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Sample records for preliminary sequence analysis

  1. Preliminary hazard analysis using sequence tree method

    International Nuclear Information System (INIS)

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

    2007-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Rene Sutherland

    2012-01-01

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

  3. 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.

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

    Directory of Open Access Journals (Sweden)

    Sally Ali Tawfik

    2018-01-01

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

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

    Science.gov (United States)

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

    2010-01-01

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

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

    KAUST Repository

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

    2013-01-01

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

  7. 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.

  8. UVISS preliminary visibility analysis

    DEFF Research Database (Denmark)

    Betto, Maurizio

    1998-01-01

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

  9. 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.

  10. Biological sequence analysis

    DEFF Research Database (Denmark)

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

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

  11. Pickering safeguards: a preliminary analysis

    International Nuclear Information System (INIS)

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

    1977-05-01

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

  12. 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 ...

  13. 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.

  14. Preliminary HECTOR analysis by Dragon

    Energy Technology Data Exchange (ETDEWEB)

    Presser, W; Woloch, F

    1972-06-02

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

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

    International Nuclear Information System (INIS)

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

    2012-01-01

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

  16. Concept Overview & Preliminary Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ruth, Mark

    2017-07-12

    'H2@Scale' is an opportunity for wide-scale use of hydrogen as an intermediate that carries energy from various production options to multiple uses. It is based on identifying and developing opportunities for low-cost hydrogen production and investigating opportunities for using that hydrogen across the electricity, industrial, and transportation sectors. One of the key production opportunities is use of low-cost electricity that may be generated under high penetrations of variable renewable generators such as wind and solar photovoltaics. The technical potential demand for hydrogen across the sectors is 60 million metric tons per year. The U.S. has sufficient domestic renewable resources so that each could meet that demand and could readily meet the demand using a portfolio of generation options. This presentation provides an overview of the concept and the technical potential demand and resources. It also motivates analysis and research on H2@Scale.

  17. Preliminary hazards analysis -- vitrification process

    International Nuclear Information System (INIS)

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

    1994-06-01

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

  18. 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.

  19. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Changqing Liu

    2013-05-01

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

  2. 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.

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

    African Journals Online (AJOL)

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

  4. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

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

  5. High-throughput transcriptome sequencing analysis provides preliminary insights into the biotransformation mechanism of Rhodopseudomonas palustris treated with alpha-rhamnetin-3-rhamnoside.

    Science.gov (United States)

    Bi, Lei; Guan, Chun-jie; Yang, Guan-e; Yang, Fei; Yan, Hong-yu; Li, Qing-shan

    2016-04-01

    The purple photosynthetic bacterium Rhodopseudomonas palustris has been widely applied to enhance the therapeutic effects of traditional Chinese medicine using novel biotransformation technology. However, comprehensive studies of the R. palustris biotransformation mechanism are rare. Therefore, investigation of the expression patterns of genes involved in metabolic pathways that are active during the biotransformation process is essential to elucidate this complicated mechanism. To promote further study of the biotransformation of R. palustris, we assembled all R. palustris transcripts using Trinity software and performed differential expression analysis of the resulting unigenes. A total of 9725, 7341 and 10,963 unigenes were obtained by assembling the alpha-rhamnetin-3-rhamnoside-treated R. palustris (RPB) reads, control R. palustris (RPS) reads and combined RPB&RPS reads, respectively. A total of 9971 unigenes assembled from the RPB&RPS reads were mapped to the nr, nt, Swiss-Prot, Gene Ontology (GO), Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (E-value biotransformation in R. palustris. Furthermore, we propose two putative ARR biotransformation mechanisms in R. palustris. These analytical results represent a useful genomic resource for in-depth research into the molecular basis of biotransformation and genetic modification in R. palustris. Copyright © 2016 Elsevier GmbH. All rights reserved.

  6. 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.

  7. Whole genome sequence analysis of Mycobacterium suricattae

    KAUST Repository

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

    2015-01-01

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

  8. 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.

  9. 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

  10. Original Article PRELIMINARY BIOAUTOGRAPHIC ANALYSIS OF ...

    African Journals Online (AJOL)

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

  11. Preliminary Analysis of Reinforced Concrete Waffle Walls

    National Research Council Canada - National Science Library

    Shugar, Theodore

    1997-01-01

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

  12. 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.

  13. 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

  14. 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)

  15. Preliminary failure mode and effect analysis

    International Nuclear Information System (INIS)

    Addison, J.V.

    1972-01-01

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

  16. Preliminary safety analysis report for the TFTR

    International Nuclear Information System (INIS)

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

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

  17. Sequence analysis of Leukemia DNA

    Science.gov (United States)

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

    2018-03-01

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

  18. Licensing Support System: Preliminary data scope analysis

    International Nuclear Information System (INIS)

    1989-01-01

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

  19. Preliminary study of pseudorandom binary sequence pulsing of ORELA

    International Nuclear Information System (INIS)

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

    1980-03-01

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

  20. Genome Sequencing and Analysis Conference IV

    Energy Technology Data Exchange (ETDEWEB)

    1993-12-31

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

  1. Preliminary Analysis of Google+'s Privacy

    OpenAIRE

    Mahmood, Shah; Desmedt, Yvo

    2011-01-01

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

  2. Robustness analysis of chiller sequencing control

    International Nuclear Information System (INIS)

    Liao, Yundan; Sun, Yongjun; Huang, Gongsheng

    2015-01-01

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

  3. Preliminary Hazards Analysis Plasma Hearth Process

    International Nuclear Information System (INIS)

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

    1993-11-01

    This Preliminary Hazards Analysis (PHA) for the Plasma Hearth Process (PHP) follows the requirements of United States Department of Energy (DOE) Order 5480.23 (DOE, 1992a), DOE Order 5480.21 (DOE, 1991d), DOE Order 5480.22 (DOE, 1992c), DOE Order 5481.1B (DOE, 1986), and the guidance provided in DOE Standards DOE-STD-1027-92 (DOE, 1992b). Consideration is given to ft proposed regulations published as 10 CFR 830 (DOE, 1993) and DOE Safety Guide SG 830.110 (DOE, 1992b). The purpose of performing a PRA is to establish an initial hazard categorization for a DOE nuclear facility and to identify those processes and structures which may have an impact on or be important to safety. The PHA is typically performed during and provides input to project conceptual design. The PRA then is followed by a Preliminary Safety Analysis Report (PSAR) performed during Title I and II design. This PSAR then leads to performance of the Final Safety Analysis Report performed during construction, testing, and acceptance and completed before routine operation. Radiological assessments indicate that a PHP facility, depending on the radioactive material inventory, may be an exempt, Category 3, or Category 2 facility. The calculated impacts would result in no significant impact to offsite personnel or the environment. Hazardous material assessments indicate that a PHP facility will be a Low Hazard facility having no significant impacts either onsite or offsite to personnel and the environment

  4. Probabilistic accident sequence recovery analysis

    International Nuclear Information System (INIS)

    Stutzke, Martin A.; Cooper, Susan E.

    2004-01-01

    Recovery analysis is a method that considers alternative strategies for preventing accidents in nuclear power plants during probabilistic risk assessment (PRA). Consideration of possible recovery actions in PRAs has been controversial, and there seems to be a widely held belief among PRA practitioners, utility staff, plant operators, and regulators that the results of recovery analysis should be skeptically viewed. This paper provides a framework for discussing recovery strategies, thus lending credibility to the process and enhancing regulatory acceptance of PRA results and conclusions. (author)

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

    International Nuclear Information System (INIS)

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

    2017-01-01

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

  6. Waste Feed Delivery System Phase 1 Preliminary RAM Analysis

    International Nuclear Information System (INIS)

    DYKES, A.A.

    2000-01-01

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

  7. Repository Subsurface Preliminary Fire Hazard Analysis

    International Nuclear Information System (INIS)

    Logan, Richard C.

    2001-01-01

    This fire hazard analysis identifies preliminary design and operations features, fire, and explosion hazards, and provides a reasonable basis to establish the design requirements of fire protection systems during development and emplacement phases of the subsurface repository. This document follows the Technical Work Plan (TWP) (CRWMS M and O 2001c) which was prepared in accordance with AP-2.21Q, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities''; Attachment 4 of AP-ESH-008, ''Hazards Analysis System''; and AP-3.11Q, ''Technical Reports''. The objective of this report is to establish the requirements that provide for facility nuclear safety and a proper level of personnel safety and property protection from the effects of fire and the adverse effects of fire-extinguishing agents

  8. Preliminary shielding analysis of VHTR reactors

    International Nuclear Information System (INIS)

    Flaspoehler, Timothy M.; Petrovic, Bojan

    2011-01-01

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

  9. Plasma brake model for preliminary mission analysis

    Science.gov (United States)

    Orsini, Leonardo; Niccolai, Lorenzo; Mengali, Giovanni; Quarta, Alessandro A.

    2018-03-01

    Plasma brake is an innovative propellantless propulsion system concept that exploits the Coulomb collisions between a charged tether and the ions in the surrounding environment (typically, the ionosphere) to generate an electrostatic force orthogonal to the tether direction. Previous studies on the plasma brake effect have emphasized the existence of a number of different parameters necessary to obtain an accurate description of the propulsive acceleration from a physical viewpoint. The aim of this work is to discuss an analytical model capable of estimating, with the accuracy required by a preliminary mission analysis, the performance of a spacecraft equipped with a plasma brake in a (near-circular) low Earth orbit. The simplified mathematical model is first validated through numerical simulations, and is then used to evaluate the plasma brake performance in some typical mission scenarios, in order to quantify the influence of the system parameters on the mission performance index.

  10. Preliminary Shielding Analysis for HCCB TBM Transport

    Science.gov (United States)

    Miao, Peng; Zhao, Fengchao; Cao, Qixiang; Zhang, Guoshu; Feng, Kaiming

    2015-09-01

    A preliminary shielding analysis on the transport of the Chinese helium cooled ceramic breeder test blanket module (HCCB TBM) from France back to China after being irradiated in ITER is presented in this contribution. Emphasis was placed on irradiation safety during transport. The dose rate calculated by MCNP/4C for the conceptual package design satisfies the relevant dose limits from IAEA that the dose rate 3 m away from the surface of the package containing low specific activity III materials should be less than 10 mSv/h. The change with location and the time evolution of dose rates after shutdown have also been studied. This will be helpful for devising the detailed transport plan of HCCB TBM back to China in the near future. supported by the Major State Basic Research Development Program of China (973 Program) (No. 2013GB108000)

  11. Sequence analysis by iterated maps, a review.

    Science.gov (United States)

    Almeida, Jonas S

    2014-05-01

    Among alignment-free methods, Iterated Maps (IMs) are on a particular extreme: they are also scale free (order free). The use of IMs for sequence analysis is also distinct from other alignment-free methodologies in being rooted in statistical mechanics instead of computational linguistics. Both of these roots go back over two decades to the use of fractal geometry in the characterization of phase-space representations. The time series analysis origin of the field is betrayed by the title of the manuscript that started this alignment-free subdomain in 1990, 'Chaos Game Representation'. The clash between the analysis of sequences as continuous series and the better established use of Markovian approaches to discrete series was almost immediate, with a defining critique published in same journal 2 years later. The rest of that decade would go by before the scale-free nature of the IM space was uncovered. The ensuing decade saw this scalability generalized for non-genomic alphabets as well as an interest in its use for graphic representation of biological sequences. Finally, in the past couple of years, in step with the emergence of BigData and MapReduce as a new computational paradigm, there is a surprising third act in the IM story. Multiple reports have described gains in computational efficiency of multiple orders of magnitude over more conventional sequence analysis methodologies. The stage appears to be now set for a recasting of IMs with a central role in processing nextgen sequencing results.

  12. Preliminary ATWS analysis for the IRIS PRA

    International Nuclear Information System (INIS)

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

    2005-01-01

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

  13. Activation analysis by filtered neutrons. Preliminary investigation

    International Nuclear Information System (INIS)

    Skarnemark, G.; Rodinson, T.; Skaalberg, M.; Tokay, R.K.

    1986-01-01

    In order to investigate if measuring sensibility and precision by epithermal neutron activation analysis may be improved, different types of geological and biologic test samples were radiated. The test samples were enclosed in an extra filter of tungsten or sodium in order to reduce the flux of those neutrons that otherwise would induce interfering activity in the sample. The geological test samples consist of granites containing lanthanides which had been crushed in tung- sten carbide grinder. Normally such test samples show a interferins 1 87W-activity. By use of a tungsten filter the activity was reduced by up to 60%, which resulted in a considerable improvement of sensibility and precision of the measurement. The biologic test samples consisted of evaporated urine from patients treated with the cell poison cis-platinol. A reliable method to measure the platinum content has not existed so far. This method, however, enables platinum contents as low as about 0.1 ppm to be determined which is quite adequate. To sum up this preliminary study has demonstrated that activation analysis using filtered neutrons, correctly applied, is a satisfactory method of reducing interferences without complicated and time-consuming chemical separation procedures. (O.S.)

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

    Science.gov (United States)

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

    2009-12-01

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

  15. Digital image sequence processing, compression, and analysis

    CERN Document Server

    Reed, Todd R

    2004-01-01

    IntroductionTodd R. ReedCONTENT-BASED IMAGE SEQUENCE REPRESENTATIONPedro M. Q. Aguiar, Radu S. Jasinschi, José M. F. Moura, andCharnchai PluempitiwiriyawejTHE COMPUTATION OF MOTIONChristoph Stiller, Sören Kammel, Jan Horn, and Thao DangMOTION ANALYSIS AND DISPLACEMENT ESTIMATION IN THE FREQUENCY DOMAINLuca Lucchese and Guido Maria CortelazzoQUALITY OF SERVICE ASSESSMENT IN NEW GENERATION WIRELESS VIDEO COMMUNICATIONSGaetano GiuntaERROR CONCEALMENT IN DIGITAL VIDEOFrancesco G.B. De NataleIMAGE SEQUENCE RESTORATION: A WIDER PERSPECTIVEAnil KokaramVIDEO SUMMARIZATIONCuneyt M. Taskiran and Edward

  16. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    Phylogenetic analysis suggests that our sequences are clustered with sequences reported from Japan. This is the first phylogenetic analysis of HCV core gene from Pakistani population. Our sequences and sequences from Japan are grouped into same cluster in the phylogenetic tree. Sequence comparison and ...

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

    Science.gov (United States)

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

    2012-10-04

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

  18. OTU analysis using metagenomic shotgun sequencing data.

    Directory of Open Access Journals (Sweden)

    Xiaolin Hao

    Full Text Available Because of technological limitations, the primer and amplification biases in targeted sequencing of 16S rRNA genes have veiled the true microbial diversity underlying environmental samples. However, the protocol of metagenomic shotgun sequencing provides 16S rRNA gene fragment data with natural immunity against the biases raised during priming and thus the potential of uncovering the true structure of microbial community by giving more accurate predictions of operational taxonomic units (OTUs. Nonetheless, the lack of statistically rigorous comparison between 16S rRNA gene fragments and other data types makes it difficult to interpret previously reported results using 16S rRNA gene fragments. Therefore, in the present work, we established a standard analysis pipeline that would help confirm if the differences in the data are true or are just due to potential technical bias. This pipeline is built by using simulated data to find optimal mapping and OTU prediction methods. The comparison between simulated datasets revealed a relationship between 16S rRNA gene fragments and full-length 16S rRNA sequences that a 16S rRNA gene fragment having a length >150 bp provides the same accuracy as a full-length 16S rRNA sequence using our proposed pipeline, which could serve as a good starting point for experimental design and making the comparison between 16S rRNA gene fragment-based and targeted 16S rRNA sequencing-based surveys possible.

  19. Sequence Matching Analysis for Curriculum Development

    Directory of Open Access Journals (Sweden)

    Liem Yenny Bendatu

    2015-06-01

    Full Text Available Many organizations apply information technologies to support their business processes. Using the information technologies, the actual events are recorded and utilized to conform with predefined model. Conformance checking is an approach to measure the fitness and appropriateness between process model and actual events. However, when there are multiple events with the same timestamp, the traditional approach unfit to result such measures. This study attempts to develop a sequence matching analysis. Considering conformance checking as the basis of this approach, this proposed approach utilizes the current control flow technique in process mining domain. A case study in the field of educational process has been conducted. This study also proposes a curriculum analysis framework to test the proposed approach. By considering the learning sequence of students, it results some measurements for curriculum development. Finally, the result of the proposed approach has been verified by relevant instructors for further development.

  20. Preliminary Analysis and Selection of Mooring Solution Candidates

    DEFF Research Database (Denmark)

    Thomsen, Jonas Bjerg; Delaney, Martin

    This report covers a preliminary analysis of mooring solutions candidates for four large floating wave energy converters. The work is part of the EUDP project “Mooring Solutions for Large Wave Energy Converters” and is the outcome of "Work Package 3: Preliminary Analysis". The report further...... compose the "Milestone 4: Report on results of preliminary analysis and selection of final candidates. The report is produced by Aalborg University with input from the partner WECs Floating Power Plant, KNSwing, LEANCON and Wave Dragon. Tension Technology International (TTI) has provided a significant...

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

    Science.gov (United States)

    Tan, M K

    1991-08-01

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

  2. Preliminary safety analysis of the Gorleben site

    International Nuclear Information System (INIS)

    Bracke, G.; Fischer-Appelt, K.

    2014-01-01

    The safety requirements governing the final disposal of heat-generating radioactive waste in Germany were implemented by the Federal Ministry of Environment, Natural Conservation and Nuclear Safety (BMU) in 2010. The Ministry considers as a fundamental objective the protection of man and the environment against the hazards of radioactive waste. Unreasonable burdens and obligation for future generations shall be avoided. The main safety principles are concentration and inclusion of radioactive and other pollutants in a containment-providing rock zone. Any release of radioactive nuclides may increase the risk for men and the environment only negligibly compared to natural radiation exposure. No intervention or maintenance work shall be necessary in the post-closure phase. Retrieval/recovery of the waste shall be possible up to 500 years after closure. The Gorleben salt dome has been discussed since the 1970's as a possible repository site for heat-generating radioactive waste in Germany. The objective of the project preliminary safety analysis of the Gorleben site (VSG) was to assess if repository concepts at the Gorleben site or other sites with a comparable geology could comply with these requirements based on currently available knowledge (Fischer-Appelt, 2013; Bracke, 2013). In addition to this it was assessed if methodological approaches can be used for a future site selection procedure and which technological and conceptual considerations can be transferred to other geological situations. The objective included the compilation and review of the available exploration data of the Gorleben site and on disposal in salt rock, the development of repository designs, and the identification of the needs for future R and D work and further site investigations. (authors)

  3. The Scrap Tire Problem: A Preliminary Economic Analysis (1985)

    Science.gov (United States)

    The purpose of the study was to conduct a preliminary economic analysis of the social benefits of EPA action to require more appropriate disposal of scrap tires versus the social costs of such an action.

  4. Original Article PRELIMINARY BIOAUTOGRAPHIC ANALYSIS OF ...

    African Journals Online (AJOL)

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

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

    International Nuclear Information System (INIS)

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

    2011-01-01

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

  6. Life cycle analysis in preliminary design stages

    OpenAIRE

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

    2014-01-01

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

  7. FAST: FAST Analysis of Sequences Toolbox

    Directory of Open Access Journals (Sweden)

    Travis J. Lawrence

    2015-05-01

    Full Text Available FAST (FAST Analysis of Sequences Toolbox provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU’s Not Unix Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics makes FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format. Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought.

  8. Bayesian Correlation Analysis for Sequence Count Data.

    Directory of Open Access Journals (Sweden)

    Daniel Sánchez-Taltavull

    Full Text Available Evaluating the similarity of different measured variables is a fundamental task of statistics, and a key part of many bioinformatics algorithms. Here we propose a Bayesian scheme for estimating the correlation between different entities' measurements based on high-throughput sequencing data. These entities could be different genes or miRNAs whose expression is measured by RNA-seq, different transcription factors or histone marks whose expression is measured by ChIP-seq, or even combinations of different types of entities. Our Bayesian formulation accounts for both measured signal levels and uncertainty in those levels, due to varying sequencing depth in different experiments and to varying absolute levels of individual entities, both of which affect the precision of the measurements. In comparison with a traditional Pearson correlation analysis, we show that our Bayesian correlation analysis retains high correlations when measurement confidence is high, but suppresses correlations when measurement confidence is low-especially for entities with low signal levels. In addition, we consider the influence of priors on the Bayesian correlation estimate. Perhaps surprisingly, we show that naive, uniform priors on entities' signal levels can lead to highly biased correlation estimates, particularly when different experiments have widely varying sequencing depths. However, we propose two alternative priors that provably mitigate this problem. We also prove that, like traditional Pearson correlation, our Bayesian correlation calculation constitutes a kernel in the machine learning sense, and thus can be used as a similarity measure in any kernel-based machine learning algorithm. We demonstrate our approach on two RNA-seq datasets and one miRNA-seq dataset.

  9. A basic analysis toolkit for biological sequences

    Directory of Open Access Journals (Sweden)

    Siragusa Enrico

    2007-09-01

    Full Text Available Abstract This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at http://www.math.unipa.it/~raffaele/BATS/ under the GNU GPL.

  10. Preliminary Analysis For Wolsong Par Effects Using ISACC Calculations

    International Nuclear Information System (INIS)

    Song, Yong Mann; Kim, Dong Ha

    2012-01-01

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

  11. Review of Preliminary Analysis Techniques for Tension Structures.

    Science.gov (United States)

    1984-02-01

    however,a linear dinamic analysis can be conducted for purposes of preliminary design, relative to the static configuration. It is noted that the amount of...16 Chapter 3. PRELIMINARY DESIGN OF TENSION STRUCTURES . . .. .. .. .... 22 S.3.1 Cable Systems . . . . . . . . . . . . .. .. .. .... 23...3.1.1 Singly-Connected Segments. .. .... ... 24 3.1.2 Multiply-Connected Segments . . .. .. .. .. 27 3.1.3 Linearized Dynamics of Cable Systems . . . . 29

  12. Computational analysis of sequence selection mechanisms.

    Science.gov (United States)

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

    2004-04-01

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

  13. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

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

  14. Time fluctuation analysis of forest fire sequences

    Science.gov (United States)

    Vega Orozco, Carmen D.; Kanevski, Mikhaïl; Tonini, Marj; Golay, Jean; Pereira, Mário J. G.

    2013-04-01

    Forest fires are complex events involving both space and time fluctuations. Understanding of their dynamics and pattern distribution is of great importance in order to improve the resource allocation and support fire management actions at local and global levels. This study aims at characterizing the temporal fluctuations of forest fire sequences observed in Portugal, which is the country that holds the largest wildfire land dataset in Europe. This research applies several exploratory data analysis measures to 302,000 forest fires occurred from 1980 to 2007. The applied clustering measures are: Morisita clustering index, fractal and multifractal dimensions (box-counting), Ripley's K-function, Allan Factor, and variography. These algorithms enable a global time structural analysis describing the degree of clustering of a point pattern and defining whether the observed events occur randomly, in clusters or in a regular pattern. The considered methods are of general importance and can be used for other spatio-temporal events (i.e. crime, epidemiology, biodiversity, geomarketing, etc.). An important contribution of this research deals with the analysis and estimation of local measures of clustering that helps understanding their temporal structure. Each measure is described and executed for the raw data (forest fires geo-database) and results are compared to reference patterns generated under the null hypothesis of randomness (Poisson processes) embedded in the same time period of the raw data. This comparison enables estimating the degree of the deviation of the real data from a Poisson process. Generalizations to functional measures of these clustering methods, taking into account the phenomena, were also applied and adapted to detect time dependences in a measured variable (i.e. burned area). The time clustering of the raw data is compared several times with the Poisson processes at different thresholds of the measured function. Then, the clustering measure value

  15. SVAMP: Sequence variation analysis, maps and phylogeny

    KAUST Repository

    Naeem, Raeece

    2014-04-03

    Summary: SVAMP is a stand-alone desktop application to visualize genomic variants (in variant call format) in the context of geographical metadata. Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate analysis in real time from variant call format (VCF) and associated metadata files. Allele frequency map, geographical map of isolates, Tajima\\'s D metric, single nucleotide polymorphism density, GC and variation density are also available for visualization in real time. We demonstrate the utility of SVAMP in tracking a methicillin-resistant Staphylococcus aureus outbreak from published next-generation sequencing data across 15 countries. We also demonstrate the scalability and accuracy of our software on 245 Plasmodium falciparum malaria isolates from three continents. Availability and implementation: The Qt/C++ software code, binaries, user manual and example datasets are available at http://cbrc.kaust.edu.sa/svamp. © The Author 2014.

  16. Statistical analysis of next generation sequencing data

    CERN Document Server

    Nettleton, Dan

    2014-01-01

    Next Generation Sequencing (NGS) is the latest high throughput technology to revolutionize genomic research. NGS generates massive genomic datasets that play a key role in the big data phenomenon that surrounds us today. To extract signals from high-dimensional NGS data and make valid statistical inferences and predictions, novel data analytic and statistical techniques are needed. This book contains 20 chapters written by prominent statisticians working with NGS data. The topics range from basic preprocessing and analysis with NGS data to more complex genomic applications such as copy number variation and isoform expression detection. Research statisticians who want to learn about this growing and exciting area will find this book useful. In addition, many chapters from this book could be included in graduate-level classes in statistical bioinformatics for training future biostatisticians who will be expected to deal with genomic data in basic biomedical research, genomic clinical trials and personalized med...

  17. Movement Pattern Analysis Based on Sequence Signatures

    Directory of Open Access Journals (Sweden)

    Seyed Hossein Chavoshi

    2015-09-01

    Full Text Available Increased affordability and deployment of advanced tracking technologies have led researchers from various domains to analyze the resulting spatio-temporal movement data sets for the purpose of knowledge discovery. Two different approaches can be considered in the analysis of moving objects: quantitative analysis and qualitative analysis. This research focuses on the latter and uses the qualitative trajectory calculus (QTC, a type of calculus that represents qualitative data on moving point objects (MPOs, and establishes a framework to analyze the relative movement of multiple MPOs. A visualization technique called sequence signature (SESI is used, which enables to map QTC patterns in a 2D indexed rasterized space in order to evaluate the similarity of relative movement patterns of multiple MPOs. The applicability of the proposed methodology is illustrated by means of two practical examples of interacting MPOs: cars on a highway and body parts of a samba dancer. The results show that the proposed method can be effectively used to analyze interactions of multiple MPOs in different domains.

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

    Directory of Open Access Journals (Sweden)

    Marta Brozynska

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

  19. Noncoding sequence classification based on wavelet transform analysis: part I

    Science.gov (United States)

    Paredes, O.; Strojnik, M.; Romo-Vázquez, R.; Vélez Pérez, H.; Ranta, R.; Garcia-Torales, G.; Scholl, M. K.; Morales, J. A.

    2017-09-01

    DNA sequences in human genome can be divided into the coding and noncoding ones. Coding sequences are those that are read during the transcription. The identification of coding sequences has been widely reported in literature due to its much-studied periodicity. Noncoding sequences represent the majority of the human genome. They play an important role in gene regulation and differentiation among the cells. However, noncoding sequences do not exhibit periodicities that correlate to their functions. The ENCODE (Encyclopedia of DNA elements) and Epigenomic Roadmap Project projects have cataloged the human noncoding sequences into specific functions. We study characteristics of noncoding sequences with wavelet analysis of genomic signals.

  20. Image sequence analysis workstation for multipoint motion analysis

    Science.gov (United States)

    Mostafavi, Hassan

    1990-08-01

    This paper describes an application-specific engineering workstation designed and developed to analyze motion of objects from video sequences. The system combines the software and hardware environment of a modem graphic-oriented workstation with the digital image acquisition, processing and display techniques. In addition to automation and Increase In throughput of data reduction tasks, the objective of the system Is to provide less invasive methods of measurement by offering the ability to track objects that are more complex than reflective markers. Grey level Image processing and spatial/temporal adaptation of the processing parameters is used for location and tracking of more complex features of objects under uncontrolled lighting and background conditions. The applications of such an automated and noninvasive measurement tool include analysis of the trajectory and attitude of rigid bodies such as human limbs, robots, aircraft in flight, etc. The system's key features are: 1) Acquisition and storage of Image sequences by digitizing and storing real-time video; 2) computer-controlled movie loop playback, freeze frame display, and digital Image enhancement; 3) multiple leading edge tracking in addition to object centroids at up to 60 fields per second from both live input video or a stored Image sequence; 4) model-based estimation and tracking of the six degrees of freedom of a rigid body: 5) field-of-view and spatial calibration: 6) Image sequence and measurement data base management; and 7) offline analysis software for trajectory plotting and statistical analysis.

  1. 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)

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

    International Nuclear Information System (INIS)

    Han, Seok Jung; Yang, Joon Eon

    2005-01-01

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

  3. Novel algorithms for protein sequence analysis

    NARCIS (Netherlands)

    Ye, Kai

    2008-01-01

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

  4. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

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

    2010-01-01

    preferentially selected for sequencing. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement the data have been released into public sequence repositories (Genbank/EMBL, NCBI/Ensembl trace repositories) in a timely manner and in advance of publication. CONCLUSIONS...

  5. The EURACOS activation experiments: preliminary uncertainty analysis

    International Nuclear Information System (INIS)

    Yeivin, Y.

    1982-01-01

    A sequence of counting rates of an irradiated sulphur pellet, r(tsub(i)), measured at different times after the end of the irradiation, are fitted to r(t)=Aexp(-lambda t)+B. A standard adjustment procedure is applied to determine the parameters A and B, their standard deviations and correlation, and chi square. It is demonstrated that if the counting-rate uncertainties are entirely due to the counting statistics, the experimental data are totally inconsistent with the ''theoretical'' model. However, assuming an additional systematic error of approximalety 1%, and eliminating a few ''bad'' data, produces a data set quite consistent with the model. The dependence of chi square on the assumed systematic error and the data elimination procedure are discussed in great detail. A review of the adjustment procedure is appended to the report

  6. Preliminary analysis of B. E. C. I

    Energy Technology Data Exchange (ETDEWEB)

    Sugimoto, H; Sato, S [Waseda Univ., Tokyo (Japan). Science and Engineering Research Lab.; Saito, T; Noma, M; Matsubayashi, T

    1974-10-01

    An emulsion chamber (B.E.C.I.) with a generating layer, mounted on a baloon, was flown as preliminary experiment in May 1973. The object of this experiment was (1) the observation of high energy cosmic ray, (2) study of ultra-high energy multiple generation phenomenon, and (3) study of ultra-high energy heavy ion nuclear reaction. The emulsion chamber comprises three portions. Upper portion is 130 sheets arranged vertically at 3 mm intervals, each sheet is a 1,500 ..mu..m methacrylic base coated on one side with 200 ..mu..m emulsion. Middle portion comprises horizontally arranged 800 ..mu..m methacrylic bases coated on both sides with 50 ..mu..m emulsion, and a 1 mm methacrylic sheet is inserted every five bases. Lower portion comprises first five layers of the sandwich of 1 mm lead sheet and 800 ..mu..m methacrylic base coated on both sides with 50 ..mu..m emulsion and second ten layers of the sandwich of 2 mm lead sheet, 800 ..mu..m methacrylic base coated on one side with 50 ..mu..m emulsion, and X-ray film of N type. The cascade having energy of Esub(o)>400 GeV as the scanning efficiency of lower E.C.C., the events having incidental energy of Esub(o)>3TeV among the jets occured in lower E.C.C., and the events having incidental energy of Esub(o)>10TeV among the jets occured in generating layer have been observed. Angle distribution of the secondary charged particles of jets produced in the generating layer can be obtained accurately.

  7. Practical Recommendations for the Preliminary Design Analysis of ...

    African Journals Online (AJOL)

    Interior-to-exterior shear ratios for equal and unequal bay frames, as well as column inflection points were obtained to serve as practical aids for preliminary analysis/design of fixed-feet multistory sway frames. Equal and unequal bay five story frames were analysed to show the validity of the recommended design ...

  8. Yucca Mountain transportation routes: Preliminary characterization and risk analysis

    International Nuclear Information System (INIS)

    Souleyrette, R.R. II; Sathisan, S.K.; di Bartolo, R.

    1991-01-01

    This report presents appendices related to the preliminary assessment and risk analysis for high-level radioactive waste transportation routes to the proposed Yucca Mountain Project repository. Information includes data on population density, traffic volume, ecologically sensitive areas, and accident history

  9. Preliminary analysis of patent trends for magnetic fusion technology

    International Nuclear Information System (INIS)

    Levine, L.O.; Ashton, W.B.; Campbell, R.S.

    1984-02-01

    This study presents a preliminary analysis of development trends in magnetic fusion technology based on data from US patents. The research is limited to identification and description of general patent activity and ownership characteristics for 373 patents. The results suggest that more detailed studies of fusion patents could provide useful R and D planning information

  10. Licensing support system preliminary needs analysis: Volume 1

    International Nuclear Information System (INIS)

    1989-01-01

    This Preliminary Needs Analysis, together with the Preliminary Data Scope Analysis (next in this series of reports), is a first effort under the LSS Design and Implementation Contract toward developing a sound requirements foundation for subsequent design work. Further refinements must be made before requirements can be specified in sufficient detail to provide a basis for suitably specific system specifications. This preliminary analysis of the LSS requirements has been divided into a ''needs'' and a ''data scope'' portion only for project management and scheduling reasons. The Preliminary Data Scope Analysis will address all issues concerning the content and size of the LSS data base; providing the requirements basis for data acquisition, cataloging and storage sizing specifications. This report addresses all other requirements for the LSS. The LSS consists of both computer subsystems and non-computer archives. This study addresses only the computer subsystems, focusing on the Access Subsystems. After providing background on previous LSS-related work, this report summarizes the findings from previous examinations of needs and describes a number of other requirements that have an impact on the LSS. The results of interviews conducted for this report are then described and analyzed. The final section of the report brings all of the key findings together and describes how these needs analyses will continue to be refined and utilized in on-going design activities. 14 refs., 2 figs., 1 tab

  11. Preliminary thermal and stress analysis of the SINQ window

    International Nuclear Information System (INIS)

    Heidenreich, G.

    1991-01-01

    Preliminary results of a finite element analysis for the SINQ proton beam window are presented. Temperatures and stresses are calculated in an axisymmetric model. As a result of these calculations, the H 2 O-cooled window (safety window) could be redesigned in such a way that plastic deformation resulting from excessive stress in some areas is avoided. (author)

  12. Preliminary Integrated Safety Analysis Status Report

    International Nuclear Information System (INIS)

    Gwyn, D.

    2001-01-01

    This report provides the status of the potential Monitored Geologic Repository (MGR) Integrated Safety Analysis (EA) by identifying the initial work scope scheduled for completion during the ISA development period, the schedules associated with the tasks identified, safety analysis issues encountered, and a summary of accomplishments during the reporting period. This status covers the period from October 1, 2000 through March 30, 2001

  13. Preliminary analysis of alternative fuel cycles for proliferation evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Steindler, M. J.; Ripfel, H. C.F.; Rainey, R. H.

    1977-01-01

    The ERDA Division of Nuclear Research and Applications proposed 67 nuclear fuel cycles for assessment as to their nonproliferation potential. The object of the assessment was to determine which fuel cycles pose inherently low risk for nuclear weapon proliferation while retaining the major benefits of nuclear energy. This report is a preliminary analysis of these fuel cycles to develop the fuel-recycle data that will complement reactor data, environmental data, and political considerations, which must be included in the overall evaluation. This report presents the preliminary evaluations from ANL, HEDL, ORNL, and SRL and is the basis for a continuing in-depth study. (DLC)

  14. Characterization and sequence analysis of cysteine and glycine-rich ...

    African Journals Online (AJOL)

    Primers specific for CSRP3 were designed using known cDNA sequences of Bos taurus published in database with different accession numbers. Polymerase chain reaction (PCR) was performed and products were purified and sequenced. Sequence analysis and alignment were carried out using CLUSTAL W (1.83).

  15. antibacterial properties and preliminary phytochemical analysis

    African Journals Online (AJOL)

    DR. AMINU

    2Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Benin, Benin City. *Correspondence ... phytochemical analysis of the dried leaves extracts revealed the presence of alkaloids, ... for the synthesis of useful drugs.

  16. Incident sequence analysis; event trees, methods and graphical symbols

    International Nuclear Information System (INIS)

    1980-11-01

    When analyzing incident sequences, unwanted events resulting from a certain cause are looked for. Graphical symbols and explanations of graphical representations are presented. The method applies to the analysis of incident sequences in all types of facilities. By means of the incident sequence diagram, incident sequences, i.e. the logical and chronological course of repercussions initiated by the failure of a component or by an operating error, can be presented and analyzed simply and clearly

  17. Computer-aided visualization and analysis system for sequence evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Chee, Mark S.; Wang, Chunwei; Jevons, Luis C.; Bernhart, Derek H.; Lipshutz, Robert J.

    2004-05-11

    A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

  18. Preliminary conceptual design and analysis on KALIMER reactor structures

    International Nuclear Information System (INIS)

    Kim, Jong Bum

    1996-10-01

    The objectives of this study are to perform preliminary conceptual design and structural analyses for KALIMER (Korea Advanced Liquid Metal Reactor) reactor structures to assess the design feasibility and to identify detailed analysis requirements. KALIMER thermal hydraulic system analysis results and neutronic analysis results are not available at present, only-limited preliminary structural analyses have been performed with the assumptions on the thermal loads. The responses of reactor vessel and reactor internal structures were based on the temperature difference of core inlet and outlet and on engineering judgments. Thermal stresses from the assumed temperatures were calculated using ANSYS code through parametric finite element heat transfer and elastic stress analyses. While, based on the results of preliminary conceptual design and structural analyses, the ASME Code limits for the reactor structures were satisfied for the pressure boundary, the needs for inelastic analyses were indicated for evaluation of design adequacy of the support barrel and the thermal liner. To reduce thermal striping effects in the bottom are of UIS due to up-flowing sodium form reactor core, installation of Inconel-718 liner to the bottom area was proposed, and to mitigate thermal shock loads, additional stainless steel liner was also suggested. The design feasibilities of these were validated through simplified preliminary analyses. In conceptual design phase, the implementation of these results will be made for the design of the reactor structures and the reactor internal structures in conjunction with the thermal hydraulic, neutronic, and seismic analyses results. 4 tabs., 24 figs., 4 refs. (Author)

  19. Experience with PET FDG - Preliminary analysis

    International Nuclear Information System (INIS)

    Massardo, Teresa; Jofre, Josefina; Canessa, Jose; Gonzalez, Patricio; Humeres, Pamela; Sierralta, Paulina; Galaz, Rodrigo; Miranda, Karina

    2004-01-01

    Full text: The objective of this preliminary communication was to analyse the indications and data in initial group of patients studied with first dedicated PET scanner in the country at Hospital Militar in Santiago Chile. The main application of positron emission tomography (PET) with 18-Fluoro deoxyglucose (FDG) is related with oncological patients management. We studied 136 patients, 131 (97%) with known or suspected malignant disease and remaining 5 for cardiological or neuropsychiatric disease. Ten patients were controlled diabetics (1 insulin dependent). Their mean age was 51.6±18 years ranging from 6 to 84 years and 65% were females. A total of 177 scans were acquired using a dedicated PET (Siemens HR + with 4mm resolution) system. Mean F18-FDG injected dose was 477±107 MBq (12.9±2.9 mCi). Mean blood glucose levels, performed prior the injection, were 94±17mg/dl (range 62-161). F18-FDG was obtained from the cyclotron IBA Cyclone 18/9 installed in the Chilean Agency of Nuclear Energy, distant about 15 miles away from the clinical PET facility. PET studies were analyzed by at least 4 independent observers visually. Standardized uptake value (SUV) was calculated in some cases. Image fusion of FDG images with recent anatomical (CT, MRI) studies was performed where available. Data acquisition protocol consisted in 7-8 beds/study from head to mid-thighs, with 6-7-min/bed acquisitions, 36% transmission with germanium 68 rods. Data was reconstructed with standard OSEM protocol. The main indications included pulmonary lesions in 31%, gastrointestinal cancers in 21%, melanoma in 13% and lymphoma in 9% patients. The remaining were of breast, thyroid, testes, ovary, musculoskeletal (soft tissue and bone), brain tumour etc. Abnormal focal tracer uptake was observed in 83/131 oncological patients, 54% corroborating with clinical diagnosis of primary tumor or recurrence while 46% showed new metastatic localization. FDG scans were normal 36/131 patients. In 9 patients

  20. Experience with PET FDG - Preliminary analysis

    Energy Technology Data Exchange (ETDEWEB)

    Massardo, Teresa; Jofre, Josefina; Canessa, Jose; Gonzalez, Patricio; Humeres, Pamela; Sierralta, Paulina; Galaz, Rodrigo; Miranda, Karina [Centro PET de Imagenes Moleculares, Hospital Militar de Santiago, Santiago (Chile)

    2004-01-01

    Full text: The objective of this preliminary communication was to analyse the indications and data in initial group of patients studied with first dedicated PET scanner in the country at Hospital Militar in Santiago Chile. The main application of positron emission tomography (PET) with 18-Fluoro deoxyglucose (FDG) is related with oncological patients management. We studied 136 patients, 131 (97%) with known or suspected malignant disease and remaining 5 for cardiological or neuropsychiatric disease. Ten patients were controlled diabetics (1 insulin dependent). Their mean age was 51.6{+-}18 years ranging from 6 to 84 years and 65% were females. A total of 177 scans were acquired using a dedicated PET (Siemens HR + with 4mm resolution) system. Mean F18-FDG injected dose was 477{+-}107 MBq (12.9{+-}2.9 mCi). Mean blood glucose levels, performed prior the injection, were 94{+-}17mg/dl (range 62-161). F18-FDG was obtained from the cyclotron IBA Cyclone 18/9 installed in the Chilean Agency of Nuclear Energy, distant about 15 miles away from the clinical PET facility. PET studies were analyzed by at least 4 independent observers visually. Standardized uptake value (SUV) was calculated in some cases. Image fusion of FDG images with recent anatomical (CT, MRI) studies was performed where available. Data acquisition protocol consisted in 7-8 beds/study from head to mid-thighs, with 6-7-min/bed acquisitions, 36% transmission with germanium 68 rods. Data was reconstructed with standard OSEM protocol. The main indications included pulmonary lesions in 31%, gastrointestinal cancers in 21%, melanoma in 13% and lymphoma in 9% patients. The remaining were of breast, thyroid, testes, ovary, musculoskeletal (soft tissue and bone), brain tumour etc. Abnormal focal tracer uptake was observed in 83/131 oncological patients, 54% corroborating with clinical diagnosis of primary tumor or recurrence while 46% showed new metastatic localization. FDG scans were normal 36/131 patients. In 9

  1. Preliminary engineering analysis for clothes washers

    Energy Technology Data Exchange (ETDEWEB)

    Biermayer, Peter J.

    1996-10-01

    The Engineering Analysis provides information on efficiencies, manufacturer costs, and other characteristics of the appliance class being analyzed. For clothes washers, there are two classes: standard and compact. Since data were not available to analyze the compact class, only clothes washers were analyzed in this report. For this analysis, individual design options were combined and ordered in a manner that resulted in the lowest cumulative cost/savings ratio. The cost/savings ratio is the increase in manufacturer cost for a design option divided by the reduction in operating costs due to fuel and water savings.

  2. Establishing a framework for comparative analysis of genome sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bansal, A.K.

    1995-06-01

    This paper describes a framework and a high-level language toolkit for comparative analysis of genome sequence alignment The framework integrates the information derived from multiple sequence alignment and phylogenetic tree (hypothetical tree of evolution) to derive new properties about sequences. Multiple sequence alignments are treated as an abstract data type. Abstract operations have been described to manipulate a multiple sequence alignment and to derive mutation related information from a phylogenetic tree by superimposing parsimonious analysis. The framework has been applied on protein alignments to derive constrained columns (in a multiple sequence alignment) that exhibit evolutionary pressure to preserve a common property in a column despite mutation. A Prolog toolkit based on the framework has been implemented and demonstrated on alignments containing 3000 sequences and 3904 columns.

  3. Preliminary analysis of the KAERI RCCS Experiment Using GAMMA+

    Energy Technology Data Exchange (ETDEWEB)

    Khoza, Samukelisiwe; Tak, Nam-il; Lim, Hong-Sik; Lee, Sung-Nam; Cho, Bong-Hyun; Kim, Jong-Hwan [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2015-05-15

    This paper describes the analysis of the KAERI RCCS experiment. GAMMA+ code was used for analysis of the RCCS 1/4-scale natural cooling experimental facility designed and built at KAERI to verify the performance of the natural circulation phenomenon. The results obtained from the GAMMA+ analysis showing the temperature profiles and flow rates at steady state were compared with the results from the preliminary experiments conducted in this facility. GAMMA+ analysis for the KAERI RCCS experimental setup was carried out to understand its natural circulation behavior. The air flow rate at the chimney exit achieved by experiments was from to be almost same as that of GAMMA+.

  4. Gravity field of Venus - A preliminary analysis

    Science.gov (United States)

    Phillips, R. J.; Sjogren, W. L.; Abbott, E. A.; Smith, J. C.; Wimberly, R. N.; Wagner, C. A.

    1979-01-01

    The gravitational field of Venus obtained by tracking the Pioneer Venus Orbiter is examined. For each spacecraft orbit, two hours of Doppler data centered around periapsis were used to estimate spacecraft position and velocity and the velocity residuals obtained were spline fit and differentiated to produce line of sight gravitational accelerations. Consistent variations in line of sight accelerations from orbit to orbit reveal the presence of gravitational anomalies. A simulation of isostatic compensation for an elevated region on the surface of Venus indicates that the mean depth of compensation is no greater than about 100 km. Gravitational spectra obtained from a Fourier analysis of line of sight accelerations from selected Venus orbits are compared to the earth's gravitational spectrum and spherical harmonic gravitational potential power spectra of the earth, the moon and Mars. The Venus power spectrum is found to be remarkably similar to that of the earth, however systematic variations in the harmonics suggest differences in dynamic processes or lithospheric behavior.

  5. Scalable Kernel Methods and Algorithms for General Sequence Analysis

    Science.gov (United States)

    Kuksa, Pavel

    2011-01-01

    Analysis of large-scale sequential data has become an important task in machine learning and pattern recognition, inspired in part by numerous scientific and technological applications such as the document and text classification or the analysis of biological sequences. However, current computational methods for sequence comparison still lack…

  6. Recurrence plot analysis of DNA sequences

    Energy Technology Data Exchange (ETDEWEB)

    Wu Zuobing [State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080 (China)]. E-mail: wuzb@lnm.imech.ac.cn

    2004-11-15

    Recurrence plot technique of DNA sequences is established on metric representation and employed to analyze correlation structure of nucleotide strings. It is found that, in the transference of nucleotide strings, a human DNA fragment has a major correlation distance, but a yeast chromosome's correlation distance has a constant increasing.

  7. Advanced high conversion PWR: preliminary analysis

    International Nuclear Information System (INIS)

    Golfier, H.; Bellanger, V.; Bergeron, A.; Dolci, F.; Gastaldi, B.; Koberl, O.; Mignot, G.; Thevenot, C.

    2007-01-01

    In this paper, physical aspects of a HCPWR (High Conversion Light Water Reactor), which is an innovative PWR fuelled with mixed oxide and having a higher conversion ratio due to a lower moderation ratio. Moderation ratios lower than unity are considered which has led to low moderation PWR fuel assembly designs. The objectives of this parametric study are to define a feasibility area with regard to the following neutronic aspects: moderation ratio, Pu loading, reactor spectrum, irradiation time, and neutronic coefficients. Important thermohydraulic parameters are the pressure drop, the critical heat flux, the maximum temperature in the fuel rod and the pumping power. The thermohydraulic analysis shows that a range of moderation ratios from 0.8 to 1.2 is technically possible. A compromise between improved fuel utilization and research and development effort has been found for the moderation ration of about 1. The parametric study shows that there are 2 ranges of interest for the moderation ratio: -) moderation ratio between 0.8 and 1.2 with reduced fissile heights (> 3 m), hexagonal arrangement fuel assembly and square arrangement fuel assembly are possible; and -) moderation between 0.6 and 0.7 with a modification of the reactor operating conditions (reduction of the primary flow and of the thermal power), the fuel rods could be arranged inside a hexagonal fuel rod assembly. (A.C.)

  8. A preliminary analysis of bidayuh Jagoi patun

    Directory of Open Access Journals (Sweden)

    Dayang Sariah Abang Suhai

    2013-12-01

    Full Text Available Bidayuh Pantun or Patun remains a under researched topic in Borneo studies and language research due to the difficulties associated with obtaining critical, poetic information in oral culture, language variations and societal mobility. Existing data from anthologies however provide little detail about the instrinsic and extrinsic features ascribed to the poem by the people who produce and use them. This paper attempts to explore patun from the Jagoi community. In this study, the structural aspects, themes and moral values of 47 patun from the Jagoi community were analysed. The initial explanations suggested by the poet were further analysed to determine the various structural features to place it alongside existing mainstream lyric poetry. The analysis of the intrinsic features showed that good rhythmic patun has four to six words per line and eight to 12 syllables per line, and the final syllables of each line has assonance and consonance patterns of a-a-a-a and a-b-a-b. The themes of the patun include love, advice, forgiveness, beliefs, hopelessness and happiness, and the moral values take the form of subtle advice and admonishments. The Bidayuh patun is indeed a projection of knowledge, experiences, beliefs, values, and emotions of the community.

  9. Surface Properties of TNOs: Preliminary Statistical Analysis

    Science.gov (United States)

    Antonieta Barucci, Maria; Fornasier, S.; Alvarez-Cantal, A.; de Bergh, C.; Merlin, F.; DeMeo, F.; Dumas, C.

    2009-09-01

    An overview of the surface properties based on the last results obtained during the Large Program performed at ESO-VLT (2007-2008) will be presented. Simultaneous high quality visible and near-infrared spectroscopy and photometry have been carried out on 40 objects with various dynamical properties, using FORS1 (V), ISAAC (J) and SINFONI (H+K bands) mounted respectively at UT2, UT1 and UT4 VLT-ESO telescopes (Cerro Paranal, Chile). For spectroscopy we computed the spectral slope for each object and searched for possible rotational inhomogeneities. A few objects show features in their visible spectra such as Eris, whose spectral bands are displaced with respect to pure methane-ice. We identify new faint absorption features on 10199 Chariklo and 42355 Typhon, possibly due to the presence of aqueous altered materials. The H+K band spectroscopy was performed with the new instrument SINFONI which is a 3D integral field spectrometer. While some objects show no diagnostic spectral bands, others reveal surface deposits of ices of H2O, CH3OH, CH4, and N2. To investigate the surface properties of these bodies, a radiative transfer model has been applied to interpret the entire 0.4-2.4 micron spectral region. The diversity of the spectra suggests that these objects represent a substantial range of bulk compositions. These different surface compositions can be diagnostic of original compositional diversity, interior source and/or different evolution with different physical processes affecting the surfaces. A statistical analysis is in progress to investigate the correlation of the TNOs’ surface properties with size and dynamical properties.

  10. Preliminary Seismic Response and Fragility Analysis for DACS Cabinet

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Jinho; Kwag, Shinyoung; Lee, Jongmin; Kim, Youngki [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2013-05-15

    A DACS cabinet is installed in the main control room. The objective of this paper is to perform seismic analyses and evaluate the preliminary structural integrity and seismic capacity of the DACS cabinet. For this purpose, a 3-D finite element model of the DACS cabinet was developed and its modal analyses are carried out to analyze the dynamic characteristics. The response spectrum analyses and the related safety evaluation are then performed for the DACS cabinet subject to seismic loads. Finally, the seismic margin and seismic fragility of the DACS cabinet are investigated. A seismic analysis and preliminary structural integrity of the DACS cabinet under self weight and SSE load have been evaluated. For this purpose, 3-D finite element models of the DACS cabinet were developed. A modal analysis, response spectrum analysis, and seismic fragility analysis were then performed. From the structural analysis results, the DACS cabinet is below the structural design limit of under SSE 0.3g, and can structurally withstand until less than SSE 3g based on an evaluation of the maximum effective stresses. The HCLPF capacity for the DGRS of the SSE 0.3g is 0.55g. A modal analysis, response spectrum analysis, and seismic fragility analysis were then performed. From the structural analysis results, the DACS cabinet is below the structural design limit of under SSE 0.3g, and can structurally withstand until less than SSE 3g based on an evaluation of the maximum effective stresses. The HCLPF capacity for the DGRS of the SSE 0.3g is 0.55g. Therefore, it is concluded that the DACS cabinet was safely designed in that no damage to the preliminary structural integrity and sufficient seismic margin is expected.

  11. Preliminary Seismic Response and Fragility Analysis for DACS Cabinet

    International Nuclear Information System (INIS)

    Oh, Jinho; Kwag, Shinyoung; Lee, Jongmin; Kim, Youngki

    2013-01-01

    A DACS cabinet is installed in the main control room. The objective of this paper is to perform seismic analyses and evaluate the preliminary structural integrity and seismic capacity of the DACS cabinet. For this purpose, a 3-D finite element model of the DACS cabinet was developed and its modal analyses are carried out to analyze the dynamic characteristics. The response spectrum analyses and the related safety evaluation are then performed for the DACS cabinet subject to seismic loads. Finally, the seismic margin and seismic fragility of the DACS cabinet are investigated. A seismic analysis and preliminary structural integrity of the DACS cabinet under self weight and SSE load have been evaluated. For this purpose, 3-D finite element models of the DACS cabinet were developed. A modal analysis, response spectrum analysis, and seismic fragility analysis were then performed. From the structural analysis results, the DACS cabinet is below the structural design limit of under SSE 0.3g, and can structurally withstand until less than SSE 3g based on an evaluation of the maximum effective stresses. The HCLPF capacity for the DGRS of the SSE 0.3g is 0.55g. A modal analysis, response spectrum analysis, and seismic fragility analysis were then performed. From the structural analysis results, the DACS cabinet is below the structural design limit of under SSE 0.3g, and can structurally withstand until less than SSE 3g based on an evaluation of the maximum effective stresses. The HCLPF capacity for the DGRS of the SSE 0.3g is 0.55g. Therefore, it is concluded that the DACS cabinet was safely designed in that no damage to the preliminary structural integrity and sufficient seismic margin is expected

  12. Analysis of Neuronal Sequences Using Pairwise Biases

    Science.gov (United States)

    2015-08-27

    semantic memory (knowledge of facts) and implicit memory (e.g., how to ride a bike ). Evidence for the participation of the hippocampus in the formation of...hippocampal formation in an attempt to be cured of severe epileptic seizures. Although the surgery was successful in regards to reducing the frequency and...very different from each other in many ways including duration and number of spikes. Still, these sequences share a similar trend in the general order

  13. Google matrix analysis of DNA sequences.

    Science.gov (United States)

    Kandiah, Vivek; Shepelyansky, Dima L

    2013-01-01

    For DNA sequences of various species we construct the Google matrix [Formula: see text] of Markov transitions between nearby words composed of several letters. The statistical distribution of matrix elements of this matrix is shown to be described by a power law with the exponent being close to those of outgoing links in such scale-free networks as the World Wide Web (WWW). At the same time the sum of ingoing matrix elements is characterized by the exponent being significantly larger than those typical for WWW networks. This results in a slow algebraic decay of the PageRank probability determined by the distribution of ingoing elements. The spectrum of [Formula: see text] is characterized by a large gap leading to a rapid relaxation process on the DNA sequence networks. We introduce the PageRank proximity correlator between different species which determines their statistical similarity from the view point of Markov chains. The properties of other eigenstates of the Google matrix are also discussed. Our results establish scale-free features of DNA sequence networks showing their similarities and distinctions with the WWW and linguistic networks.

  14. Google matrix analysis of DNA sequences.

    Directory of Open Access Journals (Sweden)

    Vivek Kandiah

    Full Text Available For DNA sequences of various species we construct the Google matrix [Formula: see text] of Markov transitions between nearby words composed of several letters. The statistical distribution of matrix elements of this matrix is shown to be described by a power law with the exponent being close to those of outgoing links in such scale-free networks as the World Wide Web (WWW. At the same time the sum of ingoing matrix elements is characterized by the exponent being significantly larger than those typical for WWW networks. This results in a slow algebraic decay of the PageRank probability determined by the distribution of ingoing elements. The spectrum of [Formula: see text] is characterized by a large gap leading to a rapid relaxation process on the DNA sequence networks. We introduce the PageRank proximity correlator between different species which determines their statistical similarity from the view point of Markov chains. The properties of other eigenstates of the Google matrix are also discussed. Our results establish scale-free features of DNA sequence networks showing their similarities and distinctions with the WWW and linguistic networks.

  15. Error Analysis of Deep Sequencing of Phage Libraries: Peptides Censored in Sequencing

    Directory of Open Access Journals (Sweden)

    Wadim L. Matochko

    2013-01-01

    Full Text Available Next-generation sequencing techniques empower selection of ligands from phage-display libraries because they can detect low abundant clones and quantify changes in the copy numbers of clones without excessive selection rounds. Identification of errors in deep sequencing data is the most critical step in this process because these techniques have error rates >1%. Mechanisms that yield errors in Illumina and other techniques have been proposed, but no reports to date describe error analysis in phage libraries. Our paper focuses on error analysis of 7-mer peptide libraries sequenced by Illumina method. Low theoretical complexity of this phage library, as compared to complexity of long genetic reads and genomes, allowed us to describe this library using convenient linear vector and operator framework. We describe a phage library as N×1 frequency vector n=ni, where ni is the copy number of the ith sequence and N is the theoretical diversity, that is, the total number of all possible sequences. Any manipulation to the library is an operator acting on n. Selection, amplification, or sequencing could be described as a product of a N×N matrix and a stochastic sampling operator (Sa. The latter is a random diagonal matrix that describes sampling of a library. In this paper, we focus on the properties of Sa and use them to define the sequencing operator (Seq. Sequencing without any bias and errors is Seq=Sa IN, where IN is a N×N unity matrix. Any bias in sequencing changes IN to a nonunity matrix. We identified a diagonal censorship matrix (CEN, which describes elimination or statistically significant downsampling, of specific reads during the sequencing process.

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

    Directory of Open Access Journals (Sweden)

    Alessandra De Cesare

    2018-04-01

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

  17. Preliminary Mass Spectrometric Analysis of Uranium on Environmental Swipe Materials

    International Nuclear Information System (INIS)

    Cheong, Chang-Sik; Jeong, Youn-Joong; Ryu, Jong-Sik; Shin, Hyung-Seon; Cha, Hyun-Ju; Ahn, Gil-Hoon; Park, Il-Jin; Min, Gyung-Sik

    2006-01-01

    It is well-known that uranium and plutonium isotopic compositions of safeguards samples are very useful to investigate the history of nuclear activities. To strengthen the capabilities of environmental sampling analysis in the ROK through MOST/DOE collaboration, round robin test for uranium and plutonium was designed in 2003. As the first round robin test, a set of dried uranium-containing solutions (∼35ng and (∼300ng) was distributed to the participating laboratories in November of 2003, with results reported in April of 2004. The KBSI (Korea Basic Science Institute) and ORNL (Oak Ridge National Laboratory) are currently in the process of analyzing uranium on cotton swipes for the second round robin test. As a preliminary test for the second round, KBSI intends to analyze home-made swipe samples into which international uranium standards are added. Here we describe technical steps of sample preparation and mass spectrometry at KBSI, and report some results of the preliminary test

  18. Active cooling for downhole instrumentation: Preliminary analysis and system selection

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, G.A.

    1988-03-01

    A feasibility study and a series of preliminary designs and analyses were done to identify candidate processes or cycles for use in active cooling systems for downhole electronic instruments. A matrix of energy types and their possible combinations was developed and the energy conversion process for each pari was identified. The feasibility study revealed conventional as well as unconventional processes and possible refrigerants and identified parameters needing further clarifications. A conceptual design or series od oesigns for each system was formulated and a preliminary analysis of each design was completed. The resulting coefficient of performance for each system was compared with the Carnot COP and all systems were ranked by decreasing COP. The system showing the best combination of COP, exchangeability to other operating conditions, failure mode, and system serviceability is chosen for use as a downhole refrigerator. 85 refs., 48 figs., 33 tabs.

  19. Preliminary study of soil permeability properties using principal component analysis

    Science.gov (United States)

    Yulianti, M.; Sudriani, Y.; Rustini, H. A.

    2018-02-01

    Soil permeability measurement is undoubtedly important in carrying out soil-water research such as rainfall-runoff modelling, irrigation water distribution systems, etc. It is also known that acquiring reliable soil permeability data is rather laborious, time-consuming, and costly. Therefore, it is desirable to develop the prediction model. Several studies of empirical equations for predicting permeability have been undertaken by many researchers. These studies derived the models from areas which soil characteristics are different from Indonesian soil, which suggest a possibility that these permeability models are site-specific. The purpose of this study is to identify which soil parameters correspond strongly to soil permeability and propose a preliminary model for permeability prediction. Principal component analysis (PCA) was applied to 16 parameters analysed from 37 sites consist of 91 samples obtained from Batanghari Watershed. Findings indicated five variables that have strong correlation with soil permeability, and we recommend a preliminary permeability model, which is potential for further development.

  20. Preliminary Safety Analysis Report for the Tokamak Physics Experiment

    International Nuclear Information System (INIS)

    Motloch, C.G.; Bonney, R.F.; Levine, J.D.; Masson, L.S.; Commander, J.C.

    1995-04-01

    This Preliminary Safety Analysis Report (PSAR), includes an indication of the magnitude of facility hazards, complexity of facility operations, and the stage of the facility life-cycle. It presents the results of safety analyses, safety assurance programs, identified vulnerabilities, compensatory measures, and, in general, the rationale describing why the Tokamak Physics Experiment (TPX) can be safely operated. It discusses application of the graded approach to the TPX safety analysis, including the basis for using Department of Energy (DOE) Order 5480.23 and DOE-STD-3009-94 in the development of the PSAR

  1. Cloning and sequence analysis of benzo-a-pyreneinducible ...

    African Journals Online (AJOL)

    The phylogenetic tree based on the amino acid sequences clearly shows tilapia CYP1A and killifish CYP1A to be more closely related to each other than to the other CYP1A subfamilies. Sequence analysis of 3727 bp of genomic DNA showed that the clone obtained was the structural gene of CYP1A which consists of ...

  2. Biological sequence analysis: probabilistic models of proteins and nucleic acids

    National Research Council Canada - National Science Library

    Durbin, Richard

    1998-01-01

    ... analysis methods are now based on principles of probabilistic modelling. Examples of such methods include the use of probabilistically derived score matrices to determine the significance of sequence alignments, the use of hidden Markov models as the basis for profile searches to identify distant members of sequence families, and the inference...

  3. Phylogenetic analysis of the genus Hordeum using repetitive DNA sequences

    DEFF Research Database (Denmark)

    Svitashev, S.; Bryngelsson, T.; Vershinin, A.

    1994-01-01

    A set of six cloned barley (Hordeum vulgare) repetitive DNA sequences was used for the analysis of phylogenetic relationships among 31 species (46 taxa) of the genus Hordeum, using molecular hybridization techniques. In situ hybridization experiments showed dispersed organization of the sequences...

  4. Parametric inference for biological sequence analysis.

    Science.gov (United States)

    Pachter, Lior; Sturmfels, Bernd

    2004-11-16

    One of the major successes in computational biology has been the unification, by using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied to these problems include hidden Markov models for annotation, tree models for phylogenetics, and pair hidden Markov models for alignment. A single algorithm, the sum-product algorithm, solves many of the inference problems that are associated with different statistical models. This article introduces the polytope propagation algorithm for computing the Newton polytope of an observation from a graphical model. This algorithm is a geometric version of the sum-product algorithm and is used to analyze the parametric behavior of maximum a posteriori inference calculations for graphical models.

  5. Recurrence time statistics: versatile tools for genomic DNA sequence analysis.

    Science.gov (United States)

    Cao, Yinhe; Tung, Wen-Wen; Gao, J B

    2004-01-01

    With the completion of the human and a few model organisms' genomes, and the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time based method for sequence analysis. The method can conveniently study all kinds of periodicity and exhaustively find all repeat-related features from a genomic DNA sequence. An efficient codon index is also derived from the recurrence time statistics, which has the salient features of being largely species-independent and working well on very short sequences. Efficient codon indices are key elements of successful gene finding algorithms, and are particularly useful for determining whether a suspected EST belongs to a coding or non-coding region. We illustrate the power of the method by studying the genomes of E. coli, the yeast S. cervisivae, the nematode worm C. elegans, and the human, Homo sapiens. Computationally, our method is very efficient. It allows us to carry out analysis of genomes on the whole genomic scale by a PC.

  6. RESEARCH NOTE Genome-based exome-sequencing analysis ...

    Indian Academy of Sciences (India)

    Navya

    2017-02-22

    Feb 22, 2017 ... Genome-based exome-sequencing analysis identifies GYG1, DIS3L, DDRGK1 genes ... Cardiology Division, Department of Internal Medicine, Severance .... with p values of <0.05 byanalyzing differences in allele distribution.

  7. Editorial: Special Issue on Algorithms for Sequence Analysis and Storage

    Directory of Open Access Journals (Sweden)

    Veli Mäkinen

    2014-03-01

    Full Text Available This special issue of Algorithms is dedicated to approaches to biological sequence analysis that have algorithmic novelty and potential for fundamental impact in methods used for genome research.

  8. Tools for integrated sequence-structure analysis with UCSF Chimera

    Directory of Open Access Journals (Sweden)

    Huang Conrad C

    2006-07-01

    Full Text Available Abstract Background Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit; (c can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals. Results The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided. Conclusion The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is

  9. Isolation and preliminary function analysis of a Na + /H + antiporter ...

    African Journals Online (AJOL)

    A full-length cDNA Na+/H+ antiporter gene (MzNHX1) was isolated from Malus zumi according to the homologous Na+/H+ antiporter gene region in plants. Sequence analysis indicated that the cDNA was 2062 bp in length, including an open reading frame (ORF) of 1629 bp, which encoded a predicted polypeptide of 542 ...

  10. Sequencing and Analysis of Neanderthal Genomic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Noonan, James P.; Coop, Graham; Kudaravalli, Sridhar; Smith,Doug; Krause, Johannes; Alessi, Joe; Chen, Feng; Platt, Darren; Paabo,Svante; Pritchard, Jonathan K.; Rubin, Edward M.

    2006-06-13

    Recovery and analysis of multiple Neanderthal autosomalsequences using a metagenomic approach reveals that modern humans andNeanderthals split ~;400,000 years ago, without significant evidence ofsubsequent admixture.

  11. SVAMP: Sequence variation analysis, maps and phylogeny

    KAUST Repository

    Naeem, Raeece; Hidayah, Lailatul; Preston, Mark D.; Clark, Taane G.; Pain, Arnab

    2014-01-01

    Summary: SVAMP is a stand-alone desktop application to visualize genomic variants (in variant call format) in the context of geographical metadata. Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate analysis

  12. DSAP: deep-sequencing small RNA analysis pipeline.

    Science.gov (United States)

    Huang, Po-Jung; Liu, Yi-Chung; Lee, Chi-Ching; Lin, Wei-Chen; Gan, Richie Ruei-Chi; Lyu, Ping-Chiang; Tang, Petrus

    2010-07-01

    DSAP is an automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a tab-delimited file as an input format, which holds the unique sequence reads (tags) and their corresponding number of copies generated by the Solexa sequencing platform. The input data will go through four analysis steps in DSAP: (i) cleanup: removal of adaptors and poly-A/T/C/G/N nucleotides; (ii) clustering: grouping of cleaned sequence tags into unique sequence clusters; (iii) non-coding RNA (ncRNA) matching: sequence homology mapping against a transcribed sequence library from the ncRNA database Rfam (http://rfam.sanger.ac.uk/); and (iv) known miRNA matching: detection of known miRNAs in miRBase (http://www.mirbase.org/) based on sequence homology. The expression levels corresponding to matched ncRNAs and miRNAs are summarized in multi-color clickable bar charts linked to external databases. DSAP is also capable of displaying miRNA expression levels from different jobs using a log(2)-scaled color matrix. Furthermore, a cross-species comparative function is also provided to show the distribution of identified miRNAs in different species as deposited in miRBase. DSAP is available at http://dsap.cgu.edu.tw.

  13. Quantiprot - a Python package for quantitative analysis of protein sequences.

    Science.gov (United States)

    Konopka, Bogumił M; Marciniak, Marta; Dyrka, Witold

    2017-07-17

    The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids. Besides basic measures, Quantiprot performs quantitative analysis of recurrence and determinism in the sequence, calculates distribution of n-grams and computes the Zipf's law coefficient. We propose three main fields of application of the Quantiprot package. First, quantitative characteristics can be used in alignment-free similarity searches, and in clustering of large and/or divergent sequence sets. Second, a feature space defined by quantitative properties can be used in comparative studies of protein families and organisms. Third, the feature space can be used for evaluating generative models, where large number of sequences generated by the model can be compared to actually observed sequences.

  14. Preliminary analysis of a target factory for laser fusion

    International Nuclear Information System (INIS)

    Sherohman, J.W.; Hendricks, C.D.

    1980-01-01

    An analysis of a target factory leading to the determination of production expressions has provided for the basis of a parametric study. Parameters involving the input and output rate of a process system, processing yield factors, and multiple processing steps and production lines have been used to develop an understanding of their dependence on the rate of target injection for laser fusion. Preliminary results have indicated that a parametric study of this type will be important in the selection of processing methods to be used in the final production scheme of a target factory

  15. Determinants of Trade Credit: A Preliminary Analysis on Construction Sector

    Directory of Open Access Journals (Sweden)

    Nicoleta Barbuta-Misu

    2016-07-01

    Full Text Available This paper introduces a preliminary analysis of the correlations between trade credit and some selected measures of financial performance for a sample of 958 firms acting in the construction sector. The examined period covers 2004-2013. The sample derived from Amadeus database contains firms that have sold and bought on credit. Results showed that larger firms offered and used more credit than counterparties. Firms offered and used in same time credit, but not in same level. Firms with higher return on assets and profit margin used and offered less credit from suppliers, respectively to clients. Moreover, more liquid firms used less trade payables.

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

    International Nuclear Information System (INIS)

    Tsuda, Kyo; Murakami, Takamichi; Sakurai, Kousuke

    1997-01-01

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

  17. CONTENT ANALYSIS, DISCOURSE ANALYSIS, AND CONVERSATION ANALYSIS: PRELIMINARY STUDY ON CONCEPTUAL AND THEORETICAL METHODOLOGICAL DIFFERENCES

    Directory of Open Access Journals (Sweden)

    Anderson Tiago Peixoto Gonçalves

    2016-08-01

    Full Text Available This theoretical essay aims to reflect on three models of text interpretation used in qualitative research, which is often confused in its concepts and methodologies (Content Analysis, Discourse Analysis, and Conversation Analysis. After the presentation of the concepts, the essay proposes a preliminary discussion on conceptual and theoretical methodological differences perceived between them. A review of the literature was performed to support the conceptual and theoretical methodological discussion. It could be verified that the models have differences related to the type of strategy used in the treatment of texts, the type of approach, and the appropriate theoretical position.

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

    NARCIS (Netherlands)

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

    2011-01-01

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

  19. Enhanced Accident Tolerant Fuels for LWRS - A Preliminary Systems Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gilles Youinou; R. Sonat Sen

    2013-09-01

    The severe accident at Fukushima Daiichi nuclear plants illustrates the need for continuous improvements through developing and implementing technologies that contribute to safe, reliable and cost-effective operation of the nuclear fleet. Development of enhanced accident tolerant fuel contributes to this effort. These fuels, in comparison with the standard zircaloy – UO2 system currently used by the LWR industry, should be designed such that they tolerate loss of active cooling in the core for a longer time period (depending on the LWR system and accident scenario) while maintaining or improving the fuel performance during normal operations, operational transients, and design-basis events. This report presents a preliminary systems analysis related to most of these concepts. The potential impacts of these innovative LWR fuels on the front-end of the fuel cycle, on the reactor operation and on the back-end of the fuel cycle are succinctly described without having the pretension of being exhaustive. Since the design of these various concepts is still a work in progress, this analysis can only be preliminary and could be updated as the designs converge on their respective final version.

  20. Nonlinear analysis of river flow time sequences

    Science.gov (United States)

    Porporato, Amilcare; Ridolfi, Luca

    1997-06-01

    Within the field of chaos theory several methods for the analysis of complex dynamical systems have recently been proposed. In light of these ideas we study the dynamics which control the behavior over time of river flow, investigating the existence of a low-dimension deterministic component. The present article follows the research undertaken in the work of Porporato and Ridolfi [1996a] in which some clues as to the existence of chaos were collected. Particular emphasis is given here to the problem of noise and to nonlinear prediction. With regard to the latter, the benefits obtainable by means of the interpolation of the available time series are reported and the remarkable predictive results attained with this nonlinear method are shown.

  1. Crystallization and preliminary X-ray analysis of isomaltase from Saccharomyces cerevisiae

    International Nuclear Information System (INIS)

    Yamamoto, Keizo; Miyake, Hideo; Kusunoki, Masami; Osaki, Shigeyoshi

    2008-01-01

    The crystallization and preliminary X-ray analysis of isomaltase is reported. Isomaltase from Saccharomyces cerevisiae is an oligo-1,6-glucosidase that preferentially hydrolyzes isomaltose, with little activity towards isomaltotriose or longer oligosaccharides. An amino-acid sequence analysis of the isomaltase revealed that it belongs to glucoside hydrolase family 13. Recombinant isomaltase was purified and crystallized by the hanging-drop vapour-diffusion method with PEG 3350 as the precipitant. The crystals belonged to space group C2, with unit-cell parameters a = 95.67, b = 115.42, c = 61.77 Å, β = 91.17°. X-ray diffraction data were collected to 1.35 Å resolution from a single crystal on a synchrotron-radiation source

  2. 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.

  3. 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

  4. 13-colour photometry of pre-main sequence stars: preliminary report and results

    Energy Technology Data Exchange (ETDEWEB)

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

    1981-01-01

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

  5. Accident sequence analysis of human-computer interface design

    International Nuclear Information System (INIS)

    Fan, C.-F.; Chen, W.-H.

    2000-01-01

    It is important to predict potential accident sequences of human-computer interaction in a safety-critical computing system so that vulnerable points can be disclosed and removed. We address this issue by proposing a Multi-Context human-computer interaction Model along with its analysis techniques, an Augmented Fault Tree Analysis, and a Concurrent Event Tree Analysis. The proposed augmented fault tree can identify the potential weak points in software design that may induce unintended software functions or erroneous human procedures. The concurrent event tree can enumerate possible accident sequences due to these weak points

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

    Science.gov (United States)

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

    2011-06-01

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

  7. Preliminary hazards analysis of thermal scrap stabilization system. Revision 1

    International Nuclear Information System (INIS)

    Lewis, W.S.

    1994-01-01

    This preliminary analysis examined the HA-21I glovebox and its supporting systems for potential process hazards. Upon further analysis, the thermal stabilization system has been installed in gloveboxes HC-21A and HC-21C. The use of HC-21C and HC-21A simplified the initial safety analysis. In addition, these gloveboxes were cleaner and required less modification for operation than glovebox HA-21I. While this document refers to glovebox HA-21I for the hazards analysis performed, glovebox HC-21C is sufficiently similar that the following analysis is also valid for HC-21C. This hazards analysis document is being re-released as revision 1 to include the updated flowsheet document (Appendix C) and the updated design basis (Appendix D). The revised Process Flow Schematic has also been included (Appendix E). This Current revision incorporates the recommendations provided from the original hazards analysis as well. The System Design Description (SDD) has also been appended (Appendix H) to document the bases for Safety Classification of thermal stabilization equipment

  8. Food Fish Identification from DNA Extraction through Sequence Analysis

    Science.gov (United States)

    Hallen-Adams, Heather E.

    2015-01-01

    This experiment exposed 3rd and 4th y undergraduates and graduate students taking a course in advanced food analysis to DNA extraction, polymerase chain reaction (PCR), and DNA sequence analysis. Students provided their own fish sample, purchased from local grocery stores, and the class as a whole extracted DNA, which was then subjected to PCR,…

  9. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

    Directory of Open Access Journals (Sweden)

    Stephan Pabinger

    Full Text Available Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM. Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage

  10. Analysis preliminary phytochemical raw extract of leaves Nephrolepis pectinata

    Directory of Open Access Journals (Sweden)

    Natally Marreiros Gomes

    2017-06-01

    Full Text Available The Nephrolepis pectinata popularly known as paulista fern, ladder-heaven, cat tail, belongs to the family Davalliaceae. For the beauty of the arrangements of their leaves ferns are quite commercialized in Brazil, however, have not been described in the literature studies on their pharmacological potential. Thus, the objective of this research was to analyze the phytochemical properties of the crude extract of the leaves of Nephrolepis pectinata. To perform the phytochemical analysis were initially made the collection of the vegetable, preparation of voucher specimen, washing, drying and grinding. Then, extraction by percolation method and end the phytochemical analysis. Preliminary results phytochemicals the crude extract of the leaves of Nephrolepis pectinata tested positive for reducing sugars, phenols/tannins (catechins tannins and catechins.

  11. Multilocus Sequence Analysis and rpoB Sequencing of Mycobacterium abscessus (Sensu Lato) Strains▿

    Science.gov (United States)

    Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

    2011-01-01

    Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536T, M. massiliense CIP 108297T, and M. bolletii CIP 108541T) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the clustering

  12. Multilocus sequence analysis and rpoB sequencing of Mycobacterium abscessus (sensu lato) strains.

    Science.gov (United States)

    Macheras, Edouard; Roux, Anne-Laure; Bastian, Sylvaine; Leão, Sylvia Cardoso; Palaci, Moises; Sivadon-Tardy, Valérie; Gutierrez, Cristina; Richter, Elvira; Rüsch-Gerdes, Sabine; Pfyffer, Gaby; Bodmer, Thomas; Cambau, Emmanuelle; Gaillard, Jean-Louis; Heym, Beate

    2011-02-01

    Mycobacterium abscessus, Mycobacterium bolletii, and Mycobacterium massiliense (Mycobacterium abscessus sensu lato) are closely related species that currently are identified by the sequencing of the rpoB gene. However, recent studies show that rpoB sequencing alone is insufficient to discriminate between these species, and some authors have questioned their current taxonomic classification. We studied here a large collection of M. abscessus (sensu lato) strains by partial rpoB sequencing (752 bp) and multilocus sequence analysis (MLSA). The final MLSA scheme developed was based on the partial sequences of eight housekeeping genes: argH, cya, glpK, gnd, murC, pgm, pta, and purH. The strains studied included the three type strains (M. abscessus CIP 104536(T), M. massiliense CIP 108297(T), and M. bolletii CIP 108541(T)) and 120 isolates recovered between 1997 and 2007 in France, Germany, Switzerland, and Brazil. The rpoB phylogenetic tree confirmed the existence of three main clusters, each comprising the type strain of one species. However, divergence values between the M. massiliense and M. bolletii clusters all were below 3% and between the M. abscessus and M. massiliense clusters were from 2.66 to 3.59%. The tree produced using the concatenated MLSA gene sequences (4,071 bp) also showed three main clusters, each comprising the type strain of one species. The M. abscessus cluster had a bootstrap value of 100% and was mostly compact. Bootstrap values for the M. massiliense and M. bolletii branches were much lower (71 and 61%, respectively), with the M. massiliense cluster having a fuzzy aspect. Mean (range) divergence values were 2.17% (1.13 to 2.58%) between the M. abscessus and M. massiliense clusters, 2.37% (1.5 to 2.85%) between the M. abscessus and M. bolletii clusters, and 2.28% (0.86 to 2.68%) between the M. massiliense and M. bolletii clusters. Adding the rpoB sequence to the MLSA-concatenated sequence (total sequence, 4,823 bp) had little effect on the

  13. An optimum analysis sequence for environmental gamma-ray spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    De la Torre, F.; Rios M, C.; Ruvalcaba A, M. G.; Mireles G, F.; Saucedo A, S.; Davila R, I.; Pinedo, J. L., E-mail: fta777@hotmail.co [Universidad Autonoma de Zacatecas, Centro Regional de Estudis Nucleares, Calle Cipres No. 10, Fracc. La Penuela, 98068 Zacatecas (Mexico)

    2010-10-15

    This work aims to obtain an optimum analysis sequence for environmental gamma-ray spectroscopy by means of Genie 2000 (Canberra). Twenty different analysis sequences were customized using different peak area percentages and different algorithms for: 1) peak finding, and 2) peak area determination, and with or without the use of a library -based on evaluated nuclear data- of common gamma-ray emitters in environmental samples. The use of an optimum analysis sequence with certified nuclear information avoids the problems originated by the significant variations in out-of-date nuclear parameters of commercial software libraries. Interference-free gamma ray energies with absolute emission probabilities greater than 3.75% were included in the customized library. The gamma-ray spectroscopy system (based on a Ge Re-3522 Canberra detector) was calibrated both in energy and shape by means of the IAEA-2002 reference spectra for software intercomparison. To test the performance of the analysis sequences, the IAEA-2002 reference spectrum was used. The z-score and the reduced {chi}{sup 2} criteria were used to determine the optimum analysis sequence. The results show an appreciable variation in the peak area determinations and their corresponding uncertainties. Particularly, the combination of second derivative peak locate with simple peak area integration algorithms provides the greater accuracy. Lower accuracy comes from the combination of library directed peak locate algorithm and Genie's Gamma-M peak area determination. (Author)

  14. An optimum analysis sequence for environmental gamma-ray spectrometry

    International Nuclear Information System (INIS)

    De la Torre, F.; Rios M, C.; Ruvalcaba A, M. G.; Mireles G, F.; Saucedo A, S.; Davila R, I.; Pinedo, J. L.

    2010-10-01

    This work aims to obtain an optimum analysis sequence for environmental gamma-ray spectroscopy by means of Genie 2000 (Canberra). Twenty different analysis sequences were customized using different peak area percentages and different algorithms for: 1) peak finding, and 2) peak area determination, and with or without the use of a library -based on evaluated nuclear data- of common gamma-ray emitters in environmental samples. The use of an optimum analysis sequence with certified nuclear information avoids the problems originated by the significant variations in out-of-date nuclear parameters of commercial software libraries. Interference-free gamma ray energies with absolute emission probabilities greater than 3.75% were included in the customized library. The gamma-ray spectroscopy system (based on a Ge Re-3522 Canberra detector) was calibrated both in energy and shape by means of the IAEA-2002 reference spectra for software intercomparison. To test the performance of the analysis sequences, the IAEA-2002 reference spectrum was used. The z-score and the reduced χ 2 criteria were used to determine the optimum analysis sequence. The results show an appreciable variation in the peak area determinations and their corresponding uncertainties. Particularly, the combination of second derivative peak locate with simple peak area integration algorithms provides the greater accuracy. Lower accuracy comes from the combination of library directed peak locate algorithm and Genie's Gamma-M peak area determination. (Author)

  15. Preliminary RAMI analysis of WCLL blanket and breeder systems

    International Nuclear Information System (INIS)

    Arroyo, Jose Manuel; Brown, Richard; Harman, Jon; Rosa, Elena; Ibarra, Angel

    2015-01-01

    Highlights: • Preliminary RAMI model for WCLL has been developed. • Critical parts and parameters influencing WCLL availability have been focused. • Necessary developments of tools/models to represent system performance have been identified. - Abstract: DEMO will be a prototype fusion reactor designed to prove the capability to produce electrical power in a commercially acceptable way. One of the key factors in that endeavor is the achievement of certain level of plant availability. Therefore, RAMI (Reliability, Availability, Maintainability and Inspectability) will be a key element in the engineering development of DEMO. Some studies have been started so as to develop the tools and models to assess different design alternatives from RAMI point of view. The main objective of these studies is to be able to evaluate the influence of different parameters on DEMO availability and to focus the critical parts that should be further researched and improved in order to develop a high-availability oriented DEMO design. A preliminary RAMI analysis of the Water Cooled Lithium-Lead (WCLL) blanket and breeder concept for DEMO has been developed. The amounts of single elements that may fail (e.g. more than 180,000 C-shaped tubes) and the mean down time associated to failures inside the vacuum vessel (around 3 months) have been highlighted as the critical parameters influencing the system availability. On the other hand, the necessary developments of tools/models to better represent the system performance have been identified and proposed for future work.

  16. Preliminary RAMI analysis of WCLL blanket and breeder systems

    Energy Technology Data Exchange (ETDEWEB)

    Arroyo, Jose Manuel, E-mail: josemanuel.arroyo@ciemat.es [Laboratorio Nacional de Fusión por Confinamiento Magnético – CIEMAT, Madrid (Spain); Brown, Richard [Culham Centre for Fusion Energy, Culham Science Centre, Abingdon (United Kingdom); Harman, Jon [EFDA Close Support Unit, Garching (Germany); Rosa, Elena; Ibarra, Angel [Laboratorio Nacional de Fusión por Confinamiento Magnético – CIEMAT, Madrid (Spain)

    2015-10-15

    Highlights: • Preliminary RAMI model for WCLL has been developed. • Critical parts and parameters influencing WCLL availability have been focused. • Necessary developments of tools/models to represent system performance have been identified. - Abstract: DEMO will be a prototype fusion reactor designed to prove the capability to produce electrical power in a commercially acceptable way. One of the key factors in that endeavor is the achievement of certain level of plant availability. Therefore, RAMI (Reliability, Availability, Maintainability and Inspectability) will be a key element in the engineering development of DEMO. Some studies have been started so as to develop the tools and models to assess different design alternatives from RAMI point of view. The main objective of these studies is to be able to evaluate the influence of different parameters on DEMO availability and to focus the critical parts that should be further researched and improved in order to develop a high-availability oriented DEMO design. A preliminary RAMI analysis of the Water Cooled Lithium-Lead (WCLL) blanket and breeder concept for DEMO has been developed. The amounts of single elements that may fail (e.g. more than 180,000 C-shaped tubes) and the mean down time associated to failures inside the vacuum vessel (around 3 months) have been highlighted as the critical parameters influencing the system availability. On the other hand, the necessary developments of tools/models to better represent the system performance have been identified and proposed for future work.

  17. System-level hazard analysis using the sequence-tree method

    International Nuclear Information System (INIS)

    Huang, H.-W.; Shih Chunkuan; Yih Swu; Chen, M.-H.

    2008-01-01

    A system-level PHA using the sequence-tree method is presented to perform safety-related digital I and C system SSA. The conventional PHA involves brainstorming among experts on various portions of the system to identify hazards through discussions. However, since the conventional PHA is not a systematic technique, the analysis results depend strongly on the experts' subjective opinions. The quality of analysis cannot be appropriately controlled. Therefore, this study presents a system-level sequence tree based PHA, which can clarify the relationship among the major digital I and C systems. This sequence-tree-based technique has two major phases. The first phase adopts a table to analyze each event in SAR Chapter 15 for a specific safety-related I and C system, such as RPS. The second phase adopts a sequence tree to recognize the I and C systems involved in the event, the working of the safety-related systems and how the backup systems can be activated to mitigate the consequence if the primary safety systems fail. The defense-in-depth echelons, namely the Control echelon, Reactor trip echelon, ESFAS echelon and Monitoring and indicator echelon, are arranged to build the sequence-tree structure. All the related I and C systems, including the digital systems and the analog back-up systems, are allocated in their specific echelons. This system-centric sequence-tree analysis not only systematically identifies preliminary hazards, but also vulnerabilities in a nuclear power plant. Hence, an effective simplified D3 evaluation can also be conducted

  18. Validation of Genotyping-By-Sequencing Analysis in Populations of Tetraploid Alfalfa by 454 Sequencing

    Science.gov (United States)

    Rocher, Solen; Jean, Martine; Castonguay, Yves; Belzile, François

    2015-01-01

    Genotyping-by-sequencing (GBS) is a relatively low-cost high throughput genotyping technology based on next generation sequencing and is applicable to orphan species with no reference genome. A combination of genome complexity reduction and multiplexing with DNA barcoding provides a simple and affordable way to resolve allelic variation between plant samples or populations. GBS was performed on ApeKI libraries using DNA from 48 genotypes each of two heterogeneous populations of tetraploid alfalfa (Medicago sativa spp. sativa): the synthetic cultivar Apica (ATF0) and a derived population (ATF5) obtained after five cycles of recurrent selection for superior tolerance to freezing (TF). Nearly 400 million reads were obtained from two lanes of an Illumina HiSeq 2000 sequencer and analyzed with the Universal Network-Enabled Analysis Kit (UNEAK) pipeline designed for species with no reference genome. Following the application of whole dataset-level filters, 11,694 single nucleotide polymorphism (SNP) loci were obtained. About 60% had a significant match on the Medicago truncatula syntenic genome. The accuracy of allelic ratios and genotype calls based on GBS data was directly assessed using 454 sequencing on a subset of SNP loci scored in eight plant samples. Sequencing depth in this study was not sufficient for accurate tetraploid allelic dosage, but reliable genotype calls based on diploid allelic dosage were obtained when using additional quality filtering. Principal Component Analysis of SNP loci in plant samples revealed that a small proportion (<5%) of the genetic variability assessed by GBS is able to differentiate ATF0 and ATF5. Our results confirm that analysis of GBS data using UNEAK is a reliable approach for genome-wide discovery of SNP loci in outcrossed polyploids. PMID:26115486

  19. 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.

  20. Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

    Directory of Open Access Journals (Sweden)

    Rebecca M. Davidson

    2011-11-01

    Full Text Available Transcriptome sequencing is a powerful method for studying global expression patterns in large, complex genomes. Evaluation of sequence-based expression profiles during reproductive development would provide functional annotation to genes underlying agronomic traits. We generated transcriptome profiles for 12 diverse maize ( L. reproductive tissues representing male, female, developing seed, and leaf tissues using high throughput transcriptome sequencing. Overall, ∼80% of annotated genes were expressed. Comparative analysis between sequence and hybridization-based methods demonstrated the utility of ribonucleic acid sequencing (RNA-seq for expression determination and differentiation of paralagous genes (∼85% of maize genes. Analysis of 4975 gene families across reproductive tissues revealed expression divergence is proportional to family size. In all pairwise comparisons between tissues, 7 (pre- vs. postemergence cobs to 48% (pollen vs. ovule of genes were differentially expressed. Genes with expression restricted to a single tissue within this study were identified with the highest numbers observed in leaves, endosperm, and pollen. Coexpression network analysis identified 17 gene modules with complex and shared expression patterns containing many previously described maize genes. The data and analyses in this study provide valuable tools through improved gene annotation, gene family characterization, and a core set of candidate genes to further characterize maize reproductive development and improve grain yield potential.

  1. Preliminary analysis of biomass potentially useful for producing biodiesel

    International Nuclear Information System (INIS)

    Cabrera Cifuentes, Gerardo; Burbano Jaramillo, Juan Carlos; Garcia Melo, Jose Isidro

    2011-01-01

    Given that biodiesel is emerging as a viable solution for some energy and environmental problems, research on raw materials appropriate for its production is a matter of growing interest. In this study we present the results of research devoted to preliminary analysis on several vegetable (biomass) species potentially useful for producing biodiesel. The bioprospection zone is a region on the Colombian Pacific coast. The candidate species collected underwent different standardized ASTM tests in order for us to define properties that facilitate their evaluation. Some of the species underwent a transesterification process. Comparisons between the thermo-physical properties of the biofuels obtained and the properties of commercial diesel were carried out. Also, performance tests for these biofuels were conducted in compression ignition engines, particularly evaluating efficiency, fuel consumption, and potency at different RPMs.

  2. Preliminary radar systems analysis for Venus orbiter missions

    Science.gov (United States)

    Brandenburg, R. K.; Spadoni, D. J.

    1971-01-01

    A short, preliminary analysis is presented of the problems involved in mapping the surface of Venus with radar from an orbiting spacecraft. Two types of radar, the noncoherent sidelooking and the focused synthetic aperture systems, are sized to fulfill two assumed levels of Venus exploration. The two exploration levels, regional and local, assumed for this study are based on previous Astro Sciences work (Klopp 1969). The regional level is defined as 1 to 3 kilometer spatial and 0.5 to 1 km vertical resolution of 100 percent 0 of the planet's surface. The local level is defined as 100 to 200 meter spatial and 50-10 m vertical resolution of about 100 percent of the surfAce (based on the regional survey). A 10cm operating frequency was chosen for both radar systems in order to minimize the antenna size and maximize the apparent radar cross section of the surface.

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

    International Nuclear Information System (INIS)

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

    2010-01-01

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

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

    Science.gov (United States)

    Hegedish, Omer; Kivilis, Naama; Hoofien, Dan

    2015-01-01

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

  5. Structural analysis of salt cavities formed by solution mining: I. Method of analysis and preliminary results for spherical cavities

    International Nuclear Information System (INIS)

    Fossum, A.F.

    1976-01-01

    The primary objective of this effort is an analysis of the structural stability of cavities formed by solution mining in salt domes. In particular, the effects of depth (i.e. initial state of in situ stress), shape, volume (i.e. physical dimensions of the cavity), and sequence of salt excavation/fluid evacuation on the timewise structural stability of a cavity are of interest. It is anticipated that an assessment can be made of the interrelation between depth, cavern size, and cavern shape or of the practical limits therewith. In general, the cavity shape is assumed to be axisymmetric and the salt is assumed to exhibit nonlinear creep behavior. The primary emphasis is placed on the methodology of the finite element analysis, and the results of preliminary calculations for a spherically shaped cavity. It is common practice for engineers to apply elasticity theory to the behavior of rock in order to obtain near field stresses and displacements around an underground excavation in an effort to assess structural stability. Rock masses, particularly at depth, may be subjected to a rather complex state of initial stress, and may be nonhomogeneous and anisotropic. If one also includes complex geometrical excavation shape, the use of analytical techniques as an analysis tool is practically impossible. Thus, it is almost a necessity that approximate solution techniques be employed. In this regard, the finite element method is ideal as it can handle complex geometries and nonlinear material behavior with relative ease. An unusual feature of the present study is the incorporation into the finite element code of a procedure for handling the gradual creation or excavation of an underground cavity. During the excavation sequence, the salt is permitted to exhibit nonlinear stress-strain-time dependence. The bulk of this report will be devoted to a description of the analysis procedures, together with a preliminary calculation for a spherically shaped cavity

  6. 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.

  7. Sequence analysis of the genome of carnation (Dianthus caryophyllus L.).

    Science.gov (United States)

    Yagi, Masafumi; Kosugi, Shunichi; Hirakawa, Hideki; Ohmiya, Akemi; Tanase, Koji; Harada, Taro; Kishimoto, Kyutaro; Nakayama, Masayoshi; Ichimura, Kazuo; Onozaki, Takashi; Yamaguchi, Hiroyasu; Sasaki, Nobuhiro; Miyahara, Taira; Nishizaki, Yuzo; Ozeki, Yoshihiro; Nakamura, Noriko; Suzuki, Takamasa; Tanaka, Yoshikazu; Sato, Shusei; Shirasawa, Kenta; Isobe, Sachiko; Miyamura, Yoshinori; Watanabe, Akiko; Nakayama, Shinobu; Kishida, Yoshie; Kohara, Mitsuyo; Tabata, Satoshi

    2014-06-01

    The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. 'Francesco' was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568,887,315 bp, consisting of 45,088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16,644 bp and 60,737 bp, respectively, and the longest scaffold was 1,287,144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼ 98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genomic sequences is available at http://carnation.kazusa.or.jp. © The Author 2013. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  8. De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae)

    Science.gov (United States)

    2014-01-01

    Background Anopheles sinensis is the major malaria vector in China and Southeast Asia. Vector control is one of the most effective measures to prevent malaria transmission. However, there is little transcriptome information available for the malaria vector. To better understand the biological basis of malaria transmission and to develop novel and effective means of vector control, there is a need to build a transcriptome dataset for functional genomics analysis by large-scale RNA sequencing (RNA-seq). Methods To provide a more comprehensive and complete transcriptome of An. sinensis, eggs, larvae, pupae, male adults and female adults RNA were pooled together for cDNA preparation, sequenced using the Illumina paired-end sequencing technology and assembled into unigenes. These unigenes were then analyzed in their genome mapping, functional annotation, homology, codon usage bias and simple sequence repeats (SSRs). Results Approximately 51.6 million clean reads were obtained, trimmed, and assembled into 38,504 unigenes with an average length of 571 bp, an N50 of 711 bp, and an average GC content 51.26%. Among them, 98.4% of unigenes could be mapped onto the reference genome, and 69% of unigenes could be annotated with known biological functions. Homology analysis identified certain numbers of An. sinensis unigenes that showed homology or being putative 1:1 orthologues with genomes of other Dipteran species. Codon usage bias was analyzed and 1,904 SSRs were detected, which will provide effective molecular markers for the population genetics of this species. Conclusions Our data and analysis provide the most comprehensive transcriptomic resource and characteristics currently available for An. sinensis, and will facilitate genetic, genomic studies, and further vector control of An. sinensis. PMID:25000941

  9. Sequence analysis corresponding to the PPE and PE proteins in ...

    Indian Academy of Sciences (India)

    Unknown

    AB repeats; Mycobacterium tuberculosis genome; PE-PPE domain; PPE, PE proteins; sequence analysis; surface antigens. J. Biosci. | Vol. ... bacterium tuberculosis genomes resulted in the identification of a previously uncharacterized 225 amino acid- ...... Vega Lopez F, Brooks L A, Dockrell H M, De Smet K A,. Thompson ...

  10. Molecular cloning, expression analysis and sequence prediction of ...

    African Journals Online (AJOL)

    CCAAT/enhancer-binding protein beta as an essential transcriptional factor, regulates the differentiation of adipocytes and the deposition of fat. Herein, we cloned the whole open reading frame (ORF) of bovine C/EBPβ gene and analyzed its putative protein structures via DNA cloning and sequence analysis. Then, the ...

  11. Multilocus sequence analysis of phytopathogenic species of the genus Streptomyces

    Science.gov (United States)

    The identification and classification of species within the genus Streptomyces is difficult because there are presently 576 validly described species and this number increases every year. The value of the application of multilocus sequence analysis scheme to the systematics of Streptomyces species h...

  12. Sequence symmetry analysis in pharmacovigilance and pharmacoepidemiologic studies

    DEFF Research Database (Denmark)

    Lai, Edward Chia Cheng; Pratt, Nicole; Hsieh, Cheng Yang

    2017-01-01

    Sequence symmetry analysis (SSA) is a method for detecting adverse drug events by utilizing computerized claims data. The method has been increasingly used to investigate safety concerns of medications and as a pharmacovigilance tool to identify unsuspected side effects. Validation studies have i...

  13. DNAApp: a mobile application for sequencing data analysis.

    Science.gov (United States)

    Nguyen, Phi-Vu; Verma, Chandra Shekhar; Gan, Samuel Ken-En

    2014-11-15

    There have been numerous applications developed for decoding and visualization of ab1 DNA sequencing files for Windows and MAC platforms, yet none exists for the increasingly popular smartphone operating systems. The ability to decode sequencing files cannot easily be carried out using browser accessed Web tools. To overcome this hurdle, we have developed a new native app called DNAApp that can decode and display ab1 sequencing file on Android and iOS. In addition to in-built analysis tools such as reverse complementation, protein translation and searching for specific sequences, we have incorporated convenient functions that would facilitate the harnessing of online Web tools for a full range of analysis. Given the high usage of Android/iOS tablets and smartphones, such bioinformatics apps would raise productivity and facilitate the high demand for analyzing sequencing data in biomedical research. The Android version of DNAApp is available in Google Play Store as 'DNAApp', and the iOS version is available in the App Store. More details on the app can be found at www.facebook.com/APDLab; www.bii.a-star.edu.sg/research/trd/apd.php The DNAApp user guide is available at http://tinyurl.com/DNAAppuser, and a video tutorial is available on Google Play Store and App Store, as well as on the Facebook page. samuelg@bii.a-star.edu.sg. © The Author 2014. Published by Oxford University Press.

  14. DNAApp: a mobile application for sequencing data analysis

    Science.gov (United States)

    Nguyen, Phi-Vu; Verma, Chandra Shekhar; Gan, Samuel Ken-En

    2014-01-01

    Summary: There have been numerous applications developed for decoding and visualization of ab1 DNA sequencing files for Windows and MAC platforms, yet none exists for the increasingly popular smartphone operating systems. The ability to decode sequencing files cannot easily be carried out using browser accessed Web tools. To overcome this hurdle, we have developed a new native app called DNAApp that can decode and display ab1 sequencing file on Android and iOS. In addition to in-built analysis tools such as reverse complementation, protein translation and searching for specific sequences, we have incorporated convenient functions that would facilitate the harnessing of online Web tools for a full range of analysis. Given the high usage of Android/iOS tablets and smartphones, such bioinformatics apps would raise productivity and facilitate the high demand for analyzing sequencing data in biomedical research. Availability and implementation: The Android version of DNAApp is available in Google Play Store as ‘DNAApp’, and the iOS version is available in the App Store. More details on the app can be found at www.facebook.com/APDLab; www.bii.a-star.edu.sg/research/trd/apd.php The DNAApp user guide is available at http://tinyurl.com/DNAAppuser, and a video tutorial is available on Google Play Store and App Store, as well as on the Facebook page. Contact: samuelg@bii.a-star.edu.sg PMID:25095882

  15. Long-read sequencing data analysis for yeasts.

    Science.gov (United States)

    Yue, Jia-Xing; Liti, Gianni

    2018-06-01

    Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here, we present a modular computational framework named long-read sequencing data analysis for yeasts (LRSDAY), the first one-stop solution that streamlines this process. Starting from the raw sequencing reads, LRSDAY can produce chromosome-level genome assembly and comprehensive genome annotation in a highly automated manner with minimal manual intervention, which is not possible using any alternative tool available to date. The annotated genomic features include centromeres, protein-coding genes, tRNAs, transposable elements (TEs), and telomere-associated elements. Although tailored for S. cerevisiae, we designed LRSDAY to be highly modular and customizable, making it adaptable to virtually any eukaryotic organism. When applying LRSDAY to an S. cerevisiae strain, it takes ∼41 h to generate a complete and well-annotated genome from ∼100× Pacific Biosciences (PacBio) running the basic workflow with four threads. Basic experience working within the Linux command-line environment is recommended for carrying out the analysis using LRSDAY.

  16. Construction of an integrated database to support genomic sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, W.; Overbeek, R.

    1994-11-01

    The central goal of this project is to develop an integrated database to support comparative analysis of genomes including DNA sequence data, protein sequence data, gene expression data and metabolism data. In developing the logic-based system GenoBase, a broader integration of available data was achieved due to assistance from collaborators. Current goals are to easily include new forms of data as they become available and to easily navigate through the ensemble of objects described within the database. This report comments on progress made in these areas.

  17. Analysis of Sequence Diagram Layout in Advanced UML Modelling Tools

    Directory of Open Access Journals (Sweden)

    Ņikiforova Oksana

    2016-05-01

    Full Text Available System modelling using Unified Modelling Language (UML is the task that should be solved for software development. The more complex software becomes the higher requirements are stated to demonstrate the system to be developed, especially in its dynamic aspect, which in UML is offered by a sequence diagram. To solve this task, the main attention is devoted to the graphical presentation of the system, where diagram layout plays the central role in information perception. The UML sequence diagram due to its specific structure is selected for a deeper analysis on the elements’ layout. The authors research represents the abilities of modern UML modelling tools to offer automatic layout of the UML sequence diagram and analyse them according to criteria required for the diagram perception.

  18. Network clustering coefficient approach to DNA sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gerhardt, Guenther J.L. [Universidade Federal do Rio Grande do Sul-Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos 2350/sala 2040/90035-003 Porto Alegre (Brazil); Departamento de Fisica e Quimica da Universidade de Caxias do Sul, Rua Francisco Getulio Vargas 1130, 95001-970 Caxias do Sul (Brazil); Lemke, Ney [Programa Interdisciplinar em Computacao Aplicada, Unisinos, Av. Unisinos, 950, 93022-000 Sao Leopoldo, RS (Brazil); Corso, Gilberto [Departamento de Biofisica e Farmacologia, Centro de Biociencias, Universidade Federal do Rio Grande do Norte, Campus Universitario, 59072 970 Natal, RN (Brazil)]. E-mail: corso@dfte.ufrn.br

    2006-05-15

    In this work we propose an alternative DNA sequence analysis tool based on graph theoretical concepts. The methodology investigates the path topology of an organism genome through a triplet network. In this network, triplets in DNA sequence are vertices and two vertices are connected if they occur juxtaposed on the genome. We characterize this network topology by measuring the clustering coefficient. We test our methodology against two main bias: the guanine-cytosine (GC) content and 3-bp (base pairs) periodicity of DNA sequence. We perform the test constructing random networks with variable GC content and imposed 3-bp periodicity. A test group of some organisms is constructed and we investigate the methodology in the light of the constructed random networks. We conclude that the clustering coefficient is a valuable tool since it gives information that is not trivially contained in 3-bp periodicity neither in the variable GC content.

  19. Evolutionary analysis of hepatitis C virus gene sequences from 1953

    Science.gov (United States)

    Gray, Rebecca R.; Tanaka, Yasuhito; Takebe, Yutaka; Magiorkinis, Gkikas; Buskell, Zelma; Seeff, Leonard; Alter, Harvey J.; Pybus, Oliver G.

    2013-01-01

    Reconstructing the transmission history of infectious diseases in the absence of medical or epidemiological records often relies on the evolutionary analysis of pathogen genetic sequences. The precision of evolutionary estimates of epidemic history can be increased by the inclusion of sequences derived from ‘archived’ samples that are genetically distinct from contemporary strains. Historical sequences are especially valuable for viral pathogens that circulated for many years before being formally identified, including HIV and the hepatitis C virus (HCV). However, surprisingly few HCV isolates sampled before discovery of the virus in 1989 are currently available. Here, we report and analyse two HCV subgenomic sequences obtained from infected individuals in 1953, which represent the oldest genetic evidence of HCV infection. The pairwise genetic diversity between the two sequences indicates a substantial period of HCV transmission prior to the 1950s, and their inclusion in evolutionary analyses provides new estimates of the common ancestor of HCV in the USA. To explore and validate the evolutionary information provided by these sequences, we used a new phylogenetic molecular clock method to estimate the date of sampling of the archived strains, plus the dates of four more contemporary reference genomes. Despite the short fragments available, we conclude that the archived sequences are consistent with a proposed sampling date of 1953, although statistical uncertainty is large. Our cross-validation analyses suggest that the bias and low statistical power observed here likely arise from a combination of high evolutionary rate heterogeneity and an unstructured, star-like phylogeny. We expect that attempts to date other historical viruses under similar circumstances will meet similar problems. PMID:23938759

  20. Confirmation of a novel siadenovirus species detected in raptors: partial sequence and phylogenetic analysis.

    Science.gov (United States)

    Kovács, Endre R; Benko, Mária

    2009-03-01

    Partial genome characterisation of a novel adenovirus, found recently in organ samples of multiple species of dead birds of prey, was carried out by sequence analysis of PCR-amplified DNA fragments. The virus, named as raptor adenovirus 1 (RAdV-1), has originally been detected by a nested PCR method with consensus primers targeting the adenoviral DNA polymerase gene. Phylogenetic analysis with the deduced amino acid sequence of the small PCR product has implied a new siadenovirus type present in the samples. Since virus isolation attempts remained unsuccessful, further characterisation of this putative novel siadenovirus was carried out with the use of PCR on the infected organ samples. The DNA sequence of the central genome part of RAdV-1, encompassing nine full (pTP, 52K, pIIIa, III, pVII, pX, pVI, hexon, protease) and two partial (DNA polymerase and DBP) genes and exceeding 12 kb pairs in size, was determined. Phylogenetic tree reconstructions, based on several genes, unambiguously confirmed the preliminary classification of RAdV-1 as a new species within the genus Siadenovirus. Further study of RAdV-1 is of interest since it represents a rare adenovirus genus of yet undetermined host origin.

  1. Using SQL Databases for Sequence Similarity Searching and Analysis.

    Science.gov (United States)

    Pearson, William R; Mackey, Aaron J

    2017-09-13

    Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

  2. Now And Next Generation Sequencing Techniques: Future of Sequence Analysis using Cloud Computing

    Directory of Open Access Journals (Sweden)

    Radhe Shyam Thakur

    2012-12-01

    Full Text Available Advancements in the field of sequencing techniques resulted in the huge sequenced data to be produced at a very faster rate. It is going cumbersome for the datacenter to maintain the databases. Data mining and sequence analysis approaches needs to analyze the databases several times to reach any efficient conclusion. To cope with such overburden on computer resources and to reach efficient and effective conclusions quickly, the virtualization of the resources and computation on pay as you go concept was introduced and termed as cloud computing. The datacenter’s hardware and software is collectively known as cloud which when available publicly is termed as public cloud. The datacenter’s resources are provided in a virtual mode to the clients via a service provider like Amazon, Google and Joyent which charges on pay as you go manner. The workload is shifted to the provider which is maintained by the required hardware and software upgradation. The service provider manages it by upgrading the requirements in the virtual mode. Basically a virtual environment is created according to the need of the user by taking permission from datacenter via internet, the task is performed and the environment is deleted after the task is over. In this discussion, we are focusing on the basics of cloud computing, the prerequisites and overall working of clouds. Furthermore, briefly the applications of cloud computing in biological systems, especially in comparative genomics, genome informatics and SNP detection with reference to traditional workflow are discussed.

  3. Now and next-generation sequencing techniques: future of sequence analysis using cloud computing.

    Science.gov (United States)

    Thakur, Radhe Shyam; Bandopadhyay, Rajib; Chaudhary, Bratati; Chatterjee, Sourav

    2012-01-01

    Advances in the field of sequencing techniques have resulted in the greatly accelerated production of huge sequence datasets. This presents immediate challenges in database maintenance at datacenters. It provides additional computational challenges in data mining and sequence analysis. Together these represent a significant overburden on traditional stand-alone computer resources, and to reach effective conclusions quickly and efficiently, the virtualization of the resources and computation on a pay-as-you-go concept (together termed "cloud computing") has recently appeared. The collective resources of the datacenter, including both hardware and software, can be available publicly, being then termed a public cloud, the resources being provided in a virtual mode to the clients who pay according to the resources they employ. Examples of public companies providing these resources include Amazon, Google, and Joyent. The computational workload is shifted to the provider, which also implements required hardware and software upgrades over time. A virtual environment is created in the cloud corresponding to the computational and data storage needs of the user via the internet. The task is then performed, the results transmitted to the user, and the environment finally deleted after all tasks are completed. In this discussion, we focus on the basics of cloud computing, and go on to analyze the prerequisites and overall working of clouds. Finally, the applications of cloud computing in biological systems, particularly in comparative genomics, genome informatics, and SNP detection are discussed with reference to traditional workflows.

  4. SEQUENCING AND SEQUENCE ANALYSIS OF MYOSTATIN GENE IN THE EXON 1 OF THE CAMEL (CAMELUS DROMEDARIUS

    Directory of Open Access Journals (Sweden)

    M. G. SHAH, A. S. QURESHI1, M. REISSMANN2 AND H. J. SCHWARTZ3

    2006-10-01

    Full Text Available Myostatin, also called growth differentiation factor-8 (GDF-8, is a member of the mammalian growth transforming family (TGF-beta superfamily, which is expressed specifically in developing an adult skeletal muscle. Muscular hypertrophy allele (mh allele in the double muscle breeds involved mutation within the myostatin gene. Genomic DNA was isolated from the camel hair using NucleoSpin Tissue kit. Two animals of each of the six breeds namely, Marecha, Dhatti, Larri, Kohi, Sakrai and Cambelpuri were used for sequencing. For PCR amplification of the gene, a primer pair was designed from homolog regions of already published sequences of farm animals from GenBank. Results showed that camel myostatin possessed more than 90% homology with that of cattle, sheep and pig. Camel formed separate cluster from the pig in spite of having high homology (98% and showed 94% homology with cattle and sheep as reported in literature. Sequence analysis of the PCR amplified part of exon 1 (256 bp of the camel myostatin was identical among six camel breeds.

  5. An Imaging And Graphics Workstation For Image Sequence Analysis

    Science.gov (United States)

    Mostafavi, Hassan

    1990-01-01

    This paper describes an application-specific engineering workstation designed and developed to analyze imagery sequences from a variety of sources. The system combines the software and hardware environment of the modern graphic-oriented workstations with the digital image acquisition, processing and display techniques. The objective is to achieve automation and high throughput for many data reduction tasks involving metric studies of image sequences. The applications of such an automated data reduction tool include analysis of the trajectory and attitude of aircraft, missile, stores and other flying objects in various flight regimes including launch and separation as well as regular flight maneuvers. The workstation can also be used in an on-line or off-line mode to study three-dimensional motion of aircraft models in simulated flight conditions such as wind tunnels. The system's key features are: 1) Acquisition and storage of image sequences by digitizing real-time video or frames from a film strip; 2) computer-controlled movie loop playback, slow motion and freeze frame display combined with digital image sharpening, noise reduction, contrast enhancement and interactive image magnification; 3) multiple leading edge tracking in addition to object centroids at up to 60 fields per second from both live input video or a stored image sequence; 4) automatic and manual field-of-view and spatial calibration; 5) image sequence data base generation and management, including the measurement data products; 6) off-line analysis software for trajectory plotting and statistical analysis; 7) model-based estimation and tracking of object attitude angles; and 8) interface to a variety of video players and film transport sub-systems.

  6. Multilocus sequence analysis of Treponema denticola strains of diverse origin

    Directory of Open Access Journals (Sweden)

    Mo Sisu

    2013-02-01

    Full Text Available Abstract Background The oral spirochete bacterium Treponema denticola is associated with both the incidence and severity of periodontal disease. Although the biological or phenotypic properties of a significant number of T. denticola isolates have been reported in the literature, their genetic diversity or phylogeny has never been systematically investigated. Here, we describe a multilocus sequence analysis (MLSA of 20 of the most highly studied reference strains and clinical isolates of T. denticola; which were originally isolated from subgingival plaque samples taken from subjects from China, Japan, the Netherlands, Canada and the USA. Results The sequences of the 16S ribosomal RNA gene, and 7 conserved protein-encoding genes (flaA, recA, pyrH, ppnK, dnaN, era and radC were successfully determined for each strain. Sequence data was analyzed using a variety of bioinformatic and phylogenetic software tools. We found no evidence of positive selection or DNA recombination within the protein-encoding genes, where levels of intraspecific sequence polymorphism varied from 18.8% (flaA to 8.9% (dnaN. Phylogenetic analysis of the concatenated protein-encoding gene sequence data (ca. 6,513 nucleotides for each strain using Bayesian and maximum likelihood approaches indicated that the T. denticola strains were monophyletic, and formed 6 well-defined clades. All analyzed T. denticola strains appeared to have a genetic origin distinct from that of ‘Treponema vincentii’ or Treponema pallidum. No specific geographical relationships could be established; but several strains isolated from different continents appear to be closely related at the genetic level. Conclusions Our analyses indicate that previous biological and biophysical investigations have predominantly focused on a subset of T. denticola strains with a relatively narrow range of genetic diversity. Our methodology and results establish a genetic framework for the discrimination and phylogenetic

  7. Molecular characterization of Giardia psittaci by multilocus sequence analysis.

    Science.gov (United States)

    Abe, Niichiro; Makino, Ikuko; Kojima, Atsushi

    2012-12-01

    Multilocus sequence analyses targeting small subunit ribosomal DNA (SSU rDNA), elongation factor 1 alpha (ef1α), glutamate dehydrogenase (gdh), and beta giardin (β-giardin) were performed on Giardia psittaci isolates from three Budgerigars (Melopsittacus undulates) and four Barred parakeets (Bolborhynchus lineola) kept in individual households or imported from overseas. Nucleotide differences and phylogenetic analyses at four loci indicate the distinction of G. psittaci from the other known Giardia species: Giardia muris, Giardia microti, Giardia ardeae, and Giardia duodenalis assemblages. Furthermore, G. psittaci was related more closely to G. duodenalis than to the other known Giardia species, except for G. microti. Conflicting signals regarded as "double peaks" were found at the same nucleotide positions of the ef1α in all isolates. However, the sequences of the other three loci, including gdh and β-giardin, which are known to be highly variable, from all isolates were also mutually identical at every locus. They showed no double peaks. These results suggest that double peaks found in the ef1α sequences are caused not by mixed infection with genetically different G. psittaci isolates but by allelic sequence heterogeneity (ASH), which is observed in diplomonad lineages including G. duodenalis. No sequence difference was found in any G. psittaci isolates at the gdh and β-giardin, suggesting that G. psittaci is indeed not more diverse genetically than other Giardia species. This report is the first to provide evidence related to the genetic characteristics of G. psittaci obtained using multilocus sequence analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

  8. CISAPS: Complex Informational Spectrum for the Analysis of Protein Sequences

    Directory of Open Access Journals (Sweden)

    Charalambos Chrysostomou

    2015-01-01

    Full Text Available Complex informational spectrum analysis for protein sequences (CISAPS and its web-based server are developed and presented. As recent studies show, only the use of the absolute spectrum in the analysis of protein sequences using the informational spectrum analysis is proven to be insufficient. Therefore, CISAPS is developed to consider and provide results in three forms including absolute, real, and imaginary spectrum. Biologically related features to the analysis of influenza A subtypes as presented as a case study in this study can also appear individually either in the real or imaginary spectrum. As the results presented, protein classes can present similarities or differences according to the features extracted from CISAPS web server. These associations are probable to be related with the protein feature that the specific amino acid index represents. In addition, various technical issues such as zero-padding and windowing that may affect the analysis are also addressed. CISAPS uses an expanded list of 611 unique amino acid indices where each one represents a different property to perform the analysis. This web-based server enables researchers with little knowledge of signal processing methods to apply and include complex informational spectrum analysis to their work.

  9. Preliminary Analysis of a Submerged Wave Energy Device

    Science.gov (United States)

    Wagner, J. R.; Wagner, J. J.; Hayatdavoodi, M.; Ertekin, R. C.

    2016-02-01

    Preliminary analysis of a submerged wave energy harvesting device is presented. The device is composed of a thin, horizontally submerged plate that is restricted to heave oscillations under the influence of surface waves. The submerged plate is oscillating, and it can be attached to a fixed rotor, or a piston, to harvest the wave energy. A fully submerged wave energy converter is preferred over a surface energy convertor due to its durability and less visual and physical distractions it presents. In this study, the device is subject to nonlinear shallow-water waves. Wave loads on the submerged oscillating plate are obtained via the Level I Green-Naghdi equations. The unsteady motion of the plate is obtained by solving the nonlinear equations of motion. The results are obtained for a range of waves with varying heights and periods. The amplitude and period of plate oscillations are analyzed as functions of the wave parameters and plate width. Particular attention is given to the selection of the site of desired wave field. Initial estimation on the amount of energy extraction from the device, located near shore at a given site, is provided.

  10. Preliminary radiation criteria and nuclear analysis for ETF

    International Nuclear Information System (INIS)

    Engholm, B.A.

    1980-09-01

    Preliminary biological and materials radiation dose criteria for the Engineering Test Facility are described and tabulated. In keeping with the ETF Mission Statement, a key biological dose criterion is a 24-hour shutdown dose rate of 2 mrem/hr on the surface of the outboard bulk shield. Materials dose criteria, which primarily govern the inboard shield design, include 10 9 rads exposure limit to epoxy insulation, 3 x 10 -4 dpa damage to the TF coil copper stabilizer, and a total nuclear heating rate of 5 kW in the inboard TF coils. Nuclear analysis performed during FY 80 was directed primarily at the inboard and outboard bulk shielding, and at radiation streaming in the neutral beam drift ducts. Inboard and outboard shield thicknesses to achieve the biological and materials radiation criteria are 75 cm inboard and 125 cm outboard, the configuration consisting of alternating layers of stainless steel and borated water. The outboard shield also includes a 5 cm layer of lead. NBI duct streaming analyses performed by ORNL and LASL will play a key role in the design of the duct and NBI shielding in FY 81. The NBI aluminum cryopanel nuclear heating rate during the heating cycle is about 1 milliwatt/cm 3 , which is far less than the permissible limit

  11. Preliminary analysis of accelerated space flight ionizing radiation testing

    Science.gov (United States)

    Wilson, J. W.; Stock, L. V.; Carter, D. J.; Chang, C. K.

    1982-01-01

    A preliminary analysis shows that radiation dose equivalent to 30 years in the geosynchronous environment can be accumulated in a typical composite material exposed to space for 2 years or less onboard a spacecraft orbiting from perigee of 300 km out to the peak of the inner electron belt (approximately 2750 km). Future work to determine spacecraft orbits better tailored to materials accelerated testing is indicated. It is predicted that a range of 10 to the 9th power to 10 to the 10th power rads would be accumulated in 3-6 mil thick epoxy/graphite exposed by a test spacecraft orbiting in the inner electron belt. This dose is equivalent to the accumulated dose that this material would be expected to have after 30 years in a geosynchronous orbit. It is anticipated that material specimens would be brought back to Earth after 2 years in the radiation environment so that space radiation effects on materials could be analyzed by laboratory methods.

  12. Investigation of Sorption and Diffusion Mechanisms, and Preliminary Economic Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Bhave, Ramesh R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Jubin, Robert Thomas [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Spencer, Barry B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Nair, Sankar [Georgia Inst. of Technology, Atlanta, GA (United States)

    2017-02-01

    This report describes the synthesis and evaluation of molecular sieve zeolite membranes to separate and concentrate tritiated water (HTO) from dilute HTO-bearing aqueous streams. Several monovalent and divalent cation exchanged silico alumino phosphate (SAPO-34) molecular sieve zeolite membranes were synthesized on disk supports and characterized with gas and vapor permeation measurements. The pervaporation process performance was evaluated for the separation and concentration of tritiated water. Experiments were performed using tritiated water feed solution containing tritium at the high end of the range (1 mCi/mL) anticipated in a nuclear fuel processing system that includes both acid and water streams recycling. The tritium concentration was about 0.1 ppm. The permeate was recovered under vacuum. The HTO/H2O selectivity and separation factor calculated from the measured tritium concentrations ranged from 0.99 to 1.23, and 0.83-0.98, respectively. Although the membrane performance for HTO separation was lower than expected, several encouraging observations including molecular sieving and high vapor permeance are reported. Additionally, several new approaches are proposed, such as tuning the sorption and diffusion properties offered by small pore LTA zeolite materials, and cation exchanged aluminosilicates with high metal loading. It is hypothesized that substantially improved preferential transport of tritium (HTO) resulting in a more concentrated permeate can be achieved. Preliminary economic analysis for the membrane-based process to concentrate tritiated water is also discussed.

  13. Preliminary analysis of public dose from CFETR gaseous tritium release

    Energy Technology Data Exchange (ETDEWEB)

    Nie, Baojie [Key Laboratory of Neutronics and Radiation Safety, Institute of Nuclear Energy Safety Technology, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); University of Science and Technology of China, Hefei, Anhui 230027 (China); Ni, Muyi, E-mail: muyi.ni@fds.org.cn [Key Laboratory of Neutronics and Radiation Safety, Institute of Nuclear Energy Safety Technology, Chinese Academy of Sciences, Hefei, Anhui 230031 (China); Lian, Chao; Jiang, Jieqiong [Key Laboratory of Neutronics and Radiation Safety, Institute of Nuclear Energy Safety Technology, Chinese Academy of Sciences, Hefei, Anhui 230031 (China)

    2015-02-15

    Highlights: • Present the amounts and limit dose of tritium release to the environment for CFETR. • Perform a preliminary simulation of radiation dose for gaseous tritium release. • Key parameters about soil types, wind speed, stability class, effective release height and age were sensitivity analyzed. • Tritium release amount is recalculated consistently with dose limit in Chinese regulation for CFETR. - Abstract: To demonstrate tritium self-sufficiency and other engineering issues, the scientific conception of Chinese Fusion Engineering Test Reactor (CFETR) has been proposed in China parallel with ITER and before DEMO reactor. Tritium environmental safety for CFETR is an important issue and must be evaluated because of the huge amounts of tritium cycling in reactor. In this work, different tritium release scenarios of CFETR and dose limit regulations in China are introduced. And the public dose is preliminarily analyzed under normal and accidental events. Furthermore, after finishing the sensitivity analysis of key input parameters, the public dose is reevaluated based on extreme parameters. Finally, tritium release amount is recalculated consistently with the dose limit in Chinese regulation for CFETR, which would provide a reference for tritium system design of CFETR.

  14. Cost risk analysis of radioactive waste management Preliminary study

    International Nuclear Information System (INIS)

    Forsstroem, J.

    2006-12-01

    This work begins with exposition of the basics of risk analysis. These basics are then applied to the Finnish radioactive waste disposal environment in which the nuclear power companies are responsible for all costs of radioactive waste management including longterm disposal of spent fuel. Nuclear power companies prepare cost estimates of the waste disposal on a yearly basis to support the decision making on accumulation of resources to the nuclear waste disposal fund. These cost estimates are based on the cost level of the ongoing year. A Monte Carlo simulation model of the costs of the waste disposal system was defined and it was used to produce preliminary results of its cost risk characteristics. Input data was synthesised by modifying the original coefficients of cost uncertainty to define a cost range for each cost item. This is a suitable method for demonstrating results obtainable by the model but it is not accurate enough for supporting decision making. Two key areas of further development were identified: the input data preparation and identifying and handling of (i.e. eliminating or merging) interacting cost elements in the simulation model. Further development in both of the mentioned areas can be carried out by co-operating with the power companies as they are the sources of the original data. (orig.)

  15. CAFE: aCcelerated Alignment-FrEe sequence analysis.

    Science.gov (United States)

    Lu, Yang Young; Tang, Kujin; Ren, Jie; Fuhrman, Jed A; Waterman, Michael S; Sun, Fengzhu

    2017-07-03

    Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, $d_2^*$ and $d_2^S$ are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  16. Grid-connected ICES: preliminary feasibility analysis and evaluation. Volume 2. Final report

    Energy Technology Data Exchange (ETDEWEB)

    1977-06-30

    The HEAL Complex in New Orleans will serve as a Demonstration Community for which the ICES Demonstration System will be designed. The complex is a group of hospitals, clinics, research facilities, and medical educational facilities. The five tasks reported on are: preliminary energy analysis; preliminary institutional assessment; conceptual design; firming-up of commitments; and detailed work management plan.

  17. Preliminary safety analysis of molten salt breeder reactor

    International Nuclear Information System (INIS)

    Cheng Maosong; Dai Zhimin

    2013-01-01

    Background: The molten salt reactor is one of the six advanced reactor concepts identified by the Generation IV International Forum as a candidate for cooperative development, which is characterized by remarkable advantages in inherent safety, fuel cycle, miniaturization, effective utilization of nuclear resources and proliferation resistance. ORNL finished the conceptual design of Molten Salt Breeder Reactor (MSBR) based on the design, building and operation of Molten Salt Reactor Experiment (MSRE). Purpose: We attempt to implement the preliminary safety analysis of MSBR in order to provide a reference for the design and optimization of MSBR in the future. Methods: According to the conceptual design of MSBR, a model of safety analysis using point kinetics coupled with the simplified heat transfer mechanism is presented. The model is applied to simulate the transient phenomena of MSBR initiated by an abnormal step reactivity addition and an abnormal ramp reactivity addition at full-power equilibrium condition. Results: The thermal power in the core increases rapidly at the beginning and is accompanied by a rise of the fuel and graphite temperatures after 100, 300, 500 and 600 pcm reactivity addition. The maximum outlet temperature of the fuel in the core is at 1250℃ in 500 pcm reactivity addition, but up to 1350℃ in 600 pcm reactivity addition. The maximum of the power and the temperature are delayed and lower in the ramp reactivity addition rather than in the step reactivity addition. Conclusions: Based on the results, when the reactivity inserted is less than 500 pcm in maximum at full power equilibrium condition, the structural material in Hastelloy-N is not melted and can keep integrity without external control action. And it is necessary to try to avoid inserting a reactivity at short time. (authors)

  18. Conversion Preliminary Safety Analysis Report for the NIST Research Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Diamond, D. J. [Brookhaven National Lab. (BNL), Upton, NY (United States); Baek, J. S. [Brookhaven National Lab. (BNL), Upton, NY (United States); Hanson, A. L. [Brookhaven National Lab. (BNL), Upton, NY (United States); Cheng, L-Y [Brookhaven National Lab. (BNL), Upton, NY (United States); Brown, N. [Brookhaven National Lab. (BNL), Upton, NY (United States); Cuadra, A. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2015-01-30

    The NIST Center for Neutron Research (NCNR) is a reactor-laboratory complex providing the National Institute of Standards and Technology (NIST) and the nation with a world-class facility for the performance of neutron-based research. The heart of this facility is the NIST research reactor (aka NBSR); a heavy water moderated and cooled reactor operating at 20 MW. It is fueled with high-enriched uranium (HEU) fuel elements. A Global Threat Reduction Initiative (GTRI) program is underway to convert the reactor to low-enriched uranium (LEU) fuel. This program includes the qualification of the proposed fuel, uranium and molybdenum alloy foil clad in an aluminum alloy, and the development of the fabrication techniques. This report is a preliminary version of the Safety Analysis Report (SAR) that would be submitted to the U.S. Nuclear Regulatory Commission (NRC) for approval prior to conversion. The report follows the recommended format and content from the NRC codified in NUREG-1537, “Guidelines for Preparing and Reviewing Applications for the Licensing of Non-power Reactors,” Chapter 18, “Highly Enriched to Low-Enriched Uranium Conversions.” The emphasis in any conversion SAR is to explain the differences between the LEU and HEU cores and to show the acceptability of the new design; there is no need to repeat information regarding the current reactor that will not change upon conversion. Hence, as seen in the report, the bulk of the SAR is devoted to Chapter 4, Reactor Description, and Chapter 13, Safety Analysis.

  19. Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages

    Directory of Open Access Journals (Sweden)

    Man-Li He

    2016-11-01

    Full Text Available Abstract Background Psoroptic mange is a chronic, refractory, contagious and infectious disease mainly caused by the mange mite Psoroptes ovis, which can infect horses, sheep, buffaloes, rabbits, other domestic animals, deer, wild camels, foxes, minks, lemurs, alpacas, elks and other wild animals. Features of the disease include intense pruritus and dermatitis, depilation and hyperkeratosis, which ultimately result in emaciation or death caused by secondary bacterial infections. The infestation is usually transmitted by close contact between animals. Psoroptic mange is widespread in the world. In this paper, the transcriptome of P. ovis is described following sequencing and analysis of transcripts from samples of larvae (i.e. the Pso_L group and nymphs and adults (i.e. the Pso_N_A group. The study describes differentially expressed genes (DEGs and genes encoding allergens, which help understanding the biology of P. ovis and lay foundations for the development of vaccine antigens and drug target screening. Methods The transcriptome of P. ovis was assembled and analyzed using bioinformatic tools. The unigenes of P. ovis from each developmental stage and the unigenes differentially between developmental stages were compared with allergen protein sequences contained in the allergen database website to predict potential allergens. Results We identified 38,836 unigenes, whose mean length was 825 bp. On the basis of sequence similarity with seven databases, a total of 17,366 unigenes were annotated. A total of 1,316 DEGs were identified, including 496 upregulated and 820 downregulated in the Pso_L group compared with the Pso_N_A group. We predicted 205 allergens genes in the two developmental stages similar to genes from other mites and ticks, of these, 14 were among the upregulated DEGs and 26 among the downregulated DEGs. Conclusion This study provides a reference transcriptome of P. ovis in absence of a reference genome. The analysis of DEGs and

  20. Environmental impact analysis for the main accidental sequences of ignitor

    International Nuclear Information System (INIS)

    Carpignano, A.; Francabandiera, S.; Vella, R.; Zucchetti, M.

    1996-01-01

    A safety analysis study has been applied to the Ignitor machine using Probabilistic Safety Assessment. The main initiating events have been identified, and accident sequences have been studied by means of traditional methods such as Failure Mode and Effect Analysis (FMEA), Fault Trees (FT) and Event Trees (ET). The consequences of the radioactive environmental releases have been assessed in terms of Effective Dose Equivalent (EDEs) to the Most Exposed Individuals (MEI) of the chosen site, by means of a population dose code. Results point out the low enviromental impact of the machine. 13 refs., 1 fig., 3 tabs

  1. A Preliminary Tsunami vulnerability analysis for Bakirkoy district in Istanbul

    Science.gov (United States)

    Tufekci, Duygu; Lutfi Suzen, M.; Cevdet Yalciner, Ahmet; Zaytsev, Andrey

    2016-04-01

    Resilience of coastal utilities after earthquakes and tsunamis has major importance for efficient and proper rescue and recovery operations soon after the disasters. Vulnerability assessment of coastal areas under extreme events has major importance for preparedness and development of mitigation strategies. The Sea of Marmara has experienced numerous earthquakes as well as associated tsunamis. There are variety of coastal facilities such as ports, small craft harbors, and terminals for maritime transportation, water front roads and business centers mainly at North Coast of Marmara Sea in megacity Istanbul. A detailed vulnerability analysis for Yenikapi region and a detailed resilience analysis for Haydarpasa port in Istanbul have been studied in previously by Cankaya et al., (2015) and Aytore et al., (2015) in SATREPS project. In this study, the methodology of vulnerability analysis under tsunami attack given in Cankaya et al., (2015) is modified and applied to Bakirkoy district of Istanbul. Bakirkoy district is located at western part of Istanbul and faces to the North Coast of Marmara Sea from 28.77oE to 28.89oE. High resolution spatial dataset of Istanbul Metropolitan Municipality (IMM) is used and analyzed. The bathymetry and topography database and the spatial dataset containing all buildings/structures/infrastructures in the district are collated and utilized for tsunami numerical modeling and following vulnerability analysis. The tsunami parameters from deterministically defined worst case scenarios are computed from the simulations using tsunami numerical model NAMI DANCE. The vulnerability assessment parameters in the district according to vulnerability and resilience are defined; and scored by implementation of a GIS based TVA with appropriate MCDA methods. The risk level is computed using tsunami intensity (level of flow depth from simulations) and TVA results at every location in Bakirkoy district. The preliminary results are presented and discussed

  2. Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species.

    Science.gov (United States)

    Liu, Y T; Chen, R K; Lin, S J; Chen, Y C; Chin, S W; Chen, F C; Lee, C Y

    2014-04-08

    The Orchidaceae is one of the largest and most diverse families of flowering plants. The Dendrobium genus has high economic potential as ornamental plants and for medicinal purposes. In addition, the species of this genus are able to produce large crops. However, many Dendrobium varieties are very similar in outward appearance, making it difficult to distinguish one species from another. This study demonstrated that the 12 Dendrobium species used in this study may be divided into 2 groups by internal transcribed spacer (ITS) sequence analysis. Red and yellow flowers may also be used to separate these species into 2 main groups. In particular, the deciduous characteristic is associated with the ITS genetic diversity of the A group. Of 53 designed simple sequence repeat (SSR) primer pairs, 7 pairs were polymorphic for polymerase chain reaction products that were amplified from a specific band. The results of this study demonstrate that these 7 SSR primer pairs may potentially be used to identify Dendrobium species and their progeny in future studies.

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

    DEFF Research Database (Denmark)

    Østergaard, Mikkel; McQueen, Fiona; Wiell, Charlotte

    2009-01-01

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

  4. Using Behavior Sequence Analysis to Map Serial Killers' Life Histories.

    Science.gov (United States)

    Keatley, David A; Golightly, Hayley; Shephard, Rebecca; Yaksic, Enzo; Reid, Sasha

    2018-03-01

    The aim of the current research was to provide a novel method for mapping the developmental sequences of serial killers' life histories. An in-depth biographical account of serial killers' lives, from birth through to conviction, was gained and analyzed using Behavior Sequence Analysis. The analyses highlight similarities in behavioral events across the serial killers' lives, indicating not only which risk factors occur, but the temporal order of these factors. Results focused on early childhood environment, indicating the role of parental abuse; behaviors and events surrounding criminal histories of serial killers, showing that many had previous convictions and were known to police for other crimes; behaviors surrounding their murders, highlighting differences in victim choice and modus operandi; and, finally, trial pleas and convictions. The present research, therefore, provides a novel approach to synthesizing large volumes of data on criminals and presenting results in accessible, understandable outcomes.

  5. Risk Assessment of Healthcare Waste by Preliminary Hazard Analysis Method

    Directory of Open Access Journals (Sweden)

    Pouran Morovati

    2017-09-01

    Full Text Available Introduction and purpose: Improper management of healthcare waste (HCW can pose considerable risks to human health and the environment and cause serious problems in developing countries such as Iran. In this study, we sought to determine the hazards of HCW in the public hospitals affiliated to Abadan School of Medicine using the preliminary hazard analysis (PHA method. Methods: In this descriptive and analytic study, health risk assessment of HCW in government hospitals affiliated to Abadan School of Medicine (4 public hospitals was carried out by using PHA in the summer of  2016. Results: We noted the high risk of sharps and infectious wastes. Considering the dual risk of injury and disease transmission, sharps were classified in the very high-risk group, and pharmaceutical and chemical and radioactive wastes were classified in the medium-risk group. Sharps posed the highest risk, while pharmaceutical and chemical wastes had the lowest risk. Among the various stages of waste management, the waste treatment stage was the most hazardous in all the studied hospitals. Conclusion: To diminish the risks associated with healthcare waste management in the studied hospitals, adequate training of healthcare workers and care providers, provision of suitable personal protective and transportation equipment, and supervision of the environmental health manager of hospitals should be considered by the authorities.  

  6. Swab-to-Sequence: Real-time Data Analysis Platform for the Biomolecule Sequencer

    Data.gov (United States)

    National Aeronautics and Space Administration — DNA was successfully sequenced on the ISS in 2016, but the DNA sequenced was prepared on the ground. With FY’16 IRAD funds, the same team developed a...

  7. Sequence comparison and phylogenetic analysis of core gene of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-07-19

    Jul 19, 2010 ... and antisense primers, a single band of 573 base pairs .... Amino acid sequence alignment of Cluster I and Cluster II of phylogenetic tree. First ten sequences ... sequence weighting, postion-spiecific gap penalties and weight.

  8. Cost analysis of small hydroelectric power plants components and preliminary estimation of global cost

    International Nuclear Information System (INIS)

    Basta, C.; Olive, W.J.; Antunes, J.S.

    1990-01-01

    An analysis of cost for each components of Small Hydroelectric Power Plant, taking into account the real costs of these projects is shown. It also presents a global equation which allows a preliminary estimation of cost for each construction. (author)

  9. Linear discriminant analysis of character sequences using occurrences of words

    KAUST Repository

    Dutta, Subhajit; Chaudhuri, Probal; Ghosh, Anil

    2014-01-01

    Classification of character sequences, where the characters come from a finite set, arises in disciplines such as molecular biology and computer science. For discriminant analysis of such character sequences, the Bayes classifier based on Markov models turns out to have class boundaries defined by linear functions of occurrences of words in the sequences. It is shown that for such classifiers based on Markov models with unknown orders, if the orders are estimated from the data using cross-validation, the resulting classifier has Bayes risk consistency under suitable conditions. Even when Markov models are not valid for the data, we develop methods for constructing classifiers based on linear functions of occurrences of words, where the word length is chosen by cross-validation. Such linear classifiers are constructed using ideas of support vector machines, regression depth, and distance weighted discrimination. We show that classifiers with linear class boundaries have certain optimal properties in terms of their asymptotic misclassification probabilities. The performance of these classifiers is demonstrated in various simulated and benchmark data sets.

  10. Planarian homeobox genes: cloning, sequence analysis, and expression.

    Science.gov (United States)

    Garcia-Fernàndez, J; Baguñà, J; Saló, E

    1991-01-01

    Freshwater planarians (Platyhelminthes, Turbellaria, and Tricladida) are acoelomate, triploblastic, unsegmented, and bilaterally symmetrical organisms that are mainly known for their ample power to regenerate a complete organism from a small piece of their body. To identify potential pattern-control genes in planarian regeneration, we have isolated two homeobox-containing genes, Dth-1 and Dth-2 [Dugesia (Girardia) tigrina homeobox], by using degenerate oligonucleotides corresponding to the most conserved amino acid sequence from helix-3 of the homeodomain. Dth-1 and Dth-2 homeodomains are closely related (68% at the nucleotide level and 78% at the protein level) and show the conserved residues characteristic of the homeodomains identified to data. Similarity with most homeobox sequences is low (30-50%), except with Drosophila NK homeodomains (80-82% with NK-2) and the rodent TTF-1 homeodomain (77-87%). Some unusual amino acid residues specific to NK-2, TTF-1, Dth-1, and Dth-2 can be observed in the recognition helix (helix-3) and may define a family of homeodomains. The deduced amino acid sequences from the cDNAs contain, in addition to the homeodomain, other domains also present in various homeobox-containing genes. The expression of both genes, detected by Northern blot analysis, appear slightly higher in cephalic regions than in the rest of the intact organism, while a slight increase is detected in the central period (5 days) or regeneration. Images PMID:1714599

  11. Analysis of correlations between sites in models of protein sequences

    International Nuclear Information System (INIS)

    Giraud, B.G.; Lapedes, A.; Liu, L.C.

    1998-01-01

    A criterion based on conditional probabilities, related to the concept of algorithmic distance, is used to detect correlated mutations at noncontiguous sites on sequences. We apply this criterion to the problem of analyzing correlations between sites in protein sequences; however, the analysis applies generally to networks of interacting sites with discrete states at each site. Elementary models, where explicit results can be derived easily, are introduced. The number of states per site considered ranges from 2, illustrating the relation to familiar classical spin systems, to 20 states, suitable for representing amino acids. Numerical simulations show that the criterion remains valid even when the genetic history of the data samples (e.g., protein sequences), as represented by a phylogenetic tree, introduces nonindependence between samples. Statistical fluctuations due to finite sampling are also investigated and do not invalidate the criterion. A subsidiary result is found: The more homogeneous a population, the more easily its average properties can drift from the properties of its ancestor. copyright 1998 The American Physical Society

  12. Linear discriminant analysis of character sequences using occurrences of words

    KAUST Repository

    Dutta, Subhajit

    2014-02-01

    Classification of character sequences, where the characters come from a finite set, arises in disciplines such as molecular biology and computer science. For discriminant analysis of such character sequences, the Bayes classifier based on Markov models turns out to have class boundaries defined by linear functions of occurrences of words in the sequences. It is shown that for such classifiers based on Markov models with unknown orders, if the orders are estimated from the data using cross-validation, the resulting classifier has Bayes risk consistency under suitable conditions. Even when Markov models are not valid for the data, we develop methods for constructing classifiers based on linear functions of occurrences of words, where the word length is chosen by cross-validation. Such linear classifiers are constructed using ideas of support vector machines, regression depth, and distance weighted discrimination. We show that classifiers with linear class boundaries have certain optimal properties in terms of their asymptotic misclassification probabilities. The performance of these classifiers is demonstrated in various simulated and benchmark data sets.

  13. Sequence analysis of PROTEOLYSIS 6 from Solanum lycopersicum

    Science.gov (United States)

    Roslan, Nur Farhana; Chew, Bee Lyn; Goh, Hoe-Han; Isa, Nurulhikma Md

    2018-04-01

    The N-end rule pathway is a protein degradation pathway that relates the protein half-life with the identity of its N-terminal residues. A destabilizing N-terminal residues is created by enzymatic reaction or chemical modifications. This destabilized substrate will be recognized by PROTEOLYSIS 6 (PRT6) protein, which encodes an E3 ligase enzyme and resulted in substrate degradation by proteasome. PRT6 has been studied in Arabidopsis thaliana and barley but not yet been studied in fleshy fruit plants. Hence, this study was carried out in tomato that is known as the model for fleshy fruit plants. BLASTX analysis identified that Solyc09g010830 which encodes for a PRT6 gene in tomato based on its sequence similarity with PRT6 in A. thaliana. In silico gene expression analysis shows that PRT6 gene was highly expressed in tomato fruits breaker +5. Co-expression analysis shows that PRT6 may not only involved in abiotic stresses but also in biotic stresses. The objective is to analyze the sequence and characterize PRT6 gene in tomato.

  14. Determining physical constraints in transcriptional initiationcomplexes using DNA sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Shultzaberger, Ryan K.; Chiang, Derek Y.; Moses, Alan M.; Eisen,Michael B.

    2007-07-01

    Eukaryotic gene expression is often under the control ofcooperatively acting transcription factors whose binding is limited bystructural constraints. By determining these structural constraints, wecan understand the "rules" that define functional cooperativity.Conversely, by understanding the rules of binding, we can inferstructural characteristics. We have developed an information theory basedmethod for approximating the physical limitations of cooperativeinteractions by comparing sequence analysis to microarray expressiondata. When applied to the coordinated binding of the sulfur amino acidregulatory protein Met4 by Cbf1 and Met31, we were able to create acombinatorial model that can correctly identify Met4 regulatedgenes.

  15. The Organic Food Market and Marketing Initiatives in Europe: a Preliminary Analysis

    DEFF Research Database (Denmark)

    Kristensen, Niels Heine; Nielsen, Thorkild; Bruselius-Jensen, Maria Louisa

    2003-01-01

    Kristensen NH, Nielsen T, Bruselius-Jensen M, Scheperlen-Bøgh P, Beckie M, Foster C, Midmore P, Padel S (2002): The Organic Food Market and Marketing Initiatives in Europe: a Preliminary Analysis. Final Report to the EU Commission......Kristensen NH, Nielsen T, Bruselius-Jensen M, Scheperlen-Bøgh P, Beckie M, Foster C, Midmore P, Padel S (2002): The Organic Food Market and Marketing Initiatives in Europe: a Preliminary Analysis. Final Report to the EU Commission...

  16. Oxygenates in automotive fuels. Consequence analysis - preliminary study

    International Nuclear Information System (INIS)

    Brandberg, Aa.; Saevbark, B.

    1994-01-01

    Oxygenates is used in gasoline due to several reasons. They are added as high-octane components in unleaded gasoline and as agents to reduce the emission of harmful substances. Oxygenates produced from biomass might constitute a coming market for alternative fuels. This preliminary study describes the prerequisites and consequences of such an oxygenate utilization. 39 refs, 9 figs, 5 tabs

  17. Preliminary analysis of Stearoyl Co-A Desaturase gene transcripts in River buffalo

    Directory of Open Access Journals (Sweden)

    L. Ramunno

    2010-02-01

    Full Text Available Stearoyl-CoA desaturase (SCD is a key enzyme in the biosynthesis of monounsaturated fatty acids (MUFAs. In cattle, SCD gene extends over a DNA segment of ~17.0 Kb, and it is organized in 6 exons and 5 introns. The SCD gene has been indicated as the candidate gene to change the saturated/unsaturated FAs ratio and hence it has been suggested as the gene influencing the fat quality. In cattle, eight SNPs have been identified and one of them, (T→C at 231st nt of 5th exon, is responsible for the Val→Ala amino acid change. The C allele has been associated with higher content of MUFAs in carcasses, and it is positively related to a higher index of desaturation (C18:0/C18:1 and C16:0/C16:1 in the milk. In this study, we report on preliminary results of analysis of transcripts of the SCD encoding gene in river buffalo. The electrophoretic analysis of the RT-PCR products and the subsequent sequencing showed at least five different populations of mRNA. The most represented population is correctly assembled (~1300 bp, followed by the one which is deleted of ~750bp, corresponding to the 3rd, 4th and 5th exon and partially to the 2nd and 6th exon.

  18. [Management of cytostatic drugs by nurses: analysis of preliminary results].

    Science.gov (United States)

    Bilski, Bartosz

    2004-01-01

    Cytostatic drugs pose a quite specific occupational risk to health care workers. There is a wide range of potential harmful effects, including remote effects, exerted by this group of drugs. In Polish and international regulations, standards of work safety and hygiene concerning these substances are clearly defined. Nevertheless working conditions in Polish health care institutions are now mostly influenced by economic and organizational problems, which may also be reflected in the compliance with the work safety rules. This paper presents a preliminary analysis of subjective assessment of practice with regard to the management of cytostatics reported by nurses, an occupational group mostly exposed to these substances. The study was carried out at hospital departments in the Warmińsko-Mazurskie Voivodship, where exposure of the staff to these drugs was observed. The study covered the whole nursing staff exposed. Completed questionnaires were obtained from 60 nurses, aged +/- 32 years (20-54 years) with job seniority +/- 8 years (2-18), including 58 nurses with secondary education and two university graduates. Undergraduate education did not develop in respondents skills to work with cytostatics. There is a need to increase the involvement of nursing schools, research institutes and teaching hospitals in the improvement of vocational training of nurses working with cytostatic drugs. To this end, all nurses should be covered with the obligatory training how to handle this group of drugs. The respondents reported that they had acquired their knowledge and experience of managing cytostatics in their work and during training organized at workplace. Despite the acquired knowledge and experience the interviewed nurses did not always comply with work safety and hygiene regulations. The problem of exposure to cytostatic drugs in the form of tablets was most frequently neglected. Some of the nurses were additionally exposed to ionizing radiation. Shortage of the nursing

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

    Directory of Open Access Journals (Sweden)

    J. Eldon Molto

    2017-10-01

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

  20. Streaming support for data intensive cloud-based sequence analysis.

    Science.gov (United States)

    Issa, Shadi A; Kienzler, Romeo; El-Kalioby, Mohamed; Tonellato, Peter J; Wall, Dennis; Bruggmann, Rémy; Abouelhoda, Mohamed

    2013-01-01

    Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of "resources-on-demand" and "pay-as-you-go", scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client's site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

  1. Streaming Support for Data Intensive Cloud-Based Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Shadi A. Issa

    2013-01-01

    Full Text Available Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client’s site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

  2. Next-generation sequence analysis of cancer xenograft models.

    Directory of Open Access Journals (Sweden)

    Fernando J Rossello

    Full Text Available Next-generation sequencing (NGS studies in cancer are limited by the amount, quality and purity of tissue samples. In this situation, primary xenografts have proven useful preclinical models. However, the presence of mouse-derived stromal cells represents a technical challenge to their use in NGS studies. We examined this problem in an established primary xenograft model of small cell lung cancer (SCLC, a malignancy often diagnosed from small biopsy or needle aspirate samples. Using an in silico strategy that assign reads according to species-of-origin, we prospectively compared NGS data from primary xenograft models with matched cell lines and with published datasets. We show here that low-coverage whole-genome analysis demonstrated remarkable concordance between published genome data and internal controls, despite the presence of mouse genomic DNA. Exome capture sequencing revealed that this enrichment procedure was highly species-specific, with less than 4% of reads aligning to the mouse genome. Human-specific expression profiling with RNA-Seq replicated array-based gene expression experiments, whereas mouse-specific transcript profiles correlated with published datasets from human cancer stroma. We conclude that primary xenografts represent a useful platform for complex NGS analysis in cancer research for tumours with limited sample resources, or those with prominent stromal cell populations.

  3. Streaming Support for Data Intensive Cloud-Based Sequence Analysis

    Science.gov (United States)

    Issa, Shadi A.; Kienzler, Romeo; El-Kalioby, Mohamed; Tonellato, Peter J.; Wall, Dennis; Bruggmann, Rémy; Abouelhoda, Mohamed

    2013-01-01

    Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client's site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation. PMID:23710461

  4. Extended -Regular Sequence for Automated Analysis of Microarray Images

    Directory of Open Access Journals (Sweden)

    Jin Hee-Jeong

    2006-01-01

    Full Text Available Microarray study enables us to obtain hundreds of thousands of expressions of genes or genotypes at once, and it is an indispensable technology for genome research. The first step is the analysis of scanned microarray images. This is the most important procedure for obtaining biologically reliable data. Currently most microarray image processing systems require burdensome manual block/spot indexing work. Since the amount of experimental data is increasing very quickly, automated microarray image analysis software becomes important. In this paper, we propose two automated methods for analyzing microarray images. First, we propose the extended -regular sequence to index blocks and spots, which enables a novel automatic gridding procedure. Second, we provide a methodology, hierarchical metagrid alignment, to allow reliable and efficient batch processing for a set of microarray images. Experimental results show that the proposed methods are more reliable and convenient than the commercial tools.

  5. Sequence Quality Analysis Tool for HIV Type 1 Protease and Reverse Transcriptase

    OpenAIRE

    DeLong, Allison K.; Wu, Mingham; Bennett, Diane; Parkin, Neil; Wu, Zhijin; Hogan, Joseph W.; Kantor, Rami

    2012-01-01

    Access to antiretroviral therapy is increasing globally and drug resistance evolution is anticipated. Currently, protease (PR) and reverse transcriptase (RT) sequence generation is increasing, including the use of in-house sequencing assays, and quality assessment prior to sequence analysis is essential. We created a computational HIV PR/RT Sequence Quality Analysis Tool (SQUAT) that runs in the R statistical environment. Sequence quality thresholds are calculated from a large dataset (46,802...

  6. Analysis of Paks NPP Personnel Activity during Safety Related Event Sequences

    International Nuclear Information System (INIS)

    Bareith, A.; Hollo, Elod; Karsa, Z.; Nagy, S.

    1998-01-01

    Within the AGNES Project (Advanced Generic and New Evaluation of Safety) the Level-1 PSA model of the Paks NPP Unit 3 was developed in form of a detailed event tree/fault tree structure (53 initiating events, 580 event sequences, 6300 basic events are involved). This model gives a good basis for quantitative evaluation of potential consequences of actually occurred safety-related events, i.e. for precursor event studies. To make these studies possible and efficient, the current qualitative event analysis practice should be reviewed and a new additional quantitative analysis procedure and system should be developed and applied. The present paper gives an overview of the method outlined for both qualitative and quantitative analyses of the operator crew activity during off-normal situations. First, the operator performance experienced during past operational events is discussed. Sources of raw information, the qualitative evaluation process, the follow-up actions, as well as the documentation requirements are described. Second, the general concept of the proposed precursor event analysis is described. Types of modeled interactions and the considered performance influences are presented. The quantification of the potential consequences of the identified precursor events is based on the task-oriented, Level-1 PSA model of the plant unit. A precursor analysis system covering the evaluation of operator activities is now under development. Preliminary results gained during a case study evaluation of a past historical event are presented. (authors)

  7. Preliminary Analysis of Helicopter Options to Support Tunisian Counterterrorism Operations

    Science.gov (United States)

    2016-04-27

    helicopters from Sikorsky to fulfill a number of roles in counterterrorism operations. Rising costs and delays in delivery raised the question of...whether other cost-effective options exist to meet Tunisia’s helicopter requirement. Approach Our team conducted a preliminary assessment of...alternative helicopters for counterterrorism air assault missions. Any decision to acquire an aircraft must consider many factors, including technical

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

    International Nuclear Information System (INIS)

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

    2005-01-01

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

  9. Sequencing Infrastructure Investments under Deep Uncertainty Using Real Options Analysis

    Directory of Open Access Journals (Sweden)

    Nishtha Manocha

    2018-02-01

    Full Text Available The adaptation tipping point and adaptation pathway approach developed to make decisions under deep uncertainty do not shed light on which among the multiple available pathways should be chosen as the preferred pathway. This creates the need to extend these approaches by means of suitable tools that can help sequence actions and subsequently enable the outlining of relevant policies. This paper presents two sequencing approaches, namely, the “Build to Target” and “Build Up” approach, to aid in sub-selecting a set of preferred pathways. Both approaches differ in the levels of flexibility they offer. They are exemplified by means of two case studies wherein the Net Present Valuation and the Real Options Analysis are employed as selection criterions. The results demonstrate the benefit of these two approaches when used in conjunction with the adaptation pathways and show how the pathways selected by means of a Build to Target approach generally have a value greater than, or at least the same as, the pathways selected by the Build Up approach. Further, this paper also demonstrates the capacity of Real Options to quantify and capture the economic value of flexibility, which cannot be done by traditional valuation approaches such as Net Present Valuation.

  10. Reverse transcriptase sequences from mulberry LTR retrotransposons: characterization analysis

    Directory of Open Access Journals (Sweden)

    Ma Bi

    2017-10-01

    Full Text Available Copia and Gypsy play important roles in structural, functional and evolutionary dynamics of plant genomes. In this study, a total of 106 and 101, Copia and Gypsy reverse transcriptase (rt were amplified respectively in the Morus notabilis genome using degenerate primers. All sequences exhibited high levels of heterogeneity, were rich in AT and possessed higher sequence divergence of Copia rt in comparison to Gypsy rt. Two reasons are likely to account for this phenomenon: a these elements often experience deletions or fragmentation by illegitimate or unequal homologous recombination in the transposition process; b strong purifying selective pressure drives the evolution of these elements through “selective silencing” with random mutation and eventual deletion from the host genome. Interestingly, mulberry rt clustered with other rt from distantly related taxa according to the phylogenetic analysis. This phenomenon did not result from horizontal transposable element transfer. Results obtained from fluorescence in situ hybridization revealed that most of the hybridization signals were preferentially concentrated in pericentromeric and distal regions of chromosomes, and these elements may play important roles in the regions in which they are found. Results of this study support the continued pursuit of further functional studies of Copia and Gypsy in the mulberry genome.

  11. Protective Alternatives of SMR against Extreme Threat Scenario – A Preliminary Risk Analysis

    International Nuclear Information System (INIS)

    Shohet, I.M.; Ornai, D.; Gal, E.; Ronen, Y.; Vidra, M.

    2014-01-01

    The article presents a preliminary risk analysis of the main features in NPP (Nuclear Power Plant) that includes SMR - Small and Modular Reactors, given an extreme threat scenario. A review of the structure and systems of the SMR is followed by systematic definitions and analysis of the threat scenario to which a preliminary risk analysis was carried out. The article outlines the basic events caused by the referred threat scenario, which had led to possible failure mechanisms according to FTA (Fault-Tree-Analysis),critical protective circuits, and todetecting critical topics for the protection and safety of the reactor

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

    Science.gov (United States)

    Borcherdt, R.D.

    1986-01-01

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

  13. Thermal Hydraulic Analysis of K-DEMO Single Blanket Module for Preliminary Accident Analysis using MELCOR

    Energy Technology Data Exchange (ETDEWEB)

    Moon, Sung Bo; Bang, In Cheol [UNIST, Ulsan (Korea, Republic of)

    2016-05-15

    To develop the Korean fusion commercial reactor, preliminary design concept for K-DEMO (Korean fusion demonstration reactor) has been announced by NFRI (National Fusion Research Institute). This pre-conceptual study of K-DEMO has been introduced to identify technical details of a fusion power plant for the future commercialization of fusion reactor in Korea. Before this consideration, to build the K-DEMO, accident analysis is essential. Since the Fukushima accident, which is severe accident from unexpected disaster, safety analysis of nuclear power plant has become important. The safety analysis of both fission and fusion reactors is deemed crucial in demonstrating the low radiological effect of these reactors on the environment, during severe accidents. A risk analysis of K-DEMO should be performed, as a prerequisite for the construction of a fusion reactor. In this research, thermal-hydraulic analysis of single blanket module of K-DEMO is conducted for preliminary accident analysis for K-DEMO. Further study about effect of flow distributer is conducted. The normal K-DEMO operation condition is applied to the boundary condition and simulated to verify the material temperature limit using MELCOR. MELCOR is fully integrated, relatively fast-running code developed by Sandia National Laboratories. MELCOR had been used for Light Water Reactors and fusion reactor version of MELCOR was developed for ITER accident analysis. This study shows the result of thermal-hydraulic simulation of single blanket module with MELCOR which is severe accident code for nuclear fusion safety analysis. The difference of mass flow rate for each coolant channel with or without flow distributer is presented. With flow distributer, advantage of broadening temperature gradient in the K-DEMO blanket module and increase mass flow toward first wall is obtained. This can enhance the safety of K-DEMO blanket module. Most 13 .deg. C temperature difference in blanket module is obtained.

  14. Nonlinear analysis of sequence repeats of multi-domain proteins

    Energy Technology Data Exchange (ETDEWEB)

    Huang Yanzhao [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Li Mingfeng [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China); Xiao Yi [Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei (China)]. E-mail: lmf_bill@sina.com

    2007-11-15

    Many multi-domain proteins have repetitive three-dimensional structures but nearly-random amino acid sequences. In the present paper, by using a modified recurrence plot proposed by us previously, we show that these amino acid sequences have hidden repetitions in fact. These results indicate that the repetitive domain structures are encoded by the repetitive sequences. This also gives a method to detect the repetitive domain structures directly from amino acid sequences.

  15. Human factors review for Severe Accident Sequence Analysis (SASA)

    International Nuclear Information System (INIS)

    Krois, P.A.; Haas, P.M.; Manning, J.J.; Bovell, C.R.

    1984-01-01

    The paper will discuss work being conducted during this human factors review including: (1) support of the Severe Accident Sequence Analysis (SASA) Program based on an assessment of operator actions, and (2) development of a descriptive model of operator severe accident management. Research by SASA analysts on the Browns Ferry Unit One (BF1) anticipated transient without scram (ATWS) was supported through a concurrent assessment of operator performance to demonstrate contributions to SASA analyses from human factors data and methods. A descriptive model was developed called the Function Oriented Accident Management (FOAM) model, which serves as a structure for bridging human factors, operations, and engineering expertise and which is useful for identifying needs/deficiencies in the area of accident management. The assessment of human factors issues related to ATWS required extensive coordination with SASA analysts. The analysis was consolidated primarily to six operator actions identified in the Emergency Procedure Guidelines (EPGs) as being the most critical to the accident sequence. These actions were assessed through simulator exercises, qualitative reviews, and quantitative human reliability analyses. The FOAM descriptive model assumes as a starting point that multiple operator/system failures exceed the scope of procedures and necessitates a knowledge-based emergency response by the operators. The FOAM model provides a functionally-oriented structure for assembling human factors, operations, and engineering data and expertise into operator guidance for unconventional emergency responses to mitigate severe accident progression and avoid/minimize core degradation. Operators must also respond to potential radiological release beyond plant protective barriers. Research needs in accident management and potential uses of the FOAM model are described. 11 references, 1 figure

  16. Sequence analysis of cereal sucrose synthase genes and isolation ...

    African Journals Online (AJOL)

    SERVER

    2007-10-18

    Oct 18, 2007 ... sequencing of sucrose synthase gene fragment from sor- ghum using primers designed at their conserved exons. MATERIALS AND METHODS. Multiple sequence alignment. Sucrose synthase gene sequences of various cereals like rice, maize, and barley were accessed from NCBI Genbank database.

  17. Chimera: construction of chimeric sequences for phylogenetic analysis

    NARCIS (Netherlands)

    Leunissen, J.A.M.

    2003-01-01

    Chimera allows the construction of chimeric protein or nucleic acid sequence files by concatenating sequences from two or more sequence files in PHYLIP formats. It allows the user to interactively select genes and species from the input files. The concatenated result is stored to one single output

  18. Accident Sequence Evaluation Program: Human reliability analysis procedure

    Energy Technology Data Exchange (ETDEWEB)

    Swain, A.D.

    1987-02-01

    This document presents a shortened version of the procedure, models, and data for human reliability analysis (HRA) which are presented in the Handbook of Human Reliability Analysis With emphasis on Nuclear Power Plant Applications (NUREG/CR-1278, August 1983). This shortened version was prepared and tried out as part of the Accident Sequence Evaluation Program (ASEP) funded by the US Nuclear Regulatory Commission and managed by Sandia National Laboratories. The intent of this new HRA procedure, called the ''ASEP HRA Procedure,'' is to enable systems analysts, with minimal support from experts in human reliability analysis, to make estimates of human error probabilities and other human performance characteristics which are sufficiently accurate for many probabilistic risk assessments. The ASEP HRA Procedure consists of a Pre-Accident Screening HRA, a Pre-Accident Nominal HRA, a Post-Accident Screening HRA, and a Post-Accident Nominal HRA. The procedure in this document includes changes made after tryout and evaluation of the procedure in four nuclear power plants by four different systems analysts and related personnel, including human reliability specialists. The changes consist of some additional explanatory material (including examples), and more detailed definitions of some of the terms. 42 refs.

  19. Accident Sequence Evaluation Program: Human reliability analysis procedure

    International Nuclear Information System (INIS)

    Swain, A.D.

    1987-02-01

    This document presents a shortened version of the procedure, models, and data for human reliability analysis (HRA) which are presented in the Handbook of Human Reliability Analysis With emphasis on Nuclear Power Plant Applications (NUREG/CR-1278, August 1983). This shortened version was prepared and tried out as part of the Accident Sequence Evaluation Program (ASEP) funded by the US Nuclear Regulatory Commission and managed by Sandia National Laboratories. The intent of this new HRA procedure, called the ''ASEP HRA Procedure,'' is to enable systems analysts, with minimal support from experts in human reliability analysis, to make estimates of human error probabilities and other human performance characteristics which are sufficiently accurate for many probabilistic risk assessments. The ASEP HRA Procedure consists of a Pre-Accident Screening HRA, a Pre-Accident Nominal HRA, a Post-Accident Screening HRA, and a Post-Accident Nominal HRA. The procedure in this document includes changes made after tryout and evaluation of the procedure in four nuclear power plants by four different systems analysts and related personnel, including human reliability specialists. The changes consist of some additional explanatory material (including examples), and more detailed definitions of some of the terms. 42 refs

  20. A Quantitative Accident Sequence Analysis for a VHTR

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jintae; Lee, Joeun; Jae, Moosung [Hanyang University, Seoul (Korea, Republic of)

    2016-05-15

    In Korea, the basic design features of VHTR are currently discussed in the various design concepts. Probabilistic risk assessment (PRA) offers a logical and structured method to assess risks of a large and complex engineered system, such as a nuclear power plant. It will be introduced at an early stage in the design, and will be upgraded at various design and licensing stages as the design matures and the design details are defined. Risk insights to be developed from the PRA are viewed as essential to developing a design that is optimized in meeting safety objectives and in interpreting the applicability of the existing demands to the safety design approach of the VHTR. In this study, initiating events which may occur in VHTRs were selected through MLD method. The initiating events were then grouped into four categories for the accident sequence analysis. Initiating events frequency and safety systems failure rate were calculated by using reliability data obtained from the available sources and fault tree analysis. After quantification, uncertainty analysis was conducted. The SR and LR frequency are calculated respectively 7.52E- 10/RY and 7.91E-16/RY, which are relatively less than the core damage frequency of LWRs.

  1. Comparing methods of classifying life courses: Sequence analysis and latent class analysis

    NARCIS (Netherlands)

    Elzinga, C.H.; Liefbroer, Aart C.; Han, Sapphire

    2017-01-01

    We compare life course typology solutions generated by sequence analysis (SA) and latent class analysis (LCA). First, we construct an analytic protocol to arrive at typology solutions for both methodologies and present methods to compare the empirical quality of alternative typologies. We apply this

  2. Comparing methods of classifying life courses: sequence analysis and latent class analysis

    NARCIS (Netherlands)

    Han, Y.; Liefbroer, A.C.; Elzinga, C.

    2017-01-01

    We compare life course typology solutions generated by sequence analysis (SA) and latent class analysis (LCA). First, we construct an analytic protocol to arrive at typology solutions for both methodologies and present methods to compare the empirical quality of alternative typologies. We apply this

  3. Preliminary Hazard Analysis applied to Uranium Hexafluoride - UF6 production plant

    International Nuclear Information System (INIS)

    Tomzhinsky, David; Bichmacher, Ricardo; Braganca Junior, Alvaro; Peixoto, Orpet Jose

    1996-01-01

    The purpose of this paper is to present the results of the Preliminary hazard Analysis applied to the UF 6 Production Process, which is part of the UF 6 Conversion Plant. The Conversion Plant has designed to produce a high purified UF 6 in accordance with the nuclear grade standards. This Preliminary Hazard Analysis is the first step in the Risk Management Studies, which are under current development. The analysis evaluated the impact originated from the production process in the plant operators, members of public, equipment, systems and installations as well as the environment. (author)

  4. RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

    Science.gov (United States)

    Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

    2012-01-01

    RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

  5. Frame sequences analysis technique of linear objects movement

    Science.gov (United States)

    Oshchepkova, V. Y.; Berg, I. A.; Shchepkin, D. V.; Kopylova, G. V.

    2017-12-01

    Obtaining data by noninvasive methods are often needed in many fields of science and engineering. This is achieved through video recording in various frame rate and light spectra. In doing so quantitative analysis of movement of the objects being studied becomes an important component of the research. This work discusses analysis of motion of linear objects on the two-dimensional plane. The complexity of this problem increases when the frame contains numerous objects whose images may overlap. This study uses a sequence containing 30 frames at the resolution of 62 × 62 pixels and frame rate of 2 Hz. It was required to determine the average velocity of objects motion. This velocity was found as an average velocity for 8-12 objects with the error of 15%. After processing dependencies of the average velocity vs. control parameters were found. The processing was performed in the software environment GMimPro with the subsequent approximation of the data obtained using the Hill equation.

  6. Transcriptome sequencing and positive selected genes analysis of Bombyx mandarina.

    Directory of Open Access Journals (Sweden)

    Tingcai Cheng

    Full Text Available The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 platform. We produced 100,004,078 high-quality reads and assembled them into 50,773 contigs with an N50 length of 1764 bp and a mean length of 941.62 bp. A total of 33,759 unigenes were identified, with 12,805 annotated in the Nr database, 8273 in the Pfam database, and 9093 in the Swiss-Prot database. Expression profile analysis found significant differential expression of 1308 unigenes between the middle silk gland (MSG and posterior silk gland (PSG. Three sericin genes (sericin 1, sericin 2, and sericin 3 were expressed specifically in the MSG and three fibroin genes (fibroin-H, fibroin-L, and fibroin/P25 were expressed specifically in the PSG. In addition, 32,297 Single-nucleotide polymorphisms (SNPs and 361 insertion-deletions (INDELs were detected. Comparison with the domesticated silkworm p50/Dazao identified 5,295 orthologous genes, among which 400 might have experienced or to be experiencing positive selection by Ka/Ks analysis. These data and analyses presented here provide insights into silkworm domestication and an invaluable resource for wild silkworm genomics research.

  7. Preliminary analysis of the transient overpower accident for CRBRP. Final report

    International Nuclear Information System (INIS)

    Kastenberg, W.E.; Frank, M.V.

    1975-07-01

    A preliminary analysis of the transient overpower accident for the Clinch River Breeder Reactor Plant (CRBRP) is presented. Several uncertainties in the analysis and the estimation of ramp rates during the transition to disassembly are discussed. The major conclusions are summarized

  8. SUMS preliminary design and data analysis development. [shuttle upper atmosphere mass spectrometer experiment

    Science.gov (United States)

    Hinson, E. W.

    1981-01-01

    The preliminary analysis and data analysis system development for the shuttle upper atmosphere mass spectrometer (SUMS) experiment are discussed. The SUMS experiment is designed to provide free stream atmospheric density, pressure, temperature, and mean molecular weight for the high altitude, high Mach number region.

  9. 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.)

  10. Cloning, sequencing, and sequence analysis of two novel plasmids from the thermophilic anaerobic bacterium Anaerocellum thermophilum

    DEFF Research Database (Denmark)

    Clausen, Anders; Mikkelsen, Marie Just; Schrøder, I.

    2004-01-01

    The nucleotide sequence of two novel plasmids isolated from the extreme thermophilic anaerobic bacterium Anaerocellum thermophilum DSM6725 (A. thermophilum), growing optimally at 70degreesC, has been determined. pBAS2 was found to be a 3653 bp plasmid with a GC content of 43%, and the sequence re...... with highest similarity to DNA repair protein from Campylobacter jejuni (25% aa). Orf34 showed similarity to sigma factors with highest similarity (28% aa) to the sporulation specific Sigma factor, Sigma 28(K) from Bacillus thuringiensis....

  11. Do pattern recognition skills transfer across sports? A preliminary analysis.

    Science.gov (United States)

    Smeeton, Nicholas J; Ward, Paul; Williams, A Mark

    2004-02-01

    The ability to recognize patterns of play is fundamental to performance in team sports. While typically assumed to be domain-specific, pattern recognition skills may transfer from one sport to another if similarities exist in the perceptual features and their relations and/or the strategies used to encode and retrieve relevant information. A transfer paradigm was employed to compare skilled and less skilled soccer, field hockey and volleyball players' pattern recognition skills. Participants viewed structured and unstructured action sequences from each sport, half of which were randomly represented with clips not previously seen. The task was to identify previously viewed action sequences quickly and accurately. Transfer of pattern recognition skill was dependent on the participant's skill, sport practised, nature of the task and degree of structure. The skilled soccer and hockey players were quicker than the skilled volleyball players at recognizing structured soccer and hockey action sequences. Performance differences were not observed on the structured volleyball trials between the skilled soccer, field hockey and volleyball players. The skilled field hockey and soccer players were able to transfer perceptual information or strategies between their respective sports. The less skilled participants' results were less clear. Implications for domain-specific expertise, transfer and diversity across domains are discussed.

  12. Automatic analysis of the 2015 Gorkha earthquake aftershock sequence.

    Science.gov (United States)

    Baillard, C.; Lyon-Caen, H.; Bollinger, L.; Rietbrock, A.; Letort, J.; Adhikari, L. B.

    2016-12-01

    The Mw 7.8 Gorkha earthquake, that partially ruptured the Main Himalayan Thrust North of Kathmandu on the 25th April 2015, was the largest and most catastrophic earthquake striking Nepal since the great M8.4 1934 earthquake. This mainshock was followed by multiple aftershocks, among them, two notable events that occurred on the 12th May with magnitudes of 7.3 Mw and 6.3 Mw. Due to these recent events it became essential for the authorities and for the scientific community to better evaluate the seismic risk in the region through a detailed analysis of the earthquake catalog, amongst others, the spatio-temporal distribution of the Gorkha aftershock sequence. Here we complement this first study by doing a microseismic study using seismic data coming from the eastern part of the Nepalese Seismological Center network associated to one broadband station in Everest. Our primary goal is to deliver an accurate catalog of the aftershock sequence. Due to the exceptional number of events detected we performed an automatic picking/locating procedure which can be splitted in 4 steps: 1) Coarse picking of the onsets using a classical STA/LTA picker, 2) phase association of picked onsets to detect and declare seismic events, 3) Kurtosis pick refinement around theoretical arrival times to increase picking and location accuracy and, 4) local magnitude calculation based amplitude of waveforms. This procedure is time efficient ( 1 sec/event), reduces considerably the location uncertainties ( 2 to 5 km errors) and increases the number of events detected compared to manual processing. Indeed, the automatic detection rate is 10 times higher than the manual detection rate. By comparing to the USGS catalog we were able to give a new attenuation law to compute local magnitudes in the region. A detailed analysis of the seismicity shows a clear migration toward the east of the region and a sudden decrease of seismicity 100 km east of Kathmandu which may reveal the presence of a tectonic

  13. A DNA Structure-Based Bionic Wavelet Transform and Its Application to DNA Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Fei Chen

    2003-01-01

    Full Text Available DNA sequence analysis is of great significance for increasing our understanding of genomic functions. An important task facing us is the exploration of hidden structural information stored in the DNA sequence. This paper introduces a DNA structure-based adaptive wavelet transform (WT – the bionic wavelet transform (BWT – for DNA sequence analysis. The symbolic DNA sequence can be separated into four channels of indicator sequences. An adaptive symbol-to-number mapping, determined from the structural feature of the DNA sequence, was introduced into WT. It can adjust the weight value of each channel to maximise the useful energy distribution of the whole BWT output. The performance of the proposed BWT was examined by analysing synthetic and real DNA sequences. Results show that BWT performs better than traditional WT in presenting greater energy distribution. This new BWT method should be useful for the detection of the latent structural features in future DNA sequence analysis.

  14. A preliminary analysis of the reactor-based plutonium disposition alternative deployment schedules

    International Nuclear Information System (INIS)

    Zurn, R.M.

    1997-09-01

    This paper discusses the preliminary analysis of the implementation schedules of the reactor-based plutonium disposition alternatives. These schedule analyses are a part of a larger process to examine the nine decision criteria used to determine the most appropriate method of disposing of U.S. surplus weapons plutonium. The preliminary analysis indicates that the mission durations for the reactor-based alternatives range from eleven years to eighteen years and the initial mission fuel assemblies containing surplus weapons-usable plutonium could be loaded into the reactors between nine and fourteen years after the Record of Decision

  15. Purification, crystallization and preliminary X-ray structure analysis of the laccase from Ganoderma lucidum

    International Nuclear Information System (INIS)

    Lyashenko, Andrey V.; Belova, Oksana; Gabdulkhakov, Azat G.; Lashkov, Alexander A.; Lisov, Alexandr V.; Leontievsky, Alexey A.; Mikhailov, Al’bert M.

    2011-01-01

    The purification, crystallization and preliminary X-ray structure analysis of the laccase from G. lucidum are reported. The ligninolytic enzymes of the basidiomycetes play a key role in the global carbon cycle. A characteristic property of these enzymes is their broad substrate specificity, which has led to their use in various biotechnologies, thus stimulating research into the three-dimensional structures of ligninolytic enzymes. This paper presents the purification, crystallization and preliminary X-ray analysis of the laccase from the ligninolytic basidiomycete Ganoderma lucidum

  16. NRC staff preliminary analysis of public comments on advance notice of proposed rulemaking on emergency planning

    International Nuclear Information System (INIS)

    Peabody, C.A.; Hickey, J.W.N.

    1980-01-01

    The Nuclear Regulatory Commission (NRC) published an advance notice of proposed rulemaking on emergency planning on July 17, 1979 (44 FR 41483). In October and November 1979, the NRC staff submitted several papers to the Commission related to the emergency planning rulemaking. One of these papers was a preliminary analysis of public comments received on the advance notice (SECY-79-591B, November 13, 1979). This document consists of the preliminary analysis as it was submitted to the Commission, with minor editorial changes

  17. A genome-wide analysis of lentivector integration sites using targeted sequence capture and next generation sequencing technology.

    Science.gov (United States)

    Ustek, Duran; Sirma, Sema; Gumus, Ergun; Arikan, Muzaffer; Cakiris, Aris; Abaci, Neslihan; Mathew, Jaicy; Emrence, Zeliha; Azakli, Hulya; Cosan, Fulya; Cakar, Atilla; Parlak, Mahmut; Kursun, Olcay

    2012-10-01

    One application of next-generation sequencing (NGS) is the targeted resequencing of interested genes which has not been used in viral integration site analysis of gene therapy applications. Here, we combined targeted sequence capture array and next generation sequencing to address the whole genome profiling of viral integration sites. Human 293T and K562 cells were transduced with a HIV-1 derived vector. A custom made DNA probe sets targeted pLVTHM vector used to capture lentiviral vector/human genome junctions. The captured DNA was sequenced using GS FLX platform. Seven thousand four hundred and eighty four human genome sequences flanking the long terminal repeats (LTR) of pLVTHM fragment sequences matched with an identity of at least 98% and minimum 50 bp criteria in both cells. In total, 203 unique integration sites were identified. The integrations in both cell lines were totally distant from the CpG islands and from the transcription start sites and preferentially located in introns. A comparison between the two cell lines showed that the lentiviral-transduced DNA does not have the same preferred regions in the two different cell lines. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing.

    Science.gov (United States)

    Boyer, François; Boutouil, Hend; Dalloul, Iman; Dalloul, Zeinab; Cook-Moreau, Jeanne; Aldigier, Jean-Claude; Carrion, Claire; Herve, Bastien; Scaon, Erwan; Cogné, Michel; Péron, Sophie

    2017-05-15

    B cells ensure humoral immune responses due to the production of Ag-specific memory B cells and Ab-secreting plasma cells. In secondary lymphoid organs, Ag-driven B cell activation induces terminal maturation and Ig isotype class switch (class switch recombination [CSR]). CSR creates a virtually unique IgH locus in every B cell clone by intrachromosomal recombination between two switch (S) regions upstream of each C region gene. Amount and structural features of CSR junctions reveal valuable information about the CSR mechanism, and analysis of CSR junctions is useful in basic and clinical research studies of B cell functions. To provide an automated tool able to analyze large data sets of CSR junction sequences produced by high-throughput sequencing (HTS), we designed CSReport, a software program dedicated to support analysis of CSR recombination junctions sequenced with a HTS-based protocol (Ion Torrent technology). CSReport was assessed using simulated data sets of CSR junctions and then used for analysis of Sμ-Sα and Sμ-Sγ1 junctions from CH12F3 cells and primary murine B cells, respectively. CSReport identifies junction segment breakpoints on reference sequences and junction structure (blunt-ended junctions or junctions with insertions or microhomology). Besides the ability to analyze unprecedentedly large libraries of junction sequences, CSReport will provide a unified framework for CSR junction studies. Our results show that CSReport is an accurate tool for analysis of sequences from our HTS-based protocol for CSR junctions, thereby facilitating and accelerating their study. Copyright © 2017 by The American Association of Immunologists, Inc.

  19. Thick Concrete Specimen Construction, Testing, and Preliminary Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Clayton, Dwight A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Hoegh, Kyle [Univ. of Minnesota, Minneapolis, MN (United States); Khazanovich, Lev [Univ. of Minnesota, Minneapolis, MN (United States)

    2015-03-01

    The purpose of the U.S. Department of Energy Office of Nuclear Energy’s Light Water Reactor Sustainability (LWRS) Program is to develop technologies and other solutions that can improve the reliability, sustain the safety, and extend the operating lifetimes of nuclear power plants (NPPs) beyond 60 years. Since many important safety structures in an NPP are constructed of concrete, inspection techniques must be developed and tested to evaluate the internal condition. In-service containment structures generally do not allow for the destructive measures necessary to validate the accuracy of these inspection techniques. This creates a need for comparative testing of the various nondestructive evaluation (NDE) measurement techniques on concrete specimens with known material properties, voids, internal microstructure flaws, and reinforcement locations. A preliminary report detailed some of the challenges associated with thick reinforced concrete sections and prioritized conceptual designs of specimens that could be fabricated to represent NPP concrete structures for using in NDE evaluation comparisons. This led to the construction of the concrete specimen presented in this report, which has sufficient reinforcement density and cross-sectional size to represent an NPP containment wall. Details on how a suitably thick concrete specimen was constructed are presented, including the construction materials, final nominal design schematic, as well as formwork and rigging required to safely meet the desired dimensions of the concrete structure. The report also details the type and methods of forming the concrete specimen as well as information on how the rebar and simulated defects were embedded. Details on how the resulting specimen was transported, safely anchored, and marked to allow access for systematic comparative NDE testing of defects in a representative NPP containment wall concrete specimen are also given. Data collection using the MIRA Ultrasonic NDE equipment and

  20. Sequencing and analysis of an Irish human genome.

    LENUS (Irish Health Repository)

    Tong, Pin

    2010-01-01

    Recent studies generating complete human sequences from Asian, African and European subgroups have revealed population-specific variation and disease susceptibility loci. Here, choosing a DNA sample from a population of interest due to its relative geographical isolation and genetic impact on further populations, we extend the above studies through the generation of 11-fold coverage of the first Irish human genome sequence.

  1. Exome Sequence Analysis of 14 Families With High Myopia

    DEFF Research Database (Denmark)

    Kloss, Bethany A.; Tompson, Stuart W.; Whisenhunt, Kristina N.

    2017-01-01

    Purpose: To identify causal gene mutations in 14 families with autosomal dominant (AD) high myopia using exome sequencing. Methods: Select individuals from 14 large Caucasian families with high myopia were exome sequenced. Gene variants were filtered to identify potential pathogenic changes. Sang...

  2. Database-driven primary analysis of raw sequencing data

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention relates to methods for identifying the source of a biological sequence containing sample from raw sequencing reads. The method may be used to identify the source of unknown DNA and can be used for diagnostic, biodefense, food safety and quality, and hygiene applications...

  3. Accelerating next generation sequencing data analysis with system level optimizations.

    Science.gov (United States)

    Kathiresan, Nagarajan; Temanni, Ramzi; Almabrazi, Hakeem; Syed, Najeeb; Jithesh, Puthen V; Al-Ali, Rashid

    2017-08-22

    Next generation sequencing (NGS) data analysis is highly compute intensive. In-memory computing, vectorization, bulk data transfer, CPU frequency scaling are some of the hardware features in the modern computing architectures. To get the best execution time and utilize these hardware features, it is necessary to tune the system level parameters before running the application. We studied the GATK-HaplotypeCaller which is part of common NGS workflows, that consume more than 43% of the total execution time. Multiple GATK 3.x versions were benchmarked and the execution time of HaplotypeCaller was optimized by various system level parameters which included: (i) tuning the parallel garbage collection and kernel shared memory to simulate in-memory computing, (ii) architecture-specific tuning in the PairHMM library for vectorization, (iii) including Java 1.8 features through GATK source code compilation and building a runtime environment for parallel sorting and bulk data transfer (iv) the default 'on-demand' mode of CPU frequency is over-clocked by using 'performance-mode' to accelerate the Java multi-threads. As a result, the HaplotypeCaller execution time was reduced by 82.66% in GATK 3.3 and 42.61% in GATK 3.7. Overall, the execution time of NGS pipeline was reduced to 70.60% and 34.14% for GATK 3.3 and GATK 3.7 respectively.

  4. The sequence and analysis of a Chinese pig genome

    Directory of Open Access Journals (Sweden)

    Fang Xiaodong

    2012-11-01

    Full Text Available Abstract Background The pig is an economically important food source, amounting to approximately 40% of all meat consumed worldwide. Pigs also serve as an important model organism because of their similarity to humans at the anatomical, physiological and genetic level, making them very useful for studying a variety of human diseases. A pig strain of particular interest is the miniature pig, specifically the Wuzhishan pig (WZSP, as it has been extensively inbred. Its high level of homozygosity offers increased ease for selective breeding for specific traits and a more straightforward understanding of the genetic changes that underlie its biological characteristics. WZSP also serves as a promising means for applications in surgery, tissue engineering, and xenotransplantation. Here, we report the sequencing and analysis of an inbreeding WZSP genome. Results Our results reveal some unique genomic features, including a relatively high level of homozygosity in the diploid genome, an unusual distribution of heterozygosity, an over-representation of tRNA-derived transposable elements, a small amount of porcine endogenous retrovirus, and a lack of type C retroviruses. In addition, we carried out systematic research on gene evolution, together with a detailed investigation of the counterparts of human drug target genes. Conclusion Our results provide the opportunity to more clearly define the genomic character of pig, which could enhance our ability to create more useful pig models.

  5. Analysis of expressed sequence tags from the Ulva prolifera (Chlorophyta)

    Science.gov (United States)

    Niu, Jianfeng; Hu, Haiyan; Hu, Songnian; Wang, Guangce; Peng, Guang; Sun, Song

    2010-01-01

    In 2008, a green tide broke out before the sailing competition of the 29th Olympic Games in Qingdao. The causative species was determined to be Enteromorpha prolifera ( Ulva prolifera O. F. Müller), a familiar green macroalga along the coastline of China. Rapid accumulation of a large biomass of floating U. prolifera prompted research on different aspects of this species. In this study, we constructed a nonnormalized cDNA library from the thalli of U. prolifera and acquired 10 072 high-quality expressed sequence tags (ESTs). These ESTs were assembled into 3 519 nonredundant gene groups, including 1 446 clusters and 2 073 singletons. After annotation with the nr database, a large number of genes were found to be related with chloroplast and ribosomal protein, GO functional classification showed 1 418 ESTs participated in photosynthesis and 1 359 ESTs were responsible for the generation of precursor metabolites and energy. In addition, rather comprehensive carbon fixation pathways were found in U. prolifera using KEGG. Some stress-related and signal transduction-related genes were also found in this study. All the evidences displayed that U. prolifera had substance and energy foundation for the intense photosynthesis and the rapid proliferation. Phylogenetic analysis of cytochrome c oxidase subunit I revealed that this green-tide causative species is most closely affiliated to Pseudendoclonium akinetum (Ulvophyceae).

  6. Preliminary Coupling of MATRA Code for Multi-physics Analysis

    International Nuclear Information System (INIS)

    Kim, Seongjin; Choi, Jinyoung; Yang, Yongsik; Kwon, Hyouk; Hwang, Daehyun

    2014-01-01

    The boundary conditions such as the inlet temperature, mass flux, averaged heat flux, power distributions of the rods, and core geometry is given by constant values or functions of time. These conditions are separately calculated and provided by other codes, such as a neutronics or a system codes, into the MATRA code. In addition, the coupling of several codes in the different physics field is focused and embodied. In this study, multiphysics coupling methods were developed for a subchannel code (MATRA) with neutronics codes (MASTER, DeCART) and a fuel performance code (FRAPCON-3). Preliminary evaluation results for representative sample cases are presented. The MASTER and DeCART codes provide the power distribution of the rods in the core to the MATRA code. In case of the FRAPCON-3 code, the variation of the rod diameter induced by the thermal expansion is yielded and provided. The MATRA code transfers the thermal-hydraulic conditions that each code needs. Moreover, the coupling method with each code is described

  7. Seismic response of transamerical building. I. Data and preliminary analysis

    Science.gov (United States)

    Celebi, M.; Safak, E.

    1991-01-01

    The objective of this paper is to present preliminary analyses of a set of acceleration response records obtained during the October 17, 1989 Loma Prieta earthquake (Ms = 7.1) from the 60-story vertically tapered, pyramid-shaped Trans-america Building-a landmark of San Francisco. The building was instrumented in 1985 with 22 channels of synchronized sensors consisting of 13 uniaxial accelerometers deployed throughout the structure and connected to a central recording system and three triaxial strong-motion accelerographs at three different levels of the structure. No free-field accelerographs are at the site. The acceleration records permit the study of the behavior of this unique structure. The predominant translational response of the building and the associated frequency at approximately 0.28 Hz are identified from the records and their Fourier amplitude spectra. The records do not indicate any significant torsional motion. However, there is rocking type soil-structure interaction, and an associated frequency of approximately 2.0 Hz is identified from the Fourier amplitude spectra of the differential motions between the ground level and that at the basement. In addition, the response spectra for the basement motions indicate significant resonance in both directions at a period of approximately 0.5 seconds.

  8. Preliminary Analysis of Species Partitioning in the DWPF Melter

    Energy Technology Data Exchange (ETDEWEB)

    Choi, A. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Kesterson, M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Johnson, F. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); McCabe, D. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-07-15

    The work described in this report is preliminary in nature since its goal was to demonstrate the feasibility of estimating the off-gas entrainment rates from the Defense Waste Processing Facility (DWPF) melter based on a simple mass balance using measured feed and glass pour stream compositions and timeaveraged melter operating data over the duration of one canister-filling cycle. The only case considered in this study involved the SB6 pour stream sample taken while Canister #3472 was being filled over a 20-hour period on 12/20/2010, approximately three months after the bubblers were installed. The analytical results for that pour stream sample provided the necessary glass composition data for the mass balance calculations. To estimate the “matching” feed composition, which is not necessarily the same as that of the Melter Feed Tank (MFT) batch being fed at the time of pour stream sampling, a mixing model was developed involving three preceding MFT batches as well as the one being fed at that time based on the assumption of perfect mixing in the glass pool but with an induction period to account for the process delays involved in the calcination/fusion step in the cold cap and the melter turnover.

  9. Crystallization and preliminary crystallographic analysis of merohedrally twinned crystals of MJ0729, a CBS-domain protein from Methanococcus jannaschii

    International Nuclear Information System (INIS)

    Fernández-Millán, Pablo; Kortazar, Danel; Lucas, María; Martínez-Chantar, María Luz; Astigarraga, Egoitz; Fernández, José Andrés; Sabas, Olatz; Albert, Armando; Mato, Jose M.; Martínez-Cruz, Luis Alfonso

    2008-01-01

    Trigonal crystals of MJ0729 showing different degrees of merohedral twinning that may vary from perfect hemihedral twinning to perfect tetartohedral twinning were obtained upon slight variation of the pH. CBS domains are small protein motifs, usually associated in tandem, that are implicated in binding to adenosyl groups. Several genetic diseases in humans have been associated with mutations in CBS sequences, which has made them very promising targets for rational drug design. Trigonal crystals of the CBS-domain protein MJ0729 from Methanococcus jannaschii were grown by the vapour-diffusion method at acidic pH. Preliminary analysis of nine X-ray diffraction data sets using Yeates statistics and Britton plots showed that slight variation in the pH as well as in the buffer used in the crystallization experiments led to crystals with different degrees of merohedral twinning that may vary from perfect hemihedral twinning to perfect tetartohedral twinning

  10. Fukushima Daiichi unit 1 uncertainty analysis--Preliminary selection of uncertain parameters and analysis methodology

    Energy Technology Data Exchange (ETDEWEB)

    Cardoni, Jeffrey N.; Kalinich, Donald A.

    2014-02-01

    Sandia National Laboratories (SNL) plans to conduct uncertainty analyses (UA) on the Fukushima Daiichi unit (1F1) plant with the MELCOR code. The model to be used was developed for a previous accident reconstruction investigation jointly sponsored by the US Department of Energy (DOE) and Nuclear Regulatory Commission (NRC). However, that study only examined a handful of various model inputs and boundary conditions, and the predictions yielded only fair agreement with plant data and current release estimates. The goal of this uncertainty study is to perform a focused evaluation of uncertainty in core melt progression behavior and its effect on key figures-of-merit (e.g., hydrogen production, vessel lower head failure, etc.). In preparation for the SNL Fukushima UA work, a scoping study has been completed to identify important core melt progression parameters for the uncertainty analysis. The study also lays out a preliminary UA methodology.

  11. Comparative sequence analysis of acid sensitive/resistance proteins in Escherichia coli and Shigella flexneri

    Science.gov (United States)

    Manikandan, Selvaraj; Balaji, Seetharaaman; Kumar, Anil; Kumar, Rita

    2007-01-01

    The molecular basis for the survival of bacteria under extreme conditions in which growth is inhibited is a question of great current interest. A preliminary study was carried out to determine residue pattern conservation among the antiporters of enteric bacteria, responsible for extreme acid sensitivity especially in Escherichia coli and Shigella flexneri. Here we found the molecular evidence that proved the relationship between E. coli and S. flexneri. Multiple sequence alignment of the gadC coded acid sensitive antiporter showed many conserved residue patterns at regular intervals at the N-terminal region. It was observed that as the alignment approaches towards the C-terminal, the number of conserved residues decreases, indicating that the N-terminal region of this protein has much active role when compared to the carboxyl terminal. The motif, FHLVFFLLLGG, is well conserved within the entire gadC coded protein at the amino terminal. The motif is also partially conserved among other antiporters (which are not coded by gadC) but involved in acid sensitive/resistance mechanism. Phylogenetic cluster analysis proves the relationship of Escherichia coli and Shigella flexneri. The gadC coded proteins are converged as a clade and diverged from other antiporters belongs to the amino acid-polyamine-organocation (APC) superfamily. PMID:21670792

  12. Preliminary Experimental Analysis of Soil Stabilizers for Contamination Control

    International Nuclear Information System (INIS)

    Lagos, L.; Varona, J.; Zidan, A.; Gudavalli, R.; Wu, Kuang-His

    2006-01-01

    A major focus of Department of Energy's (DOE's) environmental management mission at the Hanford site involves characterizing and remediating contaminated soil and groundwater; stabilizing contaminated soil; remediating disposal sites; decontaminating and decommissioning structures, and demolishing former plutonium production process buildings, nuclear reactors, and separation plants; maintaining inactive waste sites; transitioning facilities into the surveillance and maintenance program; and mitigating effects to biological and cultural resources from site development and environmental cleanup and restoration activities. For example, a total of 470,914 metric tons of contaminated soil from 100 Areas remediation activities were disposed at the Environmental Restoration Disposal Facility (ERDF) during 2004. The Applied Research Center (ARC) at Florida International University (FIU) is supporting the Hanford's site remediation program by analyzing the effectiveness of several soil stabilizers (fixatives) for contamination control during excavation activities. The study is focusing on determining the effects of varying soil conditions, temperature, humidity and wind velocity on the effectiveness of the candidate stabilizers. The test matrix consists of a soil penetration-depth study, wind tunnel experiments for determination of threshold velocity, and temperature and moisture-controlled drying/curing experiments. These three set of experiments are designed to verify performance metrics, as well as provide insight into what fundamental forces are altered by the use of the stabilizer. This paper only presents the preliminary results obtained during wind tunnel experiments using dry Hanford soil samples (with 2.7% moisture by weight). These dry soil samples were exposed to varying wind speeds from 2.22 m/sec to 8.88 m/sec. Furthermore, airborne particulate data was collected for the dry Hanford soil experiments using an aerosol analyzer instrument. (authors)

  13. Preliminary study of elemental analysis of hydroxyapatite used neutron activation analysis method

    International Nuclear Information System (INIS)

    Yustinus Purwamargapratala; Rina Mulyaningsih

    2010-01-01

    Preliminary study has been carried out elemental analysis of hydroxyapatite synthesized using the method of neutron activation analysis. Hydroxyapatite is the main component constituent of bones and teeth which can be synthesized from limestone and phosphoric acid. Hydroxyapatite can be used as a bone substitute material and human and animal teeth. Tests on the metal content is necessary to prevent the risk of damage to bones and teeth due to contamination. Results of analysis using neutron activation analysis method with samples irradiated at the neutron flux 10"3 n.det"-"1cm"-"2 for one minute, the impurities of Al (48.60±6.47 mg/kg), CI (38.00±7.47 mg/kg), Mn (1.05±0.19 mg/kg), and Mg (2095.30±203.66 mg/kg), were detected, whereas with irradiation time for 10 minutes and 40 minutes with a time decay of three days there were K (103.89 ± 26.82 mg/kg), Br (1617.06 ± 193.66 mg/kg), and Na (125.10±9.57 mg/kg). These results indicate that there is impurity Al, CI, Mn, Mg, Br, K and Na, although in very small amounts and do not cause damage to bones and teeth. (author)

  14. Event Sequence Analysis of the Air Intelligence Agency Information Operations Center Flight Operations

    National Research Council Canada - National Science Library

    Larsen, Glen

    1998-01-01

    This report applies Event Sequence Analysis, methodology adapted from aircraft mishap investigation, to an investigation of the performance of the Air Intelligence Agency's Information Operations Center (IOC...

  15. Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human.

    Science.gov (United States)

    Magness, Charles L; Fellin, P Campion; Thomas, Matthew J; Korth, Marcus J; Agy, Michael B; Proll, Sean C; Fitzgibbon, Matthew; Scherer, Christina A; Miner, Douglas G; Katze, Michael G; Iadonato, Shawn P

    2005-01-01

    We report the initial sequencing and comparative analysis of the Macaca mulatta transcriptome. Cloned sequences from 11 tissues, nine animals, and three species (M. mulatta, M. fascicularis, and M. nemestrina) were sampled, resulting in the generation of 48,642 sequence reads. These data represent an initial sampling of the putative rhesus orthologs for 6,216 human genes. Mean nucleotide diversity within M. mulatta and sequence divergence among M. fascicularis, M. nemestrina, and M. mulatta are also reported.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-02-01

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

  17. Sequence analysis of mitochondrial 16S ribosomal RNA gene ...

    Indian Academy of Sciences (India)

    Unknown

    For the understanding of their vectorial capacity, identification of disease carrying and refractory strains is essential. ... been widely used for phylogenetic studies and sequence differences in ... In order to fill up the internal gap, a new set.

  18. simple sequence repeat (SSR) markers in genetic analysis of

    African Journals Online (AJOL)

    Yomi

    2012-08-28

    1998). Cross- species amplification of soybean (Glycine max) simple sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol. Biol. Evol. 15:1275-1287.

  19. Sequence and expression analysis of gaps in human chromosome 20

    DEFF Research Database (Denmark)

    Minocherhomji, Sheroy; Seemann, Stefan; Mang, Yuan

    2012-01-01

    /or overlap disease-associated loci, including the DLGAP4 locus. In this study, we sequenced ~99% of all three unfinished gaps on human chr 20, determined their complete genomic sizes and assessed epigenetic profiles using a combination of Sanger sequencing, mate pair paired-end high-throughput sequencing......The finished human genome-assemblies comprise several hundred un-sequenced euchromatic gaps, which may be rich in long polypurine/polypyrimidine stretches. Human chromosome 20 (chr 20) currently has three unfinished gaps remaining on its q-arm. All three gaps are within gene-dense regions and...... and chromatin, methylation and expression analyses. We found histone 3 trimethylated at Lysine 27 to be distributed across all three gaps in immortalized B-lymphocytes. In one gap, five novel CpG islands were predominantly hypermethylated in genomic DNA from peripheral blood lymphocytes and human cerebellum...

  20. Identification and characterization of earthquake clusters: a comparative analysis for selected sequences in Italy

    Science.gov (United States)

    Peresan, Antonella; Gentili, Stefania

    2017-04-01

    Identification and statistical characterization of seismic clusters may provide useful insights about the features of seismic energy release and their relation to physical properties of the crust within a given region. Moreover, a number of studies based on spatio-temporal analysis of main-shocks occurrence require preliminary declustering of the earthquake catalogs. Since various methods, relying on different physical/statistical assumptions, may lead to diverse classifications of earthquakes into main events and related events, we aim to investigate the classification differences among different declustering techniques. Accordingly, a formal selection and comparative analysis of earthquake clusters is carried out for the most relevant earthquakes in North-Eastern Italy, as reported in the local OGS-CRS bulletins, compiled at the National Institute of Oceanography and Experimental Geophysics since 1977. The comparison is then extended to selected earthquake sequences associated with a different seismotectonic setting, namely to events that occurred in the region struck by the recent Central Italy destructive earthquakes, making use of INGV data. Various techniques, ranging from classical space-time windows methods to ad hoc manual identification of aftershocks, are applied for detection of earthquake clusters. In particular, a statistical method based on nearest-neighbor distances of events in space-time-energy domain, is considered. Results from clusters identification by the nearest-neighbor method turn out quite robust with respect to the time span of the input catalogue, as well as to minimum magnitude cutoff. The identified clusters for the largest events reported in North-Eastern Italy since 1977 are well consistent with those reported in earlier studies, which were aimed at detailed manual aftershocks identification. The study shows that the data-driven approach, based on the nearest-neighbor distances, can be satisfactorily applied to decompose the seismic

  1. DELIMINATE--a fast and efficient method for loss-less compression of genomic sequences: sequence analysis.

    Science.gov (United States)

    Mohammed, Monzoorul Haque; Dutta, Anirban; Bose, Tungadri; Chadaram, Sudha; Mande, Sharmila S

    2012-10-01

    An unprecedented quantity of genome sequence data is currently being generated using next-generation sequencing platforms. This has necessitated the development of novel bioinformatics approaches and algorithms that not only facilitate a meaningful analysis of these data but also aid in efficient compression, storage, retrieval and transmission of huge volumes of the generated data. We present a novel compression algorithm (DELIMINATE) that can rapidly compress genomic sequence data in a loss-less fashion. Validation results indicate relatively higher compression efficiency of DELIMINATE when compared with popular general purpose compression algorithms, namely, gzip, bzip2 and lzma. Linux, Windows and Mac implementations (both 32 and 64-bit) of DELIMINATE are freely available for download at: http://metagenomics.atc.tcs.com/compression/DELIMINATE. sharmila@atc.tcs.com Supplementary data are available at Bioinformatics online.

  2. Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform.

    Directory of Open Access Journals (Sweden)

    Hideyuki Tamaki

    Full Text Available BACKGROUND: 16S rRNA gene pyrosequencing approach has revolutionized studies in microbial ecology. While primer selection and short read length can affect the resulting microbial community profile, little is known about the influence of pyrosequencing methods on the sequencing throughput and the outcome of microbial community analyses. The aim of this study is to compare differences in output, ease, and cost among three different amplicon pyrosequencing methods for the Roche/454 Titanium platform METHODOLOGY/PRINCIPAL FINDINGS: The following three pyrosequencing methods for 16S rRNA genes were selected in this study: Method-1 (standard method is the recommended method for bi-directional sequencing using the LIB-A kit; Method-2 is a new option designed in this study for unidirectional sequencing with the LIB-A kit; and Method-3 uses the LIB-L kit for unidirectional sequencing. In our comparison among these three methods using 10 different environmental samples, Method-2 and Method-3 produced 1.5-1.6 times more useable reads than the standard method (Method-1, after quality-based trimming, and did not compromise the outcome of microbial community analyses. Specifically, Method-3 is the most cost-effective unidirectional amplicon sequencing method as it provided the most reads and required the least effort in consumables management. CONCLUSIONS: Our findings clearly demonstrated that alternative pyrosequencing methods for 16S rRNA genes could drastically affect sequencing output (e.g. number of reads before and after trimming but have little effect on the outcomes of microbial community analysis. This finding is important for both researchers and sequencing facilities utilizing 16S rRNA gene pyrosequencing for microbial ecological studies.

  3. Compilation and analysis of Escherichia coli promoter DNA sequences.

    OpenAIRE

    Hawley, D K; McClure, W R

    1983-01-01

    The DNA sequence of 168 promoter regions (-50 to +10) for Escherichia coli RNA polymerase were compiled. The complete listing was divided into two groups depending upon whether or not the promoter had been defined by genetic (promoter mutations) or biochemical (5' end determination) criteria. A consensus promoter sequence based on homologies among 112 well-defined promoters was determined that was in substantial agreement with previous compilations. In addition, we have tabulated 98 promoter ...

  4. Chemical Analysis of the Moon at the Surveyor VI Landing Site: Preliminary Results.

    Science.gov (United States)

    Turkevich, A L; Patterson, J H; Franzgrote, E J

    1968-06-07

    The alpha-scattering experiment aboard soft-landing Surveyor VI has provided a chemical analysis of the surface of the moon in Sinus Medii. The preliminary results indicate that, within experimental errors, the composition is the same as that found by Surveyor V in Mare Tranquillitatis. This finding suggests that large portions of the lunar maria resemble basalt in composition.

  5. Chemical Analysis of the Moon at the Surveyor VII Landing Site: Preliminary Results.

    Science.gov (United States)

    Turkevich, A L; Franzgrote, E J; Patterson, J H

    1968-10-04

    The alpha-scattering experiment aboard Surveyor VII has provided a chemical analysis of the moon in the area of the crater Tycho. The preliminary results indicate a chemical composition similar to that already found at two mare sites, but with a lower concentration of elements of the iron group (titanium through copper).

  6. Current Mooring Design in Partner WECs and Candidates for Preliminary Analysis

    DEFF Research Database (Denmark)

    Thomsen, Jonas Bjerg; Ferri, Francesco; Kofoed, Jens Peter

    This report is the combined report of Commercial Milestone "CM1: Design and Cost of Current Mooring Solutions of Partner WECs" and Milestone "M3: Mooring Solutions for Preliminary Analysis" of the EUDP project "Mooring Solutions for Large Wave Energy Converters". The report covers a description o...

  7. ANSI/ASHRAE/IES Standard 90.1-2013 Preliminary Determination: Quantitative Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Halverson, Mark A.; Rosenberg, Michael I.; Wang, Weimin; Zhang, Jian; Mendon, Vrushali V.; Athalye, Rahul A.; Xie, YuLong; Hart, Reid; Goel, Supriya

    2014-03-01

    This report provides a preliminary quantitative analysis to assess whether buildings constructed according to the requirements of ANSI/ASHRAE/IES Standard 90.1-2013 would result in energy savings compared with buildings constructed to ANSI/ASHRAE/IES Standard 90.1-2010.

  8. Preliminary fire hazard analysis for the PUTDR and TRU trenches in the Solid Waste Burial Ground

    International Nuclear Information System (INIS)

    Gaschott, L.J.

    1995-01-01

    This document represents the Preliminary Fire Hazards Analysis for the Pilot Unvented TRU Drum Retrieval effort and for the Transuranic drum trenches in the low level burial grounds. The FHA was developed in accordance with DOE Order 5480.7A to address major hazards inherent in the facility

  9. A Preliminary Analysis of the Outcomes of Students Assisted by VET FEE-HELP: Summary

    Science.gov (United States)

    National Centre for Vocational Education Research (NCVER), 2015

    2015-01-01

    This summary highlights the key findings from the report "A preliminary analysis of the outcomes of students assisted by VET FEE-HELP". VET FEE-HELP is an income-contingent loan scheme that assists eligible students undertaking certain vocational education training (VET) courses with an approved provider by paying for all or part of…

  10. Expression, purification, crystallization and preliminary X-ray analysis of Aeromonas hydrophilia metallo-β-lactamase

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, Nandini, E-mail: nandini-sharma@merck.com; Toney, Jeffrey H.; Fitzgerald, Paula M. D.

    2005-02-01

    Crystallization and preliminary X-ray analysis of the CphA metallo-β-lactamase from A. hydrophilia are described. The crystals belonged to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 40.75, b = 42.05, c = 128.88 Å, and diffract to 1.8 Å.

  11. Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase.

    Science.gov (United States)

    Delong, Allison K; Wu, Mingham; Bennett, Diane; Parkin, Neil; Wu, Zhijin; Hogan, Joseph W; Kantor, Rami

    2012-08-01

    Access to antiretroviral therapy is increasing globally and drug resistance evolution is anticipated. Currently, protease (PR) and reverse transcriptase (RT) sequence generation is increasing, including the use of in-house sequencing assays, and quality assessment prior to sequence analysis is essential. We created a computational HIV PR/RT Sequence Quality Analysis Tool (SQUAT) that runs in the R statistical environment. Sequence quality thresholds are calculated from a large dataset (46,802 PR and 44,432 RT sequences) from the published literature ( http://hivdb.Stanford.edu ). Nucleic acid sequences are read into SQUAT, identified, aligned, and translated. Nucleic acid sequences are flagged if with >five 1-2-base insertions; >one 3-base insertion; >one deletion; >six PR or >18 RT ambiguous bases; >three consecutive PR or >four RT nucleic acid mutations; >zero stop codons; >three PR or >six RT ambiguous amino acids; >three consecutive PR or >four RT amino acid mutations; >zero unique amino acids; or 15% genetic distance from another submitted sequence. Thresholds are user modifiable. SQUAT output includes a summary report with detailed comments for troubleshooting of flagged sequences, histograms of pairwise genetic distances, neighbor joining phylogenetic trees, and aligned nucleic and amino acid sequences. SQUAT is a stand-alone, free, web-independent tool to ensure use of high-quality HIV PR/RT sequences in interpretation and reporting of drug resistance, while increasing awareness and expertise and facilitating troubleshooting of potentially problematic sequences.

  12. Preliminary safety analysis of unscrammed events for KLFR

    International Nuclear Information System (INIS)

    Kim, S.J.; Ha, G.S.

    2005-01-01

    The report presents the design features of KLFR; Safety Analysis Code; steady-state calculation results and analysis results of unscrammed events. The calculations of the steady-state and unscrammed events have been performed for the conceptual design of KLFR using SSC-K code. UTOP event results in no fuel damage and no centre-line melting. The inherent safety features are demonstrated through the analysis of ULOHS event. Although the analysis of ULOF has much uncertainties in the pump design, the analysis results show the inherent safety characteristics. 6% flow of rated flow of natural circulation is formed in the case of ULOF. In the metallic fuel rod, the cladding temperature is somewhat high due to the low heat transfer coefficient of lead. ULOHS event should be considered in design of RVACS for long-term cooling

  13. 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.

  14. REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

    Science.gov (United States)

    Leonard, Guy; Stevens, Jamie R.; Richards, Thomas A.

    2009-01-01

    The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends. PMID:19812722

  15. REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

    Directory of Open Access Journals (Sweden)

    Guy Leonard

    2009-01-01

    Full Text Available The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment fi le, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree fi les (with a user-defined combination of species name and/or database accession number. Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file and generation of species and accession number lists for use in supplementary materials or figure legends.

  16. Preliminary design analysis of the ALT-II limiter for TEXTOR

    International Nuclear Information System (INIS)

    Koski, J.A.; Boyd, R.D.; Kempka, S.M.; Romig, A.D. Jr.; Smith, M.F.; Watson, R.D.; Whitley, J.B.; Conn, R.W.; Grotz, S.P.

    1984-01-01

    Installation of a large toroidal belt pump limiter, Advanced Limiter Test II (ALT-II), on the TEXTOR tokamak at Juelich, FRG is anticipated for early 1986. This paper discusses the preliminary mechanical design and materials considerations undertaken as part of the feasibility study phase for ALT-II. Since the actively cooled limiter blade is the component in direct contact with the plasma edge, and thus subject to the severe plasma environment, most preliminary design efforts have concentrated on analysis of the blade. The screening process which led to the recommended preliminary design consisting of a dispersion strenghthened copper or OFHC copper cover plate over an austenitic stainless steel base plate is discussed. A 1 to 3 mm thick low atomic number coating consisting of a graded plasma-sprayed Silicon Carbide-Aluminium composite is recommended subject to further experiment and evaluation. Thermal-hydraulic and stress analyses of the limiter blade are also discussed. (orig.)

  17. Corrective emotional experience in an integrative affect-focused therapy: Building a preliminary model using task analysis.

    Science.gov (United States)

    Nakamura, Kaori; Iwakabe, Shigeru

    2018-03-01

    The present study constructed a preliminary process model of corrective emotional experience (CEE) in an integrative affect-focused therapy. Task analysis was used to analyse 6 in-session events taken from 6 Japanese clients who worked with an integrative affect-focused therapist. The 6 events included 3 successful CEEs and 3 partially successful CEEs for comparison. A rational-empirical model of CEE was generated, which consisted of two parallel client change processes, intrapersonal change and interpersonal change, and the therapist interventions corresponding to each process. Therapist experiential interventions and therapist affirmation facilitated both intrapersonal and interpersonal change processes, whereas his relational interventions were associated with the interpersonal change process. The partially successful CEEs were differentiated by the absence of the component of core painful emotions or negative beliefs in intrapersonal change process, which seemed crucial for the interpersonal change process to develop. CEE is best represented by a preliminary model that depicts two parallel yet interacting change processes. Intrapersonal change process is similar to the sequence of change described by the emotional processing model (Pascual-Leone & Greenberg, ), whereas interpersonal change process is a unique contribution of this study. Interpersonal change process was facilitated when the therapist's active stance and use of immediacy responses to make their relational process explicit allowed a shared exploration. Therapist affirmation bridged intrapersonal change to interpersonal change by promoting an adaptive sense of self in clients and forging a deeper emotional connection between the two. Copyright © 2017 John Wiley & Sons, Ltd.

  18. Sequencing and analysis of the Mediterranean amphioxus (Branchiostoma lanceolatum transcriptome.

    Directory of Open Access Journals (Sweden)

    Silvan Oulion

    Full Text Available BACKGROUND: The basally divergent phylogenetic position of amphioxus (Cephalochordata, as well as its conserved morphology, development and genetics, make it the best proxy for the chordate ancestor. Particularly, studies using the amphioxus model help our understanding of vertebrate evolution and development. Thus, interest for the amphioxus model led to the characterization of both the transcriptome and complete genome sequence of the American species, Branchiostoma floridae. However, recent technical improvements allowing induction of spawning in the laboratory during the breeding season on a daily basis with the Mediterranean species Branchiostoma lanceolatum have encouraged European Evo-Devo researchers to adopt this species as a model even though no genomic or transcriptomic data have been available. To fill this need we used the pyrosequencing method to characterize the B. lanceolatum transcriptome and then compared our results with the published transcriptome of B. floridae. RESULTS: Starting with total RNA from nine different developmental stages of B. lanceolatum, a normalized cDNA library was constructed and sequenced on Roche GS FLX (Titanium mode. Around 1.4 million of reads were produced and assembled into 70,530 contigs (average length of 490 bp. Overall 37% of the assembled sequences were annotated by BlastX and their Gene Ontology terms were determined. These results were then compared to genomic and transcriptomic data of B. floridae to assess similarities and specificities of each species. CONCLUSION: We obtained a high-quality amphioxus (B. lanceolatum reference transcriptome using a high throughput sequencing approach. We found that 83% of the predicted genes in the B. floridae complete genome sequence are also found in the B. lanceolatum transcriptome, while only 41% were found in the B. floridae transcriptome obtained with traditional Sanger based sequencing. Therefore, given the high degree of sequence conservation

  19. ORNL: PWR-BDHT analysis procedure, a preliminary overview

    International Nuclear Information System (INIS)

    Cliff, S.B.

    1978-01-01

    The computer programs currently used in the analysis of the ORNL-PWR Blowdown Heat Transfer Separate-Effects Program are overviewed. The current linkages and relationships among the programs are given along with general comments about the future directions of some of these programs. The overview is strictly from the computer science point of view with only minimal information concerning the engineering aspects of the analysis procedure

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

    Directory of Open Access Journals (Sweden)

    Annika Brinkmann

    2017-11-01

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

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

    Science.gov (United States)

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

    2017-11-01

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

  2. Failure mode analysis of preliminary design of ITER divertor impurity monitor

    International Nuclear Information System (INIS)

    Kitazawa, Sin-iti; Ogawa, Hiroaki

    2016-01-01

    Highlights: • Divertor impurity influx monitor for ITER (DIM) is procured by JADA. • DIM is designed to observe light from nuclear fusion plasma directly. • DIM is under preliminary design phase. • Failure mode of DIM was prepared for RAMI analysis. • RAMI analysis on DIM was performed to reduce technical risks. - Abstract: The objective of the divertor impurity influx monitor (DIM) for ITER is to measure the parameters of impurities and hydrogen isotopes (tritium, deuterium, and hydrogen) in divertor plasma using visible and UV spectroscopic techniques in the 200–1000 nm wavelength range. In ITER, special provisions are required to ensure accuracy and full functionality of the diagnostic components under harsh conditions (high temperature, high magnetic field, high vacuum condition, and high radiation field). Japan Domestic Agency is preparing the preliminary design of the ITER DIM system, which will be installed in the upper, equatorial and lower ports. The optical and mechanical designs of the DIM are conducted to fit ITER’s requirements. The optical and mechanical designs meet the requirements of spatial resolution. Some auxiliary systems were examined via prototyping. The preliminary design of the ITER DIM system was evaluated by RAMI analysis. The availability of the designed system is adequately high to satisfy the project requirements. However, some equipment does not have certain designs, and this may cause potential technical risks. The preliminary design should be modified to reduce technical risks and to prepare the final design.

  3. Summary of the Preliminary Analysis of Savannah River Depleted Uranium Trioxide

    International Nuclear Information System (INIS)

    2010-01-01

    This report summarizes a preliminary special analysis of the Savannah River Depleted Uranium Trioxide waste stream (SVRSURANIUM03, Revision 2). The analysis is considered preliminary because a final waste profile has not been submitted for review. The special analysis is performed to determine the acceptability of the waste stream for shallow land burial at the Area 5 Radioactive Waste Management Site (RWMS) at the Nevada National Security Site (NNSS). The Savannah River Depleted Uranium Trioxide waste stream requires a special analysis because the waste stream's sum of fractions exceeds one. The 99Tc activity concentration is 98 percent of the NNSS Waste Acceptance Criteria and the largest single contributor to the sum of fractions.

  4. Bioelectrical impedance analysis for bovine milk: Preliminary results

    Science.gov (United States)

    Bertemes-Filho, P.; Valicheski, R.; Pereira, R. M.; Paterno, A. S.

    2010-04-01

    This work reports the investigation and analysis of bovine milk quality by using biological impedance measurements using electrical impedance spectroscopy (EIS). The samples were distinguished by a first chemical analysis using Fourier transform midinfrared spectroscopy (FTIR) and flow citometry. A set of milk samples (100ml each) obtained from 17 different cows in lactation with and without mastitis were analyzed with the proposed technique using EIS. The samples were adulterated by adding distilled water and hydrogen peroxide in a controlled manner. FTIR spectroscopy and flow cytometry were performed, and impedance measurements were made in a frequency range from 500Hz up to 1MHz with an implemented EIS system. The system's phase shift was compensated by measuring saline solutions. It was possible to show that the results obtained with the Bioelectrical Impedance Analysis (BIA) technique may detect changes in the milk caused by mastitis and the presence of water and hydrogen peroxide in the bovine milk.

  5. Magnetization transfer analysis of cartilage repair tissue: a preliminary study

    International Nuclear Information System (INIS)

    Palmieri, F.; Keyzer, F. de; Maes, F.; Breuseghem, I. van

    2006-01-01

    To evaluate the magnetization transfer ratio (MTR) after two different cartilage repair procedures, and to compare these data with the MTR of normal cartilage. Twenty-seven patients with a proven cartilage defect were recruited: 13 were treated with autologous chondrocyte implantation (ACI) and 14 were treated with the microfracture technique (MFR). All patients underwent MRI examinations with MT-sequences before the surgical treatment, after 12 months (26 patients) and after 24 months (11 patients). Eleven patients received a complete follow-up study at all three time points (five of the ACI group and six of the MFR group). All images were transferred to a workstation to calculate MTR images. For every MT image set, different ROIs were delineated by two radiologists. Means were calculated per ROI type in the different time frames and in both groups of cartilage repair. The data were analyzed with unpaired t- and ANOVA tests, and by calculating Pearson's correlation coefficient. No significant differences were found in the MTR of fatty bone marrow, muscle and normal cartilage in the different time frames. There was a significant but small difference between the MTR of normal cartilage and the cartilage repair area after 12 months for both procedures. After 24 months, the MTR of ACI repaired cartilage (0.31±0.07) was not significantly different from normal cartilage MTR (0.34±0.05). The MTR of MFR repaired cartilage (0.28±0.02), still showed a significant difference from normal cartilage. The differences between damaged and repaired cartilage MTR are too small to enable MT-imaging to be a useful tool for postoperative follow-up of cartilage repair procedures. There is, however, an evolution towards normal MTR-values in the cartilage repair tissue (especially after ACI repair). (orig.)

  6. A Preliminary Analysis of a Behavioral Classrooms Needs Assessment

    Science.gov (United States)

    Leaf, Justin B.; Leaf, Ronald; McCray, Cynthia; Lamkins, Carol; Taubman, Mitchell; McEachin, John; Cihon, Joseph H.

    2016-01-01

    Today many special education classrooms implement procedures based upon the principles of Applied Behavior Analysis (ABA) to establish educationally relevant skills and decrease aberrant behaviors. However, it is difficult for school staff and consultants to evaluate the implementation of various components of ABA and general classroom set up. In…

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

    International Nuclear Information System (INIS)

    Grimm, Bertrand

    1990-01-01

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

  8. Preliminary analysis of a 1:4 scale prestressed concrete containment vessel model

    International Nuclear Information System (INIS)

    Dameron, R.A.; Rashid, Y.R.; Luk, V.K.; Hessheimer, M.F.

    1997-01-01

    Sandia National Laboratories is conducting a research program to investigate the integrity of nuclear containment structures. As part of the program Sandia will construct an instrumented 1:4 scale model of a prestressed concrete containment vessel (PCCV) for pressurized water reactors (PWR), which will be pressure tested up to its ultimate capacity. One of the key program objectives is to develop validated methods to predict the structural performance of containment vessels when subjected to beyond design basis loadings. Analytical prediction of structural performance requires a stepwise, systematic approach that addresses all potential failure modes. The analysis effort includes two and three-dimensional nonlinear finite element analyses of the PCCV test model to evaluate its structural performance under very high internal pressurization. Such analyses have been performed using the nonlinear concrete constitutive model, ANACAP-U, in conjunction with the ABAQUS general purpose finite element code. The analysis effort is carried out in three phases: preliminary analysis; pretest prediction; and post-test data interpretation and analysis evaluation. The preliminary analysis phase serves to provide instrumentation support and identify candidate failure modes. The associated tasks include the preliminary prediction of failure pressure and probable failure locations and the development of models to be used in the detailed failure analyses. This paper describes the modeling approaches and some of the results obtained in the first phase of the analysis effort

  9. Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Gao Zhihong

    2010-07-01

    Full Text Available Abstract Background Expressed Sequence Tag (EST has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047, among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65% and low in the peach (46%, and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species.

  10. Preliminary Geospatial Analysis of Arctic Ocean Hydrocarbon Resources

    Energy Technology Data Exchange (ETDEWEB)

    Long, Philip E.; Wurstner, Signe K.; Sullivan, E. C.; Schaef, Herbert T.; Bradley, Donald J.

    2008-10-01

    Ice coverage of the Arctic Ocean is predicted to become thinner and to cover less area with time. The combination of more ice-free waters for exploration and navigation, along with increasing demand for hydrocarbons and improvements in technologies for the discovery and exploitation of new hydrocarbon resources have focused attention on the hydrocarbon potential of the Arctic Basin and its margins. The purpose of this document is to 1) summarize results of a review of published hydrocarbon resources in the Arctic, including both conventional oil and gas and methane hydrates and 2) develop a set of digital maps of the hydrocarbon potential of the Arctic Ocean. These maps can be combined with predictions of ice-free areas to enable estimates of the likely regions and sequence of hydrocarbon production development in the Arctic. In this report, conventional oil and gas resources are explicitly linked with potential gas hydrate resources. This has not been attempted previously and is particularly powerful as the likelihood of gas production from marine gas hydrates increases. Available or planned infrastructure, such as pipelines, combined with the geospatial distribution of hydrocarbons is a very strong determinant of the temporal-spatial development of Arctic hydrocarbon resources. Significant unknowns decrease the certainty of predictions for development of hydrocarbon resources. These include: 1) Areas in the Russian Arctic that are poorly mapped, 2) Disputed ownership: primarily the Lomonosov Ridge, 3) Lack of detailed information on gas hydrate distribution, and 4) Technical risk associated with the ability to extract methane gas from gas hydrates. Logistics may control areas of exploration more than hydrocarbon potential. Accessibility, established ownership, and leasing of exploration blocks may trump quality of source rock, reservoir, and size of target. With this in mind, the main areas that are likely to be explored first are the Bering Strait and Chukchi

  11. Pilot Workload and Speech Analysis: A Preliminary Investigation

    Science.gov (United States)

    Bittner, Rachel M.; Begault, Durand R.; Christopher, Bonny R.

    2013-01-01

    Prior research has questioned the effectiveness of speech analysis to measure the stress, workload, truthfulness, or emotional state of a talker. The question remains regarding the utility of speech analysis for restricted vocabularies such as those used in aviation communications. A part-task experiment was conducted in which participants performed Air Traffic Control read-backs in different workload environments. Participant's subjective workload and the speech qualities of fundamental frequency (F0) and articulation rate were evaluated. A significant increase in subjective workload rating was found for high workload segments. F0 was found to be significantly higher during high workload while articulation rates were found to be significantly slower. No correlation was found to exist between subjective workload and F0 or articulation rate.

  12. Preliminary analysis of productivity of fruiting fungi on Strzeleckie meadows

    Directory of Open Access Journals (Sweden)

    Barbara Sadowska

    2014-11-01

    Full Text Available Analysis demonstrated that the fresh ahd dry weight as well as the ash content of fungal fruit bodies collected on a forest-surrounded unmown meadow (Stellario-Deschampsietum Freitag 1957 and Caricetum elatae W.Koch 1926 were lower than the same values for a plot of exploited mown meadow and higher than on an exploited unmown meadow (Arrhenatheretum medioeuropaeum (Br.-Bl. Oberd. 1952.

  13. Preliminary analysis on incore performance of nuclear fuel: pt. 4

    International Nuclear Information System (INIS)

    Noh, S.K.; Chang, M.H.; Lee, C.C.; Chung, Y.H.; Kuk, K.Y.; Park, C.Y.; Lee, S.K.

    1981-01-01

    An analysis has been performed for thermal hydraulic design parameters of Wolsung-1 reactor core in steady state with the help of a computer code COBRA-IV-I. The design parameters are coolant enthalpy, flow velocity, coolant quality, pressure and fuel temperature distribution. The maximum power channel has been taken into account in this work. The results appear to be reasonably agreeable with data from PSR'S, with the maximum difference between this work and PSR'S being 4.3%

  14. Job Search Success in Local Labour Markets - A Preliminary Analysis

    OpenAIRE

    Greig, Malcolm; McQuaid, Ronald W.

    2001-01-01

    This study tests the appropriateness of current government employment policies, in particular the New Deal, in targeting specific groups of unemployed jobseekers. A sample of 169 unemployed jobseekers is divided into those who were successful and unsuccessful in finding employment and each group is analysed in terms of their attributes. A factor analysis of these attributes is then carried out in order to develop typical profiles of unsuccessful jobseekers who are possibly in need of special ...

  15. Preliminary analysis of knee stress in Full Extension Landing

    Directory of Open Access Journals (Sweden)

    Majid Davoodi Makinejad

    2013-09-01

    Full Text Available OBJECTIVE: This study provides an experimental and finite element analysis of knee-joint structure during extended-knee landing based on the extracted impact force, and it numerically identifies the contact pressure, stress distribution and possibility of bone-to-bone contact when a subject lands from a safe height. METHODS: The impact time and loads were measured via inverse dynamic analysis of free landing without knee flexion from three different heights (25, 50 and 75 cm, using five subjects with an average body mass index of 18.8. Three-dimensional data were developed from computed tomography scans and were reprocessed with modeling software before being imported and analyzed by finite element analysis software. The whole leg was considered to be a fixed middle-hinged structure, while impact loads were applied to the femur in an upward direction. RESULTS: Straight landing exerted an enormous amount of pressure on the knee joint as a result of the body's inability to utilize the lower extremity muscles, thereby maximizing the threat of injury when the load exceeds the height-safety threshold. CONCLUSIONS: The researchers conclude that extended-knee landing results in serious deformation of the meniscus and cartilage and increases the risk of bone-to-bone contact and serious knee injury when the load exceeds the threshold safety height. This risk is considerably greater than the risk of injury associated with walking downhill or flexion landing activities.

  16. Accident Sequence Precursor Analysis for SGTR by Using Dynamic PSA Approach

    International Nuclear Information System (INIS)

    Lee, Han Sul; Heo, Gyun Young; Kim, Tae Wan

    2016-01-01

    In order to address this issue, this study suggests the sequence tree model to analyze accident sequence systematically. Using the sequence tree model, all possible scenarios which need a specific safety action to prevent the core damage can be identified and success conditions of safety action under complicated situation such as combined accident will be also identified. Sequence tree is branch model to divide plant condition considering the plant dynamics. Since sequence tree model can reflect the plant dynamics, arising from interaction of different accident timing and plant condition and from the interaction between the operator action, mitigation system, and the indicators for operation, sequence tree model can be used to develop the dynamic event tree model easily. Target safety action for this study is a feed-and-bleed (F and B) operation. A F and B operation directly cools down the reactor cooling system (RCS) using the primary cooling system when residual heat removal by the secondary cooling system is not available. In this study, a TLOFW accident and a TLOFW accident with LOCA were the target accidents. Based on the conventional PSA model and indicators, the sequence tree model for a TLOFW accident was developed. Based on the results of a sampling analysis and data from the conventional PSA model, the CDF caused by Sequence no. 26 can be realistically estimated. For a TLOFW accident with LOCA, second accident timings were categorized according to plant condition. Indicators were selected as branch point using the flow chart and tables, and a corresponding sequence tree model was developed. If sampling analysis is performed, practical accident sequences can be identified based on the sequence analysis. If a realistic distribution for the variables can be obtained for sampling analysis, much more realistic accident sequences can be described. Moreover, if the initiating event frequency under a combined accident can be quantified, the sequence tree model

  17. Sequencing and phylogenetic analysis of Herpes simplex virus type ...

    African Journals Online (AJOL)

    For determination of the genetic relationship of HSV-2 glycoprotein G gene (gG) in Iran with those in other countries, DNA fragment of 1100 bp corresponding to gG from six HSV-2 strains have been isolated from human infected sera samples in Iran, it was amplified in PCR system and was sequenced for determining ...

  18. Transcriptome analysis of blueberry using 454 EST sequencing

    Science.gov (United States)

    Blueberry (Vaccinium corymbosum) is a major berry crop in the United States, and one that has great nutritional and economical value. Next generation sequencing methodologies, such as 454, have been demonstrated to be successful and efficient in producing a snap-shot of transcriptional activities du...

  19. Characterization and sequence analysis of cysteine and glycine-rich ...

    African Journals Online (AJOL)

    Tarek

    2011-04-18

    Apr 18, 2011 ... nucleotide alignment of both native buffalo and cattle CSRP3 cDNAs sequences ..... Exon III, Identities = 71/75 (94%), Gaps = 1/75 (1%) Strand=Plus/Plus ... Band MR, Larson JH, Rebeiz M, Green CA, Heyen DW, Donovan J,.

  20. Functional analysis of bipartite begomovirus coat protein promoter sequences

    International Nuclear Information System (INIS)

    Lacatus, Gabriela; Sunter, Garry

    2008-01-01

    We demonstrate that the AL2 gene of Cabbage leaf curl virus (CaLCuV) activates the CP promoter in mesophyll and acts to derepress the promoter in vascular tissue, similar to that observed for Tomato golden mosaic virus (TGMV). Binding studies indicate that sequences mediating repression and activation of the TGMV and CaLCuV CP promoter specifically bind different nuclear factors common to Nicotiana benthamiana, spinach and tomato. However, chromatin immunoprecipitation demonstrates that TGMV AL2 can interact with both sequences independently. Binding of nuclear protein(s) from different crop species to viral sequences conserved in both bipartite and monopartite begomoviruses, including TGMV, CaLCuV, Pepper golden mosaic virus and Tomato yellow leaf curl virus suggests that bipartite begomoviruses bind common host factors to regulate the CP promoter. This is consistent with a model in which AL2 interacts with different components of the cellular transcription machinery that bind viral sequences important for repression and activation of begomovirus CP promoters

  1. The DNA sequence, annotation and analysis of human chromosome 3

    DEFF Research Database (Denmark)

    Muzny, D.M.; Bolund, Lars; As part of the Chinese Human Genome Sequencing Consortium, E.T.A.L.

    2006-01-01

    as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion...

  2. Sequence analysis of mitochondrial 16S ribosomal RNA gene

    Indian Academy of Sciences (India)

    Mosquitoes are vectors for the transmission of many human pathogens that include viruses, nematodes and protozoa. For the understanding of their vectorial capacity, identification of disease carrying and refractory strains is essential. Recently, molecular taxonomic techniques have been utilized for this purpose. Sequence ...

  3. Illumina-based de novo transcriptome sequencing and analysis

    Indian Academy of Sciences (India)

    In the present study, we used Illumina HiSeq technology to perform de novo assembly of heart and musk gland transcriptomes from the Chinese forest musk deer. A total of 239,383 transcripts and 176,450 unigenes were obtained, of which 37,329 unigenes were matched to known sequences in the NCBI nonredundant ...

  4. Generation and analysis of expressed sequence tags from Botrytis cinerea

    Directory of Open Access Journals (Sweden)

    EVELYN SILVA

    2006-01-01

    Full Text Available Botrytis cinerea is a filamentous plant pathogen of a wide range of plant species, and its infection may cause enormous damage both during plant growth and in the post-harvest phase. We have constructed a cDNA library from an isolate of B. cinerea and have sequenced 11,482 expressed sequence tags that were assembled into 1,003 contigs sequences and 3,032 singletons. Approximately 81% of the unigenes showed significant similarity to genes coding for proteins with known functions: more than 50% of the sequences code for genes involved in cellular metabolism, 12% for transport of metabolites, and approximately 10% for cellular organization. Other functional categories include responses to biotic and abiotic stimuli, cell communication, cell homeostasis, and cell development. We carried out pair-wise comparisons with fungal databases to determine the B. cinerea unisequence set with relevant similarity to genes in other fungal pathogenic counterparts. Among the 4,035 non-redundant B. cinerea unigenes, 1,338 (23% have significant homology with Fusarium verticillioides unigenes. Similar values were obtained for Saccharomyces cerevisiae and Aspergillus nidulans (22% and 24%, respectively. The lower percentages of homology were with Magnaporthe grisae and Neurospora crassa (13% and 19%, respectively. Several genes involved in putative and known fungal virulence and general pathogenicity were identified. The results provide important information for future research on this fungal pathogen

  5. Whole-genome sequence-based analysis of thyroid function

    DEFF Research Database (Denmark)

    Taylor, Peter N.; Porcu, Eleonora; Chew, Shelby

    2015-01-01

    Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N = 2,287). Using additional whole-genome seque...

  6. DNA sequence and prokaryotic expression analysis of vitellogenin ...

    African Journals Online (AJOL)

    In this study, the DNA sequence of vitellogenin from Antheraea pernyi (Ap-Vg) was identified and its functional domain (30-740 aa, Ap-Vg-1) was expressed in Escherichia coli BL21 (DE3) cells. The recombinant Ap-Vg-1 proteins were purified and used for antibody preparation. The results showed that the intact DNA ...

  7. Molecular cloning, sequence analysis and structure prediction of the ...

    African Journals Online (AJOL)

    AJL

    2012-04-19

    Apr 19, 2012 ... The primers were based on the rBAT sequences of other animals deposited in GenBank. .... fragment; M1, 2000 bp DNA ladder; M2, 1000 bp DNA ladder. spliced to obtain the ..... A traffic signal for heterodimeric amino acid.

  8. A bibliometric analysis of global research on genome sequencing ...

    African Journals Online (AJOL)

    The results show that disease and protein related researches were the leading research focuses, and comparative genomics and evolution related research had strong potential in the near future. Key words: Genome sequencing, research trend, scientometrics, science citation index expanded (SCI-Expanded), word cluster ...

  9. Cloning and sequence analysis of the defective in anther ...

    African Journals Online (AJOL)

    To clone the defective in anther dehiscence1 (DAD1) gene fragment of Chinese kale, about 700 bp product was obtained by PCR amplification using Chinese kale genomic DNA as the template and a pair of specific primers designed according to the conserved sequence of DAD1 genes of Arabidopsis thaliana and ...

  10. Sequence and comparative analysis of Leuconostoc dairy bacteriophages

    DEFF Research Database (Denmark)

    Kot, Witold; Hansen, Lars Henrik; Neve, Horst

    2014-01-01

    Bacteriophages attacking Leuconostoc species may significantly influence the quality of the final product. There is however limited knowledge of this group of phages in the literature. We have determined the complete genome sequences of nine Leuconostoc bacteriophages virulent to either Leuconostoc...

  11. Analysis for preliminary evaluation of discrete fracture flow and large-scale permeability in sedimentary rocks

    International Nuclear Information System (INIS)

    Kanehiro, B.Y.; Lai, C.H.; Stow, S.H.

    1987-05-01

    Conceptual models for sedimentary rock settings that could be used in future evaluation and suitability studies are being examined through the DOE Repository Technology Program. One area of concern for the hydrologic aspects of these models is discrete fracture flow analysis as related to the estimation of the size of the representative elementary volume, evaluation of the appropriateness of continuum assumptions and estimation of the large-scale permeabilities of sedimentary rocks. A basis for preliminary analysis of flow in fracture systems of the types that might be expected to occur in low permeability sedimentary rocks is presented. The approach used involves numerical modeling of discrete fracture flow for the configuration of a large-scale hydrologic field test directed at estimation of the size of the representative elementary volume and large-scale permeability. Analysis of fracture data on the basis of this configuration is expected to provide a preliminary indication of the scale at which continuum assumptions can be made

  12. Preliminary RAMI analysis of DFLL TBS for ITER

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Dagui [Key Laboratory of Neutronics and Radiation Safety, Institute of Nuclear Energy Safety Technology, Chinese Academy of Sciences, Hefei, Anhui, 230031 (China); University of Science and Technology of China, Hefei, Anhui, 230031 (China); Yuan, Run [Key Laboratory of Neutronics and Radiation Safety, Institute of Nuclear Energy Safety Technology, Chinese Academy of Sciences, Hefei, Anhui, 230031 (China); Wang, Jiaqun, E-mail: jiaqun.wang@fds.org.cn [Key Laboratory of Neutronics and Radiation Safety, Institute of Nuclear Energy Safety Technology, Chinese Academy of Sciences, Hefei, Anhui, 230031 (China); Wang, Fang; Wang, Jin [Key Laboratory of Neutronics and Radiation Safety, Institute of Nuclear Energy Safety Technology, Chinese Academy of Sciences, Hefei, Anhui, 230031 (China)

    2016-11-15

    Highlights: • We performed the functional analysis of the DFLL TBS. • We performed a failure mode analysis of the DFLL TBS. • We estimated the reliability and availability of the DFLL TBS. • The ITER RAMI approach was applied to the DFLL TBS for technical risk control in the design phase. - Abstract: ITER is the first fusion machine fully designed to prove the physics and technological basis for next fusion power plants. Among the main technical objectives of ITER is to test and validate design concepts of tritium breeding blankets relevant to the fusion power plants. To achieve this goal, China has proposed the dual functional lithium-lead test blanket module (DFLL TBM) concept design. The DFLL TBM and its associated ancillary system were called DFLL TBS. The DFLL TBS play a key role in next fusion reactor. In order to ensure reliable and available of DFLL TBS, the risk control project of DFLL TBS has been put on the schedule. As the stage of the ITER technical risk control policy, the RAMI (Reliability, Availability, Maintainability, Inspectability) approach was used to control the technical risk of ITER. In this paper, the RAMI approach was performed on the conceptual design of DFLL TBS. A functional breakdown was prepared on DFLL TBS, and the system was divided into 3 main functions and 72 basic functions. Based on the result of functional breakdown of DFLL TBS, the reliability block diagrams were prepared to estimate the reliability and availability of each function under the stipulated operating conditions. The inherent availability of the DFLL TBS expected after implementation of mitigation actions was calculated to be 98.57% over 2 years based on the ITER reliability database. A Failure Modes Effects and Criticality Analysis (FMECA) was performed with criticality charts highlighting the risk level of the different failure modes with regard to their probability of occurrence and their effects on the availability.

  13. Preliminary safety analysis for key design features of KALIMER

    Energy Technology Data Exchange (ETDEWEB)

    Hahn, D. H.; Kwon, Y. M.; Chang, W. P.; Suk, S. D.; Lee, S. O.; Lee, Y. B.; Jeong, K. S

    2000-07-01

    KAERI is currently developing the conceptual design of a liquid metal reactor, KALIMER(Korea Advanced Liquid Metal Reactor) under the long-term nuclear R and D program. In this report, descriptions of the KALIMER safety design features and safety analyses results for selected ATWS accidents are presented. First, the basic approach to achieve the safety goal is introduced in chapter 1, and the safety evaluation procedure for the KALIMER design is described in chapter 2. It includes event selection, event categorization, description of design basis events, and beyond design basis events. In chapter 3, results of inherent safety evaluations for the KALIMER conceptual design are presented. The KALIMER core and plant system are designed to assure design performance during a selected set of events without either reactor control or protection system intervention. Safety analyses for the postulated anticipated transient without scram(ATWS) have been performed to investigate the KALIMER system response to the events. They are categorized as bounding events(BEs) because of their low probability of occurrence. In chapter 4, the design of the KALIMER containment dome and the results of its performance analysis are presented. The designs of the existing LMR containment and the KALIMER containment dome have been compared in this chapter. Procedure of the containment performance analysis and the analysis results are described along with the accident scenario and source terms. Finally, a simple methodology is introduced to investigate the core kinetics and hydraulic behavior during HCDA in chapter 5. Mathematical formulations have been developed in the framework of the modified bethe-tait method, and scoping analyses have been performed for the KALIMER core behavior during super-prompt critical excursions.

  14. Computer content analysis of schizophrenic speech: a preliminary report.

    Science.gov (United States)

    Tucker, G J; Rosenberg, S D

    1975-06-01

    Computer analysis significantly differtiated the thermatic content of the free speech of 10 schizophrenic patients from that of 10 nonschizophrenic patients and from the content of transcripts of dream material from 10 normal subjects. Schizophrenic patients used the thematic categories in factor 1 (the "schizophrenic factor") 3 times more frequently than the nonschizophrenics and 10 times more frequently than the normal subjects (p smaller than 01). In general, the language content of the schizophrenic patient mirrored an almost agitated attempt to locate oneself in time and space and to defend against internal discomfort and confusion. The authors discuss the implications of this study for future research.

  15. Preliminary report on the PIXE analysis of the squid statoliths

    International Nuclear Information System (INIS)

    Ikeda, Yuzuru; Arai, Nobuaki; Sakamoto, Wataru; Murayama, Tatsuro; Maeda, Kuniko; Yoshida, Koji.

    1996-01-01

    Micro trace elements in the squid statolith, a calcareous stone which acts as a balancer and hearing, was analyzed with Particle Induced X-ray Emission (PIXE) for the Japanese common squid for the first time. Calcium is the main component of the squid statoliths, which means that squid statolith is the pure calcified structure similar to the fish otolith. Beside Ca, Sr was detected with strong dosage, and some other elements as Mn, Fe, Cu, Zn and As were also detected. Possible assumption of intake of microelements to the statoliths and the suitability of PIXE for statoliths analysis are discussed. (author)

  16. Macroalgae as a Biomass Feedstock: A Preliminary Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Roesijadi, Guritno; Jones, Susanne B.; Snowden-Swan, Lesley J.; Zhu, Yunhua

    2010-09-26

    A thorough of macroalgae analysis as a biofuels feedstock is warranted due to the size of this biomass resource and the need to consider all potential sources of feedstock to meet current biomass production goals. Understanding how to harness this untapped biomass resource will require additional research and development. A detailed assessment of environmental resources, cultivation and harvesting technology, conversion to fuels, connectivity with existing energy supply chains, and the associated economic and life cycle analyses will facilitate evaluation of this potentially important biomass resource.

  17. Preliminary safety analysis report for the Waste Characterization Facility

    International Nuclear Information System (INIS)

    1994-10-01

    This safety analysis report outlines the safety concerns associated with the Waste Characterization Facility located in the Radioactive Waste Management Complex at the Idaho National Engineering Laboratory. The three main objectives of the report are to: define and document a safety basis for the Waste Characterization Facility activities; demonstrate how the activities will be carried out to adequately protect the workers, public, and environment; and provide a basis for review and acceptance of the identified risk that the managers, operators, and owners will assume. 142 refs., 38 figs., 39 tabs

  18. Preliminary uranium enrichment analysis results using cadmium zinc telluride detectors

    International Nuclear Information System (INIS)

    Lavietes, A.D.; McQuaid, J.H.; Paulus, T.J.

    1995-01-01

    Lawrence Livermore National Laboratory (LLNL) and EG ampersand G ORTEC have jointly developed a portable ambient-temperature detection system that can be used in a number of application scenarios. The detection system uses a planar cadmium zinc telluride (CZT) detector with custom-designed detector support electronics developed at LLNL and is based on the recently released MicroNOMAD multichannel analyzer (MCA) produced by ORTEC. Spectral analysis is performed using software developed at LLNL that was originally designed for use with high-purity germanium (HPGe) detector systems. In one application, the CZT detection system determines uranium enrichments ranging from less than 3% to over 75% to within accuracies of 20%. The analysis was performed using sample sizes of 200 g or larger and acquisition times of 30 min. The authors have demonstrated the capabilities of this system by analyzing the spectra gathered by the CZT detection system from uranium sources of several enrichments. These experiments demonstrate that current CZT detectors can, in some cases, approach performance criteria that were previously the exclusive domain of larger HPGe detector systems

  19. XplorSeq: a software environment for integrated management and phylogenetic analysis of metagenomic sequence data.

    Science.gov (United States)

    Frank, Daniel N

    2008-10-07

    Advances in automated DNA sequencing technology have accelerated the generation of metagenomic DNA sequences, especially environmental ribosomal RNA gene (rDNA) sequences. As the scale of rDNA-based studies of microbial ecology has expanded, need has arisen for software that is capable of managing, annotating, and analyzing the plethora of diverse data accumulated in these projects. XplorSeq is a software package that facilitates the compilation, management and phylogenetic analysis of DNA sequences. XplorSeq was developed for, but is not limited to, high-throughput analysis of environmental rRNA gene sequences. XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI). Through this GUI, users may perform basic sequence import and assembly steps (base-calling, vector/primer trimming, contig assembly), perform BLAST (Basic Local Alignment and Search Tool; 123) searches of NCBI and local databases, create multiple sequence alignments, build phylogenetic trees, assemble Operational Taxonomic Units, estimate biodiversity indices, and summarize data in a variety of formats. Furthermore, sequences may be annotated with user-specified meta-data, which then can be used to sort data and organize analyses and reports. A document-based architecture permits parallel analysis of sequence data from multiple clones or amplicons, with sequences and other data stored in a single file. XplorSeq should benefit researchers who are engaged in analyses of environmental sequence data, especially those with little experience using bioinformatics software. Although XplorSeq was developed for management of rDNA sequence data, it can be applied to most any sequencing project. The application is available free of charge for non-commercial use at http://vent.colorado.edu/phyloware.

  20. Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

    Science.gov (United States)

    Kisand, Veljo; Lettieri, Teresa

    2013-04-01

    De novo genome sequencing of previously uncharacterized microorganisms has the potential to open up new frontiers in microbial genomics by providing insight into both functional capabilities and biodiversity. Until recently, Roche 454 pyrosequencing was the NGS method of choice for de novo assembly because it generates hundreds of thousands of long reads (tools for processing NGS data are increasingly free and open source and are often adopted for both their high quality and role in promoting academic freedom. The error rate of pyrosequencing the Alcanivorax borkumensis genome was such that thousands of insertions and deletions were artificially introduced into the finished genome. Despite a high coverage (~30 fold), it did not allow the reference genome to be fully mapped. Reads from regions with errors had low quality, low coverage, or were missing. The main defect of the reference mapping was the introduction of artificial indels into contigs through lower than 100% consensus and distracting gene calling due to artificial stop codons. No assembler was able to perform de novo assembly comparable to reference mapping. Automated annotation tools performed similarly on reference mapped and de novo draft genomes, and annotated most CDSs in the de novo assembled draft genomes. Free and open source software (FOSS) tools for assembly and annotation of NGS data are being developed rapidly to provide accurate results with less computational effort. Usability is not high priority and these tools currently do not allow the data to be processed without manual intervention. Despite this, genome assemblers now readily assemble medium short reads into long contigs (>97-98% genome coverage). A notable gap in pyrosequencing technology is the quality of base pair calling and conflicting base pairs between single reads at the same nucleotide position. Regardless, using draft whole genomes that are not finished and remain fragmented into tens of contigs allows one to characterize

  1. Yucca Mountain transportation routes: Preliminary characterization and risk analysis

    International Nuclear Information System (INIS)

    Souleyrette, R.R. II; Sathisan, S.K.; di Bartolo, R.

    1991-01-01

    In this study, rail and highway routes which may be used for shipments of high-level nuclear waste to a proposed repository at Yucca Mountain, Nevada are characterized. This characterization facilitates three types of impact analysis: comparative study, limited worst-case assessment, and more sophisticated probabilistic risk assessment techniques. Data for relative and absolute impact measures are provided to support comparisons of routes based on selected characteristics. A worst-case scenario assessment is included to determine potentially critical and most likely places for accidents or incidents to occur. The assessment facilitated by the data in this study is limited because impact measures are restricted to the identification of potential areas or persons affected. No attempt is made to quantify the magnitude of these impacts. Most likely locations for accidents to occur are determined relative to other locations within the scope of this study. Independent factors and historical trends used to identify these likely locations are only proxies for accident probability

  2. City of Hoboken Energy Surety Analysis: Preliminary Design Summary

    Energy Technology Data Exchange (ETDEWEB)

    Stamp, Jason Edwin [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Military and Energy Systems Analysis Dept.; Baca, Michael J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Military and Energy Systems Analysis Dept.; Munoz-Ramos, Karina [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Military and Energy Systems Analysis Dept.; Schenkman, Benjamin L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Military and Energy Systems Analysis Dept.; Eddy, John P. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Systems Readiness and Sustainment Technology Dept.; Smith, Mark A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Systems Readiness and Sustainment Technology Dept.; Guttromson, Ross [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electric Power Systems Research Dept.; Henry, Jordan M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Critical Infrastructure Systems Dept.; Jensen, Richard Pearson [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Geomechanics Dept.

    2014-09-01

    In 2012, Hurricane Sandy devastated much of the U.S. northeast coastal areas. Among those hardest hit was the small community of Hoboken, New Jersey, located on the banks of the Hudson River across from Manhattan. This report describes a city-wide electrical infrastructure design that uses microgrids and other infrastructure to ensure the city retains functionality should such an event occur in the future. The designs ensure that up to 55 critical buildings will retain power during blackout or flooded conditions and include analysis for microgrid architectures, performance parameters, system control, renewable energy integration, and financial opportunities (while grid connected). The results presented here are not binding and are subject to change based on input from the Hoboken stakeholders, the integrator selected to manage and implement the microgrid, or other subject matter experts during the detailed (final) phase of the design effort.

  3. The Σ − D relation for planetary nebulae: Preliminary analysis

    Directory of Open Access Journals (Sweden)

    Urošević D.

    2007-01-01

    Full Text Available An analysis of the relation between radio surface brightness and diameter, so-called Σ − D relation, for planetary nebulae (PNe is presented: i the theoretical Σ − D relation for the evolution of bremsstrahlung surface brightness is derived; ii contrary to the results obtained earlier for the Galactic supernova remnant (SNR samples, our results show that the updated sample of Galactic PNe does not severely suffer from volume selection effect - Malmquist bias (same as for the extragalactic SNR samples and; iii we conclude that the empirical S − D relation for PNe derived in this paper is not useful for valid determination of distances for all observed PNe with unknown distances. .

  4. Sequence analysis of the Legionella micdadei groELS operon

    DEFF Research Database (Denmark)

    Hindersson, P; Høiby, N; Bangsborg, Jette Marie

    1991-01-01

    A 2.7 kb DNA fragment encoding the 60 kDa common antigen (CA) and a 13 kDa protein of Legionella micdadei was sequenced. Two open reading frames of 57,677 and 10,456 Da were identified, corresponding to the heat shock proteins GroEL and GroES, respectively. Typical -35, -10, and Shine-Dalgarno heat...

  5. A Preliminary Tsunami Vulnerability Analysis for Yenikapi Region in Istanbul

    Science.gov (United States)

    Ceren Cankaya, Zeynep; Suzen, Lutfi; Cevdet Yalciner, Ahmet; Kolat, Cagil; Aytore, Betul; Zaytsev, Andrey

    2015-04-01

    One of the main requirements during post disaster recovery operations is to maintain proper transportation and fluent communication at the disaster areas. Ports and harbors are the main transportation hubs which must work with proper performance at all times especially after the disasters. Resilience of coastal utilities after earthquakes and tsunamis have major importance for efficient and proper rescue and recovery operations soon after the disasters. Istanbul is a mega city with its various coastal utilities located at the north coast of the Sea of Marmara. At Yenikapi region of Istanbul, there are critical coastal utilities and vulnerable coastal structures and critical activities occur daily. Fishery ports, commercial ports, small craft harbors, passenger terminals of intercity maritime transportation, water front commercial and/or recreational structures are some of the examples of coastal utilization which are vulnerable against marine disasters. Therefore their vulnerability under tsunami or any other marine hazard to Yenikapi region of Istanbul is an important issue. In this study, a methodology of vulnerability analysis under tsunami attack is proposed with the applications to Yenikapi region. In the study, high resolution (1m) GIS database of Istanbul Metropolitan Municipality (IMM) is used and analyzed by using GIS implementation. The bathymetry and topography database and the vector dataset containing all buildings/structures/infrastructures in the study area are obtained for tsunami numerical modeling for the study area. GIS based tsunami vulnerability assessment is conducted by applying the Multi-criteria Decision Making Analysis (MCDA). The tsunami parameters from deterministically defined worst case scenarios are computed from the simulations using tsunami numerical model NAMI DANCE. The vulnerability parameters in the region due to two different classifications i) vulnerability of buildings/structures and ii) vulnerability of (human) evacuation

  6. Preliminary analysis of a new IAEA lichen AQCS material

    International Nuclear Information System (INIS)

    Grass, F.; Bichler, M.; Dorner, J.; Ismail, S.; Kregshammer, P.; Zamini, S.; Gwozdz, R.

    2000-01-01

    Lichen with a higher content on interesting trace elements were analyzed by activation analysis and by X-RF measurements on pressed lichen samples. The activation analyses were performed in three different ways: Short-time AA in the Fast Irradiation and Measurement System. Up to 580mg of lichen were irradiated 5-300s in polyethylene containers. Single spectra and spectra of 6 samples were summed up and evaluated. Longer irradiation at the ASTRA-Reactor: 2h at 8E13/s cm 2 . 100-150mg of lichen were irradiated in quartz suprasil vials. Longer irradiation at the Institute's TRIGA-Reactor: 6-7h at 1.8E12/s cm 2 , sample size: 7-48g of lichen were irradiated in polyethylene containers and after irradiation transferred to new measurement containers and measured in a device constructed by Gwozdz. The X-RF analysis was performed with a Spectrace 5000 energy dispersive X-ray fluorescence analyzer with a rhodium anode tube for excitation. From the activation analyses, the following elements were determined: Ag, Al, As, Au, Ba, Br, Ca, Cd, Ce, Cl, Co, Cr, Cs, Cu, Dy, Eu, Fe, Hf, Hg, I, K, La, Lu, Mg, Mn, Mo, Na, Nd, Ni, Rb, Sb, Sc, Se, Sr, Ta, Tb, Th, Ti, U, V, Yb, Zn. From the X-RF measurements, the elements Ag, Al, Ba, Br, Ca, Cd, Cu, Fe, I, K, Mg, Mn, P, Pb, Rb, S, Sb, Si, Sn, Sr, Ti, Y, Zn, and Zr were evaluated. From the X-RF data as well as from the AA-data of samples of different weight it is apparent that milling to a particle size of 200m is not sufficient for all elements, especially not for gold, cadmium, and cobalt which may be present as nuggets or accessory heavy minerals. It is therefore advisable to mill the sample to a particle size which is an order of magnitude smaller and remove the not adhering dust, even if this lowers the content of these elements. (author)

  7. The Matrix Method of Representation, Analysis and Classification of Long Genetic Sequences

    Directory of Open Access Journals (Sweden)

    Ivan V. Stepanyan

    2017-01-01

    Full Text Available The article is devoted to a matrix method of comparative analysis of long nucleotide sequences by means of presenting each sequence in the form of three digital binary sequences. This method uses a set of symmetries of biochemical attributes of nucleotides. It also uses the possibility of presentation of every whole set of N-mers as one of the members of a Kronecker family of genetic matrices. With this method, a long nucleotide sequence can be visually represented as an individual fractal-like mosaic or another regular mosaic of binary type. In contrast to natural nucleotide sequences, artificial random sequences give non-regular patterns. Examples of binary mosaics of long nucleotide sequences are shown, including cases of human chromosomes and penicillins. The obtained results are then discussed.

  8. Preliminary results of standard quantitative analysis by ED-XRF

    Energy Technology Data Exchange (ETDEWEB)

    Lara, Alessandro L. de; Franca, Alana C.; Neto, Manoel R.M.; Paschuk, Sergei A., E-mail: alellara@hotmail.com [Universidade Tecnologica Federal do Parana (UTFPR), Curitiba, PR (Brazil). Dept. de Fisica; Denyak, Valeriy, E-mail: denyak@gmail.com [Instituto de Pesquisa Pele Pequeno Principe (IPPP), Curitiba, PR (Brazil)

    2013-07-01

    A comparison between the results of elemental concentration proposed by XRS-FP software , using data obtained by EDXRF technique with those obtained by stoichiometric calculation was performed. For this purpose, five standard samples of known compounds were produced: two lead- oxide, magnesium chloride and iodine in controlled amounts. The compounds were subsequently mixed and compressed to form tablets. The samples were irradiated in three endpoints, according to an orientation. The measurements were performed at the Laboratory for Radiological UTFPR using X-123SDD the Amptek detector and X-ray tube with silver target from the same manufacturer. The operating conditions tube were 05μA current to a 40 kV voltage. Finally, the 15 spectra analyzed with the software to determine the concentration of chlorine, iodine and lead. Data from this analysis were compared with results expected in stoichiometric calculations. The data provided by the program, a convergence of results, indicating homogeneity of the samples was found. Compared to the stoichiometric calculation, a considerable discrepancy that may be the result of a misconfiguration or contamination of the sample was found. At the end, we created a proposal for continuation of the work using an auxiliary calculation should be developed in the next step.

  9. A preliminary study of DTI Fingerprinting on stroke analysis.

    Science.gov (United States)

    Ma, Heather T; Ye, Chenfei; Wu, Jun; Yang, Pengfei; Chen, Xuhui; Yang, Zhengyi; Ma, Jingbo

    2014-01-01

    DTI (Diffusion Tensor Imaging) is a well-known MRI (Magnetic Resonance Imaging) technique which provides useful structural information about human brain. However, the quantitative measurement to physiological variation of subtypes of ischemic stroke is not available. An automatically quantitative method for DTI analysis will enhance the DTI application in clinics. In this study, we proposed a DTI Fingerprinting technology to quantitatively analyze white matter tissue, which was applied in stroke classification. The TBSS (Tract Based Spatial Statistics) method was employed to generate mask automatically. To evaluate the clustering performance of the automatic method, lesion ROI (Region of Interest) is manually drawn on the DWI images as a reference. The results from the DTI Fingerprinting were compared with those obtained from the reference ROIs. It indicates that the DTI Fingerprinting could identify different states of ischemic stroke and has promising potential to provide a more comprehensive measure of the DTI data. Further development should be carried out to improve DTI Fingerprinting technology in clinics.

  10. FFTF vertical sodium storage tank preliminary thermal analysis

    International Nuclear Information System (INIS)

    Irwin, J.J.

    1995-01-01

    In the FFTF Shutdown Program, sodium from the primary and secondary heat transport loops, Interim Decay Storage (IDS), and Fuel Storage Facility (FSF) will be transferred to four large storage tanks for temporary storage. Three of the storage tanks will be cylindrical vertical tanks having a diameter of 28 feet, height of 22 feet and fabricated from carbon steel. The fourth tank is a horizontal cylindrical tank but is not the subject of this report. The storage tanks will be located near the FFTF in the 400 Area and rest on a steel-lined concrete slab in an enclosed building. The purpose of this work is to document the thermal analyses that were performed to ensure that the vertical FFTF sodium storage tank design is feasible from a thermal standpoint. The key criterion for this analysis is the time to heat up the storage tank containing frozen sodium at ambient temperature to 400 F. Normal operating conditions include an ambient temperature range of 32 F to 120 F. A key parameter in the evaluation of the sodium storage tank is the type of insulation. The baseline case assumed six inches of calcium silicate insulation. An alternate case assumed refractory fiber (Cerablanket) insulation also with a thickness of six inches. Both cases assumed a total electrical trace heat load of 60 kW, with 24 kW evenly distributed on the bottom head and 36 kW evenly distributed on the tank side wall

  11. Preliminary analysis of the proposed BN-600 benchmark core

    International Nuclear Information System (INIS)

    John, T.M.

    2000-01-01

    The Indira Gandhi Centre for Atomic Research is actively involved in the design of Fast Power Reactors in India. The core physics calculations are performed by the computer codes that are developed in-house or by the codes obtained from other laboratories and suitably modified to meet the computational requirements. The basic philosophy of the core physics calculations is to use the diffusion theory codes with the 25 group nuclear cross sections. The parameters that are very sensitive is the core leakage, like the power distribution at the core blanket interface etc. are calculated using transport theory codes under the DSN approximations. All these codes use the finite difference approximation as the method to treat the spatial variation of the neutron flux. Criticality problems having geometries that are irregular to be represented by the conventional codes are solved using Monte Carlo methods. These codes and methods have been validated by the analysis of various critical assemblies and calculational benchmarks. Reactor core design procedure at IGCAR consists of: two and three dimensional diffusion theory calculations (codes ALCIALMI and 3DB); auxiliary calculations, (neutron balance, power distributions, etc. are done by codes that are developed in-house); transport theory corrections from two dimensional transport calculations (DOT); irregular geometry treated by Monte Carlo method (KENO); cross section data library used CV2M (25 group)

  12. Social network analysis in identifying influential webloggers: A preliminary study

    Science.gov (United States)

    Hasmuni, Noraini; Sulaiman, Nor Intan Saniah; Zaibidi, Nerda Zura

    2014-12-01

    In recent years, second generation of internet-based services such as weblog has become an effective communication tool to publish information on the Web. Weblogs have unique characteristics that deserve users' attention. Some of webloggers have seen weblogs as appropriate medium to initiate and expand business. These webloggers or also known as direct profit-oriented webloggers (DPOWs) communicate and share knowledge with each other through social interaction. However, survivability is the main issue among DPOW. Frequent communication with influential webloggers is one of the way to keep survive as DPOW. This paper aims to understand the network structure and identify influential webloggers within the network. Proper understanding of the network structure can assist us in knowing how the information is exchanged among members and enhance survivability among DPOW. 30 DPOW were involved in this study. Degree centrality and betweenness centrality measurement in Social Network Analysis (SNA) were used to examine the strength relation and identify influential webloggers within the network. Thus, webloggers with the highest value of these measurements are considered as the most influential webloggers in the network.

  13. Preliminary results of standard quantitative analysis by ED-XRF

    International Nuclear Information System (INIS)

    Lara, Alessandro L. de; Franca, Alana C.; Neto, Manoel R.M.; Paschuk, Sergei A.

    2013-01-01

    A comparison between the results of elemental concentration proposed by XRS-FP software , using data obtained by EDXRF technique with those obtained by stoichiometric calculation was performed. For this purpose, five standard samples of known compounds were produced: two lead- oxide, magnesium chloride and iodine in controlled amounts. The compounds were subsequently mixed and compressed to form tablets. The samples were irradiated in three endpoints, according to an orientation. The measurements were performed at the Laboratory for Radiological UTFPR using X-123SDD the Amptek detector and X-ray tube with silver target from the same manufacturer. The operating conditions tube were 05μA current to a 40 kV voltage. Finally, the 15 spectra analyzed with the software to determine the concentration of chlorine, iodine and lead. Data from this analysis were compared with results expected in stoichiometric calculations. The data provided by the program, a convergence of results, indicating homogeneity of the samples was found. Compared to the stoichiometric calculation, a considerable discrepancy that may be the result of a misconfiguration or contamination of the sample was found. At the end, we created a proposal for continuation of the work using an auxiliary calculation should be developed in the next step

  14. Preliminary analysis of space mission applications for electromagnetic launchers

    Science.gov (United States)

    Miller, L. A.; Rice, E. E.; Earhart, R. W.; Conlon, R. J.

    1984-01-01

    The technical and economic feasibility of using electromagnetically launched EML payloads propelled from the Earth's surface to LEO, GEO, lunar orbit, or to interplanetary space was assessed. Analyses of the designs of rail accelerators and coaxial magnetic accelerators show that each is capable of launching to space payloads of 800 KG or more. A hybrid launcher in which EML is used for the first 2 KM/sec followed by chemical rocket stages was also tested. A cost estimates study shows that one to two EML launches per day are needed to break even, compared to a four-stage rocket. Development models are discussed for: (1) Earth orbital missions; (2) lunar base supply mission; (3) solar system escape mission; (4) Earth escape missions; (5) suborbital missions; (6) electromagnetic boost missions; and (7) space-based missions. Safety factors, environmental impacts, and EML systems analysis are discussed. Alternate systems examined include electrothermal thrustors, an EML rocket gun; an EML theta gun, and Soviet electromagnetic accelerators.

  15. A simplified procedure of linear regression in a preliminary analysis

    Directory of Open Access Journals (Sweden)

    Silvia Facchinetti

    2013-05-01

    Full Text Available The analysis of a statistical large data-set can be led by the study of a particularly interesting variable Y – regressed – and an explicative variable X, chosen among the remained variables, conjointly observed. The study gives a simplified procedure to obtain the functional link of the variables y=y(x by a partition of the data-set into m subsets, in which the observations are synthesized by location indices (mean or median of X and Y. Polynomial models for y(x of order r are considered to verify the characteristics of the given procedure, in particular we assume r= 1 and 2. The distributions of the parameter estimators are obtained by simulation, when the fitting is done for m= r + 1. Comparisons of the results, in terms of distribution and efficiency, are made with the results obtained by the ordinary least square methods. The study also gives some considerations on the consistency of the estimated parameters obtained by the given procedure.

  16. Preliminary Analysis of Slope Stability in Kuok and Surrounding Areas

    Directory of Open Access Journals (Sweden)

    Dewandra Bagus Eka Putra

    2016-12-01

    Full Text Available The level of slope influenced by the condition of the rocks beneath the surface. On high level of slopes, amount of surface runoff and water transport energy is also enlarged. This caused by greater gravity, in line with the surface tilt from the horizontal plane. In other words, topsoil eroded more and more. When the slope becomes twice as steep, then the amount of erosion per unit area be 2.0 - 2.5 times more. Kuok and surrounding area is the road access between the West Sumatra and Riau which plays an important role economies of both provinces. The purpose of this study is to map the locations that have fairly steep slopes and potential mode of landslides. Based on SRTM data obtained,  the roads in Kuok area has a minimum elevation of + 33 m and a maximum  + 217.329 m. Rugged road conditions with slope ranging from 24.08 ° to 44.68 ° causing this area having frequent landslides. The result of slope stability analysis in a slope near the Water Power Plant Koto Panjang, indicated that mode of active failure is toppling failure or rock fall and the potential zone of failure is in the center part of the slope.

  17. Electrical field of electrical appliances versus distance: A preliminary analysis

    International Nuclear Information System (INIS)

    Mustafa, Nur Badariah Ahmad; Nordin, Farah Hani; Ismail, Fakaruddin Ali Ahmad; Alkahtani, Ammar Ahmed; Balasubramaniam, Nagaletchumi; Hock, Goh Chin; Shariff, Z A M

    2013-01-01

    Every household electrical appliance that is plugged in emits electric field even if it is not operating. The source where the appliance is plugged into and the components of household electrical appliance contribute to electric field emission. The electric field may cause unknown disturbance to the environment or also affect the human health and the effect might depends on the strength of the electric field emitted by the appliance. This paper will investigate the strength of the electric field emitted by four different electrical appliances using spectrum analyser. The strength will be captured at three different distances; (i) 1m (ii) 2m and (iii) 3m and analysis of the strength of the electrical field is done based on the three different distances. The measurement results show that the strength of the electric field is strongest when it is captured at 1m and the weakest at 3m from the electrical appliance. The results proved that the farther an object is located from the electrical appliance; the less effect the magnetic field has.

  18. Gas cooled fast reactor 2400 MWTh, status on the conceptual design studies and preliminary safety analysis

    International Nuclear Information System (INIS)

    Malo, J.Y.; Alpy, N.; Bentivoglio, F.

    2009-01-01

    The Gas cooled Fast Reactor (GFR) is considered by the French Commissariat a l'Energie Atomique as a promising concept, combining the benefits of fast spectrum and high temperature, using Helium as coolant. A status on the GFR preliminary viability was made at the end of 2007, ending the pre-conceptual design phase. A consistent overall systems arrangement was proposed and a preliminary safety analysis based on operating transient calculations and a simplified PSA had established a global confidence in the feasibility and safety of this baseline concept. Its potential for attractive performances had been pointed out. Compare to the more mature Sodium Fast Reactor technology, no demonstrator has ever been built and the feasibility demonstration will required a longer lead time. The next main project milestone is related to the GFR viability, scheduled in 2012. The current studies consist in revisiting the reactor reference design options as selected at the end of 2007. Most of them are being consolidated by going more in depth in the analysis. Some possible alternatives are assessed. The paper will give a status on the last studies performed on the core design and corresponding neutronics and cycle performance, the Decay Heat Removal strategy and preliminary safety analysis, systems design and balance of plant... This paper is complementary to the Icapp'09 papers 9062 dealing with the Gas cooled Fast Reactor Demonstrator ALLEGRO and 9378 related to GFR transients analysis. (author)

  19. OPTSDNA: Performance evaluation of an efficient distributed bioinformatics system for DNA sequence analysis.

    Science.gov (United States)

    Khan, Mohammad Ibrahim; Sheel, Chotan

    2013-01-01

    Storage of sequence data is a big concern as the amount of data generated is exponential in nature at several locations. Therefore, there is a need to develop techniques to store data using compression algorithm. Here we describe optimal storage algorithm (OPTSDNA) for storing large amount of DNA sequences of varying length. This paper provides performance analysis of optimal storage algorithm (OPTSDNA) of a distributed bioinformatics computing system for analysis of DNA sequences. OPTSDNA algorithm is used for storing various sizes of DNA sequences into database. DNA sequences of different lengths were stored by using this algorithm. These input DNA sequences are varied in size from very small to very large. Storage size is calculated by this algorithm. Response time is also calculated in this work. The efficiency and performance of the algorithm is high (in size calculation with percentage) when compared with other known with sequential approach.

  20. Clinical registry for rheumatoid arthritis; a preliminary analysis

    International Nuclear Information System (INIS)

    Fakhr, A.; Hakim, F.; Zaidi, S.K.; Sharif, A.

    2017-01-01

    To establish a clinical registry for Rheumatoid Arthritis and delineate the most common symptoms that rheumatoid arthritis (RA) patients experience in our set up. Study Design: Cross sectional study. Place and Duration of Study: Study was carried out at Military Hospital (MH) Rawalpindi at Rheumatology Department during the period of Jan 2013 to Jun 2015. Material and Methods: A clinical registry for Rheumatoid Arthritis was developed as per criteria jointly developed by American College of Rheumatology (ACR) along with European League against Rheumatism (EULAR) (2010). Fifty-eight patients were registered after their informed consent and approval by Military Hospital (MH) Rawalpindi ethical committee. Age, gender and relevant clinical parameters of RA patients were recorded on case report forms and stored for analysis in the RA registry in Excel 2010. The figures were reported in frequencies and percentages. Results: Multiple joint pains (48.28%), fever (24.14%), morning stiffness of joints (22.41%) were the most common symptoms in RA patients. Other clinical manifestations included painful bilateral swollen joints (13.79%), pain in different parts of the body (10.34%), Raynaud's phenomenon (10.34%), malaise (8.62%), swollen body parts (8.62%), ulcers (8.62%), fatigue (6.90%), nodules on skin/elbow/interphalangeal joints (6.90%), deformities of fingers/ hand (3.45%), redness of eyes (3.45%), body rash (3.45%), inability to walk (3.45%), cervical lymphadenopathy (1.72%), stiffness of spine (1.72%) and myalgias (1.72%). Conclusion: It is concluded that multiple joint pains, fever and morning stiffness of joints are the most common symptoms of RA patients. (author)

  1. Advanced analysis of finger-tapping performance: a preliminary study.

    Science.gov (United States)

    Barut, Cağatay; Kızıltan, Erhan; Gelir, Ethem; Köktürk, Fürüzan

    2013-06-01

    The finger-tapping test is a commonly employed quantitative assessment tool used to measure motor performance in the upper extremities. This task is a complex motion that is affected by external stimuli, mood and health status. The complexity of this task is difficult to explain with a single average intertap-interval value (time difference between successive tappings) which only provides general information and neglects the temporal effects of the aforementioned factors. This study evaluated the time course of average intertap-interval values and the patterns of variation in both the right and left hands of right-handed subjects using a computer-based finger-tapping system. Cross sectional study. Thirty eight male individuals aged between 20 and 28 years (Mean±SD = 22.24±1.65) participated in the study. Participants were asked to perform single-finger-tapping test for 10 seconds of test period. Only the results of right-handed (RH) 35 participants were considered in this study. The test records the time of tapping and saves data as the time difference between successive tappings for further analysis. The average number of tappings and the temporal fluctuation patterns of the intertap-intervals were calculated and compared. The variations in the intertap-interval were evaluated with the best curve fit method. An average tapping speed or tapping rate can reliably be defined for a single-finger tapping test by analysing the graphically presented data of the number of tappings within the test period. However, a different presentation of the same data, namely the intertap-interval values, shows temporal variation as the number of tapping increases. Curve fitting applications indicate that the variation has a biphasic nature. The measures obtained in this study reflect the complex nature of the finger-tapping task and are suggested to provide reliable information regarding hand performance. Moreover, the equation reflects both the variations in and the general

  2. Diisocyanate emission from a paint product: a preliminary analysis.

    Science.gov (United States)

    Jarand, Curtis W; Akapo, Samuel O; Swenson, Lonie J; Kelman, Bruce J

    2002-07-01

    Exposure of workers to diisocyanates in the polyurethane foam manufacturing industry is well documented. However, very little quantitative data have been published on exposure to diisocyanates from the use of paints and coatings. The purpose of this study was to evaluate emission of 2,4-toluene diisocyanate, 2,6-toluene diisocyanate (2,6-TDI), and isophorone diisocyanate from a commercially available two-stage concrete coating and sealant. A laboratory model of an outdoor deck coating process was developed and diisocyanate concentrations determined by derivatization with 1-(2-methoxyphenol)-piperazine and subsequent high performance liquid chromatographic analysis with UV detection. The detection limit for 2,4-toluene diisocyanate and 2,6-toluene diisocyanate urea derivatives was 0.6 microg TDI/gm wet product, and 0.54 microg IPDI/gm wet product for the isophorone diisocyanate urea derivative. No 2,4-toluene diisocyanate or isophorone diisocyanate was detected in the mixed product. A maximum mean 2,6-TDI emission rate of 0.32 microg of 2,6-TDI/gram of wet product applied/hour was observed for the 1-hour sampling time, 0.38 microg of 2,6-TDI/gram of wet product applied/hour was observed for the 5-hour sampling time, and 0.02 micrpg of 2,6-TDI/gram of wet product applied/hour was observed for the 15-hour sampling time. The decrease in rate of 2,6-TDI emission over the 15-hour period indicates that emission of 2,6-TDI is virtually complete after 5 hours. These emission rates should allow industrial hygienists to calculate exposures to isocyanates emitted from at least one curing sealant.

  3. Cognitive Task Analysis of Business Jet Pilots' Weather Flying Behaviors: Preliminary Results

    Science.gov (United States)

    Latorella, Kara; Pliske, Rebecca; Hutton, Robert; Chrenka, Jason

    2001-01-01

    This report presents preliminary findings from a cognitive task analysis (CTA) of business aviation piloting. Results describe challenging weather-related aviation decisions and the information and cues used to support these decisions. Further, these results demonstrate the role of expertise in business aviation decision-making in weather flying, and how weather information is acquired and assessed for reliability. The challenging weather scenarios and novice errors identified in the results provide the basis for experimental scenarios and dependent measures to be used in future flight simulation evaluations of candidate aviation weather information systems. Finally, we analyzed these preliminary results to recommend design and training interventions to improve business aviation decision-making with weather information. The primary objective of this report is to present these preliminary findings and to document the extended CTA methodology used to elicit and represent expert business aviator decision-making with weather information. These preliminary findings will be augmented with results from additional subjects using this methodology. A summary of the complete results, absent the detailed treatment of methodology provided in this report, will be documented in a separate publication.

  4. 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

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

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  6. Crystallization and preliminary X-ray diffraction analysis of rat autotaxin

    International Nuclear Information System (INIS)

    Day, Jacqueline E.; Hall, Troii; Pegg, Lyle E.; Benson, Timothy E.; Hausmann, Jens; Kamtekar, Satwik

    2010-01-01

    Autotaxin (ATX), a pyrophosphatase/phosphodiesterase enzyme, is a promising drug target for many indications and is only distantly related to enzymes of previously determined structure. Here, the cloning, expression, purification, crystallization and preliminary diffraction analysis of ATX are reported. Rat autotaxin has been cloned, expressed, purified to homogeneity and crystallized via hanging-drop vapour diffusion using PEG 3350 as precipitant and ammonium iodide and sodium thiocyanate as salts. The crystals diffracted to a maximum resolution of 2.05 Å and belonged to space group P1, with unit-cell parameters a = 53.8, b = 63.3, c = 70.5 Å, α = 98.8, β = 106.2, γ = 99.8°. Preliminary X-ray diffraction analysis indicated the presence of one molecule per asymmetric unit, with a solvent content of 47%

  7. Relative risk analysis in regulating the use of radiation-emitting medical devices. A preliminary application

    Energy Technology Data Exchange (ETDEWEB)

    Jones, E.D.; Banks, W.W.; Altenbach, T.J.; Fischer, L.E. [Lawrence Livermore National Lab., CA (United States)

    1995-09-01

    This report describes a preliminary application of an analysis approach for assessing relative risks in the use of radiation- emitting medical devices. Results are presented on human-initiated actions and failure modes that are most likely to occur in the use of the Gamma Knife, a gamma irradiation therapy device. This effort represents an initial step in a US Nuclear Regulatory Commission (NRC) plan to evaluate the potential role of risk analysis in regulating the use of nuclear medical devices. For this preliminary application of risk assessment, the focus was to develop a basic process using existing techniques for identifying the most likely risk contributors and their relative importance. The approach taken developed relative risk rankings and profiles that incorporated the type and quality of data available and could present results in an easily understood form. This work was performed by the Lawrence Livermore National Laboratory for the NRC.

  8. Crystallization and preliminary X-ray diffraction analysis of West Nile virus

    International Nuclear Information System (INIS)

    Kaufmann, Bärbel; Plevka, Pavel; Kuhn, Richard J.; Rossmann, Michael G.

    2010-01-01

    Crystals of infectious West Nile virus were obtained and diffracted at best to about 25 Å resolution. Preliminary analysis of the diffraction pattern suggested tight hexagonal packing of the intact virus. West Nile virus, a human pathogen, is closely related to other medically important flaviviruses of global impact such as dengue virus. The infectious virus was purified from cell culture using polyethylene glycol (PEG) precipitation and density-gradient centrifugation. Thin amorphously shaped crystals of the lipid-enveloped virus were grown in quartz capillaries equilibrated by vapor diffusion. Crystal diffraction extended at best to a resolution of about 25 Å using synchrotron radiation. A preliminary analysis of the diffraction images indicated that the crystals had unit-cell parameters a ≃ b ≃ 480 Å, γ = 120°, suggesting a tight hexagonal packing of one virus particle per unit cell

  9. Preliminary Dynamic Feasibility and Analysis of a Spherical, Wind-Driven (Tumbleweed), Martian Rover

    Science.gov (United States)

    Flick, John J.; Toniolo, Matthew D.

    2005-01-01

    The process and findings are presented from a preliminary feasibility study examining the dynamics characteristics of a spherical wind-driven (or Tumbleweed) rover, which is intended for exploration of the Martian surface. The results of an initial feasibility study involving several worst-case mobility situations that a Tumbleweed rover might encounter on the surface of Mars are discussed. Additional topics include the evaluation of several commercially available analysis software packages that were examined as possible platforms for the development of a Monte Carlo Tumbleweed mission simulation tool. This evaluation lead to the development of the Mars Tumbleweed Monte Carlo Simulator (or Tumbleweed Simulator) using the Vortex physics software package from CM-Labs, Inc. Discussions regarding the development and evaluation of the Tumbleweed Simulator, as well as the results of a preliminary analysis using the tool are also presented. Finally, a brief conclusions section is presented.

  10. Preliminary X-ray analysis of twinned crystals of sarcosine dimethylglycine methyltransferase from Halorhodospira halochoris

    International Nuclear Information System (INIS)

    Kallio, Juha Pekka; Jänis, Janne; Nyyssölä, Antti; Hakulinen, Nina; Rouvinen, Juha

    2009-01-01

    The crystallization and preliminary X-ray diffraction analysis of sarcosine dimethylglycine methyltransferase from H. halochoris is reported. Sarcosine dimethylglycine methyltransferase (EC 2.1.1.157) is an enzyme from the extremely halophilic anaerobic bacterium Halorhodospira halochoris. This enzyme catalyzes the twofold methylation of sarcosine to betaine, with S-adenosylmethionine (AdoMet) as the methyl-group donor. This study presents the crystallization and preliminary X-ray analysis of recombinant sarcosine dimethylglycine methyltransferase produced in Escherichia coli. Mass spectroscopy was used to determine the purity and homogeneity of the enzyme material. Two different crystal forms, which initially appeared to be hexagonal and tetragonal, were obtained. However, on analyzing the diffraction data it was discovered that both crystal forms were pseudo-merohedrally twinned. The true crystal systems were monoclinic and orthorhombic. The monoclinic crystal diffracted to a maximum of 2.15 Å resolution and the orthorhombic crystal diffracted to 1.8 Å resolution

  11. Preliminary Disposal Analysis for Selected Accelerator Production of Tritium Waste Streams

    International Nuclear Information System (INIS)

    Ades, M.J.; England, J.L.

    1998-06-01

    A preliminary analysis was performed for two selected Accelerator Production of Tritium (APT) generated mixed and low-level waste streams to determine if one mixed low-level waste (MLLW) stream that includes the Mixed Waste Lead (MWL) can be disposed of at the Nevada Test Site (NTS) and at the Hanford Site and if one low-level radioactive waste (LLW) stream, that includes the Tungsten waste stream (TWS) generated by the Tungsten Neutron Source modules and used in the Target/Blanket cavity vessel, can be disposed of in the LLW Vaults at the Savannah River Plant (SRP). The preliminary disposal analysis that the radionuclide concentrations of the two selected APT waste streams are not in full compliance with the Waste Acceptance Criteria (WAC) and the Performance Assessment (PA) radionuclide limits of the disposal sites considered

  12. Relative risk analysis in regulating the use of radiation-emitting medical devices. A preliminary application

    International Nuclear Information System (INIS)

    Jones, E.D.; Banks, W.W.; Altenbach, T.J.; Fischer, L.E.

    1995-09-01

    This report describes a preliminary application of an analysis approach for assessing relative risks in the use of radiation- emitting medical devices. Results are presented on human-initiated actions and failure modes that are most likely to occur in the use of the Gamma Knife, a gamma irradiation therapy device. This effort represents an initial step in a US Nuclear Regulatory Commission (NRC) plan to evaluate the potential role of risk analysis in regulating the use of nuclear medical devices. For this preliminary application of risk assessment, the focus was to develop a basic process using existing techniques for identifying the most likely risk contributors and their relative importance. The approach taken developed relative risk rankings and profiles that incorporated the type and quality of data available and could present results in an easily understood form. This work was performed by the Lawrence Livermore National Laboratory for the NRC

  13. National Data Center Preparedness Exercise 2015 (NPE 2015): MY-NDC Preliminary Analysis Result

    International Nuclear Information System (INIS)

    Faisal Izwan Abdul Rashid; Muhammed Zulfakar Zolkaffly

    2016-01-01

    Malaysia has established the CTBT National Data Centre (MY-NDC) in December 2005. MY-NDC is tasked to perform Comprehensive Nuclear-Test-Ban-Treaty (CTBT) data management as well as provide information for Treaty related events to Nuclear Malaysia as CTBT National Authority. In 2015, MY-NDC has participated in the National Data Centre Preparedness Exercise 2015 (NPE 2015). This paper aims at presenting MY-NDC preliminary analysis result of NPE 2015. In NPE 2015, MY-NDC has performed five different analyses, namely, radionuclide, atmospheric transport modelling (ATM), data fusion, seismic analysis and site forensics. The preliminary findings show the hypothetical scenario in NPE 2015 most probably is an uncontained event resulted high release of radionuclide to the air. (author)

  14. Preliminary safety analysis of the HTTR-IS nuclear hydrogen production system

    International Nuclear Information System (INIS)

    Sato, Hiroyuki; Ohashi, Hirofumi; Tazawa, Yujiro; Tachibana, Yukio; Sakaba, Nariaki

    2010-06-01

    Japan Atomic Energy Agency is planning to demonstrate hydrogen production by thermochemical water-splitting IS process utilizing heat from the high-temperature gas-cooled reactor HTTR (HTTR-IS system). The previous study identified that the HTTR modification due to the coupling of hydrogen production plant requires an additional safety review since the scenario and quantitative values of the evaluation items would be altered from the original HTTR safety review. Hence, preliminary safety analyses are conducted by using the system analysis code. Calculation results showed that evaluation items such as a coolant pressure, temperatures of heat transfer tubes at the pressure boundary, etc., did not exceed allowable values. Also, the peak fuel temperature did not exceed allowable value and therefore the reactor core was not damaged and cooled sufficiently. This report compiles calculation conditions, event scenarios and the calculation results of the preliminary safety analysis. (author)

  15. Preliminary Hazards Analysis of K-Basin Fuel Encapsulation and Storage

    International Nuclear Information System (INIS)

    Strickland, G.C.

    1994-01-01

    This Preliminary Hazards Analysis (PHA) systematically examines the K-Basin facilities and their supporting systems for hazards created by abnormal operating conditions and external events (e.g., earthquakes) which have the potential for causing undesirable consequences to the facility worker, the onsite individual, or the public. The operational activities examined are fuel encapsulation, fuel storage and cooling. Encapsulation of sludges in the basins is not examined. A team of individuals from Westinghouse produced a set of Hazards and Operability (HAZOP) tables documenting their examination of abnormal process conditions in the systems and activities examined in K-Basins. The purpose of this report is to reevaluate and update the HAZOP in the original Preliminary Hazard Analysis of K-Basin Fuel Encapsulation and Storage originally developed in 1991

  16. Analysis of xylem formation in pine by cDNA sequencing

    Science.gov (United States)

    Allona, I.; Quinn, M.; Shoop, E.; Swope, K.; St Cyr, S.; Carlis, J.; Riedl, J.; Retzel, E.; Campbell, M. M.; Sederoff, R.; hide

    1998-01-01

    Secondary xylem (wood) formation is likely to involve some genes expressed rarely or not at all in herbaceous plants. Moreover, environmental and developmental stimuli influence secondary xylem differentiation, producing morphological and chemical changes in wood. To increase our understanding of xylem formation, and to provide material for comparative analysis of gymnosperm and angiosperm sequences, ESTs were obtained from immature xylem of loblolly pine (Pinus taeda L.). A total of 1,097 single-pass sequences were obtained from 5' ends of cDNAs made from gravistimulated tissue from bent trees. Cluster analysis detected 107 groups of similar sequences, ranging in size from 2 to 20 sequences. A total of 361 sequences fell into these groups, whereas 736 sequences were unique. About 55% of the pine EST sequences show similarity to previously described sequences in public databases. About 10% of the recognized genes encode factors involved in cell wall formation. Sequences similar to cell wall proteins, most known lignin biosynthetic enzymes, and several enzymes of carbohydrate metabolism were found. A number of putative regulatory proteins also are represented. Expression patterns of several of these genes were studied in various tissues and organs of pine. Sequencing novel genes expressed during xylem formation will provide a powerful means of identifying mechanisms controlling this important differentiation pathway.

  17. MiSeq: A Next Generation Sequencing Platform for Genomic Analysis.

    Science.gov (United States)

    Ravi, Rupesh Kanchi; Walton, Kendra; Khosroheidari, Mahdieh

    2018-01-01

    MiSeq, Illumina's integrated next generation sequencing instrument, uses reversible-terminator sequencing-by-synthesis technology to provide end-to-end sequencing solutions. The MiSeq instrument is one of the smallest benchtop sequencers that can perform onboard cluster generation, amplification, genomic DNA sequencing, and data analysis, including base calling, alignment and variant calling, in a single run. It performs both single- and paired-end runs with adjustable read lengths from 1 × 36 base pairs to 2 × 300 base pairs. A single run can produce output data of up to 15 Gb in as little as 4 h of runtime and can output up to 25 M single reads and 50 M paired-end reads. Thus, MiSeq provides an ideal platform for rapid turnaround time. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing and target enrichment), metagenomics, and gene expression studies. For these reasons, MiSeq has become one of the most widely used next generation sequencing platforms. Here, we provide a protocol to prepare libraries for sequencing using the MiSeq instrument and basic guidelines for analysis of output data from the MiSeq sequencing run.

  18. Preliminary spatial analysis of combined BATSE/Ulysses gamma-ray burst locations

    International Nuclear Information System (INIS)

    Kippen, R. Marc; Hurley, Kevin; Pendleton, Geoffrey N.

    1998-01-01

    We present the preliminary spatial analysis of 278 bursts that have been localized by BATSE and the two-spacecraft Compton/Ulysses Interplanetary Network. The large number and superior accuracy of the combined BATSE/Ulysses locations provides improved sensitivity to small-angle source properties. We find that the locations are consistent with large- and small-scale isotropy, with no significant small-angle clustering. We constrain the fraction of sources in clusters and discuss the implications for burst repetition

  19. Preliminary Failure Modes and Effects Analysis of the US DCLL Test Blanket Module

    Energy Technology Data Exchange (ETDEWEB)

    Lee C. Cadwallader

    2010-06-01

    This report presents the results of a preliminary failure modes and effects analysis (FMEA) of a small tritium-breeding test blanket module design for the International Thermonuclear Experimental Reactor. The FMEA was quantified with “generic” component failure rate data, and the failure events are binned into postulated initiating event families and frequency categories for safety assessment. An appendix to this report contains repair time data to support an occupational radiation exposure assessment for test blanket module maintenance.

  20. Preliminary Failure Modes and Effects Analysis of the US DCLL Test Blanket Module

    Energy Technology Data Exchange (ETDEWEB)

    Lee C. Cadwallader

    2007-08-01

    This report presents the results of a preliminary failure modes and effects analysis (FMEA) of a small tritium-breeding test blanket module design for the International Thermonuclear Experimental Reactor. The FMEA was quantified with “generic” component failure rate data, and the failure events are binned into postulated initiating event families and frequency categories for safety assessment. An appendix to this report contains repair time data to support an occupational radiation exposure assessment for test blanket module maintenance.

  1. Preliminary Failure Modes and Effects Analysis of the US DCLL Test Blanket Module

    International Nuclear Information System (INIS)

    Lee C. Cadwallader

    2007-01-01

    This report presents the results of a preliminary failure modes and effects analysis (FMEA) of a small tritium-breeding test blanket module design for the International Thermonuclear Experimental Reactor. The FMEA was quantified with 'generic' component failure rate data, and the failure events are binned into postulated initiating event families and frequency categories for safety assessment. An appendix to this report contains repair time data to support an occupational radiation exposure assessment for test blanket module maintenance

  2. Preliminary crystallographic analysis of a possible transcription factor encoded by the mimivirus L544 gene

    International Nuclear Information System (INIS)

    Ciaccafava, Alexandre; Lartigue, Audrey; Mansuelle, Pascal; Jeudy, Sandra; Abergel, Chantal

    2011-01-01

    The mimivirus L544 gene product was expressed in E. coli and crystallized; preliminary phasing of a MAD data set was performed using the selenium signal present in a crystal of recombinant selenomethionine-substituted protein. Mimivirus is the prototype of a new family (the Mimiviridae) of nucleocytoplasmic large DNA viruses (NCLDVs), which already include the Poxviridae, Iridoviridae, Phycodnaviridae and Asfarviridae. Mimivirus specifically replicates in cells from the genus Acanthamoeba. Proteomic analysis of purified mimivirus particles revealed the presence of many subunits of the DNA-directed RNA polymerase II complex. A fully functional pre-transcriptional complex appears to be loaded in the virions, allowing mimivirus to initiate transcription within the host cytoplasm immediately upon infection independently of the host nuclear apparatus. To fully understand this process, a systematic study of mimivirus proteins that are predicted (by bioinformatics) or suspected (by proteomic analysis) to be involved in transcription was initiated by cloning and expressing them in Escherichia coli in order to determine their three-dimensional structures. Here, preliminary crystallographic analysis of the recombinant L544 protein is reported. The crystals belonged to the orthorhombic space group C222 1 with one monomer per asymmetric unit. A MAD data set was used for preliminary phasing using the selenium signal present in a selenomethionine-substituted protein crystal

  3. Maturity onset diabetes of youth (MODY) in Turkish children: sequence analysis of 11 causative genes by next generation sequencing.

    Science.gov (United States)

    Ağladıoğlu, Sebahat Yılmaz; Aycan, Zehra; Çetinkaya, Semra; Baş, Veysel Nijat; Önder, Aşan; Peltek Kendirci, Havva Nur; Doğan, Haldun; Ceylaner, Serdar

    2016-04-01

    Maturity-onset diabetes of the youth (MODY), is a genetically and clinically heterogeneous group of diseasesand is often misdiagnosed as type 1 or type 2 diabetes. The aim of this study is to investigate both novel and proven mutations of 11 MODY genes in Turkish children by using targeted next generation sequencing. A panel of 11 MODY genes were screened in 43 children with MODY diagnosed by clinical criterias. Studies of index cases was done with MISEQ-ILLUMINA, and family screenings and confirmation studies of mutations was done by Sanger sequencing. We identified 28 (65%) point mutations among 43 patients. Eighteen patients have GCK mutations, four have HNF1A, one has HNF4A, one has HNF1B, two have NEUROD1, one has PDX1 gene variations and one patient has both HNF1A and HNF4A heterozygote mutations. This is the first study including molecular studies of 11 MODY genes in Turkish children. GCK is the most frequent type of MODY in our study population. Very high frequency of novel mutations (42%) in our study population, supports that in heterogenous disorders like MODY sequence analysis provides rapid, cost effective and accurate genetic diagnosis.

  4. Whole genome sequencing and bioinformatics analysis of two Egyptian genomes.

    Science.gov (United States)

    ElHefnawi, Mahmoud; Jeon, Sungwon; Bhak, Youngjune; ElFiky, Asmaa; Horaiz, Ahmed; Jun, JeHoon; Kim, Hyunho; Bhak, Jong

    2018-05-15

    We report two Egyptian male genomes (EGP1 and EGP2) sequenced at ~ 30× sequencing depths. EGP1 had 4.7 million variants, where 198,877 were novel variants while EGP2 had 209,109 novel variants out of 4.8 million variants. The mitochondrial haplogroup of the two individuals were identified to be H7b1 and L2a1c, respectively. We also identified the Y haplogroup of EGP1 (R1b) and EGP2 (J1a2a1a2 > P58 > FGC11). EGP1 had a mutation in the NADH gene of the mitochondrial genome ND4 (m.11778 G > A) that causes Leber's hereditary optic neuropathy. Some SNPs shared by the two genomes were associated with an increased level of cholesterol and triglycerides, probably related with Egyptians obesity. Comparison of these genomes with African and Western-Asian genomes can provide insights on Egyptian ancestry and genetic history. This resource can be used to further understand genomic diversity and functional classification of variants as well as human migration and evolution across Africa and Western-Asia. Copyright © 2017. Published by Elsevier B.V.

  5. Accident sequence precursor analysis level 2/3 model development

    International Nuclear Information System (INIS)

    Lui, C.H.; Galyean, W.J.; Brownson, D.A.

    1997-01-01

    The US Nuclear Regulatory Commission's Accident Sequence Precursor (ASP) program currently uses simple Level 1 models to assess the conditional core damage probability for operational events occurring in commercial nuclear power plants (NPP). Since not all accident sequences leading to core damage will result in the same radiological consequences, it is necessary to develop simple Level 2/3 models that can be used to analyze the response of the NPP containment structure in the context of a core damage accident, estimate the magnitude of the resulting radioactive releases to the environment, and calculate the consequences associated with these releases. The simple Level 2/3 model development work was initiated in 1995, and several prototype models have been completed. Once developed, these simple Level 2/3 models are linked to the simple Level 1 models to provide risk perspectives for operational events. This paper describes the methods implemented for the development of these simple Level 2/3 ASP models, and the linkage process to the existing Level 1 models

  6. In Vivo Enhancer Analysis Chromosome 16 Conserved NoncodingSequences

    Energy Technology Data Exchange (ETDEWEB)

    Pennacchio, Len A.; Ahituv, Nadav; Moses, Alan M.; Nobrega,Marcelo; Prabhakar, Shyam; Shoukry, Malak; Minovitsky, Simon; Visel,Axel; Dubchak, Inna; Holt, Amy; Lewis, Keith D.; Plajzer-Frick, Ingrid; Akiyama, Jennifer; De Val, Sarah; Afzal, Veena; Black, Brian L.; Couronne, Olivier; Eisen, Michael B.; Rubin, Edward M.

    2006-02-01

    The identification of enhancers with predicted specificitiesin vertebrate genomes remains a significant challenge that is hampered bya lack of experimentally validated training sets. In this study, weleveraged extreme evolutionary sequence conservation as a filter toidentify putative gene regulatory elements and characterized the in vivoenhancer activity of human-fish conserved and ultraconserved1 noncodingelements on human chromosome 16 as well as such elements from elsewherein the genome. We initially tested 165 of these extremely conservedsequences in a transgenic mouse enhancer assay and observed that 48percent (79/165) functioned reproducibly as tissue-specific enhancers ofgene expression at embryonic day 11.5. While driving expression in abroad range of anatomical structures in the embryo, the majority of the79 enhancers drove expression in various regions of the developingnervous system. Studying a set of DNA elements that specifically droveforebrain expression, we identified DNA signatures specifically enrichedin these elements and used these parameters to rank all ~;3,400human-fugu conserved noncoding elements in the human genome. The testingof the top predictions in transgenic mice resulted in a three-foldenrichment for sequences with forebrain enhancer activity. These datadramatically expand the catalogue of in vivo-characterized human geneenhancers and illustrate the future utility of such training sets for avariety of iological applications including decoding the regulatoryvocabulary of the human genome.

  7. Sequence analysis of putative swrW gene required for surfactant ...

    African Journals Online (AJOL)

    Serratia marcescens produces biosurfactant serrawettin, essential for its population migration behavior. Serrawettin W1 was revealed to be an antibiotic serratamolide that makes it significant for deoxyribonucleic acid (DNA) and protein sequence analysis. Four nucleotide and amino-acid sequences from local strains ...

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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

    2011-01-01

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

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

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  11. Preliminary CFD Analysis for HVAC System Design of a Containment Building

    Energy Technology Data Exchange (ETDEWEB)

    Son, Sung Man; Choi, Choengryul [ELSOLTEC, Yongin (Korea, Republic of); Choo, Jae Ho; Hong, Moonpyo; Kim, Hyungseok [KEPCO Engineering and Construction, Gimcheon (Korea, Republic of)

    2016-10-15

    HVAC (Heating, Ventilation, Air Conditioning) system has been mainly designed based on overall heat balance and averaging concepts, which is simple and useful for designing overall system. However, such a method has the disadvantage that cannot predict the local flow and temperature distributions in a containment building. In this study, a CFD (Computational Fluid Dynamics) preliminary analysis is carried out to obtain detailed flow and temperature distributions in a containment building and to ensure that such information can be obtained via CFD analysis. This approach can be useful for hydrogen analysis in an accident related to hydrogen released into a containment building. In this study, CFD preliminary analysis has been performed to obtain the detailed information of the reactor containment building by using the CFD analysis techniques and to ensure that such information can be obtained via CFD analysis. We confirmed that CFD analysis can offer enough detailed information about flow patterns and temperature field and that CFD technique is a useful tool for HVAC design of nuclear power plants.

  12. A symbolic dynamics approach for the complexity analysis of chaotic pseudo-random sequences

    International Nuclear Information System (INIS)

    Xiao Fanghong

    2004-01-01

    By considering a chaotic pseudo-random sequence as a symbolic sequence, authors present a symbolic dynamics approach for the complexity analysis of chaotic pseudo-random sequences. The method is applied to the cases of Logistic map and one-way coupled map lattice to demonstrate how it works, and a comparison is made between it and the approximate entropy method. The results show that this method is applicable to distinguish the complexities of different chaotic pseudo-random sequences, and it is superior to the approximate entropy method

  13. The sequence and analysis of duplication rich human chromosome 16

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Joel; Han, Cliff; Gordon, Laurie A.; Terry, Astrid; Prabhakar, Shyam; She, Xinwei; Xie, Gary; Hellsten, Uffe; Man Chan, Yee; Altherr, Michael; Couronne, Olivier; Aerts, Andrea; Bajorek, Eva; Black, Stacey; Blumer, Heather; Branscomb, Elbert; Brown, Nancy C.; Bruno, William J.; Buckingham, Judith M.; Callen, David F.; Campbell, Connie S.; Campbell, Mary L.; Campbell, Evelyn W.; Caoile, Chenier; Challacombe, Jean F.; Chasteen, Leslie A.; Chertkov, Olga; Chi, Han C.; Christensen, Mari; Clark, Lynn M.; Cohn, Judith D.; Denys, Mirian; Detter, John C.; Dickson, Mark; Dimitrijevic-Bussod, Mira; Escobar, Julio; Fawcett, Joseph J.; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Goodwin, Lynne A.; Grady, Deborah L.; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Hildebrand, Carl E.; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Jewett, Phillip E.; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Krawczyk, Marie-Claude; Leyba, Tina; Longmire, Jonathan L.; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Ludeman, Thom; Mark, Graham A.; Mcmurray, Kimberly L.; Meincke, Linda J.; Morgan, Jenna; Moyzis, Robert K.; Mundt, Mark O.; Munk, A. Christine; Nandkeshwar, Richard D.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Parson-Quintana, Beverly; Ramirez, Lucia; Rash, Sam; Retterer, James; Ricke, Darryl O.; Robinson, Donna L.; Rodriguez, Alex; Salamov, Asaf; Saunders, Elizabeth H.; Scott, Duncan; Shough, Timothy; Stallings, Raymond L.; Stalvey, Malinda; Sutherland, Robert D.; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Torney, David C.; Tran-Gyamfi, Mary; Tsai, Ming; Ulanovsky, Levy E.; Ustaszewska, Anna; Vo, Nu; White, P. Scott; Williams, Albert L.; Wills, Patricia L.; Wu, Jung-Rung; Wu, Kevin; Yang, Joan; DeJong, Pieter; Bruce, David; Doggett, Norman; Deaven, Larry; Schmutz, Jeremy; Grimwood, Jane; Richardson, Paul; et al.

    2004-08-01

    We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

  14. Analysis of decision procedures for a sequence of inventory periods

    International Nuclear Information System (INIS)

    Avenhaus, R.

    1982-07-01

    Optimal test procedures for a sequence of inventory periods will be discussed. Starting with a game theoretical description of the conflict situation between the plant operator and the inspector, the objectives of the inspector as well as the general decision theoretical problem will be formulated. In the first part the objective of 'secure' detection will be emphasized which means that only at the end of the reference time a decision is taken by the inspector. In the second part the objective of 'timely' detection will be emphasized which will lead to sequential test procedures. At the end of the paper all procedures will be summarized, and in view of the multitude of procedures available at the moment some comments about future work will be given. (orig./HP) [de

  15. The Sequence and Analysis of Duplication Rich Human Chromosome 16

    Science.gov (United States)

    Martin, Joel; Han, Cliff; Gordon, Laurie A.; Terry, Astrid; Prabhakar, Shyam; She, Xinwei; Xie, Gary; Hellsten, Uffe; Man Chan, Yee; Altherr, Michael; Couronne, Olivier; Aerts, Andrea; Bajorek, Eva; Black, Stacey; Blumer, Heather; Branscomb, Elbert; Brown, Nancy C.; Bruno, William J.; Buckingham, Judith M.; Callen, David F.; Campbell, Connie S.; Campbell, Mary L.; Campbell, Evelyn W.; Caoile, Chenier; Challacombe, Jean F.; Chasteen, Leslie A.; Chertkov, Olga; Chi, Han C.; Christensen, Mari; Clark, Lynn M.; Cohn, Judith D.; Denys, Mirian; Detter, John C.; Dickson, Mark; Dimitrijevic-Bussod, Mira; Escobar, Julio; Fawcett, Joseph J.; Flowers, Dave; Fotopulos, Dea; Glavina, Tijana; Gomez, Maria; Gonzales, Eidelyn; Goodstein, David; Goodwin, Lynne A.; Grady, Deborah L.; Grigoriev, Igor; Groza, Matthew; Hammon, Nancy; Hawkins, Trevor; Haydu, Lauren; Hildebrand, Carl E.; Huang, Wayne; Israni, Sanjay; Jett, Jamie; Jewett, Phillip E.; Kadner, Kristen; Kimball, Heather; Kobayashi, Arthur; Krawczyk, Marie-Claude; Leyba, Tina; Longmire, Jonathan L.; Lopez, Frederick; Lou, Yunian; Lowry, Steve; Ludeman, Thom; Mark, Graham A.; Mcmurray, Kimberly L.; Meincke, Linda J.; Morgan, Jenna; Moyzis, Robert K.; Mundt, Mark O.; Munk, A. Christine; Nandkeshwar, Richard D.; Pitluck, Sam; Pollard, Martin; Predki, Paul; Parson-Quintana, Beverly; Ramirez, Lucia; Rash, Sam; Retterer, James; Ricke, Darryl O.; Robinson, Donna L.; Rodriguez, Alex; Salamov, Asaf; Saunders, Elizabeth H.; Scott, Duncan; Shough, Timothy; Stallings, Raymond L.; Stalvey, Malinda; Sutherland, Robert D.; Tapia, Roxanne; Tesmer, Judith G.; Thayer, Nina; Thompson, Linda S.; Tice, Hope; Torney, David C.; Tran-Gyamfi, Mary; Tsai, Ming; Ulanovsky, Levy E.; Ustaszewska, Anna; Vo, Nu; White, P. Scott; Williams, Albert L.; Wills, Patricia L.; Wu, Jung-Rung; Wu, Kevin; Yang, Joan; DeJong, Pieter; Bruce, David; Doggett, Norman; Deaven, Larry; Schmutz, Jeremy; Grimwood, Jane; Richardson, Paul; et al.

    2004-01-01

    We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

  16. Factoring local sequence composition in motif significance analysis.

    Science.gov (United States)

    Ng, Patrick; Keich, Uri

    2008-01-01

    We recently introduced a biologically realistic and reliable significance analysis of the output of a popular class of motif finders. In this paper we further improve our significance analysis by incorporating local base composition information. Relying on realistic biological data simulation, as well as on FDR analysis applied to real data, we show that our method is significantly better than the increasingly popular practice of using the normal approximation to estimate the significance of a finder's output. Finally we turn to leveraging our reliable significance analysis to improve the actual motif finding task. Specifically, endowing a variant of the Gibbs Sampler with our improved significance analysis we demonstrate that de novo finders can perform better than has been perceived. Significantly, our new variant outperforms all the finders reviewed in a recently published comprehensive analysis of the Harbison genome-wide binding location data. Interestingly, many of these finders incorporate additional information such as nucleosome positioning and the significance of binding data.

  17. Peptide Pattern Recognition for high-throughput protein sequence analysis and clustering

    DEFF Research Database (Denmark)

    Busk, Peter Kamp

    2017-01-01

    Large collections of protein sequences with divergent sequences are tedious to analyze for understanding their phylogenetic or structure-function relation. Peptide Pattern Recognition is an algorithm that was developed to facilitate this task but the previous version does only allow a limited...... number of sequences as input. I implemented Peptide Pattern Recognition as a multithread software designed to handle large numbers of sequences and perform analysis in a reasonable time frame. Benchmarking showed that the new implementation of Peptide Pattern Recognition is twenty times faster than...... the previous implementation on a small protein collection with 673 MAP kinase sequences. In addition, the new implementation could analyze a large protein collection with 48,570 Glycosyl Transferase family 20 sequences without reaching its upper limit on a desktop computer. Peptide Pattern Recognition...

  18. Information-Theoretical Analysis of EEG Microstate Sequences in Python

    Directory of Open Access Journals (Sweden)

    Frederic von Wegner

    2018-06-01

    Full Text Available We present an open-source Python package to compute information-theoretical quantities for electroencephalographic data. Electroencephalography (EEG measures the electrical potential generated by the cerebral cortex and the set of spatial patterns projected by the brain's electrical potential on the scalp surface can be clustered into a set of representative maps called EEG microstates. Microstate time series are obtained by competitively fitting the microstate maps back into the EEG data set, i.e., by substituting the EEG data at a given time with the label of the microstate that has the highest similarity with the actual EEG topography. As microstate sequences consist of non-metric random variables, e.g., the letters A–D, we recently introduced information-theoretical measures to quantify these time series. In wakeful resting state EEG recordings, we found new characteristics of microstate sequences such as periodicities related to EEG frequency bands. The algorithms used are here provided as an open-source package and their use is explained in a tutorial style. The package is self-contained and the programming style is procedural, focusing on code intelligibility and easy portability. Using a sample EEG file, we demonstrate how to perform EEG microstate segmentation using the modified K-means approach, and how to compute and visualize the recently introduced information-theoretical tests and quantities. The time-lagged mutual information function is derived as a discrete symbolic alternative to the autocorrelation function for metric time series and confidence intervals are computed from Markov chain surrogate data. The software package provides an open-source extension to the existing implementations of the microstate transform and is specifically designed to analyze resting state EEG recordings.

  19. Massively parallel sequencing and analysis of the Necator americanus transcriptome.

    Directory of Open Access Journals (Sweden)

    Cinzia Cantacessi

    2010-05-01

    Full Text Available The blood-feeding hookworm Necator americanus infects hundreds of millions of people worldwide. In order to elucidate fundamental molecular biological aspects of this hookworm, the transcriptome of the adult stage of Necator americanus was explored using next-generation sequencing and bioinformatic analyses.A total of 19,997 contigs were assembled from the sequence data; 6,771 of these contigs had known orthologues in the free-living nematode Caenorhabditis elegans, and most of them encoded proteins with WD40 repeats (10.6%, proteinase inhibitors (7.8% or calcium-binding EF-hand proteins (6.7%. Bioinformatic analyses inferred that the C. elegans homologues are involved mainly in biological pathways linked to ribosome biogenesis (70%, oxidative phosphorylation (63% and/or proteases (60%; most of these molecules were predicted to be involved in more than one biological pathway. Comparative analyses of the transcriptomes of N. americanus and the canine hookworm, Ancylostoma caninum, revealed qualitative and quantitative differences. For instance, proteinase inhibitors were inferred to be highly represented in the former species, whereas SCP/Tpx-1/Ag5/PR-1/Sc7 proteins ( = SCP/TAPS or Ancylostoma-secreted proteins were predominant in the latter. In N. americanus, essential molecules were predicted using a combination of orthology mapping and functional data available for C. elegans. Further analyses allowed the prioritization of 18 predicted drug targets which did not have homologues in the human host. These candidate targets were inferred to be linked to mitochondrial (e.g., processing proteins or amino acid metabolism (e.g., asparagine t-RNA synthetase.This study has provided detailed insights into the transcriptome of the adult stage of N. americanus and examines similarities and differences between this species and A. caninum. Future efforts should focus on comparative transcriptomic and proteomic investigations of the other predominant human

  20. First phylogenetic analysis of Ehrlichia canis in dogs and ticks from Mexico. Preliminary study

    Directory of Open Access Journals (Sweden)

    Carolina G. Sosa-Gutiérrez

    2016-09-01

    Full Text Available Objective. Phylogenetic characterization of Ehrlichia canis in dogs naturally infected and ticks, diagnosed by PCR and sequencing of 16SrRNA gene; compare different isolates found in American countries. Materials and methods. Were collected Blood samples from 139 dogs with suggestive clinical manifestations of this disease and they were infested with ticks; part of 16SrRNA gene was sequenced and aligned, with 17 sequences reported in American countries. Two phylogenetic trees were constructed using the Maximum likelihood method, and Maximum parsimony. Results. They were positive to E. canis 25/139 (18.0% dogs and 29/139 (20.9% ticks. The clinical manifestations presented were fever, fatigue, depression and vomiting. Rhipicephalus sanguineus Dermacentor variabilis and Haemaphysalis leporis-palustris ticks were positive for E. canis. Phylogenetic analysis showed that the sequences of dogs and ticks in Mexico form a third group diverging of sequences from South America and USA. Conclusions. This is the first phylogenetic analysis of E. canis in Mexico. There are differences in the sequences of Mexico with those reported in South America and USA. This research lays the foundation for further study of genetic variability.

  1. Preliminary hazard analysis for the Brayton Isotope Ground Demonstration System (including vacuum test chamber)

    International Nuclear Information System (INIS)

    Miller, L.G.

    1975-01-01

    The Preliminary Hazard Analysis (PHA) of the BIPS-GDS is a tabular summary of hazards and undesired events which may lead to system damage or failure and/or hazard to personnel. The PHA reviews the GDS as it is envisioned to operate in the Vacuum Test Chamber (VTC) of the GDS Test Facility. The VTC and other equipment which will comprise the test facility are presently in an early stage of preliminary design and will undoubtedly undergo numerous changes before the design is frozen. The PHA and the FMECA to follow are intended to aid the design effort by identifying areas of concern which are critical to the safety and reliability of the BIPS-GDS and test facility

  2. Expression, purification, crystallization and preliminary crystallographic analysis of the proliferation-associated protein Ebp1

    International Nuclear Information System (INIS)

    Kowalinski, Eva; Bange, Gert; Wild, Klemens; Sinning, Irmgard

    2007-01-01

    Preliminary X-ray analysis of the proliferation-associated protein Ebp1 from Homo sapiens is provided. ErbB-3-binding protein 1 (Ebp1) is a member of the family of proliferation-associated 2G4 proteins (PA2G4s) and plays a role in cellular growth and differentiation. Ligand-induced activation of the transmembrane receptor ErbB3 leads to dissociation of Ebp1 from the receptor in a phosphorylation-dependent manner. The non-associated protein is involved in transcriptional and translational regulation in the cell. Here, the overexpression, purification, crystallization and preliminary crystallographic studies of Ebp1 from Homo sapiens are reported. Initially observed crystals were improved by serial seeding to single crystals suitable for data collection. The optimized crystals belong to the tetragonal space group P4 1 2 1 2 or P4 3 2 1 2 and diffracted to a resolution of 1.6 Å

  3. Most significant preliminary results of the probabilistic safety analysis on the Juragua nuclear power plant

    International Nuclear Information System (INIS)

    Perdomo, Manuel

    1995-01-01

    Since 1990 the Group for PSA Development and Applications (GDA/APS) is working on the Level-1 PSA for the Juragua-1 NPP, as a part of an IAEA Technical Assistance Project. The main objective of this study, which is still under way, is to assess, in a preliminary way, the Reactor design safety to find its potential 'weak points' at the construction stage, using a eneric data base. At the same time, the study allows the PSA team to familiarize with the plant design and analysis techniques for the future operational PSA of the plant. This paper presents the most significant preliminary results of the study, which reveal some advantages of the safety characteristics of the plant design in comparison with the homologous VVER-440 reactors and some areas, where including slight modifications would improve the plant safety, considering the level of detail at which the study is carried out. (author). 13 refs, 1 fig, 2 tabs

  4. Combined DECS Analysis and Next-Generation Sequencing Enable Efficient Detection of Novel Plant RNA Viruses

    Directory of Open Access Journals (Sweden)

    Hironobu Yanagisawa

    2016-03-01

    Full Text Available The presence of high molecular weight double-stranded RNA (dsRNA within plant cells is an indicator of infection with RNA viruses as these possess genomic or replicative dsRNA. DECS (dsRNA isolation, exhaustive amplification, cloning, and sequencing analysis has been shown to be capable of detecting unknown viruses. We postulated that a combination of DECS analysis and next-generation sequencing (NGS would improve detection efficiency and usability of the technique. Here, we describe a model case in which we efficiently detected the presumed genome sequence of Blueberry shoestring virus (BSSV, a member of the genus Sobemovirus, which has not so far been reported. dsRNAs were isolated from BSSV-infected blueberry plants using the dsRNA-binding protein, reverse-transcribed, amplified, and sequenced using NGS. A contig of 4,020 nucleotides (nt that shared similarities with sequences from other Sobemovirus species was obtained as a candidate of the BSSV genomic sequence. Reverse transcription (RT-PCR primer sets based on sequences from this contig enabled the detection of BSSV in all BSSV-infected plants tested but not in healthy controls. A recombinant protein encoded by the putative coat protein gene was bound by the BSSV-antibody, indicating that the candidate sequence was that of BSSV itself. Our results suggest that a combination of DECS analysis and NGS, designated here as “DECS-C,” is a powerful method for detecting novel plant viruses.

  5. Data Analysis of Sequences and qPCR for Microbial Communities during Algal Blooms

    Science.gov (United States)

    A training opportunity is open to a highly microbial-research-motivated student to conduct sequence analysis, explore novel genes and metabolic pathways, validate resultant findings using qPCR/RT-qPCR and summarize the findings

  6. Sequence analysis of the N-acetyltransferase 2 gene (NAT2) among ...

    African Journals Online (AJOL)

    Yazun Bashir Jarrar

    2017-11-26

    Nov 26, 2017 ... Sequence analysis of the N-acetyltransferase 2 gene (NAT2) among Jordanian volunteers, Libyan. Journal of Medicine .... For molecular modeling of NAT2 protein, visualized ..... cal clustering. .... cular dynamics simulation.

  7. Analysis of common SHOX gene sequence variants and ∼4.9-kb ...

    Indian Academy of Sciences (India)

    [Solc R., Hirschfeldova K., Kebrdlova V. and Baxova A. 2014 Analysis of common SHOX gene sequence variants ... based on a Gibbs sampling strategy were done using .... SHOX (short stature homeobox) are an important cause of growth.

  8. Comparative sequence analysis of Sordaria macrospora and Neurospora crassa as a means to improve genome annotation.

    Science.gov (United States)

    Nowrousian, Minou; Würtz, Christian; Pöggeler, Stefanie; Kück, Ulrich

    2004-03-01

    One of the most challenging parts of large scale sequencing projects is the identification of functional elements encoded in a genome. Recently, studies of genomes of up to six different Saccharomyces species have demonstrated that a comparative analysis of genome sequences from closely related species is a powerful approach to identify open reading frames and other functional regions within genomes [Science 301 (2003) 71, Nature 423 (2003) 241]. Here, we present a comparison of selected sequences from Sordaria macrospora to their corresponding Neurospora crassa orthologous regions. Our analysis indicates that due to the high degree of sequence similarity and conservation of overall genomic organization, S. macrospora sequence information can be used to simplify the annotation of the N. crassa genome.

  9. Probabilistic topic modeling for the analysis and classification of genomic sequences

    Science.gov (United States)

    2015-01-01

    Background Studies on genomic sequences for classification and taxonomic identification have a leading role in the biomedical field and in the analysis of biodiversity. These studies are focusing on the so-called barcode genes, representing a well defined region of the whole genome. Recently, alignment-free techniques are gaining more importance because they are able to overcome the drawbacks of sequence alignment techniques. In this paper a new alignment-free method for DNA sequences clustering and classification is proposed. The method is based on k-mers representation and text mining techniques. Methods The presented method is based on Probabilistic Topic Modeling, a statistical technique originally proposed for text documents. Probabilistic topic models are able to find in a document corpus the topics (recurrent themes) characterizing classes of documents. This technique, applied on DNA sequences representing the documents, exploits the frequency of fixed-length k-mers and builds a generative model for a training group of sequences. This generative model, obtained through the Latent Dirichlet Allocation (LDA) algorithm, is then used to classify a large set of genomic sequences. Results and conclusions We performed classification of over 7000 16S DNA barcode sequences taken from Ribosomal Database Project (RDP) repository, training probabilistic topic models. The proposed method is compared to the RDP tool and Support Vector Machine (SVM) classification algorithm in a extensive set of trials using both complete sequences and short sequence snippets (from 400 bp to 25 bp). Our method reaches very similar results to RDP classifier and SVM for complete sequences. The most interesting results are obtained when short sequence snippets are considered. In these conditions the proposed method outperforms RDP and SVM with ultra short sequences and it exhibits a smooth decrease of performance, at every taxonomic level, when the sequence length is decreased. PMID:25916734

  10. Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer

    Science.gov (United States)

    2017-09-01

    AWARD NUMBER: W81XWH-14-1-0080 TITLE: Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer . PRINCIPAL INVESTIGATOR...TITLE AND SUBTITLE Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer . 5a. CONTRACT NUMBER 5b. GRANT NUMBER GRANT11489...institutional, NIH-funded study of genetic and epigenetic alterations of pre-invasive DCIS that did or did not progress to invasive breast cancer , with an

  11. Seismically induced accident sequence analysis of the advanced test reactor

    International Nuclear Information System (INIS)

    Khericha, S.T.; Henry, D.M.; Ravindra, M.K.; Hashimoto, P.S.; Griffin, M.J.; Tong, W.H.; Nafday, A.M.

    1991-01-01

    A seismic probabilistic risk assessment (PRA) was performed for the Department of Energy (DOE) Advanced Test Reactor (ATR) as part of the external events analysis. The risk from seismic events to the fuel in the core and in the fuel storage canal was evaluated. The key elements of this paper are the integration of seismically induced internal flood and internal fire, and the modeling of human error rates as a function of the magnitude of earthquake. The systems analysis was performed by EG ampersand G Idaho, Inc. and the fragility analysis and quantification were performed by EQE International, Inc. (EQE)

  12. Recent advances in nanopore-based nucleic acid analysis and sequencing

    International Nuclear Information System (INIS)

    Shi, Jidong; Fang, Ying; Hou, Junfeng

    2016-01-01

    Nanopore-based sequencing platforms are transforming the field of genomic science. This review (containing 116 references) highlights some recent progress on nanopore-based nucleic acid analysis and sequencing. These studies are classified into three categories, biological, solid-state, and hybrid nanopores, according to their nanoporous materials. We begin with a brief description of the translocation-based detection mechanism of nanopores. Next, specific examples are given in nanopore-based nucleic acid analysis and sequencing, with an emphasis on identifying strategies that can improve the resolution of nanopores. This review concludes with a discussion of future research directions that will advance the practical applications of nanopore technology. (author)

  13. Microscopic Analysis and Modeling of Airport Surface Sequencing, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The complexity and interdependence of operations on the airport surface motivate the need for a comprehensive and detailed, yet flexible and validated analysis and...

  14. BioMatriX: Sequence analysis, structure visualization, phylogenetics ...

    African Journals Online (AJOL)

    bmx-biomatrix.blogspot.com) developed for biological science community to augment scientific research regarding genomics, proteomics, phylogenetics and linkage analysis in one platform. BioMatriX offers multi-functional services to perform ...

  15. Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii genome.

    Directory of Open Access Journals (Sweden)

    Byrappa Venkatesh

    2007-04-01

    Full Text Available Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4x coverage and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element-like and long interspersed element-like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.

  16. Sequence analysis of L RNA of Lassa virus

    International Nuclear Information System (INIS)

    Vieth, Simon; Torda, Andrew E.; Asper, Marcel; Schmitz, Herbert; Guenther, Stephan

    2004-01-01

    The L RNA of three Lassa virus strains originating from Nigeria, Ghana/Ivory Coast, and Sierra Leone was sequenced and the data subjected to structure predictions and phylogenetic analyses. The L gene products had 2218-2221 residues, diverged by 18% at the amino acid level, and contained several conserved regions. Only one region of 504 residues (positions 1043-1546) could be assigned a function, namely that of an RNA polymerase. Secondary structure predictions suggest that this domain is very similar to RNA-dependent RNA polymerases of known structure encoded by plus-strand RNA viruses, permitting a model to be built. Outside the polymerase region, there is little structural data, except for regions of strong alpha-helical content and probably a coiled-coil domain at the N terminus. No evidence for reassortment or recombination during Lassa virus evolution was found. The secondary structure-assisted alignment of the RNA polymerase region permitted a reliable reconstruction of the phylogeny of all negative-strand RNA viruses, indicating that Arenaviridae are most closely related to Nairoviruses. In conclusion, the data provide a basis for structural and functional characterization of the Lassa virus L protein and reveal new insights into the phylogeny of negative-strand RNA viruses

  17. Reproducible analysis of sequencing-based RNA structure probing data with user-friendly tools

    DEFF Research Database (Denmark)

    Kielpinski, Lukasz Jan; Sidiropoulos, Nikos; Vinther, Jeppe

    2015-01-01

    time also made analysis of the data challenging for scientists without formal training in computational biology. Here, we discuss different strategies for data analysis of massive parallel sequencing-based structure-probing data. To facilitate reproducible and standardized analysis of this type of data...

  18. Stratigraphical analysis of the neoproterozoic sedimentary sequences of the Sao Francisco Basin

    International Nuclear Information System (INIS)

    Martins, Mariela; Lemos, Valesca Brasil

    2007-01-01

    A stratigraphic analysis was performed under the principles of Sequence Stratigraphy on the neoproterozoic sedimentary sequences of the Sao Francisco Basin (Central Brazil). Three periods of deposition separated by unconformities were recognized in the Sao Francisco Megasequence: (1) Sequences 1 and 2, a cryogenian glaciogenic sequence, followed by a distal scarp carbonate ramp, developed during stable conditions, (2) Sequence 3, a Upper Cryogenian stack homoclinal ramps with mixed carbonate-siliciclastic sedimentation, deposited under a progressive influence of compressional stresses of the Brasiliano Cycle, (3) Sequence 4, a Lower Ediacaran shallow platform dominated by siliciclastic sedimentation of molassic nature, the erosion product of the nearby uplifted thrust sheets. Each of the carbonate-bearing sequences presents a distinct δ 13 C isotopic signature. The superposition to the global curve for carbon isotopic variation allowed the recognition of a major depositional hiatus between the Paranoa and Sao Francisco Megasequences, and suggested that the glacial diamictite deposition (Jequitai Formation) took place most probably around 800 Ma. This constrains the Sao Francisco Megasequence deposition to the interval between 800 and 600 Ma (the known ages of the Brasiliano Orogeny defines the upper limit). A minor depositional hiatus (700.680 Ma) was also identified separating sequences 2 and 3. Isotopic analyses suggest that from then on, more restricted environmental conditions were established in the basin, probably associated with a first order global event, which prevailed throughout deposition of the Sequence 3. (author)

  19. Isolation and sequence analysis of a cDNA clone encoding the fifth complement component

    DEFF Research Database (Denmark)

    Lundwall, Åke B; Wetsel, Rick A; Kristensen, Torsten

    1985-01-01

    DNA clone of 1.85 kilobase pairs was isolated. Hybridization of the mixed-sequence probe to the complementary strand of the plasmid insert and sequence analysis by the dideoxy method predicted the expected protein sequence of C5a (positions 1-12), amino-terminal to the anticipated priming site. The sequence......, subcloned into M13 mp8, and sequenced at random by the dideoxy technique, thereby generating a contiguous sequence of 1703 base pairs. This clone contained coding sequence for the C-terminal 262 amino acid residues of the beta-chain, the entire C5a fragment, and the N-terminal 98 residues of the alpha......'-chain. The 3' end of the clone had a polyadenylated tail preceded by a polyadenylation recognition site, a 3'-untranslated region, and base pairs homologous to the human Alu concensus sequence. Comparison of the derived partial human C5 protein sequence with that previously determined for murine C3 and human...

  20. Oasis: online analysis of small RNA deep sequencing data.

    Science.gov (United States)

    Capece, Vincenzo; Garcia Vizcaino, Julio C; Vidal, Ramon; Rahman, Raza-Ur; Pena Centeno, Tonatiuh; Shomroni, Orr; Suberviola, Irantzu; Fischer, Andre; Bonn, Stefan

    2015-07-01

    Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis' exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. Oasis generates downloadable interactive web reports for easy visualization, exploration and analysis of data on a local system. Finally, Oasis' modular workflow enables for the rapid (re-) analysis of data. Oasis is implemented in Python, R, Java, PHP, C++ and JavaScript. It is freely available at http://oasis.dzne.de. stefan.bonn@dzne.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  1. Establishment of screening technique for mutant cell and analysis of base sequence in the mutation

    International Nuclear Information System (INIS)

    Sofuni, Toshio; Nomi, Takehiko; Yamada, Masami; Masumura, Kenichi

    2000-01-01

    This research project aimed to establish an easy and quick detection method for radiation-induced mutation using molecular-biological techniques and an effective analyzing method for the molecular changes in base sequence. In this year, Spi mutants derived from γ-radiation exposed mouse were analyzed by PCR method and DNA sequence method. Male transgenic mice were exposed to γ-ray at 5,10, 50 Gy and the transgene was taken out from the genome DNA from the spleen in vivo packaging method. Spi mutant plaques were obtained by infecting the recovered phage to E. coli. Sequence analysis for the mutants was made using ALFred DNA sequencer and SequiTherm TM Long-Red Cycle sequencing kit. Sequence analysis was carried out for 41 of 50 independent Spi mutants obtained. The deletions were classified into 4 groups; Group 1 included 15 mutants that were characterized with a large deletion (43 bp-10 kb) with a short homologous sequence. Group 2 included 11 mutants of a large deletion having no homologous sequence at the connecting region. Group 3 included 11 mutants having a short deletion of less than 20 bp, which occurred in the non-repetitive sequence of gam gene and possibly caused by oxidative breakage of DNA or recombination of DNA fragment produced by the breakage. Group 4 included 4 mutants having deletions as short as 20 bp or less in the repetitive sequence of gam gene, resulting in an alteration of the reading frame. Thus, the synthesis of Gam protein was terminated by the appearance of TGA between code 13 and 14 of redB gene, leading to inactivation of gam gene and redBA gene. These results indicated that most of Spi mutants had a deletion in red/gam region and the deletions in more than half mutants occurred in homologous sequences as short as 8 bp. (M.N.)

  2. The BsaHI restriction-modification system: Cloning, sequencing and analysis of conserved motifs

    Directory of Open Access Journals (Sweden)

    Roberts Richard J

    2008-05-01

    Full Text Available Abstract Background Restriction and modification enzymes typically recognise short DNA sequences of between two and eight bases in length. Understanding the mechanism of this recognition represents a significant challenge that we begin to address for the BsaHI restriction-modification system, which recognises the six base sequence GRCGYC. Results The DNA sequences of the genes for the BsaHI methyltransferase, bsaHIM, and restriction endonuclease, bsaHIR, have been determined (GenBank accession #EU386360, cloned and expressed in E. coli. Both the restriction endonuclease and methyltransferase enzymes share significant similarity with a group of 6 other enzymes comprising the restriction-modification systems HgiDI and HgiGI and the putative HindVP, NlaCORFDP, NpuORFC228P and SplZORFNP restriction-modification systems. A sequence alignment of these homologues shows that their amino acid sequences are largely conserved and highlights several motifs of interest. We target one such conserved motif, reading SPERRFD, at the C-terminal end of the bsaHIR gene. A mutational analysis of these amino acids indicates that the motif is crucial for enzymatic activity. Sequence alignment of the methyltransferase gene reveals a short motif within the target recognition domain that is conserved among enzymes recognising the same sequences. Thus, this motif may be used as a diagnostic tool to define the recognition sequences of the cytosine C5 methyltransferases. Conclusion We have cloned and sequenced the BsaHI restriction and modification enzymes. We have identified a region of the R. BsaHI enzyme that is crucial for its activity. Analysis of the amino acid sequence of the BsaHI methyltransferase enzyme led us to propose two new motifs that can be used in the diagnosis of the recognition sequence of the cytosine C5-methyltransferases.

  3. A base composition analysis of natural patterns for the preprocessing of metagenome sequences.

    Science.gov (United States)

    Bonham-Carter, Oliver; Ali, Hesham; Bastola, Dhundy

    2013-01-01

    On the pretext that sequence reads and contigs often exhibit the same kinds of base usage that is also observed in the sequences from which they are derived, we offer a base composition analysis tool. Our tool uses these natural patterns to determine relatedness across sequence data. We introduce spectrum sets (sets of motifs) which are permutations of bacterial restriction sites and the base composition analysis framework to measure their proportional content in sequence data. We suggest that this framework will increase the efficiency during the pre-processing stages of metagenome sequencing and assembly projects. Our method is able to differentiate organisms and their reads or contigs. The framework shows how to successfully determine the relatedness between these reads or contigs by comparison of base composition. In particular, we show that two types of organismal-sequence data are fundamentally different by analyzing their spectrum set motif proportions (coverage). By the application of one of the four possible spectrum sets, encompassing all known restriction sites, we provide the evidence to claim that each set has a different ability to differentiate sequence data. Furthermore, we show that the spectrum set selection having relevance to one organism, but not to the others of the data set, will greatly improve performance of sequence differentiation even if the fragment size of the read, contig or sequence is not lengthy. We show the proof of concept of our method by its application to ten trials of two or three freshly selected sequence fragments (reads and contigs) for each experiment across the six organisms of our set. Here we describe a novel and computationally effective pre-processing step for metagenome sequencing and assembly tasks. Furthermore, our base composition method has applications in phylogeny where it can be used to infer evolutionary distances between organisms based on the notion that related organisms often have much conserved code.

  4. Expressed sequence tags as a tool for phylogenetic analysis of placental mammal evolution.

    Directory of Open Access Journals (Sweden)

    Morgan Kullberg

    Full Text Available BACKGROUND: We investigate the usefulness of expressed sequence tags, ESTs, for establishing divergences within the tree of placental mammals. This is done on the example of the established relationships among primates (human, lagomorphs (rabbit, rodents (rat and mouse, artiodactyls (cow, carnivorans (dog and proboscideans (elephant. METHODOLOGY/PRINCIPAL FINDINGS: We have produced 2000 ESTs (1.2 mega bases from a marsupial mouse and characterized the data for their use in phylogenetic analysis. The sequences were used to identify putative orthologous sequences from whole genome projects. Although most ESTs stem from single sequence reads, the frequency of potential sequencing errors was found to be lower than allelic variation. Most of the sequences represented slowly evolving housekeeping-type genes, with an average amino acid distance of 6.6% between human and mouse. Positive Darwinian selection was identified at only a few single sites. Phylogenetic analyses of the EST data yielded trees that were consistent with those established from whole genome projects. CONCLUSIONS: The general quality of EST sequences and the general absence of positive selection in these sequences make ESTs an attractive tool for phylogenetic analysis. The EST approach allows, at reasonable costs, a fast extension of data sampling from species outside the genome projects.

  5. Preliminary design and off-design performance analysis of an Organic Rankine Cycle for geothermal sources

    International Nuclear Information System (INIS)

    Hu, Dongshuai; Li, Saili; Zheng, Ya; Wang, Jiangfeng; Dai, Yiping

    2015-01-01

    Highlights: • A method for preliminary design and performance prediction is established. • Preliminary data of radial inflow turbine and plate heat exchanger are obtained. • Off-design performance curves of critical components are researched. • Performance maps in sliding pressure operation are illustrated. - Abstract: Geothermal fluid of 90 °C and 10 kg/s can be exploited together with oil in Huabei Oilfield of China. Organic Rankine Cycle is regarded as a reasonable method to utilize these geothermal sources. This study conducts a detailed design and off-design performance analysis based on the preliminary design of turbines and heat exchangers. The radial inflow turbine and plate heat exchanger are selected in this paper. Sliding pressure operation is applied in the simulation and three parameters are considered: geothermal fluid mass flow rate, geothermal fluid temperature and condensing pressure. The results indicate that in all considered conditions the designed radial inflow turbine has smooth off-design performance and no choke or supersonic flow are found at the nozzle and rotor exit. The lager geothermal fluid mass flow rate, the higher geothermal fluid temperature and the lower condensing pressure contribute to the increase of cycle efficiency and net power. Performance maps are illustrated to make system meet different load requirements especially when the geothermal fluid temperature and condensing pressure deviate from the design condition. This model can be used to provide basic data for future detailed design, and predict off-design performance in the initial design phase

  6. Preliminary Analysis of Severe Accident Progression Initiated from Small Break LOCA of a SMART Reactor

    International Nuclear Information System (INIS)

    Jin, Young Ho; Park, Jong Hwa; Kim, Dong Ha; Cho, Seong Won

    2010-01-01

    SMART (System integrated Modular Advanced ReacTor), is under the development at Korea Atomic Energy Research Institute (KAERI). SMART is an integral type pressurized water reactor which contains a pressurizer, 4 reactor coolant pumps (RCPs), and 8 steam generator cassettes(S/Gs) in a single reactor vessel. This reactor has substantially enhanced its safety with an integral layout of its major components, 4 trains of safety injection systems (SISs), and an adoption of 4 trains of passive residual heat removal systems (PRHRS) instead of an active auxiliary feedwater system . The thermal power is 330 MWth. During the conceptual design stage, a preliminary PSA was performed. PSA results identified that a small break loss of coolant accident (SLOCA) with all safety injections unavailable is one of important severe core damage sequences. Clear understanding of this sequence helps in the developing accident mitigation strategies. MIDAS/SMR computer code is used to simulate the severe accident progression initiated from a small break LOCA in SMART reactor. This code has capability to model a helical steam generator which is adopted in SMART reactor. The important accident progression results for SMART reactor are then compared with the typical pressurized water reactor (PWR) result

  7. Cloning and sequence analysis of hyaluronoglucosaminidase (nagH gene of Clostridium chauvoei

    Directory of Open Access Journals (Sweden)

    Saroj K. Dangi

    2017-09-01

    Full Text Available Aim: Blackleg disease is caused by Clostridium chauvoei in ruminants. Although virulence factors such as C. chauvoei toxin A, sialidase, and flagellin are well characterized, hyaluronidases of C. chauvoei are not characterized. The present study was aimed at cloning and sequence analysis of hyaluronoglucosaminidase (nagH gene of C. chauvoei. Materials and Methods: C. chauvoei strain ATCC 10092 was grown in ATCC 2107 media and confirmed by polymerase chain reaction (PCR using the primers specific for 16-23S rDNA spacer region. nagH gene of C. chauvoei was amplified and cloned into pRham-SUMO vector and transformed into Escherichia cloni 10G cells. The construct was then transformed into E. cloni cells. Colony PCR was carried out to screen the colonies followed by sequencing of nagH gene in the construct. Results: PCR amplification yielded nagH gene of 1143 bp product, which was cloned in prokaryotic expression system. Colony PCR, as well as sequencing of nagH gene, confirmed the presence of insert. Sequence was then subjected to BLAST analysis of NCBI, which confirmed that the sequence was indeed of nagH gene of C. chauvoei. Phylogenetic analysis of the sequence showed that it is closely related to Clostridium perfringens and Clostridium paraputrificum. Conclusion: The gene for virulence factor nagH was cloned into a prokaryotic expression vector and confirmed by sequencing.

  8. Preliminary analysis for model development of groundwater evolution in Horonobe area

    International Nuclear Information System (INIS)

    Yoshida, Yasushi; Yui, Mikazu

    2003-03-01

    The preliminary analysis for model development of groundwater evolution in Horonobe area was performed with data at D-1, HDB-1 and HDB-2 bore hole where hydrogen / oxygen isotope concentration, mineral property in sedimentary rock and physico-chemical parameters (pH, Eh and ionic concentrations) were measured. As a result of analysis for hydrogen and oxygen isotope concentration, saline water in marine sediment was diluted by the mixing with shallow groundwater and diffusion. And as a result of analysis for a concentration of bicarbonate from the difference of pH values measured between in-situ and under air, the estimated in-situ concentration of bicarbonate differs from that measured under air. And minerals which were assumed to be equilibrium with groundwater were selected by thermodynamic calculation. This report presents the results of preliminary analysis for groundwater evolution by using data derived from D-1, HDB-1 and HDB-2 boring research. In order to establish the model which interprets the groundwater evolution as a next step, data which satisfy the representative in-situ property of groundwater chemistry in Horonobe area are needed. Reliable measurements for physico-chemical parameter and property of minerals in sedimentary rock in dominant layer and at the variety of depth are also needed. (author)

  9. Ares-I-X Vehicle Preliminary Range Safety Malfunction Turn Analysis

    Science.gov (United States)

    Beaty, James R.; Starr, Brett R.; Gowan, John W., Jr.

    2008-01-01

    Ares-I-X is the designation given to the flight test version of the Ares-I rocket (also known as the Crew Launch Vehicle - CLV) being developed by NASA. As part of the preliminary flight plan approval process for the test vehicle, a range safety malfunction turn analysis was performed to support the launch area risk assessment and vehicle destruct criteria development processes. Several vehicle failure scenarios were identified which could cause the vehicle trajectory to deviate from its normal flight path, and the effects of these failures were evaluated with an Ares-I-X 6 degrees-of-freedom (6-DOF) digital simulation, using the Program to Optimize Simulated Trajectories Version 2 (POST2) simulation framework. The Ares-I-X simulation analysis provides output files containing vehicle state information, which are used by other risk assessment and vehicle debris trajectory simulation tools to determine the risk to personnel and facilities in the vicinity of the launch area at Kennedy Space Center (KSC), and to develop the vehicle destruct criteria used by the flight test range safety officer. The simulation analysis approach used for this study is described, including descriptions of the failure modes which were considered and the underlying assumptions and ground rules of the study, and preliminary results are presented, determined by analysis of the trajectory deviation of the failure cases, compared with the expected vehicle trajectory.

  10. Analysis of Multiple Genomic Sequence Alignments: A Web Resource, Online Tools, and Lessons Learned From Analysis of Mammalian SCL Loci

    Science.gov (United States)

    Chapman, Michael A.; Donaldson, Ian J.; Gilbert, James; Grafham, Darren; Rogers, Jane; Green, Anthony R.; Göttgens, Berthold

    2004-01-01

    Comparative analysis of genomic sequences is becoming a standard technique for studying gene regulation. However, only a limited number of tools are currently available for the analysis of multiple genomic sequences. An extensive data set for the testing and training of such tools is provided by the SCL gene locus. Here we have expanded the data set to eight vertebrate species by sequencing the dog SCL locus and by annotating the dog and rat SCL loci. To provide a resource for the bioinformatics community, all SCL sequences and functional annotations, comprising a collation of the extensive experimental evidence pertaining to SCL regulation, have been made available via a Web server. A Web interface to new tools specifically designed for the display and analysis of multiple sequence alignments was also implemented. The unique SCL data set and new sequence comparison tools allowed us to perform a rigorous examination of the true benefits of multiple sequence comparisons. We demonstrate that multiple sequence alignments are, overall, superior to pairwise alignments for identification of mammalian regulatory regions. In the search for individual transcription factor binding sites, multiple alignments markedly increase the signal-to-noise ratio compared to pairwise alignments. PMID:14718377

  11. WebMGA: a customizable web server for fast metagenomic sequence analysis.

    Science.gov (United States)

    Wu, Sitao; Zhu, Zhengwei; Fu, Liming; Niu, Beifang; Li, Weizhong

    2011-09-07

    The new field of metagenomics studies microorganism communities by culture-independent sequencing. With the advances in next-generation sequencing techniques, researchers are facing tremendous challenges in metagenomic data analysis due to huge quantity and high complexity of sequence data. Analyzing large datasets is extremely time-consuming; also metagenomic annotation involves a wide range of computational tools, which are difficult to be installed and maintained by common users. The tools provided by the few available web servers are also limited and have various constraints such as login requirement, long waiting time, inability to configure pipelines etc. We developed WebMGA, a customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing artifacts and contaminations, taxonomic analysis, functional annotation etc. WebMGA provides users with rapid metagenomic data analysis using fast and effective tools, which have been implemented to run in parallel on our local computer cluster. Users can access WebMGA through web browsers or programming scripts to perform individual analysis or to configure and run customized pipelines. WebMGA is freely available at http://weizhongli-lab.org/metagenomic-analysis. WebMGA offers to researchers many fast and unique tools and great flexibility for complex metagenomic data analysis.

  12. WebMGA: a customizable web server for fast metagenomic sequence analysis

    Directory of Open Access Journals (Sweden)

    Niu Beifang

    2011-09-01

    Full Text Available Abstract Background The new field of metagenomics studies microorganism communities by culture-independent sequencing. With the advances in next-generation sequencing techniques, researchers are facing tremendous challenges in metagenomic data analysis due to huge quantity and high complexity of sequence data. Analyzing large datasets is extremely time-consuming; also metagenomic annotation involves a wide range of computational tools, which are difficult to be installed and maintained by common users. The tools provided by the few available web servers are also limited and have various constraints such as login requirement, long waiting time, inability to configure pipelines etc. Results We developed WebMGA, a customizable web server for fast metagenomic analysis. WebMGA includes over 20 commonly used tools such as ORF calling, sequence clustering, quality control of raw reads, removal of sequencing artifacts and contaminations, taxonomic analysis, functional annotation etc. WebMGA provides users with rapid metagenomic data analysis using fast and effective tools, which have been implemented to run in parallel on our local computer cluster. Users can access WebMGA through web browsers or programming scripts to perform individual analysis or to configure and run customized pipelines. WebMGA is freely available at http://weizhongli-lab.org/metagenomic-analysis. Conclusions WebMGA offers to researchers many fast and unique tools and great flexibility for complex metagenomic data analysis.

  13. The scale analysis sequence for LWR fuel depletion

    International Nuclear Information System (INIS)

    Hermann, O.W.; Parks, C.V.

    1991-01-01

    The SCALE (Standardized Computer Analyses for Licensing Evaluation) code system is used extensively to perform away-from-reactor safety analysis (particularly criticality safety, shielding, heat transfer analyses) for spent light water reactor (LWR) fuel. Spent fuel characteristics such as radiation sources, heat generation sources, and isotopic concentrations can be computed within SCALE using the SAS2 control module. A significantly enhanced version of the SAS2 control module, which is denoted as SAS2H, has been made available with the release of SCALE-4. For each time-dependent fuel composition, SAS2H performs one-dimensional (1-D) neutron transport analyses (via XSDRNPM-S) of the reactor fuel assembly using a two-part procedure with two separate unit-cell-lattice models. The cross sections derived from a transport analysis at each time step are used in a point-depletion computation (via ORIGEN-S) that produces the burnup-dependent fuel composition to be used in the next spectral calculation. A final ORIGEN-S case is used to perform the complete depletion/decay analysis using the burnup-dependent cross sections. The techniques used by SAS2H and two recent applications of the code are reviewed in this paper. 17 refs., 5 figs., 5 tabs

  14. Sequence determination and analysis of the NSs genes of two tospoviruses.

    Science.gov (United States)

    Hallwass, Mariana; Leastro, Mikhail O; Lima, Mirtes F; Inoue-Nagata, Alice K; Resende, Renato O

    2012-03-01

    The tospoviruses groundnut ringspot virus (GRSV) and zucchini lethal chlorosis virus (ZLCV) cause severe losses in many crops, especially in solanaceous and cucurbit species. In this study, the non-structural NSs gene and the 5'UTRs of these two biologically distinct tospoviruses were cloned and sequenced. The NSs sequence of GRSV and ZLCV were both 1,404 nucleotides long. Pairwise comparison showed that the NSs amino acid sequence of GRSV shared 69.6% identity with that of ZLCV and 75.9% identity with that of TSWV, while the NSs sequence of ZLCV and TSWV shared 67.9% identity. Phylogenetic analysis based on NSs sequences confirmed that these viruses cluster in the American clade.

  15. Sequencing and phylogenetic analysis of tobacco virus 2, a polerovirus from Nicotiana tabacum.

    Science.gov (United States)

    Zhou, Benguo; Wang, Fang; Zhang, Xuesong; Zhang, Lina; Lin, Huafeng

    2017-07-01

    The complete genome sequence of a new virus, provisionally named tobacco virus 2 (TV2), was determined and identified from leaves of tobacco (Nicotiana tabacum) exhibiting leaf mosaic, yellowing, and deformity, in Anhui Province, China. The genome sequence of TV2 comprises 5,979 nucleotides, with 87% nucleotide sequence identity to potato leafroll virus (PLRV). Its genome organization is similar to that of PLRV, containing six open reading frames (ORFs) that potentially encode proteins with putative functions in cell-to-cell movement and suppression of RNA silencing. Phylogenetic analysis of the nucleotide sequence placed TV2 alongside members of the genus Polerovirus in the family Luteoviridae. To the best our knowledge, this study is the first report of a complete genome sequence of a new polerovirus identified in tobacco.

  16. An analysis of LOCA sequences in the development of severe accident analysis DB

    International Nuclear Information System (INIS)

    Choi, Young; Park, Soo Yong; Ahn, Kwang-Il; Kim, D.H.

    2006-01-01

    Although a Level 2 PSA was performed for the Korean Standard Power Plants (KSNPs), and it considered the necessary sequences for an assessment of the containment integrity and source term analysis. In terms of an accident management, however, more cases causing severe core damage need to be analyzed and arranged systematically for an easy access to the results. At present, KAERI is calculating the severe accident sequences intensively for various initiating events and generating a database for the accident progression including thermal hydraulic and source term behaviours. The developed Database (DB) system includes a graphical display for a plant and equipment status, previous research results by knowledge-base technique, and the expected plant behaviour. The plant model used in this paper is oriented to the case of LOCAs related severe accident phenomena and thus can simulate the plant behaviours for a severe accident. Therefore the developed system may play a central role as an information source for decision-making for a severe accident management, and will be used as a training simulator for a severe accident management. (author)

  17. A preliminary analysis of the risk of transporting nuclear waste to potential candidate commercial repository sites

    International Nuclear Information System (INIS)

    Madsen, M.M.

    1984-01-01

    In accordance with the provisions of the Nuclear Waste Policy Act of 1982, environmental assessments for potential candidate sites are required to provide a basis for selection of the first site for disposal of commercial radioactive waste in deep geologic repositories. A preliminary analysis of the impacts of transportation for each of the five potential sites will be described. Transportation was assumed to be entirely by truck or entirely by rail in order to obtain bounding impacts. This paper presents both radiological and nonradiological risks for the once-through fuel cycle

  18. Foregrounds in the BOOMERANG-LDB data: a preliminary rms analysis

    OpenAIRE

    Masi, S.; Ade, P. A. R.; Bock, J.; Boscaleri, A.; Crill, B. P.; de Bernardis, P.; Ganga, K.; Giacometti, M.; Hivon, E.; Hristov, V. V.; Lange, A. E.; Martinis, L.; Mauskopf, P. D.; Montroy, T.; Netterfield, C. B.

    2000-01-01

    We present a preliminary analysis of the BOOMERanG LDB maps, focused on foregrounds. BOOMERanG detects dust emission at moderately low galactic latitudes ($b > -20^o$) in bands centered at 90, 150, 240, 410 GHz. At higher Galactic latitudes, we use the BOOMERanG data to set conservative upper limits on the level of contamination at 90 and 150 GHz. We find that the mean square signal correlated with the IRAS/DIRBE dust template is less than 3% of the mean square signal due to CMB anisotropy.

  19. Documentation of Hanford Site independent review of the Hanford Waste Vitrification Plant Preliminary Safety Analysis Report

    International Nuclear Information System (INIS)

    Herborn, D.I.

    1991-10-01

    The requirements for Westinghouse Hanford independent review of the Preliminary Safety Analysis Report (PSAR) are contained in Section 1.0, Subsection 4.3 of WCH-CM-4-46. Specifically, this manual requires the following: (1) Formal functional reviews of the HWVP PSAR by the future operating organization (HWVP Operations), and the independent review organizations (HWVP and Environmental Safety Assurance, Environmental Assurance, and Quality Assurance); and (2) Review and approval of the HWVP PSAR by the Tank Waste Disposal (TWD) Subcouncil of the Safety and Environmental Advisory Council (SEAC), which provides independent advice to the Westinghouse Hanford President and executives on matters of safety and environmental protection. 7 refs

  20. Preliminary study of energy confinement data with a statistical analysis system in HL-2A tokamak

    International Nuclear Information System (INIS)

    Xu Yuan; Cui Zhengying; Ji Xiaoquan; Dong Chunfeng; Yang Qingwei; O J W F Kardaun

    2010-01-01

    Taking advantage of the HL-2A experimental data,an energy confinement database facing ITERL DB2.0 version has been originally established. As for this database,a world widely used statistical analysis system (SAS) has been adopted for the first time to analyze and evaluate the confinement data from HL-2A and the research on scaling laws of energy confinement time corresponding to plasma density is developed, some preliminary results having been achieved. Finally, through comparing with both ITER scaling law and previous ASDEX database, the investigation about L-mode confinement quality on HL-2A and influence of temperature on Spitzer resistivity will be discussed. (authors)

  1. Geoscientific long-term prognosis. Preliminary safety analysis for the site Gorleben

    International Nuclear Information System (INIS)

    Mrugalla, Sabine

    2011-07-01

    The preliminary safety analysis of the site Gorleben includes the following chapters: (1) Introduction; (2) Aim and content of the geoscientific long-term prognosis for the site Gorleben; (3) Boundary conditions at the site Gorleben: climate; geomorphology; overlying rocks and adjoining rocks; hydrogeology; salt deposit Gorleben. (4) Probable future geological developments at the site Gorleben: supraregional developments with effects on the site Gorleben; glacial period developments; developments of the geomorphology, overlying and adjoining rocks; future developments of the hydrological systems at the site Gorleben; future saliniferous specific developments of the salt deposit Gorleben. (5) Commentary on the unlikely or excludable developments of the site Gorleben.

  2. Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

    Science.gov (United States)

    Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

    2012-01-01

    Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

  3. Generation and analysis of expressed sequence tags from the ciliate protozoan parasite Ichthyophthirius multifiliis

    Directory of Open Access Journals (Sweden)

    Arias Covadonga

    2007-06-01

    Full Text Available Abstract Background The ciliate protozoan Ichthyophthirius multifiliis (Ich is an important parasite of freshwater fish that causes 'white spot disease' leading to significant losses. A genomic resource for large-scale studies of this parasite has been lacking. To study gene expression involved in Ich pathogenesis and virulence, our goal was to generate expressed sequence tags (ESTs for the development of a powerful microarray platform for the analysis of global gene expression in this species. Here, we initiated a project to sequence and analyze over 10,000 ESTs. Results We sequenced 10,368 EST clones using a normalized cDNA library made from pooled samples of the trophont, tomont, and theront life-cycle stages, and generated 9,769 sequences (94.2% success rate. Post-sequencing processing led to 8,432 high quality sequences. Clustering analysis of these ESTs allowed identification of 4,706 unique sequences containing 976 contigs and 3,730 singletons. These unique sequences represent over two million base pairs (~10% of Plasmodium falciparum genome, a phylogenetically related protozoan. BLASTX searches produced 2,518 significant (E-value -5 hits and further Gene Ontology (GO analysis annotated 1,008 of these genes. The ESTs were analyzed comparatively against the genomes of the related protozoa Tetrahymena thermophila and P. falciparum, allowing putative identification of additional genes. All the EST sequences were deposited by dbEST in GenBank (GenBank: EG957858–EG966289. Gene discovery and annotations are presented and discussed. Conclusion This set of ESTs represents a significant proportion of the Ich transcriptome, and provides a material basis for the development of microarrays useful for gene expression studies concerning Ich development, pathogenesis, and virulence.

  4. Genetic mutation analysis of human gastric adenocarcinomas using ion torrent sequencing platform.

    Directory of Open Access Journals (Sweden)

    Zhi Xu

    Full Text Available Gastric cancer is the one of the major causes of cancer-related death, especially in Asia. Gastric adenocarcinoma, the most common type of gastric cancer, is heterogeneous and its incidence and cause varies widely with geographical regions, gender, ethnicity, and diet. Since unique mutations have been observed in individual human cancer samples, identification and characterization of the molecular alterations underlying individual gastric adenocarcinomas is a critical step for developing more effective, personalized therapies. Until recently, identifying genetic mutations on an individual basis by DNA sequencing remained a daunting task. Recent advances in new next-generation DNA sequencing technologies, such as the semiconductor-based Ion Torrent sequencing platform, makes DNA sequencing cheaper, faster, and more reliable. In this study, we aim to identify genetic mutations in the genes which are targeted by drugs in clinical use or are under development in individual human gastric adenocarcinoma samples using Ion Torrent sequencing. We sequenced 737 loci from 45 cancer-related genes in 238 human gastric adenocarcinoma samples using the Ion Torrent Ampliseq Cancer Panel. The sequencing analysis revealed a high occurrence of mutations along the TP53 locus (9.7% in our sample set. Thus, this study indicates the utility of a cost and time efficient tool such as Ion Torrent sequencing to screen cancer mutations for the development of personalized cancer therapy.

  5. Crystallization, characterization and preliminary X-ray crystallographic analysis of GK2848, a putative carbonic anhydrase of Geobacillus kaustophilus

    International Nuclear Information System (INIS)

    Ragunathan, Preethi; Raghunath, Gokul; Kuramitsu, Seiki; Yokoyama, Shigeyuki; Kumarevel, Thirumananseri; Ponnuraj, Karthe

    2013-01-01

    The expression, purification, characterization and crystallization of GK2848, a carbonic anhydrase from G. kaustophilus, are described. The crystals diffracted to a resolution of 2.70 Å. GK2848, a hypothetical protein from the thermophilic organism Geobacillus kaustophilus, was cloned and overexpressed in Escherichia coli. The protein was purified to homogeneity using Ni–NTA affinity-column and gel-filtration chromatography. The purified protein was crystallized using the sitting-drop vapour-diffusion method. The crystals diffracted to a resolution of 2.70 Å and belonged to the orthorhombic space group P2 1 2 1 2. GK2848 bears sequence homology to carbonic anhydrases of various bacterial species, indicating that it belongs to the carbonic anhydrase family of proteins. A subsequent carbonic anhydrase activity assay of GK2848 using the Wilbur–Anderson method confirmed its function as a carbonic anhydrase. A preliminary structure solution was obtained by molecular replacement using MOLREP. Mutation and biochemical characterization of the protein are in progress. The structure and functional analysis of GK2848 might provide valuable information on a novel class of carbonic anhydrases, as none of its homologous structures have been characterized

  6. Crystallization and preliminary crystallographic analysis of LipC12, a true lipase isolated through a metagenomics approach

    International Nuclear Information System (INIS)

    Martini, V. P.; Glogauer, A.; Iulek, J.; Souza, E. M.; Pedrosa, F. O.; Krieger, N.

    2012-01-01

    The preliminary X-ray analysis of LipC12, the first lipase isolated through a metagenomics approach to be crystallized, is reported. LipC12, a true lipase from family I.1 of bacterial lipases which was previously isolated through a metagenomics approach, contains 293 amino acids. Among lipases of known three-dimensional structure, it has a sequence identity of 47% to the lipase from Pseudomonas aeruginosa PAO1. Recombinant N-terminally His 6 -tagged LipC12 protein was expressed in Escherichia coli, purified in a homogenous form and crystallized in several conditions, with the best crystals being obtained using 2.0 M sodium formate and 0.1 M bis-tris propane pH 7.0. X-ray diffraction data were collected to 2.70 Å resolution. The crystals belonged to the tetragonal space group P4 1 22, with unit-cell parameters a = b = 58.62, c = 192.60 Å

  7. Preliminary Report: Analysis of the baseline study on the prevalence of Salmonella in laying hen flocks of Gallus gallus

    DEFF Research Database (Denmark)

    Hald, Tine

    This is a preliminary report on the analysis of the Community-wide baseline study to estimate the prevalence of Salmonella in laying hen flocks. It is being published pending the full analysis of the entire dataset from the baseline study. The report contains the elements necessary for the establ......This is a preliminary report on the analysis of the Community-wide baseline study to estimate the prevalence of Salmonella in laying hen flocks. It is being published pending the full analysis of the entire dataset from the baseline study. The report contains the elements necessary...

  8. Plastome Sequence Determination and Comparative Analysis for Members of the Lolium-Festuca Grass Species Complex

    Science.gov (United States)

    Hand, Melanie L.; Spangenberg, German C.; Forster, John W.; Cogan, Noel O. I.

    2013-01-01

    Chloroplast genome sequences are of broad significance in plant biology, due to frequent use in molecular phylogenetics, comparative genomics, population genetics, and genetic modification studies. The present study used a second-generation sequencing approach to determine and assemble the plastid genomes (plastomes) of four representatives from the agriculturally important Lolium-Festuca species complex of pasture grasses (Lolium multiflorum, Festuca pratensis, Festuca altissima, and Festuca ovina). Total cellular DNA was extracted from either roots or leaves, was sequenced, and the output was filtered for plastome-related reads. A comparison between sources revealed fewer plastome-related reads from root-derived template but an increase in incidental bacterium-derived sequences. Plastome assembly and annotation indicated high levels of sequence identity and a conserved organization and gene content between species. However, frequent deletions within the F. ovina plastome appeared to contribute to a smaller plastid genome size. Comparative analysis with complete plastome sequences from other members of the Poaceae confirmed conservation of most grass-specific features. Detailed analysis of the rbcL–psaI intergenic region, however, revealed a “hot-spot” of variation characterized by independent deletion events. The evolutionary implications of this observation are discussed. The complete plastome sequences are anticipated to provide the basis for potential organelle-specific genetic modification of pasture grasses. PMID:23550121

  9. galaxie--CGI scripts for sequence identification through automated phylogenetic analysis.

    Science.gov (United States)

    Nilsson, R Henrik; Larsson, Karl-Henrik; Ursing, Björn M

    2004-06-12

    The prevalent use of similarity searches like BLAST to identify sequences and species implicitly assumes the reference database to be of extensive sequence sampling. This is often not the case, restraining the correctness of the outcome as a basis for sequence identification. Phylogenetic inference outperforms similarity searches in retrieving correct phylogenies and consequently sequence identities, and a project was initiated to design a freely available script package for sequence identification through automated Web-based phylogenetic analysis. Three CGI scripts were designed to facilitate qualified sequence identification from a Web interface. Query sequences are aligned to pre-made alignments or to alignments made by ClustalW with entries retrieved from a BLAST search. The subsequent phylogenetic analysis is based on the PHYLIP package for inferring neighbor-joining and parsimony trees. The scripts are highly configurable. A service installation and a version for local use are found at http://andromeda.botany.gu.se/galaxiewelcome.html and http://galaxie.cgb.ki.se

  10. QTL analysis by sequencing of Water Use Efficiency (WUE) in potato

    DEFF Research Database (Denmark)

    Kaminski, Kacper Piotr; Sønderkær, Mads; Sørensen, Kirsten Kørup

    2013-01-01

    The traditional approach to potato breeding, the classical “mate and phenotype” approach is relatively costly and because phenotyping and growth capacity is limited, this are being slowly replaced by Marker Assisted Selection (MAS) breeding schemes. MAS is based on the presence of DNA polymorphic.......sparsipilum), phenotyped for water use efficiency. This population has also previously been phenotyped for the total glycoalkaloid (TGA) content....... and time consuming process. Here, a novel method for Quantitative Trait Locus (QTL) analysis has been developed, that allows for development of specific markers by use of genomic sequence reads and the recently published reference genome sequence for potato. Prior to sequencing the mapping population...

  11. Sequence length variation, indel costs, and congruence in sensitivity analysis

    DEFF Research Database (Denmark)

    Aagesen, Lone; Petersen, Gitte; Seberg, Ole

    2005-01-01

    The behavior of two topological and four character-based congruence measures was explored using different indel treatments in three empirical data sets, each with different alignment difficulties. The analyses were done using direct optimization within a sensitivity analysis framework in which...... the cost of indels was varied. Indels were treated either as a fifth character state, or strings of contiguous gaps were considered single events by using linear affine gap cost. Congruence consistently improved when indels were treated as single events, but no congruence measure appeared as the obviously...... preferable one. However, when combining enough data, all congruence measures clearly tended to select the same alignment cost set as the optimal one. Disagreement among congruence measures was mostly caused by a dominant fragment or a data partition that included all or most of the length variation...

  12. Accident sequences and causes analysis in a hydrogen production process

    Energy Technology Data Exchange (ETDEWEB)

    Jae, Moo Sung; Hwang, Seok Won; Kang, Kyong Min; Ryu, Jung Hyun; Kim, Min Soo; Cho, Nam Chul; Jeon, Ho Jun; Jung, Gun Hyo; Han, Kyu Min; Lee, Seng Woo [Hanyang Univ., Seoul (Korea, Republic of)

    2006-03-15

    Since hydrogen production facility using IS process requires high temperature of nuclear power plant, safety assessment should be performed to guarantee the safety of facility. First of all, accident cases of hydrogen production and utilization has been surveyed. Based on the results, risk factors which can be derived from hydrogen production facility were identified. Besides the correlation between risk factors are schematized using influence diagram. Also initiating events of hydrogen production facility were identified and accident scenario development and quantification were performed. PSA methodology was used for identification of initiating event and master logic diagram was used for selection method of initiating event. Event tree analysis was used for quantification of accident scenario. The sum of all the leakage frequencies is 1.22x10{sup -4} which is similar value (1.0x10{sup -4}) for core damage frequency that International Nuclear Safety Advisory Group of IAEA suggested as a criteria.

  13. Image registration based on virtual frame sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chen, H.; Ng, W.S. [Nanyang Technological University, Computer Integrated Medical Intervention Laboratory, School of Mechanical and Aerospace Engineering, Singapore (Singapore); Shi, D. (Nanyang Technological University, School of Computer Engineering, Singapore, Singpore); Wee, S.B. [Tan Tock Seng Hospital, Department of General Surgery, Singapore (Singapore)

    2007-08-15

    This paper is to propose a new framework for medical image registration with large nonrigid deformations, which still remains one of the biggest challenges for image fusion and further analysis in many medical applications. Registration problem is formulated as to recover a deformation process with the known initial state and final state. To deal with large nonlinear deformations, virtual frames are proposed to be inserted to model the deformation process. A time parameter is introduced and the deformation between consecutive frames is described with a linear affine transformation. Experiments are conducted with simple geometric deformation as well as complex deformations presented in MRI and ultrasound images. All the deformations are characterized with nonlinearity. The positive results demonstrated the effectiveness of this algorithm. The framework proposed in this paper is feasible to register medical images with large nonlinear deformations and is especially useful for sequential images. (orig.)

  14. Next-generation sequencing of multiple individuals per barcoded library by deconvolution of sequenced amplicons using endonuclease fragment analysis

    DEFF Research Database (Denmark)

    Andersen, Jeppe D; Pereira, Vania; Pietroni, Carlotta

    2014-01-01

    The simultaneous sequencing of samples from multiple individuals increases the efficiency of next-generation sequencing (NGS) while also reducing costs. Here we describe a novel and simple approach for sequencing DNA from multiple individuals per barcode. Our strategy relies on the endonuclease...... digestion of PCR amplicons prior to library preparation, creating a specific fragment pattern for each individual that can be resolved after sequencing. By using both barcodes and restriction fragment patterns, we demonstrate the ability to sequence the human melanocortin 1 receptor (MC1R) genes from 72...... individuals using only 24 barcoded libraries....

  15. VisRseq: R-based visual framework for analysis of sequencing data

    OpenAIRE

    Younesy, Hamid; Möller, Torsten; Lorincz, Matthew C; Karimi, Mohammad M; Jones, Steven JM

    2015-01-01

    Background Several tools have been developed to enable biologists to perform initial browsing and exploration of sequencing data. However the computational tool set for further analyses often requires significant computational expertise to use and many of the biologists with the knowledge needed to interpret these data must rely on programming experts. Results We present VisRseq, a framework for analysis of sequencing datasets that provides a computationally rich and accessible framework for ...

  16. Targeted DNA Methylation Analysis by High Throughput Sequencing in Porcine Peri-attachment Embryos

    OpenAIRE

    MORRILL, Benson H.; COX, Lindsay; WARD, Anika; HEYWOOD, Sierra; PRATHER, Randall S.; ISOM, S. Clay

    2013-01-01

    Abstract The purpose of this experiment was to implement and evaluate the effectiveness of a next-generation sequencing-based method for DNA methylation analysis in porcine embryonic samples. Fourteen discrete genomic regions were amplified by PCR using bisulfite-converted genomic DNA derived from day 14 in vivo-derived (IVV) and parthenogenetic (PA) porcine embryos as template DNA. Resulting PCR products were subjected to high-throughput sequencing using the Illumina Genome Analyzer IIx plat...

  17. CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

    OpenAIRE

    Agrawal, Sonia; Arze, Cesar; Adkins, Ricky S.; Crabtree, Jonathan; Riley, David; Vangala, Mahesh; Galens, Kevin; Fraser, Claire M.; Tettelin, Herv?; White, Owen; Angiuoli, Samuel V.; Mahurkar, Anup; Fricke, W. Florian

    2017-01-01

    Background The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. Results CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. ...

  18. Preliminary phytochemical screening, Antibacterial potential and GC-MS analysis of two medicinal plant extracts.

    Science.gov (United States)

    Vijayaram, Seerangaraj; Kannan, Suruli; Saravanan, Konda Mani; Vasantharaj, Seerangaraj; Sathiyavimal, Selvam; P, Palanisamy Senthilkumar

    2016-05-01

    The presence study was aimed to catalyze the primary metabolites and their confirmation by using GC-MS analysis and antibacterial potential of leaf extract of two important medicinal plant viz., Eucalyptus and Azadirachta indica. The antibacterial potential of the methanol leaf extract of the studied species was tested against Escherichia coli, Pseudomonas aeruginosa, Klebsiellap neumoniae, Streptococcus pyogens, Staphylococcus aureus using by agar well diffusion method. The higher zone of inhibition (16mm) was observed against the bacterium Pseudomonas aeruginosa at 100μl concentration of methanol leaf extract. Preliminary phytochemical analysis of studied species shows that presence of phytochemical compounds like steroids, phenolic compounds and flavonoids. GC-MS analysis confirms the occurrence of 20 different compounds in the methanol leaf extract of the both studied species.

  19. 1972 preliminary safety analysis report based on a conceptual design of a proposed repository in Kansas

    International Nuclear Information System (INIS)

    Blomeke, J.O.

    1977-08-01

    This preliminary safety analysis report is based on a proposed Federal Repository at Lyons, Kansas, for receiving, handling, and depositing radioactive solid wastes in bedded salt during the remainder of this century. The safety analysis applies to a hypothetical site in central Kansas identical to the Lyons site, except that it is free of nearby salt solution-mining operations and bore holes that cannot be plugged to Repository specifications. This PSAR contains much information that also appears in the conceptual design report. Much of the geological-hydrological information was gathered in the Lyons area. This report is organized in 16 sections: considerations leading to the proposed Repository, design requirements and criteria, a description of the Lyons site and its environs, land improvements, support facilities, utilities, different impacts of Repository operations, safety analysis, design confirmation program, operational management, requirements for eventually decommissioning the facility, design criteria for protection from severe natural events, and the proposed program of experimental investigations

  20. Modeling and preliminary thermal analysis of the capsule for a creep test in HANARO

    International Nuclear Information System (INIS)

    Choi, Myoung Hwan; Cho, Man Soon; Choo, Kee Nam; Kang, Young Hwan; Sohn, Jae Min; Shin, Yoon Taeg; Park, Sung Jae; Kim, Bong Goo; Kim, Young Jin

    2005-01-01

    A creep capsule is a device to investigate the creep characteristics of nuclear materials during inpile irradiation tests. To obtain the design data of the capsule through a preliminary thermal analysis, a 2-dimensional model for the cross section of the capsule including the specimens and components is generated, and an analysis using the ANSYS program is performed. The gamma-heating rates of the materials for the HANARO power of 30MW are considered, and the effect of the gap size and the control rod position on the temperature of the specimen is discussed. From the analysis it is found that the gap between the thermal media and the external tube has a significant effect on the temperature of the specimen. The temperature by increasing the position of the control rod is decreased

  1. 1972 preliminary safety analysis report based on a conceptual design of a proposed repository in Kansas

    Energy Technology Data Exchange (ETDEWEB)

    Blomeke, J.O.

    1977-08-01

    This preliminary safety analysis report is based on a proposed Federal Repository at Lyons, Kansas, for receiving, handling, and depositing radioactive solid wastes in bedded salt during the remainder of this century. The safety analysis applies to a hypothetical site in central Kansas identical to the Lyons site, except that it is free of nearby salt solution-mining operations and bore holes that cannot be plugged to Repository specifications. This PSAR contains much information that also appears in the conceptual design report. Much of the geological-hydrological information was gathered in the Lyons area. This report is organized in 16 sections: considerations leading to the proposed Repository, design requirements and criteria, a description of the Lyons site and its environs, land improvements, support facilities, utilities, different impacts of Repository operations, safety analysis, design confirmation program, operational management, requirements for eventually decommissioning the facility, design criteria for protection from severe natural events, and the proposed program of experimental investigations. (DLC)

  2. Preliminary Computational Analysis of the (HIRENASD) Configuration in Preparation for the Aeroelastic Prediction Workshop

    Science.gov (United States)

    Chwalowski, Pawel; Florance, Jennifer P.; Heeg, Jennifer; Wieseman, Carol D.; Perry, Boyd P.

    2011-01-01

    This paper presents preliminary computational aeroelastic analysis results generated in preparation for the first Aeroelastic Prediction Workshop (AePW). These results were produced using FUN3D software developed at NASA Langley and are compared against the experimental data generated during the HIgh REynolds Number Aero- Structural Dynamics (HIRENASD) Project. The HIRENASD wind-tunnel model was tested in the European Transonic Windtunnel in 2006 by Aachen University0s Department of Mechanics with funding from the German Research Foundation. The computational effort discussed here was performed (1) to obtain a preliminary assessment of the ability of the FUN3D code to accurately compute physical quantities experimentally measured on the HIRENASD model and (2) to translate the lessons learned from the FUN3D analysis of HIRENASD into a set of initial guidelines for the first AePW, which includes test cases for the HIRENASD model and its experimental data set. This paper compares the computational and experimental results obtained at Mach 0.8 for a Reynolds number of 7 million based on chord, corresponding to the HIRENASD test conditions No. 132 and No. 159. Aerodynamic loads and static aeroelastic displacements are compared at two levels of the grid resolution. Harmonic perturbation numerical results are compared with the experimental data using the magnitude and phase relationship between pressure coefficients and displacement. A dynamic aeroelastic numerical calculation is presented at one wind-tunnel condition in the form of the time history of the generalized displacements. Additional FUN3D validation results are also presented for the AGARD 445.6 wing data set. This wing was tested in the Transonic Dynamics Tunnel and is commonly used in the preliminary benchmarking of computational aeroelastic software.

  3. Third-Generation Sequencing and Analysis of Four Complete Pig Liver Esterase Gene Sequences in Clones Identified by Screening BAC Library.

    Science.gov (United States)

    Zhou, Qiongqiong; Sun, Wenjuan; Liu, Xiyan; Wang, Xiliang; Xiao, Yuncai; Bi, Dingren; Yin, Jingdong; Shi, Deshi

    2016-01-01

    Pig liver carboxylesterase (PLE) gene sequences in GenBank are incomplete, which has led to difficulties in studying the genetic structure and regulation mechanisms of gene expression of PLE family genes. The aim of this study was to obtain and analysis of complete gene sequences of PLE family by screening from a Rongchang pig BAC library and third-generation PacBio gene sequencing. After a number of existing incomplete PLE isoform gene sequences were analysed, primers were designed based on conserved regions in PLE exons, and the whole pig genome used as a template for Polymerase chain reaction (PCR) amplification. Specific primers were then selected based on the PCR amplification results. A three-step PCR screening method was used to identify PLE-positive clones by screening a Rongchang pig BAC library and PacBio third-generation sequencing was performed. BLAST comparisons and other bioinformatics methods were applied for sequence analysis. Five PLE-positive BAC clones, designated BAC-10, BAC-70, BAC-75, BAC-119 and BAC-206, were identified. Sequence analysis yielded the complete sequences of four PLE genes, PLE1, PLE-B9, PLE-C4, and PLE-G2. Complete PLE gene sequences were defined as those containing regulatory sequences, exons, and introns. It was found that, not only did the PLE exon sequences of the four genes show a high degree of homology, but also that the intron sequences were highly similar. Additionally, the regulatory region of the genes contained two 720bps reverse complement sequences that may have an important function in the regulation of PLE gene expression. This is the first report to confirm the complete sequences of four PLE genes. In addition, the study demonstrates that each PLE isoform is encoded by a single gene and that the various genes exhibit a high degree of sequence homology, suggesting that the PLE family evolved from a single ancestral gene. Obtaining the complete sequences of these PLE genes provides the necessary foundation for

  4. Genome sequencing and analysis of BCG vaccine strains.

    Directory of Open Access Journals (Sweden)

    Wen Zhang

    Full Text Available BACKGROUND: Although the Bacillus Calmette-Guérin (BCG vaccine against tuberculosis (TB has been available for more than 75 years, one third of the world's population is still infected with Mycobacterium tuberculosis and approximately 2 million people die of TB every year. To reduce this immense TB burden, a clearer understanding of the functional genes underlying the action of BCG and the development of new vaccines are urgently needed. METHODS AND FINDINGS: Comparative genomic analysis of 19 M. tuberculosis complex strains showed that BCG strains underwent repeated human manipulation, had higher region of deletion rates than those of natural M. tuberculosis strains, and lost several essential components such as T-cell epitopes. A total of 188 BCG strain T-cell epitopes were lost to various degrees. The non-virulent BCG Tokyo strain, which has the largest number of T-cell epitopes (359, lost 124. Here we propose that BCG strain protection variability results from different epitopes. This study is the first to present BCG as a model organism for genetics research. BCG strains have a very well-documented history and now detailed genome information. Genome comparison revealed the selection process of BCG strains under human manipulation (1908-1966. CONCLUSIONS: Our results revealed the cause of BCG vaccine strain protection variability at the genome level and supported the hypothesis that the restoration of lost BCG Tokyo epitopes is a useful future vaccine development strategy. Furthermore, these detailed BCG vaccine genome investigation results will be useful in microbial genetics, microbial engineering and other research fields.

  5. Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.

    KAUST Repository

    Doan, Ryan; Cohen, Noah D; Sawyer, Jason; Ghaffari, Noushin; Johnson, Charlie D; Dindot, Scott V

    2012-01-01

    BACKGROUND: The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. RESULTS: Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse's genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. CONCLUSIONS: This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.

  6. Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare.

    KAUST Repository

    Doan, Ryan

    2012-02-17

    BACKGROUND: The catalog of genetic variants in the horse genome originates from a few select animals, the majority originating from the Thoroughbred mare used for the equine genome sequencing project. The purpose of this study was to identify genetic variants, including single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (INDELs), and copy number variants (CNVs) in the genome of an individual Quarter Horse mare sequenced by next-generation sequencing. RESULTS: Using massively parallel paired-end sequencing, we generated 59.6 Gb of DNA sequence from a Quarter Horse mare resulting in an average of 24.7X sequence coverage. Reads were mapped to approximately 97% of the reference Thoroughbred genome. Unmapped reads were de novo assembled resulting in 19.1 Mb of new genomic sequence in the horse. Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs. Genetic variants were annotated to determine their impact on gene structure and function. Additionally, we genotyped this Quarter Horse for mutations of known diseases and for variants associated with particular traits. Functional clustering analysis of genetic variants revealed that most of the genetic variation in the horse\\'s genome was enriched in sensory perception, signal transduction, and immunity and defense pathways. CONCLUSIONS: This is the first sequencing of a horse genome by next-generation sequencing and the first genomic sequence of an individual Quarter Horse mare. We have increased the catalog of genetic variants for use in equine genomics by the addition of novel SNPs, INDELs, and CNVs. The genetic variants described here will be a useful resource for future studies of genetic variation regulating performance traits and diseases in equids.

  7. The purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum

    International Nuclear Information System (INIS)

    Dobson, Renwick C. J.; Atkinson, Sarah C.; Gorman, Michael A.; Newman, Janet M.; Parker, Michael W.; Perugini, Matthew A.

    2008-01-01

    Dihydrodipicolinate synthase (DHDPS), an enzyme in the lysine-biosynthetic pathway, is a promising target for antibiotic development against pathogenic bacteria. Here, the expression, purification, crystallization and preliminary diffraction analysis of DHDPS from C. botulinum are reported. In recent years, dihydrodipicolinate synthase (DHDPS; EC 4.2.1.52) has received considerable attention from both mechanistic and structural viewpoints. This enzyme, which is part of the diaminopimelate pathway leading to lysine, couples (S)-aspartate-β-semialdehyde with pyruvate via a Schiff base to a conserved active-site lysine. In this paper, the expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPS from Clostridium botulinum, an important bacterial pathogen, are presented. The enzyme was crystallized in a number of forms, predominantly using PEG precipitants, with the best crystal diffracting to beyond 1.9 Å resolution and displaying P4 2 2 1 2 symmetry. The unit-cell parameters were a = b = 92.9, c = 60.4 Å. The crystal volume per protein weight (V M ) was 2.07 Å 3 Da −1 , with an estimated solvent content of 41%. The structure of the enzyme will help guide the design of novel therapeutics against the C. botulinum pathogen

  8. A Preliminary Analysis of Reactor Performance Test (LOEP) for a Research Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyeonil; Park, Su-Ki [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2015-10-15

    The final phase of commissioning is reactor performance test, which is to prove the integrated performance and safety of the research reactor at full power with fuel loaded such as neutron power calibration, Control Absorber Rod/Second Shutdown Rod drop time, InC function test, Criticality, Rod worth, Core heat removal with natural mechanism, and so forth. The last test will be safety-related one to assure the result of the safety analysis of the research reactor is marginal enough to be sure about the nuclear safety by showing the reactor satisfies the acceptance criteria of the safety functions such as for reactivity control, maintenance of auxiliaries, reactor pool water inventory control, core heat removal, and confinement isolation. After all, the fuel integrity will be ensured by verifying there is no meaningful change in the radiation levels. To confirm the performance of safety equipment, loss of normal electric power (LOEP), possibly categorized as Anticipated Operational Occurrence (AOO), is selected as a key experiment to figure out how safe the research reactor is before turning over the research reactor to the owner. This paper presents a preliminary analysis of the reactor performance test (LOEP) for a research reactor. The results showed how different the transient between conservative estimate and best estimate will look. Preliminary analyses have shown all probable thermal-hydraulic transient behavior of importance as to opening of flap valve, minimum critical heat flux ratio, the change of flow direction, and important values of thermal-hydraulic parameters.

  9. Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase from Escherichia coli

    International Nuclear Information System (INIS)

    Hor, Lilian; Dobson, Renwick C. J.; Dogovski, Con; Hutton, Craig A.; Perugini, Matthew A.

    2009-01-01

    Diaminopimelate (DAP) epimerase, an enzyme in the lysine-biosynthetic pathway, is a promising target for antibiotic development against pathogenic bacteria. Here, the cloning, expression, purification, crystallization and preliminary diffraction analysis of DAP epimerase from E. coli are reported. Diaminopimelate (DAP) epimerase (EC 5.1.1.7) catalyzes the penultimate step of lysine biosynthesis in bacteria and plants, converting l,l-diaminopimelate to meso-diaminopimelate. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DAP epimerase from Escherichia coli are presented. Crystals were obtained in space group P4 1 2 1 2 and diffracted to 2.0 Å resolution, with unit-cell parameters a = b = 89.4, c = 179.6 Å. Molecular replacement was conducted using Bacillus anthracis DAP epimerase as a search model and showed the presence of two molecules in the asymmetric unit, with an initial R free of 0.456 and R work of 0.416

  10. Mini-DIAL system measurements coupled with multivariate data analysis to identify TIC and TIM simulants: preliminary absorption database analysis

    International Nuclear Information System (INIS)

    Gaudio, P; Malizia, A; Gelfusa, M; Poggi, L.A.; Martinelli, E.; Di Natale, C.; Bellecci, C.

    2017-01-01

    Nowadays Toxic Industrial Components (TICs) and Toxic Industrial Materials (TIMs) are one of the most dangerous and diffuse vehicle of contamination in urban and industrial areas. The academic world together with the industrial and military one are working on innovative solutions to monitor the diffusion in atmosphere of such pollutants. In this phase the most common commercial sensors are based on “point detection” technology but it is clear that such instruments cannot satisfy the needs of the smart cities. The new challenge is developing stand-off systems to continuously monitor the atmosphere. Quantum Electronics and Plasma Physics (QEP) research group has a long experience in laser system development and has built two demonstrators based on DIAL (Differential Absorption of Light) technology could be able to identify chemical agents in atmosphere. In this work the authors will present one of those DIAL system, the miniaturized one, together with the preliminary results of an experimental campaign conducted on TICs and TIMs simulants in cell with aim of use the absorption database for the further atmospheric an analysis using the same DIAL system. The experimental results are analysed with standard multivariate data analysis technique as Principal Component Analysis (PCA) to develop a classification model aimed at identifying organic chemical compound in atmosphere. The preliminary results of absorption coefficients of some chemical compound are shown together pre PCA analysis. (paper)

  11. mESAdb: microRNA expression and sequence analysis database.

    Science.gov (United States)

    Kaya, Koray D; Karakülah, Gökhan; Yakicier, Cengiz M; Acar, Aybar C; Konu, Ozlen

    2011-01-01

    microRNA expression and sequence analysis database (http://konulab.fen.bilkent.edu.tr/mirna/) (mESAdb) is a regularly updated database for the multivariate analysis of sequences and expression of microRNAs from multiple taxa. mESAdb is modular and has a user interface implemented in PHP and JavaScript and coupled with statistical analysis and visualization packages written for the R language. The database primarily comprises mature microRNA sequences and their target data, along with selected human, mouse and zebrafish expression data sets. mESAdb analysis modules allow (i) mining of microRNA expression data sets for subsets of microRNAs selected manually or by motif; (ii) pair-wise multivariate analysis of expression data sets within and between taxa; and (iii) association of microRNA subsets with annotation databases, HUGE Navigator, KEGG and GO. The use of existing and customized R packages facilitates future addition of data sets and analysis tools. Furthermore, the ability to upload and analyze user-specified data sets makes mESAdb an interactive and expandable analysis tool for microRNA sequence and expression data.

  12. Novel primer specific false terminations during DNA sequencing reactions: danger of inaccuracy of mutation analysis in molecular diagnostics

    Science.gov (United States)

    Anwar, R; Booth, A; Churchill, A J; Markham, A F

    1996-01-01

    The determination of nucleotide sequence is fundamental to the identification and molecular analysis of genes. Direct sequencing of PCR products is now becoming a commonplace procedure for haplotype analysis, and for defining mutations and polymorphism within genes, particularly for diagnostic purposes. A previously unrecognised phenomenon, primer related variability, observed in sequence data generated using Taq cycle sequencing and T7 Sequenase sequencing, is reported. This suggests that caution is necessary when interpreting DNA sequence data. This is particularly important in situations where treatment may be dependent on the accuracy of the molecular diagnosis. Images PMID:16696096

  13. The calorimetric spectrum of the electron-capture decay of $^{163}$Ho. A preliminary analysis of the preliminary data

    CERN Document Server

    De Rújula, A.

    2015-01-01

    It is in principle possible to measure directly the electron neutrino mass (or masses and mixing angles) in weak electron-capture decays. The optimal nuclide in this respect is $^{163}$Ho. The favoured experimental technique, currently pursued in various experiments (ECHo, HOLMES and NuMECS) is "calorimetric". The calorimetric energy spectrum is a sum over the unstable vacant orbitals, or "holes", left by the electrons weakly captured by the nucleus. We discuss the current progress in this field and analize the preliminary data. Our conclusion is that, as pointed out by Robertson, the contribution of two-hole states is not negligible. But --in strong contradistinction with the tacit conclusion of previous comparisons of theory and observations-- we find a quite satisfactory agreement. A crucial point is that, in the creation of secondary holes, electron shakeoff and not only electron shakeup must be taken into account.

  14. A priori Considerations When Conducting High-Throughput Amplicon-Based Sequence Analysis

    Directory of Open Access Journals (Sweden)

    Aditi Sengupta

    2016-03-01

    Full Text Available Amplicon-based sequencing strategies that include 16S rRNA and functional genes, alongside “meta-omics” analyses of communities of microorganisms, have allowed researchers to pose questions and find answers to “who” is present in the environment and “what” they are doing. Next-generation sequencing approaches that aid microbial ecology studies of agricultural systems are fast gaining popularity among agronomy, crop, soil, and environmental science researchers. Given the rapid development of these high-throughput sequencing techniques, researchers with no prior experience will desire information about the best practices that can be used before actually starting high-throughput amplicon-based sequence analyses. We have outlined items that need to be carefully considered in experimental design, sampling, basic bioinformatics, sequencing of mock communities and negative controls, acquisition of metadata, and in standardization of reaction conditions as per experimental requirements. Not all considerations mentioned here may pertain to a particular study. The overall goal is to inform researchers about considerations that must be taken into account when conducting high-throughput microbial DNA sequencing and sequences analysis.

  15. Regularized rare variant enrichment analysis for case-control exome sequencing data.

    Science.gov (United States)

    Larson, Nicholas B; Schaid, Daniel J

    2014-02-01

    Rare variants have recently garnered an immense amount of attention in genetic association analysis. However, unlike methods traditionally used for single marker analysis in GWAS, rare variant analysis often requires some method of aggregation, since single marker approaches are poorly powered for typical sequencing study sample sizes. Advancements in sequencing technologies have rendered next-generation sequencing platforms a realistic alternative to traditional genotyping arrays. Exome sequencing in particular not only provides base-level resolution of genetic coding regions, but also a natural paradigm for aggregation via genes and exons. Here, we propose the use of penalized regression in combination with variant aggregation measures to identify rare variant enrichment in exome sequencing data. In contrast to marginal gene-level testing, we simultaneously evaluate the effects of rare variants in multiple genes, focusing on gene-based least absolute shrinkage and selection operator (LASSO) and exon-based sparse group LASSO models. By using gene membership as a grouping variable, the sparse group LASSO can be used as a gene-centric analysis of rare variants while also providing a penalized approach toward identifying specific regions of interest. We apply extensive simulations to evaluate the performance of these approaches with respect to specificity and sensitivity, comparing these results to multiple competing marginal testing methods. Finally, we discuss our findings and outline future research. © 2013 WILEY PERIODICALS, INC.

  16. Molecular characterization, sequence analysis and tissue expression of a porcine gene – MOSPD2

    Directory of Open Access Journals (Sweden)

    Yang Jie

    2017-01-01

    Full Text Available The full-length cDNA sequence of a porcine gene, MOSPD2, was amplified using the rapid amplification of cDNA ends method based on a pig expressed sequence tag sequence which was highly homologous to the coding sequence of the human MOSPD2 gene. Sequence prediction analysis revealed that the open reading frame of this gene encodes a protein of 491 amino acids that has high homology with the motile sperm domain-containing protein 2 (MOSPD2 of five species: horse (89%, human (90%, chimpanzee (89%, rhesus monkey (89% and mouse (85%; thus, it could be defined as a porcine MOSPD2 gene. This novel porcine gene was assigned GeneID: 100153601. This gene is structured in 15 exons and 14 introns as revealed by computer-assisted analysis. The phylogenetic analysis revealed that the porcine MOSPD2 gene has a closer genetic relationship with the MOSPD2 gene of horse. Tissue expression analysis indicated that the porcine MOSPD2 gene is generally and differentially expressed in the spleen, muscle, skin, kidney, lung, liver, fat and heart. Our experiment is the first to establish the primary foundation for further research on the porcine MOSPD2 gene.

  17. Preliminary design and thermal analysis of device for finish cooling Jaffa biscuits in a.d. 'Jaffa'- Crvenka

    Directory of Open Access Journals (Sweden)

    Salemović Duško R.

    2015-01-01

    Full Text Available In this paper preliminary design of device for finish cooling chocolate topping of biscuits in A.D. 'Jaffa'- Crvenka was done. The proposed preliminary design followed by the required technological process of finish cooling biscuits and required parameters of process which was supposed to get and which represented part of project task. Thermal analysis was made and obtained percentage error between surface contact of the air and chocolate topping, obtained from heat balance and geometrical over proposed preliminary design, wasn't more than 0.67%. This is a preliminary design completely justified because using required length of belt conveyor receive required temperature of chocolate topping at the end of the cooling process.

  18. Sequence and phylogenetic analysis of chicken anaemia virus obtained from backyard and commercial chickens in Nigeria.

    Science.gov (United States)

    Oluwayelu, D O; Todd, D; Olaleye, O D

    2008-12-01

    This work reports the first molecular analysis study of chicken anaemia virus (CAV) in backyard chickens in Africa using molecular cloning and sequence analysis to characterize CAV strains obtained from commercial chickens and Nigerian backyard chickens. Partial VP1 gene sequences were determined for three CAVs from commercial chickens and for six CAV variants present in samples from a backyard chicken. Multiple alignment analysis revealed that the 6% and 4% nucleotide diversity obtained respectively for the commercial and backyard chicken strains translated to only 2% amino acid diversity for each breed. Overall, the amino acid composition of Nigerian CAVs was found to be highly conserved. Since the partial VP1 gene sequence of two backyard chicken cloned CAV strains (NGR/CI-8 and NGR/CI-9) were almost identical and evolutionarily closely related to the commercial chicken strains NGR-1, and NGR-4 and NGR-5, respectively, we concluded that CAV infections had crossed the farm boundary.

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

    Directory of Open Access Journals (Sweden)

    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.

  20. PMS2 gene mutational analysis: direct cDNA sequencing to circumvent pseudogene interference.

    Science.gov (United States)

    Wimmer, Katharina; Wernstedt, Annekatrin

    2014-01-01

    The presence of highly homologous pseudocopies can compromise the mutation analysis of a gene of interest. In particular, when using PCR-based strategies, pseudogene co-amplification has to be effectively prevented. This is often achieved by using primers designed to be parental gene specific according to the reference sequence and by applying stringent PCR conditions. However, there are cases in which this approach is of limited utility. For example, it has been shown that the PMS2 gene exchanges sequences with one of its pseudogenes, named PMS2CL. This results in functional PMS2 alleles containing pseudogene-derived sequences at their 3'-end and in nonfunctional PMS2CL pseudogene alleles that contain gene-derived sequences. Hence, the paralogues cannot be distinguished according to the reference sequence. This shortcoming can be effectively circumvented by using direct cDNA sequencing. This approach is based on the selective amplification of PMS2 transcripts in two overlapping 1.6-kb RT-PCR products. In addition to avoiding pseudogene co-amplification and allele dropout, this method has also the advantage that it allows to effectively identify deletions, splice mutations, and de novo retrotransposon insertions that escape the detection of most DNA-based mutation analysis protocols.

  1. An integrative variant analysis suite for whole exome next-generation sequencing data

    Directory of Open Access Journals (Sweden)

    Challis Danny

    2012-01-01

    Full Text Available Abstract Background Whole exome capture sequencing allows researchers to cost-effectively sequence the coding regions of the genome. Although the exome capture sequencing methods have become routine and well established, there is currently a lack of tools specialized for variant calling in this type of data. Results Using statistical models trained on validated whole-exome capture sequencing data, the Atlas2 Suite is an integrative variant analysis pipeline optimized for variant discovery on all three of the widely used next generation sequencing platforms (SOLiD, Illumina, and Roche 454. The suite employs logistic regression models in conjunction with user-adjustable cutoffs to accurately separate true SNPs and INDELs from sequencing and mapping errors with high sensitivity (96.7%. Conclusion We have implemented the Atlas2 Suite and applied it to 92 whole exome samples from the 1000 Genomes Project. The Atlas2 Suite is available for download at http://sourceforge.net/projects/atlas2/. In addition to a command line version, the suite has been integrated into the Genboree Workbench, allowing biomedical scientists with minimal informatics expertise to remotely call, view, and further analyze variants through a simple web interface. The existing genomic databases displayed via the Genboree browser also streamline the process from variant discovery to functional genomics analysis, resulting in an off-the-shelf toolkit for the broader community.

  2. Cloning and sequence analysis of cDNA coding for rat nucleolar protein C23

    International Nuclear Information System (INIS)

    Ghaffari, S.H.; Olson, M.O.J.

    1986-01-01

    Using synthetic oligonucleotides as primers and probes, the authors have isolated and sequenced cDNA clones encoding protein C23, a putative nucleolus organizer protein. Poly(A + ) RNA was isolated from rat Novikoff hepatoma cells and enriched in C23 mRNA by sucrose density gradient ultracentrifugation. Two deoxyoligonuleotides, a 48- and a 27-mer, were synthesized on the basis of amino acid sequence from the C-terminal half of protein C23 and cDNA sequence data from CHO cell protein. The 48-mer was used a primer for synthesis of cDNA which was then inserted into plasmid pUC9. Transformed bacterial colonies were screened by hybridization with 32 P labeled 27-mer. Two clones among 5000 gave a strong positive signal. Plasmid DNAs from these clones were purified and characterized by blotting and nucleotide sequence analysis. The length of C23 mRNA was estimated to be 3200 bases in a northern blot analysis. The sequence of a 267 b.p. insert shows high homology with the CHO cDNA with only 9 nucleotide differences and an identical amino acid sequence. These studies indicate that this region of the protein is highly conserved

  3. Preliminary Nuclear Analysis for the HANARO Fuel Element with Burnable Absorber

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Chul Gyo; Kim, So Young; In, Won Ho [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2015-10-15

    Burnable absorber is used for reducing reactivity swing and power peaking in high performance research reactors. Development of the HANARO fuel element with burnable absorber was started in the U-Mo fuel development program at HANARO, but detailed full core analysis was not performed because the current HANARO fuel management system is uncertain to analysis the HANARO core with burnable absorber. A sophisticated reactor physics system is required to analysis the core. The McCARD code was selected and the detailed McCARD core models, in which the basic HANARO core model was developed by one of the McCARD developers, are used in this study. The development of nuclear fuel requires a long time and correct developing direction especially by the nuclear analysis. This paper presents a preliminary nuclear analysis to promote the fuel development. Based on the developed fuel, the further nuclear analysis will improve reactor performance and safety. Basic nuclear analysis for the HANARO and the AHR were performed for getting the proper fuel elements with burnable absorber. Addition of 0.3 - 0.4% Cd to the fuel meat is promising for the current HANARO fuel element. Small addition of burnable absorber may not change any fuel characteristics of the HANARO fuel element, but various basic tests and irradiation tests at the HANARO core are required.

  4. Preliminary Uncertainty Analysis for SMART Digital Core Protection and Monitoring System

    International Nuclear Information System (INIS)

    Koo, Bon Seung; In, Wang Kee; Hwang, Dae Hyun

    2012-01-01

    The Korea Atomic Energy Research Institute (KAERI) developed on-line digital core protection and monitoring systems, called SCOPS and SCOMS as a part of SMART plant protection and monitoring system. SCOPS simplified the protection system by directly connecting the four RSPT signals to each core protection channel and eliminated the control element assembly calculator (CEAC) hardware. SCOMS adopted DPCM3D method in synthesizing core power distribution instead of Fourier expansion method being used in conventional PWRs. The DPCM3D method produces a synthetic 3-D power distribution by coupling a neutronics code and measured in-core detector signals. The overall uncertainty analysis methodology which is used statistically combining uncertainty components of SMART core protection and monitoring system was developed. In this paper, preliminary overall uncertainty factors for SCOPS/SCOMS of SMART initial core were evaluated by applying newly developed uncertainty analysis method

  5. Preliminary Evaluation of MapReduce for High-Performance Climate Data Analysis

    Science.gov (United States)

    Duffy, Daniel Q.; Schnase, John L.; Thompson, John H.; Freeman, Shawn M.; Clune, Thomas L.

    2012-01-01

    MapReduce is an approach to high-performance analytics that may be useful to data intensive problems in climate research. It offers an analysis paradigm that uses clusters of computers and combines distributed storage of large data sets with parallel computation. We are particularly interested in the potential of MapReduce to speed up basic operations common to a wide range of analyses. In order to evaluate this potential, we are prototyping a series of canonical MapReduce operations over a test suite of observational and climate simulation datasets. Our initial focus has been on averaging operations over arbitrary spatial and temporal extents within Modern Era Retrospective- Analysis for Research and Applications (MERRA) data. Preliminary results suggest this approach can improve efficiencies within data intensive analytic workflows.

  6. Preliminary Analysis of the Bundle-Duct Interaction for the fuel of SFR

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Byoung Oon; Cheon, Jin Sik; Hahn, Do Hee; Lee, Chan Bock [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2008-10-15

    BDI (Bundle-Duct Interaction) occurs in the fuel of SFR (Sodium-cooled Fast Reactor) due to the radial expansion and bowing of a fuel pin bundle. Under the BDI condition, excess cladding strain and hot spots would occur. Therefore, BDI, which is the dominant deformation mechanisms in a fuel pin bundle, should be considered to evaluate the FBR fuel integrity. The analysis codes such as ETOILE and BMBOO, have been developed to evaluate the BDI behavior. The bundle duct interaction model is also being developed for SFR in Korea. This model is based on ANSYS. In this paper, the fuel pin configuration model for the BDI calculation was established. The preliminary analysis of the bundle-duct interaction was performed to evaluate the fuel design concept.

  7. Los Alamos National Laboratory corregated metal pipe saw facility preliminary safety analysis report. Volume I

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1990-09-19

    This Preliminary Safety Analysis Report addresses site assessment, facility design and construction, and design operation of the processing systems in the Corrugated Metal Pipe Saw Facility with respect to normal and abnormal conditions. Potential hazards are identified, credible accidents relative to the operation of the facility and the process systems are analyzed, and the consequences of postulated accidents are presented. The risk associated with normal operations, abnormal operations, and natural phenomena are analyzed. The accident analysis presented shows that the impact of the facility will be acceptable for all foreseeable normal and abnormal conditions of operation. Specifically, under normal conditions the facility will have impacts within the limits posted by applicable DOE guidelines, and in accident conditions the facility will similarly meet or exceed the requirements of all applicable standards. 16 figs., 6 tabs.

  8. Preliminary analysis on hybrid Box-Jenkins - GARCH modeling in forecasting gold price

    Science.gov (United States)

    Yaziz, Siti Roslindar; Azizan, Noor Azlinna; Ahmad, Maizah Hura; Zakaria, Roslinazairimah; Agrawal, Manju; Boland, John

    2015-02-01

    Gold has been regarded as a valuable precious metal and the most popular commodity as a healthy return investment. Hence, the analysis and prediction of gold price become very significant to investors. This study is a preliminary analysis on gold price and its volatility that focuses on the performance of hybrid Box-Jenkins models together with GARCH in analyzing and forecasting gold price. The Box-Cox formula is used as the data transformation method due to its potential best practice in normalizing data, stabilizing variance and reduces heteroscedasticity using 41-year daily gold price data series starting 2nd January 1973. Our study indicates that the proposed hybrid model ARIMA-GARCH with t-innovation can be a new potential approach in forecasting gold price. This finding proves the strength of GARCH in handling volatility in the gold price as well as overcomes the non-linear limitation in the Box-Jenkins modeling.

  9. Preliminary X-ray crystallographic analysis of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans

    International Nuclear Information System (INIS)

    Zhang, Yanfei; Cherney, Maia M.; Solomonson, Matthew; Liu, Jianshe; James, Michael N. G.; Weiner, Joel H.

    2009-01-01

    The sulfide:quinone oxidoreductase from A. ferrooxidans ATCC 23270 was overexpressed in E. coli and purified. Crystallization and preliminarily X-ray crystallographic analysis were performed for the recombinant enzyme. The gene product of open reading frame AFE-1293 from Acidithiobacillus ferrooxidans ATCC 23270 is annotated as encoding a sulfide:quinone oxidoreductase, an enzyme that catalyses electron transfer from sulfide to quinone. Following overexpression in Escherichia coli, the enzyme was purified and crystallized using the hanging-drop vapour-diffusion method. The native crystals belonged to the tetragonal space group P4 2 2 1 2, with unit-cell parameters a = b = 131.7, c = 208.8 Å, and diffracted to 2.3 Å resolution. Preliminary crystallographic analysis indicated the presence of a dimer in the asymmetric unit, with an extreme value of the Matthews coefficient (V M ) of 4.53 Å 3 Da −1 and a solvent content of 72.9%

  10. Preliminary code development for seismic signal analysis related to test ban treaty questions

    International Nuclear Information System (INIS)

    Brolley, J.E.

    1977-01-01

    Forensic seismology, from a present day viewpoint, appears to be divided into several areas. Overwhelmingly important, in view of current Complete Test Ban (CTB) discussions, is the seismological study of waves generated in the earth by underground nuclear explosions. Over the last two decades intensive effort has been devoted to developing improved observational apparatus and to the interpretation of the data produced by this equipment. It is clearly desirable to extract the maximum amount of information from seismic signals. It is, therefore, necessary to quantitatively compare various modes of analysis to establish which mode or combination of modes provides the most useful information. Preliminary code development for application of some modern developments in signal processing to seismic signals is described. Applications of noncircular functions are considered and compared with circular function results. The second portion of the discussion concerns maximum entropy analysis. Lastly, the multivariate aspects of the general problem are considered

  11. Treatment by gliding arc of epoxy resin: preliminary analysis of surface modifications

    Science.gov (United States)

    Faubert, F.; Wartel, M.; Pellerin, N.; Pellerin, S.; Cochet, V.; Regnier, E.; Hnatiuc, B.

    2016-12-01

    Treatments with atmospheric pressure non-thermal plasma are easy to implement and inexpensive. Among them gliding arc (GlidArc) remains rarely used in surface treatment of polymers. However, it offers economic and flexible way to treat quickly large areas. In addition the choice of carrier gas makes it possible to bring the active species and other radicals allowing different types of grafting and functionalization of the treated surfaces, for example in order to apply for anti-biofouling prevention. This preliminary work includes analysis of the surface of epoxy resins by infrared spectroscopy: the different affected chemical bonds were studied depending on the duration of treatment. The degree of oxidation (the C/O ratio) is obtained by X-ray microanalysis and contact angle analysis have been performed to determinate the wettability properties of the treated surface. A spectroscopic study of the plasma allows to determine the possible active species in the different zones of the discharge.

  12. PseudoMLSA: a database for multigenic sequence analysis of Pseudomonas species

    Directory of Open Access Journals (Sweden)

    Lalucat Jorge

    2010-04-01

    Full Text Available Abstract Background The genus Pseudomonas comprises more than 100 species of environmental, clinical, agricultural, and biotechnological interest. Although, the recommended method for discriminating bacterial species is DNA-DNA hybridisation, alternative techniques based on multigenic sequence analysis are becoming a common practice in bacterial species discrimination studies. Since there is not a general criterion for determining which genes are more useful for species resolution; the number of strains and genes analysed is increasing continuously. As a result, sequences of different genes are dispersed throughout several databases. This sequence information needs to be collected in a common database, in order to be useful for future identification-based projects. Description The PseudoMLSA Database is a comprehensive database of multiple gene sequences from strains of Pseudomonas species. The core of the database is composed of selected gene sequences from all Pseudomonas type strains validly assigned to the genus through 2008. The database is aimed to be useful for MultiLocus Sequence Analysis (MLSA procedures, for the identification and characterisation of any Pseudomonas bacterial isolate. The sequences are available for download via a direct connection to the National Center for Biotechnology Information (NCBI. Additionally, the database includes an online BLAST interface for flexible nucleotide queries and similarity searches with the user's datasets, and provides a user-friendly output for easily parsing, navigating, and analysing BLAST results. Conclusions The PseudoMLSA database amasses strains and sequence information of validly described Pseudomonas species, and allows free querying of the database via a user-friendly, web-based interface available at http://www.uib.es/microbiologiaBD/Welcome.html. The web-based platform enables easy retrieval at strain or gene sequence information level; including references to published peer

  13. Comparative analysis of the prion protein gene sequences in African lion.

    Science.gov (United States)

    Wu, Chang-De; Pang, Wan-Yong; Zhao, De-Ming

    2006-10-01

    The prion protein gene of African lion (Panthera Leo) was first cloned and polymorphisms screened. The results suggest that the prion protein gene of eight African lions is highly homogenous. The amino acid sequences of the prion protein (PrP) of all samples tested were identical. Four single nucleotide polymorphisms (C42T, C81A, C420T, T600C) in the prion protein gene (Prnp) of African lion were found, but no amino acid substitutions. Sequence analysis showed that the higher homology is observed to felis catus AF003087 (96.7%) and to sheep number M31313.1 (96.2%) Genbank accessed. With respect to all the mammalian prion protein sequences compared, the African lion prion protein sequence has three amino acid substitutions. The homology might in turn affect the potential intermolecular interactions critical for cross species transmission of prion disease.

  14. Capillary electrophoresis fragment analysis and clone sequencing in detection of dynamic mutations of spinocerebellar ataxia

    Directory of Open Access Journals (Sweden)

    Yuan-yuan CHEN

    2018-04-01

    Full Text Available Objective To estimate the accuracy and stability of capillary electrophoresis fragment analysis and clone sequencing in detecting dynamic mutations of spinocerebellar ataxia (SCA. Methods Capillary electrophoresis fragment analysis and clone sequencing were used in detecting trinucleotide repeated sequence of 14 SCA patients (3 cases of SCA2, 2 cases of SCA7, 7 cases of SCA8 and 2 cases of SCA17. Results Capillary electrophoresis fragment analysis of 3 SCA2 cases showed the expanded cytosine-adenine-guanine (CAG repeats were 31, 30 and 32, and the copy numbers of 3 clone sequencing for 3 colonies in each case were 37/40/40, 37/38/39 and 38/39/40 respectively. Capillary electrophoresis fragment analysis of 2 SCA7 cases showed the expanded CAG repeats were 57 and 34, and the copy numbers of repeats were 69, 74, 75 in 3 colonies of one case, and was 45 in the other case. For the 7 SCA8 cases with the expanded cytosine-thymine-adenine (CTA/cytosine-thymine-guanine (CTG repeats of 99, 111, 104, 92, 89, 104 and 75, the results of clone sequencing were 97, 116, 104, 90, 90, 102 and 76 respectively. For 2 SCA17 cases with the short/expanded CAG repeats of 37/50 and 36/45, the results of clone sequencing were 51/50/52 and 45/44 for 3 and 2 colonies. Conclusions Although the higher mobility of polymerase chain reaction (PCR products containing dynamic mutation in the capillary electrophoresis fragment analysis might cause the deviation for analysis of copy numbers, the deviation was predictable and the results were repeatable. The clone sequencing results showed obvious instability, especially for SCA2 and SCA7 genes, which might owing to their simple CAG repeats. Consequently, clone sequencing is not suited for detection of dynamic mutation, not to mention the quantitative criteria of dynamic mutation sequencing. DOI: 10.3969/j.issn.1672-6731.2018.03.008

  15. Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing.

    Science.gov (United States)

    González, Roberto; Zato, Carolina; Benito, Rocío; Bajo, Javier; Hernández, Jesús M; De Paz, Juan F; Vera, Vicente; Corchado, Juan M

    2012-12-01

    Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms.

  16. Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing

    Directory of Open Access Journals (Sweden)

    González Roberto

    2012-12-01

    Full Text Available Advances in bioinformatics have contributed towards a significant increase in available information. Information analysis requires the use of distributed computing systems to best engage the process of data analysis. This study proposes a multiagent system that incorporates grid technology to facilitate distributed data analysis by dynamically incorporating the roles associated to each specific case study. The system was applied to genetic sequencing data to extract relevant information about insertions, deletions or polymorphisms.

  17. Characterization of Liaoning cashmere goat transcriptome: sequencing, de novo assembly, functional annotation and comparative analysis.

    Directory of Open Access Journals (Sweden)

    Hongliang Liu

    Full Text Available Liaoning cashmere goat is a famous goat breed for cashmere wool. In order to increase the transcriptome data and accelerate genetic improvement for this breed, we performed de novo transcriptome sequencing to generate the first expressed sequence tag dataset for the Liaoning cashmere goat, using next-generation sequencing technology.Transcriptome sequencing of Liaoning cashmere goat on a Roche 454 platform yielded 804,601 high-quality reads. Clustering and assembly of these reads produced a non-redundant set of 117,854 unigenes, comprising 13,194 isotigs and 104,660 singletons. Based on similarity searches with known proteins, 17,356 unigenes were assigned to 6,700 GO categories, and the terms were summarized into three main GO categories and 59 sub-categories. 3,548 and 46,778 unigenes had significant similarity to existing sequences in the KEGG and COG databases, respectively. Comparative analysis revealed that 42,254 unigenes were aligned to 17,532 different sequences in NCBI non-redundant nucleotide databases. 97,236 (82.51% unigenes were mapped to the 30 goat chromosomes. 35,551 (30.17% unigenes were matched to 11,438 reported goat protein-coding genes. The remaining non-matched unigenes were further compared with cattle and human reference genes, 67 putative new goat genes were discovered. Additionally, 2,781 potential simple sequence repeats were initially identified from all unigenes.The transcriptome of Liaoning cashmere goat was deep sequenced, de novo assembled, and annotated, providing abundant data to better understand the Liaoning cashmere goat transcriptome. The potential simple sequence repeats provide a material basis for future genetic linkage and quantitative trait loci analyses.

  18. Genomic sequence around butterfly wing development genes: annotation and comparative analysis.

    Directory of Open Access Journals (Sweden)

    Inês C Conceição

    Full Text Available BACKGROUND: Analysis of genomic sequence allows characterization of genome content and organization, and access beyond gene-coding regions for identification of functional elements. BAC libraries, where relatively large genomic regions are made readily available, are especially useful for species without a fully sequenced genome and can increase genomic coverage of phylogenetic and biological diversity. For example, no butterfly genome is yet available despite the unique genetic and biological properties of this group, such as diversified wing color patterns. The evolution and development of these patterns is being studied in a few target species, including Bicyclus anynana, where a whole-genome BAC library allows targeted access to large genomic regions. METHODOLOGY/PRINCIPAL FINDINGS: We characterize ∼1.3 Mb of genomic sequence around 11 selected genes expressed in B. anynana developing wings. Extensive manual curation of in silico predictions, also making use of a large dataset of expressed genes for this species, identified repetitive elements and protein coding sequence, and highlighted an expansion of Alcohol dehydrogenase genes. Comparative analysis with orthologous regions of the lepidopteran reference genome allowed assessment of conservation of fine-scale synteny (with detection of new inversions and translocations and of DNA sequence (with detection of high levels of conservation of non-coding regions around some, but not all, developmental genes. CONCLUSIONS: The general properties and organization of the available B. anynana genomic sequence are similar to the lepidopteran reference, despite the more than 140 MY divergence. Our results lay the groundwork for further studies of new interesting findings in relation to both coding and non-coding sequence: 1 the Alcohol dehydrogenase expansion with higher similarity between the five tandemly-repeated B. anynana paralogs than with the corresponding B. mori orthologs, and 2 the high

  19. Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida

    Science.gov (United States)

    Pirooznia, Mehdi; Gong, Ping; Guan, Xin; Inouye, Laura S; Yang, Kuan; Perkins, Edward J; Deng, Youping

    2007-01-01

    Background Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to environmental contaminants, we cloned 4032 cDNAs or expressed sequence tags (ESTs) from two E. fetida libraries enriched with genes responsive to ten ordnance related compounds using suppressive subtractive hybridization-PCR. Results A total of 3144 good quality ESTs (GenBank dbEST accession number EH669363–EH672369 and EL515444–EL515580) were obtained from the raw clone sequences after cleaning. Clustering analysis yielded 2231 unique sequences including 448 contigs (from 1361 ESTs) and 1783 singletons. Comparative genomic analysis showed that 743 or 33% of the unique sequences shared high similarity with existing genes in the GenBank nr database. Provisional function annotation assigned 830 Gene Ontology terms to 517 unique sequences based on their homology with the annotated genomes of four model organisms Drosophila melanogaster, Mus musculus, Saccharomyces cerevisiae, and Caenorhabditis elegans. Seven percent of the unique sequences were further mapped to 99 Kyoto Encyclopedia of Genes and Genomes pathways based on their matching Enzyme Commission numbers. All the information is stored and retrievable at a highly performed, web-based and user-friendly relational database called EST model database or ESTMD version 2. Conclusion The ESTMD containing the sequence and annotation information of 4032 E. fetida ESTs is publicly accessible at . PMID:18047730

  20. Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly.

    Science.gov (United States)

    Bai, Yongsheng; Kinne, Jeff; Ding, Lizhong; Rath, Ethan C; Cox, Aaron; Naidu, Siva Dharman

    2017-10-03

    It is generally thought that most canonical or non-canonical splicing events involving U2- and U12 spliceosomes occur within nuclear pre-mRNAs. However, the question of whether at least some U12-type splicing occurs in the cytoplasm is still unclear. In recent years next-generation sequencing technologies have revolutionized the field. The "Read-Split-Walk" (RSW) and "Read-Split-Run" (RSR) methods were developed to identify genome-wide non-canonical spliced regions including special events occurring in cytoplasm. As the significant amount of genome/transcriptome data such as, Encyclopedia of DNA Elements (ENCODE) project, have been generated, we have advanced a newer more memory-efficient version of the algorithm, "Read-Split-Fly" (RSF), which can detect non-canonical spliced regions with higher sensitivity and improved speed. The RSF algorithm also outputs the spliced sequences for further downstream biological function analysis. We used open access ENCODE project RNA-Seq data to search spliced intron sequences against the U12-type spliced intron sequence database to examine whether some events could occur as potential signatures of U12-type splicing. The check was performed by searching spliced sequences against 5'ss and 3'ss sequences from the well-known orthologous U12-type spliceosomal intron database U12DB. Preliminary results of searching 70 ENCODE samples indicated that the presence of 5'ss with U12-type signature is more frequent than U2-type and prevalent in non-canonical junctions reported by RSF. The selected spliced sequences have also been further studied using miRBase to elucidate their functionality. Preliminary results from 70 samples of ENCODE datasets show that several miRNAs are prevalent in studied ENCODE samples. Two of these are associated with many diseases as suggested in the literature. Specifically, hsa-miR-1273 and hsa-miR-548 are associated with many diseases and cancers. Our RSF pipeline is able to detect many possible junctions