abbreviation of Beijing Isotope-Separation-On-Line neutron beam facility. It is proposed jointly by Peking University (PKU) and China Institute of Atomic Energy (CIAE) for basic science study and application. It is a double driven facility that can be driven by a reactor or a deuteron accelerator. The deuteron driver accelerator should accelerate the deuteron beam up to 40 MeV with maximum beam current of 10 mA. Proton beams up to 33 MeV and He{sup 2+} beams up to 81.2 MeV can also be accelerated in this accelerator. The accelerator can be operated on either CW (continuous waveform) or pulsed mode, and the ion energy can be adjusted in a wide range. The accelerator will also allow independent operation of the RIB (Radioactive Ion Beams) system. It will be mainly charged by PKU group. Details of the deuteron accelerator preliminary design for BISOL will be given in this paper.

  15. Guidance for performing preliminary assessments under CERCLA

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1991-09-01

    EPA headquarters and a national site assessment workgroup produced this guidance for Regional, State, and contractor staff who manage or perform preliminary assessments (PAs). EPA has focused this guidance on the types of sites and site conditions most commonly encountered. The PA approach described in this guidance is generally applicable to a wide variety of sites. However, because of the variability among sites, the amount of information available, and the level of investigative effort required, it is not possible to provide guidance that is equally applicable to all sites. PA investigators should recognize this and be aware that variation from this guidance may be necessary for some sites, particularly for PAs performed at Federal facilities, PAs conducted under EPA`s Environmental Priorities Initiative (EPI), and PAs at sites that have previously been extensively investigated by EPA or others. The purpose of this guidance is to provide instructions for conducting a PA and reporting results. This guidance discusses the information required to evaluate a site and how to obtain it, how to score a site, and reporting requirements. This document also provides guidelines and instruction on PA evaluation, scoring, and the use of standard PA scoresheets. The overall goal of this guidance is to assist PA investigators in conducting high-quality assessments that result in correct site screening or further action recommendations on a nationally consistent basis.

  16. STACEE-32: Design, performance, and preliminary results

    Science.gov (United States)

    Ong, Rene A.

    2000-06-01

    The Solar Tower Atmospheric Cherenkov Effect Experiment (STACEE) is designed to detect astrophysical sources of γ-rays at energies between 25 and 500 GeV. STACEE uses large solar mirrors (heliostats) to collect the atmospheric Cherenkov radiation produced in γ-ray air showers. The use of a large mirror collection area will allow STACEE to probe γ-ray sources at energies above the reach of the Compton Gamma Ray Observatory (CGRO), but below the reach of conventional Cherenkov telescopes. During the 1998-99 observing season, a portion of STACEE using 32 heliostats was installed at the National Solar Thermal Test Facility (NSTTF) of Sandia National Laboratories (Albuquerque, NM). This initial configuration (STACEE-32) observed a number of astronomical sources, including the Crab and several active galactic nuclei (AGN). Here we report on these observations. We highlight the experimental configuration and the preliminary results from the Crab data. The full STACEE experiment using 64 heliostats will be commissioned in 2000. .

  17. Preliminary pharmacognostic screening of Achyranthes coynei stem

    Directory of Open Access Journals (Sweden)

    Vinayak Upadhya

    2015-01-01

    Full Text Available Achyranthes coynei is a rare, endemic perennial shrub reported from Karnataka and Maharashtra states of India. The plant is used to treat various disorders by folk healers and was proven to have antimicrobial and antioxidant properties. The present study was undertaken to evaluate microscopic and macroscopic characters of A. coynei stem, along with its physicochemical parameters. ProgRes ® CapturePro and Microsoft Excel were used for statistical analysis. Perennial, shrubby nature and woody stem were the distinguishing morphological characters observed. Transverse section (TS illustrated quadrangular outline of the stem and showed the presence of two types of trichomes on the thick-walled epidermis. TS also showed number of rosette calcium oxalates crystals; prismatic and microsphenoid crystals; conjoint, collateral open secondary vascular bundles; and two amphixylic medullary bundles in the pith. Ash and extractive values, micro and macro elements and nutritive factors were estimated in the present study. The presence of alkaloids, saponins and triterpenoids were observed in preliminary phytochemical screening. High-performance thin layer chromatographic analysis yielded different bands and also indicated the presence of oleanolic acid. The studied parameters for A. coynei stem will be useful for identification and authentication of the plant material.

  18. Preliminary safety design analysis of KALIMER

    Energy Technology Data Exchange (ETDEWEB)

    Suk, Soo Dong; Kwon, Y. M.; Kim, K. D. [Korea Atomic Energy Research Institute, Taejon (Korea)

    1999-03-01

    The national long-term R and D program updated in 1997 requires Korea Atomic Energy Research Institute(KAERI) to complete by the year 2006 the basic design of Korea Advanced Liquid Metal Reactor (KALIMER), along with supporting R and D work, with the capability of resolving the issue of spent fuel storage as well as with significantly enhanced safety. KALIMER is a 150 MWe pool-type sodium cooled prototype reactor that uses metallic fuel. The conceptual design is currently under way to establish a self consistent design meeting a set of the major safety design requirements for accident prevention. Some of current emphasis include those for inherent and passive means of negative reactivity insertion and decay heat removal, high shutdown reliability, prevention of and protection from sodium chemical reaction, and high seismic margin, among others. All of these requirements affect the reactor design significantly and involve supporting R and D programs of substance. This document first introduces a set of safety design requirements and accident evaluation criteria established for the conceptual design of KALIMER and then summarizes some of the preliminary results of engineering and design analyses performed for the safety of KALIMER. 19 refs., 19 figs., 6 tabs. (Author)

  19. Preliminary study natural gas; Foerstudie naturgas

    Energy Technology Data Exchange (ETDEWEB)

    Lamnevik, Stefan; Carlsson, Tomas; Dyhr, Kurt

    2000-09-01

    FOA has carried out a preliminary study on natural gas for the Swedish National Energy Administration. To use natural gas as an energy source could be one step towards use of carbon-free fuels such as hydrogen. Natural gas, consisting mainly of methane, is the hydrocarbon with the highest hydrogen content. It has a high heat of combustion, 55 MJ/kg, and a low emission of carbon dioxide, 2.8 kg/kg fuel or 0.051 kg/MJ. The carbon dioxide emission per energy unit is twice as high for coal, 75% higher for wood fuels, and 27% higher for fuel oils. The Swedish natural gas network starts at Malmoe and ends at Hyltebruk. The natural gas used is imported from Denmark by Sydgas AB. It would be possible in the future to get connections to the Russian and the Norwegian networks and also to import LNG by ship and store it to buffer the different consumption demands during summer and winter. Natural gas is non-toxic but can be suffocating due to too low oxygen content at high concentrations. Combustion with an inadequate air supply will form toxic carbon monoxide like other carbonaceous fuels. Natural gas/air mixtures may explode like other gaseous fuels. The gas is lighter than air and is therefore dispersed better than heavier gases like LPG. Natural gas is difficult to detonate unlike other gases.

  20. Modeling Malaysia's Energy System: Some Preliminary Results

    Directory of Open Access Journals (Sweden)

    Ahmad M. Yusof

    2011-01-01

    Full Text Available Problem statement: The current dynamic and fragile world energy environment necessitates the development of new energy model that solely caters to analyze Malaysia’s energy scenarios. Approach: The model is a network flow model that traces the flow of energy carriers from its sources (import and mining through some conversion and transformation processes for the production of energy products to final destinations (energy demand sectors. The integration to the economic sectors is done exogeneously by specifying the annual sectoral energy demand levels. The model in turn optimizes the energy variables for a specified objective function to meet those demands. Results: By minimizing the inter temporal petroleum product imports for the crude oil system the annual extraction level of Tapis blend is projected at 579600 barrels per day. The aggregate demand for petroleum products is projected to grow at 2.1% year-1 while motor gasoline and diesel constitute 42 and 38% of the petroleum products demands mix respectively over the 5 year planning period. Petroleum products import is expected to grow at 6.0% year-1. Conclusion: The preliminary results indicate that the model performs as expected. Thus other types of energy carriers such as natural gas, coal and biomass will be added to the energy system for the overall development of Malaysia energy model.