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Sample records for large gene pool

  1. Gene pool conservation of teak in Myanmar

    International Nuclear Information System (INIS)

    Tin-Tun

    1995-01-01

    Myanmar with an area of 261, 228 Sq. miles is endowed with various types of forests which occupied nearly 50% of the country. Teak (Tectona grandis Linn. f.) is one of the most valuable timber species for its excellent wood quality and properties which are not observed with other timbers. Gene pool can be defined as a group of individual trees growing over a wide range of environmental conditions, and constituting different genetic complexes which can be transmitted to the offsprings. Topics such as: objectives of gene pool conservation, genetically improved seeds for large scale forest plantations, methodology of conservation, are discussed in the article. Myanmar teak dominates the world's teak market, and thus it is crucial to maintain the superiority in the conservation of gene complexes of teak. To some extent, the conservation of gene pools of teak and tree improvements are being undertaken by the Forest Research Institute of Myanmar. It is felt that the dissemination of the philosophy and concept of gene conservation to the personal involved in the forestry activities of the country are still inadequate

  2. Conjugative plasmids: Vessels of the communal gene pool

    DEFF Research Database (Denmark)

    Norman, Anders; Hansen, Lars H.; Sørensen, Søren Johannes

    2009-01-01

    to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important...... mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized ‘private genes'....

  3. Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species

    Directory of Open Access Journals (Sweden)

    Bolhuis Henk

    2006-07-01

    Full Text Available Abstract Background Mature saturated brine (crystallizers communities are largely dominated (>80% of cells by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and thesequencing of its genome allows comparison with the metagenome of this taxonomically simplified environment. Similar studies carried out in other extreme environments have revealed very little diversity in gene content among the cell lineages present. Results The metagenome of the microbial community of a crystallizer pond has been analyzed by end sequencing a 2000 clone fosmid library and comparing the sequences obtained with the genome sequence of "Haloquadratum walsbyi". The genome of the sequenced strain was retrieved nearly complete within this environmental DNA library. However, many ORF's that could be ascribed to the "Haloquadratum" metapopulation by common genome characteristics or scaffolding to the strain genome were not present in the specific sequenced isolate. Particularly, three regions of the sequenced genome were associated with multiple rearrangements and the presence of different genes from the metapopulation. Many transposition and phage related genes were found within this pool which, together with the associated atypical GC content in these areas, supports lateral gene transfer mediated by these elements as the most probable genetic cause of this variability. Additionally, these sequences were highly enriched in putative regulatory and signal transduction functions. Conclusion These results point to a large pan-genome (total gene repertoire of the genus/species even in this highly specialized extremophile and at a single geographic location. The extensive gene repertoire is what might be expected of a population that exploits a diverse nutrient pool, resulting from the degradation of biomass produced at lower salinities.

  4. Model of large pool fires

    Energy Technology Data Exchange (ETDEWEB)

    Fay, J.A. [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)]. E-mail: jfay@mit.edu

    2006-08-21

    A two zone entrainment model of pool fires is proposed to depict the fluid flow and flame properties of the fire. Consisting of combustion and plume zones, it provides a consistent scheme for developing non-dimensional scaling parameters for correlating and extrapolating pool fire visible flame length, flame tilt, surface emissive power, and fuel evaporation rate. The model is extended to include grey gas thermal radiation from soot particles in the flame zone, accounting for emission and absorption in both optically thin and thick regions. A model of convective heat transfer from the combustion zone to the liquid fuel pool, and from a water substrate to cryogenic fuel pools spreading on water, provides evaporation rates for both adiabatic and non-adiabatic fires. The model is tested against field measurements of large scale pool fires, principally of LNG, and is generally in agreement with experimental values of all variables.

  5. Model of large pool fires

    International Nuclear Information System (INIS)

    Fay, J.A.

    2006-01-01

    A two zone entrainment model of pool fires is proposed to depict the fluid flow and flame properties of the fire. Consisting of combustion and plume zones, it provides a consistent scheme for developing non-dimensional scaling parameters for correlating and extrapolating pool fire visible flame length, flame tilt, surface emissive power, and fuel evaporation rate. The model is extended to include grey gas thermal radiation from soot particles in the flame zone, accounting for emission and absorption in both optically thin and thick regions. A model of convective heat transfer from the combustion zone to the liquid fuel pool, and from a water substrate to cryogenic fuel pools spreading on water, provides evaporation rates for both adiabatic and non-adiabatic fires. The model is tested against field measurements of large scale pool fires, principally of LNG, and is generally in agreement with experimental values of all variables

  6. Gene Pools and the Genetic Architecture of Domesticated Cowpea

    Directory of Open Access Journals (Sweden)

    Bao-Lam Huynh

    2013-11-01

    Full Text Available Cowpea [ (L. Walp.] is a major tropical legume crop grown in warm to hot areas throughout the world and especially important to the people of sub-Saharan Africa where the crop was domesticated. To date, relatively little is understood about its domestication origins and patterns of genetic variation. In this study, a worldwide collection of cowpea landraces and African ancestral wild cowpea was genotyped with more than 1200 single nucleotide polymorphism markers. Bayesian inference revealed the presence of two major gene pools in cultivated cowpea in Africa. Landraces from gene pool 1 are mostly distributed in western Africa while the majority of gene pool 2 are located in eastern Africa. Each gene pool is most closely related to wild cowpea in the same geographic region, indicating divergent domestication processes leading to the formation of two gene pools. The total genetic variation within landraces from countries outside Africa was slightly greater than within African landraces. Accessions from Asia and Europe were more related to those from western Africa while accessions from the Americas appeared more closely related to those from eastern Africa. This delineation of cowpea germplasm into groups of genetic relatedness will be valuable for guiding introgression efforts in breeding programs and for improving the efficiency of germplasm management.

  7. Frozen gene pools - A future for species otherwise destined for extinction

    Science.gov (United States)

    Gee, G.F.

    1986-01-01

    Conclusion: Semen banks and ova and embryo banks can be practical methods to maintain gene pools. Gene pool preservation is desperately needed today due to the rapid decline in number of species and their habitat, a matter that is of concern to.biologists, economists, and politicians worldwide. Techniques are available for the cryopreservation of semen from many animals (and embryos from a few mammals) and adaptations of these techniques to other animals should be possible. A frozen gene pool in conjunction with existing programs makes it possible to preserve gene pools at less cost or in.some cases where no other alternative to extinction existed.

  8. Sculpting the Barnyard Gene Pool

    Science.gov (United States)

    Childers, Gina; Wolfe, Kim; Dupree, Alan; Young, Sheila; Caver, Jessica; Quintanilla, Ruby; Thornton, Laura

    2016-01-01

    Project-based learning (PBL) takes student engagement to a higher level through reflective collaboration, inquiry, critical thinking, problem solving, and personal relevance. This article explains how six high school teachers developed an interconnected, interdisciplinary STEM-focused PBL called "Sculpting the Barnyard Gene Pool." The…

  9. Large-scale pool fires

    Directory of Open Access Journals (Sweden)

    Steinhaus Thomas

    2007-01-01

    Full Text Available A review of research into the burning behavior of large pool fires and fuel spill fires is presented. The features which distinguish such fires from smaller pool fires are mainly associated with the fire dynamics at low source Froude numbers and the radiative interaction with the fire source. In hydrocarbon fires, higher soot levels at increased diameters result in radiation blockage effects around the perimeter of large fire plumes; this yields lower emissive powers and a drastic reduction in the radiative loss fraction; whilst there are simplifying factors with these phenomena, arising from the fact that soot yield can saturate, there are other complications deriving from the intermittency of the behavior, with luminous regions of efficient combustion appearing randomly in the outer surface of the fire according the turbulent fluctuations in the fire plume. Knowledge of the fluid flow instabilities, which lead to the formation of large eddies, is also key to understanding the behavior of large-scale fires. Here modeling tools can be effectively exploited in order to investigate the fluid flow phenomena, including RANS- and LES-based computational fluid dynamics codes. The latter are well-suited to representation of the turbulent motions, but a number of challenges remain with their practical application. Massively-parallel computational resources are likely to be necessary in order to be able to adequately address the complex coupled phenomena to the level of detail that is necessary.

  10. Seismic analysis of large pools

    Energy Technology Data Exchange (ETDEWEB)

    Dong, R.G.; Tokarz, F.J.

    1976-11-17

    Large pools for storing spent, nuclear fuel elements are being proposed to augment present storage capacity. To preserve the ability to isolate portions of these pools, a modularization requirement appears desirable. The purpose of this project was to investigate the effects of modularization on earthquake resistance and to assess the adequacy of current design methods for seismic loads. After determining probable representative pool geometries, three rectangular pool configurations, all 240 x 16 ft and 40 ft deep, were examined. One was unmodularized; two were modularized into 80 x 40 ft cells in one case and 80 x 80 ft cells in the other. Both embedded and above-ground installations for a hard site and embedded installations for an intermediate hard site were studied. It was found that modularization was unfavorable in terms of reducing the total structural load attributable to dynamic effects, principally because one or more cells could be left unfilled. The walls of unfilled cells would be subjected to significantly higher loads than the walls of a filled, unmodularized pool. Generally, embedded installations were preferable to above-ground installations, and the hard site was superior to the intermediate hard site. It was determined that Housner's theory was adequate for calculating hydrodynamic effects on spent fuel storage pools. Current design methods for seismic loads were found to be satisfactory when results from these methods were compared with those from LUSH analyses. As a design method for dynamic soil pressure, we found the Mononobe-Okabe theory, coupled with correction factors as suggested by Seed, to be acceptable. The factors we recommend for spent fuel storage pools are tabulated.

  11. Seismic analysis of large pools

    International Nuclear Information System (INIS)

    Dong, R.G.; Tokarz, F.J.

    1976-01-01

    Large pools for storing spent, nuclear fuel elements are being proposed to augment present storage capacity. To preserve the ability to isolate portions of these pools, a modularization requirement appears desirable. The purpose of this project was to investigate the effects of modularization on earthquake resistance and to assess the adequacy of current design methods for seismic loads. After determining probable representative pool geometries, three rectangular pool configurations, all 240 x 16 ft and 40 ft deep, were examined. One was unmodularized; two were modularized into 80 x 40 ft cells in one case and 80 x 80 ft cells in the other. Both embedded and above-ground installations for a hard site and embedded installations for an intermediate hard site were studied. It was found that modularization was unfavorable in terms of reducing the total structural load attributable to dynamic effects, principally because one or more cells could be left unfilled. The walls of unfilled cells would be subjected to significantly higher loads than the walls of a filled, unmodularized pool. Generally, embedded installations were preferable to above-ground installations, and the hard site was superior to the intermediate hard site. It was determined that Housner's theory was adequate for calculating hydrodynamic effects on spent fuel storage pools. Current design methods for seismic loads were found to be satisfactory when results from these methods were compared with those from LUSH analyses. As a design method for dynamic soil pressure, we found the Mononobe-Okabe theory, coupled with correction factors as suggested by Seed, to be acceptable. The factors we recommend for spent fuel storage pools are tabulated

  12. Dried blood spots of pooled samples for RHD gene screening in blood donors of mixed ancestry.

    Science.gov (United States)

    Silva-Malta, M C F; Araujo, N C Fidélis; Vieira, O V Neves; Schmidt, L Cayres; Gonçalves, P de Cassia; Martins, M Lobato

    2015-10-01

    In this study, we present a strategy for RHD gene screening based on real-time polymerase chain reaction (PCR) using dried blood spots of pooled samples. Molecular analysis of blood donors may be used to detect RHD variants among the presumed D-negative individuals. RHD genotyping using pooled samples is a strategy to test a large number of samples at a more reasonable cost. RHD gene detection based on real-time PCR using dried blood spots of pooled samples was standardised and used to evaluate 1550 Brazilian blood donors phenotyped as RhD-negative. Positive results were re-evaluated by retesting single samples using real-time PCR and conventional multiplex PCR to amplify five RHD-specific exons. PCR-sequence-specific primers was used to amplify RHDψ allele. We devised a strategy for RHD gene screening using dried blood spots of five pooled samples. Among 1550 serologically D-negative blood donors, 58 (3.74%) had the RHD gene. The non-functional RHDψ allele was detected in 47 samples (3.02%). The present method is a promising strategy to detect the RHD gene among presumed RhD-negative blood donors, particularly for populations with African ancestry. © 2015 British Blood Transfusion Society.

  13. Parts & Pools: A Framework for Modular Design of Synthetic Gene Circuits

    Energy Technology Data Exchange (ETDEWEB)

    Marchisio, Mario Andrea, E-mail: marchisio@hit.edu.cn [School of Life Science and Technology, Harbin Institute of Technology, Harbin (China)

    2014-10-06

    Published in 2008, Parts & Pools represents one of the first attempts to conceptualize the modular design of bacterial synthetic gene circuits with Standard Biological Parts (DNA segments) and Pools of molecules referred to as common signal carriers (e.g., RNA polymerases and ribosomes). The original framework for modeling bacterial components and designing prokaryotic circuits evolved over the last years and brought, first, to the development of an algorithm for the automatic design of Boolean gene circuits. This is a remarkable achievement since gene digital circuits have a broad range of applications that goes from biosensors for health and environment care to computational devices. More recently, Parts & Pools was enabled to give a proper formal description of eukaryotic biological circuit components. This was possible by employing a rule-based modeling approach, a technique that permits a faithful calculation of all the species and reactions involved in complex systems such as eukaryotic cells and compartments. In this way, Parts & Pools is currently suitable for the visual and modular design of synthetic gene circuits in yeast and mammalian cells too.

  14. Parts & Pools: A Framework for Modular Design of Synthetic Gene Circuits

    International Nuclear Information System (INIS)

    Marchisio, Mario Andrea

    2014-01-01

    Published in 2008, Parts & Pools represents one of the first attempts to conceptualize the modular design of bacterial synthetic gene circuits with Standard Biological Parts (DNA segments) and Pools of molecules referred to as common signal carriers (e.g., RNA polymerases and ribosomes). The original framework for modeling bacterial components and designing prokaryotic circuits evolved over the last years and brought, first, to the development of an algorithm for the automatic design of Boolean gene circuits. This is a remarkable achievement since gene digital circuits have a broad range of applications that goes from biosensors for health and environment care to computational devices. More recently, Parts & Pools was enabled to give a proper formal description of eukaryotic biological circuit components. This was possible by employing a rule-based modeling approach, a technique that permits a faithful calculation of all the species and reactions involved in complex systems such as eukaryotic cells and compartments. In this way, Parts & Pools is currently suitable for the visual and modular design of synthetic gene circuits in yeast and mammalian cells too.

  15. Review of events at large pool-type irradiators

    International Nuclear Information System (INIS)

    Trager, E.A. Jr.

    1989-03-01

    Large pool-type gamma irradiators are used in applications such as the ''cold'' sterilization of medical and pharmaceutical supplies, and recent changes in federal regulations make it possible they will be used extensively in the preservation of foodstuffs. Because of this possible large increase in the use of irradiators, the Office of Nuclear Materials Safety and Safeguards was interested in knowing what events had occurred at irradiators. The event data would be used as background in developing new regulations on irradiators. Therefore, AEOD began a study of the operating experience at large, wet source storage gamma irradiators. The scope of the study was to assess all available operating information on large (≥ 250,000 curie), pool-type irradiators licensed by both the NRC and the Agreement States, and events at foreign facilities. The study found that about 0.12 events have been reported per irradiator-year. Most of these events were precursor events, in that there was no evidence of damage to the radioactive sources or degradation in the level of safety of the facility. Events with more significant impacts had a reported frequency of about 0.01 event per irradiator-year. However, the actual rate of occurrence of events of concern to the staff may be higher because there are few specific reporting requirements for events at irradiators. It is suggested that during development of a regulation for large pool-type irradiators consideration be given to specifying requirements for: reporting breakdowns in access control systems; periodic inspection of the source movement and suspension system; systems to detect source leakage and product contamination; allowable pool leakage; and feedback of information on operational events involving safety-important systems

  16. Balancing gene expression without library construction via a reusable sRNA pool.

    Science.gov (United States)

    Ghodasara, Amar; Voigt, Christopher A

    2017-07-27

    Balancing protein expression is critical when optimizing genetic systems. Typically, this requires library construction to vary the genetic parts controlling each gene, which can be expensive and time-consuming. Here, we develop sRNAs corresponding to 15nt 'target' sequences that can be inserted upstream of a gene. The targeted gene can be repressed from 1.6- to 87-fold by controlling sRNA expression using promoters of different strength. A pool is built where six sRNAs are placed under the control of 16 promoters that span a ∼103-fold range of strengths, yielding ∼107 combinations. This pool can simultaneously optimize up to six genes in a system. This requires building only a single system-specific construct by placing a target sequence upstream of each gene and transforming it with the pre-built sRNA pool. The resulting library is screened and the top clone is sequenced to determine the promoter controlling each sRNA, from which the fold-repression of the genes can be inferred. The system is then rebuilt by rationally selecting parts that implement the optimal expression of each gene. We demonstrate the versatility of this approach by using the same pool to optimize a metabolic pathway (β-carotene) and genetic circuit (XNOR logic gate). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Rapid protein production from stable CHO cell pools using plasmid vector and the cumate gene-switch.

    Science.gov (United States)

    Poulain, Adeline; Perret, Sylvie; Malenfant, Félix; Mullick, Alaka; Massie, Bernard; Durocher, Yves

    2017-08-10

    To rapidly produce large amounts of recombinant proteins, the generation of stable Chinese Hamster Ovary (CHO) cell pools represents a useful alternative to large-scale transient gene expression (TGE). We have developed a cell line (CHO BRI/rcTA ) allowing the inducible expression of recombinant proteins, based on the cumate gene switch. After the identification of optimal plasmid DNA topology (supercoiled vs linearized plasmid) for PEIpro™ mediated transfection and of optimal conditions for methionine sulfoximine (MSX) selection, we were able to generate CHO BRI/rcTA pools producing high levels of recombinant proteins. Volumetric productivities of up to 900mg/L were reproducibly achieved for a Fc fusion protein and up to 350mg/L for an antibody after 14days post-induction in non-optimized fed-batch cultures. In addition, we show that CHO pool volumetric productivities are not affected by a freeze-thaw cycle or following maintenance in culture for over one month in the presence of MSX. Finally, we demonstrate that volumetric protein production with the CR5 cumate-inducible promoter is three- to four-fold higher than with the human CMV or hybrid EF1α-HTLV constitutive promoters. These results suggest that the cumate-inducible CHO BRI/rcTA stable pool platform is a powerful and robust system for the rapid production of gram amounts of recombinant proteins. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  18. Pooled Resequencing of 122 Ulcerative Colitis Genes in a Large Dutch Cohort Suggests Population-Specific Associations of Rare Variants in MUC2.

    Science.gov (United States)

    Visschedijk, Marijn C; Alberts, Rudi; Mucha, Soren; Deelen, Patrick; de Jong, Dirk J; Pierik, Marieke; Spekhorst, Lieke M; Imhann, Floris; van der Meulen-de Jong, Andrea E; van der Woude, C Janneke; van Bodegraven, Adriaan A; Oldenburg, Bas; Löwenberg, Mark; Dijkstra, Gerard; Ellinghaus, David; Schreiber, Stefan; Wijmenga, Cisca; Rivas, Manuel A; Franke, Andre; van Diemen, Cleo C; Weersma, Rinse K

    2016-01-01

    Genome-wide association studies have revealed several common genetic risk variants for ulcerative colitis (UC). However, little is known about the contribution of rare, large effect genetic variants to UC susceptibility. In this study, we performed a deep targeted re-sequencing of 122 genes in Dutch UC patients in order to investigate the contribution of rare variants to the genetic susceptibility to UC. The selection of genes consists of 111 established human UC susceptibility genes and 11 genes that lead to spontaneous colitis when knocked-out in mice. In addition, we sequenced the promoter regions of 45 genes where known variants exert cis-eQTL-effects. Targeted pooled re-sequencing was performed on DNA of 790 Dutch UC cases. The Genome of the Netherlands project provided sequence data of 500 healthy controls. After quality control and prioritization based on allele frequency and pathogenicity probability, follow-up genotyping of 171 rare variants was performed on 1021 Dutch UC cases and 1166 Dutch controls. Single-variant association and gene-based analyses identified an association of rare variants in the MUC2 gene with UC. The associated variants in the Dutch population could not be replicated in a German replication cohort (1026 UC cases, 3532 controls). In conclusion, this study has identified a putative role for MUC2 on UC susceptibility in the Dutch population and suggests a population-specific contribution of rare variants to UC.

  19. Feasibility study on large pool-type LMFBR

    International Nuclear Information System (INIS)

    1984-01-01

    A feasibility study has been conducted from 1981 FY to 1983 FY, in order to evaluate the feasibility of a large pool-type LMFBR under the Japanese seismic design condition and safety design condition, etc. This study was aimed to establish an original reactor structure concept which meets those design conditions especially required in Japan. In the first year, preceding design concepts had been reviewed and several concepts were originated to be suitable to Japan. For typical two of them being selected by preliminary analysis, test programs were planned. In the second year, more than twenty tests with basic models had been conducted under severe conditions, concurrently analytical approaches were promoted. In the last year, larger model tests were conducted and analytical methods have been verified concerning hydrodynamic effects on structure vibration, thermo-hydraulic behaviours in reactor plena and so on. Finally the reactor structure concepts for a large pool-type LMFBR have been acknowledged to be feasible in Japan. (author)

  20. Measurements in large JP-4 pool fires

    International Nuclear Information System (INIS)

    Keltner, N.R.; Kent, L.A.; Schneider, M.E.

    1987-01-01

    Over the past four years, Sandia National Laboratories has conducted a number of large pool fire tests to evaluate the design of radioactive material (RAM) shipping containers. Some of these tests have been designed to define the thermal environment and some have been used for certification testing. In each test there have been a number of fire diagnostic measurements. The simplest sets of diagnostics have involved measurements of temperature at several elevations on arrays of towers, measurements of hot wall heat flux with small calorimeters suspended from the towers, the average fuel recession rate, and the wind speed and direction. The most complex sets of diagnostics have included the above and in various tests added radiometers in the lower flame zone, centerline velocity measurements at a number of elevations, radiometers and calorimeters at the fuel surface, large cylindrical and flat plate calorimeters, infrared imaging, time resolved fuel recession rates, and a variety of soot particle concentration and size measurements made in the plume with a tethered balloon and an instrumented airplane. All of the large fires have been conducted in a 9.1 m by 18.3 m pool using JP-4 as the fuel. Typical duration is one-half hour. Covering all of the results is beyond the scope of a single paper. Conditionally sampled temperature and velocity measurements from one fire will be presented; for this fire, a 20 cm layer of fuel was floated on 61 cm of water. Pool surface heat flux, fuel recession rate data, and smoke emission data from a second fire are given. Because the wind has a strong effect on the temperature and velocity measurements, conditional sampling has been used to try to obtain data during periods of low winds. 10 refs., 3 figs

  1. PDA: Pooled DNA analyzer

    Directory of Open Access Journals (Sweden)

    Lin Chin-Yu

    2006-04-01

    Full Text Available Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer, to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

  2. DATA-POOL : a direct-access data base for large-scale nuclear codes

    International Nuclear Information System (INIS)

    Yamano, Naoki; Koyama, Kinji; Naito, Yoshitaka; Minami, Kazuyoshi.

    1991-12-01

    A direct-access data base DATA-POOL has been developed for large-scale nuclear codes. The data can be stored and retrieved with specifications of simple node names, by using the DATA-POOL access package written in the FORTRAN 77 language. A management utility POOL for the DATA-POOL is also provided. A typical application of the DATA-POOL is shown to the RADHEAT-V4 code system developed for performing safety analyses of radiation shielding. Many samples and error messages are also noted to apply the DATA-POOL for the other code systems. This report is provided for a manual of DATA-POOL. (author)

  3. Gene pool conservation and tree improvement in Serbia

    Directory of Open Access Journals (Sweden)

    Isajev Vasilije

    2009-01-01

    Full Text Available This paper presents the concepts applied in the gene pool conservation and tree improvement in Serbia. Gene pool conservation of tree species in Serbia includes a series of activities aiming at the sustainability and protection of genetic and species variability. This implies the investigation of genetic resources and their identification through the research of the genetic structure and the breeding system of individual species. Paper also includes the study of intra- and inter-population variability in experiments - provenance tests, progeny tests, half- and full-sib lines, etc. The increased use of the genetic potential in tree improvement in Serbia should be intensified by the following activities: improvement of production of normal forest seed, application of the concept of new selections directed primarily to the improvement of only one character, because in that case the result would be certain, establishment and management of seed orchards as specialized plantations for long-term production of genetically good-quality forest seeds, and the shortening of the improvement process by introducing new techniques and methods (molecular markers, somaclonal variation, genetic engineering, protoplast fusion, micropropagation, etc..

  4. Nucleotide Pool Depletion Induces G-Quadruplex-Dependent Perturbation of Gene Expression

    Directory of Open Access Journals (Sweden)

    Charikleia Papadopoulou

    2015-12-01

    Full Text Available Nucleotide pool imbalance has been proposed to drive genetic instability in cancer. Here, we show that slowing replication forks by depleting nucleotide pools with hydroxyurea (HU can also give rise to both transient and permanent epigenetic instability of a reporter locus, BU-1, in DT40 cells. HU induces stochastic formation of Bu-1low variants in dividing cells, which have lost the H3K4me3 present in untreated cells. This instability is potentiated by an intragenic G quadruplex, which also promotes local H2Ax phosphorylation and transient heterochromatinization. Genome-wide, gene expression changes induced by HU significantly overlap with those resulting from loss of the G4-helicases FANCJ, WRN, and BLM. Thus, the effects of global replication stress induced by nucleotide pool depletion can be focused by local replication impediments caused by G quadruplex formation to induce epigenetic instability and changes in gene expression, a mechanism that may contribute to selectable transcriptional changes in cancer.

  5. Expansion of the known Klebsiella pneumoniae species gene pool by characterization of novel alien DNA islands integrated into tmRNA gene sites.

    Science.gov (United States)

    Zhang, Jie; van Aartsen, Jon Jurriaan; Jiang, Xiaofei; Shao, Yucheng; Tai, Cui; He, Xinyi; Tan, Zhilei; Deng, Zixin; Jia, Shiru; Rajakumar, Kumar; Ou, Hong-Yu

    2011-02-01

    Klebsiella pneumoniae is an important bacterial pathogen of man that is commonly associated with opportunistic and hospital-associated infections. Increasing levels of multiple-antibiotic resistance associated with this species pose a major emerging clinical problem. This organism also occurs naturally in other diverse environments, including the soil. Consistent with its varied lifestyle and membership of the Enterobacteriaceae family, K. pneumoniae genomes exhibit highly plastic architecture comprising a core genome backbone interspersed with numerous and varied alien genomic islands. In this study the size of the presently known K. pneumoniae pan-genome gene pool was estimated through analysis of complete sequences of three chromosomes and 31 plasmids belonging to K. pneumoniae strains. In addition, using a PCR-based strategy the genomic content of eight tRNA/tmRNA gene sites that serve as DNA insertion hotspots were investigated in 28 diverse environmental and clinical strains of K. pneumoniae. Sequencing and characterization of five newly identified horizontally-acquired tmRNA-associated islands further expanded the archived K. pneumoniae gene pool to a total of 7648 unique gene members. Large-scale investigation of the content of tRNA/tmRNA hotspots will be useful to identify and/or survey accessory sequences dispersed amongst hundreds to thousands of members of many key bacterial species. Copyright © 2010 Elsevier B.V. All rights reserved.

  6. The care and handling of the forest gene pool

    Science.gov (United States)

    Roy R. Silen; Ivan Doig

    1976-01-01

    What must be the world's most magnificent pool of forest genes has timbered our Pacific slopes.Why else do the tallest firs, pines, spruces, hemlocks, redwoods, and larches all rise along the Pacific Coast of North America? Does their hugeness simply thrust up from our deep soils and mild, rainy climate? From a vantage point of three...

  7. Gene expression changes in blood RNA after swimming in a chlorinated pool.

    Science.gov (United States)

    Salas, Lucas A; Font-Ribera, Laia; Bustamante, Mariona; Sumoy, Lauro; Grimalt, Joan O; Bonnin, Sarah; Aguilar, Maria; Mattlin, Heidi; Hummel, Manuela; Ferrer, Anna; Kogevinas, Manolis; Villanueva, Cristina M

    2017-08-01

    Exposure to disinfection by-products (DBP) such as trihalomethanes (THM) in swimming pools has been linked to adverse health effects in humans, but their biological mechanisms are unclear. We evaluated short-term changes in blood gene expression of adult recreational swimmers after swimming in a chlorinated pool. Volunteers swam 40min in an indoor chlorinated pool. Blood samples were drawn and four THM (chloroform, bromodichloromethane, dibromochloromethane and bromoform) were measured in exhaled breath before and after swimming. Intensity of physical activity was measured as metabolic equivalents (METs). Gene expression in whole blood mRNA was evaluated using IlluminaHumanHT-12v3 Expression-BeadChip. Linear mixed models were used to evaluate the relationship between gene expression changes and THM exposure. Thirty-seven before-after pairs were analyzed. The median increase from baseline to after swimming were: 0.7 to 2.3 for MET, and 1.4 to 7.1μg/m 3 for exhaled total THM (sum of the four THM). Exhaled THM increased on average 0.94μg/m 3 per 1 MET. While 1643 probes were differentially expressed post-exposure. Of them, 189 were also associated with exhaled levels of individual/total THM or MET after False Discovery Rate. The observed associations with the exhaled THM were low to moderate (Log-fold change range: -0.17 to 0.15). In conclusion, we identified short-term gene expression changes associated with swimming in a pool that were minor in magnitude and their biological meaning was unspecific. The high collinearity between exhaled THM levels and intensity of physical activity precluded mutually adjusted models with both covariates. These exploratory results should be validated in future studies. Copyright © 2017. Published by Elsevier B.V.

  8. Modular design of synthetic gene circuits with biological parts and pools.

    Science.gov (United States)

    Marchisio, Mario Andrea

    2015-01-01

    Synthetic gene circuits can be designed in an electronic fashion by displaying their basic components-Standard Biological Parts and Pools of molecules-on the computer screen and connecting them with hypothetical wires. This procedure, achieved by our add-on for the software ProMoT, was successfully applied to bacterial circuits. Recently, we have extended this design-methodology to eukaryotic cells. Here, highly complex components such as promoters and Pools of mRNA contain hundreds of species and reactions whose calculation demands a rule-based modeling approach. We showed how to build such complex modules via the joint employment of the software BioNetGen (rule-based modeling) and ProMoT (modularization). In this chapter, we illustrate how to utilize our computational tool for synthetic biology with the in silico implementation of a simple eukaryotic gene circuit that performs the logic AND operation.

  9. The Phoenix series large scale LNG pool fire experiments.

    Energy Technology Data Exchange (ETDEWEB)

    Simpson, Richard B.; Jensen, Richard Pearson; Demosthenous, Byron; Luketa, Anay Josephine; Ricks, Allen Joseph; Hightower, Marion Michael; Blanchat, Thomas K.; Helmick, Paul H.; Tieszen, Sheldon Robert; Deola, Regina Anne; Mercier, Jeffrey Alan; Suo-Anttila, Jill Marie; Miller, Timothy J.

    2010-12-01

    The increasing demand for natural gas could increase the number and frequency of Liquefied Natural Gas (LNG) tanker deliveries to ports across the United States. Because of the increasing number of shipments and the number of possible new facilities, concerns about the potential safety of the public and property from an accidental, and even more importantly intentional spills, have increased. While improvements have been made over the past decade in assessing hazards from LNG spills, the existing experimental data is much smaller in size and scale than many postulated large accidental and intentional spills. Since the physics and hazards from a fire change with fire size, there are concerns about the adequacy of current hazard prediction techniques for large LNG spills and fires. To address these concerns, Congress funded the Department of Energy (DOE) in 2008 to conduct a series of laboratory and large-scale LNG pool fire experiments at Sandia National Laboratories (Sandia) in Albuquerque, New Mexico. This report presents the test data and results of both sets of fire experiments. A series of five reduced-scale (gas burner) tests (yielding 27 sets of data) were conducted in 2007 and 2008 at Sandia's Thermal Test Complex (TTC) to assess flame height to fire diameter ratios as a function of nondimensional heat release rates for extrapolation to large-scale LNG fires. The large-scale LNG pool fire experiments were conducted in a 120 m diameter pond specially designed and constructed in Sandia's Area III large-scale test complex. Two fire tests of LNG spills of 21 and 81 m in diameter were conducted in 2009 to improve the understanding of flame height, smoke production, and burn rate and therefore the physics and hazards of large LNG spills and fires.

  10. Workshop on large molten pool heat transfer summary and conclusions

    International Nuclear Information System (INIS)

    1994-01-01

    The CSNI Workshop on Large Molten Heat Transfer held at Grenoble (France) in March 1994 was organised by CSNI's Principal Working Group on the Confinement of Accidental Radioactive Releases (PWG4) with the cooperation of the Principal Working Group on Coolant System Behaviour (FWG2) and in collaboration with the Grenoble Nuclear Research Centre of the French Commissariat a l'Energie Atomique (CEA). Conclusions and recommendations are given for each of the five sessions of the workshops: Feasibility of in-vessel core debris cooling through external cooling of the vessel; Experiments on molten pool heat transfer; Calculational efforts on molten pool convection; Heat transfer to the surrounding water - experimental techniques; Future experiments and ex-vessel studies (open forum discussion)

  11. Nanobiotechnologies in the System of Farm Animals' Gene Pool Preservation

    Science.gov (United States)

    Kovtun, S. I.; Galagan, N. P.; Shcherbak, O. V.; Klymenko, N. Y.; Osypchuk, O. S.

    It has been determined that sperm viability and mobility upon long storage in liquid nitrogen is being reduced. This issue is relevant for gene pool objects' preservation and for reproductive medicine. The use of nanomaterials (NM) in reproductive biotechnology can expand to the methodology of the rational gene pool preservation technology, especially of valuable biomaterial. Use of nanoparticles, based on ultrafine silica (UFS) with different agents located on its surface gives a positive effect on the thawed sperm mobility, increasing its activity and survival rate and leading to increased fertilization ability. After thawing, the sperm of bulls had an average activity level of 47 %. This activity index of gametes in control was being maintained for 30 min. In the experimental groups after 30 min, the most active gametes were those with UFS + sucrose (52 %). A lower activity compared with the control and UFS + sucrose had gametes with UFS + D-galactosamine. Sperm activity with UFS + D-galactosamine decreased by 14 % compared with the control and by 19 % compared to the UFS + sucrose. So, the feasibility of adding NM with UFS + sucrose at a concentration of 0.001 % to thawed bull sperm that has been cryopreserved for a long time was proved.

  12. Formation and maintenance of a forced pool-riffle couplet following loading of large wood

    Science.gov (United States)

    Thompson, D. M.; Fixler, S. A.

    2017-11-01

    Pool-riffle maintenance has been documented in numerous studies, but it has been almost impossible to characterize detailed natural pool-riffle formation mechanisms because of the lack of baseline data prior to pool establishment. In 2013, a study was conducted on the Blackledge River in Connecticut to document the formation of a new pool-riffle couplet on a section of river that had previously been studied from 1999 to 2001. In 2001, the study reach contained a scour hole with a residual depth of 0.08 ± 0.09 m downstream of a 1930s paired deflector with no identifiable riffle immediately downstream. At this time, a large, severely undercut, hemlock tree was noted along the left bank. Sometime between fall 2001 and 2004, the tree fell perpendicular to flow across the channel and formed a large wood (LW) jam and new pool-riffle couplet several meters downstream of the old scour hole. Pool spacing along the reach decreased from 4.47 bankfull widths (BFW) in 1999 to 3.83 BFW after the new pool-riffle couplet formed. The new pool has a residual depth, the water depth of the streambed depression below the elevation of the immediate downstream hydraulic control, of 1.36 ± 0.075 to 1.59 ± 0.075 m, which resulted from a combination of 1.32 ± 0.09 m or less of incision below the old scour hole (95.6% or less of the depth increase) and up to 0.18 ± 0.09 m of downstream deposition and associated backwater formation (13.2% or less of the depth increase). To assess dynamic stability of the pool-riffle couplet over several flood cycles, surficial fine-sediment and organic material along the reach were quantified. The 23-m-long pool stores 25.7% of the surficial fine grained sediments and 15.4% of organic material along a 214-m-long reach that includes one additional artificially created pool. An adjacent 50-m-long secondary channel impacted by the LW jam stores 65.3% of the surficial fine-grained sediments and 54.8% of organic material along the full reach.

  13. Measurements in large pool fires with an actively cooled calorimeter

    International Nuclear Information System (INIS)

    Koski, J.A.; Wix, S.D.

    1995-01-01

    The pool fire thermal test described in Safety Series 6 published by the International Atomic Energy Agency (IAEA) or Title 10, Code of Federal Regulations, Part 71 (10CFR71) in the United States is one of the most difficult tests that a container for larger ''Type B'' quantities of nuclear materials must pass. If retests of a container are required, costly redesign and project delays can result. Accurate measurements and modeling of the pool fire environment will ultimately lower container costs by assuring that containers past the pool fire test on the first attempt. Experiments indicate that the object size or surface temperature of the container can play a role in determining local heat fluxes that are beyond the effects predicted from the simple radiative heat transfer laws. An analytical model described by Nicolette and Larson 1990 can be used to understand many of these effects. In this model a gray gas represents soot particles present in the flame structure. Close to the container surface, these soot particles are convectively and radiatively cooled and interact with incident energy from the surrounding fire. This cooler soot cloud effectively prevents some thermal radiation from reaching the container surface, reducing the surface heat flux below the value predicted by a transparent medium model. With some empirical constants, the model suggested by Nicolette and Larson can be used to more accurately simulate the pool fire environment. Properly formulated, the gray gas approaches also fast enough to be used with standard commercial computer codes to analyze shipping containers. To calibrate this type of model, accurate experimental measurements of radiative absorption coefficients, flame temperatures, and other parameters are necessary. A goal of the calorimeter measurements described here is to obtain such parameters so that a fast, useful design tool for large pool fires can be constructed

  14. Gene coexpression measures in large heterogeneous samples using count statistics.

    Science.gov (United States)

    Wang, Y X Rachel; Waterman, Michael S; Huang, Haiyan

    2014-11-18

    With the advent of high-throughput technologies making large-scale gene expression data readily available, developing appropriate computational tools to process these data and distill insights into systems biology has been an important part of the "big data" challenge. Gene coexpression is one of the earliest techniques developed that is still widely in use for functional annotation, pathway analysis, and, most importantly, the reconstruction of gene regulatory networks, based on gene expression data. However, most coexpression measures do not specifically account for local features in expression profiles. For example, it is very likely that the patterns of gene association may change or only exist in a subset of the samples, especially when the samples are pooled from a range of experiments. We propose two new gene coexpression statistics based on counting local patterns of gene expression ranks to take into account the potentially diverse nature of gene interactions. In particular, one of our statistics is designed for time-course data with local dependence structures, such as time series coupled over a subregion of the time domain. We provide asymptotic analysis of their distributions and power, and evaluate their performance against a wide range of existing coexpression measures on simulated and real data. Our new statistics are fast to compute, robust against outliers, and show comparable and often better general performance.

  15. Next generation semiconductor based-sequencing of a nutrigenetics target gene (GPR120) and association with growth rate in Italian Large White pigs.

    Science.gov (United States)

    Fontanesi, Luca; Bertolini, Francesca; Scotti, Emilio; Schiavo, Giuseppina; Colombo, Michela; Trevisi, Paolo; Ribani, Anisa; Buttazzoni, Luca; Russo, Vincenzo; Dall'Olio, Stefania

    2015-01-01

    The GPR120 gene (also known as FFAR4 or O3FAR1) encodes for a functional omega-3 fatty acid receptor/sensor that mediates potent insulin sensitizing effects by repressing macrophage-induced tissue inflammation. For its functional role, GPR120 could be considered a potential target gene in animal nutrigenetics. In this work we resequenced the porcine GPR120 gene by high throughput Ion Torrent semiconductor sequencing of amplified fragments obtained from 8 DNA pools derived, on the whole, from 153 pigs of different breeds/populations (two Italian Large White pools, Italian Duroc, Italian Landrace, Casertana, Pietrain, Meishan, and wild boars). Three single nucleotide polymorphisms (SNPs), two synonymous substitutions and one in the putative 3'-untranslated region (g.114765469C > T), were identified and their allele frequencies were estimated by sequencing reads count. The g.114765469C > T SNP was also genotyped by PCR-RFLP confirming estimated frequency in Italian Large White pools. Then, this SNP was analyzed in two Italian Large White cohorts using a selective genotyping approach based on extreme and divergent pigs for back fat thickness (BFT) estimated breeding value (EBV) and average daily gain (ADG) EBV. Significant differences of allele and genotype frequencies distribution was observed between the extreme ADG-EBV groups (P < 0.001) whereas this marker was not associated with BFT-EBV.

  16. Approaches to gene pool conservation of medicinal plant Oxytropis lanata (Pall. DC. (Fabaceae

    Directory of Open Access Journals (Sweden)

    A. B. Kholina

    2015-05-01

    Full Text Available In order to preserve the gene pool of medicinal plant Oxytropis lanata (Pall. DC. we analyzed allozyme polymorphism and identified reliable and informative marker enzyme systems of this species; also we studied the response of seeds to deep freezing in liquid nitrogen (–196 ºС. Population has an average level of polymorphism (P95 = 41,2 %, P99 = 52,9 %, A = 1,58, Ho = 0,158, He = 0,171 in general typical for herbaceous legumes, and can serve as a source of material for gene pool conservation of the species. Deep freezing has not led to the death of the seeds; it was marked stimulatory effect of ultralow temperatures, expressed as an acceleration of germination and sharp increase of germinability (98,6 ± 2,3 % compared to the control (12,0 ± 3,5 % that is associated with overcoming physical dormancy. There were no abnormalities in the development of seedlings from seeds passed cryopreservation.

  17. Modelling of decay heat removal using large water pools

    International Nuclear Information System (INIS)

    Munther, R.; Raussi, P.; Kalli, H.

    1992-01-01

    The main task for investigating of passive safety systems typical for ALWRs (Advanced Light Water Reactors) has been reviewing decay heat removal systems. The reference system for calculations has been represented in Hitachi's SBWR-concept. The calculations for energy transfer to the suppression pool were made using two different fluid mechanics codes, namely FIDAP and PHOENICS. FIDAP is based on finite element methodology and PHOENICS uses finite differences. The reason choosing these codes has been to compare their modelling and calculating abilities. The thermal stratification behaviour and the natural circulation was modelled with several turbulent flow models. Also, energy transport to the suppression pool was calculated for laminar flow conditions. These calculations required a large amount of computer resources and so the CRAY-supercomputer of the state computing centre was used. The results of the calculations indicated that the capabilities of these codes for modelling the turbulent flow regime are limited. Output from these codes should be considered carefully, and whenever possible, experimentally determined parameters should be used as input to enhance the code reliability. (orig.). (31 refs., 21 figs., 3 tabs.)

  18. Analysis of pools of targeted Salmonella deletion mutants identifies novel genes affecting fitness during competitive infection in mice.

    Directory of Open Access Journals (Sweden)

    Carlos A Santiviago

    2009-07-01

    Full Text Available Pools of mutants of minimal complexity but maximal coverage of genes of interest facilitate screening for genes under selection in a particular environment. We constructed individual deletion mutants in 1,023 Salmonella enterica serovar Typhimurium genes, including almost all genes found in Salmonella but not in related genera. All mutations were confirmed simultaneously using a novel amplification strategy to produce labeled RNA from a T7 RNA polymerase promoter, introduced during the construction of each mutant, followed by hybridization of this labeled RNA to a Typhimurium genome tiling array. To demonstrate the ability to identify fitness phenotypes using our pool of mutants, the pool was subjected to selection by intraperitoneal injection into BALB/c mice and subsequent recovery from spleens. Changes in the representation of each mutant were monitored using T7 transcripts hybridized to a novel inexpensive minimal microarray. Among the top 120 statistically significant spleen colonization phenotypes, more than 40 were mutations in genes with no previously known role in this model. Fifteen phenotypes were tested using individual mutants in competitive assays of intraperitoneal infection in mice and eleven were confirmed, including the first two examples of attenuation for sRNA mutants in Salmonella. We refer to the method as Array-based analysis of cistrons under selection (ABACUS.

  19. Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

    Science.gov (United States)

    Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R.; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J.

    2013-01-01

    For the vast majority of species – including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding. PMID:23592960

  20. Combinatorial pooling enables selective sequencing of the barley gene space.

    Directory of Open Access Journals (Sweden)

    Stefano Lonardi

    2013-04-01

    Full Text Available For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

  1. Combinatorial pooling enables selective sequencing of the barley gene space.

    Science.gov (United States)

    Lonardi, Stefano; Duma, Denisa; Alpert, Matthew; Cordero, Francesca; Beccuti, Marco; Bhat, Prasanna R; Wu, Yonghui; Ciardo, Gianfranco; Alsaihati, Burair; Ma, Yaqin; Wanamaker, Steve; Resnik, Josh; Bozdag, Serdar; Luo, Ming-Cheng; Close, Timothy J

    2013-04-01

    For the vast majority of species - including many economically or ecologically important organisms, progress in biological research is hampered due to the lack of a reference genome sequence. Despite recent advances in sequencing technologies, several factors still limit the availability of such a critical resource. At the same time, many research groups and international consortia have already produced BAC libraries and physical maps and now are in a position to proceed with the development of whole-genome sequences organized around a physical map anchored to a genetic map. We propose a BAC-by-BAC sequencing protocol that combines combinatorial pooling design and second-generation sequencing technology to efficiently approach denovo selective genome sequencing. We show that combinatorial pooling is a cost-effective and practical alternative to exhaustive DNA barcoding when preparing sequencing libraries for hundreds or thousands of DNA samples, such as in this case gene-bearing minimum-tiling-path BAC clones. The novelty of the protocol hinges on the computational ability to efficiently compare hundred millions of short reads and assign them to the correct BAC clones (deconvolution) so that the assembly can be carried out clone-by-clone. Experimental results on simulated data for the rice genome show that the deconvolution is very accurate, and the resulting BAC assemblies have high quality. Results on real data for a gene-rich subset of the barley genome confirm that the deconvolution is accurate and the BAC assemblies have good quality. While our method cannot provide the level of completeness that one would achieve with a comprehensive whole-genome sequencing project, we show that it is quite successful in reconstructing the gene sequences within BACs. In the case of plants such as barley, this level of sequence knowledge is sufficient to support critical end-point objectives such as map-based cloning and marker-assisted breeding.

  2. Seismic loads in modularized and unmodularized large pools located on hard or intermediate hard sites

    Energy Technology Data Exchange (ETDEWEB)

    Dong, R G [California Univ., Livermore (USA). Lawrence Livermore Lab.

    1977-12-01

    To augment the present capacity of pools for storing spent nuclear fuel elements, pools larger than those in current use are being planned. These pools may or may not be modularized into cells. Because of the large size of the pools, seismic loads are of significant interest. In particular, the effects of modularization and site hardness are of concern. The study presented in this paper reveals that modularization is generally unfavourable, because it creates the option of leaving one or more cells empty which in turn results in higher structural loads. The wall which separates a filled cell from an empty cell, or the wall which bears against earth on one side and faces an empty cell on the other, becomes very highly stressed. For the particular pool geometries examined, a hard site is generally preferred over an intermediate hard site in terms of structural loads.

  3. Population structure of the malaria vector Anopheles sinensis (Diptera: Culicidae in China: two gene pools inferred by microsatellites.

    Directory of Open Access Journals (Sweden)

    Yajun Ma

    Full Text Available BACKGROUND: Anopheles sinensis is a competent malaria vector in China. An understanding of vector population structure is important to the vector-based malaria control programs. However, there is no adequate data of A. sinensis population genetics available yet. METHODOLOGY/PRINCIPAL FINDINGS: This study used 5 microsatellite loci to estimate population genetic diversity, genetic differentiation and demographic history of A. sinensis from 14 representative localities in China. All 5 microsatellite loci were highly polymorphic across populations, with high allelic richness and heterozygosity. Hardy-Weinberg disequilibrium was found in 12 populations associated with heterozygote deficits, which was likely caused by the presence of null allele and the Wahlund effect. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes six and the other includes eight populations. Out of 14 samples, six samples were mixed with individuals from both gene pools, indicating the coexistence of two genetic units in the areas sampled. The overall differentiation between two genetic pools was moderate (F(ST = 0.156. Pairwise differentiation between populations were lower within clusters (F(ST = 0.008-0.028 in cluster I and F(ST = 0.004-0.048 in cluster II than between clusters (F(ST = 0.120-0.201. A reduced gene flow (Nm = 1-1.7 was detected between clusters. No evidence of isolation by distance was detected among populations neither within nor between the two clusters. There are differences in effective population size (Ne = 14.3-infinite across sampled populations. CONCLUSIONS/SIGNIFICANCE: Two genetic pools with moderate genetic differentiation were identified in the A. sinensis populations in China. The population divergence was not correlated with geographic distance or barrier in the range. Variable effective population size and other demographic effects of historical population

  4. Voluntary rewards mediate the evolution of pool punishment for maintaining public goods in large populations

    Science.gov (United States)

    Sasaki, Tatsuya; Uchida, Satoshi; Chen, Xiaojie

    2015-03-01

    Punishment is a popular tool when governing commons in situations where free riders would otherwise take over. It is well known that sanctioning systems, such as the police and courts, are costly and thus can suffer from those who free ride on other's efforts to maintain the sanctioning systems (second-order free riders). Previous game-theory studies showed that if populations are very large, pool punishment rarely emerges in public good games, even when participation is optional, because of second-order free riders. Here we show that a matching fund for rewarding cooperation leads to the emergence of pool punishment, despite the presence of second-order free riders. We demonstrate that reward funds can pave the way for a transition from a population of free riders to a population of pool punishers. A key factor in promoting the transition is also to reward those who contribute to pool punishment, yet not abstaining from participation. Reward funds eventually vanish in raising pool punishment, which is sustainable by punishing the second-order free riders. This suggests that considering the interdependence of reward and punishment may help to better understand the origins and transitions of social norms and institutions.

  5. Cold pool organization and the merging of convective updrafts in a Large Eddy Simulation

    Science.gov (United States)

    Glenn, I. B.; Krueger, S. K.

    2016-12-01

    Cold pool organization is a process that accelerates the transition from shallow to deep cumulus convection, and leads to higher deep convective cloud top heights. The mechanism by which cold pool organization enhances convection remains not well understood, but the basic idea is that since precipitation evaporation and a low equivalent potential temperature in the mid-troposphere lead to strong cold pools, the net cold pool effect can be accounted for in a cumulus parameterization as a relationship involving those factors. Understanding the actual physical mechanism at work will help quantify the strength of the relationship between cold pools and enhanced deep convection. One proposed mechanism of enhancement is that cold pool organization leads to reduced distances between updrafts, creating a local environment more conducive to convection as updrafts entrain parcels of air recently detrained by their neighbors. We take this hypothesis one step further and propose that convective updrafts actually merge, not just exchange recently processed air. Because entrainment and detrainment around an updraft draws nearby air in or pushes it out, respectively, they act like dynamic flow sources and sinks, drawing each other in or pushing each other away. The acceleration is proportional to the inverse square of the distance between two updrafts, so a small reduction in distance can make a big difference in the rate of merging. We have shown in previous research how merging can be seen as collisions between different updraft air parcels using Lagrangian Parcel Trajectories (LPTs) released in a Large Eddy Simulation (LES) during a period with organized deep convection. Now we use a Eulerian frame of reference to examine the updraft merging process during the transition from shallow to organized deep convection. We use a case based on the Large-Scale Biosphere-Atmosphere Experiment in Amazonia (LBA) for our LES. We directly measure the rate of entrainment and the properties

  6. Large sodium pool fires in a closed or in a naturally vented cell

    International Nuclear Information System (INIS)

    Rzekiecki, R.; Malet, J.C.; Sophy, Y.; Joly, C.; Claverie, J.

    1986-01-01

    Within the framework of R and D studies related to LMFBR sodium handling safety, a facility named ESMERALDA 1 was provided. This permits full scale demonstration of the control of sodium fires. ESMERALDA is a French-Italian project including EDF, CEA, NERSA, NOVATOME, partners. Large pool fires studies are a part of it. (author)

  7. Pooled Enrichment Sequencing Identifies Diversity and Evolutionary Pressures at NLR Resistance Genes within a Wild Tomato Population

    Science.gov (United States)

    Stam, Remco; Scheikl, Daniela; Tellier, Aurélien

    2016-01-01

    Nod-like receptors (NLRs) are nucleotide-binding domain and leucine-rich repeats containing proteins that are important in plant resistance signaling. Many of the known pathogen resistance (R) genes in plants are NLRs and they can recognize pathogen molecules directly or indirectly. As such, divergence and copy number variants at these genes are found to be high between species. Within populations, positive and balancing selection are to be expected if plants coevolve with their pathogens. In order to understand the complexity of R-gene coevolution in wild nonmodel species, it is necessary to identify the full range of NLRs and infer their evolutionary history. Here we investigate and reveal polymorphism occurring at 220 NLR genes within one population of the partially selfing wild tomato species Solanum pennellii. We use a combination of enrichment sequencing and pooling ten individuals, to specifically sequence NLR genes in a resource and cost-effective manner. We focus on the effects which different mapping and single nucleotide polymorphism calling software and settings have on calling polymorphisms in customized pooled samples. Our results are accurately verified using Sanger sequencing of polymorphic gene fragments. Our results indicate that some NLRs, namely 13 out of 220, have maintained polymorphism within our S. pennellii population. These genes show a wide range of πN/πS ratios and differing site frequency spectra. We compare our observed rate of heterozygosity with expectations for this selfing and bottlenecked population. We conclude that our method enables us to pinpoint NLR genes which have experienced natural selection in their habitat. PMID:27189991

  8. The Polynesian gene pool: an early contribution by Amerindians to Easter Island.

    Science.gov (United States)

    Thorsby, Erik

    2012-03-19

    It is now generally accepted that Polynesia was first settled by peoples from southeast Asia. An alternative that eastern parts of Polynesia were first inhabited by Amerindians has found little support. There are, however, many indications of a 'prehistoric' (i.e. before Polynesia was discovered by Europeans) contact between Polynesia and the Americas, but genetic evidence of a prehistoric Amerindian contribution to the Polynesian gene pool has been lacking. We recently carried out genomic HLA (human leucocyte antigen) typing as well as typing for mitochondrial DNA (mtDNA) and Y chromosome markers of blood samples collected in 1971 and 2008 from reputedly non-admixed Easter Islanders. All individuals carried HLA alleles and mtDNA types previously found in Polynesia, and most of the males carried Y chromosome markers of Polynesian origin (a few had European Y chromosome markers), further supporting an initial Polynesian population on Easter Island. The HLA investigations revealed, however, that some individuals also carried HLA alleles which have previously almost only been found in Amerindians. We could trace the introduction of these Amerindian alleles to before the Peruvian slave trades, i.e. before the 1860s, and provide suggestive evidence that they were introduced already in prehistoric time. Our results demonstrate an early Amerindian contribution to the Polynesian gene pool on Easter Island, and illustrate the usefulness of typing for immunogenetic markers such as HLA to complement mtDNA and Y chromosome analyses in anthropological investigations.

  9. Two endornaviruses show differential infection patterns between gene pools of Phaseolus vulgaris.

    Science.gov (United States)

    Khankhum, Surasak; Valverde, Rodrigo A; Pastor-Corrales, Marcial A; Osorno, Juan M; Sabanadzovic, Sead

    2015-04-01

    We investigated the occurrence of two plant endornaviruses, Phaseolus vulgaris endornavirus 1 and Phaseolus vulgaris endornavirus 2, in breeding lines, cultivars, landraces, and wild genotypes of common bean (Phaseolus vulgaris) collected from the two centers of common bean domestication: Mesoamerica and the Andes. The two endornaviruses were detected in many genotypes of Mesoamerican origin but rarely in genotypes of Andean origin. The results suggest that these two endornaviruses were introduced into the Mesoamerican modern genotypes during common bean domestication and provide more evidence for the existence of two divergent gene pools of common bean.

  10. Pooled Enrichment Sequencing Identifies Diversity and Evolutionary Pressures at NLR Resistance Genes within a Wild Tomato Population.

    Science.gov (United States)

    Stam, Remco; Scheikl, Daniela; Tellier, Aurélien

    2016-06-02

    Nod-like receptors (NLRs) are nucleotide-binding domain and leucine-rich repeats containing proteins that are important in plant resistance signaling. Many of the known pathogen resistance (R) genes in plants are NLRs and they can recognize pathogen molecules directly or indirectly. As such, divergence and copy number variants at these genes are found to be high between species. Within populations, positive and balancing selection are to be expected if plants coevolve with their pathogens. In order to understand the complexity of R-gene coevolution in wild nonmodel species, it is necessary to identify the full range of NLRs and infer their evolutionary history. Here we investigate and reveal polymorphism occurring at 220 NLR genes within one population of the partially selfing wild tomato species Solanum pennellii. We use a combination of enrichment sequencing and pooling ten individuals, to specifically sequence NLR genes in a resource and cost-effective manner. We focus on the effects which different mapping and single nucleotide polymorphism calling software and settings have on calling polymorphisms in customized pooled samples. Our results are accurately verified using Sanger sequencing of polymorphic gene fragments. Our results indicate that some NLRs, namely 13 out of 220, have maintained polymorphism within our S. pennellii population. These genes show a wide range of πN/πS ratios and differing site frequency spectra. We compare our observed rate of heterozygosity with expectations for this selfing and bottlenecked population. We conclude that our method enables us to pinpoint NLR genes which have experienced natural selection in their habitat. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. The Roles of Mitochondrion in Intergenomic Gene Transfer in Plants: A Source and a Pool

    Directory of Open Access Journals (Sweden)

    Nan Zhao

    2018-02-01

    Full Text Available Intergenomic gene transfer (IGT is continuous in the evolutionary history of plants. In this field, most studies concentrate on a few related species. Here, we look at IGT from a broader evolutionary perspective, using 24 plants. We discover many IGT events by assessing the data from nuclear, mitochondrial and chloroplast genomes. Thus, we summarize the two roles of the mitochondrion: a source and a pool. That is, the mitochondrion gives massive sequences and integrates nuclear transposons and chloroplast tRNA genes. Though the directions are opposite, lots of likenesses emerge. First, mitochondrial gene transfer is pervasive in all 24 plants. Second, gene transfer is a single event of certain shared ancestors during evolutionary divergence. Third, sequence features of homologies vary for different purposes in the donor and recipient genomes. Finally, small repeats (or micro-homologies contribute to gene transfer by mediating recombination in the recipient genome.

  12. Comparison of individual and pooled samples for quantification of antimicrobial resistance genes in swine feces by high-throughput qPCR

    DEFF Research Database (Denmark)

    Clasen, Julie; Mellerup, Anders; Olsen, J. E.

    2015-01-01

    There is a considerable societal interest in the careful monitoring of antimicrobial resistance (AMR) levels in human and animal populations. Sampling and data analysis can be both costly and time consuming. Optimization of sample pooling procedures is therefore important to reduce costs...... and analysis times. The objective of this study was to estimate how many individual fecal samples are needed to pool to get a representative sample for quantification of AMR-genes in a Danish pig herd. 20 individual fecal samples were collected from one section in a Danish pig herd. One to five rectal fecal...... samples were taken from each pen with respect to the number of pigs in the pen. A total of 48 pools were made of increasing number of individual samples. The levels of 9 different AMR-genes were quantified using dynamic qPCR arrays on the BioMark HD system(Fluidigm®).DNA was extracted using the Maxwell...

  13. Genomics of crop wild relatives: expanding the gene pool for crop improvement.

    Science.gov (United States)

    Brozynska, Marta; Furtado, Agnelo; Henry, Robert J

    2016-04-01

    Plant breeders require access to new genetic diversity to satisfy the demands of a growing human population for more food that can be produced in a variable or changing climate and to deliver the high-quality food with nutritional and health benefits demanded by consumers. The close relatives of domesticated plants, crop wild relatives (CWRs), represent a practical gene pool for use by plant breeders. Genomics of CWR generates data that support the use of CWR to expand the genetic diversity of crop plants. Advances in DNA sequencing technology are enabling the efficient sequencing of CWR and their increased use in crop improvement. As the sequencing of genomes of major crop species is completed, attention has shifted to analysis of the wider gene pool of major crops including CWR. A combination of de novo sequencing and resequencing is required to efficiently explore useful genetic variation in CWR. Analysis of the nuclear genome, transcriptome and maternal (chloroplast and mitochondrial) genome of CWR is facilitating their use in crop improvement. Genome analysis results in discovery of useful alleles in CWR and identification of regions of the genome in which diversity has been lost in domestication bottlenecks. Targeting of high priority CWR for sequencing will maximize the contribution of genome sequencing of CWR. Coordination of global efforts to apply genomics has the potential to accelerate access to and conservation of the biodiversity essential to the sustainability of agriculture and food production. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  14. Multiplexed resequencing analysis to identify rare variants in pooled DNA with barcode indexing using next-generation sequencer.

    Science.gov (United States)

    Mitsui, Jun; Fukuda, Yoko; Azuma, Kyo; Tozaki, Hirokazu; Ishiura, Hiroyuki; Takahashi, Yuji; Goto, Jun; Tsuji, Shoji

    2010-07-01

    We have recently found that multiple rare variants of the glucocerebrosidase gene (GBA) confer a robust risk for Parkinson disease, supporting the 'common disease-multiple rare variants' hypothesis. To develop an efficient method of identifying rare variants in a large number of samples, we applied multiplexed resequencing using a next-generation sequencer to identification of rare variants of GBA. Sixteen sets of pooled DNAs from six pooled DNA samples were prepared. Each set of pooled DNAs was subjected to polymerase chain reaction to amplify the target gene (GBA) covering 6.5 kb, pooled into one tube with barcode indexing, and then subjected to extensive sequence analysis using the SOLiD System. Individual samples were also subjected to direct nucleotide sequence analysis. With the optimization of data processing, we were able to extract all the variants from 96 samples with acceptable rates of false-positive single-nucleotide variants.

  15. Extra-binomial variation approach for analysis of pooled DNA sequencing data

    Science.gov (United States)

    Wallace, Chris

    2012-01-01

    Motivation: The invention of next-generation sequencing technology has made it possible to study the rare variants that are more likely to pinpoint causal disease genes. To make such experiments financially viable, DNA samples from several subjects are often pooled before sequencing. This induces large between-pool variation which, together with other sources of experimental error, creates over-dispersed data. Statistical analysis of pooled sequencing data needs to appropriately model this additional variance to avoid inflating the false-positive rate. Results: We propose a new statistical method based on an extra-binomial model to address the over-dispersion and apply it to pooled case-control data. We demonstrate that our model provides a better fit to the data than either a standard binomial model or a traditional extra-binomial model proposed by Williams and can analyse both rare and common variants with lower or more variable pool depths compared to the other methods. Availability: Package ‘extraBinomial’ is on http://cran.r-project.org/ Contact: chris.wallace@cimr.cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics Online. PMID:22976083

  16. CFD modeling of pool swell during large break LOCA

    International Nuclear Information System (INIS)

    Yan, Jin; Bolger, Francis; Li, Guangjun; Mintz, Saul; Pappone, Daniel

    2009-01-01

    GE had conducted a series of one-third scale three-vent air tests in support the horizontal vent pressure suppression system used in Mark III containment design for General Electric BWR plants. During the test, the air-water interface has been tracked by conductivity probes. There are many pressure monitors inside the test rig. The purpose of the test was to provide a basis for the pool swell load definition for the Mark III containment. In this paper, a transient 3-Dimensional CFD model of the one-third scale Mark III suppression pool swell process is constructed. The Volume of Fluid (VOF) multiphase model is used to explicitly track the interface between the water liquid and the air. The CFD results such as flow velocity, pressure, interface locations are compared to those from the test. Through the comparisons, a technical approach to numerically model the pool swell phenomenon is established and benchmarked. (author)

  17. Decrypting the mitochondrial gene pool of modern Panamanians.

    Directory of Open Access Journals (Sweden)

    Ugo A Perego

    Full Text Available The Isthmus of Panama--the narrow neck of land connecting the northern and southern American landmasses--was an obligatory corridor for the Paleo-Indians as they moved into South America. Archaeological evidence suggests an unbroken link between modern natives and their Paleo-Indian ancestors in some areas of Panama, even if the surviving indigenous groups account for only 12.3% of the total population. To evaluate if modern Panamanians have retained a larger fraction of the native pre-Columbian gene pool in their maternally-inherited mitochondrial genome, DNA samples and historical records were collected from more than 1500 volunteer participants living in the nine provinces and four indigenous territories of the Republic. Due to recent gene-flow, we detected ~14% African mitochondrial lineages, confirming the demographic impact of the Atlantic slave trade and subsequent African immigration into Panama from Caribbean islands, and a small European (~2% component, indicating only a minor influence of colonialism on the maternal side. The majority (~83% of Panamanian mtDNAs clustered into native pan-American lineages, mostly represented by haplogroup A2 (51%. These findings reveal an overwhelming native maternal legacy in today's Panama, which is in contrast with the overall concept of personal identity shared by many Panamanians. Moreover, the A2 sub-clades A2ad and A2af (with the previously named 6 bp Huetar deletion, when analyzed at the maximum level of resolution (26 entire mitochondrial genomes, confirm the major role of the Pacific coastal path in the peopling of North, Central and South America, and testify to the antiquity of native mitochondrial genomes in Panama.

  18. poolHiTS: A Shifted Transversal Design based pooling strategy for high-throughput drug screening

    Directory of Open Access Journals (Sweden)

    Woolf Peter J

    2008-05-01

    Full Text Available Abstract Background A key goal of drug discovery is to increase the throughput of small molecule screens without sacrificing screening accuracy. High-throughput screening (HTS in drug discovery involves testing a large number of compounds in a biological assay to identify active compounds. Normally, molecules from a large compound library are tested individually to identify the activity of each molecule. Usually a small number of compounds are found to be active, however the presence of false positive and negative testing errors suggests that this one-drug one-assay screening strategy can be significantly improved. Pooling designs are testing schemes that test mixtures of compounds in each assay, thereby generating a screen of the whole compound library in fewer tests. By repeatedly testing compounds in different combinations, pooling designs also allow for error-correction. These pooled designs, for specific experiment parameters, can be simply and efficiently created using the Shifted Transversal Design (STD pooling algorithm. However, drug screening contains a number of key constraints that require specific modifications if this pooling approach is to be useful for practical screen designs. Results In this paper, we introduce a pooling strategy called poolHiTS (Pooled High-Throughput Screening which is based on the STD algorithm. In poolHiTS, we implement a limit on the number of compounds that can be mixed in a single assay. In addition, we show that the STD-based pooling strategy is limited in the error-correction that it can achieve. Due to the mixing constraint, we show that it is more efficient to split a large library into smaller blocks of compounds, which are then tested using an optimized strategy repeated for each block. We package the optimal block selection algorithm into poolHiTS. The MATLAB codes for the poolHiTS algorithm and the corresponding decoding strategy are also provided. Conclusion We have produced a practical version

  19. Seismic sloshing experiments of large pool-type fast breeder reactors

    International Nuclear Information System (INIS)

    Sakurai, A.; Masuko, Y.; Kurihara, C.; Ishihama, K.; Yashiro, T.; Rodwell, E.

    1989-01-01

    This paper presents the results of seismic sloshing experiments performed on large pool-type LMFBR vessels. Two types of tests were performed. The first type of test was designed to understand the basis phenomena of sloshing (limited to linear sloshing only) and evaluate the effects of the deck-mounted components (i.e., IHXs, pumps, and UIS) on sloshing wave heights using a 1/10-scale model (diameter 2.23 m x H 1.03 m) of the LSPB 1340 MWe pool plant. The second type of test was designed to evaluate the structural integrity of the thermal baffles of the roof-deck to withstand sloshing impulsive pressures (focused on nonlinear sloshing), using a two-dimensional 1/3-scale model (L 8 m x W 3 m x H 2.6 m) of a typical 1000 MWe pool plant. The results of the linear sloshing tests have shown that: 1. the vessel wall stiffness has no effect on the sloshing natural frequency; 2. sloshing wave heights are lowered by 30% to 50% in the presence of the deck-mounted components; and 3. damping factors of sloshing are not influenced by the wall stiffness while they are increased by the presence of the deck-mounted components. The results of the nonlinear sloshing tests are that: 1. the maximum impulsive pressure occurs when the first effective wave strikes at the roof-deck, and thereafter the impulsive pressure decreases irrespective of the impact velocity of the fluid; 2. the first effective wave refers to the case in which the height of the fluid free surface becomes nearly twice the height of the cover gas space; and 3. the structural integrity of the thermal baffles for the roof-deck against the sloshing load was confirmed. In addition to these results, two sloshing-caused problems were identified. The first one is the spillover of hot sodium into the gas-dam type thermal insulator. The second one is cover-gas entrainment into sodium which might lead to a transient overpower (TOP) incident because of the presence of gas bubbles in the reactor core. (orig./HP)

  20. 454 sequencing of pooled BAC clones on chromosome 3H of barley

    Directory of Open Access Journals (Sweden)

    Yamaji Nami

    2011-05-01

    Full Text Available Abstract Background Genome sequencing of barley has been delayed due to its large genome size (ca. 5,000Mbp. Among the fast sequencing systems, 454 liquid phase pyrosequencing provides the longest reads and is the most promising method for BAC clones. Here we report the results of pooled sequencing of BAC clones selected with ESTs genetically mapped to chromosome 3H. Results We sequenced pooled barley BAC clones using a 454 parallel genome sequencer. A PCR screening system based on primer sets derived from genetically mapped ESTs on chromosome 3H was used for clone selection in a BAC library developed from cultivar "Haruna Nijo". The DNA samples of 10 or 20 BAC clones were pooled and used for shotgun library development. The homology between contig sequences generated in each pooled library and mapped EST sequences was studied. The number of contigs assigned on chromosome 3H was 372. Their lengths ranged from 1,230 bp to 58,322 bp with an average 14,891 bp. Of these contigs, 240 showed homology and colinearity with the genome sequence of rice chromosome 1. A contig annotation browser supplemented with query search by unique sequence or genetic map position was developed. The identified contigs can be annotated with barley cDNAs and reference sequences on the browser. Homology analysis of these contigs with rice genes indicated that 1,239 rice genes can be assigned to barley contigs by the simple comparison of sequence lengths in both species. Of these genes, 492 are assigned to rice chromosome 1. Conclusions We demonstrate the efficiency of sequencing gene rich regions from barley chromosome 3H, with special reference to syntenic relationships with rice chromosome 1.

  1. Subgenomic Diversity Patterns Caused by Directional Selection in Bread Wheat Gene Pools

    Directory of Open Access Journals (Sweden)

    Kai Voss-Fels

    2015-07-01

    Full Text Available Genetic diversity represents the fundamental key to breeding success, providing the basis for breeders to select varieties with constantly improving yield performance. On the other hand, strong selection during domestication and breeding have eliminated considerable genetic diversity in the breeding pools of major crops, causing erosion of genetic potential for adaptation to emerging challenges like climate change. High-throughput genomic technologies can address this dilemma by providing detailed knowledge to characterize and replenish genetic diversity in breeding programs. In hexaploid bread wheat ( L., the staple food for 35% of the world’s population, bottlenecks during allopolyploidisation followed by strong artificial selection have considerably narrowed diversity to the extent that yields in many regions appear to be unexpectedly stagnating. In this study, we used a 90,000 single nucleotide polymorphism (SNP wheat genotyping array to assay high-frequency, polymorphic SNP markers in 460 accessions representing different phenological diversity groups from Asian, Australian, European, and North American bread wheat breeding materials. Detailed analysis of subgroup diversity at the chromosome and subgenome scale revealed highly distinct patterns of conserved linkage disequilibrium between different gene pools. The data enable identification of genome regions in most need of rejuvenation with novel diversity and provide a high-resolution molecular basis for genomic-assisted introgression of new variation into chromosome segments surrounding directionally selected metaloci conferring important adaptation and quality traits.

  2. Impact and quantification of the sources of error in DNA pooling designs.

    Science.gov (United States)

    Jawaid, A; Sham, P

    2009-01-01

    The analysis of genome wide variation offers the possibility of unravelling the genes involved in the pathogenesis of disease. Genome wide association studies are also particularly useful for identifying and validating targets for therapeutic intervention as well as for detecting markers for drug efficacy and side effects. The cost of such large-scale genetic association studies may be reduced substantially by the analysis of pooled DNA from multiple individuals. However, experimental errors inherent in pooling studies lead to a potential increase in the false positive rate and a loss in power compared to individual genotyping. Here we quantify various sources of experimental error using empirical data from typical pooling experiments and corresponding individual genotyping counts using two statistical methods. We provide analytical formulas for calculating these different errors in the absence of complete information, such as replicate pool formation, and for adjusting for the errors in the statistical analysis. We demonstrate that DNA pooling has the potential of estimating allele frequencies accurately, and adjusting the pooled allele frequency estimates for differential allelic amplification considerably improves accuracy. Estimates of the components of error show that differential allelic amplification is the most important contributor to the error variance in absolute allele frequency estimation, followed by allele frequency measurement and pool formation errors. Our results emphasise the importance of minimising experimental errors and obtaining correct error estimates in genetic association studies.

  3. Genotyping common and rare variation using overlapping pool sequencing

    Directory of Open Access Journals (Sweden)

    Pasaniuc Bogdan

    2011-07-01

    Full Text Available Abstract Background Recent advances in sequencing technologies set the stage for large, population based studies, in which the ANA or RNA of thousands of individuals will be sequenced. Currently, however, such studies are still infeasible using a straightforward sequencing approach; as a result, recently a few multiplexing schemes have been suggested, in which a small number of ANA pools are sequenced, and the results are then deconvoluted using compressed sensing or similar approaches. These methods, however, are limited to the detection of rare variants. Results In this paper we provide a new algorithm for the deconvolution of DNA pools multiplexing schemes. The presented algorithm utilizes a likelihood model and linear programming. The approach allows for the addition of external data, particularly imputation data, resulting in a flexible environment that is suitable for different applications. Conclusions Particularly, we demonstrate that both low and high allele frequency SNPs can be accurately genotyped when the DNA pooling scheme is performed in conjunction with microarray genotyping and imputation. Additionally, we demonstrate the use of our framework for the detection of cancer fusion genes from RNA sequences.

  4. Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels

    Directory of Open Access Journals (Sweden)

    Hinds David A

    2004-11-01

    Full Text Available Abstract Association studies are used to identify genetic determinants of complex human traits of medical interest. With the large number of validated single nucleotide polymorphisms (SNPs currently available, two limiting factors in association studies are genotyping capability and costs. Pooled DNA genotyping has been proposed as an efficient means of screening SNPs for allele frequency differences in case-control studies and for prioritising them for subsequent individual genotyping analysis. Here, we apply quantitative pooled genotyping followed by individual genotyping and replication to identify associations with human serum high-density lipoprotein (HDL cholesterol levels. The DNA from individuals with low and high HDL cholesterol levels was pooled separately, each pool was amplified by polymerase chain reaction in triplicate and each amplified product was separately hybridised to a high-density oligonucleotide array. Allele frequency differences between case and control groups with low and high HDL cholesterol levels were estimated for 7,283 SNPs distributed across 71 candidate gene regions spanning a total of 17.1 megabases. A novel method was developed to take advantage of independently derived haplotype map information to improve the pooled estimates of allele frequency differences. A subset of SNPs with the largest estimated allele frequency differences between low and high HDL cholesterol groups was chosen for individual genotyping in the study population, as well as in a separate replication population. Four SNPs in a single haplotype block within the cholesteryl ester transfer protein (CETP gene interval were significantly associated with HDL cholesterol levels in both populations. Our study is among the first to demonstrate the application of pooled genotyping followed by confirmation with individual genotyping to identify genetic determinants of a complex trait.

  5. Further evidence of an Amerindian contribution to the Polynesian gene pool on Easter Island.

    Science.gov (United States)

    Thorsby, E; Flåm, S T; Woldseth, B; Dupuy, B M; Sanchez-Mazas, A; Fernandez-Vina, M A

    2009-06-01

    Available evidence suggests a Polynesian origin of the Easter Island population. We recently found that some native Easter Islanders also carried some common American Indian (Amerindian) human leukocyte antigen (HLA) alleles, which probably were introduced before Europeans discovered the island in 1722. In this study, we report molecular genetic investigations of 21 other selected native Easter Islanders. Analysis of mitochondrial DNA and Y chromosome markers showed no traces of an Amerindian contribution. However, high-resolution genomic HLA typing showed that two individuals carried some other common Amerindian HLA alleles, different from those found in our previous investigations. The new data support our previous evidence of an Amerindian contribution to the gene pool on Easter Island.

  6. [Structure of the gene pool of ethnic groups from the Altai-Sayan region from data on mitochondrial polymorphism].

    Science.gov (United States)

    Derenko, M V; Denisova, G A; Maliarchuk, B A; Dambueva, I K; Luzina, F A; Lotosh, E A; Dorzhu, Ch M; Karamchakova, O N; Solovenchuk, L L; Zakharov, I A

    2001-10-01

    Using the data on mitochondrial DNA (mtDNA) polymorphism, genetic structures of the four Turkic-speaking ethnic groups of Altai-Sayan highlands, Southern Altaians (Altai-Kizhi), Khakassians, Shorians, and Sojots, were described. Mitochondrial gene pools of the populations examined were characterized by different ratios between Mongoloid (M*, C, D, E, G, A, B, and F) and Caucasoid (H, U, T, J, and K) mtDNA lineages. All the populations studied had a strongly pronounced Mongoloid component, the frequency of which was 88.2% in Sojots, 75.9% in Khakassians, 67.4% in Altaians, and 64.3% in Shorians. Maximum frequency of the Caucasoid component (35.7%) was observed in Shorians. Phylogenetic and statistical analyses of the mtDNA group frequency distribution patterns in the gene pools of the ethnic populations of Altai-Sayan highlands and the adjacent territories showed that the populations of the region fell into three groups. The first group included Khakassians, Tuvinians and Altaians, the second group consisted of Sojots, Buryats, and Mongols, while the third group was composed of Uigurs, Kazakhs, and Kyrgyzes. The isolated position of Shorians among the populations examined can be explained by their different anthropological composition and their presumptive relatedness to Finno-Ugric populations of Siberia.

  7. Assessing the general safety and tolerability of vildagliptin: value of pooled analyses from a large safety database versus evaluation of individual studies

    Science.gov (United States)

    Schweizer, Anja; Dejager, Sylvie; Foley, James E; Kothny, Wolfgang

    2011-01-01

    Aim: Analyzing safety aspects of a drug from individual studies can lead to difficult-to-interpret results. The aim of this paper is therefore to assess the general safety and tolerability, including incidences of the most common adverse events (AEs), of vildagliptin based on a large pooled database of Phase II and III clinical trials. Methods: Safety data were pooled from 38 studies of ≥12 to ≥104 weeks’ duration. AE profiles of vildagliptin (50 mg bid; N = 6116) were evaluated relative to a pool of comparators (placebo and active comparators; N = 6210). Absolute incidence rates were calculated for all AEs, serious AEs (SAEs), discontinuations due to AEs, and deaths. Results: Overall AEs, SAEs, discontinuations due to AEs, and deaths were all reported with a similar frequency in patients receiving vildagliptin (69.1%, 8.9%, 5.7%, and 0.4%, respectively) and patients receiving comparators (69.0%, 9.0%, 6.4%, and 0.4%, respectively), whereas drug-related AEs were seen with a lower frequency in vildagliptin-treated patients (15.7% vs 21.7% with comparators). The incidences of the most commonly reported specific AEs were also similar between vildagliptin and comparators, except for increased incidences of hypoglycemia, tremor, and hyperhidrosis in the comparator group related to the use of sulfonylureas. Conclusions: The present pooled analysis shows that vildagliptin was overall well tolerated in clinical trials of up to >2 years in duration. The data further emphasize the value of a pooled analysis from a large safety database versus assessing safety and tolerability from individual studies. PMID:21415917

  8. Validation of Effective Models for Simulation of Thermal Stratification and Mixing Induced by Steam Injection into a Large Pool of Water

    Directory of Open Access Journals (Sweden)

    Hua Li

    2014-01-01

    Full Text Available The Effective Heat Source (EHS and Effective Momentum Source (EMS models have been proposed to predict the development of thermal stratification and mixing during a steam injection into a large pool of water. These effective models are implemented in GOTHIC software and validated against the POOLEX STB-20 and STB-21 tests and the PPOOLEX MIX-01 test. First, the EHS model is validated against STB-20 test which shows the development of thermal stratification. Different numerical schemes and grid resolutions have been tested. A 48×114 grid with second order scheme is sufficient to capture the vertical temperature distribution in the pool. Next, the EHS and EMS models are validated against STB-21 test. Effective momentum is estimated based on the water level oscillations in the blowdown pipe. An effective momentum selected within the experimental measurement uncertainty can reproduce the mixing details. Finally, the EHS-EMS models are validated against MIX-01 test which has improved space and time resolution of temperature measurements inside the blowdown pipe. Excellent agreement in averaged pool temperature and water level in the pool between the experiment and simulation has been achieved. The development of thermal stratification in the pool is also well captured in the simulation as well as the thermal behavior of the pool during the mixing phase.

  9. Genomic analyses of tropical beef cattle fertility based on genotyping pools of Brahman cows with unknown pedigree.

    Science.gov (United States)

    Reverter, A; Porto-Neto, L R; Fortes, M R S; McCulloch, R; Lyons, R E; Moore, S; Nicol, D; Henshall, J; Lehnert, S A

    2016-10-01

    We introduce an innovative approach to lowering the overall cost of obtaining genomic EBV (GEBV) and encourage their use in commercial extensive herds of Brahman beef cattle. In our approach, the DNA genotyping of cow herds from 2 independent properties was performed using a high-density bovine SNP chip on DNA from pooled blood samples, grouped according to the result of a pregnancy test following their first and second joining opportunities. For the DNA pooling strategy, 15 to 28 blood samples from the same phenotype and contemporary group were allocated to pools. Across the 2 properties, a total of 183 pools were created representing 4,164 cows. In addition, blood samples from 309 bulls from the same properties were also taken. After genotyping and quality control, 74,584 remaining SNP were used for analyses. Pools and individual DNA samples were related by means of a "hybrid" genomic relationship matrix. The pooled genotyping analysis of 2 large and independent commercial populations of tropical beef cattle was able to recover significant and plausible associations between SNP and pregnancy test outcome. We discuss 24 SNP with significant association ( < 1.0 × 10) and mapped within 40 kb of an annotated gene. We have established a method to estimate the GEBV in young herd bulls for a trait that is currently unable to be predicted at all. In summary, our novel approach allowed us to conduct genomic analyses of fertility in 2 large commercial Brahman herds managed under extensive pastoral conditions.

  10. Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq.

    Science.gov (United States)

    Dennenmoser, Stefan; Vamosi, Steven M; Nolte, Arne W; Rogers, Sean M

    2017-01-01

    Understanding the genomic basis of adaptive divergence in the presence of gene flow remains a major challenge in evolutionary biology. In prickly sculpin (Cottus asper), an abundant euryhaline fish in northwestern North America, high genetic connectivity among brackish-water (estuarine) and freshwater (tributary) habitats of coastal rivers does not preclude the build-up of neutral genetic differentiation and emergence of different life history strategies. Because these two habitats present different osmotic niches, we predicted high genetic differentiation at known teleost candidate genes underlying salinity tolerance and osmoregulation. We applied whole-genome sequencing of pooled DNA samples (Pool-Seq) to explore adaptive divergence between two estuarine and two tributary habitats. Paired-end sequence reads were mapped against genomic contigs of European Cottus, and the gene content of candidate regions was explored based on comparisons with the threespine stickleback genome. Genes showing signals of repeated differentiation among brackish-water and freshwater habitats included functions such as ion transport and structural permeability in freshwater gills, which suggests that local adaptation to different osmotic niches might contribute to genomic divergence among habitats. Overall, the presence of both repeated and unique signatures of differentiation across many loci scattered throughout the genome is consistent with polygenic adaptation from standing genetic variation and locally variable selection pressures in the early stages of life history divergence. © 2016 John Wiley & Sons Ltd.

  11. Estimation of the algal-available phosphorus pool in sediments of a large, shallow eutrophic lake (Taihu, China) using profiled SMT fractional analysis

    International Nuclear Information System (INIS)

    Zhu Mengyuan; Zhu Guangwei; Li Wei; Zhang Yunlin; Zhao Linlin; Gu Zhao

    2013-01-01

    Because large, shallow lakes are heavily influenced by wind–wave disturbance, it is difficult to estimate internal phosphorus load using traditional methods. To estimate the potential contribution of phosphorus from sediment to overlying water in eutrophic Lake Taihu, phosphorus fractions of surface and deep layer sediments were quantified and analyzed for algal bloom potential using a Standard Measurements and Testing (SMT) sequential extraction method and incubation experiments. Phosphorus bound to Fe, Al and Mn oxides and hydroxides (Fe–P) and organic phosphorus (OP) were to be found bioactive. The difference in Fe–P and OP contents between surface and deep layers equates to the sediment pool of potentially algal-available phosphorus. This pool was estimated at 5168 tons for the entire lake and was closely related to pollution input and algal blooms. Profiled SMT fractionation analysis is thus a potentially useful tool for estimating internal phosphorus loading in large, shallow lakes. - Highlights: ► We used profiled sediment P activity by SMT fractionation to evaluate the P release potential in large and shallow lakes. ► We built the relationship between sediment SMT fractionations of P and the P release by algal bloom degradation process. ► We discussed the supporting mechanism of sediment P release to Microcystis algal bloom in a large and shallow lake. ► We discussed the nutrient control strategy of algal bloom in shallow lakes in highly human activities disturbance catchment. - Profiled SMT fractional analysis of internal phosphorus pool in large, shallow lake.

  12. Web service discovery among large service pools utilising semantic similarity and clustering

    Science.gov (United States)

    Chen, Fuzan; Li, Minqiang; Wu, Harris; Xie, Lingli

    2017-03-01

    With the rapid development of electronic business, Web services have attracted much attention in recent years. Enterprises can combine individual Web services to provide new value-added services. An emerging challenge is the timely discovery of close matches to service requests among large service pools. In this study, we first define a new semantic similarity measure combining functional similarity and process similarity. We then present a service discovery mechanism that utilises the new semantic similarity measure for service matching. All the published Web services are pre-grouped into functional clusters prior to the matching process. For a user's service request, the discovery mechanism first identifies matching services clusters and then identifies the best matching Web services within these matching clusters. Experimental results show that the proposed semantic discovery mechanism performs better than a conventional lexical similarity-based mechanism.

  13. Ultra Large Gene Families: A Matter of Adaptation or Genomic Parasites?

    Directory of Open Access Journals (Sweden)

    Philipp H. Schiffer

    2016-08-01

    Full Text Available Gene duplication is an important mechanism of molecular evolution. It offers a fast track to modification, diversification, redundancy or rescue of gene function. However, duplication may also be neutral or (slightly deleterious, and often ends in pseudo-geneisation. Here, we investigate the phylogenetic distribution of ultra large gene families on long and short evolutionary time scales. In particular, we focus on a family of NACHT-domain and leucine-rich-repeat-containing (NLR-genes, which we previously found in large numbers to occupy one chromosome arm of the zebrafish genome. We were interested to see whether such a tight clustering is characteristic for ultra large gene families. Our data reconfirm that most gene family inflations are lineage-specific, but we can only identify very few gene clusters. Based on our observations we hypothesise that, beyond a certain size threshold, ultra large gene families continue to proliferate in a mechanism we term “run-away evolution”. This process might ultimately lead to the failure of genomic integrity and drive species to extinction.

  14. Measurement of temperature distributions in large pool fires with the use of directional flame thermometers

    International Nuclear Information System (INIS)

    Koski, Jorman A.

    2000-01-01

    Temperatures inside the flame zone of large regulatory pool fires measured during tests of radioactive materials packages vary widely with both time and position. Measurements made with several Directional Flame Thermometers, in which a thermocouple is attached to a thin metal sheet that quickly approaches flame temperatures, have been used to construct fire temperature distributions and cumulative probability distributions. As an aid to computer simulations of these large fires, these distributions are presented. The distributions are constructed by sorting fire temperature data into bins 10 C wide. A typical fire temperature distribution curve has a gradual increase starting at about 600 C, with the number of observations increasing to a peak near 1000 C, followed by an abrupt decrease in frequency, with no temperatures observed above 1200 C

  15. Pooling and correlated neural activity

    Directory of Open Access Journals (Sweden)

    Robert Rosenbaum

    2010-04-01

    Full Text Available Correlations between spike trains can strongly modulate neuronal activity and affect the ability of neurons to encode information. Neurons integrate inputs from thousands of afferents. Similarly, a number of experimental techniques are designed to record pooled cell activity. We review and generalize a number of previous results that show how correlations between cells in a population can be amplified and distorted in signals that reflect their collective activity. The structure of the underlying neuronal response can significantly impact correlations between such pooled signals. Therefore care needs to be taken when interpreting pooled recordings, or modeling networks of cells that receive inputs from large presynaptic populations. We also show that the frequently observed runaway synchrony in feedforward chains is primarily due to the pooling of correlated inputs.

  16. Vitamin D Pooling Project

    Science.gov (United States)

    The Vitamin D Pooling Project of Rarer Cancers brought together investigators from 10 cohorts to conduct a large prospective epidemiologic study of the association between vitamin D status and seven rarer cancers.

  17. Finding Biomarker Signatures in Pooled Sample Designs: A Simulation Framework for Methodological Comparisons

    Directory of Open Access Journals (Sweden)

    Anna Telaar

    2010-01-01

    Full Text Available Detection of discriminating patterns in gene expression data can be accomplished by using various methods of statistical learning. It has been proposed that sample pooling in this context would have negative effects; however, pooling cannot always be avoided. We propose a simulation framework to explicitly investigate the parameters of patterns, experimental design, noise, and choice of method in order to find out which effects on classification performance are to be expected. We use a two-group classification task and simulated gene expression data with independent differentially expressed genes as well as bivariate linear patterns and the combination of both. Our results show a clear increase of prediction error with pool size. For pooled training sets powered partial least squares discriminant analysis outperforms discriminance analysis, random forests, and support vector machines with linear or radial kernel for two of three simulated scenarios. The proposed simulation approach can be implemented to systematically investigate a number of additional scenarios of practical interest.

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

    Directory of Open Access Journals (Sweden)

    Baumgarten Andrew

    2004-06-01

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

  19. SBWR PCCS vent phenomena and suppression pool mixing

    Energy Technology Data Exchange (ETDEWEB)

    Coddington, P. [Thermal-Hydraulics Lab., Paul Scherrer Institute, Villigen (Switzerland); Andreani, M. [Nuclear Engineering Lab., Swiss Federal Institute of Technology, Zurich (Switzerland)

    1995-09-01

    The most important phenomena influencing the effectiveness of the pressure suppression capability of the water pool within the Wetwell compartment of the SBWR Containment, during the period of Passive Containment Cooling System (PCCS) venting, have been critically reviewed. In addition, calculations have been carried-out to determine the condensation of the vented steam and the distribution of the energy deposited in the liquid pool. It has been found that a large contribution to the vapour suppression is due to condensation inside the vent pipe. The condensation rate of the steam inside the bubbles, produced at the vent exit, during their rise to the surface, may however be rather low, because of the large size bubbles. This can lead to vapour channelling to the Wetwell gas space. The above comments are likely to be ameliorated if the vent exit is a distributed source or sparger. Due to the large water flow rates within the {open_quotes}bubbly two-phase plume{close_quotes} generated by the gas injection, the water in the pool above the vent exit is likely to be heated nearly isothermally (perfect mixing). The effect of the suppression pool walls would be to enhance the recirculation and, consequently to promote mixing. The large size of the bubbles therein and of the walls on pool mixing are the most severe difficulties in extrapolating the results from scaled experiments to prototypical conditions.

  20. Pooling knowledge and improving safety for contracted works at a large industrial park.

    Science.gov (United States)

    Agnello, Patrizia; Ansaldi, Silvia; Bragatto, Paolo

    2015-01-01

    At a large chemical park maintenance is contracted by the major companies operating the plants to many small firms. The cultural and psychological isolation of contractor workers was recognized a root cause of severe accidents in the recent years. That problem is common in chemical industry. The knowledge sharing has been assumed a good key to involve contractors and sub contractors in safety culture and contributing to injuries prevention. The selection of personal protective equipment PPE for the maintenance works has been taken as benchmark to demonstrate the adequateness of the proposed approach. To support plant operators, contractors and subcontractors in PPE discussion, a method has been developed. Its core is a knowledge-base, organized in an Ontology, as suitable for inferring decisions. By means of this tool all stakeholders have merged experience and information and find out the right PPE, to be provided, with adequate training and information package. PPE selection requires sound competencies about process and environmental hazards, including major accident, preventive and protective measures, maintenance activities. These pieces of knowledge previously fragmented among plant operators and contractors, have to be pooled, and used to find out the adequate PPE for a number of maintenance works. The PPE selection is per se important, but it is also a good chance to break the contractors' isolation and involve them in safety objectives. Thus by pooling experience and practical knowledge, the common understanding of safety issues has been strengthened.

  1. Genes Involved in Initial Follicle Recruitment May Be Associated with Age at Menopause

    NARCIS (Netherlands)

    Voorhuis, Marlies; Broekmans, Frank J.; Fauser, Bart C. J. M.; Onland-Moret, N. Charlotte; van der Schouw, Yvonne T.

    Context: Timing of menopause is largely influenced by genetic factors. Because menopause occurs when the follicle pool in the ovaries has become exhausted, genes involved in primordial follicle recruitment can be considered as candidate genes for timing of menopause. Objective: The aim was to study

  2. Effects of thin-layer boilover on flame geometry and dynamics in large hydrocarbon pool fires

    Energy Technology Data Exchange (ETDEWEB)

    Ferrero, Fabio; Munoz, Miguel; Arnaldos, Josep [Centre d' Estudis del Risc Tecnologic (CERTEC), Chemical Engineering Department, Universitat Politecnica de Catalunya, Diagonal 647, 08028-Barcelona, Catalonia (Spain)

    2007-03-15

    This work aims to estimate the effects of thin-layer boilover on flame geometry and dynamics. A series of large scale experiments (in pools ranging from 1.5 to 6 m in diameter) were performed using gasoline and diesel as fuel. As expected, only diesel showed evidence of this phenomenon. This article presents a summary of the results obtained for flame height, tilt and pulsation. Flame height increases during water ebullition, though the increase is no longer detectable when wind speed exceeds certain values. Correlations previously presented in the literature to predict flame length and tilt were modified in order to fit the results obtained during thin-layer boilover. However, the influence on flame tilt is not as great and the equations for the stationary period seem suitable for the entire fire. Results of flame pulsation during the stationary period fill the gap in the literature for fires between 1.5 and 6 m and fit previous correlations. On the other hand, during ebullition, the flame pulsates faster, as air entrainment is greater and, as one would expect, this effect decreases with pool size. A new equation for estimating pulsation frequency during boilover is proposed. (author)

  3. Pool fires in a large scale ventilation system

    International Nuclear Information System (INIS)

    Smith, P.R.; Leslie, I.H.; Gregory, W.S.; White, B.

    1991-01-01

    A series of pool fire experiments was carried out in the Large Scale Flow Facility of the Mechanical Engineering Department at New Mexico State University. The various experiments burned alcohol, hydraulic cutting oil, kerosene, and a mixture of kerosene and tributylphosphate. Gas temperature and wall temperature measurements as a function of time were made throughout the 23.3m 3 burn compartment and the ducts of the ventilation system. The mass of the smoke particulate deposited upon the ventilation system 0.61m x 0.61m high efficiency particulate air filter for the hydraulic oil, kerosene, and kerosene-tributylphosphate mixture fires was measured using an in situ null balance. Significant increases in filter resistance were observed for all three fuels for burning time periods ranging from 10 to 30 minutes. This was found to be highly dependent upon initial ventilation system flow rate, fuel type, and flow configuration. The experimental results were compared to simulated results predicted by the Los Alamos National Laboratory FIRAC computer code. In general, the experimental and the computer results were in reasonable agreement, despite the fact that the fire compartment for the experiments was an insulated steel tank with 0.32 cm walls, while the compartment model FIRIN of FIRAC assumes 0.31 m thick concrete walls. This difference in configuration apparently caused FIRAC to consistently underpredict the measured temperatures in the fire compartment. The predicted deposition of soot proved to be insensitive to ventilation system flow rate, but the measured values showed flow rate dependence. However, predicted soot deposition was of the same order of magnitude as measured soot deposition

  4. Polymorphisms in Genes of Relevance for Oestrogen and Oxytocin Pathways and Risk of Barrett's Oesophagus and Oesophageal Adenocarcinoma: A Pooled Analysis from the BEACON Consortium.

    Science.gov (United States)

    Lagergren, Katarina; Ek, Weronica E; Levine, David; Chow, Wong-Ho; Bernstein, Leslie; Casson, Alan G; Risch, Harvey A; Shaheen, Nicholas J; Bird, Nigel C; Reid, Brian J; Corley, Douglas A; Hardie, Laura J; Wu, Anna H; Fitzgerald, Rebecca C; Pharoah, Paul; Caldas, Carlos; Romero, Yvonne; Vaughan, Thomas L; MacGregor, Stuart; Whiteman, David; Westberg, Lars; Nyren, Olof; Lagergren, Jesper

    2015-01-01

    The strong male predominance in oesophageal adenocarcinoma (OAC) and Barrett's oesophagus (BO) continues to puzzle. Hormonal influence, e.g. oestrogen or oxytocin, might contribute. This genetic-epidemiological study pooled 14 studies from three continents, Australia, Europe, and North America. Polymorphisms in 3 key genes coding for the oestrogen pathway (receptor alpha (ESR1), receptor beta (ESR2), and aromatase (CYP19A1)), and 3 key genes of the oxytocin pathway (the oxytocin receptor (OXTR), oxytocin protein (OXT), and cyclic ADP ribose hydrolase glycoprotein (CD38)), were analysed using a gene-based approach, versatile gene-based test association study (VEGAS). Among 1508 OAC patients, 2383 BO patients, and 2170 controls, genetic variants within ESR1 were associated with BO in males (p = 0.0058) and an increased risk of OAC and BO combined in males (p = 0.0023). Genetic variants within OXTR were associated with an increased risk of BO in both sexes combined (p = 0.0035) and in males (p = 0.0012). We followed up these suggestive findings in a further smaller data set, but found no replication. There were no significant associations between the other 4 genes studied and risk of OAC, BO, separately on in combination, in males and females combined or in males only. Genetic variants in the oestrogen receptor alpha and the oxytocin receptor may be associated with an increased risk of BO or OAC, but replication in other large samples are needed.

  5. Polymorphisms in Genes of Relevance for Oestrogen and Oxytocin Pathways and Risk of Barrett's Oesophagus and Oesophageal Adenocarcinoma: A Pooled Analysis from the BEACON Consortium.

    Directory of Open Access Journals (Sweden)

    Katarina Lagergren

    Full Text Available The strong male predominance in oesophageal adenocarcinoma (OAC and Barrett's oesophagus (BO continues to puzzle. Hormonal influence, e.g. oestrogen or oxytocin, might contribute.This genetic-epidemiological study pooled 14 studies from three continents, Australia, Europe, and North America. Polymorphisms in 3 key genes coding for the oestrogen pathway (receptor alpha (ESR1, receptor beta (ESR2, and aromatase (CYP19A1, and 3 key genes of the oxytocin pathway (the oxytocin receptor (OXTR, oxytocin protein (OXT, and cyclic ADP ribose hydrolase glycoprotein (CD38, were analysed using a gene-based approach, versatile gene-based test association study (VEGAS.Among 1508 OAC patients, 2383 BO patients, and 2170 controls, genetic variants within ESR1 were associated with BO in males (p = 0.0058 and an increased risk of OAC and BO combined in males (p = 0.0023. Genetic variants within OXTR were associated with an increased risk of BO in both sexes combined (p = 0.0035 and in males (p = 0.0012. We followed up these suggestive findings in a further smaller data set, but found no replication. There were no significant associations between the other 4 genes studied and risk of OAC, BO, separately on in combination, in males and females combined or in males only.Genetic variants in the oestrogen receptor alpha and the oxytocin receptor may be associated with an increased risk of BO or OAC, but replication in other large samples are needed.

  6. Studies of thermal stratification in water pool

    International Nuclear Information System (INIS)

    Verma, P.K.; Chandraker, D.K.; Nayak, A.K.; Vijayan, P.K.

    2015-01-01

    Large water pools are used as a heat sink for various cooling systems used in industry. In context of advance nuclear reactors like AHWR, it is used as ultimate heat sink for passive systems for decay heat removal and containment cooling. This system incorporates heat exchangers submerged in the large water pool. However, heat transfer by natural convection in pool poses a problem of thermal stratification. Due to thermal stratification hot layers of water accumulate over the relatively cold one. The heat transfer performance of heat exchanger gets deteriorated as a hot fluid envelops it. In the nuclear reactors, the walls of the pool are made of concrete and it may subject to high temperature due to thermal stratification which is not desirable. In this paper, a concept of employing shrouds around the heat source is studied. These shrouds provide a bulk flow in the water pool, thereby facilitating mixing of hot and cold fluid, which eliminate stratification. The concept has been applied to the a scaled model of Gravity Driven Water Pool (GDWP) of AHWR in which Isolation Condensers (IC) tubes are submerged for decay heat removal of AHWR using ICS and thermal stratification phenomenon was predicted with and without shrouds. To demonstrate the adequacy of the effectiveness of shroud arrangement and to validate the simulation methodology of RELAP5/Mod3.2, experiments has been conducted on a scaled model of the pool with and without shroud. (author)

  7. Assessing the general safety and tolerability of vildagliptin: value of pooled analyses from a large safety database versus evaluation of individual studies

    Directory of Open Access Journals (Sweden)

    Schweizer A

    2011-02-01

    Full Text Available Anja Schweizer1, Sylvie Dejager2, James E Foley3, Wolfgang Kothny31Novartis Pharma AG, Basel, Switzerland; 2Novartis Pharma SAS, Rueil-Malmaison, France; 3Novartis Pharmaceuticals Corporation, East Hanover, NJ, USAAim: Analyzing safety aspects of a drug from individual studies can lead to difficult-to-interpret results. The aim of this paper is therefore to assess the general safety and tolerability, including incidences of the most common adverse events (AEs, of vildagliptin based on a large pooled database of Phase II and III clinical trials.Methods: Safety data were pooled from 38 studies of ≥12 to ≥104 weeks' duration. AE profiles of vildagliptin (50 mg bid; N = 6116 were evaluated relative to a pool of comparators (placebo and active comparators; N = 6210. Absolute incidence rates were calculated for all AEs, serious AEs (SAEs, discontinuations due to AEs, and deaths.Results: Overall AEs, SAEs, discontinuations due to AEs, and deaths were all reported with a similar frequency in patients receiving vildagliptin (69.1%, 8.9%, 5.7%, and 0.4%, respectively and patients receiving comparators (69.0%, 9.0%, 6.4%, and 0.4%, respectively, whereas drug-related AEs were seen with a lower frequency in vildagliptin-treated patients (15.7% vs 21.7% with comparators. The incidences of the most commonly reported specific AEs were also similar between vildagliptin and comparators, except for increased incidences of hypoglycemia, tremor, and hyperhidrosis in the comparator group related to the use of sulfonylureas.Conclusions: The present pooled analysis shows that vildagliptin was overall well tolerated in clinical trials of up to >2 years in duration. The data further emphasize the value of a pooled analysis from a large safety database versus assessing safety and tolerability from individual studies.Keywords: type 2 diabetes, dipeptidyl peptidase-4, edema, safety, vildagliptin

  8. Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

    Directory of Open Access Journals (Sweden)

    Mullen Michael P

    2012-01-01

    Full Text Available Abstract Background The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and although technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Therefore using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility. Results In total, 4,135 SNPs and 893 indels were identified during the resequencing of the 83 candidate genes. Nineteen percent (n = 952 of variants were located within 5' and 3' UTRs. Seventy-two percent (n = 3,612 were intronic and 9% (n = 464 were exonic, including 65 indels and 236 SNPs resulting in non-synonymous substitutions (NSS. Significant (P ® MassARRAY. No significant differences (P > 0.1 were observed between the two methods for any of the 43 SNPs across both pools (i.e., 86 tests in total. Conclusions The results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post-natal growth and development and subsequent lactogenesis and fertility. We have identified a large number of variants segregating at significantly different frequencies between cattle groups divergent for calving

  9. 13 CFR 120.611 - Pools backing Pool Certificates.

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Pools backing Pool Certificates. 120.611 Section 120.611 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION BUSINESS LOANS Secondary Market Certificates § 120.611 Pools backing Pool Certificates. (a) Pool characteristics. As set...

  10. De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley

    Directory of Open Access Journals (Sweden)

    Scholz Uwe

    2009-11-01

    Full Text Available Abstract Background De novo sequencing the entire genome of a large complex plant genome like the one of barley (Hordeum vulgare L. is a major challenge both in terms of experimental feasibility and costs. The emergence and breathtaking progress of next generation sequencing technologies has put this goal into focus and a clone based strategy combined with the 454/Roche technology is conceivable. Results To test the feasibility, we sequenced 91 barcoded, pooled, gene containing barley BACs using the GS FLX platform and assembled the sequences under iterative change of parameters. The BAC assemblies were characterized by N50 of ~50 kb (N80 ~31 kb, N90 ~21 kb and a Q40 of 94%. For ~80% of the clones, the best assemblies consisted of less than 10 contigs at 24-fold mean sequence coverage. Moreover we show that gene containing regions seem to assemble completely and uninterrupted thus making the approach suitable for detecting complete and positionally anchored genes. By comparing the assemblies of four clones to their complete reference sequences generated by the Sanger method, we evaluated the distribution, quality and representativeness of the 454 sequences as well as the consistency and reliability of the assemblies. Conclusion The described multiplex 454 sequencing of barcoded BACs leads to sequence consensi highly representative for the clones. Assemblies are correct for the majority of contigs. Though the resolution of complex repetitive structures requires additional experimental efforts, our approach paves the way for a clone based strategy of sequencing the barley genome.

  11. Identification and characterization of two novel bla(KLUC resistance genes through large-scale resistance plasmids sequencing.

    Directory of Open Access Journals (Sweden)

    Teng Xu

    Full Text Available Plasmids are important antibiotic resistance determinant carriers that can disseminate various drug resistance genes among species or genera. By using a high throughput sequencing approach, two groups of plasmids of Escherichia coli (named E1 and E2, each consisting of 160 clinical E. coli strains isolated from different periods of time were sequenced and analyzed. A total of 20 million reads were obtained and mapped onto the known resistance gene sequences. As a result, a total of 9 classes, including 36 types of antibiotic resistant genes, were identified. Among these genes, 25 and 27 single nucleotide polymorphisms (SNPs appeared, of which 9 and 12 SNPs are nonsynonymous substitutions in the E1 and E2 samples. It is interesting to find that a novel genotype of bla(KLUC, whose close relatives, bla(KLUC-1 and bla(KLUC-2, have been previously reported as carried on the Kluyvera cryocrescens chromosome and Enterobacter cloacae plasmid, was identified. It shares 99% and 98% amino acid identities with Kluc-1 and Kluc-2, respectively. Further PCR screening of 608 Enterobacteriaceae family isolates yielded a second variant (named bla(KLUC-4. It was interesting to find that Kluc-3 showed resistance to several cephalosporins including cefotaxime, whereas bla(KLUC-4 did not show any resistance to the antibiotics tested. This may be due to a positively charged residue, Arg, replaced by a neutral residue, Leu, at position 167, which is located within an omega-loop. This work represents large-scale studies on resistance gene distribution, diversification and genetic variation in pooled multi-drug resistance plasmids, and provides insight into the use of high throughput sequencing technology for microbial resistance gene detection.

  12. Horizontal gene transfer and nucleotide compositional anomaly in large DNA viruses

    Directory of Open Access Journals (Sweden)

    Ogata Hiroyuki

    2007-12-01

    Full Text Available Abstract Background DNA viruses have a wide range of genome sizes (5 kb up to 1.2 Mb, compared to 0.16 Mb to 1.5 Mb for obligate parasitic bacteria that do not correlate with their virulence or the taxonomic distribution of their hosts. The reasons for such large variation are unclear. According to the traditional view of viruses as gifted "gene pickpockets", large viral genome sizes could originate from numerous gene acquisitions from their hosts. We investigated this hypothesis by studying 67 large DNA viruses with genome sizes larger than 150 kb, including the recently characterized giant mimivirus. Given that horizontally transferred DNA often have anomalous nucleotide compositions differing from the rest of the genome, we conducted a detailed analysis of the inter- and intra-genome compositional properties of these viruses. We then interpreted their compositional heterogeneity in terms of possible causes, including strand asymmetry, gene function/expression, and horizontal transfer. Results We first show that the global nucleotide composition and nucleotide word usage of viral genomes are species-specific and distinct from those of their hosts. Next, we identified compositionally anomalous (cA genes in viral genomes, using a method based on Bayesian inference. The proportion of cA genes is highly variable across viruses and does not exhibit a significant correlation with genome size. The vast majority of the cA genes were of unknown function, lacking homologs in the databases. For genes with known homologs, we found a substantial enrichment of cA genes in specific functional classes for some of the viruses. No significant association was found between cA genes and compositional strand asymmetry. A possible exogenous origin for a small fraction of the cA genes could be confirmed by phylogenetic reconstruction. Conclusion At odds with the traditional dogma, our results argue against frequent genetic transfers to large DNA viruses from their

  13. Mining a database of single amplified genomes from Red Sea brine pool extremophiles—improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA)

    Science.gov (United States)

    Grötzinger, Stefan W.; Alam, Intikhab; Ba Alawi, Wail; Bajic, Vladimir B.; Stingl, Ulrich; Eppinger, Jörg

    2014-01-01

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile's genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  14. Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA).

    KAUST Repository

    Grötzinger, Stefan W.

    2014-04-07

    Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile\\'s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available

  15. What’s old is new again: yeast mutant screens in the era of pooled segregant analysis by genome sequencing

    Directory of Open Access Journals (Sweden)

    Chris Curtin

    2016-04-01

    Full Text Available While once de-rigueur for identification of genes involved in biological processes, screening of chemically induced mutant populations is an approach that has largely been superseded for model organisms such as Saccharomyces cerevisiae. Availability of single gene deletion/overexpression libraries and combinatorial synthetic genetic arrays provide yeast researchers more structured ways to probe genetic networks. Furthermore, in the age of inexpensive DNA sequencing, methodologies such as mapping of quantitative trait loci (QTL by pooled segregant analysis and genome-wide association enable the identification of multiple naturally occurring allelic variants that contribute to polygenic phenotypes of interest. This is, however, contingent on the capacity to screen large numbers of individuals and existence of sufficient natural phenotypic variation within the available population. The latter cannot be guaranteed and non-selectable, industrially relevant phenotypes, such as production of volatile aroma compounds, pose severe limitations on the use of modern genetic techniques due to expensive and time-consuming downstream analyses. An interesting approach to overcome these issues can be found in Den Abt et al.[1] (this issue of Microbial Cell, where a combination of repeated rounds of chemical mutagenesis and pooled segregant analysis by whole genome sequencing was applied to identify genes involved in ethyl acetate formation, demonstrating a new path for industrial yeast strain development and bringing classical mutant screens into the 21st century.

  16. Beta-Binomial Model for the Detection of Rare Mutations in Pooled Next-Generation Sequencing Experiments.

    Science.gov (United States)

    Jakaitiene, Audrone; Avino, Mariano; Guarracino, Mario Rosario

    2017-04-01

    Against diminishing costs, next-generation sequencing (NGS) still remains expensive for studies with a large number of individuals. As cost saving, sequencing genome of pools containing multiple samples might be used. Currently, there are many software available for the detection of single-nucleotide polymorphisms (SNPs). Sensitivity and specificity depend on the model used and data analyzed, indicating that all software have space for improvement. We use beta-binomial model to detect rare mutations in untagged pooled NGS experiments. We propose a multireference framework for pooled data with ability being specific up to two patients affected by neuromuscular disorders (NMD). We assessed the results comparing with The Genome Analysis Toolkit (GATK), CRISP, SNVer, and FreeBayes. Our results show that the multireference approach applying beta-binomial model is accurate in predicting rare mutations at 0.01 fraction. Finally, we explored the concordance of mutations between the model and software, checking their involvement in any NMD-related gene. We detected seven novel SNPs, for which the functional analysis produced enriched terms related to locomotion and musculature.

  17. Mining a database of single amplified genomes from Red Sea brine pool extremophiles – Improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA

    Directory of Open Access Journals (Sweden)

    Stefan Wolfgang Grötzinger

    2014-04-01

    Full Text Available Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs and poor homology of novel extremophile’s genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the INDIGO data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes may translate into false positives when searching for specific functions. The Profile & Pattern Matching (PPM strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO-terms (which represent enzyme function profiles and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern. The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2,577 E.C. numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from 6 different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter and PROSITE IDs (pattern filter. Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns are present. Scripts for annotation, as well as for the PPM algorithm, are available through the INDIGO website.

  18. Experience on Maintenance of Thai Research Reactor's 'Small-Section' Pool

    International Nuclear Information System (INIS)

    Tippayakul, Chanatip

    2013-01-01

    The reactor pool of TRR-1/M1 has been used since 1962 when the reactor building was constructed. Periodic maintenance of the reactor pool has been conducted by cleaning the pool surface and re-painting with epoxy coating. The TRR-1/M1 pool basically consists of two sections referred as 'large-section' and 'small-section'. The latest re-painting activity of the 'large-section' pool was performed in 2006 but the 'small-section' pool had not been re-painted for more than 10 years. Therefore, to assure that the 'small-section' pool can maintain leak-proof condition, the re-painting of the 'small-section' pool was performed in the early 2012. A project team was organized specially for this project and a detailed execution plan was developed. The project activities include removing foreign objects and highly activated materials from the pool section, cleaning, inspecting, re-painting the pool surface and testing for water leaks. Preparation of the repainting activities had begun 2 years in advance. During the time, the reactor core had been relocated to operate in the large-section pool away from the working area in order to minimize radioactivity. The challenge of this project was to handle 4 sets of highly radioactive bolts and nuts which support the weight of the 'void tank' irradiation facility. These bolts and nuts were made from stainless steel and had been in the flux region since the installation of the 'void tank' irradiation facility approximately 30 years ago. Dose rate measurement at the contacts of these bolts and nuts were found to be in the range of 10 . 20 R/hr. The strategy to minimize the dose rate of the workers to conduct the pool repainting in the area was to remove the bolts and nuts and replace with new ones before entering the area. Special tools were improvised in order to remove the bolts and nuts under water. During the execution of the project, close radiation monitoring was performed by the radiation protection team. The project was conducted

  19. Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies.

    Science.gov (United States)

    Chen, Jun; Källman, Thomas; Ma, Xiao-Fei; Zaina, Giusi; Morgante, Michele; Lascoux, Martin

    2016-07-07

    The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower FST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both FST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI. Copyright © 2016 Chen et al.

  20. Swimming pools as heat sinks for air conditioners: Model design and experimental validation for natural thermal behavior of the pool

    Energy Technology Data Exchange (ETDEWEB)

    Woolley, Jonathan; Harrington, Curtis; Modera, Mark [University of California Davis, Western Cooling Efficiency Center, 1450 Drew Avenue, Suite 100, Davis, CA 95618 (United States)

    2011-01-15

    Swimming pools as thermal sinks for air conditioners could save approximately 40% on peak cooling power and 30% of overall cooling energy, compared to standard residential air conditioning. Heat dissipation from pools in semi-arid climates with large diurnal temperature shifts is such that pool heating and space cooling may occur concurrently; in which case heat rejected from cooling equipment could directly displace pool heating energy, while also improving space cooling efficiency. The performance of such a system relies on the natural temperature regulation of swimming pools governed by evaporative and convective heat exchange with the air, radiative heat exchange with the sky, and conductive heat exchange with the ground. This paper describes and validates a model that uses meteorological data to accurately predict the hourly temperature of a swimming pool to within 1.1 C maximum error over the period of observation. A thorough review of literature guided our choice of the most appropriate set of equations to describe the natural mass and energy exchange between a swimming pool and the environment. Monitoring of a pool in Davis, CA, was used to confirm the resulting simulations. Comparison of predicted and observed pool temperature for all hours over a 56 day experimental period shows an R-squared relatedness of 0.967. (author)

  1. Corium quench in deep pool mixing experiments

    International Nuclear Information System (INIS)

    Spencer, B.W.; McUmber, L.; Gregorash, D.; Aeschlimann, R.; Sienicki, J.J.

    1985-01-01

    The results of two recent corium-water thermal interaction (CWTI) tests are described in which a stream of molten corium was poured into a deep pool of water in order to determine the mixing behavior, the corium-to-water heat transfer rates, and the characteristic sizes of the quenched debris. The corium composition was 60% UO 2 , 16% ZrO 2 , and 24% stainless steel by weight; its initial temperature was 3080 K, approx.160 K above the oxide phase liquidus temperature. The corium pour stream was a single-phase 2.2 cm dia liquid column which entered the water pool in film boiling at approx.4 m/s. The water subcooling was 6 and 75C in the two tests. Test results showed that with low subcooling, rapid steam generation caused the pool to boil up into a high void fraction regime. In contrast, with large subcooling no net steam generation occurred, and the pool remained relatively quiescent. Breakup of the jet appeared to occur by surface stripping. In neither test was the breakup complete during transit through the 32 cm deep water pool, and molten corium channeled to the base where it formed a melt layer. The characteristic heat transfer rates measured 3.5 MJ/s and 2.7 MJ/s during the fall stage for small and large subcooling, respectively; during the initial stage of bed quench, the surface heat fluxes measured 2.4 MW/m 2 and 3.7 MW/m 2 , respectively. A small mass of particles was formed in each test, measuring typically 0.1 to 1 mm and 1 to 5 mm dia for the large and small subcooling conditions, respectively. 9 refs., 13 figs., 1 tab

  2. Hawaii ESI: POOLS (Anchialine Pool Points)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for anchialine pools in Hawaii. Anchialine pools are small, relatively shallow coastal ponds that occur...

  3. Cash pooling

    OpenAIRE

    Lozovaya, Karina

    2009-01-01

    This work makes a mention of cash management. At next chapter describes two most known theoretical models of cash management -- Baumol Model and Miller-Orr Model. Principal part of work is about cash pooling, types of cash pooling, cash pooling at Czech Republic and influence of cash pooling over accounting and taxes.

  4. Steam blowdown experiments with the condensation pool test rig

    International Nuclear Information System (INIS)

    Purhonen, H.; Puustinen, M.; Laine, J.; Raesaenen, A.; Kyrki-Rajamaeki, R.; Vihavainen, J.

    2005-01-01

    During a possible loss-of-coolant accident (Local) a large amount of non-condensable (nitrogen) and condensable (steam) gas is blown from the upper drywell of the containment to the condensation pool through the blowdown pipes at the boiling water reactors (BWRs). The wet well pool serves as the major heat sink for condensation of steam. The blowdown causes both dynamic and structural loads to the condensation pool. There might also be a risk that the gas discharging to the pool could push its way to the emergency core cooling systems (ECCS) and undermine their performance. (author)

  5. Spent fuel pool cleanup and stabilization

    International Nuclear Information System (INIS)

    Miller, R.L.

    1987-06-01

    Each of the plutonium production reactors at Hanford had a large water-filled spent fuel pool to provide interim storage of irradiated fuel while awaiting shipment to the separation facilities. After cessation of reactor operations the fuel was removed from the pools and the water levels were drawn down to a 5- to 10-foot depth. The pools were maintained with the water to provide shielding and radiological control. What appeared to be a straightforward project to process the water, remove the sediments from the basin, and stabilize the contamination on the floors and walls became a very complex and time consuming operation. The sediment characteristics varied from pool to pool, the ion exchange system required modification, areas of hard-pack sediments were discovered on the floors, special arrangements to handle and package high dose rate items for shipment were required, and contract problems ensued with the subcontractor. The original schedule to complete the project from preliminary engineering to final stabilization of the pools was 15 months. The actual time required was about 25 months. The original cost estimate to perform the work was $2,651,000. The actual cost of the project was $5,120,000, which included $150,000 for payment of claims to the subcontractor. This paper summarizes the experiences associated with the cleanup and radiological stabilization of the 100-B, -C, -D, and -DR spent fuel pools, and discusses a number of lessons learned items

  6. Harnessing Genetic Diversity of Wild Gene Pools to Enhance Wheat Crop Production and Sustainability: Challenges and Opportunities

    Directory of Open Access Journals (Sweden)

    Carla Ceoloni

    2017-12-01

    Full Text Available Wild species are extremely rich resources of useful genes not available in the cultivated gene pool. For species providing staple food to mankind, such as the cultivated Triticum species, including hexaploid bread wheat (Triticum aestivum, 6x and tetraploid durum wheat (T. durum, 4x, widening the genetic base is a priority and primary target to cope with the many challenges that the crop has to face. These include recent climate changes, as well as actual and projected demographic growth, contrasting with reduction of arable land and water reserves. All of these environmental and societal modifications pose major constraints to the required production increase in the wheat crop. A sustainable approach to address this task implies resorting to non-conventional breeding strategies, such as “chromosome engineering”. This is based on cytogenetic methodologies, which ultimately allow for the incorporation into wheat chromosomes of targeted, and ideally small, chromosomal segments from the genome of wild relatives, containing the gene(s of interest. Chromosome engineering has been successfully applied to introduce into wheat genes/QTL for resistance to biotic and abiotic stresses, quality attributes, and even yield-related traits. In recent years, a substantial upsurge in effective alien gene exploitation for wheat improvement has come from modern technologies, including use of molecular markers, molecular cytogenetic techniques, and sequencing, which have greatly expanded our knowledge and ability to finely manipulate wheat and alien genomes. Examples will be provided of various types of stable introgressions, including pyramiding of different alien genes/QTL, into the background of bread and durum wheat genotypes, representing valuable materials for both species to respond to the needed novelty in current and future breeding programs. Challenging contexts, such as that inherent to the 4x nature of durum wheat when compared to 6x bread wheat, or

  7. Molecular genetic studies of natives on Easter Island: evidence of an early European and Amerindian contribution to the Polynesian gene pool.

    Science.gov (United States)

    Lie, B A; Dupuy, B M; Spurkland, A; Fernández-Viña, M A; Hagelberg, E; Thorsby, E

    2007-01-01

    Most archaeological and linguistic evidence suggest a Polynesian origin of the population of Easter Island (Rapanui), and this view has been supported by the identification of Polynesian mitochondrial DNA (mtDNA) polymorphisms in prehistoric skeletal remains. However, some evidence of an early South American contact also exists (the sweet potato, bottle gourd etc.), but genetic studies have so far failed to show an early Amerindian contribution to the gene pool on Easter Island. To address this issue, we analyzed mtDNA and Y chromosome markers and performed high-resolution human leukocyte antigen (HLA) genotyping of DNA harvested from previously collected sera of 48 reputedly nonadmixed native Easter Islanders. All individuals carried mtDNA types and HLA alleles previously found in Polynesia, and most men carried Y chromosome markers of Polynesian origin, providing further evidence of a Polynesian origin of the population of Easter Island. A few individuals carried HLA alleles and/or Y chromosome markers of European origin. More interestingly, some individuals carried the HLA alleles A*0212 and B*3905, which are of typical Amerindian origin. The genealogy of some of the individuals carrying these non-Polynesian HLA alleles and their haplotypic backgrounds suggest an introduction into Easter Island in the early 1800s, or earlier. Thus, there may have been an early European and Amerindian contribution to the Polynesian gene pool of Easter Island.

  8. Tax credits and purchasing pools: will this marriage work?

    Science.gov (United States)

    Trude, S; Ginsburg, P B

    2001-04-01

    Bipartisan interest is growing in Congress for using federal tax credits to help low-income families buy health insurance. Regardless of the approach taken, tax credit policies must address risk selection issues to ensure coverage for the chronically ill. Proposals that link tax credits to purchasing pools would avoid risk selection by grouping risks similar to the way large employers do. Voluntary purchasing pools have had only limited success, however. This Issue Brief discusses linking tax credits to purchasing pools. It uses information from the Center for Studying Health System Change's (HSC) site visits to 12 communities as well as other research to assess the role of purchasing pools nationwide and the key issues and implications of linking tax credits and pools.

  9. AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees.

    Science.gov (United States)

    Zhou, Chan; Mao, Fenglou; Yin, Yanbin; Huang, Jinling; Gogarten, Johann Peter; Xu, Ying

    2014-01-01

    A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.

  10. Genomic and Transcriptomic Evidence for Carbohydrate Consumption Among Microorganisms in a Cold Seep Brine Pool

    Directory of Open Access Journals (Sweden)

    Weipeng Zhang

    2016-11-01

    Full Text Available The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC, and F420H2 dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT. Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs is a dominant process performed by microorganisms from various phyla within this ecosystem.

  11. Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool

    KAUST Repository

    Zhang, Weipeng

    2016-11-15

    The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC), and F420H2 dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT). Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs) is a dominant process performed by microorganisms from various phyla within this ecosystem.

  12. Research program on the feasibility of pool type LMFBR in Japan

    International Nuclear Information System (INIS)

    Hattori, Sadao

    1982-01-01

    The Central Research Institute of Electric Power Industry has started the feasibility study to evaluate the possiblity of existence of large pool type FBR plants in Japan as the three-year project from fiscal 1981. The development of FBRs is indispensable for the effective use of nuclear fuel and the establishment of energy security. The knowledge on the characteristics of FBR core, sodium technology and others has advanced rapidly in Japan. At the stage of the practical reactors with large capacity, the pool type is naturally considered as the object of selection, but the aseismatic capability and safety of the large containment vessels for the pool type and the qualitative and quantitative acceptability of the research and development for the pool type are the problems. The difference between the loop type and the pool type is only the structural change arising from the difference in the arrangement of equipment. The pool type reactors have been operated already in the UK and France. The objective of the research and main subjects, the total plan and research organization, the fundamental condition of investigation, the research procedure for respective subjects, and the outline of model test are discribed. The change of design and safety standards in the future must be predicted and taken in consideration in the research. (Kako, I.)

  13. Bioreactor scale up and protein product quality characterization of piggyBac transposon derived CHO pools.

    Science.gov (United States)

    Rajendra, Yashas; Balasubramanian, Sowmya; Peery, Robert B; Swartling, James R; McCracken, Neil A; Norris, Dawn L; Frye, Christopher C; Barnard, Gavin C

    2017-03-01

    Chinese hamster ovary (CHO) cells remain the most popular host for the production of biopharmaceutical drugs, particularly monoclonal antibodies (mAbs), bispecific antibodies, and Fc-fusion proteins. Creating and characterizing the stable CHO clonally-derived cell lines (CDCLs) needed to manufacture these therapeutic proteins is a lengthy and laborious process. Therefore, CHO pools have increasingly been used to rapidly produce protein to support and enable preclinical drug development. We recently described the generation of CHO pools yielding mAb titers as high as 7.6 g/L in a 16 day bioprocess using piggyBac transposon-mediated gene integration. In this study, we wanted to understand why the piggyBac pool titers were significantly higher (2-10 fold) than the control CHO pools. Higher titers were the result of a combination of increased average gene copy number, significantly higher messenger RNA levels and the homogeneity (i.e. less diverse population distribution) of the piggyBac pools, relative to the control pools. In order to validate the use of piggyBac pools to support preclinical drug development, we then performed an in-depth product quality analysis of purified protein. The product quality of protein obtained from the piggyBac pools was very similar to the product quality profile of protein obtained from the control pools. Finally, we demonstrated the scalability of these pools from shake flasks to 36L bioreactors. Overall, these results suggest that gram quantities of therapeutic protein can be rapidly obtained from piggyBac CHO pools without significantly changing product quality attributes. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:534-540, 2017. © 2017 American Institute of Chemical Engineers.

  14. Large-scale gene function analysis with the PANTHER classification system.

    Science.gov (United States)

    Mi, Huaiyu; Muruganujan, Anushya; Casagrande, John T; Thomas, Paul D

    2013-08-01

    The PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system.

  15. Sample pooling for real-time PCR detection and virulence determination of the footrot pathogen Dichelobacter nodosus.

    Science.gov (United States)

    Frosth, Sara; König, Ulrika; Nyman, Ann-Kristin; Aspán, Anna

    2017-09-01

    Dichelobacter nodosus is the principal cause of ovine footrot and strain virulence is an important factor in disease severity. Therefore, detection and virulence determination of D. nodosus is important for proper diagnosis of the disease. Today this is possible by real-time PCR analysis. Analysis of large numbers of samples is costly and laborious; therefore, pooling of individual samples is common in surveillance programs. However, pooling can reduce the sensitivity of the method. The aim of this study was to develop a pooling method for real-time PCR analysis that would allow sensitive detection and simultaneous virulence determination of D. nodosus. A total of 225 sheep from 17 flocks were sampled using ESwabs within the Swedish Footrot Control Program in 2014. Samples were first analysed individually and then in pools of five by real-time PCR assays targeting the 16S rRNA and aprV2/B2 genes of D. nodosus. Each pool consisted of four negative and one positive D. nodosus samples with varying amounts of the bacterium. In the individual analysis, 61 (27.1%) samples were positive in the 16S rRNA and the aprV2/B2 PCR assays and 164 (72.9%) samples were negative. All samples positive in the aprV2/B2 PCR-assay were of aprB2 variant. The pooled analysis showed that all 41 pools were also positive for D. nodosus 16S rRNA and the aprB2 variant. The diagnostic sensitivity for pooled and individual samples was therefore similar. Our method includes concentration of the bacteria before DNA-extraction. This may account for the maintenance of diagnostic sensitivity. Diagnostic sensitivity in the real-time PCR assays of the pooled samples were comparable to the sensitivity obtained for individually analysed samples. Even sub-clinical infections were able to be detected in the pooled PCR samples which is important for control of the disease. This method may therefore be implemented in footrot control programs where it can replace analysis of individual samples.

  16. Solar swimming pool

    Energy Technology Data Exchange (ETDEWEB)

    1985-01-01

    This report examines the feasibility of using solar collectors to heat the water in a previously unheated outdoor swimming pool. The solar system is used in conjunction with a pool blanket, to conserve heat when the pool is not in use. Energy losses through evaporation can be reduced by as much as 70% by a pool blanket. A total of 130 m{sup 2} of highly durable black synthetic collectors were installed on a support structure at a 30{degree} angle from the horizontal, oriented to the south. Circulation of pool water though the collectors, which is controlled by a differential thermostat, was done with the existing pool pump. Before installation the pool temperature averaged 16{degree}C; after installation it ranged from 20{degree} to 26{degree}C. It was hard to distinguish how much pool heating was due to the solar system and how much heat was retained by the pool blanket. However, the pool season was extended by five weeks and attendance tripled. 2 figs.

  17. Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka.

    Science.gov (United States)

    Mardanov, Andrey V; Gumerov, Vadim M; Beletsky, Alexey V; Ravin, Nikolai V

    2018-01-01

    Microbial communities of four acidic thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied using amplification and pyrosequencing of 16S rRNA gene fragments. The sites differed in temperature and pH: 1805 (60 °C, pH 3.7), 1810 (90 °C, pH 4.1), 1818 (80 °C, pH 3.5), and 1807 (86 °C, pH 5.6). Archaea of the order Sulfolobales were present among the dominant groups in all four pools. Acidilobales dominated in pool 1818 but were a minor fraction at the higher temperature in pool 1810. Uncultivated Archaea of the Hot Thaumarchaeota-related clade were present in significant quantities in pools 1805 and 1807, but they were not abundant in pools 1810 and 1818, where high temperatures were combined with low pH. Nanoarchaeota were present in all pools, but were more abundant in pools 1810 and 1818. A similar abundance pattern was observed for Halobacteriales. Thermophilic Bacteria were less diverse and were mostly represented by aerobic hydrogen- and sulfur-oxidizers of the phylum Aquificae and sulfur-oxidising Proteobacteria of the genus Acidithiobacillus. Thus we showed that extremely acidic hot pools contain diverse microbial communities comprising different metabolic groups of prokaryotes, including putative lithoautotrophs using energy sources of volcanic origin, and various facultative and obligate heterotrophs.

  18. System seismic analysis of an innovative primary system for a large pool type LMFBR plant

    International Nuclear Information System (INIS)

    Pan, Y.C.; Wu, T.S.; Cha, B.K.; Burelbach, J.; Seidensticker, R.

    1984-01-01

    The system seismic analysis of an innovative primary system for a large pool type liquid metal fast breeder reactor (LMFBR) plant is presented. In this primary system, the reactor core is supported in a way which differs significantly from that used in previous designs. The analytical model developed for this study is a three-dimensional finite element model including one-half of the primary system cut along the plane of symmetry. The model includes the deck and deck mounted components,the reactor vessel, the core support structure, the core barrel, the radial neutron shield, the redan, and the conical support skirt. The sodium contained in the primary system is treated as a lumped mass appropriately distributed among various components. The significant seismic behavior as well as the advantages of this primary system design are discussed in detail

  19. Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean.

    Science.gov (United States)

    Galeano, Carlos H; Fernandez, Andrea C; Franco-Herrera, Natalia; Cichy, Karen A; McClean, Phillip E; Vanderleyden, Jos; Blair, Matthew W

    2011-01-01

    Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364 × BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364 × G19833 (DG) and BAT93 × JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.

  20. Livestock Grazing as a Driver of Vernal Pool Ecohydrology

    Science.gov (United States)

    Michaels, J.; McCarten, N. F.

    2017-12-01

    Vernal pools are seasonal wetlands that host rare plant communities of high conservation priority. Plant community composition is largely driven by pool hydroperiod. A previous study found that vernal pools grazed by livestock had longer hydroperiods compared with pools excluded from grazing for 10 years, and suggests that livestock grazing can be used to protect plant diversity. It is important to assess whether observed differences are due to the grazing or due to water balance variables including upland discharge into or out of the pools since no a priori measurements were made of the hydrology prior to grazing. To address this question, in 2016 we compared 15 pools that have been grazed continuously and 15 pools that have been fenced off for over 40 years at a site in Sacramento County. We paired pools based on abiotic characteristics (size, shape, slope, soil type) to minimize natural variation. We sampled vegetation and water depth using Solinst level loggers. We found that plant diversity and average hydroperiod was significantly higher in the grazed pools. We are currently measuring groundwater connectivity and upland inputs in order to compare the relative strength of livestock grazing as a driver of hydroperiod to these other drivers.

  1. Distributed Technologies in a Data Pool

    Science.gov (United States)

    Keiser, K.; Conover, H.; Graves, S.; He, Y.; Regner, K.; Smith, M.

    2004-12-01

    A Data Pool is an on-line repository providing interactive and programmatic access to data products through a variety of services. The University of Alabama in Huntsville has developed and deployed such a Data Pool in conjunction with the DISCOVER project, a collaboration with NASA and Remote Sensing Systems. DISCOVER provides long-term ocean and climate data from a variety of passive microwave satellite instruments, including such products as sea-surface temperature and wind, air temperature, atmospheric water vapor, cloud water and rain rate. The Data Pool provides multiple methods to access and visualize these products, including conventional HTTP and FTP access, as well as data services that provide for enhanced usability and interoperability, such as GridFTP, OPeNDAP, OpenGIS-compliant web mapping and coverage services, and custom subsetting and packaging services. This paper will focus on the distributed service technologies used in the Data Pool, which spans heterogeneous machines at multiple locations. For example, in order to provide seamless access to data at multiple sites, the Data Pool provides catalog services for all data products at the various data server locations. Under development is an automated metadata generation tool that crawls the online data repositories regularly to dynamically update the Data Pool catalog with information about newly generated data files. For efficient handling of data orders across distributed repositories, the Data Pool also implements distributed data processing services on the file servers where the data resides. Ontologies are planned to support automated service chaining for custom user requests. The UAH Data Pool is based on a configurable technology framework that integrates distributed data services with a web interface and a set of centralized database services for catalogs and order tracking. While this instantiation of the Data Pool was implemented to meet the needs of the DISCOVER project, the framework was

  2. A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool

    Science.gov (United States)

    Bloom-Ackermann, Zohar; Navon, Sivan; Gingold, Hila; Towers, Ruth; Pilpel, Yitzhak; Dahan, Orna

    2014-01-01

    Deciphering the architecture of the tRNA pool is a prime challenge in translation research, as tRNAs govern the efficiency and accuracy of the process. Towards this challenge, we created a systematic tRNA deletion library in Saccharomyces cerevisiae, aimed at dissecting the specific contribution of each tRNA gene to the tRNA pool and to the cell's fitness. By harnessing this resource, we observed that the majority of tRNA deletions show no appreciable phenotype in rich medium, yet under more challenging conditions, additional phenotypes were observed. Robustness to tRNA gene deletion was often facilitated through extensive backup compensation within and between tRNA families. Interestingly, we found that within tRNA families, genes carrying identical anti-codons can contribute differently to the cellular fitness, suggesting the importance of the genomic surrounding to tRNA expression. Characterization of the transcriptome response to deletions of tRNA genes exposed two disparate patterns: in single-copy families, deletions elicited a stress response; in deletions of genes from multi-copy families, expression of the translation machinery increased. Our results uncover the complex architecture of the tRNA pool and pave the way towards complete understanding of their role in cell physiology. PMID:24453985

  3. Discs Large Homolog 5 (DLG5 Gene Polymorphism and Crohn’s Disease: A Meta-Analysis of the Published Studies

    Directory of Open Access Journals (Sweden)

    Arezoo Shafieyoun

    2016-05-01

    Full Text Available The real pathophysiology of Crohn’s disease is unknown. The higher prevalence of Crohn’s disease in Caucasian and Jewish ethnicities, as well as its familial aggregation and higher concordance among monozygotic twins, suggest some roles for genes in its development, clinical progression, and outcome. Recent original studies have indicated DLG5113G/A gene polymorphism as a risk factor for Crohn’s disease. Meanwhile, the results of these studies are not consistent. We performed the current meta-analysis to understand whether there is any association between DLG5 gene polymorphism and the risk of Crohn’s disease. PubMed was searched to find the case-control studies on DLG5 gene polymorphisms and Crohn’s disease. This search compiled 65 articles and based on our criteria. 11 articles were included in this meta-analysis. The association between the DLG5 113G/A polymorphism and the risk of disease was assessed using odds ratio (OR and 95% confidence interval (95% CI. Heterogeneity was evaluated based on I2 values.  Random and fixed-effect models were used when I2>50% and I2≤50%, respectively. Eleven studies with a total of 4648 cases and 5677 controls were pooled. Based on our meta-analysis, DLG5113G/A gene polymorphism both at genotypic and allelic levels were not associated with the risk of Crohn’s disease. Pooled data indicated no significant association between DLG5113G/A gene polymorphism and the development of Crohn’s disease. In order to achieve a superior conclusion, multicenter studies on larger number of patients are recommended.

  4. Microdiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool

    Science.gov (United States)

    Schmidt, Johanna; Jezberová, Jitka; Koll, Ulrike; Hahn, Martin W.

    2016-01-01

    ABSTRACT Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to Polynucleobacter species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of Polynucleobacter bacteria. IMPORTANCE Assessing the ecological relevance of bacterial diversity is a key challenge for current microbial ecology. The polyphasic approach which was applied in this study, including targeted isolation of strains, genome analysis, and ecophysiological tests, is crucial for the linkage of genetic and ecological knowledge. Particularly great importance is attached to the high number of closely related strains which were investigated, represented by genome-wide average nucleotide identities (ANI) larger than 97%. The extent of functional diversification found on this narrow phylogenetic scale is compelling. Moreover, the transfer of

  5. Determining the optimal number of individual samples to pool for quantification of average herd levels of antimicrobial resistance genes in Danish pig herds using high-throughput qPCR

    DEFF Research Database (Denmark)

    Clasen, Julie; Mellerup, Anders; Olsen, John Elmerdahl

    2016-01-01

    The primary objective of this study was to determine the minimum number of individual fecal samples to pool together in order to obtain a representative sample for herd level quantification of antimicrobial resistance (AMR) genes in a Danish pig herd, using a novel high-throughput qPCR assay...

  6. Genic regions of a large salamander genome contain long introns and novel genes

    Directory of Open Access Journals (Sweden)

    Bryant Susan V

    2009-01-01

    Full Text Available Abstract Background The basis of genome size variation remains an outstanding question because DNA sequence data are lacking for organisms with large genomes. Sixteen BAC clones from the Mexican axolotl (Ambystoma mexicanum: c-value = 32 × 109 bp were isolated and sequenced to characterize the structure of genic regions. Results Annotation of genes within BACs showed that axolotl introns are on average 10× longer than orthologous vertebrate introns and they are predicted to contain more functional elements, including miRNAs and snoRNAs. Loci were discovered within BACs for two novel EST transcripts that are differentially expressed during spinal cord regeneration and skin metamorphosis. Unexpectedly, a third novel gene was also discovered while manually annotating BACs. Analysis of human-axolotl protein-coding sequences suggests there are 2% more lineage specific genes in the axolotl genome than the human genome, but the great majority (86% of genes between axolotl and human are predicted to be 1:1 orthologs. Considering that axolotl genes are on average 5× larger than human genes, the genic component of the salamander genome is estimated to be incredibly large, approximately 2.8 gigabases! Conclusion This study shows that a large salamander genome has a correspondingly large genic component, primarily because genes have incredibly long introns. These intronic sequences may harbor novel coding and non-coding sequences that regulate biological processes that are unique to salamanders.

  7. Analysis of sodium pool fire in SFEF for assessing the limiting pool fire

    International Nuclear Information System (INIS)

    Mangarjuna Rao, P.; Ramesh, S.S.; Nashine, B.K.; Kasinathan, N.; Chellapandi, P.

    2011-01-01

    Accidental sodium leaks and resultant sodium fires in Liquid Metal Fast Breeder Reactor (LMFBR) systems can create a threat to the safe operation of the plant. To avoid this defence-in depth approach is implemented from the design stage of reactor itself. Rapid detection of sodium leak and fast dumping of the sodium into the storage tank of a defective circuit, leak collection trays, adequate lining of load bearing structural concrete and extinguishment of the sodium fire are the important defensive measures in the design, construction and operation of a LMFBR for protection against sodium leaks and their resultant fires. Evaluation of sodium leak events and their consequences by conducting large scale engineering experiments is very essential for effective implementation of the above protection measures for sodium fire safety. For this purpose a Sodium Fire Experimental Facility (SFEF) is constructed at SED, IGCAR. SFEF is having an experimental hall of size 9 m x 6 m x 10 m with 540 m 3 volume and its design pressure is 50 kPa. It is a concrete structure and provided with SS 304 liner, which is fixed to the inside surfaces of walls, ceiling and floor. A leak tight door of size (1.8 m x 2.0 m) is provided to the experimental hall and the facility is provided with a sodium equipment hall and a control room. Experimental evaluation of sodium pool fire consequences is an important activity in the LMFBR sodium fire safety related studies. An experimental program has been planned for different types of sodium fire studies in SFEF. A prior to that numerical analysis have been carried out for enclosed sodium pool fires using SOFIRE-II sodium pool fire code for SFEF experimental hall configuration to evaluate the limiting pool fire. This paper brings out results of the analysis carried out for this purpose. Limiting pool fire of SFEF depends on the exposed surface area of the pool, amount of sodium in the pool, oxygen concentration and initial sodium temperature. Limiting

  8. Construction of the BAC Library of Small Abalone (Haliotis diversicolor) for Gene Screening and Genome Characterization.

    Science.gov (United States)

    Jiang, Likun; You, Weiwei; Zhang, Xiaojun; Xu, Jian; Jiang, Yanliang; Wang, Kai; Zhao, Zixia; Chen, Baohua; Zhao, Yunfeng; Mahboob, Shahid; Al-Ghanim, Khalid A; Ke, Caihuan; Xu, Peng

    2016-02-01

    The small abalone (Haliotis diversicolor) is one of the most important aquaculture species in East Asia. To facilitate gene cloning and characterization, genome analysis, and genetic breeding of it, we constructed a large-insert bacterial artificial chromosome (BAC) library, which is an important genetic tool for advanced genetics and genomics research. The small abalone BAC library includes 92,610 clones with an average insert size of 120 Kb, equivalent to approximately 7.6× of the small abalone genome. We set up three-dimensional pools and super pools of 18,432 BAC clones for target gene screening using PCR method. To assess the approach, we screened 12 target genes in these 18,432 BAC clones and identified 16 positive BAC clones. Eight positive BAC clones were then sequenced and assembled with the next generation sequencing platform. The assembled contigs representing these 8 BAC clones spanned 928 Kb of the small abalone genome, providing the first batch of genome sequences for genome evaluation and characterization. The average GC content of small abalone genome was estimated as 40.33%. A total of 21 protein-coding genes, including 7 target genes, were annotated into the 8 BACs, which proved the feasibility of PCR screening approach with three-dimensional pools in small abalone BAC library. One hundred fifty microsatellite loci were also identified from the sequences for marker development in the future. The BAC library and clone pools provided valuable resources and tools for genetic breeding and conservation of H. diversicolor.

  9. A swimming pool array for ultra high energy showers

    Science.gov (United States)

    Yodh, Gaurang B.; Shoup, Anthony; Barwick, Steve; Goodman, Jordan A.

    1992-11-01

    A very preliminary design concept for an array using water Cherenkov counters, built out of commercially available backyard swimming pools, to sample the electromagnetic and muonic components of ultra high energy showers at large lateral distances is presented. The expected performance of the pools is estimated using the observed lateral distributions by scintillator and water Cherenkov arrays at energies above 1019 eV and simulations.

  10. Gene prediction in metagenomic fragments: A large scale machine learning approach

    Directory of Open Access Journals (Sweden)

    Morgenstern Burkhard

    2008-04-01

    Full Text Available Abstract Background Metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. The amount of metagenomic sequence data is growing fast while computational methods for metagenome analysis are still in their infancy. In contrast to genomic sequences of single species, which can usually be assembled and analyzed by many available methods, a large proportion of metagenome data remains as unassembled anonymous sequencing reads. One of the aims of all metagenomic sequencing projects is the identification of novel genes. Short length, for example, Sanger sequencing yields on average 700 bp fragments, and unknown phylogenetic origin of most fragments require approaches to gene prediction that are different from the currently available methods for genomes of single species. In particular, the large size of metagenomic samples requires fast and accurate methods with small numbers of false positive predictions. Results We introduce a novel gene prediction algorithm for metagenomic fragments based on a two-stage machine learning approach. In the first stage, we use linear discriminants for monocodon usage, dicodon usage and translation initiation sites to extract features from DNA sequences. In the second stage, an artificial neural network combines these features with open reading frame length and fragment GC-content to compute the probability that this open reading frame encodes a protein. This probability is used for the classification and scoring of gene candidates. With large scale training, our method provides fast single fragment predictions with good sensitivity and specificity on artificially fragmented genomic DNA. Additionally, this method is able to predict translation initiation sites accurately and distinguishes complete from incomplete genes with high reliability. Conclusion Large scale machine learning methods are well-suited for gene

  11. Evaluation of Decontamination Factor of Aerosol in Pool Scrubber according to Bubble Shape and Size

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Hyun Joung; Ha, Kwang Soon; Jang, Dong Soon [KAERI, Daejeon (Korea, Republic of)

    2016-05-15

    The scrubbing pool could play an important role in the wet type FCVS because a large amount of aerosol is captured in the water pool. The pool scrubbing phenomena have been modelled and embedded in several computer codes, such as SPARC (Suppression Pool Aerosol Removal Code), BUSCA (BUbble Scrubbing Algorithm) and SUPRA (Suppression Pool Retention Analysis). These codes aim at simulating the pool scrubbing process and estimating the decontamination factors (DFs) of the radioactive aerosol and iodine gas in the water pool, which is defined as the ratio of initial mass of the specific radioactive material to final massy after passing through the water pool. The pool scrubbing models were reviewed and an aerosol scrubbing code has been prepared to calculate decontamination factor through the pool. The developed code has been verified using the experimental results and parametric studies the decontamination factor according to bubble shape and size. To evaluate the decontamination factor more accurate whole pool scrubber phenomena, the code was improved to consider the variety shape and size of bubbles. The decontamination factor were largely evaluated in ellipsoid bubble rather than in sphere bubble. The pool scrubbing models will be enhanced to apply more various model such as aerosol condensation of hygroscopic. And, it is need to experiment to measure to bubble shape and size distribution in pool to improve bubble model.

  12. Effective Momentum and heat flux models for simulation of stratification and mixing in a large pool of water

    Energy Technology Data Exchange (ETDEWEB)

    Hua Li; Villanueva, W.; Kudinov, P. [Royal Institute of Technology (KTH). Div. of Nuclear Power Safety, Stockholm (Sweden)

    2012-06-15

    Performance of a boiling water reactor (BWR) containment is mostly determined by reliable operation of pressure suppression pool which serves as a heat sink to cool and condense steam released from the core vessel. Thermal stratification in the pool can significantly impede the pool's pressure suppression capacity. A source of momentum is required in order to break stratification and mix the pool. It is important to have reliable prediction of transient development of stratification and mixing in the pool in different regimes of steam injection. Previously, we have proposed to model the effect of steam injection on the mixing and stratification with the Effective Heat Source (EHS) and the Effective Momentum Source (EMS) models. The EHS model is used to provide thermal effect of steam injection on the pool, preserving heat and mass balance. The EMS model is used to simulate momentum induced by steam injection in different flow regimes. The EMS model is based on the combination of (1) synthetic jet theory, which predicts effective momentum if amplitude and frequency of flow oscillations in the pipe are given, and (2) model proposed by Aya and Nariai for prediction of the amplitude and frequency of oscillations at a given pool temperature and steam mass flux. The complete EHS/EMS models only require the steam mass flux, initial pool bulk temperature, and design-specific parameters, to predict thermal stratification and mixing in a pressure suppression pool. In this work we use EHS/EMS models implemented in containment thermal hydraulic code GOTHIC. The POOLEX/PPOOLEX experiments (Lappeenranta University of Technology, Finland) are utilized, to (a) quantify errors due to GOTHIC's physical models and numerical schemes, (b) propose necessary improvements in GOTHIC sub-grid scale modeling, and (c) validate our proposed models. Specifically the data from POOLEX STB-21 and PPOOLEX STR-03 and STR-04 tests are used for validation of the EHS and EMS models in this

  13. Effective Momentum and heat flux models for simulation of stratification and mixing in a large pool of water

    International Nuclear Information System (INIS)

    Hua Li; Villanueva, W.; Kudinov, P.

    2012-06-01

    Performance of a boiling water reactor (BWR) containment is mostly determined by reliable operation of pressure suppression pool which serves as a heat sink to cool and condense steam released from the core vessel. Thermal stratification in the pool can significantly impede the pool's pressure suppression capacity. A source of momentum is required in order to break stratification and mix the pool. It is important to have reliable prediction of transient development of stratification and mixing in the pool in different regimes of steam injection. Previously, we have proposed to model the effect of steam injection on the mixing and stratification with the Effective Heat Source (EHS) and the Effective Momentum Source (EMS) models. The EHS model is used to provide thermal effect of steam injection on the pool, preserving heat and mass balance. The EMS model is used to simulate momentum induced by steam injection in different flow regimes. The EMS model is based on the combination of (1) synthetic jet theory, which predicts effective momentum if amplitude and frequency of flow oscillations in the pipe are given, and (2) model proposed by Aya and Nariai for prediction of the amplitude and frequency of oscillations at a given pool temperature and steam mass flux. The complete EHS/EMS models only require the steam mass flux, initial pool bulk temperature, and design-specific parameters, to predict thermal stratification and mixing in a pressure suppression pool. In this work we use EHS/EMS models implemented in containment thermal hydraulic code GOTHIC. The POOLEX/PPOOLEX experiments (Lappeenranta University of Technology, Finland) are utilized, to (a) quantify errors due to GOTHIC's physical models and numerical schemes, (b) propose necessary improvements in GOTHIC sub-grid scale modeling, and (c) validate our proposed models. Specifically the data from POOLEX STB-21 and PPOOLEX STR-03 and STR-04 tests are used for validation of the EHS and EMS models in this work. We

  14. Sampling and Pooling Methods for Capturing Herd Level Antibiotic Resistance in Swine Feces using qPCR and CFU Approaches

    DEFF Research Database (Denmark)

    Schmidt, Gunilla Veslemøy; Mellerup, Anders; Christiansen, Lasse Engbo

    2015-01-01

    The aim of this article was to define the sampling level and method combination that captures antibiotic resistance at pig herd level utilizing qPCR antibiotic resistance gene quantification and culture-based quantification of antibiotic resistant coliform indicator bacteria. Fourteen qPCR assays...... for commonly detected antibiotic resistance genes were developed, and used to quantify antibiotic resistance genes in total DNA from swine fecal samples that were obtained using different sampling and pooling methods. In parallel, the number of antibiotic resistant coliform indicator bacteria was determined...... when comparing individual sampling and pooling methods. qPCR on pooled samples was found to be a good representative for the general resistance level in a pig herd compared to the coliform CFU counts. It had significantly reduced relative standard deviations compared to coliform CFU counts in the same...

  15. Controls on the size and occurrence of pools in coarse-grained forest rivers

    Science.gov (United States)

    John M. Buffington; Thomas E. Lisle; Richard D. Woodsmith; Sue Hilton

    2002-01-01

    Controls on pool formation are examined in gravel- and cobble-bed rivers in forest mountain drainage basins of northern California, southern Oregon, and southeastern Alaska. We demonstrate that the majority of pools at our study sites are formed by flow obstructions and that pool geometry and frequency largely depend on obstruction characteristics (size, type, and...

  16. Gene expression in colorectal cancer

    DEFF Research Database (Denmark)

    Birkenkamp-Demtroder, Karin; Christensen, Lise Lotte; Olesen, Sanne Harder

    2002-01-01

    Understanding molecular alterations in colorectal cancer (CRC) is needed to define new biomarkers and treatment targets. We used oligonucleotide microarrays to monitor gene expression of about 6,800 known genes and 35,000 expressed sequence tags (ESTs) on five pools (four to six samples in each...... pool) of total RNA from left-sided sporadic colorectal carcinomas. We compared normal tissue to carcinoma tissue from Dukes' stages A-D (noninvasive to distant metastasis) and identified 908 known genes and 4,155 ESTs that changed remarkably from normal to tumor tissue. Based on intensive filtering 226...

  17. Welding pool measurement using thermal array sensor

    Science.gov (United States)

    Cho, Chia-Hung; Hsieh, Yi-Chen; Chen, Hsin-Yi

    2015-08-01

    Selective laser melting (SLM) is an additive manufacturing (AM) technology that uses a high-power laser beam to melt metal powder in chamber of inert gas. The process starts by slicing the 3D CAD data as a digital information source into layers to create a 2D image of each layer. Melting pool was formed by using laser irradiation on metal powders which then solidified to consolidated structure. In a selective laser melting process, the variation of melt pool affects the yield of a printed three-dimensional product. For three dimensional parts, the border conditions of the conductive heat transport have a very large influence on the melt pool dimensions. Therefore, melting pool is an important behavior that affects the final quality of the 3D object. To meet the temperature and geometry of the melting pool for monitoring in additive manufacturing technology. In this paper, we proposed the temperature sensing system which is composed of infrared photodiode, high speed camera, band-pass filter, dichroic beam splitter and focus lens. Since the infrared photodiode and high speed camera look at the process through the 2D galvanometer scanner and f-theta lens, the temperature sensing system can be used to observe the melting pool at any time, regardless of the movement of the laser spot. In order to obtain a wide temperature detecting range, 500 °C to 2500 °C, the radiation from the melting pool to be measured is filtered into a plurality of radiation portions, and since the intensity ratio distribution of the radiation portions is calculated by using black-body radiation. The experimental result shows that the system is suitable for melting pool to measure temperature.

  18. Mathematical modelling and simulation of the thermal performance of a solar heated indoor swimming pool

    OpenAIRE

    Mančić Marko V.; Živković Dragoljub S.; Milosavljević Peđa M.; Todorović Milena N.

    2014-01-01

    Buildings with indoor swimming pools have a large energy footprint. The source of major energy loss is the swimming pool hall where air humidity is increased by evaporation from the pool water surface. This increases energy consumption for heating and ventilation of the pool hall, fresh water supply loss and heat demand for pool water heating. In this paper, a mathematical model of the swimming pool was made to assess energy demands of an indoor swimming po...

  19. Experimental investigation of particulate debris spreading in a pool

    Energy Technology Data Exchange (ETDEWEB)

    Konovalenko, A., E-mail: kono@kth.se [Division of Nuclear Power Safety, Royal Institute of Technology (KTH) , Roslagstullsbacken 21, Stockholm 106 91 (Sweden); Basso, S., E-mail: simoneb@kth.se [Division of Nuclear Power Safety, Royal Institute of Technology (KTH) , Roslagstullsbacken 21, Stockholm 106 91 (Sweden); Kudinov, P., E-mail: pkudinov@kth.se [Division of Nuclear Power Safety, Royal Institute of Technology (KTH) , Roslagstullsbacken 21, Stockholm 106 91 (Sweden); Yakush, S.E., E-mail: yakush@ipmnet.ru [Institute for Problems in Mechanics of the Russian Academy of Sciences, Ave. Vernadskogo 101 Bldg 1, Moscow 119526 (Russian Federation)

    2016-02-15

    Termination of severe accident progression by core debris cooling in a deep pool of water under reactor vessel is considered in several designs of light water reactors. However, success of this accident mitigation strategy is contingent upon the effectiveness of heat removal by natural circulation from the debris bed. It is assumed that a porous bed will be formed in the pool in the process of core melt fragmentation and quenching. Debris bed coolability depends on its properties and system conditions. The properties of the bed, including its geometry are the outcomes of the debris bed formation process. Spreading of the debris particles in the pool by two-phase turbulent flows induced by the heat generated in the bed can affect the shape of the bed and thus influence its coolability. The goal of this work is to provide experimental data on spreading of solid particles in the pool by large-scale two-phase flow. The aim is to provide data necessary for understanding of separate effects and for development and validation of models and codes. Validated codes can be then used for prediction of debris bed formation under prototypic severe accident conditions. In PDS-P (Particulate Debris Spreading in the Pool) experiments, air injection at the bottom of the test section is employed as a means to create large-scale flow in the pool in isothermal conditions. The test section is a rectangular tank with a 2D slice geometry, it has fixed width (72 mm), adjustable length (up to 1.5 m) and allows water filling to the depth of up to 1 m. Variable pool length and depth allows studying two-phase circulating flows of different characteristic sizes and patterns. The average void fraction in the pool is determined by video recording and subsequent image processing. Particles are supplied from the top of the facility above the water surface. Results of several series of PDS-P experiments are reported in this paper. The influence of the gas flow rate, pool dimensions, particle density

  20. Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio

    Directory of Open Access Journals (Sweden)

    Gillings Michael R

    2006-01-01

    Full Text Available Abstract Background Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombination site known as a 59-base element (59-be. Multiple insertion events can lead to the assembly of large integron-associated cassette arrays. The most striking examples are found in Vibrio, where such cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron gene cassette arrays from bacterial strains. Results The complete Vibrio sp. DAT722 integron cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phylogenetic analyses for all of its components (integrase, 59-be sites, gene cassette encoded genes. It differs extensively in terms of genomic context as well as gene cassette content and organization. The phylogenetic tree of the 59-be sites collectively found in the Vibrio gene cassette pool suggests frequent transfer of cassettes within and between Vibrio species, with slower transfer rates between more phylogenetically distant relatives. We also identify multiple cases where non-integron chromosomal genes seem to have been assembled into gene cassettes and others where cassettes have been inserted into chromosomal locations outside integrons. Conclusion Our systematic approach greatly facilitates the isolation and annotation of large integrons gene cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this genetic element in promoting lateral gene transfer and suggests a high rate of gene

  1. Estimated environmental radionuclide transfer and deposition into outdoor swimming pools

    International Nuclear Information System (INIS)

    Tagami, Kazumi; Nagata, Izumi; Sueki, Keisuke

    2014-01-01

    In 2011, a large radioactive discharge occurred at the Fukushima Daiichi nuclear power plant. This plant is located within a climatically temperate region where outdoor swimming pools are popular. Although it is relatively easy to decontaminate pools by refilling them with fresh water, it is difficult to maintain safe conditions given highly contaminated diurnal dust falls from the surrounding contaminated ground. Our objectives in this paper were to conduct daily radioactivity measurements, to determine the quantity of radioactive contaminants from the surrounding environment that invade outdoor pools, and to investigate the efficacy of traditional pool cleaners in removing radioactive contaminants. The depositions in the paper filterable particulates ranged from 0 to 62,5 Bq/m 2 /day, with the highest levels found in the southern Tohoku District containing Fukushima Prefecture and in the Kanto District containing Tokyo Metro. They were approximately correlated with the ground contamination. Traditional pool cleaners eliminated 99% of contaminants at the bottom of the pool, reducing the concentration to 41 Bq/m 2 after cleaning. Authors recommended the deposition or the blown radionuclides into outdoor swimming pools must be considered into pool regulations when the environments exactly polluted with radionuclides. - Highlights: • Deposition into outdoor swimming pool in a habitable areas estimated 72 Bq/m 2 /day. • More than 500 Bq/m 2 /day deposition will exceed our national guideline (10 Bq/l) of swimming pool. • Vacuum pool cleaner eliminates 99% radionuclides deposition

  2. Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

    Directory of Open Access Journals (Sweden)

    Blackmon Barbara P

    2011-07-01

    Full Text Available Abstract Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

  3. Domestication of the neotropical tree Chrysophyllum cainito from a geographically limited yet genetically diverse gene pool in Panama.

    Science.gov (United States)

    Petersen, Jennifer J; Parker, Ingrid M; Potter, Daniel

    2014-03-01

    Species in the early stages of domestication, in which wild and cultivated forms co-occur, provide important opportunities to develop and test hypotheses about the origins of crop species. Chrysophyllum cainito (Sapotaceae), the star apple or caimito, is a semidomesticated tree widely cultivated for its edible fruits; it is known to be native to the neotropics, but its precise geographic origins have not been firmly established. Here, we report results of microsatellite marker analyses supporting the hypothesis that the center of domestication for caimito was the Isthmus of Panama, a region in which few crop species are believed to have originated, despite its importance as a crossroads for the dispersal of domesticated plants between North and South America. Our data suggest that caimito was domesticated in a geographically restricted area while incorporating a diverse gene pool. These results refute the generally accepted Antillean origin of caimito, as well as alternative hypotheses that the species was domesticated independently in the two areas or over a broad geographic range including both. Human-mediated dispersal from Panama to the north and east was accompanied by strong reductions in both genotypic and phenotypic diversity. Within Panama, cultivated and wild trees show little neutral genetic divergence, in contrast to striking phenotypic differentiation in fruit and seed traits. In addition to providing a rare example of data that support the hypothesis of a narrow geographic origin on the Isthmus of Panama for a now widespread cultivated plant species, this study is one of the first investigations of the origins of an edible species of the large pantropical family Sapotaceae.

  4. Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.

    Science.gov (United States)

    Ramos, Enrique; Levinson, Benjamin T; Chasnoff, Sara; Hughes, Andrew; Young, Andrew L; Thornton, Katherine; Li, Allie; Vallania, Francesco L M; Province, Michael; Druley, Todd E

    2012-12-06

    Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regions and comparing against unaffected cohorts. However, despite persistent declines in sequencing costs, population-based rare variant detection across large genomic target regions remains cost prohibitive for most investigators. In addition, DNA samples are often precious and hybridization methods typically require large amounts of input DNA. Pooled sample DNA sequencing is a cost and time-efficient strategy for surveying populations of individuals for rare variants. We set out to 1) create a scalable, multiplexing method for custom capture with or without individual DNA indexing that was amenable to low amounts of input DNA and 2) expand the functionality of the SPLINTER algorithm for calling substitutions, insertions and deletions across either candidate genes or the entire exome by integrating the variant calling algorithm with the dynamic programming aligner, Novoalign. We report methodology for pooled hybridization capture with pre-enrichment, indexed multiplexing of up to 48 individuals or non-indexed pooled sequencing of up to 92 individuals with as little as 70 ng of DNA per person. Modified solid phase reversible immobilization bead purification strategies enable no sample transfers from sonication in 96-well plates through adapter ligation, resulting in 50% less library preparation reagent consumption. Custom Y-shaped adapters containing novel 7 base pair index sequences with a Hamming distance of ≥2 were directly ligated onto fragmented source DNA eliminating the need for PCR to incorporate indexes, and was followed by a custom blocking strategy using a single oligonucleotide regardless of index sequence. These results were obtained aligning raw

  5. Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing

    Directory of Open Access Journals (Sweden)

    Ramos Enrique

    2012-12-01

    Full Text Available Abstract Background Rare genetic variation in the human population is a major source of pathophysiological variability and has been implicated in a host of complex phenotypes and diseases. Finding disease-related genes harboring disparate functional rare variants requires sequencing of many individuals across many genomic regions and comparing against unaffected cohorts. However, despite persistent declines in sequencing costs, population-based rare variant detection across large genomic target regions remains cost prohibitive for most investigators. In addition, DNA samples are often precious and hybridization methods typically require large amounts of input DNA. Pooled sample DNA sequencing is a cost and time-efficient strategy for surveying populations of individuals for rare variants. We set out to 1 create a scalable, multiplexing method for custom capture with or without individual DNA indexing that was amenable to low amounts of input DNA and 2 expand the functionality of the SPLINTER algorithm for calling substitutions, insertions and deletions across either candidate genes or the entire exome by integrating the variant calling algorithm with the dynamic programming aligner, Novoalign. Results We report methodology for pooled hybridization capture with pre-enrichment, indexed multiplexing of up to 48 individuals or non-indexed pooled sequencing of up to 92 individuals with as little as 70 ng of DNA per person. Modified solid phase reversible immobilization bead purification strategies enable no sample transfers from sonication in 96-well plates through adapter ligation, resulting in 50% less library preparation reagent consumption. Custom Y-shaped adapters containing novel 7 base pair index sequences with a Hamming distance of ≥2 were directly ligated onto fragmented source DNA eliminating the need for PCR to incorporate indexes, and was followed by a custom blocking strategy using a single oligonucleotide regardless of index sequence

  6. More to NAD+ than meets the eye: A regulator of metabolic pools and gene expression in Arabidopsis.

    Science.gov (United States)

    Gakière, Bertrand; Fernie, Alisdair R; Pétriacq, Pierre

    2018-01-05

    Since its discovery more than a century ago, nicotinamide adenine dinucleotide (NAD + ) is recognised as a fascinating cornerstone of cellular metabolism. This ubiquitous energy cofactor plays vital roles in metabolic pathways and regulatory processes, a fact emphasised by the essentiality of a balanced NAD + metabolism for normal plant growth and development. Research on the role of NAD in plants has been predominantly carried out in the model plant Arabidopsis thaliana (Arabidopsis) with emphasis on the redox properties and cellular signalling functions of the metabolite. This review examines the current state of knowledge concerning how NAD can regulate both metabolic pools and gene expression in Arabidopsis. Particular focus is placed on recent studies highlighting the complexity of metabolic regulations involving NAD, more particularly in the mitochondrial compartment, and of signalling roles with respect to interactions with environmental fluctuations most specifically those involving plant immunity. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Diets high in resistant starch and arabinoxylan modulate digestion processes and SCFA pool size in the large intestine and faecal microbial composition in pigs.

    Science.gov (United States)

    Nielsen, Tina S; Lærke, Helle N; Theil, Peter K; Sørensen, Jens F; Saarinen, Markku; Forssten, Sofia; Knudsen, Knud E Bach

    2014-12-14

    The effects of a high level of dietary fibre (DF) either as arabinoxylan (AX) or resistant starch (RS) on digestion processes, SCFA concentration and pool size in various intestinal segments and on the microbial composition in the faeces were studied in a model experiment with pigs. A total of thirty female pigs (body weight 63.1 (sem 4.4) kg) were fed a low-DF, high-fat Western-style control diet (WSD), an AX-rich diet (AXD) or a RS-rich diet (RSD) for 3 weeks. Diet significantly affected the digestibility of DM, protein, fat, NSP and NSP components, and the arabinose:xylose ratio, as well as the disappearance of NSP and AX in the large intestine. RS was mainly digested in the caecum. AX was digested at a slower rate than RS. The digesta from AXD-fed pigs passed from the ileum to the distal colon more than twice as fast as those from WSD-fed pigs, with those from RSD-fed pigs being intermediate (PEubacterium rectale, Bifidobacterium spp. and Lactobacillus spp. in the faeces sampled at week 3 of the experimental period (P< 0.05). In the caecum, proximal and mid colon, AXD feeding resulted in a 3- to 5-fold higher pool size of butyrate compared with WSD feeding, with the RSD being intermediate (P <0.001). In conclusion, the RSD and AXD differently affected digestion processes compared with the WSD, and the AXD most efficiently shifted the microbial composition towards butyrogenic species in the faeces and increased the large-intestinal butyrate pool size.

  8. DNA pooling strategies for categorical (ordinal) traits

    Science.gov (United States)

    Despite reduced genotyping costs in recent years, obtaining genotypes for all individuals in a population may still not be feasible when sample size is large. DNA pooling provides a useful alternative to determining genotype effects. Clustering algorithms allow for grouping of individuals (observati...

  9. Effect of pool rotation on three-dimensional flow in a shallow annular pool of silicon melt with bidirectional temperature gradients

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Quan-Zhuang; Peng, Lan; Liu, Jia [Key Laboratory of Low-grade Energy Utilization Technologies and Systems of Ministry of Education, College of Power Engineering, Chongqing University, Chongqing, 400044 (China); Wang, Fei, E-mail: penglan@cqu.edu.cn [Chongqing Special Equipment Inspection and Research Institute, Chongqing, 401121 (China)

    2016-08-15

    In order to understand the effect of pool rotation on silicon melt flow with the bidirectional temperature gradients, we conducted a series of unsteady three-dimensional (3D) numerical simulations in a shallow annular pool. The bidirectional temperature gradients are produced by the temperature difference between outer and inner walls as well as a constant heat flux at the bottom. Results show that when Marangoni number is small, a 3D steady flow is common without pool rotation. But it bifurcates to a 3D oscillatory flow at a low rotation Reynolds number. Subsequently, the flow becomes steady and axisymmetric at a high rotation Reynolds number. When the Marangoni number is large, pool rotation can effectively suppress the temperature fluctuation on the free surface, meanwhile, it improves the flow stability. The critical heat flux density diagrams are mapped, and the effects of radial and vertical temperature gradients on the flow are discussed. Additionally, the transition process from the flow dominated by the radial temperature gradient to the one dominated by the vertical temperature gradient is presented. (paper)

  10. Controls on Filling and Evacuation of Sediment in Waterfall Plunge Pools

    Science.gov (United States)

    Scheingross, J. S.; Lamb, M. P.

    2014-12-01

    Many waterfalls are characterized by the presence of deep plunge pools that experience periods of sediment fill and evacuation. These cycles of sediment fill are a first order control on the relative magnitude of lateral versus vertical erosion at the base of waterfalls, as vertical incision requires cover-free plunge pools to expose the bedrock floor, while lateral erosion can occur when pools are partially filled and plunge-pool walls are exposed. Currently, there exists no mechanistic model describing sediment transport through waterfall plunge pools, limiting our ability to predict waterfall retreat. To address this knowledge gap, we performed detailed laboratory experiments measuring plunge-pool sediment transport capacity (Qsc_pool) under varying waterfall and plunge-pool geometries, flow hydraulics, and sediment size. Our experimental plunge-pool sediment transport capacity measurements match well with a mechanistic model we developed which combines existing waterfall jet theory with a modified Rouse profile to predict sediment transport capacity as a function of water discharge and suspended sediment concentration at the plunge-pool lip. Comparing the transport capacity of plunge pools to lower gradient portions of rivers (Qsc_river) shows that, for transport limited conditions, plunge pools fill with sediment under modest water discharges when Qsc_river > Qsc_pool, and empty to bedrock under high discharges when Qsc_pool > Qsc_river. These results are consistent with field observations of sand-filled plunge pools with downstream boulder rims, implying filling and excavation of plunge pools over single-storm timescales. Thus, partial filling of waterfall plunge pools may provide a mechanism to promote lateral undercutting and retreat of waterfalls in homogeneous rock in which plunge-pool vertical incision occurs during brief large floods that expose bedrock, whereas lateral erosion may prevail during smaller events.

  11. Exciting Pools

    Science.gov (United States)

    Wright, Bradford L.

    1975-01-01

    Advocates the creation of swimming pool oscillations as part of a general investigation of mechanical oscillations. Presents the equations, procedure for deriving the slosh modes, and methods of period estimation for exciting swimming pool oscillations. (GS)

  12. Sodium-water reaction in double pool LMFBR, (5)

    International Nuclear Information System (INIS)

    Yoshida, Kazuo; Kumagai, Hiromichi; Nishi, Yoshihisa; Uotani, Masaki

    1990-01-01

    Experiments were conducted using a 1/5 scale model of the Double Pool in order to evaluate a pressure rise caused by a large scale sodium-water reaction. The experiments were focused on the pressure rise caused by the piston motion of liquid sodium. It appeared from the results that the magnitude of this pressure rise depends on the depth of reaction point, and that a pressure rise more than 1 MPa would arise in the real Double Pool plant. A new design of steam generator is proposed to mitigate the pressure rise. (author)

  13. Pooled Sequencing of 531 Genes in Inflammatory Bowel Disease Identifies an Associated Rare Variant in BTNL2 and Implicates Other Immune Related Genes

    Science.gov (United States)

    Prescott, Natalie J.; Lehne, Benjamin; Stone, Kristina; Lee, James C.; Taylor, Kirstin; Knight, Jo; Papouli, Efterpi; Mirza, Muddassar M.; Simpson, Michael A.; Spain, Sarah L.; Lu, Grace; Fraternali, Franca; Bumpstead, Suzannah J.; Gray, Emma; Amar, Ariella; Bye, Hannah; Green, Peter; Chung-Faye, Guy; Hayee, Bu’Hussain; Pollok, Richard; Satsangi, Jack; Parkes, Miles; Barrett, Jeffrey C.; Mansfield, John C.; Sanderson, Jeremy; Lewis, Cathryn M.; Weale, Michael E.; Schlitt, Thomas; Mathew, Christopher G.

    2015-01-01

    The contribution of rare coding sequence variants to genetic susceptibility in complex disorders is an important but unresolved question. Most studies thus far have investigated a limited number of genes from regions which contain common disease associated variants. Here we investigate this in inflammatory bowel disease by sequencing the exons and proximal promoters of 531 genes selected from both genome-wide association studies and pathway analysis in pooled DNA panels from 474 cases of Crohn’s disease and 480 controls. 80 variants with evidence of association in the sequencing experiment or with potential functional significance were selected for follow up genotyping in 6,507 IBD cases and 3,064 population controls. The top 5 disease associated variants were genotyped in an extension panel of 3,662 IBD cases and 3,639 controls, and tested for association in a combined analysis of 10,147 IBD cases and 7,008 controls. A rare coding variant p.G454C in the BTNL2 gene within the major histocompatibility complex was significantly associated with increased risk for IBD (p = 9.65x10−10, OR = 2.3[95% CI = 1.75–3.04]), but was independent of the known common associated CD and UC variants at this locus. Rare (T) or decreased risk (IL12B p.V298F, and NICN p.H191R) of IBD. These results provide additional insights into the involvement of the inhibition of T cell activation in the development of both sub-phenotypes of inflammatory bowel disease. We suggest that although rare coding variants may make a modest overall contribution to complex disease susceptibility, they can inform our understanding of the molecular pathways that contribute to pathogenesis. PMID:25671699

  14. 3-dimensional thermohydraulic analysis of KALIMER reactor pool during unprotected accidents

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Yong Bum; Hahn Do Hee

    2003-01-01

    During a normal reactor scram, the heat generation is reduced almost instantaneously while the coolant flow rate follows the pump coastdown. This mismatch between power and flow results in a situation where the core flow entering the hot pool is at a lower temperature than the temperature of the bulk pool sodium. This temperature difference leads to thermal stratification. Thermal stratification can occur in the hot pool region if the entering coolant is colder than the existing hot pool coolant and the flow momentum is not large enough to overcome the negative buoyancy force. Since the fluid of hot pool enters IHXs, the temperature distribution of hot pool can alter the overall system response. Hence, it is necessary to predict the pool coolant temperature distribution with sufficient accuracy to determine the inlet temperature conditions for the IHXs and its contribution to the net buoyancy head. Therefore, two-dimensional hot pool thermohydraulic model named HP2D has been developed. In this report code-to-code comparison analysis between HP2D and COMMIX-1AR/P has been performed in the case of steady-state and UTOP.

  15. Theoretical assessment of particle generation from sodium pool fires

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, M., E-mail: monica.gmartin@ciemat.es [CIEMAT, Unit of Nuclear Safety Research, Av. Complutense, 40, 28040 Madrid (Spain); Herranz, L.E., E-mail: luisen.herranz@ciemat.es [CIEMAT, Unit of Nuclear Safety Research, Av. Complutense, 40, 28040 Madrid (Spain); Kissane, M.P., E-mail: Martin.KISSANE@oecd.org [Nuclear Safety Technology and Regulation Division, OECD Nuclear Energy Agency (NEA), 46 quai Alphonse Le Gallo, 92100 Boulogne-Billancourt (France)

    2016-12-15

    Highlights: • Development of particle generation model for sodium-oxides aerosol formation. • Development of partially validated numerical simulations to build up maps of saturation ratio. • Nucleation of supersaturated vapours as relevant source of aerosols over sodium pools. • Prediction of high concentrations of primary particles in the combustion zone. - Abstract: Potential sodium discharge in the containment during postulated Beyond Design Basis Accidents (BDBAs) in Sodium-cooled Fast Reactors (SFRs) would have major consequences for accident development in terms of energetics and source term. In the containment, sodium vaporization and subsequent oxidation would result in supersaturated oxide vapours that would undergo rapid nucleation creating toxic aerosols. Therefore, modelling this vapour nucleation is essential to proper source term assessment in SFRs. In the frame of the EU-JASMIN project, a particle generation model to calculate the particle generation rate and their primary size during an in-containment sodium pool fire has been developed. Based on a suite of individual models for sodium vaporization, oxygen natural circulation (3D modelling), sodium-oxygen chemical reactions, sodium-oxides-vapour nucleation and condensation, its consistency has been partially validated by comparing with available experimental data. As an outcome, large temperature and vapour concentration gradients set over the sodium pool have been found which result in large particle concentrations in the close vicinity of the pool.

  16. Prioritization of gene regulatory interactions from large-scale modules in yeast

    Directory of Open Access Journals (Sweden)

    Bringas Ricardo

    2008-01-01

    Full Text Available Abstract Background The identification of groups of co-regulated genes and their transcription factors, called transcriptional modules, has been a focus of many studies about biological systems. While methods have been developed to derive numerous modules from genome-wide data, individual links between regulatory proteins and target genes still need experimental verification. In this work, we aim to prioritize regulator-target links within transcriptional modules based on three types of large-scale data sources. Results Starting with putative transcriptional modules from ChIP-chip data, we first derive modules in which target genes show both expression and function coherence. The most reliable regulatory links between transcription factors and target genes are established by identifying intersection of target genes in coherent modules for each enriched functional category. Using a combination of genome-wide yeast data in normal growth conditions and two different reference datasets, we show that our method predicts regulatory interactions with significantly higher predictive power than ChIP-chip binding data alone. A comparison with results from other studies highlights that our approach provides a reliable and complementary set of regulatory interactions. Based on our results, we can also identify functionally interacting target genes, for instance, a group of co-regulated proteins related to cell wall synthesis. Furthermore, we report novel conserved binding sites of a glycoprotein-encoding gene, CIS3, regulated by Swi6-Swi4 and Ndd1-Fkh2-Mcm1 complexes. Conclusion We provide a simple method to prioritize individual TF-gene interactions from large-scale transcriptional modules. In comparison with other published works, we predict a complementary set of regulatory interactions which yields a similar or higher prediction accuracy at the expense of sensitivity. Therefore, our method can serve as an alternative approach to prioritization for

  17. Swimming-pool piles

    International Nuclear Information System (INIS)

    Trioulaire, M.

    1959-01-01

    In France two swimming-pool piles, Melusine and Triton, have just been set in operation. The swimming-pool pile is the ideal research tool for neutron fluxes of the order of 10 13 . This type of pile can be of immediate interest to many research centres, but its cost must be reduced and a break with tradition should be observed in its design. It would be an advantage: - to bury the swimming-pool; - to reject the experimental channel; - to concentrate the cooling circuit in the swimming-pool; - to carry out all manipulations in the water; - to double the core. (author) [fr

  18. Preliminary Calculation on a Spent Fuel Pool Accident using GOTHIC

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jaehwan; Choi, Yu Jung; Hong, Tae Hyub; Kim, Hyeong-Taek [KHNP-CRI, Daejeon (Korea, Republic of)

    2015-10-15

    The probability of an accident happening at the spent fuel pool was believed to be quite low until the 2011 Fukushima accident occurred. Notably, large amount of spent fuel are normally stored in the spent fuel pool for a long time compared to the amount of fuel in the reactor core and the total heat released from the spent fuel is high enough to boil the water of the spent fuel pool when the cooling system does not operate. In addition, the enrichment and the burnup of the fuel have both increased in the past decade and heat generation from the spent fuel thereby has also increased. The failure of the cooling system at the spent fuel pool (hereafter, a loss-of-cooling accident) is one of the principal hypothetical causes of an accident that could occur at the spent fuel pool. In this paper, the preliminary calculation of a loss-of-cooling accident was performed. In this paper, the preliminary calculation of a loss-of cooling accident was performed with GOTHIC. The calculation results show boiling away of water in the spent fuel pool due to the loss-of-cooling accident and similar thermal performance of the spent fuel pool with previous research results.

  19. Study on velocity distribution in a pool by submersible mixers

    International Nuclear Information System (INIS)

    Tian, F; Shi, W D; Lu, X N; Chen, B; Jiang, H

    2012-01-01

    To study the distribution of submersible mixers and agitating effect in the sewage treatment pool, Pro/E software was utilized to build the three-dimensional model. Then, the large-scale computational fluid dynamics software FLUENT6.3 was used. ICEM software was used to build unstructured grid of sewage treatment pool. After that, the sewage treatment pool was numerically simulated by dynamic coordinate system technology and RNG k-ε turbulent model and PIOS algorithm. The macro fluid field and each section velocity flow field distribution were analyzed to observe the efficiency of each submersible mixer. The average velocity and mixing area in the sewage pool were studied simultaneously. Results show that: the preferred project B, two submersible mixers speed is 980 r/min, and setting angles are all 30°. Fluid mixing area in the pool has reached more than 95%. Under the action of two mixers, the fluid in the sewage pool form a continuous circulating water flow. The fluid is mixed adequately and average velocity of fluid in the pool is at around 0.241m/s, which agreed with the work requirements. Consequently it can provide a reference basis for practical engineering application of submersible mixers by using this method.

  20. An accurate clone-based haplotyping method by overlapping pool sequencing.

    Science.gov (United States)

    Li, Cheng; Cao, Changchang; Tu, Jing; Sun, Xiao

    2016-07-08

    Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand.

    Science.gov (United States)

    Hug, Katrin; Maher, William A; Stott, Matthew B; Krikowa, Frank; Foster, Simon; Moreau, John W

    2014-01-01

    Acid-sulfide hot springs are analogs of early Earth geothermal systems where microbial metal(loid) resistance likely first evolved. Arsenic is a metalloid enriched in the acid-sulfide hot spring Champagne Pool (Waiotapu, New Zealand). Arsenic speciation in Champagne Pool follows reaction paths not yet fully understood with respect to biotic contributions and coupling to biogeochemical sulfur cycling. Here we present quantitative arsenic speciation from Champagne Pool, finding arsenite dominant in the pool, rim and outflow channel (55-75% total arsenic), and dithio- and trithioarsenates ubiquitously present as 18-25% total arsenic. In the outflow channel, dimethylmonothioarsenate comprised ≤9% total arsenic, while on the outflow terrace thioarsenates were present at 55% total arsenic. We also quantified sulfide, thiosulfate, sulfate and elemental sulfur, finding sulfide and sulfate as major species in the pool and outflow terrace, respectively. Elemental sulfur concentration reached a maximum at the terrace. Phylogenetic analysis of 16S rRNA genes from metagenomic sequencing revealed the dominance of Sulfurihydrogenibium at all sites and an increased archaeal population at the rim and outflow channel. Several phylotypes were found closely related to known sulfur- and sulfide-oxidizers, as well as sulfur- and sulfate-reducers. Bioinformatic analysis revealed genes underpinning sulfur redox transformations, consistent with sulfur speciation data, and illustrating a microbial role in sulfur-dependent transformation of arsenite to thioarsenate. Metagenomic analysis also revealed genes encoding for arsenate reductase at all sites, reflecting the ubiquity of thioarsenate and a need for microbial arsenate resistance despite anoxic conditions. Absence of the arsenite oxidase gene, aio, at all sites suggests prioritization of arsenite detoxification over coupling to energy conservation. Finally, detection of methyl arsenic in the outflow channel, in conjunction with

  2. CO{sub 2} flooding performance prediction for Alberta oil pools

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, J.C. [Adams Pearson Associates Inc., Calgary, AB (Canada); Bachu, S. [Alberta Energy and Utilities Board, Calgary, AB (Canada)

    2002-06-01

    An advanced technical screening program was used to successfully screen and rank a very large number of Alberta oil pools for enhanced oil recovery using carbon dioxide (CO{sub 2}) flooding. This paper is a continuation paper describing the results of using the Microsoft Excel program with VBA to estimate production forecasts for several candidate pools in Alberta. A total of 6 ranking parameters were used, including API gravity of oil, residual oil saturation, ratio between reservoir pressure and minimum miscibility pressure, reservoir temperature, net pay thickness and porosity. The screening program provides a technical ranking of approximately 8,000 Alberta pools. After compilation of the Alberta oil pools, it was determined that most of the deep carbonate oil pools are excellent candidates for CO{sub 2} miscible flooding. Other Devonian carbonate pools are also ranked as having high potential for the process. An environmental benefit of CO{sub 2} miscible flooding process is that carbon sequestration has the potential to reduce anthropogenic carbon dioxide emissions from reaching the atmosphere. Ongoing studies are currently addressing CO{sub 2} capture and transportation, making EOR technology viable for maintaining light oil production in western Canada. 11 refs., 2 tabs., 2 figs.

  3. Dynamics of inorganic nutrients in intertidal sediments: porewater, exchangeable and intracellular pools

    Directory of Open Access Journals (Sweden)

    Emilio eGarcia-Robledo

    2016-05-01

    Full Text Available The study of inorganic nutrients dynamics in shallow sediments usually focuses on two main pools: the porewater (PW nutrients and the exchangeable (EX ammonium and phosphate. Recently, it has been found that microphytobenthos (MPB and other microorganisms can accumulate large amounts of nutrients intracellularly (IC, highlighting the biogeochemical importance of this nutrient pool. Storing nutrients could support the growth of autotrophs when nutrients are not available, and could also provide alternative electron acceptors for dissimilatory processes such as nitrate reduction. Here, we studied the magnitude and relative importance of these three nutrient pools (PW, IC and EX and their relation to chlorophylls (used as a proxy for MPB abundance and organic matter (OM contents in an intertidal mudflat of Cadiz Bay (Spain. MPB was localized in the first 4 mm of the sediment and showed a clear seasonal pattern; highest chlorophylls content was found during autumn and lowest during spring-summer. The temporal and spatial distribution of nutrients pools and MPB were largely correlated. Ammonium was higher in the IC and EX fractions, representing on average 59 and 37% of the total ammonium pool, respectively. Similarly, phosphate in the IC and EX fractions accounted on average for 40 and 31% of the total phosphate pool, respectively. Nitrate in the PW was low, suggesting low nitrification activity and rapid consumption. Nitrate accumulated in the IC pool during periods of moderate MPB abundance, being up to 66% of the total nitrate pool, whereas it decreased when chlorophyll concentration peaked likely due to a high nitrogen demand. EX-Nitrate accounted for the largest fraction of total sediment nitrate, 66% on average. The distribution of EX-Nitrate was significantly correlated with chlorophyll and OM, which probably indicates a relation of this pool to an increased availability of sites for ionic adsorption. This EX-Nitrate pool could represent an

  4. Addressing data privacy in matched studies via virtual pooling.

    Science.gov (United States)

    Saha-Chaudhuri, P; Weinberg, C R

    2017-09-07

    Data confidentiality and shared use of research data are two desirable but sometimes conflicting goals in research with multi-center studies and distributed data. While ideal for straightforward analysis, confidentiality restrictions forbid creation of a single dataset that includes covariate information of all participants. Current approaches such as aggregate data sharing, distributed regression, meta-analysis and score-based methods can have important limitations. We propose a novel application of an existing epidemiologic tool, specimen pooling, to enable confidentiality-preserving analysis of data arising from a matched case-control, multi-center design. Instead of pooling specimens prior to assay, we apply the methodology to virtually pool (aggregate) covariates within nodes. Such virtual pooling retains most of the information used in an analysis with individual data and since individual participant data is not shared externally, within-node virtual pooling preserves data confidentiality. We show that aggregated covariate levels can be used in a conditional logistic regression model to estimate individual-level odds ratios of interest. The parameter estimates from the standard conditional logistic regression are compared to the estimates based on a conditional logistic regression model with aggregated data. The parameter estimates are shown to be similar to those without pooling and to have comparable standard errors and confidence interval coverage. Virtual data pooling can be used to maintain confidentiality of data from multi-center study and can be particularly useful in research with large-scale distributed data.

  5. Macroinvertebrate community assembly in pools created during peatland restoration.

    Science.gov (United States)

    Brown, Lee E; Ramchunder, Sorain J; Beadle, Jeannie M; Holden, Joseph

    2016-11-01

    providing extensive new habitat that is largely equivalent to natural pools. More generally, we suggest that assembly theory could provide new benchmarks for planning and evaluating ecological restoration success. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  6. Simulation of droplet impact onto a deep pool for large Froude numbers in different open-source codes

    Science.gov (United States)

    Korchagova, V. N.; Kraposhin, M. V.; Marchevsky, I. K.; Smirnova, E. V.

    2017-11-01

    A droplet impact on a deep pool can induce macro-scale or micro-scale effects like a crown splash, a high-speed jet, formation of secondary droplets or thin liquid films, etc. It depends on the diameter and velocity of the droplet, liquid properties, effects of external forces and other factors that a ratio of dimensionless criteria can account for. In the present research, we considered the droplet and the pool consist of the same viscous incompressible liquid. We took surface tension into account but neglected gravity forces. We used two open-source codes (OpenFOAM and Gerris) for our computations. We review the possibility of using these codes for simulation of processes in free-surface flows that may take place after a droplet impact on the pool. Both codes simulated several modes of droplet impact. We estimated the effect of liquid properties with respect to the Reynolds number and Weber number. Numerical simulation enabled us to find boundaries between different modes of droplet impact on a deep pool and to plot corresponding mode maps. The ratio of liquid density to that of the surrounding gas induces several changes in mode maps. Increasing this density ratio suppresses the crown splash.

  7. Malaria diagnosis from pooled blood samples: comparative analysis of real-time PCR, nested PCR and immunoassay as a platform for the molecular and serological diagnosis of malaria on a large-scale

    Directory of Open Access Journals (Sweden)

    Giselle FMC Lima

    2011-09-01

    Full Text Available Malaria diagnoses has traditionally been made using thick blood smears, but more sensitive and faster techniques are required to process large numbers of samples in clinical and epidemiological studies and in blood donor screening. Here, we evaluated molecular and serological tools to build a screening platform for pooled samples aimed at reducing both the time and the cost of these diagnoses. Positive and negative samples were analysed in individual and pooled experiments using real-time polymerase chain reaction (PCR, nested PCR and an immunochromatographic test. For the individual tests, 46/49 samples were positive by real-time PCR, 46/49 were positive by nested PCR and 32/46 were positive by immunochromatographic test. For the assays performed using pooled samples, 13/15 samples were positive by real-time PCR and nested PCR and 11/15 were positive by immunochromatographic test. These molecular methods demonstrated sensitivity and specificity for both the individual and pooled samples. Due to the advantages of the real-time PCR, such as the fast processing and the closed system, this method should be indicated as the first choice for use in large-scale diagnosis and the nested PCR should be used for species differentiation. However, additional field isolates should be tested to confirm the results achieved using cultured parasites and the serological test should only be adopted as a complementary method for malaria diagnosis.

  8. Microbial contributions to coupled arsenic and sulfur cycling in the acid-sulfide hot spring Champagne Pool, New Zealand

    Directory of Open Access Journals (Sweden)

    Katrin eHug

    2014-11-01

    Full Text Available Acid-sulfide hot springs are analogs of early Earth geothermal systems where microbial metal(loid resistance likely first evolved. Arsenic is a metalloid enriched in the acid-sulfide hot spring Champagne Pool (Waiotapu, New Zealand. Arsenic speciation in Champagne Pool follows reaction paths not yet fully understood with respect to biotic contributions and coupling to biogeochemical sulfur cycling. Here we present quantitative arsenic speciation from Champagne Pool, finding arsenite dominant in the pool, rim and outflow channel (55-75% total arsenic, and dithio- and trithioarsenates ubiquitously present as 18-25% total arsenic. In the outflow channel, dimethylmonothioarsenate comprised ≤9% total arsenic, while on the outflow terrace thioarsenates were present at 55% total arsenic. We also quantified sulfide, thiosulfate, sulfate and elemental sulfur, finding sulfide and sulfate as major species in the pool and outflow terrace, respectively. Elemental sulfur reached a maximum at the terrace. Phylogenetic analysis of 16S rRNA genes from metagenomic sequencing revealed the dominance of Sulfurihydrogenibium at all sites and an increased archaeal population at the rim and outflow channel. Several phylotypes were found closely related to known sulfur- and sulfide-oxidizers, as well as sulfur- and sulfate-reducers. Bioinformatic analysis revealed genes underpinning sulfur redox transformations, consistent with sulfur speciation data, and illustrating a microbial role in sulfur-dependent transformation of arsenite to thioarsenate. Metagenomic analysis also revealed genes encoding for arsenate reductase at all sites, reflecting the ubiquity of thioarsenate and a need for microbial arsenate resistance despite anoxic conditions. Absence of the arsenite oxidase gene, aio, at all sites suggests prioritization of arsenite detoxification over coupling to energy conservation. Finally, detection of methyl arsenic in the outflow channel, in conjunction with

  9. Spent fuel storage pool

    International Nuclear Information System (INIS)

    Murakami, Naoshi.

    1996-01-01

    Fences are disposed to a fuel exchange floor surrounding the upper surface of a fuel pool for preventing overflow of pool water. The fences comprise a plurality of flat boards arranged in parallel with each other in the longitudinal direction while being vertically inclined, and slits are disposed between the boards for looking down the pool. Further, the fences comprise wide boards and are constituted so as to be laid horizontally on the fuel exchange floor in a normal state and uprisen by means of the signals from an earthquake sensing device. Even if pool water is overflow from the fuel pool by the vibrations occurred upon earthquake and flown out to the floor of the fuel exchange floor, the overflow from the fuel exchange floor is prevented by the fences. An operator who monitors the fuel pool can observe the inside of the fuel pool through the slits formed to the fences during normal operation. The fences act as resistance against overflowing water upon occurrence of an earthquake thereby capable of reducing the overflowing amount of water due to the vibrations of pool water. The effect of preventing overflowing water can be enhanced. (N.H.)

  10. UPDG: Utilities package for data analysis of Pooled DNA GWAS

    Directory of Open Access Journals (Sweden)

    Ho Daniel WH

    2012-01-01

    Full Text Available Abstract Background Despite being a well-established strategy for cost reduction in disease gene mapping, pooled DNA association study is much less popular than the individual DNA approach. This situation is especially true for pooled DNA genomewide association study (GWAS, for which very few computer resources have been developed for its data analysis. This motivates the development of UPDG (Utilities package for data analysis of Pooled DNA GWAS. Results UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background. Conclusions UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy.

  11. Quantifying aboveground forest carbon pools and fluxes from repeat LiDAR surveys

    Science.gov (United States)

    Andrew T. Hudak; Eva K. Strand; Lee A. Vierling; John C. Byrne; Jan U. H. Eitel; Sebastian Martinuzzi; Michael J. Falkowski

    2012-01-01

    Sound forest policy and management decisions to mitigate rising atmospheric CO2 depend upon accurate methodologies to quantify forest carbon pools and fluxes over large tracts of land. LiDAR remote sensing is a rapidly evolving technology for quantifying aboveground biomass and thereby carbon pools; however, little work has evaluated the efficacy of repeat LiDAR...

  12. Peculiarities of natural convective heat removal from complex pools

    International Nuclear Information System (INIS)

    Groetzbach, Guenther

    2002-01-01

    Considerable sensitivities are investigated in using natural convection for cooling large pools. Such a flow occurred in a sump cooling concept for a water cooled reactor. The related SUCOS model experiments were analyzed by means of the FLUTAN code. The numerical interpretations show, the natural convection in large pools is strongly influenced by local thermal disturbances, either due to structures in the fluid domain, or by bounding structures interacting thermally with the fluid. These experiment specific disturbances must be recorded in the numerical model in order to achieve adequate simulations of the heat transport. Some geometric imperfections of horizontal coolers or heaters could also have tremendous influences. As a consequence, not only the numerical model has to record all relevant phenomena as realistic as possible, but also the model experiment. (author)

  13. Macroinvertebrate community assembly in pools created during peatland restoration

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Lee E., E-mail: l.brown@leeds.ac.uk; Ramchunder, Sorain J.; Beadle, Jeannie M.; Holden, Joseph

    2016-11-01

    providing extensive new habitat that is largely equivalent to natural pools. More generally, we suggest that assembly theory could provide new benchmarks for planning and evaluating ecological restoration success. - Highlights: • We assessed the benefits of peatland pool restoration for aquatic biodiversity. • Biomonitoring metrics and community composition suggested different outcomes to restoration. • Null model approaches provided a clearer suggestion that restoration was successful. • Analysis of assembly processes should be used when planning and evaluating ecological restorations.

  14. Macroinvertebrate community assembly in pools created during peatland restoration

    International Nuclear Information System (INIS)

    Brown, Lee E.; Ramchunder, Sorain J.; Beadle, Jeannie M.; Holden, Joseph

    2016-01-01

    providing extensive new habitat that is largely equivalent to natural pools. More generally, we suggest that assembly theory could provide new benchmarks for planning and evaluating ecological restoration success. - Highlights: • We assessed the benefits of peatland pool restoration for aquatic biodiversity. • Biomonitoring metrics and community composition suggested different outcomes to restoration. • Null model approaches provided a clearer suggestion that restoration was successful. • Analysis of assembly processes should be used when planning and evaluating ecological restorations.

  15. Identification of candidate new cancer susceptibility genes using yeast genomics

    International Nuclear Information System (INIS)

    Brown, M.; Brown, J.A.; Game, J.C.

    2003-01-01

    A large proportion of cancer susceptibility syndromes are the result of mutations in genes in DNA repair or in cell-cycle checkpoints in response to DNA damage, such as ataxia telangiectasia (AT), Fanconi's anemia (FA), Bloom's syndrome (BS), Nijmegen breakage syndrome (NBS), and xeroderma pigmentosum (XP). Mutations in these genes often cause gross chromosomal instability leading to an increased mutation rate of all genes including those directly responsible for cancer. We have proposed that because the orthologs of these genes in budding yeast, S. cerevisiae, confer protection against killing by DNA damaging agents it should be possible to identify new cancer susceptibility genes by identifying yeast genes whose deletion causes sensitivity to DNA damage. We therefore screened the recently completed collection of individual gene deletion mutants to identify genes that affect sensitivity to DNA-damaging agents. Screening for sensitivity in this obtained up to now with the F98 glioma model othe fact that each deleted gene is replaced by a cassette containing two molecular 'barcodes', or 20-mers, that uniquely identify the strain when DNA from a pool of strains is hybridized to an oligonucleotide array containing the complementary sequences of the barcodes. We performed the screen with UV, IR, H 2 0 2 and other DNA damaging agents. In addition to identifying genes already known to confer resistance to DNA damaging agents we have identified, and individually confirmed, several genes not previously associated with resistance. Several of these are of unknown function. We have also examined the chromosomal stability of selected strains and found that IR sensitive strains often but not always exhibit genomic instability. We are presently constructing a yeast artificial chromosome to globally interrogate all the genes in the deletion pool for their involvement in genomic stability. This work shows that budding yeast is a valuable eukaryotic model organism to identify

  16. Study of Microbial Contamination of the Public Swimming Pools with Escherichia coli and Pseudomonas aeruginosa and Their Physical Parameters in Kermanshah, Iran

    Directory of Open Access Journals (Sweden)

    Afsaneh Haghmorad Korasti

    2016-09-01

    Full Text Available Background and Objectives: Public swimming pools' waters are contaminated with a wide variety of pathogenic microorganisms and are a suitable environment for transmission of different diseases. The aim of this study was to investigate the microbial contamination of the public swimming pools' waters with Escherichia coli and Pseudomonas aeruginosa and to determine certain parameters such as residual chlorine, pH, temperature and turbidity in these pools' waters in Kermanshah. In this descriptive, cross-sectional study, 129 water samples were taken from all active pools in Kermanshah and their bacteriologic and physicochemical properties were investigated. Phosphatase alkaline (PHO-A gene was used for molecular confirmation of E. coli isolates, and exotoxin A (ETA gene in PCR was employed to confirm pathogenicity of P. aeruginosa isolates. Data were analyzed by chi-square and t-test. p0.05. Conclusion: The results of this study indicated that appropriate amount of residual chlorine caused reduction in microbial contamination in the public swimming pools' waters in Kermanshah.

  17. Velocity Fields Measurement of Natural Circulation Flow inside a Pool Using PIV Technique

    International Nuclear Information System (INIS)

    Kim, Seok; Kim, Dong Eok; Youn, Young Jung; Euh, Dong Jin; Song, Chul Hwa

    2012-01-01

    Thermal stratification is encountered in large pool of water increasingly being used as heat sink in new generation of advanced reactors. These large pools at near atmospheric pressure provide a heat sink for heat removal from the reactor or steam generator, and the containment by natural circulation as well as a source of water for core cooling. For examples, the PAFS (passive auxiliary feedwater system) is one of the advanced safety features adopted in the APR+ (Advanced Power Reactor Plus), which is intended to completely replace the conventional active auxiliary feedwater system. The PAFS cools down the steam generator secondary side and eventually removes the decay heat from the reactor core by adopting a natural convection mechanism. In a pool, the heat transfer from the PCHX (passive condensation heat exchanger) contributed to increase the pool temperature up to the saturation condition and induce the natural circulation flow of the PCCT (passive condensate cooling tank) pool water. When a heat rod is placed horizontally in a pool of water, the fluid adjacent to the heat rod gets heated up. In the process, its density reduces and by virtue of the buoyancy force, the fluid in this region moves up. After reaching the top free surface, the heated water moves towards the other side wall of the pool along the free surface. Since this heated water is cooling, it goes downward along the wall at the other side wall. Above heater rod, a natural circulation flow is formed. However, there is no flow below heater rod until pool water temperature increases to saturation temperature. In this study, velocity measurement was conducted to reveal a natural circulation flow structure in a small pool using PIV (particle image velocimetry) measurement technique

  18. Fragmentation of the large subunit ribosomal RNA gene in oyster mitochondrial genomes

    Directory of Open Access Journals (Sweden)

    Milbury Coren A

    2010-09-01

    Full Text Available Abstract Background Discontinuous genes have been observed in bacteria, archaea, and eukaryotic nuclei, mitochondria and chloroplasts. Gene discontinuity occurs in multiple forms: the two most frequent forms result from introns that are spliced out of the RNA and the resulting exons are spliced together to form a single transcript, and fragmented gene transcripts that are not covalently attached post-transcriptionally. Within the past few years, fragmented ribosomal RNA (rRNA genes have been discovered in bilateral metazoan mitochondria, all within a group of related oysters. Results In this study, we have characterized this fragmentation with comparative analysis and experimentation. We present secondary structures, modeled using comparative sequence analysis of the discontinuous mitochondrial large subunit rRNA genes of the cupped oysters C. virginica, C. gigas, and C. hongkongensis. Comparative structure models for the large subunit rRNA in each of the three oyster species are generally similar to those for other bilateral metazoans. We also used RT-PCR and analyzed ESTs to determine if the two fragmented LSU rRNAs are spliced together. The two segments are transcribed separately, and not spliced together although they still form functional rRNAs and ribosomes. Conclusions Although many examples of discontinuous ribosomal genes have been documented in bacteria and archaea, as well as the nuclei, chloroplasts, and mitochondria of eukaryotes, oysters are some of the first characterized examples of fragmented bilateral animal mitochondrial rRNA genes. The secondary structures of the oyster LSU rRNA fragments have been predicted on the basis of previous comparative metazoan mitochondrial LSU rRNA structure models.

  19. Code Development of Radioactive Aerosol Scrubbing in Pool-Injection Zone

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Hyun Joung; Ha, Kwang Soon [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of); Jang, Dong Soon [Chungnam National University, Daejeon (Korea, Republic of)

    2015-10-15

    The pool scrubbing models were reviewed and an aerosol scrubbing code has been prepared to calculate decontamination factor through the injection zone. The developed code has been verified using the experimental results and evaluated parametrically on the input variables. In injection zone, the initial steam condensation was most effective mechanism for the aerosol removal, and the steam fraction and pool temperature were highly affected on the decontamination factor by initial steam condensation. The aerosol scrubbing code will be updated to evaluate the decontamination factor at rise zone and finally whole pool scrubber phenomena. If a severe accident occurs in a nuclear power plant (NPP), the aerosol and gaseous fission products might be produced in the reactor vessel, and then released to the environment after the containment failure. FCVS (Filtered Containment Venting System) is one of the severe accident mitigation systems for retaining the containment integrity by discharging the high-temperature and high-pressure fission products to the environment after passing through the filtration system. In general, the FCVS is categorized into two types, wet and dry types. The scrubbing pool could play an important role in the wet type FCVS because a large amount of aerosol is captured in the water pool. The pool scrubbing phenomena have been modelled and embedded in several computer codes, such as SPARC (Suppression Pool Aerosol Removal Code), BUSCA (BUbble Scrubbing Algorithm) and SUPRA (Suppression Pool Retention Analysis). These codes aim at simulating the pool scrubbing process and estimating the decontamination factors (DFs) of the radioactive aerosol and iodine gas in the water pool, which is defined as the ratio of initial mass of the specific radioactive material to final massy after passing through the water pool. The pool scrubbing models were reviewed and an aerosol scrubbing code has been prepared to calculate decontamination factor through the injection

  20. Zebrafish Expression Ontology of Gene Sets (ZEOGS): A Tool to Analyze Enrichment of Zebrafish Anatomical Terms in Large Gene Sets

    Science.gov (United States)

    Marsico, Annalisa

    2013-01-01

    Abstract The zebrafish (Danio rerio) is an established model organism for developmental and biomedical research. It is frequently used for high-throughput functional genomics experiments, such as genome-wide gene expression measurements, to systematically analyze molecular mechanisms. However, the use of whole embryos or larvae in such experiments leads to a loss of the spatial information. To address this problem, we have developed a tool called Zebrafish Expression Ontology of Gene Sets (ZEOGS) to assess the enrichment of anatomical terms in large gene sets. ZEOGS uses gene expression pattern data from several sources: first, in situ hybridization experiments from the Zebrafish Model Organism Database (ZFIN); second, it uses the Zebrafish Anatomical Ontology, a controlled vocabulary that describes connected anatomical structures; and third, the available connections between expression patterns and anatomical terms contained in ZFIN. Upon input of a gene set, ZEOGS determines which anatomical structures are overrepresented in the input gene set. ZEOGS allows one for the first time to look at groups of genes and to describe them in terms of shared anatomical structures. To establish ZEOGS, we first tested it on random gene selections and on two public microarray datasets with known tissue-specific gene expression changes. These tests showed that ZEOGS could reliably identify the tissues affected, whereas only very few enriched terms to none were found in the random gene sets. Next we applied ZEOGS to microarray datasets of 24 and 72 h postfertilization zebrafish embryos treated with beclomethasone, a potent glucocorticoid. This analysis resulted in the identification of several anatomical terms related to glucocorticoid-responsive tissues, some of which were stage-specific. Our studies highlight the ability of ZEOGS to extract spatial information from datasets derived from whole embryos, indicating that ZEOGS could be a useful tool to automatically analyze gene

  1. Zebrafish Expression Ontology of Gene Sets (ZEOGS): a tool to analyze enrichment of zebrafish anatomical terms in large gene sets.

    Science.gov (United States)

    Prykhozhij, Sergey V; Marsico, Annalisa; Meijsing, Sebastiaan H

    2013-09-01

    The zebrafish (Danio rerio) is an established model organism for developmental and biomedical research. It is frequently used for high-throughput functional genomics experiments, such as genome-wide gene expression measurements, to systematically analyze molecular mechanisms. However, the use of whole embryos or larvae in such experiments leads to a loss of the spatial information. To address this problem, we have developed a tool called Zebrafish Expression Ontology of Gene Sets (ZEOGS) to assess the enrichment of anatomical terms in large gene sets. ZEOGS uses gene expression pattern data from several sources: first, in situ hybridization experiments from the Zebrafish Model Organism Database (ZFIN); second, it uses the Zebrafish Anatomical Ontology, a controlled vocabulary that describes connected anatomical structures; and third, the available connections between expression patterns and anatomical terms contained in ZFIN. Upon input of a gene set, ZEOGS determines which anatomical structures are overrepresented in the input gene set. ZEOGS allows one for the first time to look at groups of genes and to describe them in terms of shared anatomical structures. To establish ZEOGS, we first tested it on random gene selections and on two public microarray datasets with known tissue-specific gene expression changes. These tests showed that ZEOGS could reliably identify the tissues affected, whereas only very few enriched terms to none were found in the random gene sets. Next we applied ZEOGS to microarray datasets of 24 and 72 h postfertilization zebrafish embryos treated with beclomethasone, a potent glucocorticoid. This analysis resulted in the identification of several anatomical terms related to glucocorticoid-responsive tissues, some of which were stage-specific. Our studies highlight the ability of ZEOGS to extract spatial information from datasets derived from whole embryos, indicating that ZEOGS could be a useful tool to automatically analyze gene expression

  2. Operation and maintenance techniques of pool and pool water purification system in IMEF

    Energy Technology Data Exchange (ETDEWEB)

    Soong, Woong Sup

    1999-03-01

    IMEF pool is used pass way between pool and hot cell in order to inlet and outlet of fuel pin in cask. All operation is performed conforming with naked eyes. Therefore floating matter is filtered so as to easy under water handling. Also radioactivity in pool water is controlled according to the nuclear law, radioactivity ration maintained less than 15mR/hr on pool side. Perfect operation and maintenance can be achieved well trained operator. Result obtained from the perfection can give more influence over restrain, spreading contamination of radioactivity materials. This report describes operation and maintenance technique of pool water purification system in IMEF. (Author). 7 refs., 13 figs.

  3. Operation and maintenance techniques of pool and pool water purification system in IMEF

    International Nuclear Information System (INIS)

    Soong, Woong Sup

    1999-03-01

    IMEF pool is used pass way between pool and hot cell in order to inlet and outlet of fuel pin in cask. All operation is performed conforming with naked eyes. Therefore floating matter is filtered so as to easy under water handling. Also radioactivity in pool water is controlled according to the nuclear law, radioactivity ration maintained less than 15mR/hr on pool side. Perfect operation and maintenance can be achieved well trained operator. Result obtained from the perfection can give more influence over restrain, spreading contamination of radioactivity materials. This report describes operation and maintenance technique of pool water purification system in IMEF. (Author). 7 refs., 13 figs

  4. Swimming pool granuloma

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/001357.htm Swimming pool granuloma To use the sharing features on this page, please enable JavaScript. A swimming pool granuloma is a long-term (chronic) skin ...

  5. Evaluation of a pooled strategy for high-throughput sequencing of cosmid clones from metagenomic libraries.

    Science.gov (United States)

    Lam, Kathy N; Hall, Michael W; Engel, Katja; Vey, Gregory; Cheng, Jiujun; Neufeld, Josh D; Charles, Trevor C

    2014-01-01

    High-throughput sequencing methods have been instrumental in the growing field of metagenomics, with technological improvements enabling greater throughput at decreased costs. Nonetheless, the economy of high-throughput sequencing cannot be fully leveraged in the subdiscipline of functional metagenomics. In this area of research, environmental DNA is typically cloned to generate large-insert libraries from which individual clones are isolated, based on specific activities of interest. Sequence data are required for complete characterization of such clones, but the sequencing of a large set of clones requires individual barcode-based sample preparation; this can become costly, as the cost of clone barcoding scales linearly with the number of clones processed, and thus sequencing a large number of metagenomic clones often remains cost-prohibitive. We investigated a hybrid Sanger/Illumina pooled sequencing strategy that omits barcoding altogether, and we evaluated this strategy by comparing the pooled sequencing results to reference sequence data obtained from traditional barcode-based sequencing of the same set of clones. Using identity and coverage metrics in our evaluation, we show that pooled sequencing can generate high-quality sequence data, without producing problematic chimeras. Though caveats of a pooled strategy exist and further optimization of the method is required to improve recovery of complete clone sequences and to avoid circumstances that generate unrecoverable clone sequences, our results demonstrate that pooled sequencing represents an effective and low-cost alternative for sequencing large sets of metagenomic clones.

  6. An analytical framework for common-pool resource–large technical system (CPR-LTS constellations

    Directory of Open Access Journals (Sweden)

    Pär Blomkvist

    2013-02-01

    Full Text Available This paper introduces an analytical framework for a special phenomenon: when a common-pool resource (CPR institution and a large technical system (LTS are connected and mutually interdependent. The CPR in this case is a node managed by its appropriators within a centrally planned and managed system; here named CPR-LTS constellations. Our framework is empirically derived from two historical investigations of CPR institutions within two LTSs, the agricultural-technical system and the road transport system of Sweden. By comparing similarities and differences it is possible to identify paths to successes and failures. To understand why one survived and the other disappeared we connect Elinor Ostrom’s theories about management of CPRs with Thomas P. Hughes’s theories about LTSs. We are proposing a framework that can bridge the gap between theories about management of CPRs and LTSs. By combining the two theories it should be possible to better understand how small-scale producers using bottom-up CPRs can be linked to top-down LTSs.We will argue that to fit within an LTS, a CPR needs alignment between different parts or components within the constellation/system and alignment with other systems and institutions in society. We propose three analytical levels to deal with the phenomenon of aligning a CPR project to an existing, large sociotechnical system:Local alignment (CPR: How are CPRs organized and managed at local sites?Sociotechnical alignment (CPR-LTS: How are CPRs connected to the sociotechnical system?Contextual alignment: How are CPR-LTS constellations aligned with neighboring institutions and systems in society?Our work indicates that for successful management of a CPR-LTS constellation it is important that the CPR be included in legislation and that government agencies support the CPR in alignment with the LTS. Legislators must recognize the CPR-part in the CPR-LTS constellation so that its institutional body is firmly established in

  7. Swimming pool hydraulics and their significance for public pools. Bedeutung der Beckenhydraulik in oeffentlichen Schwimmbaedern

    Energy Technology Data Exchange (ETDEWEB)

    Gansloser, G

    1989-11-01

    The term of swimming pool hydraulics means the process of letting in and drawing off water to and from the pool while ensuring that no inadmissible water-borne contaminant concentrations will occur anywhere within the pool. Measurements were performed on a pool to study the significance of correct pool hydraulics. The author points out that a wrong water recirculation design will bring to nought the effects of an elaborate water treatment system; by contrast, poor pool water quality can be greatly improved by redesigning the pool water hydraulics approach. In principle, systems with with water inlet at one side and water outlet at the far side will fall short of hygienic requirements. (BWI).

  8. Vertebrate gene predictions and the problem of large genes

    DEFF Research Database (Denmark)

    Wang, Jun; Li, ShengTing; Zhang, Yong

    2003-01-01

    To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistent...

  9. Analysis of accidental loss of pool coolant due to leakage in a PWR SFP

    International Nuclear Information System (INIS)

    Wu, Xiaoli; Li, Wei; Zhang, Yapei; Tian, Wenxi; Su, Guanghui; Qiu, Suizheng

    2015-01-01

    Highlights: • Accidental loss of pool coolant due to leakage in a PWR SFP was studied using MAAP5. • The effect of emergency ventilation on the accident progression was investigated. • The effect of emergency injection on the accident progression was discussed. - Abstract: A large loss of pool coolant/water accident may be caused by extreme accidents such as the pool wall or bottom floor punctures due to a large aircraft strike. The safety of SFP under this circumstance is very important. Large amounts of radioactive materials would be easily released into the environment if a severe accident happened in the SFP, because the spent fuel pool (SFP) in a PWR nuclear power station (NPS) is often located in the fuel handing building outside the reactor containment. To gain insight into the loss of pool coolant accident progression for a pressurized water reactor (PWR) SFP, a computational model was established by using the Modular Accident Analysis Program (MAAP5). Important factors such as Zr oxidation by air, air natural circulation and thermal radiation were considered for partial and complete drainage accidents without mitigation measures. The calculation indicated that even if the residual water level was in the active fuel region, there was a chance to effectively remove the decay heat through axial heat conduction (if the pool cooling system failed) or steam cooling (if the pool cooling system was working). For sensitivity study, the effects of emergency ventilation and water injection on the accident progression were analyzed. The analysis showed that for the current configuration of high-density storage racks, it was difficult to cool the spent fuels by air natural circulation. Enlarging the space between the adjacent assemblies was a way of increasing air natural circulation flow rate and maintaining the coolability of SFP. Water injection to the bottom of the SFP helped to recover water inventory, quenching the high temperature assemblies to prevent

  10. A protocol for measuring spatial variables in soft-sediment tide pools

    Directory of Open Access Journals (Sweden)

    Marina R. Brenha-Nunes

    2016-01-01

    Full Text Available ABSTRACT We present a protocol for measuring spatial variables in large (>50 m2 soft-sediment tide pool. Secondarily, we present the fish capture efficiency of a sampling protocol that based on such spatial variables to calculate relative abundances. The area of the pool is estimated by summing areas of basic geometric forms; the depth, by taken representative measurements of the depth variability of each pool's sector, previously determined according to its perimeter; and the volume, by considering the pool as a prism. These procedures were a trade-off between the acquisition of reliable estimates and the minimization of both the cost of operating and the time spent in field. The fish sampling protocol is based on two con secutive stages: 1 two people search for fishes under structures (e.g., rocks and litters on the pool and capture them with hand seines; 2 these structures are removed and then a beach-seine is hauled over the whole pool. Our method is cheaper than others and fast to operate considering the time in low tides. The method to sample fish is quite efficient resulting in a capture efficiency of 89%.

  11. Wheat Landraces Are Better Qualified as Potential Gene Pools at Ultraspaced rather than Densely Grown Conditions

    Directory of Open Access Journals (Sweden)

    Elissavet G. Ninou

    2014-01-01

    Full Text Available The negative relationship between the yield potential of a genotype and its competitive ability may constitute an obstacle to recognize outstanding genotypes within heterogeneous populations. This issue was investigated by growing six heterogeneous wheat landraces along with a pure-line commercial cultivar under both dense and widely spaced conditions. The performance of two landraces showed a perfect match to the above relationship. Although they lagged behind the cultivar by 64 and 38% at the dense stand, the reverse was true with spaced plants where they succeeded in out-yielding the cultivar by 58 and 73%, respectively. It was concluded that dense stand might undervalue a landrace as potential gene pool in order to apply single-plant selection targeting pure-line cultivars, attributable to inability of plants representing high yielding genotypes to exhibit their capacity due to competitive disadvantage. On the other side, the yield expression of individuals is optimized when density is low enough to preclude interplant competition. Therefore, the latter condition appears ideal to identify the most promising landrace for breeding and subsequently recognize the individuals representing the most outstanding genotypes.

  12. An efficient modeling method for thermal stratification simulation in a BWR suppression pool

    Energy Technology Data Exchange (ETDEWEB)

    Haihua Zhao; Ling Zou; Hongbin Zhang; Hua Li; Walter Villanueva; Pavel Kudinov

    2012-09-01

    The suppression pool in a BWR plant not only is the major heat sink within the containment system, but also provides major emergency cooling water for the reactor core. In several accident scenarios, such as LOCA and extended station blackout, thermal stratification tends to form in the pool after the initial rapid venting stage. Accurately predicting the pool stratification phenomenon is important because it affects the peak containment pressure; and the pool temperature distribution also affects the NPSHa (Available Net Positive Suction Head) and therefore the performance of the pump which draws cooling water back to the core. Current safety analysis codes use 0-D lumped parameter methods to calculate the energy and mass balance in the pool and therefore have large uncertainty in prediction of scenarios in which stratification and mixing are important. While 3-D CFD methods can be used to analyze realistic 3D configurations, these methods normally require very fine grid resolution to resolve thin substructures such as jets and wall boundaries, therefore long simulation time. For mixing in stably stratified large enclosures, the BMIX++ code has been developed to implement a highly efficient analysis method for stratification where the ambient fluid volume is represented by 1-D transient partial differential equations and substructures such as free or wall jets are modeled with 1-D integral models. This allows very large reductions in computational effort compared to 3-D CFD modeling. The POOLEX experiments at Finland, which was designed to study phenomena relevant to Nordic design BWR suppression pool including thermal stratification and mixing, are used for validation. GOTHIC lumped parameter models are used to obtain boundary conditions for BMIX++ code and CFD simulations. Comparison between the BMIX++, GOTHIC, and CFD calculations against the POOLEX experimental data is discussed in detail.

  13. The pool chlorine hypothesis and asthma among boys.

    LENUS (Irish Health Repository)

    Cotter, A

    2012-01-31

    Swimming pool sanitation has largely been concerned with the microbiological quality of pool water, which is normally treated using a number of chlorine products. Recent studies have pointed to the potential hazards of chlorine by-products to the respiratory epithelium, particularly in indoor, poorly ventilated, pools. The aim of our study was to elucidate whether chronic exposure to indoor chlorinated swimming pools was associated with an increased likelihood of the development of asthma in boys. METHODS: The subjects were boys aged between 6 and 12 years. Data was collected by means of parental responses to a standardized asthma questionnaire (ISAAC: International Study of Asthma and Allergies in Childhood), supplemented with additional questions regarding frequency of attendance, number of years attendance, whether the child is a swimming team member. The questionnaire return rate was 71\\/% (n = 121). 23 boys were excluded on the basis that they had asthma before they started swimming (n = 97). There was a significant association between number of years a boy had been swimming and the likelihood of wheezing in the last 12 months (p = 0.009; OR = 1.351; 95% CI = 1.077-1.693) and diagnosed asthma (p = 0.046; OR = 1.299; 95% CI = 1.004-1.506). The greater the number the number of years a boy had been attending an indoor, chlorinated pool, the greater the likelihood of wheezing in the last 12 months or "had asthma". Age, parental smoking habits and being a swimming team member had no association with any of the asthma variables examined. Swimming pool attendance may be a risk factor in asthma in boys.

  14. 13 CFR 120.1706 - Pool Originator's retained interest in Pool.

    Science.gov (United States)

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Pool Originator's retained interest in Pool. 120.1706 Section 120.1706 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION BUSINESS LOANS Establishment of SBA Secondary Market Guarantee Program for First Lien Position 504 Loan...

  15. Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools

    Directory of Open Access Journals (Sweden)

    Thomson Pippa

    2003-09-01

    Full Text Available Abstract In a project on the biodiversity of chickens funded by the European Commission (EC, eight laboratories collaborated to assess the genetic variation within and between 52 populations from a wide range of chicken types. Twenty-two di-nucleotide microsatellite markers were used to genotype DNA pools of 50 birds from each population. The polymorphism measures for the average, the least polymorphic population (inbred C line and the most polymorphic population (Gallus gallus spadiceus were, respectively, as follows: number of alleles per locus, per population: 3.5, 1.3 and 5.2; average gene diversity across markers: 0.47, 0.05 and 0.64; and proportion of polymorphic markers: 0.91, 0.25 and 1.0. These were in good agreement with the breeding history of the populations. For instance, unselected populations were found to be more polymorphic than selected breeds such as layers. Thus DNA pools are effective in the preliminary assessment of genetic variation of populations and markers. Mean genetic distance indicates the extent to which a given population shares its genetic diversity with that of the whole tested gene pool and is a useful criterion for conservation of diversity. The distribution of population-specific (private alleles and the amount of genetic variation shared among populations supports the hypothesis that the red jungle fowl is the main progenitor of the domesticated chicken.

  16. Interleukin 10 gene promoter polymorphism and risk of diffuse large ...

    African Journals Online (AJOL)

    Purpose: Given the importance of understanding the genetic variations involved in the pathogenesis of non-Hodgkin's lymphoma (NHL), this work was designed to study the impact of IL-10 (1082 G/A; rs1800896 and 819 C/T; rs1800871) gene promoter polymorphism on susceptibility of Egyptians to diffuse large B cell ...

  17. Longevity of Wood-Forced Pools in an Old-Growth Forest

    Science.gov (United States)

    Buffington, J. M.; Woodsmith, R. D.; Johnson, A. C.

    2009-12-01

    Wood debris plays an important role in scouring pools in forest channels and providing resultant habitat for aquatic organisms. We investigated the longevity of such pools in a gravel-bed river flowing through old-growth forest in southeastern Alaska by aging trees and “bear’s bread” fungi (Ganoderma applanatum, Fomitopsis pinicola) growing on pool-forming wood debris. Ages were determined by counting annual growth rings from cores and cross sections of trees and fungi growing on the wood debris. These ages are minimum values because they do not account for lag time between debris recruitment and seedling/spore establishment on the debris, nor do they account for flood scour that may periodically reset tree and fungi growth on the debris. The study stream has a gradient of about 1%, bankfull width and depth of 13.3 and 0.78 m, respectively, median grain size of 18 mm, a high wood loading (0.8 pieces/m), and a correspondingly low pool spacing (0.3 bankfull widths/pool), with 81% of the pools forced by wood debris. The size of wood debris in the study stream is large relative to the channel (average log length of 7.6 m and diameter of 0.35 m), rendering most debris immobile. Eighty-one pool-forming pieces of wood were dated over 1.2 km of stream length, with 28% of these pieces causing scour of more than one pool. In all, 122 wood-forced pools were dated, accounting for 38% of all pools at the site and 47% of the wood-forced pools. Fifty-three percent of the wood-forced pools lacked datable wood because these pieces either: were newly recruited; had been scoured by floods; or were contained below the active channel elevation, prohibiting vegetation establishment on the wood debris (the most common cause). The debris age distribution declined exponentially from 2 to 113 yrs., with a median value of 18 yrs. Similar exponential residence time distributions have been reported in other studies, but our analysis focused specifically on the ages of pool-forming wood

  18. A new asynchronous parallel algorithm for inferring large-scale gene regulatory networks.

    Directory of Open Access Journals (Sweden)

    Xiangyun Xiao

    Full Text Available The reconstruction of gene regulatory networks (GRNs from high-throughput experimental data has been considered one of the most important issues in systems biology research. With the development of high-throughput technology and the complexity of biological problems, we need to reconstruct GRNs that contain thousands of genes. However, when many existing algorithms are used to handle these large-scale problems, they will encounter two important issues: low accuracy and high computational cost. To overcome these difficulties, the main goal of this study is to design an effective parallel algorithm to infer large-scale GRNs based on high-performance parallel computing environments. In this study, we proposed a novel asynchronous parallel framework to improve the accuracy and lower the time complexity of large-scale GRN inference by combining splitting technology and ordinary differential equation (ODE-based optimization. The presented algorithm uses the sparsity and modularity of GRNs to split whole large-scale GRNs into many small-scale modular subnetworks. Through the ODE-based optimization of all subnetworks in parallel and their asynchronous communications, we can easily obtain the parameters of the whole network. To test the performance of the proposed approach, we used well-known benchmark datasets from Dialogue for Reverse Engineering Assessments and Methods challenge (DREAM, experimentally determined GRN of Escherichia coli and one published dataset that contains more than 10 thousand genes to compare the proposed approach with several popular algorithms on the same high-performance computing environments in terms of both accuracy and time complexity. The numerical results demonstrate that our parallel algorithm exhibits obvious superiority in inferring large-scale GRNs.

  19. A new asynchronous parallel algorithm for inferring large-scale gene regulatory networks.

    Science.gov (United States)

    Xiao, Xiangyun; Zhang, Wei; Zou, Xiufen

    2015-01-01

    The reconstruction of gene regulatory networks (GRNs) from high-throughput experimental data has been considered one of the most important issues in systems biology research. With the development of high-throughput technology and the complexity of biological problems, we need to reconstruct GRNs that contain thousands of genes. However, when many existing algorithms are used to handle these large-scale problems, they will encounter two important issues: low accuracy and high computational cost. To overcome these difficulties, the main goal of this study is to design an effective parallel algorithm to infer large-scale GRNs based on high-performance parallel computing environments. In this study, we proposed a novel asynchronous parallel framework to improve the accuracy and lower the time complexity of large-scale GRN inference by combining splitting technology and ordinary differential equation (ODE)-based optimization. The presented algorithm uses the sparsity and modularity of GRNs to split whole large-scale GRNs into many small-scale modular subnetworks. Through the ODE-based optimization of all subnetworks in parallel and their asynchronous communications, we can easily obtain the parameters of the whole network. To test the performance of the proposed approach, we used well-known benchmark datasets from Dialogue for Reverse Engineering Assessments and Methods challenge (DREAM), experimentally determined GRN of Escherichia coli and one published dataset that contains more than 10 thousand genes to compare the proposed approach with several popular algorithms on the same high-performance computing environments in terms of both accuracy and time complexity. The numerical results demonstrate that our parallel algorithm exhibits obvious superiority in inferring large-scale GRNs.

  20. Mixed convection and stratification phenomena in a heavy liquid metal pool

    Energy Technology Data Exchange (ETDEWEB)

    Tarantino, Mariano, E-mail: mariano.tarantino@enea.it [Italian National Agency for New Technologies, Energy and Sustainable Economic Development, C.R. ENEA Brasimone (Italy); Martelli, Daniele; Barone, Gianluca [Dipartimento di Ingegneria Civile e Industriale, University of Pisa, Largo Lucio Lazzarino, 1-56100 Pisa Italy (Italy); Di Piazza, Ivan [Italian National Agency for New Technologies, Energy and Sustainable Economic Development, C.R. ENEA Brasimone (Italy); Forgione, Nicola [Dipartimento di Ingegneria Civile e Industriale, University of Pisa, Largo Lucio Lazzarino, 1-56100 Pisa Italy (Italy)

    2015-05-15

    Highlights: • Results related to experiments reproducing PLOHS + LOF accident in CIRCE pool facility. • Vertical thermal stratification in large HLM pool. • Transition from forced to natural circulation in HLM pool under DHR conditions. • Heat transfer coefficient measurement in HLM pin bundle. • Nusselt numbers calculations and comparison with correlations. - Abstract: This work deals with an analysis of the first experimental series of tests performed to investigate mixed convection and stratification phenomena in CIRCE HLM large pool. In particular, the tests concern the transition from nominal flow to natural circulation regime, typical of decay heat removal (DHR) regime. To this purpose the CIRCE pool facility has been updated to host a suitable test section in order to reproduce the thermal-hydraulic behaviour of a HLM pool-type reactor. The test section basically consists of an electrical bundle (FPS) made up of 37 pins arranged in a hexagonal wrapped lattice with a pitch diameter ratio of 1.8. Along the FPS active length, three sections were instrumented to monitor the heat transfer coefficient along the bundle as well as the cladding temperatures at different ranks of the sub-channels. This paper reports the experimental data as well as a preliminary analysis and discussion of the results, focusing on the most relevant tests of the campaign, namely Test I (48 h) and Test II (97 h). Temperatures along three sections of the FPS and at inlet and outlet sections of the main components were reported and the Nusselt number in the FPS sub-channels was investigated together with the void fraction in the riser. Concerning the investigation of in-pool thermal stratification phenomena, the temperatures in the whole LBE pool were monitored at different elevations and radial locations. The analysis of experimental data obtained from Tests I and II underline the occurrence of thermal stratification phenomena in the region placed between the outlet sections of

  1. Benthic assemblages of rock pools in northern Portugal: seasonal and between-pool variability

    Directory of Open Access Journals (Sweden)

    Iacopo Bertocci

    2012-11-01

    Full Text Available We investigated the seasonal (winter vs summer and within season and spatial (between-pool variability of benthic assemblages of rock pools at mid-intertidal level along the shore of Viana do Castelo (North Portugal. Physical traits of rock pools, including size, depth and position along the shore, were also compared between pools. While pools did not differ for any of the examined physical traits, results indicated a clear seasonal difference in the structure of assemblages, including a total of 49 macroalgal and 13 animal taxa. This finding was driven by six taxa that are more abundant in winter (the reef-forming polychaete Sabellaria alveolata, the articulated coralline algae Corallina spp., the brown alga Bifurcaria bifurcata, the encrusting coralline alga Lithophyllum incrustans, the red alga Chondracanthus acicularis and the grazing snails Gibbula spp. and four algal taxa that are more abundant in summer (the invasive brown Sargassum muticum, the green Ulva spp., the kelp Laminaria ochroleuca and the filamentous red Ceramium spp.. These data provide a new contribution to the knowledge of rock pool systems and have potential implications for monitoring programmes aimed at assessing ecological modifications related to natural and anthropogenic disturbances and for identifying processes responsible for the variability of rock pool assemblages.

  2. Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments

    KAUST Repository

    Adel, Mustafa

    2016-09-06

    The central rift of the Red Sea has 25 brine pools with different physical and geochemical characteristics. Atlantis II (ATIID), Discovery Deeps (DD) and Chain Deep (CD) are characterized by high salinity, temperature and metal content. Several studies reported microbial communities in these brine pools, but few studies addressed the brine pool sediments. Therefore, sediment cores were collected from ATIID, DD, CD brine pools and an adjacent brine-influenced site. Sixteen different lithologic sediment sections were subjected to shotgun DNA pyrosequencing to generate 1.47 billion base pairs (1.47 × 109 bp). We generated sediment-specific reads and attempted to annotate all reads. We report the phylogenetic and biochemical uniqueness of the deepest ATIID sulfur-rich brine pool sediments. In contrary to all other sediment sections, bacteria dominate the deepest ATIID sulfur-rich brine pool sediments. This decrease in virus-to-bacteria ratio in selected sections and depth coincided with an overrepresentation of mobile genetic elements. Skewing in the composition of viruses-to-mobile genetic elements may uniquely contribute to the distinct microbial consortium in sediments in proximity to hydrothermally active vents of the Red Sea and possibly in their surroundings, through differential horizontal gene transfer.

  3. Neurogenomics and the role of a large mutational target on rapid behavioral change.

    Science.gov (United States)

    Stanley, Craig E; Kulathinal, Rob J

    2016-11-08

    Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage. However, unlike other rapidly evolving functional systems such as sperm-egg interactions and immune defense, the genetic basis of rapid behavioral change remains elusive. Here we propose that the rapid divergence and widespread novelty of innate and adaptive behavior is primarily a function of its genomic architecture. Specifically, we hypothesize that the broad diversity of behavioral phenotypes present at micro- and macroevolutionary scales is promoted by a disproportionately large mutational target of neurogenic genes. We present evidence that these large neuro-behavioral targets are significant and ubiquitous in animal genomes and suggest that behavior's novelty and rapid emergence are driven by a number of factors including more selection on a larger pool of variants, a greater role of phenotypic plasticity, and/or unique molecular features present in large genes. We briefly discuss the origins of these large neurogenic genes, as they relate to the remarkable diversity of metazoan behaviors, and highlight key consequences on both behavioral traits and neurogenic disease across, respectively, evolutionary and ontogenetic time scales. Current approaches to studying the genetic mechanisms underlying rapid phenotypic change primarily focus on identifying signatures of Darwinian selection in protein-coding regions. In contrast

  4. Targeted sequencing of established and candidate colorectal cancer genes in the Colon Cancer Family Registry Cohort.

    Science.gov (United States)

    Raskin, Leon; Guo, Yan; Du, Liping; Clendenning, Mark; Rosty, Christophe; Lindor, Noralane M; Gruber, Stephen B; Buchanan, Daniel D

    2017-11-07

    The underlying genetic cause of colorectal cancer (CRC) can be identified for 5-10% of all cases, while at least 20% of CRC cases are thought to be due to inherited genetic factors. Screening for highly penetrant mutations in genes associated with Mendelian cancer syndromes using next-generation sequencing (NGS) can be prohibitively expensive for studies requiring large samples sizes. The aim of the study was to identify rare single nucleotide variants and small indels in 40 established or candidate CRC susceptibility genes in 1,046 familial CRC cases (including both MSS and MSI-H tumor subtypes) and 1,006 unrelated controls from the Colon Cancer Family Registry Cohort using a robust and cost-effective DNA pooling NGS strategy. We identified 264 variants in 38 genes that were observed only in cases, comprising either very rare (minor allele frequency cancer susceptibility genes BAP1, CDH1, CHEK2, ENG, and MSH3 . For the candidate CRC genes, we identified likely pathogenic variants in the helicase domain of POLQ and in the LRIG1 , SH2B3 , and NOS1 genes and present their clinicopathological characteristics. Using a DNA pooling NGS strategy, we identified novel germline mutations in established CRC susceptibility genes in familial CRC cases. Further studies are required to support the role of POLQ , LRIG1 , SH2B3 and NOS1 as CRC susceptibility genes.

  5. Pooling data for the analysis of dynamic marketing systems

    NARCIS (Netherlands)

    Horvath, C.; Wieringa, J.E.

    Vector autoregressive (VAR) models have become popular in marketing literature for analyzing the behavior of competitive marketing systems. One drawback of these models is that the number of parameters can become very large, potentially leading to estimation problems. Pooling data for multiple

  6. Big city consultants shut down our pool : a shocking community pool gets checked for stray voltage

    Energy Technology Data Exchange (ETDEWEB)

    Lynch, P. [Power Line Systems Engineering Inc., Markham, ON (Canada)

    2009-12-15

    This article discussed an investigation conducted at a community pool where swimmers complained of receiving electrical shocks both in the pool and on the pool's deck area. Electrical measurements taken at the pool revealed current flows from the pool water to various points around the deck area. Measured current flow in the pool area was 30 amps even when the main pool service breaker was opened to shut off power to the entire facility. Thirty amps of primary neutral current was then measured on the primary side aerial neutral in front of the pool. A 10 amp primary feeder from the pool joined up with the complex's primary neutral wire to increase the neutral current to 40 amps. The combined 40 amps current then returned to the secondary side of a nearby utility transformer substation. The study showed that the underground wet low-resistance grounded surface area of the pool was attracting the 30 amps of utility current from the surrounding ground area. The local utility disconnected the primary and secondary neutral interconnection at the pool's main 600-volt step-down transformer. The pool deck was removed in order to install additional copper bonding grounds. In order to avert serious injuries, many experts propose that all electric utilities should be required by law to reconfigure their power systems to prevent primary power neutral currents from entering private buildings. 1 tab., 2 figs.

  7. Biomass production and energy source of thermophiles in a Japanese alkaline geothermal pool.

    Science.gov (United States)

    Kimura, Hiroyuki; Mori, Kousuke; Nashimoto, Hiroaki; Hattori, Shohei; Yamada, Keita; Koba, Keisuke; Yoshida, Naohiro; Kato, Kenji

    2010-02-01

    Microbial biomass production has been measured to investigate the contribution of planktonic bacteria to fluxations in dissolved organic matter in marine and freshwater environments, but little is known about biomass production of thermophiles inhabiting geothermal and hydrothermal regions. The biomass production of thermophiles inhabiting an 85 degrees C geothermal pool was measured by in situ cultivation using diffusion chambers. The thermophiles' growth rates ranged from 0.43 to 0.82 day(-1), similar to those of planktonic bacteria in marine and freshwater habitats. Biomass production was estimated based on cellular carbon content measured directly from the thermophiles inhabiting the geothermal pool, which ranged from 5.0 to 6.1 microg C l(-1) h(-1). This production was 2-75 times higher than that of planktonic bacteria in other habitats, because the cellular carbon content of the thermophiles was much higher. Quantitative PCR and phylogenetic analysis targeting 16S rRNA genes revealed that thermophilic H2-oxidizing bacteria closely related to Calderobacterium and Geothermobacterium were dominant in the geothermal pool. Chemical analysis showed the presence of H2 in gases bubbling from the bottom of the geothermal pool. These results strongly suggested that H2 plays an important role as a primary energy source of thermophiles in the geothermal pool.

  8. Large changes in anatomy and physiology between diploid Rangpur lime (Citrus limonia) and its autotetraploid are not associated with large changes in leaf gene expression.

    Science.gov (United States)

    Allario, Thierry; Brumos, Javier; Colmenero-Flores, Jose Manuel; Tadeo, Francisco; Froelicher, Yann; Talon, Manuel; Navarro, Luis; Ollitrault, Patrick; Morillon, Raphaël

    2011-05-01

    Very little is known about the molecular origin of the large phenotypic differentiation between genotypes arising from somatic chromosome set doubling and their diploid parents. In this study, the anatomy and physiology of diploid (2x) and autotetraploid (4x) Rangpur lime (Citrus limonia Osbeck) seedlings has been characterized. Growth of 2x was more vigorous than 4x although leaves, stems, and roots of 4x plants were thicker and contained larger cells than 2x that may have a large impact on cell-to-cell water exchanges. Leaf water content was higher in 4x than in 2x. Leaf transcriptome expression using a citrus microarray containing 21 081 genes revealed that the number of genes differentially expressed in both genotypes was less than 1% and the maximum rate of gene expression change within a 2-fold range. Six up-regulated genes in 4x were targeted to validate microarray results by real-time reverse transcription-PCR. Five of these genes were apparently involved in the response to water deficit, suggesting that, in control conditions, the genome expression of citrus autotetraploids may act in a similar way to diploids under water-deficit stress condition. The sixth up-regulated gene which codes for a histone may also play an important role in regulating the transcription of growth processes. These results show that the large phenotypic differentiation in 4x Rangpur lime compared with 2x is not associated with large changes in genome expression. This suggests that, in 4x Rangpur lime, subtle changes in gene expression may be at the origin of the phenotypic differentiation of 4x citrus when compared with 2x.

  9. Utilizing the ultrasensitive Schistosoma up-converting phosphor lateral flow circulating anodic antigen (UCP-LF CAA) assay for sample pooling-strategies.

    Science.gov (United States)

    Corstjens, Paul L A M; Hoekstra, Pytsje T; de Dood, Claudia J; van Dam, Govert J

    2017-11-01

    Methodological applications of the high sensitivity genus-specific Schistosoma CAA strip test, allowing detection of single worm active infections (ultimate sensitivity), are discussed for efficient utilization in sample pooling strategies. Besides relevant cost reduction, pooling of samples rather than individual testing can provide valuable data for large scale mapping, surveillance, and monitoring. The laboratory-based CAA strip test utilizes luminescent quantitative up-converting phosphor (UCP) reporter particles and a rapid user-friendly lateral flow (LF) assay format. The test includes a sample preparation step that permits virtually unlimited sample concentration with urine, reaching ultimate sensitivity (single worm detection) at 100% specificity. This facilitates testing large urine pools from many individuals with minimal loss of sensitivity and specificity. The test determines the average CAA level of the individuals in the pool thus indicating overall worm burden and prevalence. When requiring test results at the individual level, smaller pools need to be analysed with the pool-size based on expected prevalence or when unknown, on the average CAA level of a larger group; CAA negative pools do not require individual test results and thus reduce the number of tests. Straightforward pooling strategies indicate that at sub-population level the CAA strip test is an efficient assay for general mapping, identification of hotspots, determination of stratified infection levels, and accurate monitoring of mass drug administrations (MDA). At the individual level, the number of tests can be reduced i.e. in low endemic settings as the pool size can be increased as opposed to prevalence decrease. At the sub-population level, average CAA concentrations determined in urine pools can be an appropriate measure indicating worm burden. Pooling strategies allowing this type of large scale testing are feasible with the various CAA strip test formats and do not affect

  10. Mathematical modelling and simulation of the thermal performance of a solar heated indoor swimming pool

    Directory of Open Access Journals (Sweden)

    Mančić Marko V.

    2014-01-01

    Full Text Available Buildings with indoor swimming pools have a large energy footprint. The source of major energy loss is the swimming pool hall where air humidity is increased by evaporation from the pool water surface. This increases energy consumption for heating and ventilation of the pool hall, fresh water supply loss and heat demand for pool water heating. In this paper, a mathematical model of the swimming pool was made to assess energy demands of an indoor swimming pool building. The mathematical model of the swimming pool is used with the created multi-zone building model in TRNSYS software to determine pool hall energy demand and pool losses. Energy loss for pool water and pool hall heating and ventilation are analyzed for different target pool water and air temperatures. The simulation showed that pool water heating accounts for around 22%, whereas heating and ventilation of the pool hall for around 60% of the total pool hall heat demand. With a change of preset controller air and water temperatures in simulations, evaporation loss was in the range 46-54% of the total pool losses. A solar thermal sanitary hot water system was modelled and simulated to analyze it's potential for energy savings of the presented demand side model. The simulation showed that up to 87% of water heating demands could be met by the solar thermal system, while avoiding stagnation. [Projekat Ministarstva nauke Republike Srbije, br. III 42006: Research and development of energy and environmentally highly effective polygeneration systems based on using renewable energy sources

  11. Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

    Energy Technology Data Exchange (ETDEWEB)

    Makarova, Kira S.; Omelchenko, Marina V.; Gaidamakova, Elena K.; Matrosova, Vera Y.; Vasilenko, Alexander; Zhai, Min; Lapidus, Alla; Copeland, Alex; Kim, Edwin; Land, Miriam; Mavrommatis, Konstantinos; Pitluck, Samuel; Richardson, Paul M.; Detter, Chris; Brettin, Thomas; Saunders, Elizabeth; Lai, Barry; Ravel, Bruce; Kemner, Kenneth M.; Wolf, Yuri I.; Sorokin, Alexander; Gerasimova, Anna V.; Gelfand, Mikhail S.; Fredrickson, James K.; Koonin, Eugene V.; Daly, Michael J.

    2007-07-24

    Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at itsoptimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to

  12. Prediction of pool void fraction by new drift flux correlation

    International Nuclear Information System (INIS)

    Kataoka, I.; Ishii, M.

    1986-06-01

    A void fraction for a bubbling or boiling pool system is one of the important parameters in analyzing heat and mass transfer processes. Using the drift flux formulation, correlations for the pool void fraction have been developed in collaboration with a large number of experimental data. It has been found that the drift velocity in a pool system depends upon vessel diameter, system pressure, gas flux and fluid physical properties. The results show that the relative velocity and void fraction can be quite different from those predicted by conventional correlations. In terms of the rise velocity, four different regimes are identified. These are bubbly, churn-turbulent, slug and cap bubble regimes. The present correlations are shown to agree with the experimental data over wide ranges of parameters such as vessel diameter, system pressure, gas flux and physical properties. 39 refs., 41 figs

  13. Pool scrubbing

    International Nuclear Information System (INIS)

    Lopez-Jimenez, J.; Herranz, J.; Escudero, M.J.; Espigares, M.M.; Peyres, V.; Polo, J.; Kortz, Ch.; Koch, M.K.; Brockmeier, U.; Unger, H.; Dutton, L.M.C.; Smedley, Ch.; Trow, W.; Jones, A.V.; Bonanni, E.; Calvo, M.; Alonso, A.

    1996-12-01

    The Source Term Project in the Third Frame Work Programme of the European Union Was conducted under and important joined effort on pool scrubbing research. CIEMAT was the Task Manager of the project and several other organizations participated in it: JRC-Ispra, NNC Limited, RUB-NES and UPM. The project was divided into several tasks. A peer review of the models in the pool scrubbing codes SPARC90 and BUSCA-AUG92 was made, considering the different aspects in the hydrodynamic phenomenology, particle retention and fission product vapor abortions. Several dominant risk accident sequences were analyzed with MAAP, SPARC90 and BUSCA-AUG92 codes, and the predictions were compared. A churn-turbulent model was developed for the hydrodynamic behaviour of the pool. Finally, an experimental programme in the PECA facility of CIEMAT was conducted in order to study the decontamination factor under jet injection regime, and the experimental observations were compared with the SPARC and BUSCA codes. (Author)

  14. Simulation of Thermal Stratification in BWR Suppression Pools with One Dimensional Modeling Method

    Energy Technology Data Exchange (ETDEWEB)

    Haihua Zhao; Ling Zou; Hongbin Zhang

    2014-01-01

    The suppression pool in a boiling water reactor (BWR) plant not only is the major heat sink within the containment system, but also provides the major emergency cooling water for the reactor core. In several accident scenarios, such as a loss-of-coolant accident and extended station blackout, thermal stratification tends to form in the pool after the initial rapid venting stage. Accurately predicting the pool stratification phenomenon is important because it affects the peak containment pressure; the pool temperature distribution also affects the NPSHa (available net positive suction head) and therefore the performance of the Emergency Core Cooling System and Reactor Core Isolation Cooling System pumps that draw cooling water back to the core. Current safety analysis codes use zero dimensional (0-D) lumped parameter models to calculate the energy and mass balance in the pool; therefore, they have large uncertainties in the prediction of scenarios in which stratification and mixing are important. While three-dimensional (3-D) computational fluid dynamics (CFD) methods can be used to analyze realistic 3-D configurations, these methods normally require very fine grid resolution to resolve thin substructures such as jets and wall boundaries, resulting in a long simulation time. For mixing in stably stratified large enclosures, the BMIX++ code (Berkeley mechanistic MIXing code in C++) has been developed to implement a highly efficient analysis method for stratification where the ambient fluid volume is represented by one-dimensional (1-D) transient partial differential equations and substructures (such as free or wall jets) are modeled with 1-D integral models. This allows very large reductions in computational effort compared to multi-dimensional CFD modeling. One heat-up experiment performed at the Finland POOLEX facility, which was designed to study phenomena relevant to Nordic design BWR suppression pool including thermal stratification and mixing, is used for

  15. Pooled-DNA sequencing identifies genomic regions of selection in Nigerian isolates of Plasmodium falciparum.

    Science.gov (United States)

    Oyebola, Kolapo M; Idowu, Emmanuel T; Olukosi, Yetunde A; Awolola, Taiwo S; Amambua-Ngwa, Alfred

    2017-06-29

    The burden of falciparum malaria is especially high in sub-Saharan Africa. Differences in pressure from host immunity and antimalarial drugs lead to adaptive changes responsible for high level of genetic variations within and between the parasite populations. Population-specific genetic studies to survey for genes under positive or balancing selection resulting from drug pressure or host immunity will allow for refinement of interventions. We performed a pooled sequencing (pool-seq) of the genomes of 100 Plasmodium falciparum isolates from Nigeria. We explored allele-frequency based neutrality test (Tajima's D) and integrated haplotype score (iHS) to identify genes under selection. Fourteen shared iHS regions that had at least 2 SNPs with a score > 2.5 were identified. These regions code for genes that were likely to have been under strong directional selection. Two of these genes were the chloroquine resistance transporter (CRT) on chromosome 7 and the multidrug resistance 1 (MDR1) on chromosome 5. There was a weak signature of selection in the dihydrofolate reductase (DHFR) gene on chromosome 4 and MDR5 genes on chromosome 13, with only 2 and 3 SNPs respectively identified within the iHS window. We observed strong selection pressure attributable to continued chloroquine and sulfadoxine-pyrimethamine use despite their official proscription for the treatment of uncomplicated malaria. There was also a major selective sweep on chromosome 6 which had 32 SNPs within the shared iHS region. Tajima's D of circumsporozoite protein (CSP), erythrocyte-binding antigen (EBA-175), merozoite surface proteins - MSP3 and MSP7, merozoite surface protein duffy binding-like (MSPDBL2) and serine repeat antigen (SERA-5) were 1.38, 1.29, 0.73, 0.84 and 0.21, respectively. We have demonstrated the use of pool-seq to understand genomic patterns of selection and variability in P. falciparum from Nigeria, which bears the highest burden of infections. This investigation identified known

  16. Suppression of the E. coli SOS response by dNTP pool changes.

    Science.gov (United States)

    Maslowska, Katarzyna H; Makiela-Dzbenska, Karolina; Fijalkowska, Iwona J; Schaaper, Roel M

    2015-04-30

    The Escherichia coli SOS system is a well-established model for the cellular response to DNA damage. Control of SOS depends largely on the RecA protein. When RecA is activated by single-stranded DNA in the presence of a nucleotide triphosphate cofactor, it mediates cleavage of the LexA repressor, leading to expression of the 30(+)-member SOS regulon. RecA activation generally requires the introduction of DNA damage. However, certain recA mutants, like recA730, bypass this requirement and display constitutive SOS expression as well as a spontaneous (SOS) mutator effect. Presently, we investigated the possible interaction between SOS and the cellular deoxynucleoside triphosphate (dNTP) pools. We found that dNTP pool changes caused by deficiencies in the ndk or dcd genes, encoding nucleoside diphosphate kinase and dCTP deaminase, respectively, had a strongly suppressive effect on constitutive SOS expression in recA730 strains. The suppression of the recA730 mutator effect was alleviated in a lexA-deficient background. Overall, the findings suggest a model in which the dNTP alterations in the ndk and dcd strains interfere with the activation of RecA, thereby preventing LexA cleavage and SOS induction. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  17. One-Dimensional Analysis of Thermal Stratification in AHTR and SFR Coolant Pools

    International Nuclear Information System (INIS)

    Haihua Zhao; Per F. Peterson

    2007-01-01

    Thermal stratification phenomena are very common in pool type reactor systems, such as the liquid-salt cooled Advanced High Temperature Reactor (AHTR) and liquid-metal cooled fast reactor systems such as the Sodium Fast Reactor (SFR). It is important to accurately predict the temperature and density distributions both for design optimation and accident analysis. Current major reactor system analysis codes such as RELAP5 (for LWR's, and recently extended to analyze high temperature reactors), TRAC (for LWR's), and SASSYS (for liquid metal fast reactors) only provide lumped-volume based models which can only give very approximate results and can only handle simple cases with one mixing source. While 2-D or 3-D CFD methods can be used to analyze simple configurations, these methods require very fine grid resolution to resolve thin substructures such as jets and wall boundaries, yet such fine grid resolution is difficult or impossible to provide for studying the reactor response to transients due to computational expense. Therefore, new methods are needed to support design optimization and safety analysis of Generation IV pool type reactor systems. Previous scaling has shown that stratified mixing processes in large stably stratified enclosures can be described using one-dimensional differential equations, with the vertical transport by free and wall jets modeled using standard integral techniques. This allows very large reductions in computational effort compared to three-dimensional numerical modeling of turbulent mixing in large enclosures. The BMIX++ (Berkeley mechanistic MIXing code in C++) code was originally developed at UC Berkeley to implement such ideas. This code solves mixing and heat transfer problems in stably stratified enclosures. The code uses a Lagrangian approach to solve 1-D transient governing equations for the ambient fluid and uses analytical or 1-D integral models to compute substructures. By including liquid salt properties, BMIX++ code is

  18. Experimental investigation on the weld pool formation process in plasma keyhole arc welding

    Science.gov (United States)

    Van Anh, Nguyen; Tashiro, Shinichi; Van Hanh, Bui; Tanaka, Manabu

    2018-01-01

    This paper seeks to clarify the weld pool formation process in plasma keyhole arc welding (PKAW). We adopted, for the first time, the measurement of the 3D convection inside the weld pool in PKAW by stereo synchronous imaging of tungsten tracer particles using two sets of x-ray transmission systems. The 2D convection on the weld pool surface was also measured using zirconia tracer particles. Through these measurements, the convection in a wide range of weld pools from the vicinity of the keyhole to the rear region was successfully visualized. In order to discuss the heat transport process in a weld pool, the 2D temperature distribution on the weld pool surface was also measured by two-color pyrometry. The results of the comprehensive experimental measurement indicate that the shear force due to plasma flow is found to be the dominant driving force in the weld pool formation process in PKAW. Thus, heat transport in a weld pool is considered to be governed by two large convective patterns near the keyhole: (1) eddy pairs on the surface (perpendicular to the torch axis), and (2) eddy pairs on the bulk of the weld pool (on the plane of the torch). They are formed with an equal velocity of approximately 0.35 m s-1 and are mainly driven by shear force. Furthermore, the flow velocity of the weld pool convection becomes considerably higher than that of other welding processes, such as TIG welding and GMA welding, due to larger plasma flow velocity.

  19. Design of hydrotherapy exercise pools.

    Science.gov (United States)

    Edlich, R F; Abidin, M R; Becker, D G; Pavlovich, L J; Dang, M T

    1988-01-01

    Several hydrotherapy pools have been designed specifically for a variety of aquatic exercise. Aqua-Ark positions the exerciser in the center of the pool for deep-water exercise. Aqua-Trex is a shallow underwater treadmill system for water walking or jogging. Swim-Ex generates an adjustable laminar flow that permits swimming without turning. Musculoskeletal conditioning can be accomplished in the above-ground Arjo shallow-water exercise pool. A hydrotherapy pool also can be custom designed for musculoskeletal conditioning in its shallow part and cardiovascular conditioning in a deeper portion of the pool. Regardless of the type of exercise, there is general agreement that the specific exercise conducted in water requires significantly more energy expenditure than when the same exercise is performed on land.

  20. Large-scale gene-centric analysis identifies novel variants for coronary artery disease

    NARCIS (Netherlands)

    Butterworth, A.S.; Braund, P.S.; Hardwick, R.J.; Saleheen, D.; Peden, J.F.; Soranzo, N.; Chambers, J.C.; Kleber, M.E.; Keating, B.; Qasim, A.; Klopp, N.; Erdmann, J.; Basart, H.; Baumert, J.H.; Bezzina, C.R.; Boehm, B.O.; Brocheton, J.; Bugert, P.; Cambien, F.; Collins, R.; Couper, D.; Jong, J.S. de; Diemert, P.; Ejebe, K.; Elbers, C.C.; Elliott, P.; Fornage, M.; Frossard, P.; Garner, S.; Hunt, S.E.; Kastelein, J.J.; Klungel, O.H.; Kluter, H.; Koch, K.; Konig, I.R.; Kooner, A.S.; Liu, K.; McPherson, R.; Musameh, M.D.; Musani, S.; Papanicolaou, G.; Peters, A.; Peters, B.J.; Potter, S.; Psaty, B.M.; Rasheed, A.; Scott, J.; Seedorf, U.; Sehmi, J.S.; Sotoodehnia, N.; Stark, K.; Stephens, J.; Schoot, C.E. van der; Schouw, Y.T. van der; Harst, P. van der; Vasan, R.S.; Wilde, A.A.; Willenborg, C.; Winkelmann, B.R.; Zaidi, M.; Zhang, W.; Ziegler, A.; Koenig, W.; Matz, W.; Trip, M.D.; Reilly, M.P.; Kathiresan, S.; Schunkert, H.; Hamsten, A.; Hall, A.S.; Kooner, J.S.; Thompson, S.G.; Thompson, J.R.; Watkins, H.; Danesh, J.; Barnes, T.; Rafelt, S.; Codd, V.; Bruinsma, N.; Dekker, L.R.; Henriques, J.P.; Koch, K.T.; Winter, R.J. de; Alings, M.; Allaart, C.F.; Gorgels, A.P.; Verheugt, F.W.A.; Mueller, M.; Meisinger, C.; DerOhannessian, S.; Mehta, N.N.; Ferguson, J.; Hakonarson, H.; Matthai, W.; Wilensky, R.; Hopewell, J.C.; Parish, S.; Linksted, P.; Notman, J.; Gonzalez, H.; Young, A.; Ostley, T.; Munday, A.; Goodwin, N.; Verdon, V.; Shah, S.; Edwards, C.; Mathews, C.; Gunter, R.; Benham, J.; Davies, C.; Cobb, M.; Cobb, L.; Crowther, J.; Richards, A.; Silver, M.; Tochlin, S.; Mozley, S.; Clark, S.; Radley, M.; Kourellias, K.; Olsson, P.; Barlera, S.; Tognoni, G.; Rust, S.; Assmann, G.; Heath, S.; Zelenika, D.; Gut, I.; Green, F.; Farrall, M.; Goel, A.; Ongen, H.; Franzosi, M.G.; Lathrop, M.; Clarke, R.; Aly, A.; Anner, K.; Bjorklund, K.; Blomgren, G.; Cederschiold, B.; Danell-Toverud, K.; Eriksson, P.; Grundstedt, U.; Heinonen, M.; Hellenius, M.L.; Hooft, F. van 't; Husman, K.; Lagercrantz, J.; Larsson, A.; Larsson, M.; Mossfeldt, M.; Malarstig, A.; Olsson, G.; Sabater-Lleal, M.; Sennblad, B.; Silveira, A.; Strawbridge, R.; Soderholm, B.; Ohrvik, J.; Zaman, K.S.; Mallick, N.H.; Azhar, M.; Samad, A.; Ishaq, M.; Shah, N.; Samuel, M.; Kathiresan, S.C.; Assimes, T.L.; Holm, H.; Preuss, M.; Stewart, A.F.; Barbalic, M.; Gieger, C.; Absher, D.; Aherrahrou, Z.; Allayee, H.; Altshuler, D.; Anand, S.; Andersen, K.; Anderson, J.L.; Ardissino, D.; Ball, S.G.; Balmforth, A.J.; Barnes, T.A.; Becker, L.C.; Becker, D.M.; Berger, K.; Bis, J.C.; Boekholdt, S.M.; Boerwinkle, E.; Brown, M.J.; Burnett, M.S.; Buysschaert, I.; Carlquist, J.F.; Chen, L.; Davies, R.W.; Dedoussis, G.; Dehghan, A.; Demissie, S.; Devaney, J.; Do, R.; Doering, A.; El Mokhtari, N.E.; Ellis, S.G.; Elosua, R.; Engert, J.C.; Epstein, S.; Faire, U. de; Fischer, M.; Folsom, A.R.; Freyer, J.; Gigante, B.; Girelli, D.; Gretarsdottir, S.; Gudnason, V.; Gulcher, J.R.; Tennstedt, S.; Halperin, E.; Hammond, N.; Hazen, S.L.; Hofman, A.; Horne, B.D.; Illig, T.; Iribarren, C.; Jones, G.T.; Jukema, J.W.; Kaiser, M.A.; Kaplan, L.M.; Khaw, K.T.; Knowles, J.W.; Kolovou, G.; Kong, A.; Laaksonen, R.; Lambrechts, D.; Leander, K.; Li, M.; Lieb, W.; Lettre, G.; Loley, C.; Lotery, A.J.; Mannucci, P.M.; Martinelli, N.; McKeown, P.P.; Meitinger, T.; Melander, O.; Merlini, P.A.; Mooser, V.; Morgan, T.; Muhleisen T.W., .; Muhlestein, J.B.; Musunuru, K.; Nahrstaedt, J.; Nothen, Markus; Olivieri, O.; Peyvandi, F.; Patel, R.S.; Patterson, C.C.; Qu, L.; Quyyumi, A.A.; Rader, D.J.; Rallidis, L.S.; Rice, C.; Roosendaal, F.R.; Rubin, D.; Salomaa, V.; Sampietro, M.L.; Sandhu, M.S.; Schadt, E.; Schafer, A.; Schillert, A.; Schreiber, S.; Schrezenmeir, J.; Schwartz, S.M.; Siscovick, D.S.; Sivananthan, M.; Sivapalaratnam, S.; Smith, A.V.; Smith, T.B.; Snoep, J.D.; Spertus, J.A.; Stefansson, K.; Stirrups, K.; Stoll, M.; Tang, W.H.; Thorgeirsson, G.; Thorleifsson, G.; Tomaszewski, M.; Uitterlinden, A.G.; Rij, A.M. van; Voight, B.F.; Wareham, N.J.; AWells, G.; Wichmann, H.E.; Witteman, J.C.; Wright, B.J.; Ye, S.; Cupples, L.A.; Quertermous, T.; Marz, W.; Blankenberg, S.; Thorsteinsdottir, U.; Roberts, R.; O'Donnell, C.J.; Onland-Moret, N.C.; Setten, J. van; Bakker, P.I. de; Verschuren, W.M.; Boer, J.M.; Wijmenga, C.; Hofker, M.H.; Maitland-van der Zee, A.H.; Boer, A. de; Grobbee, D.E.; Attwood, T.; Belz, S.; Cooper, J.; Crisp-Hihn, A.; Deloukas, P.; Foad, N.; Goodall, A.H.; Gracey, J.; Gray, E.; Gwilliams, R.; Heimerl, S.; Hengstenberg, C.; Jolley, J.; Krishnan, U.; Lloyd-Jones, H.; Lugauer, I.; Lundmark, P.; Maouche, S.; Moore, J.S.; Muir, D.; Murray, E.; Nelson, C.P.; Neudert, J.; Niblett, D.; O'Leary, K.; Ouwehand, W.H.; Pollard, H.; Rankin, A.; Rice, C.M.; Sager, H.; Samani, N.J.; Sambrook, J.; Schmitz, G.; Scholz, M.; Schroeder, L.; Syvannen, A.C.; Wallace, C.

    2011-01-01

    Coronary artery disease (CAD) has a significant genetic contribution that is incompletely characterized. To complement genome-wide association (GWA) studies, we conducted a large and systematic candidate gene study of CAD susceptibility, including analysis of many uncommon and functional variants.

  1. Swimming pool cleaner poisoning

    Science.gov (United States)

    Swimming pool cleaner poisoning occurs when someone swallows this type of cleaner, touches it, or breathes in ... The harmful substances in swimming pool cleaner are: Bromine ... copper Chlorine Soda ash Sodium bicarbonate Various mild acids

  2. Efficient pooling designs for library screening

    OpenAIRE

    Bruno, William J.; Knill, Emanuel; Balding, David J.; Bruce, D. C.; Doggett, N. A.; Sawhill, W. W.; Stallings, R. L.; Whittaker, Craig C.; Torney, David C.

    1994-01-01

    We describe efficient methods for screening clone libraries, based on pooling schemes which we call ``random $k$-sets designs''. In these designs, the pools in which any clone occurs are equally likely to be any possible selection of $k$ from the $v$ pools. The values of $k$ and $v$ can be chosen to optimize desirable properties. Random $k$-sets designs have substantial advantages over alternative pooling schemes: they are efficient, flexible, easy to specify, require fewer pools, and have er...

  3. GECKO: a complete large-scale gene expression analysis platform

    Directory of Open Access Journals (Sweden)

    Heuer Michael

    2004-12-01

    Full Text Available Abstract Background Gecko (Gene Expression: Computation and Knowledge Organization is a complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. Results Based on a client-server architecture, with a centralized repository of typically many tens of thousands of Affymetrix scans, Gecko includes automatic processing pipelines for uploading data from remote sites, a data base, a computational engine implementing ~ 50 different analysis tools, and a client application. Among available analysis tools are clustering methods, principal component analysis, supervised classification including feature selection and cross-validation, multi-factorial ANOVA, statistical contrast calculations, and various post-processing tools for extracting data at given error rates or significance levels. On account of its open architecture, Gecko also allows for the integration of new algorithms. The Gecko framework is very general: non-Affymetrix and non-gene expression data can be analyzed as well. A unique feature of the Gecko architecture is the concept of the Analysis Tree (actually, a directed acyclic graph, in which all successive results in ongoing analyses are saved. This approach has proven invaluable in allowing a large (~ 100 users and distributed community to share results, and to repeatedly return over a span of years to older and potentially very complex analyses of gene expression data. Conclusions The Gecko system is being made publicly available as free software http://sourceforge.net/projects/geckoe. In totality or in parts, the Gecko framework should prove useful to users and system developers with a broad range of analysis needs.

  4. 21 CFR 1250.89 - Swimming pools.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Swimming pools. 1250.89 Section 1250.89 Food and... SANITATION Sanitation Facilities and Conditions on Vessels § 1250.89 Swimming pools. (a) Fill and draw swimming pools shall not be installed or used. (b) Swimming pools of the recirculation type shall be...

  5. Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

    Science.gov (United States)

    Feuermann, Marc; Gaudet, Pascale; Mi, Huaiyu; Lewis, Suzanna E; Thomas, Paul D

    2016-01-01

    We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This 'GO Phylogenetic Annotation' approach integrates GO annotations from evolutionarily related genes across ∼100 different organisms in the context of a gene family tree, in which curators build an explicit model of the evolution of gene functions. GO Phylogenetic Annotation models the gain and loss of functions in a gene family tree, which is used to infer the functions of uncharacterized (or incompletely characterized) gene products, even for human proteins that are relatively well studied. Here, we report our results from applying this paradigm to two well-characterized cellular processes, apoptosis and autophagy. This revealed several important observations with respect to GO annotations and how they can be used for function inference. Notably, we applied only a small fraction of the experimentally supported GO annotations to infer function in other family members. The majority of other annotations describe indirect effects, phenotypes or results from high throughput experiments. In addition, we show here how feedback from phylogenetic annotation leads to significant improvements in the PANTHER trees, the GO annotations and GO itself. Thus GO phylogenetic annotation both increases the quantity and improves the accuracy of the GO annotations provided to the research community. We expect these phylogenetically based annotations to be of broad use in gene enrichment analysis as well as other applications of GO annotations.Database URL: http://amigo.geneontology.org/amigo. © The Author(s) 2016. Published by Oxford University Press.

  6. Parallelizing Gene Expression Programming Algorithm in Enabling Large-Scale Classification

    Directory of Open Access Journals (Sweden)

    Lixiong Xu

    2017-01-01

    Full Text Available As one of the most effective function mining algorithms, Gene Expression Programming (GEP algorithm has been widely used in classification, pattern recognition, prediction, and other research fields. Based on the self-evolution, GEP is able to mine an optimal function for dealing with further complicated tasks. However, in big data researches, GEP encounters low efficiency issue due to its long time mining processes. To improve the efficiency of GEP in big data researches especially for processing large-scale classification tasks, this paper presents a parallelized GEP algorithm using MapReduce computing model. The experimental results show that the presented algorithm is scalable and efficient for processing large-scale classification tasks.

  7. Topography Battles Surface Texture: An Experimental Study of Pool-riffle Formation

    Science.gov (United States)

    Chartrand, S. M.; Hassan, M. A.; Jellinek, M.

    2016-12-01

    Pool-riffles are perhaps the most common streambed shape found in streams and rivers, and not surprisingly, they are essential to salmon ecology, and are a central focus of many restoration actions. Yet, when an applied earth scientist or engineer is faced with developing a pool-riffle design, there is a lack of clear and rigorously developed design guidelines. Given the volumes of money spent annually within the restoration industry, this is a real problem. Recognition of this problem is growing, however, and an increasing level of attention has been directed to questions of pool-riffle formation in the past decade. At this point and given certain landscape characteristics, it is well established that streamwise gradients in channel width are associated with pool-riffles. Specifically, pools are associated with negative gradients in width, and riffles with positive gradients. Importantly, these associations have now been documented from field-derived data, as well as via experimental and numerical investigations. There is much to build from the present knowledge base, and central to this are questions related to (a) how pool-riffles evolve during the formative process, (b) what are the basic set of ingredients necessary for pool-riffle formation within systems characterized by relatively non-erodible channel margins, and (c) do pool-riffles persist, once formed, under a broad range of forcing conditions? We have completed four physical experiments examining the process and evolution of pool-riffle formation under a large range of upstream boundary, as well as physical channel conditions. We will report on two of the completed experiments. Our work will highlight two new non-dimensional channel evolution numbers, derived to help describe and characterize bedform development, as well as response to perturbations from near-equilibrium conditions. The channel evolution numbers lay the foundation for development of a new regime diagram, which quantifies the basic

  8. Comparing large covariance matrices under weak conditions on the dependence structure and its application to gene clustering.

    Science.gov (United States)

    Chang, Jinyuan; Zhou, Wen; Zhou, Wen-Xin; Wang, Lan

    2017-03-01

    Comparing large covariance matrices has important applications in modern genomics, where scientists are often interested in understanding whether relationships (e.g., dependencies or co-regulations) among a large number of genes vary between different biological states. We propose a computationally fast procedure for testing the equality of two large covariance matrices when the dimensions of the covariance matrices are much larger than the sample sizes. A distinguishing feature of the new procedure is that it imposes no structural assumptions on the unknown covariance matrices. Hence, the test is robust with respect to various complex dependence structures that frequently arise in genomics. We prove that the proposed procedure is asymptotically valid under weak moment conditions. As an interesting application, we derive a new gene clustering algorithm which shares the same nice property of avoiding restrictive structural assumptions for high-dimensional genomics data. Using an asthma gene expression dataset, we illustrate how the new test helps compare the covariance matrices of the genes across different gene sets/pathways between the disease group and the control group, and how the gene clustering algorithm provides new insights on the way gene clustering patterns differ between the two groups. The proposed methods have been implemented in an R-package HDtest and are available on CRAN. © 2016, The International Biometric Society.

  9. Applications of pooled DNA samples to the assessment of population affinities: short tandem repeats.

    Science.gov (United States)

    Crawford, M H; Banerjee, P; Demarchi, D A; Zlojutro, M; McComb, J; Livshits, G; Henneberg, M; Mosher, M J; Schanfield, M S; Knowles, J A

    2005-12-01

    Pooled DNA samples have been used in association studies of Mendelian disease genes. This method involves combining equal quantities of DNA from patients and control subjects into separate pools and comparing the pools for distributions of genetic markers. In this study identical quantities of DNA from 300 individuals representing 6 populations were pooled and amplified for 296 loci using the touchdown polymerase chain reaction (PCR) method. The purpose of this study is to test the efficacy of pooled DNA markers in the reconstruction of the genetic structure of human populations. The populations sampled included Chuvash, Buryats, Kizhi, Native Americans, South Africans, and New York City whites. To test the accuracy of the allele-frequency distributions, we genotyped the Buryats and New York samples individually for six microsatellite markers and compared their frequencies to the allele frequencies derived from the electropherogram peak heights for the pooled DNA, producing a correlation of 0.9811 with a variance of less than 0.04. Two-dimensional scaling of genetic distances among the six populations produced clusters that reflected known historical relationships. A distance matrix was created using all 296 loci, and matrices based on individual chromosomes were correlated against the total matrix. As expected, the largest chromosomes had the highest correlations with the total matrix, whereas one of the smallest chromosomes, chromosome 22, had the lowest correlation and differed most from the combined STR distance matrix.

  10. Evolutionary conservation of essential and highly expressed genes in Pseudomonas aeruginosa

    Directory of Open Access Journals (Sweden)

    Scharfe Maren

    2010-04-01

    Full Text Available Abstract Background The constant increase in development and spread of bacterial resistance to antibiotics poses a serious threat to human health. New sequencing technologies are now on the horizon that will yield massive increases in our capacity for DNA sequencing and will revolutionize the drug discovery process. Since essential genes are promising novel antibiotic targets, the prediction of gene essentiality based on genomic information has become a major focus. Results In this study we demonstrate that pooled sequencing is applicable for the analysis of sequence variations of strain collections with more than 10 individual isolates. Pooled sequencing of 36 clinical Pseudomonas aeruginosa isolates revealed that essential and highly expressed proteins evolve at lower rates, whereas extracellular proteins evolve at higher rates. We furthermore refined the list of experimentally essential P. aeruginosa genes, and identified 980 genes that show no sequence variation at all. Among the conserved nonessential genes we found several that are involved in regulation, motility and virulence, indicating that they represent factors of evolutionary importance for the lifestyle of a successful environmental bacterium and opportunistic pathogen. Conclusion The detailed analysis of a comprehensive set of P. aeruginosa genomes in this study clearly disclosed detailed information of the genomic makeup and revealed a large set of highly conserved genes that play an important role for the lifestyle of this microorganism. Sequencing strain collections enables for a detailed and extensive identification of sequence variations as potential bacterial adaptation processes, e.g., during the development of antibiotic resistance in the clinical setting and thus may be the basis to uncover putative targets for novel treatment strategies.

  11. Modal analysis of pool door in water tank

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kang Soo; Jeong, Kyeong Hoon; Park, Chan Gook; Koo, In Soo [KAERI, Daejeon (Korea, Republic of)

    2012-10-15

    A pool door is installed at the chase of the pool gate by means of an overhead crane in the building of a research reactor. The principal function of the pool door, which is located between the reactor pool and service pool, is to separate the reactor pool from the service pool for the maintenance and/or the removal of the equipment either in the reactor pool or service pool. The pool door consists of stainless steel plates supported by structural steel frames and sealing components. The pool door is equipped with double inflatable gaskets. The configuration of the pool door is shown in Figure 1. The FEM analysis and theoretical calculation by the formula were performed to evaluate the natural frequency for the pool door in the water. The results from the two methods were compared.

  12. Characterisation of silent and active genes for a variable large protein of Borrelia recurrentis

    Directory of Open Access Journals (Sweden)

    Scragg Ian G

    2002-10-01

    Full Text Available Abstract Background We report the characterisation of the variable large protein (vlp gene expressed by clinical isolate A1 of Borrelia recurrentis; the agent of the life-threatening disease louse-borne relapsing fever. Methods The major vlp protein of this isolate was characterised and a DNA probe created. Use of this together with standard molecular methods was used to determine the location of the vlp1B. recurrentis A1 gene in both this and other isolates. Results This isolate was found to carry silent and expressed copies of the vlp1B. recurrentis A1 gene on plasmids of 54 kbp and 24 kbp respectively, whereas a different isolate, A17, had only the silent vlp1B. recurrentis A17 on a 54 kbp plasmid. Silent and expressed vlp1 have identical mature protein coding regions but have different 5' regions, both containing different potential lipoprotein leader sequences. Only one form of vlp1 is transcribed in the A1 isolate of B. recurrentis, yet both 5' upstream sequences of this vlp1 gene possess features of bacterial promoters. Conclusion Taken together these results suggest that antigenic variation in B. recurrentis may result from recombination of variable large and small protein genes at the junction between lipoprotein leader sequence and mature protein coding region. However, this hypothetical model needs to be validated by further identification of expressed and silent variant protein genes in other B. recurrentis isolates.

  13. An experimental study on sodium-water reaction in the double pool LMFBR, (4)

    International Nuclear Information System (INIS)

    Kumagai, Hiromichi; Yoshida, Kazuo; Uotani, Masaki; Akimoto, Tokuzo

    1989-01-01

    Double Pool type LMFBR set the rectangular cross-sectional steam generator (SGs) inside a secondary vessel. The initial spike pressure rise caused by large sodium-water reaction in SGs might be radiated into a large sodium pool in the secondary vessel. Therefore basic experiments on pressure wave propagation were carried out by generating pressure wave in water by mean of a set of drop hummer and piston. But the experimental apparatus in water was not convenience to simulate the structure near the bottom end of the SGs shell. In this reports, experiments were carried out by generating pulse sound pressure in air, and compared with the results pressure waves in water. (author)

  14. Hygiene trap in swimming pools? Planning decisions with consequences; Hygienefalle Wasseraufbereitung in Schwimmbaedern. Planungsentscheidungen mit Folgen

    Energy Technology Data Exchange (ETDEWEB)

    Schellhorn, Martin [SHK-Presseagentur Kommunikations-Management Schellhorn GmbH, Haltern am See (Germany)

    2008-03-15

    Planning decisions often can be influenced by a domino effect. A causality pulls the other causality up until clear problems for example in a technical operational sequence are developed. A typical example for this is a water treatment plant in swimming pools. Finally, here it is decided how well the bather feels, how much bathers use the swimming pool and how large the economic success is. Just in the water purification and filtering of swimming pools the market shows a strongly differentiated picture.

  15. Transcriptome sequencing of two phenotypic mosaic Eucalyptus trees reveals large scale transcriptome re-modelling.

    Directory of Open Access Journals (Sweden)

    Amanda Padovan

    Full Text Available Phenotypic mosaic trees offer an ideal system for studying differential gene expression. We have investigated two mosaic eucalypt trees from two closely related species (Eucalyptus melliodora and E. sideroxylon, which each support two types of leaves: one part of the canopy is resistant to insect herbivory and the remaining leaves are susceptible. Driving this ecological distinction are differences in plant secondary metabolites. We used these phenotypic mosaics to investigate genome wide patterns of foliar gene expression with the aim of identifying patterns of differential gene expression and the somatic mutation(s that lead to this phenotypic mosaicism. We sequenced the mRNA pool from leaves of the resistant and susceptible ecotypes from both mosaic eucalypts using the Illumina HiSeq 2000 platform. We found large differences in pathway regulation and gene expression between the ecotypes of each mosaic. The expression of the genes in the MVA and MEP pathways is reflected by variation in leaf chemistry, however this is not the case for the terpene synthases. Apart from the terpene biosynthetic pathway, there are several other metabolic pathways that are differentially regulated between the two ecotypes, suggesting there is much more phenotypic diversity than has been described. Despite the close relationship between the two species, they show large differences in the global patterns of gene and pathway regulation.

  16. Screening and ranking Alberta oil pools for CO{sub 2} flooding and sequestration

    Energy Technology Data Exchange (ETDEWEB)

    Shaw, J.C. [Adams Pearson Associates Inc., Calgary, AB (Canada); Bachu, S. [Alberta Energy and Utilities Board, Calgary, AB (Canada)

    2001-06-01

    This paper presented the results of a technical screening program using Excel VBA to successfully screen and rank a very large number of oil pools for enhanced oil recovery using carbon dioxide (CO{sub 2}) flooding. A total of 6 ranking parameters were used, including API gravity of oil, residual oil saturation, ratio between reservoir pressure and minimum miscibility pressure, reservoir temperature, net pay thickness and porosity. The screening program provided a technical ranking of approximately 8,800 Alberta pools in less than 2 minutes. After compilation of the Alberta oil pools, it was determined that most of the deep carbonate oil pools are excellent candidates for CO{sub 2} miscible flooding. Other Devonian carbonate pools were also ranked as having high potential for the process. An environmental benefit of CO{sub 2} miscible flooding process is that carbon sequestration has the potential to reduce anthropogenic carbon dioxide emissions from reaching the atmosphere. Ongoing studies are currently addressing CO{sub 2} capture and transportation, making EOR technology viable for maintaining light oil production in western Canada. 11 refs., 7 tabs., 1 fig.

  17. Numerical modeling of sodium fire – Part II: Pool combustion and combined spray and pool combustion

    International Nuclear Information System (INIS)

    Sathiah, Pratap; Roelofs, Ferry

    2014-01-01

    Highlights: • A CFD based method is proposed for the simulation of sodium pool combustion. • A sodium evaporation based model is proposed to model sodium pool evaporation. • The proposed method is validated against sodium pool experiments of Newman and Payne. • The results obtained using the proposed method are in good agreement with the experiments. - Abstract: The risk of sodium-air reaction has received considerable attention after the sodium-fire accident in Monju reactor. The fires resulting from the sodium-air reaction can be detrimental to the safety of a sodium fast reactor. Therefore, predicting the consequences of a sodium fire is important from a safety point of view. A computational method based on CFD is proposed here to simulate sodium pool fire and understand its characteristics. The method solves the Favre-averaged Navier-Stokes equation and uses a non-premixed mixture fraction based combustion model. The mass transfer of sodium vapor from the pool surface to the flame is obtained using a sodium evaporation model. The proposed method is then validated against well-known sodium pool experiments of Newman and Payne. The flame temperature and location predicted by the model are in good agreement with experiments. Furthermore, the trends of the mean burning rate with initial pool temperature and oxygen concentration are captured well. Additionally, parametric studies have been performed to understand the effects of pool diameter and initial air temperature on the mean burning rate. Furthermore, the sodium spray and sodium pool combustion models are combined to simulate simultaneous spray and pool combustion. Simulations were performed to demonstrate that the combined code could be applied to simulate this. Once sufficiently validated, the present code can be used for safety evaluation of a sodium fast reactor

  18. Numerical modeling of sodium fire – Part II: Pool combustion and combined spray and pool combustion

    Energy Technology Data Exchange (ETDEWEB)

    Sathiah, Pratap, E-mail: pratap.sathiah78@gmail.com [Shell Global Solutions Ltd., Brabazon House, Concord Business Park, Threapwood Road, Manchester M220RR (United Kingdom); Roelofs, Ferry, E-mail: roelofs@nrg.eu [Nuclear Research and Consultancy Group (NRG), Westerduinweg 3, 1755ZG Petten (Netherlands)

    2014-10-15

    Highlights: • A CFD based method is proposed for the simulation of sodium pool combustion. • A sodium evaporation based model is proposed to model sodium pool evaporation. • The proposed method is validated against sodium pool experiments of Newman and Payne. • The results obtained using the proposed method are in good agreement with the experiments. - Abstract: The risk of sodium-air reaction has received considerable attention after the sodium-fire accident in Monju reactor. The fires resulting from the sodium-air reaction can be detrimental to the safety of a sodium fast reactor. Therefore, predicting the consequences of a sodium fire is important from a safety point of view. A computational method based on CFD is proposed here to simulate sodium pool fire and understand its characteristics. The method solves the Favre-averaged Navier-Stokes equation and uses a non-premixed mixture fraction based combustion model. The mass transfer of sodium vapor from the pool surface to the flame is obtained using a sodium evaporation model. The proposed method is then validated against well-known sodium pool experiments of Newman and Payne. The flame temperature and location predicted by the model are in good agreement with experiments. Furthermore, the trends of the mean burning rate with initial pool temperature and oxygen concentration are captured well. Additionally, parametric studies have been performed to understand the effects of pool diameter and initial air temperature on the mean burning rate. Furthermore, the sodium spray and sodium pool combustion models are combined to simulate simultaneous spray and pool combustion. Simulations were performed to demonstrate that the combined code could be applied to simulate this. Once sufficiently validated, the present code can be used for safety evaluation of a sodium fast reactor.

  19. 10 CFR 36.63 - Pool water purity.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Pool water purity. 36.63 Section 36.63 Energy NUCLEAR... § 36.63 Pool water purity. (a) Pool water purification system must be run sufficiently to maintain the conductivity of the pool water below 20 microsiemens per centimeter under normal circumstances. If pool water...

  20. Large-scale image-based profiling of single-cell phenotypes in arrayed CRISPR-Cas9 gene perturbation screens.

    Science.gov (United States)

    de Groot, Reinoud; Lüthi, Joel; Lindsay, Helen; Holtackers, René; Pelkmans, Lucas

    2018-01-23

    High-content imaging using automated microscopy and computer vision allows multivariate profiling of single-cell phenotypes. Here, we present methods for the application of the CISPR-Cas9 system in large-scale, image-based, gene perturbation experiments. We show that CRISPR-Cas9-mediated gene perturbation can be achieved in human tissue culture cells in a timeframe that is compatible with image-based phenotyping. We developed a pipeline to construct a large-scale arrayed library of 2,281 sequence-verified CRISPR-Cas9 targeting plasmids and profiled this library for genes affecting cellular morphology and the subcellular localization of components of the nuclear pore complex (NPC). We conceived a machine-learning method that harnesses genetic heterogeneity to score gene perturbations and identify phenotypically perturbed cells for in-depth characterization of gene perturbation effects. This approach enables genome-scale image-based multivariate gene perturbation profiling using CRISPR-Cas9. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

  1. Identification of gene pools used in restoration and conservation by chloroplast microsatellite markers in Iberian pine species

    Directory of Open Access Journals (Sweden)

    Enrique Hernández-Tecles

    2017-10-01

    Full Text Available Aim of study: To contribute to the characterization of the origin of material used in afforestation, restoration or conservation activities by using Cp-SSR markers. Area of study: We used information from the natural range of Iberian pines, from Spain. Materials and methods: We used Iberian pines as an example to undertook gene pool characterization based on a wide Iberian sample of 97 populations from five Pinus species (Pinus halepensis, Pinus pinaster, Pinus nigra, Pinus sylvestris and Pinus uncinata. Haplotypes from each analyzed tree (derived from nine chloroplast microsatellites markers in P. halepensis and six in the rest of the species were obtained. Based on this information we subdivided each species in regions (considering both genetic structure and its application in afforestation, restoration and conservation programs and tested the assignation of populations to the different groups based on the genetic distance among samples. Main results: The rate of successful identification of populations among the different species was very high (> 94 % for P. nigra, P. sylvestris and P. uncinata, high (81 % for P. pinaster, and low (< 65 % for P. halepensis. Research highlights: Chloroplast DNA markers from extensive population datasets can be used to assign the origin of the forest reproductive material in some pine species.

  2. Identification of gene pools used in restoration and conservation by chloroplast microsatellite markers in Iberian pine species

    International Nuclear Information System (INIS)

    Hernández-Tecles, Enrique; De las Heras, Jorge; Lorenzo, Zaida; Navascués, Miguel; Alia, Ricardo

    2017-01-01

    Aim of study: To contribute to the characterization of the origin of material used in afforestation, restoration or conservation activities by using Cp-SSR markers. Area of study: We used information from the natural range of Iberian pines, from Spain. Materials and methods: We used Iberian pines as an example to undertook gene pool characterization based on a wide Iberian sample of 97 populations from five Pinus species (Pinus halepensis, Pinus pinaster, Pinus nigra, Pinus sylvestris and Pinus uncinata). Haplotypes from each analyzed tree (derived from nine chloroplast microsatellites markers in P. halepensis and six in the rest of the species) were obtained. Based on this information we subdivided each species in regions (considering both genetic structure and its application in afforestation, restoration and conservation programs) and tested the assignation of populations to the different groups based on the genetic distance among samples. Main results: The rate of successful identification of populations among the different species was very high (> 94 %) for P. nigra, P. sylvestris and P. uncinata, high (81 %) for P. pinaster, and low (< 65 %) for P. halepensis. Research highlights: Chloroplast DNA markers from extensive population datasets can be used to assign the origin of the forest reproductive material in some pine species.

  3. Identification of gene pools used in restoration and conservation by chloroplast microsatellite markers in Iberian pine species

    Energy Technology Data Exchange (ETDEWEB)

    Hernández-Tecles, Enrique; De las Heras, Jorge; Lorenzo, Zaida; Navascués, Miguel; Alia, Ricardo

    2017-11-01

    Aim of study: To contribute to the characterization of the origin of material used in afforestation, restoration or conservation activities by using Cp-SSR markers. Area of study: We used information from the natural range of Iberian pines, from Spain. Materials and methods: We used Iberian pines as an example to undertook gene pool characterization based on a wide Iberian sample of 97 populations from five Pinus species (Pinus halepensis, Pinus pinaster, Pinus nigra, Pinus sylvestris and Pinus uncinata). Haplotypes from each analyzed tree (derived from nine chloroplast microsatellites markers in P. halepensis and six in the rest of the species) were obtained. Based on this information we subdivided each species in regions (considering both genetic structure and its application in afforestation, restoration and conservation programs) and tested the assignation of populations to the different groups based on the genetic distance among samples. Main results: The rate of successful identification of populations among the different species was very high (> 94 %) for P. nigra, P. sylvestris and P. uncinata, high (81 %) for P. pinaster, and low (< 65 %) for P. halepensis. Research highlights: Chloroplast DNA markers from extensive population datasets can be used to assign the origin of the forest reproductive material in some pine species.

  4. Evolution of the pilot infrastructure of CMS towards a single glideinWMS pool

    OpenAIRE

    Gutsche, Oliver

    2013-01-01

    CMS production and analysis job submission is based largely on glideinWMS and pilot submissions. The transition from multiple different submission solutions like gLite WMS and HTCondor-based implementations was carried out over years and is coming now to a conclusion. The historically explained separate glideinWMS pools for different types of production jobs and analysis jobs are being unified into a single global pool. This enables CMS to benefit from global prioritization and scheduling pos...

  5. A fundamental study on sodium-water reaction in the double-pool-type LMFBR

    International Nuclear Information System (INIS)

    Yoshida, Kazuo; Akimoto, Tokuzo

    1987-01-01

    In order to evaluate the pressure rise by large sodium-water reaction in the Double-Pool LMFBR, basic tests on pressure wave celerity in rectangular tube are carried out. The initial spike pressure in rectangular-shelled steam generator of the Double Pool reactor, strongly depends on pressure wave celerity. In this study, celerity was measured as a function of pressure wave rising time and pulse height, and influence of water around the test section on celerity was investigated. (author)

  6. Vortex-ring-induced large bubble entrainment during drop impact

    KAUST Repository

    Thoraval, Marie-Jean

    2016-03-29

    For a limited set of impact conditions, a drop impacting onto a pool can entrap an air bubble as large as its own size. The subsequent rise and rupture of this large bubble plays an important role in aerosol formation and gas transport at the air-sea interface. The large bubble is formed when the impact crater closes up near the pool surface and is known to occur only for drops that are prolate at impact. Herein we use experiments and numerical simulations to show that a concentrated vortex ring, produced in the neck between the drop and the pool, controls the crater deformations and pinchoff. However, it is not the strongest vortex rings that are responsible for the large bubbles, as they interact too strongly with the pool surface and self-destruct. Rather, it is somewhat weaker vortices that can deform the deeper craters, which manage to pinch off the large bubbles. These observations also explain why the strongest and most penetrating vortex rings emerging from drop impacts are not produced by oblate drops but by more prolate drop shapes, as had been observed in previous experiments.

  7. Human-caused Indo-Pacific warm pool expansion

    OpenAIRE

    Weller, Evan; Min, Seung-Ki; Cai, Wenju; Zwiers, Francis W.; Kim, Yeon-Hee; Lee, Donghyun

    2016-01-01

    The Indo-Pacific warm pool (IPWP) has warmed and grown substantially during the past century. The IPWP is Earth?s largest region of warm sea surface temperatures (SSTs), has the highest rainfall, and is fundamental to global atmospheric circulation and hydrological cycle. The region has also experienced the world?s highest rates of sea-level rise in recent decades, indicating large increases in ocean heat content and leading to substantial impacts on small island states in the region. Previou...

  8. Key asset - inherent safety of LMFBR Pool Plant

    International Nuclear Information System (INIS)

    Marchaterre, J.F.; Sevy, R.H.; Lancet, R.T.; Mills, J.C.

    1984-04-01

    The safety approach used in the design of the Large Pool Plant emphasizes use of the intrinsic characteristics of Liquid Metal Fast Breeder Reactors to incorporate a high degree of safety in the design and reduce cost by providing simpler (more reliable) dedicated safety systems. Correspondingly, a goal was not to require the action of active systems to prevent significant core damage and/or provide large grace periods for all anticipated transients. The key safety features of the plant are presented and the analysis of representative flow and power transients are presented to show that the design goal has been satisfied

  9. Key asset--Inherent safety of LFMBR pool plant

    International Nuclear Information System (INIS)

    Marchaterre, J.F.; Lancet, R.T.; Mills, J.C.; Sevy, R.H.

    1984-01-01

    The safety approach used in the design of the Large Pool Plant emphasizes use of the intrinsic characteristics of Liquid Metal Fast Breeder Reactors to incorporate a high degree of safety in the design and reduce cost by providing simpler (more reliable) dedicated safety systems. Correspondingly, a goal was not to require the action of active systems to prevent significant core damage and/or provide large grace periods for all anticipated transients. The key safety features of the plant are presented and the analysis of representative flow and power transients are presented to show that the design goal has been satisfied

  10. Mutation scanning of peach floral genes

    Directory of Open Access Journals (Sweden)

    Wilde H Dayton

    2011-05-01

    Full Text Available Abstract Background Mutation scanning technology has been used to develop crop species with improved traits. Modifications that improve screening throughput and sensitivity would facilitate the targeted mutation breeding of crops. Technical innovations for high-resolution melting (HRM analysis are enabling the clinic-based screening for human disease gene polymorphism. We examined the application of two HRM modifications, COLD-PCR and QMC-PCR, to the mutation scanning of genes in peach, Prunus persica. The targeted genes were the putative floral regulators PpAGAMOUS and PpTERMINAL FLOWER I. Results HRM analysis of PpAG and PpTFL1 coding regions in 36 peach cultivars found one polymorphic site in each gene. PpTFL1 and PpAG SNPs were used to examine approaches to increase HRM throughput. Cultivars with SNPs could be reliably detected in pools of twelve genotypes. COLD-PCR was found to increase the sensitivity of HRM analysis of pooled samples, but worked best with small amplicons. Examination of QMC-PCR demonstrated that primary PCR products for further analysis could be produced from variable levels of genomic DNA. Conclusions Natural SNPs in exons of target peach genes were discovered by HRM analysis of cultivars from a southeastern US breeding program. For detecting natural or induced SNPs in larger populations, HRM efficiency can be improved by increasing sample pooling and template production through approaches such as COLD-PCR and QMC-PCR. Technical advances developed to improve clinical diagnostics can play a role in the targeted mutation breeding of crops.

  11. De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries.

    Science.gov (United States)

    Cho, Namjin; Hwang, Byungjin; Yoon, Jung-ki; Park, Sangun; Lee, Joongoo; Seo, Han Na; Lee, Jeewon; Huh, Sunghoon; Chung, Jinsoo; Bang, Duhee

    2015-09-21

    Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.

  12. POOL WATER TREATMENT AND COOLING SYSTEM DESCRIPTION DOCUMENT

    International Nuclear Information System (INIS)

    King, V.

    2000-01-01

    The Pool Water Treatment and Cooling System is located in the Waste Handling Building (WHB), and is comprised of various process subsystems designed to support waste handling operations. This system maintains the pool water temperature within an acceptable range, maintains water quality standards that support remote underwater operations and prevent corrosion, detects leakage from the pool liner, provides the capability to remove debris from the pool, controls the pool water level, and helps limit radiological exposure to personnel. The pool structure and liner, pool lighting, and the fuel staging racks in the pool are not within the scope of the Pool Water Treatment and Cooling System. Pool water temperature control is accomplished by circulating the pool water through heat exchangers. Adequate circulation and mixing of the pool water is provided to prevent localized thermal hotspots in the pool. Treatment of the pool water is accomplished by a water treatment system that circulates the pool water through filters, and ion exchange units. These water treatment units remove radioactive and non-radioactive particulate and dissolved solids from the water, thereby providing the water clarity needed to conduct waste handling operations. The system also controls pool water chemistry to prevent advanced corrosion of the pool liner, pool components, and fuel assemblies. Removal of radioactivity from the pool water contributes to the project ALARA (as low as is reasonably achievable) goals. A leak detection system is provided to detect and alarm leaks through the pool liner. The pool level control system monitors the water level to ensure that the minimum water level required for adequate radiological shielding is maintained. Through interface with a demineralized water system, adequate makeup is provided to compensate for loss of water inventory through evaporation and waste handling operations. Interface with the Site Radiological Monitoring System provides continuous

  13. A deeper look at the relationship between root carbon pools and the vertical distribution of the soil carbon pool

    Directory of Open Access Journals (Sweden)

    R. Dietzel

    2017-08-01

    Full Text Available Plant root material makes a substantial contribution to the soil organic carbon (C pool, but this contribution is disproportionate below 20 cm where 30 % of root mass and 50 % of soil organic C is found. Root carbon inputs changed drastically when native perennial plant systems were shifted to cultivated annual plant systems. We used the reconstruction of a native prairie and a continuous maize field to examine both the relationship between root carbon and soil carbon and the fundamental rooting system differences between the vegetation under which the soils developed versus the vegetation under which the soils continue to change. In all treatments we found that root C  :  N ratios increased with depth, and this plays a role in why an unexpectedly large proportion of soil organic C is found below 20 cm. Measured root C  :  N ratios and turnover times along with modeled root turnover dynamics showed that in the historical shift from prairie to maize, a large, structural-tissue-dominated root C pool with slow turnover concentrated at shallow depths was replaced by a small, nonstructural-tissue-dominated root C pool with fast turnover evenly distributed in the soil profile. These differences in rooting systems suggest that while prairie roots contribute more C to the soil than maize at shallow depths, maize may contribute more C to soil C stocks than prairies at deeper depths.

  14. Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells.

    Directory of Open Access Journals (Sweden)

    João A Paredes

    Full Text Available Loss of thymidine kinase 2 (TK2 causes a heterogeneous myopathic form of mitochondrial DNA (mtDNA depletion syndrome (MDS in humans that predominantly affects skeletal muscle tissue. In mice, TK2 deficiency also affects several tissues in addition to skeletal muscle, including brain, heart, adipose tissue, kidneys and causes death about 3 weeks after birth. We analysed skeletal muscle and heart muscle tissues of Tk2 knockout mice at postnatal development phase and observed that TK2 deficient pups grew slower and their skeletal muscles appeared significantly underdeveloped, whereas heart was close to normal in size. Both tissues showed mtDNA depletion and mitochondria with altered ultrastructure, as revealed by transmission electron microscopy. Gene expression microarray analysis showed a strong down-regulation of genes involved in cell cycle and cell proliferation in both tissues, suggesting a lower pool of undifferentiated proliferating cells. Analysis of isolated primary myoblasts from Tk2 knockout mice showed slow proliferation, less ability to differentiate and signs of premature senescence, even in absence of mtDNA depletion. Our data demonstrate that TK2 deficiency disturbs myogenic progenitor cells function in postnatal skeletal muscle and we propose this as one of the causes of underdeveloped phenotype and myopathic characteristic of the TK2 deficient mice, in addition to the progressive mtDNA depletion, mitochondrial damage and respiratory chain deficiency in post-mitotic differentiated tissue.

  15. Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells.

    Science.gov (United States)

    Paredes, João A; Zhou, Xiaoshan; Höglund, Stefan; Karlsson, Anna

    2013-01-01

    Loss of thymidine kinase 2 (TK2) causes a heterogeneous myopathic form of mitochondrial DNA (mtDNA) depletion syndrome (MDS) in humans that predominantly affects skeletal muscle tissue. In mice, TK2 deficiency also affects several tissues in addition to skeletal muscle, including brain, heart, adipose tissue, kidneys and causes death about 3 weeks after birth. We analysed skeletal muscle and heart muscle tissues of Tk2 knockout mice at postnatal development phase and observed that TK2 deficient pups grew slower and their skeletal muscles appeared significantly underdeveloped, whereas heart was close to normal in size. Both tissues showed mtDNA depletion and mitochondria with altered ultrastructure, as revealed by transmission electron microscopy. Gene expression microarray analysis showed a strong down-regulation of genes involved in cell cycle and cell proliferation in both tissues, suggesting a lower pool of undifferentiated proliferating cells. Analysis of isolated primary myoblasts from Tk2 knockout mice showed slow proliferation, less ability to differentiate and signs of premature senescence, even in absence of mtDNA depletion. Our data demonstrate that TK2 deficiency disturbs myogenic progenitor cells function in postnatal skeletal muscle and we propose this as one of the causes of underdeveloped phenotype and myopathic characteristic of the TK2 deficient mice, in addition to the progressive mtDNA depletion, mitochondrial damage and respiratory chain deficiency in post-mitotic differentiated tissue.

  16. Neurons That Underlie Drosophila melanogaster Reproductive Behaviors: Detection of a Large Male-Bias in Gene Expression in fruitless-Expressing Neurons

    Directory of Open Access Journals (Sweden)

    Nicole R. Newell

    2016-08-01

    Full Text Available Male and female reproductive behaviors in Drosophila melanogaster are vastly different, but neurons that express sex-specifically spliced fruitless transcripts (fru P1 underlie these behaviors in both sexes. How this set of neurons can generate such different behaviors between the two sexes is an unresolved question. A particular challenge is that fru P1-expressing neurons comprise only 2–5% of the adult nervous system, and so studies of adult head tissue or whole brain may not reveal crucial differences. Translating Ribosome Affinity Purification (TRAP identifies the actively translated pool of mRNAs from fru P1-expressing neurons, allowing a sensitive, cell-type-specific assay. We find four times more male-biased than female-biased genes in TRAP mRNAs from fru P1-expressing neurons. This suggests a potential mechanism to generate dimorphism in behavior. The male-biased genes may direct male behaviors by establishing cell fate in a similar context of gene expression observed in females. These results suggest a possible global mechanism for how distinct behaviors can arise from a shared set of neurons.

  17. Spatially pooled contrast responses predict neural and perceptual similarity of naturalistic image categories.

    Directory of Open Access Journals (Sweden)

    Iris I A Groen

    Full Text Available The visual world is complex and continuously changing. Yet, our brain transforms patterns of light falling on our retina into a coherent percept within a few hundred milliseconds. Possibly, low-level neural responses already carry substantial information to facilitate rapid characterization of the visual input. Here, we computationally estimated low-level contrast responses to computer-generated naturalistic images, and tested whether spatial pooling of these responses could predict image similarity at the neural and behavioral level. Using EEG, we show that statistics derived from pooled responses explain a large amount of variance between single-image evoked potentials (ERPs in individual subjects. Dissimilarity analysis on multi-electrode ERPs demonstrated that large differences between images in pooled response statistics are predictive of more dissimilar patterns of evoked activity, whereas images with little difference in statistics give rise to highly similar evoked activity patterns. In a separate behavioral experiment, images with large differences in statistics were judged as different categories, whereas images with little differences were confused. These findings suggest that statistics derived from low-level contrast responses can be extracted in early visual processing and can be relevant for rapid judgment of visual similarity. We compared our results with two other, well- known contrast statistics: Fourier power spectra and higher-order properties of contrast distributions (skewness and kurtosis. Interestingly, whereas these statistics allow for accurate image categorization, they do not predict ERP response patterns or behavioral categorization confusions. These converging computational, neural and behavioral results suggest that statistics of pooled contrast responses contain information that corresponds with perceived visual similarity in a rapid, low-level categorization task.

  18. Spatially Pooled Contrast Responses Predict Neural and Perceptual Similarity of Naturalistic Image Categories

    Science.gov (United States)

    Groen, Iris I. A.; Ghebreab, Sennay; Lamme, Victor A. F.; Scholte, H. Steven

    2012-01-01

    The visual world is complex and continuously changing. Yet, our brain transforms patterns of light falling on our retina into a coherent percept within a few hundred milliseconds. Possibly, low-level neural responses already carry substantial information to facilitate rapid characterization of the visual input. Here, we computationally estimated low-level contrast responses to computer-generated naturalistic images, and tested whether spatial pooling of these responses could predict image similarity at the neural and behavioral level. Using EEG, we show that statistics derived from pooled responses explain a large amount of variance between single-image evoked potentials (ERPs) in individual subjects. Dissimilarity analysis on multi-electrode ERPs demonstrated that large differences between images in pooled response statistics are predictive of more dissimilar patterns of evoked activity, whereas images with little difference in statistics give rise to highly similar evoked activity patterns. In a separate behavioral experiment, images with large differences in statistics were judged as different categories, whereas images with little differences were confused. These findings suggest that statistics derived from low-level contrast responses can be extracted in early visual processing and can be relevant for rapid judgment of visual similarity. We compared our results with two other, well- known contrast statistics: Fourier power spectra and higher-order properties of contrast distributions (skewness and kurtosis). Interestingly, whereas these statistics allow for accurate image categorization, they do not predict ERP response patterns or behavioral categorization confusions. These converging computational, neural and behavioral results suggest that statistics of pooled contrast responses contain information that corresponds with perceived visual similarity in a rapid, low-level categorization task. PMID:23093921

  19. Seismic responses of a pool-type fast reactor with different core support designs

    International Nuclear Information System (INIS)

    Wu, Ting-shu; Seidensticker, R.W.

    1989-01-01

    In designing the core support system for a pool-type fast reactor, there are many issues which must be considered in order to achieve an optimum and balanced design. These issues include safety, reliability, as well as costs. Several design options are possible to support the reactor core. Different core support options yield different frequency ranges and responses. Seismic responses of a large pool-type fast reactor incorporated with different core support designs have been investigated. 4 refs., 3 figs

  20. Pool scrubbing models for iodine components

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, K [Battelle Ingenieurtechnik GmbH, Eschborn (Germany)

    1996-12-01

    Pool scrubbing is an important mechanism to retain radioactive fission products from being carried into the containment atmosphere or into the secondary piping system. A number of models and computer codes has been developed to predict the retention of aerosols and fission product vapours that are released from the core and injected into water pools of BWR and PWR type reactors during severe accidents. Important codes in this field are BUSCA, SPARC and SUPRA. The present paper summarizes the models for scrubbing of gaseous Iodine components in these codes, discusses the experimental validation, and gives an assessment of the state of knowledge reached and the open questions which persist. The retention of gaseous Iodine components is modelled by the various codes in a very heterogeneous manner. Differences show up in the chemical species considered, the treatment of mass transfer boundary layers on the gaseous and liquid sides, the gas-liquid interface geometry, calculation of equilibrium concentrations and numerical procedures. Especially important is the determination of the pool water pH value. This value is affected by basic aerosols deposited in the water, e.g. Cesium and Rubidium compounds. A consistent model requires a mass balance of these compounds in the pool, thus effectively coupling the pool scrubbing phenomena of aerosols and gaseous Iodine species. Since the water pool conditions are also affected by drainage flow of condensate water from different regions in the containment, and desorption of dissolved gases on the pool surface is determined by the gas concentrations above the pool, some basic limitations of specialized pool scrubbing codes are given. The paper draws conclusions about the necessity of coupling between containment thermal-hydraulics and pool scrubbing models, and proposes ways of further simulation model development in order to improve source term predictions. (author) 2 tabs., refs.

  1. Pool scrubbing models for iodine components

    International Nuclear Information System (INIS)

    Fischer, K.

    1996-01-01

    Pool scrubbing is an important mechanism to retain radioactive fission products from being carried into the containment atmosphere or into the secondary piping system. A number of models and computer codes has been developed to predict the retention of aerosols and fission product vapours that are released from the core and injected into water pools of BWR and PWR type reactors during severe accidents. Important codes in this field are BUSCA, SPARC and SUPRA. The present paper summarizes the models for scrubbing of gaseous Iodine components in these codes, discusses the experimental validation, and gives an assessment of the state of knowledge reached and the open questions which persist. The retention of gaseous Iodine components is modelled by the various codes in a very heterogeneous manner. Differences show up in the chemical species considered, the treatment of mass transfer boundary layers on the gaseous and liquid sides, the gas-liquid interface geometry, calculation of equilibrium concentrations and numerical procedures. Especially important is the determination of the pool water pH value. This value is affected by basic aerosols deposited in the water, e.g. Cesium and Rubidium compounds. A consistent model requires a mass balance of these compounds in the pool, thus effectively coupling the pool scrubbing phenomena of aerosols and gaseous Iodine species. Since the water pool conditions are also affected by drainage flow of condensate water from different regions in the containment, and desorption of dissolved gases on the pool surface is determined by the gas concentrations above the pool, some basic limitations of specialized pool scrubbing codes are given. The paper draws conclusions about the necessity of coupling between containment thermal-hydraulics and pool scrubbing models, and proposes ways of further simulation model development in order to improve source term predictions. (author) 2 tabs., refs

  2. On heat transfer characteristics of real and simulant melt pool experiments

    Energy Technology Data Exchange (ETDEWEB)

    Dinh, T.N.; Nourgaliev R.R.; Sehgal, B.R. [Royal Institute of Technology, Stockholm (Sweden)

    1995-09-01

    The paper presents results of analytical studies of natural convection heat transfer in scaled and/or simulant melt pool experiments related to the PWR in-vessel melt retention issue. Specific reactor-scale effects of a large decay-heated core melt pool in the reactor pressure vessel lower plenum are first reviewed, and then the current analytical capability of describing physical processes under prototypical situations is examined. Experiments and experimental approaches are analysed by focusing on their ability to represent prototypical situations. Calculations are carried out in order to assess the significance of some selected effects, including variations in melt properties, pool geometry and heating conditions. Rayleigh numbers in the present analysis are limited to 10{sup 12}, where uncertainties in turbulence modeling are not overriding other uncertainties. The effects of fluid Prandtl number on heat transfer to the lowermost part of cooled pool walls are examined for square and semicircular cavities. Calculations are performed also to explore limitations of using side-wall heating and direct electrical heating in reproducing the physical picture of interest. Needs for further experimental and analytical efforts are discussed as well.

  3. Muon reconstruction in the Daya Bay water pools

    International Nuclear Information System (INIS)

    Hackenburg, R. W.

    2017-01-01

    Muon reconstruction in the Daya Bay water pools would serve to verify the simulated muon fluxes and offer the possibility of studying cosmic muons in general. This reconstruction is, however, complicated by many optical obstacles and the small coverage of photomultiplier tubes (PMTs) as compared to other large water Cherenkov detectors. The PMTs’ timing information is useful only in the case of direct, unreflected Cherenkov light. This requires PMTs to be added and removed as an hypothesized muon trajectory is iteratively improved, to account for the changing effects of obstacles and direction of light. Therefore, muon reconstruction in the Daya Bay water pools does not lend itself to a general fitting procedure employing smoothly varying functions with continuous derivatives. Here, we describe an algorithm which overcomes these complications. It employs the method of Least Mean Squares to determine an hypothesized trajectory from the PMTs’ charge-weighted positions. This initially hypothesized trajectory is then iteratively refined using the PMTs’ timing information. Reconstructions with simulated data reproduce the simulated trajectory to within about 5° in direction and about 45 cm in position at the pool surface, with a bias that tends to pull tracks away from the vertical by about 3°.

  4. Sodium pool fires consequences on a confined vessel and on the environment

    International Nuclear Information System (INIS)

    Rzekiecki, R.; Charpenel, J.; Malet, J.C.; Cucinotta, A.

    1989-01-01

    This paper presents the PYROS I Code used in France to calculate the effects of a sodium pool fire on a vessel and his validation range. The results or the atmospheric behaviour of the aerosol are given. Predicting the consequences of large sodium fires in large cells from the results of small scaled experiments, claim attention on scale effects. (author)

  5. Self-formed waterfall plunge pools in homogeneous rock

    Science.gov (United States)

    Scheingross, Joel S.; Lo, Daniel Y.; Lamb, Michael P.

    2017-01-01

    Waterfalls are ubiquitous, and their upstream propagation can set the pace of landscape evolution, yet no experimental studies have examined waterfall plunge pool erosion in homogeneous rock. We performed laboratory experiments, using synthetic foam as a bedrock simulant, to produce self-formed waterfall plunge pools via particle impact abrasion. Plunge pool vertical incision exceeded lateral erosion by approximately tenfold until pools deepened to the point that the supplied sediment could not be evacuated and deposition armored the pool bedrock floor. Lateral erosion of plunge pool sidewalls continued after sediment deposition, but primarily at the downstream pool wall, which might lead to undermining of the plunge pool lip, sediment evacuation, and continued vertical pool floor incision in natural streams. Undercutting of the upstream pool wall was absent, and our results suggest that vertical drilling of successive plunge pools is a more efficient waterfall retreat mechanism than the classic model of headwall undercutting and collapse in homogeneous rock.

  6. A large-scale international meta-analysis of paraoxonase gene polymorphisms in sporadic ALS

    NARCIS (Netherlands)

    Wills, A-M.; Cronin, S.; Slowik, A.; Kasperaviciute, D.; Van Es, M. A.; Morahan, J. M.; Valdmanis, P. N.; Meininger, V.; Melki, J.; Shaw, C. E.; Rouleau, G. A.; Fisher, E. M. C.; Shaw, P. J.; Morrison, K. E.; Pamphlett, R.; Van den Berg, L. H.; Figlewicz, D. A.; Andersen, P. M.; Al-Chalabi, A.; Hardiman, O.; Purcell, S.; Landers, J. E.; Brown, R. H.

    2009-01-01

    Background: Six candidate gene studies report a genetic association of DNA variants within the paraoxonase locus with sporadic amyotrophic lateral sclerosis (ALS). However, several other large studies, including five genome-wide association studies, have not duplicated this finding. Methods: We

  7. Convective Cold Pool Structure and Boundary Layer Recovery in DYNAMO

    Science.gov (United States)

    Savarin, A.; Chen, S. S.; Kerns, B. W.; Lee, C.; Jorgensen, D. P.

    2012-12-01

    One of the key factors controlling convective cloud systems in the Madden-Julian Oscillation (MJO) over the tropical Indian Ocean is the property of the atmospheric boundary layer. Convective downdrafts and precipitation from the cloud systems produce cold pools in the boundary layer, which can inhibit subsequent development of convection. The recovery time is the time it takes for the boundary layer to return to pre convective conditions. It may affect the variability of the convection on various time scales during the initiation of MJO. This study examines the convective cold pool structure and boundary layer recovery using the NOAA WP-3D aircraft observations, include the flight-level, Doppler radar, and GPS dropsonde data, collected during the Dynamics of MJO (DYNAMO) field campaign from November-December 2011. The depth and strength of convective cold pools are defined by the negative buoyancy, which can be computed from the dropsonde data. Convective downdraft can be affected by environmental water vapor due to entrainment. Mid-level dry air observed during the convectively suppressed phase of MJO seems to enhance convective downdraft, making the cold pools stronger and deeper. Recovery of the cold pools in the boundary layer is determined by the strength and depth of the cold pools and also the air-sea heat and moisture fluxes. Given that the water vapor and surface winds are distinct for the convectively active and suppressed phases of MJO over the Indian Ocean, the aircraft data are stratified by the two different large-scale regimes of MJO. Preliminary results show that the strength and depth of the cold pools are inversely correlated with the surrounding mid-level moisture. During the convectively suppressed phase, the recovery time is ~5-20 hours in relative weak wind condition with small air-sea fluxes. The recovery time is generally less than 6 hours during the active phase of MJO with moist mid-levels and stronger surface wind and air-sea fluxes.

  8. Patent pools: Intellectual property rights and competition.

    NARCIS (Netherlands)

    Rodriguez, V.F.

    2010-01-01

    Patent pools do not correct all problems associated with patent thickets. In this respect, patent pools might not stop the outsider problem from striking pools. Moreover, patent pools can be expensive to negotiate, can exclude patent holders with smaller numbers of patents or enable a group of major

  9. Transcriptome Analysis of Three Sheep Intestinal Regions reveals Key Pathways and Hub Regulatory Genes of Large Intestinal Lipid Metabolism.

    Science.gov (United States)

    Chao, Tianle; Wang, Guizhi; Ji, Zhibin; Liu, Zhaohua; Hou, Lei; Wang, Jin; Wang, Jianmin

    2017-07-13

    The large intestine, also known as the hindgut, is an important part of the animal digestive system. Recent studies on digestive system development in ruminants have focused on the rumen and the small intestine, but the molecular mechanisms underlying sheep large intestine metabolism remain poorly understood. To identify genes related to intestinal metabolism and to reveal molecular regulation mechanisms, we sequenced and compared the transcriptomes of mucosal epithelial tissues among the cecum, proximal colon and duodenum. A total of 4,221 transcripts from 3,254 genes were identified as differentially expressed transcripts. Between the large intestine and duodenum, differentially expressed transcripts were found to be significantly enriched in 6 metabolism-related pathways, among which PPAR signaling was identified as a key pathway. Three genes, CPT1A, LPL and PCK1, were identified as higher expression hub genes in the large intestine. Between the cecum and colon, differentially expressed transcripts were significantly enriched in 5 lipid metabolism related pathways, and CEPT1 and MBOAT1 were identified as hub genes. This study provides important information regarding the molecular mechanisms of intestinal metabolism in sheep and may provide a basis for further study.

  10. Steam CFD simulation of injection in suppression pool

    International Nuclear Information System (INIS)

    Naveen Samad, A.M.; Ghosh, Sumana

    2015-01-01

    Boiling water reactor (BWR) is one of the common types of electricity generating nuclear reactor. Suppression pool system is a major component of the BWR which has to be designed efficiently for the safe operations. During some accidents like Loss of Coolant Accident (LOCA) large amount of steam are injected to the pressure suppression system resulting in increase in temperature of the pool and thereby increasing the pressure. The present work discuss about the Computational Fluid Dynamics (CFD) simulation of steam injected to the wet well of BWR through the blow down pipes and there by investigating the hydrodynamic and thermal characteristics of the system. The simulations were carried out for three different steam injection velocities. The numerical simulations were performed with ANSYS FLUENT using multiphase 3D Volume of Fluid (VOF) model and k-ε model was adopted for modelling turbulence flow. (author)

  11. Flow behavior of volume-heated boiling pools: implications with respect to transition phase accident conditions

    International Nuclear Information System (INIS)

    Ginsberg, T.; Jones, O.C. Jr.; Chen, J.C.

    1979-01-01

    Observations of two-phase flow fields in single-component volume-heated boiling pools were made. Photographic observations, together with pool-average void fraction measurements, indicate that the churn-turbulent flow regime is stable for superficial vapor velocities up to nearly five times the Kutateladze dispersal limit. Within this range of conditions, a churn-turbulent drift flux model provides a reasonable prediction of the pool-average void fraction data. An extrapolation of the data to transition phase accident conditions suggests that intense boilup could occur where the pool-average void fraction would be >0.6 for steel vaporization rates equivalent to power levels >1% of nominal liquid-metal fast breeder reactor power density. The extended stability of bubbly flow to unusually large vapor fluxes and void fractions, observed in some experiments, is a major unresolved issue

  12. Groundwater dependent pools in seasonal and permanent streams in the Clare Valley of South Australia

    Directory of Open Access Journals (Sweden)

    Erick Bestland

    2017-02-01

    In this Mediterranean climate with cool wet winters and dry hot summers strong salinity changes (up to 2.5 times due to seasonal cycles of wetting and drying were observed in surface water. Oxygen and hydrogen isotope values from pool sites showed strong evaporative enrichment during the dry season with up to 50% net evaporation calculated. Water isotopes from groundwater, however, cluster at the depleted end of the local meteoric water line and most do not show change despite significant seasonal salinity changes. Strontium isotope values and concentrations from the pools over the one year period do not define a mixing relationship. Instead, most pool sites have unchanging strontium isotope values despite the large seasonal change in salinity indicating strong evaporation of groundwater fed pools during this drought year.

  13. “Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

    Science.gov (United States)

    Fondi, Marco; Karkman, Antti; Tamminen, Manu V.; Bosi, Emanuele; Virta, Marko; Fani, Renato; Alm, Eric; McInerney, James O.

    2016-01-01

    The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as “everything is everywhere but the environment selects.” While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge. PMID:27190206

  14. Building a Better Applicant Pool--A Case Study of the Use of Predictive Modeling and Market Segmentation to Build and Enroll Better Pools of Students

    Science.gov (United States)

    Herridge, Bart; Heil, Robert

    2003-01-01

    Predictive modeling has been a popular topic in higher education for the last few years. This case study shows an example of an effective use of modeling combined with market segmentation to strategically divide large, unmanageable prospect and inquiry pools and convert them into applicants, and eventually, enrolled students. (Contains 6 tables.)

  15. 13 CFR 120.1705 - Pool formation requirements.

    Science.gov (United States)

    2010-01-01

    ... requirements. SBA may adjust the Pool characteristics periodically based on program experience and market... a Pool involving a Pool Loan it does not own, it must purchase the Loan Interest it proposes to pool... purchase the Loan Interest and take it into inventory or settle the purchase of the Loan Interest through...

  16. Microbiota composition, gene pool and its expression in Gir cattle (Bos indicus) rumen under different forage diets using metagenomic and metatranscriptomic approaches.

    Science.gov (United States)

    Pandit, Ramesh J; Hinsu, Ankit T; Patel, Shriram H; Jakhesara, Subhash J; Koringa, Prakash G; Bruno, Fosso; Psifidi, Androniki; Shah, S V; Joshi, Chaitanya G

    2018-03-09

    Zebu (Bos indicus) is a domestic cattle species originating from the Indian subcontinent and now widely domesticated on several continents. In this study, we were particularly interested in understanding the functionally active rumen microbiota of an important Zebu breed, the Gir, under different dietary regimes. Metagenomic and metatranscriptomic data were compared at various taxonomic levels to elucidate the differential microbial population and its functional dynamics in Gir cattle rumen under different roughage dietary regimes. Different proportions of roughage rather than the type of roughage (dry or green) modulated microbiome composition and the expression of its gene pool. Fibre degrading bacteria (i.e. Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Bacillus and Roseburia) were higher in the solid fraction of rumen (Pcomparison of metagenomic shotgun and metatranscriptomic sequencing appeared to be a much richer source of information compared to conventional metagenomic analysis. Copyright © 2018 Elsevier GmbH. All rights reserved.

  17. The c.IVS1+1G>A mutation inthe GJB2 gene is prevalent and large ...

    Indian Academy of Sciences (India)

    IVS1+1G>A mutation inthe GJB2 gene is prevalent and large deletions involving the GJB6 gene are not present in the Turkish population. ASLI SIRMACI, DUYGU AKCAYOZ-DUMAN and MUSTAFA TEKIN∗. Division of Pediatric Molecular Genetics, Ankara University School of Medicine, Ankara 06100, Turkey. Introduction.

  18. 1968 Listing of Swimming Pool Equipment.

    Science.gov (United States)

    National Sanitation Foundation, Ann Arbor, MI. Testing Lab.

    An up-to-date listing of swimming pool equipment including--(1) companies authorized to display the National Sanitation Foundation seal of approval, (2) equipment listed as meeting NSF swimming pool equipment standards relating to diatomite type filters, (3) equipment listed as meeting NSF swimming pool equipment standard relating to sand type…

  19. Large-scale event extraction from literature with multi-level gene normalization.

    Directory of Open Access Journals (Sweden)

    Sofie Van Landeghem

    Full Text Available Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/. Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from

  20. Microbial profile comparisons of saliva, pooled and site-specific subgingival samples in periodontitis patients.

    Directory of Open Access Journals (Sweden)

    Daniel Belstrøm

    Full Text Available The purpose of this study was to compare microbial profiles of saliva, pooled and site-specific subgingival samples in patients with periodontitis. We tested the hypotheses that saliva can be an alternative to pooled subgingival samples, when screening for presence of periopathogens.Site specific subgingival plaque samples (n = 54, pooled subgingival plaque samples (n = 18 and stimulated saliva samples (n = 18 were collected from 18 patients with generalized chronic periodontitis. Subgingival and salivary microbiotas were characterized by means of HOMINGS (Human Oral Microbe Identification using Next Generation Sequencing and microbial community profiles were compared using Spearman rank correlation coefficient.Pronounced intraindividual differences were recorded in site-specific microbial profiles, and site-specific information was in general not reflected by pooled subgingival samples. Presence of Porphyromonas gingivalis, Treponema denticola, Prevotella intermedia, Filifactor alocis, Tannerella forsythia and Parvimona micra in site-specific subgingival samples were detected in saliva with an AUC of 0.79 (sensitivity: 0.61, specificity: 0.94, compared to an AUC of 0.76 (sensitivity: 0.56, specificity: 0.94 in pooled subgingival samples.Site-specific presence of periodontal pathogens was detected with comparable accuracy in stimulated saliva samples and pooled subgingival plaque samples. Consequently, saliva may be a reasonable surrogate for pooled subgingival samples when screening for presence of periopathogens. Future large-scale studies are needed to confirm findings from this study.

  1. A strategy for optimizing item-pool management

    NARCIS (Netherlands)

    Ariel, A.; van der Linden, Willem J.; Veldkamp, Bernard P.

    2006-01-01

    Item-pool management requires a balancing act between the input of new items into the pool and the output of tests assembled from it. A strategy for optimizing item-pool management is presented that is based on the idea of a periodic update of an optimal blueprint for the item pool to tune item

  2. Mathematical model development of heat and mass exchange processes in the outdoor swimming pool

    OpenAIRE

    M. V. Shaptala; D. E. Shaptala

    2014-01-01

    Purpose. Currently exploitation of outdoor swimming pools is often not cost-effective and, despite of their relevance, such pools are closed in large quantities. At this time there is no the whole mathematical model which would allow assessing qualitatively the effect of energy-saving measures. The aim of this work is to develop a mathematical model of heat and mass exchange processes for calculating basic heat and mass losses that occur during its exploitation. Methodology. The m...

  3. Swimming Pools and Molluscum Contagiosum

    Science.gov (United States)

    ... Travelers’ Health: Smallpox & Other Orthopoxvirus-Associated Infections Poxvirus Swimming Pools Recommend on Facebook Tweet Share Compartir The ... often ask if molluscum virus can spread in swimming pools. There is also concern that it can ...

  4. Method of measuring a liquid pool volume

    Science.gov (United States)

    Garcia, G.V.; Carlson, N.M.; Donaldson, A.D.

    1991-03-19

    A method of measuring a molten metal liquid pool volume and in particular molten titanium liquid pools is disclosed, including the steps of (a) generating an ultrasonic wave at the surface of the molten metal liquid pool, (b) shining a light on the surface of a molten metal liquid pool, (c) detecting a change in the frequency of light, (d) detecting an ultrasonic wave echo at the surface of the molten metal liquid pool, and (e) computing the volume of the molten metal liquid. 3 figures.

  5. Design and Construction of Pool Door for Research Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Jung, Kwangsub; Lee, Sangjin; Choi, Jinbok; Oh, Jinho; Lee, Jongmin [KAERI, Daejeon (Korea, Republic of)

    2016-05-15

    The pool door is a structure to isolate the reactor pool from the service pool for maintenance. The pool door is installed before the reactor pool is drained. The pool door consists of structural component and sealing component. The main structures of the pool door are stainless steel plates and side frames. The plates and frames are assembled by welded joints. Lug is welded at the top of the plate. The pool door is submerged in the pool water when it is used. Materials of the pool door should be resistive to corrosion and radiation. Stainless steel is used in structural components and air nozzle assemblies. Features of design and construction of the pool door for the research reactor are introduced. The pool door is designed to isolate the reactor pool for maintenance. Structural analysis is performed to evaluate the structural integrity during earthquake. Tests and inspections are also carried out during construction to identify the safety and function of the pool door.

  6. Design and Construction of Pool Door for Research Reactor

    International Nuclear Information System (INIS)

    Jung, Kwangsub; Lee, Sangjin; Choi, Jinbok; Oh, Jinho; Lee, Jongmin

    2016-01-01

    The pool door is a structure to isolate the reactor pool from the service pool for maintenance. The pool door is installed before the reactor pool is drained. The pool door consists of structural component and sealing component. The main structures of the pool door are stainless steel plates and side frames. The plates and frames are assembled by welded joints. Lug is welded at the top of the plate. The pool door is submerged in the pool water when it is used. Materials of the pool door should be resistive to corrosion and radiation. Stainless steel is used in structural components and air nozzle assemblies. Features of design and construction of the pool door for the research reactor are introduced. The pool door is designed to isolate the reactor pool for maintenance. Structural analysis is performed to evaluate the structural integrity during earthquake. Tests and inspections are also carried out during construction to identify the safety and function of the pool door

  7. Structural integrity assessment of HANARO pool cover

    International Nuclear Information System (INIS)

    Ryu, Jeong Soo

    2001-11-01

    This report is for the seismic analysis and the structural integrity evaluation of HANARO Pool Cover in accordances with the requirement of the Technical Specification for Seismic Analysis of HANARO Pool Cover. For performing the seismic analysis and evaluating the structural integrity for HANARO Pool Cover, the finite element analysis model using ANSYS 5.7 was developed and the dynamic characteristics were analyzed. The seismic response spectrum analyses of HANARO Pool Cover under the design floor response spectrum loads of OBE and SSE were performed. The analysis results show that the stress values in HANARO Pool Cover for the seismic loads are within the ASME Code limits. It is also confirmed that the fatigue usage factor is less than 1.0. Therefore any damage on structural integrity is not expected when an HANARO Pool Cover is installed in the upper part of the reactor pool

  8. Gene Expression Browser: Large-Scale and Cross-Experiment Microarray Data Management, Search & Visualization

    Science.gov (United States)

    The amount of microarray gene expression data in public repositories has been increasing exponentially for the last couple of decades. High-throughput microarray data integration and analysis has become a critical step in exploring the large amount of expression data for biological discovery. Howeve...

  9. [Investigation of toxigenic microcystis and microcystin pollution in Huayuankou Conservation Pool of Yellow River].

    Science.gov (United States)

    Ban, Haiqun; Ba, Yue; Cheng, Xuemin; Wang, Guangzhou

    2007-09-01

    To investigate the contaminative, condition of planktonic algae, cyanobacteria, toxigenic microcystis and microcystin in Huayuankou Conservation Pool of Yellow River. From March 2005 to January 2006, water samples were taken 15 times by 2. 5L plastic sampler from Huayuankou Conservation Pool. The density of algae were counted by using blood cell counter. Phycocyanin intergenic spacer region (PC-IGS) and microcystin synthetase gene B (mcyB) of toxigenic microcystis was identified by the whole cell PCR. The concentration of microcystin was determined by ELISA kit. The positive results of PCR and ELISA were compared. Bacillariophyta, chlorophyta, cyanophyta (cyanobacteria) and euglenophyta were main algaes in Huayuankou conservation pool, and the dominant algae and cell density changed seasonally. Algae cell density and cyanobacteria cell density were higher in summer and autumn than in spring and winter. From July to November, 2005, PC-IGS and mcyB were detected positively by whole cell PCR. Microcystin was positively detected from July, the concentration of microcystin changed from 0 to 0.25microg/L, it was more higher in summer than other seasons. Toxigenic microcystis and microcystin could be detected in Huayuankou Conservation Pool of Yellow River. Whole cell PCR could be used to identify toxigenic microcystis.

  10. Collaborative Car Pooling System

    OpenAIRE

    João Ferreira; Paulo Trigo; Porfírio Filipe

    2009-01-01

    This paper describes the architecture for a collaborative Car Pooling System based on a credits mechanism to motivate the cooperation among users. Users can spend the accumulated credits on parking facilities. For this, we propose a business model to support the collaboration between a car pooling system and parking facilities. The Portuguese Lisbon-s Metropolitan area is used as application scenario.

  11. The carB gene encoding the large subunit of carbamoylphosphate synthetase from Lactococcus lactis is transcribed monocistronically

    DEFF Research Database (Denmark)

    Martinussen, Jan; Hammer, Karin

    1998-01-01

    The biosynthesis of carbamoylphosphate is catalysed by the heterodimeric enzyme carbamoylphosphate synthetase (CPSase). The genes encoding the two subunits in procaryotes are normally transcribed as an operon, whereas in Lactococcus lactis, the gene encoding the large subunit (carB) is shown...

  12. Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution.

    Science.gov (United States)

    Gu, Xun; Wang, Yufeng; Gu, Jianying

    2002-06-01

    The classical (two-round) hypothesis of vertebrate genome duplication proposes two successive whole-genome duplication(s) (polyploidizations) predating the origin of fishes, a view now being seriously challenged. As the debate largely concerns the relative merits of the 'big-bang mode' theory (large-scale duplication) and the 'continuous mode' theory (constant creation by small-scale duplications), we tested whether a significant proportion of paralogous genes in the contemporary human genome was indeed generated in the early stage of vertebrate evolution. After an extensive search of major databases, we dated 1,739 gene duplication events from the phylogenetic analysis of 749 vertebrate gene families. We found a pattern characterized by two waves (I, II) and an ancient component. Wave I represents a recent gene family expansion by tandem or segmental duplications, whereas wave II, a rapid paralogous gene increase in the early stage of vertebrate evolution, supports the idea of genome duplication(s) (the big-bang mode). Further analysis indicated that large- and small-scale gene duplications both make a significant contribution during the early stage of vertebrate evolution to build the current hierarchy of the human proteome.

  13. Mathematical model development of heat and mass exchange processes in the outdoor swimming pool

    Directory of Open Access Journals (Sweden)

    M. V. Shaptala

    2014-12-01

    Full Text Available Purpose. Currently exploitation of outdoor swimming pools is often not cost-effective and, despite of their relevance, such pools are closed in large quantities. At this time there is no the whole mathematical model which would allow assessing qualitatively the effect of energy-saving measures. The aim of this work is to develop a mathematical model of heat and mass exchange processes for calculating basic heat and mass losses that occur during its exploitation. Methodology. The method for determination of heat and mass loses based on the theory of similarity criteria equations is used. Findings. The main types of heat and mass losses of outdoor pool were analyzed. The most significant types were allocated and mathematically described. Namely: by evaporation of water from the surface of the pool, by natural and forced convection, by radiation to the environment, heat consumption for water heating. Originality. The mathematical model of heat and mass exchange process of the outdoor swimming pool was developed, which allows calculating the basic heat and mass loses that occur during its exploitation. Practical value. The method of determining heat and mass loses of outdoor swimming pool as a software system was developed and implemented. It is based on the mathematical model proposed by the authors. This method can be used for the conceptual design of energy-efficient structures of outdoor pools, to assess their use of energy-intensive and selecting the optimum energy-saving measures. A further step in research in this area is the experimental validation of the method of calculation of heat losses in outdoor swimming pools with its use as an example the pool of Dnipropetrovsk National University of Railway Transport named after Academician V. Lazaryan. The outdoor pool, with water heating- up from the boiler room of the university, is operated year-round.

  14. p-STAT3 in luminal breast cancer: Integrated RNA-protein pooled analysis and results from the BIG 2-98 phase III trial.

    Science.gov (United States)

    Sonnenblick, Amir; Salgado, Roberto; Brohée, Sylvain; Zahavi, Tamar; Peretz, Tamar; Van den Eynden, Gert; Rouas, Ghizlane; Salmon, Asher; Francis, Prudence A; Di Leo, Angelo; Crown, John P A; Viale, Giuseppe; Daly, Laura; Javdan, Bahar; Fujisawa, Sho; De Azambuja, Evandro; Lieveke, Ameye; Piccart, Martine J; Bromberg, Jacqueline F; Sotiriou, Christos

    2018-02-01

    In the present study, in order to investigate the role of signal transducer and activator of transcription 3 (STAT3) in estrogen receptor (ER)-positive breast cancer prognosis, we evaluated the phosphorylated STAT3 (p-STAT3) status and investigated its effect on the outcome in a pooled analysis and in a large prospective adjuvant trial. By using the TCGA repository, we developed gene signatures that reflected the level of p-STAT3. Using pooled analysis of the expression data from luminal breast cancer patients, we assessed the effects of the p-STAT3 expression signature on prognosis. We further validated the p-STAT3 prognostic effect using immunohistochemistry (IHC) and immunofluorescence staining of p-STAT3 tissue microarrays from a large randomised prospective trial. Our analysis demonstrated that p-STAT3 expression was elevated in luminal A-type breast cancer (Kruskal-Wallis test, PBIG 2-98 randomised trial. With a median follow-up of 10.1 years, p-STAT3 was associated with a reduced risk of recurrence in ER-positive/HER2-negative breast cancer (Cox univariate HR, 0.66; 95% CI, 0.44-0.98; P=0.04). On the whole, our data indicate that p-STAT3 is associated with an improved outcome in ER-positive breast cancer.

  15. Identification of Phosphoglycerate Kinase 1 (PGK1 as a reference gene for quantitative gene expression measurements in human blood RNA

    Directory of Open Access Journals (Sweden)

    Unger Elizabeth R

    2011-09-01

    Full Text Available Abstract Background Blood is a convenient sample and increasingly used for quantitative gene expression measurements with a variety of diseases including chronic fatigue syndrome (CFS. Quantitative gene expression measurements require normalization of target genes to reference genes that are stable and independent from variables being tested in the experiment. Because there are no genes that are useful for all situations, reference gene selection is an essential step to any quantitative reverse transcription-PCR protocol. Many publications have described appropriate genes for a wide variety of tissues and experimental conditions, however, reference genes that may be suitable for the analysis of CFS, or human blood RNA derived from whole blood as well as isolated peripheral blood mononuclear cells (PBMCs, have not been described. Findings Literature review and analyses of our unpublished microarray data were used to narrow down the pool of candidate reference genes to six. We assayed whole blood RNA from Tempus tubes and cell preparation tube (CPT-collected PBMC RNA from 46 subjects, and used the geNorm and NormFinder algorithms to select the most stable reference genes. Phosphoglycerate kinase 1 (PGK1 was one of the optimal normalization genes for both whole blood and PBMC RNA, however, additional genes differed for the two sample types; Ribosomal protein large, P0 (RPLP0 for PBMC RNA and Peptidylprolyl isomerase B (PPIB for whole blood RNA. We also show that the use of a single reference gene is sufficient for normalization when the most stable candidates are used. Conclusions We have identified PGK1 as a stable reference gene for use with whole blood RNA and RNA derived from PBMC. When stable genes are selected it is possible to use a single gene for normalization rather than two or three. Optimal normalization will improve the ability of results from PBMC RNA to be compared with those from whole blood RNA and potentially allows comparison of

  16. GeneChip expression profiling reveals the alterations of energy metabolism related genes in osteocytes under large gradient high magnetic fields.

    Science.gov (United States)

    Wang, Yang; Chen, Zhi-Hao; Yin, Chun; Ma, Jian-Hua; Li, Di-Jie; Zhao, Fan; Sun, Yu-Long; Hu, Li-Fang; Shang, Peng; Qian, Ai-Rong

    2015-01-01

    The diamagnetic levitation as a novel ground-based model for simulating a reduced gravity environment has recently been applied in life science research. In this study a specially designed superconducting magnet with a large gradient high magnetic field (LG-HMF), which can provide three apparent gravity levels (μ-g, 1-g, and 2-g), was used to simulate a space-like gravity environment. Osteocyte, as the most important mechanosensor in bone, takes a pivotal position in mediating the mechano-induced bone remodeling. In this study, the effects of LG-HMF on gene expression profiling of osteocyte-like cell line MLO-Y4 were investigated by Affymetrix DNA microarray. LG-HMF affected osteocyte gene expression profiling. Differentially expressed genes (DEGs) and data mining were further analyzed by using bioinfomatic tools, such as DAVID, iReport. 12 energy metabolism related genes (PFKL, AK4, ALDOC, COX7A1, STC1, ADM, CA9, CA12, P4HA1, APLN, GPR35 and GPR84) were further confirmed by real-time PCR. An integrated gene interaction network of 12 DEGs was constructed. Bio-data mining showed that genes involved in glucose metabolic process and apoptosis changed notablly. Our results demostrated that LG-HMF affected the expression of energy metabolism related genes in osteocyte. The identification of sensitive genes to special environments may provide some potential targets for preventing and treating bone loss or osteoporosis.

  17. GeneChip expression profiling reveals the alterations of energy metabolism related genes in osteocytes under large gradient high magnetic fields.

    Directory of Open Access Journals (Sweden)

    Yang Wang

    Full Text Available The diamagnetic levitation as a novel ground-based model for simulating a reduced gravity environment has recently been applied in life science research. In this study a specially designed superconducting magnet with a large gradient high magnetic field (LG-HMF, which can provide three apparent gravity levels (μ-g, 1-g, and 2-g, was used to simulate a space-like gravity environment. Osteocyte, as the most important mechanosensor in bone, takes a pivotal position in mediating the mechano-induced bone remodeling. In this study, the effects of LG-HMF on gene expression profiling of osteocyte-like cell line MLO-Y4 were investigated by Affymetrix DNA microarray. LG-HMF affected osteocyte gene expression profiling. Differentially expressed genes (DEGs and data mining were further analyzed by using bioinfomatic tools, such as DAVID, iReport. 12 energy metabolism related genes (PFKL, AK4, ALDOC, COX7A1, STC1, ADM, CA9, CA12, P4HA1, APLN, GPR35 and GPR84 were further confirmed by real-time PCR. An integrated gene interaction network of 12 DEGs was constructed. Bio-data mining showed that genes involved in glucose metabolic process and apoptosis changed notablly. Our results demostrated that LG-HMF affected the expression of energy metabolism related genes in osteocyte. The identification of sensitive genes to special environments may provide some potential targets for preventing and treating bone loss or osteoporosis.

  18. Bioinformatic analysis of patient-derived ASPS gene expressions and ASPL-TFE3 fusion transcript levels identify potential therapeutic targets.

    Directory of Open Access Journals (Sweden)

    David G Covell

    Full Text Available Gene expression data, collected from ASPS tumors of seven different patients and from one immortalized ASPS cell line (ASPS-1, was analyzed jointly with patient ASPL-TFE3 (t(X;17(p11;q25 fusion transcript data to identify disease-specific pathways and their component genes. Data analysis of the pooled patient and ASPS-1 gene expression data, using conventional clustering methods, revealed a relatively small set of pathways and genes characterizing the biology of ASPS. These results could be largely recapitulated using only the gene expression data collected from patient tumor samples. The concordance between expression measures derived from ASPS-1 and both pooled and individual patient tumor data provided a rationale for extending the analysis to include patient ASPL-TFE3 fusion transcript data. A novel linear model was exploited to link gene expressions to fusion transcript data and used to identify a small set of ASPS-specific pathways and their gene expression. Cellular pathways that appear aberrantly regulated in response to the t(X;17(p11;q25 translocation include the cell cycle and cell adhesion. The identification of pathways and gene subsets characteristic of ASPS support current therapeutic strategies that target the FLT1 and MET, while also proposing additional targeting of genes found in pathways involved in the cell cycle (CHK1, cell adhesion (ARHGD1A, cell division (CDC6, control of meiosis (RAD51L3 and mitosis (BIRC5, and chemokine-related protein tyrosine kinase activity (CCL4.

  19. Large scale gene expression profiles of regenerating inner ear sensory epithelia.

    Directory of Open Access Journals (Sweden)

    R David Hawkins

    2007-06-01

    Full Text Available Loss of inner ear sensory hair cells (HC is a leading cause of human hearing loss and balance disorders. Unlike mammals, many lower vertebrates can regenerate these cells. We used cross-species microarrays to examine this process in the avian inner ear. Specifically, changes in expression of over 1700 transcription factor (TF genes were investigated in hair cells of auditory and vestibular organs following treatment with two different damaging agents and regeneration in vitro. Multiple components of seven distinct known signaling pathways were clearly identifiable: TGFbeta, PAX, NOTCH, WNT, NFKappaB, INSULIN/IGF1 and AP1. Numerous components of apoptotic and cell cycle control pathways were differentially expressed, including p27(KIP and TFs that regulate its expression. A comparison of expression trends across tissues and treatments revealed identical patterns of expression that occurred at identical times during regenerative proliferation. Network analysis of the patterns of gene expression in this large dataset also revealed the additional presence of many components (and possible network interactions of estrogen receptor signaling, circadian rhythm genes and parts of the polycomb complex (among others. Equal numbers of differentially expressed genes were identified that have not yet been placed into any known pathway. Specific time points and tissues also exhibited interesting differences: For example, 45 zinc finger genes were specifically up-regulated at later stages of cochlear regeneration. These results are the first of their kind and should provide the starting point for more detailed investigations of the role of these many pathways in HC recovery, and for a description of their possible interactions.

  20. "Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis.

    Science.gov (United States)

    Fondi, Marco; Karkman, Antti; Tamminen, Manu V; Bosi, Emanuele; Virta, Marko; Fani, Renato; Alm, Eric; McInerney, James O

    2016-05-13

    The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as "everything is everywhere but the environment selects." While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  1. Large-scale deletions of the ABCA1 gene in patients with hypoalphalipoproteinemia.

    Science.gov (United States)

    Dron, Jacqueline S; Wang, Jian; Berberich, Amanda J; Iacocca, Michael A; Cao, Henian; Yang, Ping; Knoll, Joan; Tremblay, Karine; Brisson, Diane; Netzer, Christian; Gouni-Berthold, Ioanna; Gaudet, Daniel; Hegele, Robert A

    2018-06-04

    Copy-number variations (CNVs) have been studied in the context of familial hypercholesterolemia but have not yet been evaluated in patients with extremes of high-density lipoprotein (HDL) cholesterol levels. We evaluated targeted next-generation sequencing data from patients with very low HDL cholesterol (i.e. hypoalphalipoproteinemia) using the VarSeq-CNV caller algorithm to screen for CNVs disrupting the ABCA1, LCAT or APOA1 genes. In four individuals, we found three unique deletions in ABCA1: a heterozygous deletion of exon 4, a heterozygous deletion spanning exons 8 to 31, and a heterozygous deletion of the entire ABCA1 gene. Breakpoints were identified using Sanger sequencing, and the full-gene deletion was also confirmed using exome sequencing and the Affymetrix CytoScanTM HD Array. Before now, large-scale deletions in candidate HDL genes have not been associated with hypoalphalipoproteinemia; our findings indicate that CNVs in ABCA1 may be a previously unappreciated genetic determinant of low HDL cholesterol levels. By coupling bioinformatic analyses with next-generation sequencing data, we can successfully assess the spectrum of genetic determinants of many dyslipidemias, now including hypoalphalipoproteinemia. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Reconstruction of Oomycete Genome Evolution Identifies Differences in Evolutionary Trajectories Leading to Present-Day Large Gene Families

    NARCIS (Netherlands)

    Seidl, M.F.; Ackerveken, van den G.; Govers, F.; Snel, B.

    2012-01-01

    The taxonomic class of oomycetes contains numerous pathogens of plants and animals but is related to nonpathogenic diatoms and brown algae. Oomycetes have flexible genomes comprising large gene families that play roles in pathogenicity. The evolutionary processes that shaped the gene content have

  3. Directed partial correlation: inferring large-scale gene regulatory network through induced topology disruptions.

    Directory of Open Access Journals (Sweden)

    Yinyin Yuan

    Full Text Available Inferring regulatory relationships among many genes based on their temporal variation in transcript abundance has been a popular research topic. Due to the nature of microarray experiments, classical tools for time series analysis lose power since the number of variables far exceeds the number of the samples. In this paper, we describe some of the existing multivariate inference techniques that are applicable to hundreds of variables and show the potential challenges for small-sample, large-scale data. We propose a directed partial correlation (DPC method as an efficient and effective solution to regulatory network inference using these data. Specifically for genomic data, the proposed method is designed to deal with large-scale datasets. It combines the efficiency of partial correlation for setting up network topology by testing conditional independence, and the concept of Granger causality to assess topology change with induced interruptions. The idea is that when a transcription factor is induced artificially within a gene network, the disruption of the network by the induction signifies a genes role in transcriptional regulation. The benchmarking results using GeneNetWeaver, the simulator for the DREAM challenges, provide strong evidence of the outstanding performance of the proposed DPC method. When applied to real biological data, the inferred starch metabolism network in Arabidopsis reveals many biologically meaningful network modules worthy of further investigation. These results collectively suggest DPC is a versatile tool for genomics research. The R package DPC is available for download (http://code.google.com/p/dpcnet/.

  4. Recombinant protein production from stable mammalian cell lines and pools.

    Science.gov (United States)

    Hacker, David L; Balasubramanian, Sowmya

    2016-06-01

    We highlight recent developments for the production of recombinant proteins from suspension-adapted mammalian cell lines. We discuss the generation of stable cell lines using transposons and lentivirus vectors (non-targeted transgene integration) and site-specific recombinases (targeted transgene integration). Each of these methods results in the generation of cell lines with protein yields that are generally superior to those achievable through classical plasmid transfection that depends on the integration of the transfected DNA by non-homologous DNA end-joining. This is the main reason why these techniques can also be used for the generation of stable cell pools, heterogenous populations of recombinant cells generated by gene delivery and genetic selection without resorting to single cell cloning. This allows the time line from gene transfer to protein production to be reduced. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Large scale experiments simulating hydrogen distribution in a spent fuel pool building during a hypothetical fuel uncovery accident scenario

    Energy Technology Data Exchange (ETDEWEB)

    Mignot, Guillaume; Paranjape, Sidharth; Paladino, Domenico; Jaeckel, Bernd; Rydl, Adolf [Paul Scherrer Institute, Villigen (Switzerland)

    2016-08-15

    Following the Fukushima accident and its extended station blackout, attention was brought to the importance of the spent fuel pools' (SFPs) behavior in case of a prolonged loss of the cooling system. Since then, many analytical works have been performed to estimate the timing of hypothetical fuel uncovery for various SFP types. Experimentally, however, little was done to investigate issues related to the formation of a flammable gas mixture, distribution, and stratification in the SFP building itself and to some extent assess the capability for the code to correctly predict it. This paper presents the main outcomes of the Experiments on Spent Fuel Pool (ESFP) project carried out under the auspices of Swissnuclear (Framework 2012–2013) in the PANDA facility at the Paul Scherrer Institut in Switzerland. It consists of an experimental investigation focused on hydrogen concentration build-up into a SFP building during a predefined scaled scenario for different venting positions. Tests follow a two-phase scenario. Initially steam is released to mimic the boiling of the pool followed by a helium/steam mixture release to simulate the deterioration of the oxidizing spent fuel. Results shows that while the SFP building would mainly be inerted by the presence of a high concentration of steam, the volume located below the level of the pool in adjacent rooms would maintain a high air content. The interface of the two-gas mixture presents the highest risk of flammability. Additionally, it was observed that the gas mixture could become stagnant leading locally to high hydrogen concentration while steam condenses. Overall, the experiments provide relevant information for the potentially hazardous gas distribution formed in the SFP building and hints on accident management and on eventual retrofitting measures to be implemented in the SFP building.

  6. Life cycle environmental implications of residential swimming pools.

    Science.gov (United States)

    Forrest, Nigel; Williams, Eric

    2010-07-15

    Ownership of private swimming pools in the U.S. grew 2 to 4% per annum from 1997 to 2007. The environmental implications of pool ownership are analyzed by hybrid life cycle assessment (LCA) for nine U.S. cities. An operational model is constructed estimating consumption of chemicals, water, and energy for a typical residential pool. The model incorporates geographical climatic variations and upstream water and energy use from electricity and water supply networks. Results vary considerably by city: a factor of 5-6 for both water and energy use. Water use is driven by aridness and length of the swimming season, while energy use is mainly driven by length of the swimming season. Water and energy impacts of pools are significant, particularly in arid climates. In Phoenix for example pools account for 22% and 13% of a household's electricity and water use, respectively. Measures to reduce water and energy use in pools such as optimizing the pump schedule and covering the pool in winter can realize greater savings than many common household efficiency improvements. Private versus community pools are also compared. Community pools in Phoenix use 60% less swimming pool water and energy per household than subdivisions without community pools.

  7. Microbial Diversity and Ecology in the Interfaces of the Deep-sea Anoxic Brine Pools in the Red Sea

    KAUST Repository

    Hikmawan, Tyas I.

    2015-05-01

    Deep-sea anoxic brine pools are one of the most extreme ecosystems on Earth, which are characterized by drastic changes in salinity, temperature, and oxygen concentration. The interface between the brine and overlaying seawater represents a boundary of oxic-anoxic layer and a steep gradient of redox potential that would initiate favorable conditions for divergent metabolic activities, mainly methanogenesis and sulfate reduction. This study aimed to investigate the diversity of Bacteria, particularly sulfate-reducing communities, and their ecological roles in the interfaces of five geochemically distinct brine pools in the Red Sea. Performing a comprehensive study would enable us to understand the significant role of the microbial groups in local geochemical cycles. Therefore, we combined culture-dependent approach and molecular methods, such as 454 pyrosequencing of 16S rRNA gene, phylogenetic analysis of functional marker gene encoding for the alpha subunits of dissimilatory sulfite reductase (dsrA), and single-cell genomic analysis to address these issues. Community analysis based on 16S rRNA gene sequences demonstrated high bacterial diversity and domination of Bacteria over Archaea in most locations. In the hot and multilayered Atlantis II Deep, the bacterial communities were stratified and hardly overlapped. Meanwhile in the colder brine pools, sulfatereducing Deltaproteobacteria were the most prominent bacterial groups inhabiting the interfaces. Corresponding to the bacterial community profile, the analysis of dsrA gene sequences revealed collectively high diversity of sulfate-reducing communities. Desulfatiglans-like dsrA was the prevalent group and conserved across the Red Sea brine pools. In addition to the molecular studies, more than thirty bacterial strains were successfully isolated and remarkably were found to be cytotoxic against the cancer cell lines. However, none of them were sulfate reducers. Thus, a single-cell genomic analysis was used to study

  8. Uniparental genetic heritage of belarusians: encounter of rare middle eastern matrilineages with a central European mitochondrial DNA pool.

    Science.gov (United States)

    Kushniarevich, Alena; Sivitskaya, Larysa; Danilenko, Nina; Novogrodskii, Tadeush; Tsybovsky, Iosif; Kiseleva, Anna; Kotova, Svetlana; Chaubey, Gyaneshwer; Metspalu, Ene; Sahakyan, Hovhannes; Bahmanimehr, Ardeshir; Reidla, Maere; Rootsi, Siiri; Parik, Jüri; Reisberg, Tuuli; Achilli, Alessandro; Hooshiar Kashani, Baharak; Gandini, Francesca; Olivieri, Anna; Behar, Doron M; Torroni, Antonio; Davydenko, Oleg; Villems, Richard

    2013-01-01

    Ethnic Belarusians make up more than 80% of the nine and half million people inhabiting the Republic of Belarus. Belarusians together with Ukrainians and Russians represent the East Slavic linguistic group, largest both in numbers and territory, inhabiting East Europe alongside Baltic-, Finno-Permic- and Turkic-speaking people. Till date, only a limited number of low resolution genetic studies have been performed on this population. Therefore, with the phylogeographic analysis of 565 Y-chromosomes and 267 mitochondrial DNAs from six well covered geographic sub-regions of Belarus we strove to complement the existing genetic profile of eastern Europeans. Our results reveal that around 80% of the paternal Belarusian gene pool is composed of R1a, I2a and N1c Y-chromosome haplogroups - a profile which is very similar to the two other eastern European populations - Ukrainians and Russians. The maternal Belarusian gene pool encompasses a full range of West Eurasian haplogroups and agrees well with the genetic structure of central-east European populations. Our data attest that latitudinal gradients characterize the variation of the uniparentally transmitted gene pools of modern Belarusians. In particular, the Y-chromosome reflects movements of people in central-east Europe, starting probably as early as the beginning of the Holocene. Furthermore, the matrilineal legacy of Belarusians retains two rare mitochondrial DNA haplogroups, N1a3 and N3, whose phylogeographies were explored in detail after de novo sequencing of 20 and 13 complete mitogenomes, respectively, from all over Eurasia. Our phylogeographic analyses reveal that two mitochondrial DNA lineages, N3 and N1a3, both of Middle Eastern origin, might mark distinct events of matrilineal gene flow to Europe: during the mid-Holocene period and around the Pleistocene-Holocene transition, respectively.

  9. Adding to Yersinia enterocolitica Gene Pool Diversity: Two Cryptic Plasmids from a Biotype 1A Isolate

    Directory of Open Access Journals (Sweden)

    Daniela Lepka

    2009-01-01

    Full Text Available We report the nucleotide sequence of two novel cryptic plasmids (4357 and 14 662 base pairs carried by a Yersinia enterocolitica biotype 1A strain isolated from pork. As distinguished from most biotype 1A strains, this isolate, designated 07-04449, exhibited adherence to eukaryotic cells. The smaller plasmid pYe4449-1 carries five attributable open reading frames (ORFs encoding the first CcdA/CcdB-like antitoxin/toxin system described for a Yersinia plasmid, a RepA-like replication initiation protein, and mobilizing factors MobA and MobC. The deduced amino acid sequences showed highest similarity to proteins described in Salmonella (CcdA/B, Klebsiella (RepA, and Plesiomonas (MobA/C indicating genomic fluidity among members of the Enterobacteriaceae. One additional ORF with unknown function, termed ORF5, was identified with an ancestry distinct from the rest of the plasmid. While the C+G content of ORF5 is 38.3%, the rest of pYe4449-1 shows a C+G content of 55.7%. The C+G content of the larger plasmid pYe4449-2 (54.9% was similar to that of pYe4449-1 (53.7% and differed from that of the Y. enterocolitica genome (47.3%. Of the 14 ORFs identified on pYe4449-2, only six ORFs showed significant similarity to database entries. For three of these ORFs likely functions could be ascribed: a TnpR-like resolvase and a phage replication protein, localized each on a low C+G island, and DNA primase TraC. Two ORFs of pYe4449-2, ORF3 and ORF7, seem to encode secretable proteins. Epitope-tagging of ORF3 revealed protein expression at 4°C but not at or above 27°C suggesting adaptation to a habitat outside swine. The hypothetical protein encoded by ORF7 is the member of a novel repeat protein family sharing the DxxGN(xnDxxGN motif. Our findings illustrate the exceptional gene pool diversity within the species Y. enterocolitica driven by horizontal gene transfer events.

  10. Structure for nuclear fuel storage pools

    International Nuclear Information System (INIS)

    Ebata, Sakae; Nichiei, Shinji.

    1979-01-01

    Purpose: To enable leak detection in nuclear fuel storage pools, as well as prevent external leakages while keeping the strength of the constructional structures. Constitution: Protection plates are provided around pool linear plates and a leak reception is provided to the bottom. Leakages are detected by leak detecting pipeways and the external leakages are prevented by collecting them in a detection area provided in the intermediate layer. Since ferro-reinforcements at the bottom wall of the pool are disconnected by the protection plate making it impossible to form the constructional body, body hunches are provided to the bottom wall of the pool for processing the ferro-reinforcements. (Yoshino, Y.)

  11. Study on the polymorphism of POU1F1 gene in sheep

    Directory of Open Access Journals (Sweden)

    Jun Yan Bai

    Full Text Available ABSTRACT In this study, POU1F1 gene polymorphism was detected in five sheep populations (large-tailed Han, small-tailed Han, Yuxi fat-tailed, Lanzhou large-tailed, and Mongolian sheep, using DNA pooling and sequencing, to provide theoretical basis for the breeding of excellent sheep varieties. Three single-nucleotide polymorphism (SNP loci of POU1F1 gene were detected in five sheep populations, namely C355T (C/T, C71G (C/G, and C330G (C/G. C and T frequencies of C355T were 0.67/0.33, 0.81/0.19, 0.67/0.33, 1.00/0.00, and 0.93/0.07, respectively, in large-tailed Han, small-tailed Han, Yuxi fat-tailed, Mongolian, and Lanzhou large-tailed sheep. C of C355T locus was the dominant allele in five sheep populations. C and G allele frequencies of C330G locus were detected in Yuxi fat-tailed sheep; their frequencies were 0.75 and 0.25, respectively. C and G allele of C71G locus were only detected in Yuxi fat-tailed and large-tailed Han sheep; their frequencies were 0.87/0.13 and 0.87/0.13, respectively. The cluster analysis based on POU1F1 gene sequence showed that bactrian camel, dromedary, and wild camel clustered first, and dolphin and killer whales clustered according to taxonomy. Although the four species Tibetan antelope, buffalo, goat, and sheep were alone, they got close and the relative genetic relationship was intimate according to the dendrogram. The mutation site analysis of the POU1F1 gene in five sheep populations in this study would be favorable for uncovering the function of POU1F1 gene deeply.

  12. Gene decay in Shigella as an incipient stage of host-adaptation.

    Directory of Open Access Journals (Sweden)

    Ye Feng

    Full Text Available BACKGROUND: Many facultative bacterial pathogens have undergone extensive gene decay processes, possibly due to lack of selection pressure during evolutionary conversion from free-living to intracellular lifestyle. Shigella, the causative agents of human shigellosis, have arisen from different E. coli-like ancestors independently by convergent paths. As these bacteria all have lost large numbers of genes by mutation or deletion, they can be used as ideal models for systematically studying the process of gene function loss in different bacteria living under similar selection pressures. METHODOLOGIES/PRINCIPAL FINDINGS: We compared the sequenced Shigella genomes and re-defined decayed genes (pseudogenes plus deleted genes in these bacteria. Altogether, 85 genes are commonly decayed in the five analyzed Shigella strains and 1456 genes are decayed in at least one Shigella strain. Genes coding for carbon utilization, cell motility, transporter or membrane proteins are prone to be inactivated. Decayed genes tend to concentrate in certain operons rather than distribute averagely across the whole genome. Genes in the decayed operon accumulated more non-synonymous mutations than the rest genes and meanwhile have lower expression levels. CONCLUSIONS: Different Shigella lineages underwent convergent gene decay processes, and inactivation of one gene would lead to a lesser selection pressure for the other genes in the same operon. The pool of superfluous genes for Shigella may contain at least two thousand genes and the gene decay processes may still continue in Shigella until a minimum genome harboring only essential genes is reached.

  13. Evaporation-preventive device for nuclear reactor pool water

    International Nuclear Information System (INIS)

    Kurusu, Yoshihisa; Akabori, Shiro.

    1986-01-01

    Purpose: To prevent pool water from evaporating by a great amount in a reactor pool such as a spent fuel storing pool. Constitution: Air discharge and in-take ports are disposed just above the surface of the pool water and charge and discharge of airs are forcively carried out to form air curtains above the pool water. Water vapor evaporated from the surface of the pool water does not diffuse above the air curtains due to the air stream of the curtains, but is intaken into the intake port and then condensated into water by a steam condensator and re-supplied to the pool. Since diffusion of water vapor and radioactive materials are suppressed above the air curtains, the working circumstance in the pool chamber can be maintained desirably thereby keeping the radioactivity dose in the atmosphere. Further, incorporation of dusts from above into the pool can also be prevented by the air curtains to provide an effect for the prevention of radioactive contamination. Further, since covers are not used, visual observation can be insured. (Kawakami, Y.)

  14. Evolution of the pilot infrastructure of CMS towards a single glideinWMS pool

    CERN Document Server

    Gutsche, Oliver

    2013-01-01

    CMS production and analysis job submission is based largely on glideinWMS and pilot submissions. The transition from multiple different submission solutions like gLite WMS and HTCondor-based implementations was carried out over years and is coming now to a conclusion. The historically explained separate glideinWMS pools for different types of production jobs and analysis jobs are being unified into a single global pool. This enables CMS to benefit from global prioritization and scheduling possibilities. It also presents the sites with only one kind of pilots and eliminates the need of having to make scheduling decisions on the CE level. This paper provides an analysis of the benefits of a unified resource pool, as well as a description of the resulting global policy. It will explain the technical challenges moving forward and present solutions to some of them.

  15. Evolution of the pilot infrastructure of CMS: towards a single glideinWMS pool

    Science.gov (United States)

    Belforte, S.; Gutsche, O.; Letts, J.; Majewski, K.; McCrea, A.; Sfiligoi, I.

    2014-06-01

    CMS production and analysis job submission is based largely on glideinWMS and pilot submissions. The transition from multiple different submission solutions like gLite WMS and HTCondor-based implementations was carried out over years and is coming now to a conclusion. The historically explained separate glideinWMS pools for different types of production jobs and analysis jobs are being unified into a single global pool. This enables CMS to benefit from global prioritization and scheduling possibilities. It also presents the sites with only one kind of pilots and eliminates the need of having to make scheduling decisions on the CE level. This paper provides an analysis of the benefits of a unified resource pool, as well as a description of the resulting global policy. It will explain the technical challenges moving forward and present solutions to some of them.

  16. Evolution of the pilot infrastructure of CMS: towards a single glideinWMS pool

    International Nuclear Information System (INIS)

    Belforte, S; Gutsche, O; Majewski, K; Letts, J; McCrea, A; Sfiligoi, I

    2014-01-01

    CMS production and analysis job submission is based largely on glideinWMS and pilot submissions. The transition from multiple different submission solutions like gLite WMS and HTCondor-based implementations was carried out over years and is coming now to a conclusion. The historically explained separate glideinWMS pools for different types of production jobs and analysis jobs are being unified into a single global pool. This enables CMS to benefit from global prioritization and scheduling possibilities. It also presents the sites with only one kind of pilots and eliminates the need of having to make scheduling decisions on the CE level. This paper provides an analysis of the benefits of a unified resource pool, as well as a description of the resulting global policy. It will explain the technical challenges moving forward and present solutions to some of them.

  17. Ripples in a superconducting tidal pool

    CERN Document Server

    Hudson, E

    2003-01-01

    The behaviour of electrons in a metal is often compared to that of water in a pool. An empty pool is like a material that has all of its electrons removed. As electrons are 'poured' into the metal, they first occupy the lowest energies available - the bottom of the pool - and eventually fill up to the Fermi energy, the top of the pool. At this point we no longer discuss electrons but quasiparticles. These are electrons that have modified properties due to their interactions within the material. Waves in a pool can be excited, and their properties will depend on the depth of the water. Similarly in a metal, quasiparticles behave like waves that have a material-dependent dispersion relation between their energy and their wavevector, which specifies their direction and wavelength. This simple analogy also hints at an indirect method of measuring the dispersion relation of a metal, and hence the myriad of properties that depend on it. (U.K.)

  18. Screening for Residual Disease in Pediatric Burkitt Lymphoma Using Consensus Primer Pools

    Directory of Open Access Journals (Sweden)

    Melissa Agsalda

    2009-01-01

    Full Text Available Assessing molecular persistent or minimal residual disease (PD/MRD in childhood Burkitt lymphoma (BL is challenging because access to original tumor is usually needed to design patient-specific primers (PSPs. Because BL is characterized by rearranged immunoglobulin heavy chain (IgVH genes, IgVH primer pools from IgVH1–IgVH7 regions were tested to detect PD/MRD, thus eliminating the need for original tumor. The focus of the current study was to assess the feasibility of using IgVH primer pools to detect disease in clinical specimens. Fourteen children diagnosed with B-NHL had follow-up repository specimens available to assess PD/MRD. Of the 14 patients, 12 were PD/MRD negative after 2 months of therapy and remained in remission at the end of therapy; 2/14 patients were PD/MRD positive at 2-3 months and later relapsed. PSP-based assays from these 14 patients showed 100% concordance with the current assay. This feasibility study warrants further investigation to assess PD/MRD using IgVH primer pools, which could have clinical significance as a real-time assessment tool to monitor pediatric BL and possibly other B-cell non-Hodgkin lymphoma therapy.

  19. Screening for residual disease in pediatric burkitt lymphoma using consensus primer pools.

    Science.gov (United States)

    Agsalda, Melissa; Kusao, Ian; Troelstrup, David; Shiramizu, Bruce

    2009-01-01

    Assessing molecular persistent or minimal residual disease (PD/MRD) in childhood Burkitt lymphoma (BL) is challenging because access to original tumor is usually needed to design patient-specific primers (PSPs). Because BL is characterized by rearranged immunoglobulin heavy chain (IgV(H)) genes, IgV(H) primer pools from IgV(H1)-IgV(H7) regions were tested to detect PD/MRD, thus eliminating the need for original tumor. The focus of the current study was to assess the feasibility of using IgV(H) primer pools to detect disease in clinical specimens. Fourteen children diagnosed with B-NHL had follow-up repository specimens available to assess PD/MRD. Of the 14 patients, 12 were PD/MRD negative after 2 months of therapy and remained in remission at the end of therapy; 2/14 patients were PD/MRD positive at 2-3 months and later relapsed. PSP-based assays from these 14 patients showed 100% concordance with the current assay. This feasibility study warrants further investigation to assess PD/MRD using IgV(H) primer pools, which could have clinical significance as a real-time assessment tool to monitor pediatric BL and possibly other B-cell non-Hodgkin lymphoma therapy.

  20. Vortex-ring-induced large bubble entrainment during drop impact

    KAUST Repository

    Thoraval, Marie-Jean; Li, Yangfan; Thoroddsen, Sigurdur T

    2016-01-01

    , produced in the neck between the drop and the pool, controls the crater deformations and pinchoff. However, it is not the strongest vortex rings that are responsible for the large bubbles, as they interact too strongly with the pool surface and self

  1. Evaluation of the phospholamban gene in purebred large-breed dogs with dilated cardiomyopathy.

    Science.gov (United States)

    Stabej, Polona; Leegwater, Peter A; Stokhof, Arnold A; Domanjko-Petric, Aleksandra; van Oost, Bernard A

    2005-03-01

    To evaluate the role of the phospholamban gene in purebred large-breed dogs with dilated cardiomyopathy (DCM). 6 dogs with DCM, including 2 Doberman Pinschers, 2 Newfoundlands, and 2 Great Danes. All dogs had clinical signs of congestive heart failure, and a diagnosis of DCM was made on the basis of echocardiographic findings. Blood samples were collected from each dog, and genomic DNA was isolated by a salt extraction method. Specific oligonucleotides were designed to amplify the promoter, exon 1, the 5'-part of exon 2 including the complete coding region, and part of intron 1 of the canine phospholamban gene via polymerase chain reaction procedures. These regions were screened for mutations in DNA obtained from the 6 dogs with DCM. No mutations were identified in the promoter, 5' untranslated region, part of intron 1, part of the 3' untranslated region, and the complete coding region of the phospholamban gene in dogs with DCM. Results indicate that mutations in the phospholamban gene are not a frequent cause of DCM in Doberman Pinschers, Newfoundlands, and Great Danes.

  2. Generalizing Pooling Functions in CNNs: Mixed, Gated, and Tree.

    Science.gov (United States)

    Lee, Chen-Yu; Gallagher, Patrick; Tu, Zhuowen

    2018-04-01

    In this paper, we seek to improve deep neural networks by generalizing the pooling operations that play a central role in the current architectures. We pursue a careful exploration of approaches to allow pooling to learn and to adapt to complex and variable patterns. The two primary directions lie in: (1) learning a pooling function via (two strategies of) combining of max and average pooling, and (2) learning a pooling function in the form of a tree-structured fusion of pooling filters that are themselves learned. In our experiments every generalized pooling operation we explore improves performance when used in place of average or max pooling. We experimentally demonstrate that the proposed pooling operations provide a boost in invariance properties relative to conventional pooling and set the state of the art on several widely adopted benchmark datasets. These benefits come with only a light increase in computational overhead during training (ranging from additional 5 to 15 percent in time complexity) and a very modest increase in the number of model parameters (e.g., additional 1, 9, and 27 parameters for mixed, gated, and 2-level tree pooling operators, respectively). To gain more insights about our proposed pooling methods, we also visualize the learned pooling masks and the embeddings of the internal feature responses for different pooling operations. Our proposed pooling operations are easy to implement and can be applied within various deep neural network architectures.

  3. Large-scale pattern of genetic differentiation within African rainforest trees: insights on the roles of ecological gradients and past climate changes on the evolution of Erythrophleum spp (Fabaceae).

    Science.gov (United States)

    Duminil, Jerome; Brown, Richard P; Ewédjè, Eben-Ezer B K; Mardulyn, Patrick; Doucet, Jean-Louis; Hardy, Olivier J

    2013-09-12

    The evolutionary events that have shaped biodiversity patterns in the African rainforests are still poorly documented. Past forest fragmentation and ecological gradients have been advocated as important drivers of genetic differentiation but their respective roles remain unclear. Using nuclear microsatellites (nSSRs) and chloroplast non-coding sequences (pDNA), we characterised the spatial genetic structure of Erythrophleum (Fabaceae) forest trees in West and Central Africa (Guinea Region, GR). This widespread genus displays a wide ecological amplitude and taxonomists recognize two forest tree species, E. ivorense and E. suaveolens, which are difficult to distinguish in the field and often confused. Bayesian-clustering applied on nSSRs of a blind sample of 648 specimens identified three major gene pools showing no or very limited introgression. They present parapatric distributions correlated to rainfall gradients and forest types. One gene pool is restricted to coastal evergreen forests and corresponds to E. ivorense; a second one is found in gallery forests from the dry forest zone of West Africa and North-West Cameroon and corresponds to West-African E. suaveolens; the third gene pool occurs in semi-evergreen forests and corresponds to Central African E. suaveolens. These gene pools have mostly unique pDNA haplotypes but they do not form reciprocally monophyletic clades. Nevertheless, pDNA molecular dating indicates that the divergence between E. ivorense and Central African E. suaveolens predates the Pleistocene. Further Bayesian-clustering applied within each major gene pool identified diffuse genetic discontinuities (minor gene pools displaying substantial introgression) at a latitude between 0 and 2°N in Central Africa for both species, and at a longitude between 5° and 8°E for E. ivorense. Moreover, we detected evidence of past population declines which are consistent with historical habitat fragmentation induced by Pleistocene climate changes. Overall

  4. Gravity and Heater Size Effects on Pool Boiling Heat Transfer

    Science.gov (United States)

    Kim, Jungho; Raj, Rishi

    2014-01-01

    The current work is based on observations of boiling heat transfer over a continuous range of gravity levels between 0g to 1.8g and varying heater sizes with a fluorinert as the test liquid (FC-72/n-perfluorohexane). Variable gravity pool boiling heat transfer measurements over a wide range of gravity levels were made during parabolic flight campaigns as well as onboard the International Space Station. For large heaters and-or higher gravity conditions, buoyancy dominated boiling and heat transfer results were heater size independent. The power law coefficient for gravity in the heat transfer equation was found to be a function of wall temperature under these conditions. Under low gravity conditions and-or for smaller heaters, surface tension forces dominated and heat transfer results were heater size dependent. A pool boiling regime map differentiating buoyancy and surface tension dominated regimes was developed along with a unified framework that allowed for scaling of pool boiling over a wide range of gravity levels and heater sizes. The scaling laws developed in this study are expected to allow performance quantification of phase change based technologies under variable gravity environments eventually leading to their implementation in space based applications.

  5. Formation of trihalomethanes as disinfection byproducts in herbal spa pools.

    Science.gov (United States)

    Fakour, Hoda; Lo, Shang-Lien

    2018-04-09

    Herbal spa treatments are favorite recreational activities throughout the world. The water in spas is often disinfected to control pathogenic microorganisms and guarantee hygiene. However, chlorinated water may cause the formation of disinfection byproducts (DBPs). Although there have been many studies on DBP formation in swimming pools, the role of organic matter derived from herbal medicines applied in herbal spa water has been largely neglected. Accordingly, the present study investigated the effect of herbal medicines on the formation of trihalomethanes (THMs) in simulated herbal spa water. Water samples were collected from a spa pool, and then, disinfection and herbal addition experiments were performed in a laboratory. The results showed that the organic molecules introduced by the herbal medicines are significant precursors to the formation of THMs in spa pool water. Since at least 50% of THMs were produced within the first six hours of the reaction time, the presence of herbal medicines in spa water could present a parallel route for THM exposure. Therefore, despite the undeniable benefits of herbal spas, the effect of applied herbs on DBP formation in chlorinated water should be considered to improve the water quality and health benefits of spa facilities.

  6. Preliminary results of the US pool-boiling coils from the IFSMTF full-array tests

    International Nuclear Information System (INIS)

    Lue, J.W.; Dresner, L.; Lubell, M.S.; Luton, J.N.; McManamy, T.J.; Shen, S.S.

    1986-01-01

    The Large Coil Task to develop superconducting magnets for fusion reactors, is now in the midst of full-array tests in the International Fusion Superconducting Magnet Test Facility at Oak Ridge National Laboratory. Included in the test array are two pool-boiling coils designed and fabricated by US manufacturers, General Dynamics/Convair Division and General Electric/Union Carbide Corporation. So far, both coils have been energized to full design currents in the single-coil tests, and the General Dynamics coil has reached the design point in the first Standard-I full-array test. Both coils performed well in the charging experiments. Extensive heating tests and the heavy instrumentation of these coils have, however, revealed some generic limitations of large pool-boiling superconducting coils. Details of these results and their analyses are reported

  7. XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing.

    Science.gov (United States)

    Piton, Amélie; Redin, Claire; Mandel, Jean-Louis

    2013-08-08

    Because of the unbalanced sex ratio (1.3-1.4 to 1) observed in intellectual disability (ID) and the identification of large ID-affected families showing X-linked segregation, much attention has been focused on the genetics of X-linked ID (XLID). Mutations causing monogenic XLID have now been reported in over 100 genes, most of which are commonly included in XLID diagnostic gene panels. Nonetheless, the boundary between true mutations and rare non-disease-causing variants often remains elusive. The sequencing of a large number of control X chromosomes, required for avoiding false-positive results, was not systematically possible in the past. Such information is now available thanks to large-scale sequencing projects such as the National Heart, Lung, and Blood (NHLBI) Exome Sequencing Project, which provides variation information on 10,563 X chromosomes from the general population. We used this NHLBI cohort to systematically reassess the implication of 106 genes proposed to be involved in monogenic forms of XLID. We particularly question the implication in XLID of ten of them (AGTR2, MAGT1, ZNF674, SRPX2, ATP6AP2, ARHGEF6, NXF5, ZCCHC12, ZNF41, and ZNF81), in which truncating variants or previously published mutations are observed at a relatively high frequency within this cohort. We also highlight 15 other genes (CCDC22, CLIC2, CNKSR2, FRMPD4, HCFC1, IGBP1, KIAA2022, KLF8, MAOA, NAA10, NLGN3, RPL10, SHROOM4, ZDHHC15, and ZNF261) for which replication studies are warranted. We propose that similar reassessment of reported mutations (and genes) with the use of data from large-scale human exome sequencing would be relevant for a wide range of other genetic diseases. Copyright © 2013 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  8. Technical specification for fabrication of HANARO pool cover

    Energy Technology Data Exchange (ETDEWEB)

    Ryu, Jeong Soo; Woo, Sang Ik

    2001-06-01

    This technical specification details the requirements and the acceptance criteria for design, seismic analysis, function test, installation and quality assurance for HANARO pool cover which will be installed at the top of reactor pool. The pool cover is classified as non-nuclear safety, seismic category II and quality class T. The basic design of the pool cover for increasing HANARO applications has been carried out for supporting the driving devices which can load, unload and rotate the irradiation targets in the in-core and out-core vertical irradiation holes under on-power operation. The comments of HANARO user group related with irradiation tests have optimally considered in the process of design. The interference between fuel handling and control absorber units in the reactor pool and activities to load, unload and rotate the irradiation targets at the top of the reactor pool have been minimized. The pool cover can be moved for maintenance and can protect the reactor pool from unexpected drop of foreign materials. It provides the space to vertical access of driving devices for NTD, CT/IR and OR4/OR5 under on-power operation. And the pool cover assembly must maintain its structural integrity under seismic load. Based on the above design concept, the HANARO pool cover has been proposed as supporting structure of driving devices for NTD, fission moly and RI production under on-power operation.

  9. A large-scale benchmark of gene prioritization methods.

    Science.gov (United States)

    Guala, Dimitri; Sonnhammer, Erik L L

    2017-04-21

    In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations. The Gene Ontology(GO) contains genes clustered around annotation terms. This intrinsic property of GO can be utilized in construction of robust benchmarks, objective to the problem domain. We demonstrate how this can be achieved for network-based gene prioritization tools, utilizing the FunCoup network. We use cross-validation and a set of appropriate performance measures to compare state-of-the-art gene prioritization algorithms: three based on network diffusion, NetRank and two implementations of Random Walk with Restart, and MaxLink that utilizes network neighborhood. Our benchmark suite provides a systematic and objective way to compare the multitude of available and future gene prioritization tools, enabling researchers to select the best gene prioritization tool for the task at hand, and helping to guide the development of more accurate methods.

  10. Vortex-induced buckling of a viscous drop impacting a pool

    KAUST Repository

    Li, Erqiang

    2017-07-20

    We study the intricate buckling patterns which can form when a viscous drop impacts a much lower viscosity miscible pool. The drop enters the pool by its impact inertia, flattens, and sinks by its own weight while stretching into a hemispheric bowl. Upward motion along the outer bottom surface of this bowl produces a vortical boundary layer which separates along its top and rolls up into a vortex ring. The vorticity is therefore produced in a fundamentally different way than for a drop impacting a pool of the same liquid. The vortex ring subsequently advects into the bowl, thereby stretching the drop liquid into ever thinner sheets, reaching the micron level. The rotating motion around the vortex pulls in folds to form multiple windings of double-walled toroidal viscous sheets. The axisymmetric velocity field thereby stretches the drop liquid into progressively finer sheets, which are susceptible to both axial and azimuthal compression-induced buckling. The azimuthal buckling of the sheets tends to occur on the inner side of the vortex ring, while their folds can be stretched and straightened on the outside edge. We characterize the total stretching from high-speed video imaging and use particle image velocimetry to track the formation and evolution of the vortex ring. The total interfacial area between the drop and the pool liquid can grow over 40-fold during the first 50 ms after impact. Increasing pool viscosity shows entrapment of a large bubble on top of the drop, while lowering the drop viscosity produces intricate buckled shapes, appearing at the earliest stage and being promoted by the crater motions. We also present an image collage of the most intriguing and convoluted structures observed. Finally, a simple point-vortex model reproduces some features from the experiments and shows variable stretching along the wrapping sheets.

  11. Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness

    Directory of Open Access Journals (Sweden)

    Samuele Bovo

    2015-01-01

    Full Text Available The aim of this study was to identify single nucleotide polymorphisms (SNPs that could be associated with back fat thickness (BFT in pigs. To achieve this goal, we evaluated the potential and limits of an experimental design that combined several methodologies. DNA samples from two groups of Italian Large White pigs with divergent estimating breeding value (EBV for BFT were separately pooled and sequenced, after preparation of reduced representation libraries (RRLs, on the Ion Torrent technology. Taking advantage from SNAPE for SNPs calling in sequenced DNA pools, 39,165 SNPs were identified; 1/4 of them were novel variants not reported in dbSNP. Combining sequencing data with Illumina PorcineSNP60 BeadChip genotyping results on the same animals, 661 genomic positions overlapped with a good approximation of minor allele frequency estimation. A total of 54 SNPs showing enriched alleles in one or in the other RRLs might be potential markers associated with BFT. Some of these SNPs were close to genes involved in obesity related phenotypes.

  12. Analysis of large deletions in BRCA1, BRCA2 and PALB2 genes in Finnish breast and ovarian cancer families

    International Nuclear Information System (INIS)

    Pylkäs, Katri; Erkko, Hannele; Nikkilä, Jenni; Sólyom, Szilvia; Winqvist, Robert

    2008-01-01

    BRCA1 and BRCA2 are the two most important genes associated with familial breast and ovarian cancer susceptibility. In addition, PALB2 has recently been identified as a breast cancer susceptibility gene in several populations. Here we have evaluated whether large genomic rearrangement in these genes could explain some of Finnish breast and/or ovarian cancer families. Altogether 61 index patients of Northern Finnish breast and/or ovarian cancer families were analyzed by Multiplex ligation-dependent probe amplification (MLPA) method in order to identify exon deletions and duplications in BRCA1, BRCA2 and PALB2. The families have been comprehensively screened for germline mutation in these genes by conventional methods of mutation analysis and were found negative. We identified one large deletion in BRCA1, deleting the most part of the gene (exon 1A-13) in one family with family history of ovarian cancer. No large genomic rearrangements were identified in either BRCA2 or PALB2. In Finland, women eligible for BRCA1 or BRCA2 mutation screening, when found negative, could benefit from screening for large genomic rearrangements at least in BRCA1. On the contrary, the genomic rearrangements in PALB2 seem not to contribute to the hereditary breast cancer susceptibility

  13. Decontamination of outdoor school swimming pools in Fukushima

    International Nuclear Information System (INIS)

    Saegusa, Jun

    2013-01-01

    After the Fukushima Daiichi NPP accident following the Great East Japan Earthquake, many school swimming pools in Fukushima have suspended water discharge, due to concerns that pool water which contains radioactive fallout is discharged into a river or waterway for agricultural use. The Japan Atomic Energy Agency conducted researches and examinations on the existing absorbent method and the flocculation method as ways for decontaminating pool water. By reviewing and improving these methods through decontamination demonstrations at eight pools in Fukushima, a practical decontamination method for outdoor pools has been established. This report summarizes the methods and results of the decontamination demonstrations carried out at the schools. Also, the surface density of fallout estimated at one of the pools is also presented and discussed in connection with the overall collection ratio of radiocesium at the pool. (author)

  14. 48 CFR 873.114 - Best value pool.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Best value pool. 873.114... SUPPLEMENTARY REGULATIONS SIMPLIFIED ACQUISITION PROCEDURES FOR HEALTH-CARE RESOURCES 873.114 Best value pool... solicitation. These vendors constitute the best value pool. This determination is within the sole discretion of...

  15. Biological consequences of ancient gene acquisition and duplication in the large genome soil bacterium, ""solibacter usitatus"" strain Ellin6076

    Energy Technology Data Exchange (ETDEWEB)

    Challacombe, Jean F [Los Alamos National Laboratory; Eichorst, Stephanie A [Los Alamos National Laboratory; Xie, Gary [Los Alamos National Laboratory; Kuske, Cheryl R [Los Alamos National Laboratory; Hauser, Loren [ORNL; Land, Miriam [ORNL

    2009-01-01

    Bacterial genome sizes range from ca. 0.5 to 10Mb and are influenced by gene duplication, horizontal gene transfer, gene loss and other evolutionary processes. Sequenced genomes of strains in the phylum Acidobacteria revealed that 'Solibacter usistatus' strain Ellin6076 harbors a 9.9 Mb genome. This large genome appears to have arisen by horizontal gene transfer via ancient bacteriophage and plasmid-mediated transduction, as well as widespread small-scale gene duplications. This has resulted in an increased number of paralogs that are potentially ecologically important (ecoparalogs). Low amino acid sequence identities among functional group members and lack of conserved gene order and orientation in the regions containing similar groups of paralogs suggest that most of the paralogs were not the result of recent duplication events. The genome sizes of cultured subdivision 1 and 3 strains in the phylum Acidobacteria were estimated using pulsed-field gel electrophoresis to determine the prevalence of the large genome trait within the phylum. Members of subdivision 1 were estimated to have smaller genome sizes ranging from ca. 2.0 to 4.8 Mb, whereas members of subdivision 3 had slightly larger genomes, from ca. 5.8 to 9.9 Mb. It is hypothesized that the large genome of strain Ellin6076 encodes traits that provide a selective metabolic, defensive and regulatory advantage in the variable soil environment.

  16. Modeling of condensation, stratification, and mixing phenomena in a pool of water

    Energy Technology Data Exchange (ETDEWEB)

    Li, H.; Kudinov, P.; Villanueva, W. (Royal Institute of Technology (KTH). Div. of Nuclear Power Safety, Stockholm (Sweden))

    2010-12-15

    This work pertains to the research program on Containment Thermal-Hydraulics at KTH. The objective is to evaluate and improve performance of methods, which are used to analyze thermal-hydraulics of steam suppression pools in a BWR plant under different abnormal transient and accident conditions. As a passive safety system, the function of steam pressure suppression pools is paramount to the containment performance. In the present work, the focus is on apparently-benign but intricate and potentially risk-significant scenarios in which thermal stratification could significantly impede the pool's pressure suppression capacity. For the case of small flow rates of steam influx, the steam condenses rapidly in the pool and the hot condensate rises in a narrow plume above the steam injection plane and spreads into a thin layer at the pool's free surface. When the steam flow rate increases significantly, momentum introduced by the steam injection and/or periodic expansion and shrink of large steam bubbles due to direct contact condensation can cause breakdown of the stratified layers and lead to mixing of the pool water. Accurate prediction of the pool thermal-hydraulics in such scenarios presents a computational challenge. Lumped-parameter models have no capability to predict temperature distribution of water pool during thermal stratification development. While high-order-accurate CFD (RANS, LES) methods are not practical due to excessive computing power needed to calculate 3D high-Rayleighnumber natural circulation flow in long transients. In the present work, a middleground approach is used, namely CFD-like model of the general purpose thermalhydraulic code GOTHIC. Each cell of 3D GOTHIC grid uses lumped parameter volume type closures for modeling of various heat and mass transfer processes at subgrid scale. We use GOTHIC to simulate POOLEX/PPOOLEX experiment, in order to (a) quantify errors due to GOTHIC's physical models and numerical schemes, and (b

  17. Just-in-Time Compound Pooling Increases Primary Screening Capacity without Compromising Screening Quality.

    Science.gov (United States)

    Elkin, L L; Harden, D G; Saldanha, S; Ferguson, H; Cheney, D L; Pieniazek, S N; Maloney, D P; Zewinski, J; O'Connell, J; Banks, M

    2015-06-01

    Compound pooling, or multiplexing more than one compound per well during primary high-throughput screening (HTS), is a controversial approach with a long history of limited success. Many issues with this approach likely arise from long-term storage of library plates containing complex mixtures of compounds at high concentrations. Due to the historical difficulties with using multiplexed library plates, primary HTS often uses a one-compound-one-well approach. However, as compound collections grow, innovative strategies are required to increase the capacity of primary screening campaigns. Toward this goal, we have developed a novel compound pooling method that increases screening capacity without compromising data quality. This method circumvents issues related to the long-term storage of complex compound mixtures by using acoustic dispensing to enable "just-in-time" compound pooling directly in the assay well immediately prior to assay. Using this method, we can pool two compounds per well, effectively doubling the capacity of a primary screen. Here, we present data from pilot studies using just-in-time pooling, as well as data from a large >2-million-compound screen using this approach. These data suggest that, for many targets, this method can be used to vastly increase screening capacity without significant reduction in the ability to detect screening hits. © 2015 Society for Laboratory Automation and Screening.

  18. Pooled nucleic acid testing to identify antiretroviral treatment failure during HIV infection.

    Science.gov (United States)

    May, Susanne; Gamst, Anthony; Haubrich, Richard; Benson, Constance; Smith, Davey M

    2010-02-01

    Pooling strategies have been used to reduce the costs of polymerase chain reaction-based screening for acute HIV infection in populations in which the prevalence of acute infection is low (less than 1%). Only limited research has been done for conditions in which the prevalence of screening positivity is higher (greater than 1%). We present data on a variety of pooling strategies that incorporate the use of polymerase chain reaction-based quantitative measures to monitor for virologic failure among HIV-infected patients receiving antiretroviral therapy. For a prevalence of virologic failure between 1% and 25%, we demonstrate relative efficiency and accuracy of various strategies. These results could be used to choose the best strategy based on the requirements of individual laboratory and clinical settings such as required turnaround time of results and availability of resources. Virologic monitoring during antiretroviral therapy is not currently being performed in many resource-constrained settings largely because of costs. The presented pooling strategies may be used to significantly reduce the cost compared with individual testing, make such monitoring feasible, and limit the development and transmission of HIV drug resistance in resource-constrained settings. They may also be used to design efficient pooling strategies for other settings with quantitative screening measures.

  19. Factors driving semi-aquatic predator occurrence in traditional cattle drinking pools: conservation issues

    Directory of Open Access Journals (Sweden)

    Raoul Manenti

    2016-08-01

    Full Text Available In several cases, human impact on water bodies and on their freshwater communities is detrimental, but in some cases the human activity may favour and enhance the biodiversity of small water bodies, as traditional cattle drinking pools. Despite their small size, small water bodies may constitute hot spot of biodiversity often representing the only lentic aquatic biotope in landscapes where superficial water lacks or flows in lotic environments like creeks and streams. Predators are good indicators of biodiversity in ponds and give information of food chain web complexity. In particular, semi-aquatic predators like amphibians and dragonflies may account for a substantial percentage of energy flow between aquatic and terrestrial ecosystems. In this study, we evaluated the conservation value of traditional cattle drinking pools building by assessing the factors determining the occurrence and distribution of the semi-aquatic predators. From April to August 2015, we investigated 30 distinct pools recording several abiotic and biotic environmental variables. We detected 4 semi-aquatic predators: Salamandra salamandra larvae, Triturus carnifex, Aeshna sp. larvae and Libellula sp. larvae. Abiotic features played a major role in shaping the predator community that resulted linked to stable, with no dryness period, and large drinking pools. Invertebrate prey biomass was not particularly important, while vegetation cover and occurrence of unpalatable tadpoles were the most important biotic features of the pools. Our study provides novel evidence on the importance of cattle drinking pools management to preserve biodiversity especially in areas where traditional pastoral activity is disappearing.

  20. Distribution and elevated soil pools of mercury in an acidic subtropical forest of southwestern China

    International Nuclear Information System (INIS)

    Zhou, Jun; Wang, Zhangwei; Zhang, Xiaoshan; Chen, Jian

    2015-01-01

    Tieshanping catchment in southwest China was supposed to a large pool of atmospheric mercury. This work was aimed to examine THg (total mercury) concentrations, pools and influence factors in the acidic forest. THg concentrations were highly elevated in the study area, which was significantly depended on TOM (total organic matter) concentrations and altitudinal elevation, whereas negatively correlated with soil pH. The pools of mercury accumulated in soils were correlated strongly with the stocks of TOM and altitude, ranged from 5.9 to 32 mg m −2 and averaged 14.5 mg m −2 , indicating that the acidic forest was a great sink of atmospheric mercury in southwest China. THg concentrations in stream waters decreased with altitude increasing and regression analyses showed that soil/air exchange flux would be increased with the decrease of altitude. Present results suggest that elevation increasing decreases THg losses as low THg concentrations in runoffs and volatilization from soils. - Highlights: • Soil THg pools and influence factors were studied at an acidic catchment in southwestern China. • THg concentrations was increased significantly with TOM concentrations and altitude increasing, decreased with pH. • THg pools in soils were highly elevated and deepened on TOM pools and altitude. • Difference in THg output by volatilization and runoff was a major reason for THg distribution at different altitudes. - Mercury pools increased with altitude increasing as mercury lost more at low elevation area in acidic subtropical forest

  1. Investigation of Processes Controlling Elution of Solutes from Nonaqueous Phase Liquid (NAPL) Pools into Groundwater

    Science.gov (United States)

    Seyedabbasi, M.; Pirestani, K.; Holland, S. B.; Imhoff, P. T.

    2005-12-01

    Two major processes influencing the elution of solutes from porous media contaminated with nonaqueous phase liquids (NAPLs) are external mass transfer between the NAPL and groundwater and internal diffusion through NAPL ganglia and pools. There is a relatively large body of literature on the dissolution of single-species NAPLs. Less is known about the rates of elution of compounds dissolving from multicomponent NAPLs. We examined the mass transfer of one solute, 2,3-dimethyl-2-butanol (DMB) - a partitioning tracer, between groundwater and a dense NAPL - trichloroethylene (TCE). Diffusion cell experiments were used to measure the molecular diffusion coefficient of DMB in pure TCE and in porous media contaminated with a TCE pool. Measured diffusion coefficients were compared with empirical correlations (pure TCE) and a parallel resistance model (TCE pool). Based on the results from these analyses, a dimensionless Biot number was derived to express the ratio of the external rate of mass transfer from a NAPL pool to the internal rate of diffusion within the pool, which varies with NAPL saturation and NAPL-water partition coefficient. Biot numbers were then estimated for several laboratory scale experiments involving DMB transport between NAPL pools and groundwater. The estimated Biot numbers were in good agreement with experimental results. The expression for the Biot number developed here may be used to assess the processes controlling the elution of solutes from NAPL pools, which has implications on long-term predictions of solute dissolution from NAPLs in the field.

  2. A large-scale RNA interference screen identifies genes that regulate autophagy at different stages.

    Science.gov (United States)

    Guo, Sujuan; Pridham, Kevin J; Virbasius, Ching-Man; He, Bin; Zhang, Liqing; Varmark, Hanne; Green, Michael R; Sheng, Zhi

    2018-02-12

    Dysregulated autophagy is central to the pathogenesis and therapeutic development of cancer. However, how autophagy is regulated in cancer is not well understood and genes that modulate cancer autophagy are not fully defined. To gain more insights into autophagy regulation in cancer, we performed a large-scale RNA interference screen in K562 human chronic myeloid leukemia cells using monodansylcadaverine staining, an autophagy-detecting approach equivalent to immunoblotting of the autophagy marker LC3B or fluorescence microscopy of GFP-LC3B. By coupling monodansylcadaverine staining with fluorescence-activated cell sorting, we successfully isolated autophagic K562 cells where we identified 336 short hairpin RNAs. After candidate validation using Cyto-ID fluorescence spectrophotometry, LC3B immunoblotting, and quantitative RT-PCR, 82 genes were identified as autophagy-regulating genes. 20 genes have been reported previously and the remaining 62 candidates are novel autophagy mediators. Bioinformatic analyses revealed that most candidate genes were involved in molecular pathways regulating autophagy, rather than directly participating in the autophagy process. Further autophagy flux assays revealed that 57 autophagy-regulating genes suppressed autophagy initiation, whereas 21 candidates promoted autophagy maturation. Our RNA interference screen identifies identified genes that regulate autophagy at different stages, which helps decode autophagy regulation in cancer and offers novel avenues to develop autophagy-related therapies for cancer.

  3. Molecular Identification and Quantification of Tetracycline and Erythromycin Resistance Genes in Spanish and Italian Retail Cheeses

    Directory of Open Access Journals (Sweden)

    Ana Belén Flórez

    2014-01-01

    Full Text Available Large antibiotic resistance gene pools in the microbiota of foods may ultimately pose a risk for human health. This study reports the identification and quantification of tetracycline- and erythromycin-resistant populations, resistance genes, and gene diversity in traditional Spanish and Italian cheeses, via culturing, conventional PCR, real-time quantitative PCR (qPCR, and denaturing gradient gel electrophoresis (DGGE. The numbers of resistant bacteria varied widely among the antibiotics and the different cheese varieties; in some cheeses, all the bacterial populations seemed to be resistant. Up to eight antibiotic resistance genes were sought by gene-specific PCR, six with respect to tetracycline, that is, tet(K, tet(L, tet(M, tet(O, tet(S, and tet(W, and two with respect to erythromycin, that is, erm(B and erm(F. The most common resistance genes in the analysed cheeses were tet(S, tet(W, tet(M, and erm(B. The copy numbers of these genes, as quantified by qPCR, ranged widely between cheeses (from 4.94 to 10.18log⁡10/g. DGGE analysis revealed distinct banding profiles and two polymorphic nucleotide positions for tet(W-carrying cheeses, though the similarity of the sequences suggests this tet(W to have a monophyletic origin. Traditional cheeses would therefore appear to act as reservoirs for large numbers of many types of antibiotic resistance determinants.

  4. FARO tests corium-melt cooling in water pool: Roles of melt superheat and sintering in sediment

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Gisuk [Department of Mechanical Engineering, Wichita State University, Wichita, KS 67260 (United States); Kaviany, Massoud [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Division of Advance Nuclear Engineering, POSTECH, Pohang, Gyeongbuk 790-784 (Korea, Republic of); Moriyama, Kiyofumi [Division of Advance Nuclear Engineering, POSTECH, Pohang, Gyeongbuk 790-784 (Korea, Republic of); Park, Hyun Sun, E-mail: hejsunny@postech.ac.kr [Division of Advance Nuclear Engineering, POSTECH, Pohang, Gyeongbuk 790-784 (Korea, Republic of); Hwang, Byoungcheol; Lee, Mooneon; Kim, Eunho; Park, Jin Ho [Division of Advance Nuclear Engineering, POSTECH, Pohang, Gyeongbuk 790-784 (Korea, Republic of); Nasersharifi, Yahya [Department of Mechanical Engineering, Wichita State University, Wichita, KS 67260 (United States)

    2016-08-15

    Highlights: • The numerical approach for FARO experimental data is suggested. • The cooling mechanism of ex-vessel corium is suggested. • The predicted minimum pool depth for no cake formation is suggested. - Abstract: The FARO tests have aimed at understanding an important severe accident mitigation action in a light water reactor when the accident progresses from the reactor pressure vessel boundary. These tests have aimed to measure the coolability of a molten core material (corium) gravity dispersed as jet into a water pool, quantifying the loose particle diameter distribution and fraction converted to cake under range of initial melt superheat and pool temperature and depth. Under complete hydrodynamic breakup of corium and consequent sedimentation in the pool, the initially superheated corium can result in debris bed consisting of discrete solid particles (loose debris) and/or a solid cake at the bottom of the pool. The success of the debris bed coolability requires cooling of the cake, and this is controlled by the large internal resistance. We postulate that the corium cake forms when there is a remelting part in the sediment. We show that even though a solid shell forms around the melt particles transiting in the water pool due to film-boiling heat transfer, the superheated melt allows remelting of the large particles in the sediment (depending on the water temperature and the transit time) using the COOLAP (Coolability Analysis with Parametric fuel-cooant interaction models) code. With this remelting and its liquid-phase sintering of the non-remelted particles, we predict the fraction of the melt particles converting to a cake through liquid sintering. Our predictions are in good agreement with the existing results of the FARO experiments. We address only those experiments with pool depths sufficient/exceeding the length required for complete breakup of the molten jet. Our analysis of the fate of molten corium aimed at devising the effective

  5. Pharmacokinetics and pharmacogenetics of the MEK1/2 inhibitor, selumetinib, in Asian and Western healthy subjects: a pooled analysis.

    Science.gov (United States)

    Dymond, Angela W; Elks, Cathy; Martin, Paul; Carlile, David J; Mariani, Gabriella; Lovick, Susan; Huang, Yifan; Lorch, Ulrike; Brown, Helen; So, Karen

    2017-06-01

    Emerging data on selumetinib, a MEK1/2 inhibitor in clinical development, suggest a possible difference in pharmacokinetics (PK) between Japanese and Western patients. This pooled analysis sought to assess the effect of ethnicity on selumetinib exposure in healthy Western and Asian subjects, and to identify any association between genetic variants in the UGT1A1, CYP2C19 and ABCG2 genes and observed differences in selumetinib PK. A pooled analysis of data from ten Phase I studies, one in Asian subjects (encompassing Japanese, non-Japanese Asian and Indian Asian subjects) and nine in Western subjects, was conducted. Key findings were derived from the collective exposure data across doses of 25, 35, 50 and 75 mg selumetinib; primary variables were dose-normalized AUC and C max . PK data from 308 subjects (10 studies) were available for the pooled analysis; genetic data from 87 subjects (3 studies) were available for the pharmacogenetic analysis. Dose-normalized AUC and C max were 35% (95% CI: 25-47%) and 39% (95% CI: 24-56%) higher in the pooled Asian group, respectively, compared with Western subjects. PK exposure parameters were similar between the Japanese, non-Japanese Asian and Indian groups. There was no evidence that the polymorphisms assessed in the genes UGT1A1, CYP2C19 and ABCG2 account for observed PK differences. Selumetinib exposure was higher in healthy Asian subjects compared with Western subjects, and these data provide valuable insight for clinicians to consider when treating patients of Asian ethnicity with selumetinib.

  6. Delineating probabilistic species pools in ecology and biogeography

    OpenAIRE

    Karger, Dirk Nikolaus; Cord, Anna F; Kessler, Michael; Kreft, Holger; Kühn, Ingolf; Pompe, Sven; Sandel, Brody; Sarmento Cabral, Juliano; Smith, Adam B; Svenning, Jens-Christian; Tuomisto, Hanna; Weigelt, Patrick; Wesche, Karsten

    2016-01-01

    Aim To provide a mechanistic and probabilistic framework for defining the species pool based on species-specific probabilities of dispersal, environmental suitability and biotic interactions within a specific temporal extent, and to show how probabilistic species pools can help disentangle the geographical structure of different community assembly processes. Innovation Probabilistic species pools provide an improved species pool definition based on probabilities in conjuncti...

  7. Gene expression changes governing extreme dehydration tolerance in an Antarctic insect

    Science.gov (United States)

    Teets, Nicholas M.; Peyton, Justin T.; Colinet, Herve; Renault, David; Kelley, Joanna L.; Kawarasaki, Yuta; Lee, Richard E.; Denlinger, David L.

    2012-01-01

    Among terrestrial organisms, arthropods are especially susceptible to dehydration, given their small body size and high surface area to volume ratio. This challenge is particularly acute for polar arthropods that face near-constant desiccating conditions, as water is frozen and thus unavailable for much of the year. The molecular mechanisms that govern extreme dehydration tolerance in insects remain largely undefined. In this study, we used RNA sequencing to quantify transcriptional mechanisms of extreme dehydration tolerance in the Antarctic midge, Belgica antarctica, the world’s southernmost insect and only insect endemic to Antarctica. Larvae of B. antarctica are remarkably tolerant of dehydration, surviving losses up to 70% of their body water. Gene expression changes in response to dehydration indicated up-regulation of cellular recycling pathways including the ubiquitin-mediated proteasome and autophagy, with concurrent down-regulation of genes involved in general metabolism and ATP production. Metabolomics results revealed shifts in metabolite pools that correlated closely with changes in gene expression, indicating that coordinated changes in gene expression and metabolism are a critical component of the dehydration response. Finally, using comparative genomics, we compared our gene expression results with a transcriptomic dataset for the Arctic collembolan, Megaphorura arctica. Although B. antarctica and M. arctica are adapted to similar environments, our analysis indicated very little overlap in expression profiles between these two arthropods. Whereas several orthologous genes showed similar expression patterns, transcriptional changes were largely species specific, indicating these polar arthropods have developed distinct transcriptional mechanisms to cope with similar desiccating conditions. PMID:23197828

  8. Pool water cleaning facility

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Kazuhiro; Kinoshita, Shoichiro [Hitachi Ltd., Tokyo (Japan); Asano, Takashi

    1998-05-29

    Only one system comprising a suppression poor water cleaning system (SPCU) and a filtration desalting tower (F/D) is connected for a plurality of nuclear power plants. Pipelines/valves for connecting the one system of the SPCU pump, the F/D and the plurality of nuclear power plants are disposed, and the system is used in common with the plurality of nuclear power plants. Pipelines/valves for connecting a pipeline for passing SP water to the commonly used SPCU pump and a skimmer surge tank are disposed, and fuel pool water is cooled and cleaned by the commonly used SPCU pump and the commonly used F/D. The number of SPCU pumps and the F/D facilities can be reduced, and a fuel pool water cooling operation mode and a fuel pool water cleaning operation mode which were conducted by an FPC pump so far are conducted by the SPCU pump. (N.H.)

  9. Hydrodynamics of AHWR gravity driven water pool under simulated LOCA conditions

    International Nuclear Information System (INIS)

    Thangamani, I.; Verma, Vishnu; Ali, Seik Mansoor

    2015-01-01

    The Advanced Heavy Water Reactor (AHWR) employs a double containment concept with a large inventory of water within the Gravity Driven Water Pool (GDWP) located at a high elevation within the primary containment building. GDWP performs several important safety functions in a passive manner, and hence it is essential to understand the hydrodynamics that this pool will be subjected to in case of an accident such as LOCA. In this paper, a detailed thermal hydraulic analysis for AHWR containment transients is presented for postulated LOCA scenarios involving RIH break sizes ranging from 2% to 50%. The analysis is carried out using in-house containment thermal hydraulics code 'CONTRAN'. The blowdown mass and energy discharge data for each break size, along with the geometrical details of the AHWR containment forms the main input for the analysis. Apart from obtaining the pressure and temperature transients within the containment building, the focus of this work is on simulating the hydrodynamic phenomena of vent clearing and pool swell occurring in the GDWP. The variation of several key parameters such as primary containment V1 and V2 volume pressure, temperature and V1-V2 differential pressure with time, BOP rupture time, vent clearing velocity, effect of pool swell on the V2 air-space pressure, GDWP water level etc. are discussed in detail and important findings are highlighted. Further, the effect of neglecting the pool swell phenomenon on the containment transients is also clearly brought out by a comparative study. The numerical studies presented in this paper give insight into containment transients that would be useful to both the system designer as well as the regulator. (author)

  10. Disease gene characterization through large-scale co-expression analysis.

    Directory of Open Access Journals (Sweden)

    Allen Day

    2009-12-01

    Full Text Available In the post genome era, a major goal of biology is the identification of specific roles for individual genes. We report a new genomic tool for gene characterization, the UCLA Gene Expression Tool (UGET.Celsius, the largest co-normalized microarray dataset of Affymetrix based gene expression, was used to calculate the correlation between all possible gene pairs on all platforms, and generate stored indexes in a web searchable format. The size of Celsius makes UGET a powerful gene characterization tool. Using a small seed list of known cartilage-selective genes, UGET extended the list of known genes by identifying 32 new highly cartilage-selective genes. Of these, 7 of 10 tested were validated by qPCR including the novel cartilage-specific genes SDK2 and FLJ41170. In addition, we retrospectively tested UGET and other gene expression based prioritization tools to identify disease-causing genes within known linkage intervals. We first demonstrated this utility with UGET using genetically heterogeneous disorders such as Joubert syndrome, microcephaly, neuropsychiatric disorders and type 2 limb girdle muscular dystrophy (LGMD2 and then compared UGET to other gene expression based prioritization programs which use small but discrete and well annotated datasets. Finally, we observed a significantly higher gene correlation shared between genes in disease networks associated with similar complex or Mendelian disorders.UGET is an invaluable resource for a geneticist that permits the rapid inclusion of expression criteria from one to hundreds of genes in genomic intervals linked to disease. By using thousands of arrays UGET annotates and prioritizes genes better than other tools especially with rare tissue disorders or complex multi-tissue biological processes. This information can be critical in prioritization of candidate genes for sequence analysis.

  11. Cardiac tumours: non invasive detection and assessment by gated cardiac blood pool radionuclide imaging

    International Nuclear Information System (INIS)

    Pitcher, D.; Wainwright, R.; Brennand-Roper, D.; Deverall, P.; Sowton, E.; Maisey, M.

    1980-01-01

    Four patients with cardiac tumours were investigated by gated cardiac blood pool radionuclide imaging and echocardiography. Contrast angiocardiography was performed in three of the cases. Two left atrial tumours were detected by all three techniques. In one of these cases echocardiography alone showed additional mitral valve stenosis, but isotope imaging indicated tumour size more accurately. A large septal mass was detected by all three methods. In this patient echocardiography showed evidence of left ventricular outflow obstruction, confirmed at cardiac catheterisation, but gated isotope imaging provided a more detailed assessment of the abnormal cardiac anatomy. In the fourth case gated isotope imaging detected a large right ventricular tumour which had not been identified by echocardiography. Gated cardiac blood pool isotope imaging is a complementary technique to echocardiography for the non-invasive detection and assessment of cardiac tumours. (author)

  12. In Silico Pooling of ChIP-seq Control Experiments

    Science.gov (United States)

    Sun, Guannan; Srinivasan, Rajini; Lopez-Anido, Camila; Hung, Holly A.; Svaren, John; Keleş, Sündüz

    2014-01-01

    As next generation sequencing technologies are becoming more economical, large-scale ChIP-seq studies are enabling the investigation of the roles of transcription factor binding and epigenome on phenotypic variation. Studying such variation requires individual level ChIP-seq experiments. Standard designs for ChIP-seq experiments employ a paired control per ChIP-seq sample. Genomic coverage for control experiments is often sacrificed to increase the resources for ChIP samples. However, the quality of ChIP-enriched regions identifiable from a ChIP-seq experiment depends on the quality and the coverage of the control experiments. Insufficient coverage leads to loss of power in detecting enrichment. We investigate the effect of in silico pooling of control samples within multiple biological replicates, multiple treatment conditions, and multiple cell lines and tissues across multiple datasets with varying levels of genomic coverage. Our computational studies suggest guidelines for performing in silico pooling of control experiments. Using vast amounts of ENCODE data, we show that pairwise correlations between control samples originating from multiple biological replicates, treatments, and cell lines/tissues can be grouped into two classes representing whether or not in silico pooling leads to power gain in detecting enrichment between the ChIP and the control samples. Our findings have important implications for multiplexing samples. PMID:25380244

  13. Genetic diversity within and between broodstocks of the white shrimp Litopenaeus vannamei (Boone, 1931 (Decapoda, Penaeidae and its implication for the gene pool conservation

    Directory of Open Access Journals (Sweden)

    PD. Freitas

    Full Text Available Genetic variation within and between fifteen closed broodstock lines of the Pacific white shrimp Litopenaeus vannamei, reared at different hatcheries in the Brazilian coast, was assessed by RAPD analysis. Fifty two polymorphic loci were identified when a set of five decamer primers was used in PCR. The genetic diversity analysis within lines evidenced genetic variation loss probably related to bottleneck effects and inbreeding. In addition, the genetic divergence values between the different samples appear to reflect the initial founder composition of such stocks, in some cases, sharing a common origin, suggesting a putative importance of interbreeding for the establishment of genetic improvement programs for these broodstocks. The genetic variation monitoring appears to be helpful to the gene pool conservation of this aquaculture species, mainly if considered its exotic status in Brazil and the current impossibility of new introduction of wild individuals.

  14. Current operating practices of nuclear insurance pools

    International Nuclear Information System (INIS)

    O'Connell, J.M.

    1993-01-01

    This paper discusses the nuclear pooling system and co-operation between the pools, present practice and capacity, with a breakdown of the limits for third party liability and material damage. The author also describes the relationship between the pools and the nuclear operators (the policyholders), and concludes that the nuclear pools have been successful in serving the interests of their member companies, their policyholders and the governments as they have provided a stable insurance market by making available capacity in amounts that had never before been assembled and placed at risk in a single location. 2 tabs

  15. Heat transfer from internally heated hemispherical pools

    International Nuclear Information System (INIS)

    Gabor, J.D.; Ellsion, P.G.; Cassulo, J.C.

    1980-01-01

    Experiments were conducted on heat transfer from internally heated ZnSO 4 -H 2 O pools to the walls of hemispherical containers. This experimental technique provides data for a heat transfer system that has to date been only theoretically treated. Three different sizes of copper hemispherical containers were used: 240, 280, 320 mm in diameter. The pool container served both as a heat transfer surface and as an electrode. The opposing electrode was a copper disk, 50 mm in diameter located at the top of the pool in the center. The top surface of the pool was open to the atmosphere

  16. High-throughput strategy for molecular identification of Vel- blood donors employing nucleic acids extracted from plasma pools used for viral nucleic acid test screening.

    Science.gov (United States)

    Dezan, Marcia R; Dinardo, Carla L; Bosi, Silvia R A; Vega, Sileni; Salles, Nanci A; Mendrone-Júnior, Alfredo; Levi, José E

    2016-06-01

    Serologic methods to determine the Vel- phenotype require the use of rare human antisera and do not allow for many samples to be tested simultaneously, which limits their application as a tool to search for rare donors. This study developed a low-cost molecular screening strategy using real-time polymerase chain reaction (PCR) and DNA, extracted from plasma pools for viral nucleic acid test (NAT) screening, to identify Vel- and Vel+(W) donors. A total of 4680 blood donors from the Brazilian southeast region were genotyped through real-time PCR targeting the 17-nucleotide (c.64_80del) deletion in the SMIM1 gene, which determines the Vel- phenotype, by using remaining nucleic acid from plasma pools of six donors, routinely discarded after the release of viral NAT results. Twenty pools tested reactive and individual testing of samples from reactive pools identified 19 heterozygous donors with the SMIM1*64_80del deletion (0.40%) and one homozygous donor (0.02%). Fourteen of the 19 donors were confirmed as Vel- or Vel+(W) using anti-Vel human antiserum. The DNA pool genotyping strategy using real-time PCR designed to detect the deletion in the SMIM1 gene proved effective and accurate in identifying donors with the Vel- and Vel+(W) phenotypes. The fact that remaining nucleic acid from routine viral NAT screening was used makes this technique economically attractive and definitely superior to the serologic techniques available to search for this rare phenotype. © 2016 AABB.

  17. Cooling device for reactor suppression pool

    International Nuclear Information System (INIS)

    Togasaki, Susumu; Kato, Kiyoshi.

    1994-01-01

    In a cooling device of a reactor suppression pool, when a temperature of pool water is abnormally increased and a heat absorbing portion is heated by, for example, occurrence of an accident, coolants are sent to the outside of the reactor container to actuates a thermally operating portion by the heat energy of coolants and drive heat exchanging fluids of a secondary cooling system. If the heat exchanging fluids are sent to a cooling portion, the coolants are cooled and returned to the heat absorbing portion of the suppression pool water. If the heat absorbing portion is heat pipes, the coolants are evaporated by heat absorbed from the suppression pool water, steams are sent to the thermally operating portion, then coolants are liquefied and caused to return to the heat absorbing portion. If the thermal operation portion is a gas turbine, the gas turbine is operated by the coolants, and it is converted to a rotational force to drive heat exchanging fluids by pumps. By constituting the cooling portion with a condensator, the coolants are condensed and liquefied and returned to the heat absorbing portion of the suppression pool water. (N.H.)

  18. Structure of pool in reactor building

    International Nuclear Information System (INIS)

    Yokoyama, Shigeki.

    1997-01-01

    Shielding walls made of iron-reinforced concrete having a metal liner including two body walls rigidly combined to the upper surface of a reactor container are disposed at least to one of an equipment pool or spent fuel storage pool in a reactor building. A rack for temporarily placing an upper lattice plate is detachably attached at least above one of a steam dryer or a gas/liquid separator temporarily placed in the temporary pool, and the height from the bottom portion to the upper end of the shielding wall is determined based on the height of an upper lattice plate temporary placed on the rack and the water depth required for shielding radiation from the upper lattice plate. An operator's exposure on the operation floor can be reduced by the shielding wall, and radiation dose from the spent fuels is reduced. The increase of the height of a pool guarder enhances bending resistance as a ceiling. In addition, the total height of them is made identical with the depth of the spent fuel storage pool thereby enabling to increase storage area for spent fuels. (N.H.)

  19. Mercury concentrations and pools in four adjacent coniferous and deciduous upland forests in Beijing, China

    Science.gov (United States)

    Zhou, Jun; Wang, Zhangwei; Zhang, Xiaoshan; Gao, Yu

    2017-05-01

    Understanding of forest mercury (Hg) pools is important for quantifying the global atmospheric Hg removal. We studied gaseous elemental Hg (GEM) concentrations, litterfall Hg depositions, and pool sizes in four adjacent stands at Mount Dongling to assess Hg dynamics in the forested catchment and the potential of Hg release during wildfires. The average GEM concentration was 2.5 ± 0.5 ng m-3, about 1.5 times of the background levels in the Northern Hemisphere. In all four stands, Hg concentrations increase in the following order: bole wood mineral soil litter < Oe soil < Oa organic soil. The Hg pools of aboveground biomass were comparable in the forests of larch, oak, and Chinese pine, which were much greater than that of mixed broadleaf stands due to lower biomass. The total Hg pools in ecosystems were similar in the four stands, because of the comparable Hg pool in the soil horizons (0-40 cm), which accounted for over 97% of the total ecosystem Hg storage in the four stands. Although Hg pools of the forest ecosystem in north China were comparable to North America and North Europe, Hg storage in forests constituted a high threat for large Hg emission pulses to the atmosphere by wildfires. The potential Hg emissions from the combustion at the four stands were ranged from 0.675 to 1.696 mg m-2.

  20. Conditional estimation of local pooled dispersion parameter in small-sample RNA-Seq data improves differential expression test.

    Science.gov (United States)

    Gim, Jungsoo; Won, Sungho; Park, Taesung

    2016-10-01

    High throughput sequencing technology in transcriptomics studies contribute to the understanding of gene regulation mechanism and its cellular function, but also increases a need for accurate statistical methods to assess quantitative differences between experiments. Many methods have been developed to account for the specifics of count data: non-normality, a dependence of the variance on the mean, and small sample size. Among them, the small number of samples in typical experiments is still a challenge. Here we present a method for differential analysis of count data, using conditional estimation of local pooled dispersion parameters. A comprehensive evaluation of our proposed method in the aspect of differential gene expression analysis using both simulated and real data sets shows that the proposed method is more powerful than other existing methods while controlling the false discovery rates. By introducing conditional estimation of local pooled dispersion parameters, we successfully overcome the limitation of small power and enable a powerful quantitative analysis focused on differential expression test with the small number of samples.

  1. Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria

    DEFF Research Database (Denmark)

    Farnelid, Hanna; Andersson, Anders F.; Bertilsson, Stefan

    2011-01-01

    analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity...... by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least...

  2. Optimization of heat pump system in indoor swimming pool using particle swarm algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Wen-Shing; Kung, Chung-Kuan [Department of Energy and Refrigerating Air-Conditioning Engineering, National Taipei University of Technology, 1, Section 3, Chung-Hsiao East Road, Taipei (China)

    2008-09-15

    When it comes to indoor swimming pool facilities, a large amount of energy is required to heat up low-temperature outdoor air before it is being introduced indoors to maintain indoor humidity. Since water is evaporated from the pool surface, the exhausted air contains more water and specific enthalpy. In response to this indoor air, heat pump is generally used in heat recovery for indoor swimming pools. To reduce the cost in energy consumption, this paper utilizes particle swarm algorithm to optimize the design of heat pump system. The optimized parameters include continuous parameters and discrete parameters. The former consists of outdoor air mass flow and heat conductance of heat exchangers; the latter comprises compressor type and boiler type. In a case study, life cycle energy cost is considered as an objective function. In this regard, the optimized outdoor air flow and the optimized design for heating system can be deduced by using particle swarm algorithm. (author)

  3. Salmonella testing of pooled pre-enrichment broth cultures for screening multiple food samples.

    Science.gov (United States)

    Price, W R; Olsen, R A; Hunter, J E

    1972-04-01

    A method has been described for testing multiple food samples for Salmonella without loss in sensitivity. The method pools multiple pre-enrichment broth cultures into single enrichment broths. The subsequent stages of the Salmonella analysis are not altered. The method was found applicable to several dry food materials including nonfat dry milk, dried egg albumin, cocoa, cottonseed flour, wheat flour, and shredded coconut. As many as 25 pre-enrichment broth cultures were pooled without apparent loss in the sensitivity of Salmonella detection as compared to individual sample analysis. The procedure offers a simple, yet effective, way to increase sample capacity in the Salmonella testing of foods, particularly where a large proportion of samples ordinarily is negative. It also permits small portions of pre-enrichment broth cultures to be retained for subsequent individual analysis if positive tests are found. Salmonella testing of pooled pre-enrichment broths provides increased consumer protection for a given amount of analytical effort as compared to individual sample analysis.

  4. Aspects of DNA repair and nucleotide pool imbalance

    Energy Technology Data Exchange (ETDEWEB)

    Holliday, R.

    1985-01-01

    Evidence that optimum repair depends on adequate pools of deoxynucleotide triphosphates (dNTPs) comes from the study of pyrimidine auxotrophs of Ustilago maydis. These strains are sensitive to UV light and X-rays, and for pyr1-1 it has been shown that the intracellular concentration of dTTP is reduced about 7-fold. The survival curve of pyr1-1 after UV-treatment, and split dose experiments with wild-type cells, provide evidence for an inducible repair mechanism, which probably depends on genetic recombination. Although inducible repair saves cellular resources, it has the disadvantage of becoming ineffective at doses which are high enough to inactivate the repressed structural gene(s) for repair enzymes. It is clear that a wide variety of repair mechanisms have evolved to remove lesions which arise either spontaneously or as a result of damage from external agents. Nevertheless, it would be incorrect to assume that all species require all possible pathways of repair. It is now well established that the accuracy of DNA and protein synthesis depends on proof-reading or editing mechanisms. Optimum accuracy levels will evolve from the balance between error avoidance in macromolecular synthesis and physiological efficiency in growth and propagation.

  5. Pool gateway seal

    International Nuclear Information System (INIS)

    Starr, J.A.; Steinert, L.A.

    1983-01-01

    A device for sealing a gateway between interconnectable pools in a nuclear facility comprising a frame supporting a liquid impermeable sheet positioned in a u-shaped gateway between the pools. An inflatable tube carried in a channel in the periphery of the frame and adjoining the gateway provides a seal therebetween when inflated. A restraining arrangement on the bottom edge of the frame is releasably engagable with an adjacent portion of the gateway to restrict the movement of the frame in the u-shaped gateway upon inflation of the tube, thereby enhancing the seal. The impermeable sheet is formed of an elastomer and thus is conformable to a liquid permeable supportive wall upon application of liquid pressure to the side of the sheet opposite the wall

  6. Recent advances in probabilistic species pool delineations

    Directory of Open Access Journals (Sweden)

    Dirk Nikolaus Karger

    2016-07-01

    Full Text Available A species pool is the set of species that could potentially colonize and establish within a community. It has been a commonly used concept in biogeography since the early days of MacArthur and Wilson’s work on Island Biogeography. Despite their simple and appealing definition, an operational application of species pools is bundled with a multitude of problems, which have often resulted in arbitrary decisions and workarounds when defining species pools. Two recently published papers address the operational problems of species pool delineations, and show ways of delineating them in a probabilistic fashion. In both papers, species pools were delineated using a process-based, mechanistical approach, which opens the door for a multitude of new applications in biogeography. Such applications include detecting the hidden signature of biotic interactions, disentangling the geographical structure of community assembly processes, and incorporating a temporal extent into species pools. Although similar in their conclusions, both ‘probabilistic approaches’ differ in their implementation and definitions. Here I give a brief overview of the differences and similarities of both approaches, and identify the challenges and advantages in their application.

  7. Genome organization and expression of the rat ACBP gene family

    DEFF Research Database (Denmark)

    Mandrup, S; Andreasen, P H; Knudsen, J

    1993-01-01

    pool former. We have molecularly cloned and characterized the rat ACBP gene family which comprises one expressed and four processed pseudogenes. One of these was shown to exist in two allelic forms. A comprehensive computer-aided analysis of the promoter region of the expressed ACBP gene revealed...

  8. Large-scale modeling of condition-specific gene regulatory networks by information integration and inference.

    Science.gov (United States)

    Ellwanger, Daniel Christian; Leonhardt, Jörn Florian; Mewes, Hans-Werner

    2014-12-01

    Understanding how regulatory networks globally coordinate the response of a cell to changing conditions, such as perturbations by shifting environments, is an elementary challenge in systems biology which has yet to be met. Genome-wide gene expression measurements are high dimensional as these are reflecting the condition-specific interplay of thousands of cellular components. The integration of prior biological knowledge into the modeling process of systems-wide gene regulation enables the large-scale interpretation of gene expression signals in the context of known regulatory relations. We developed COGERE (http://mips.helmholtz-muenchen.de/cogere), a method for the inference of condition-specific gene regulatory networks in human and mouse. We integrated existing knowledge of regulatory interactions from multiple sources to a comprehensive model of prior information. COGERE infers condition-specific regulation by evaluating the mutual dependency between regulator (transcription factor or miRNA) and target gene expression using prior information. This dependency is scored by the non-parametric, nonlinear correlation coefficient η(2) (eta squared) that is derived by a two-way analysis of variance. We show that COGERE significantly outperforms alternative methods in predicting condition-specific gene regulatory networks on simulated data sets. Furthermore, by inferring the cancer-specific gene regulatory network from the NCI-60 expression study, we demonstrate the utility of COGERE to promote hypothesis-driven clinical research. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Large-Scale Gene-Centric Meta-Analysis across 39 Studies Identifies Type 2 Diabetes Loci

    NARCIS (Netherlands)

    Saxena, Richa; Elbers, Clara C.; Guo, Yiran; Peter, Inga; Gaunt, Tom R.; Mega, Jessica L.; Lanktree, Matthew B.; Tare, Archana; Almoguera Castillo, Berta; Li, Yun R.; Johnson, Toby; Bruinenberg, Marcel; Gilbert-Diamond, Diane; Rajagopalan, Ramakrishnan; Voight, Benjamin F.; Balasubramanyam, Ashok; Barnard, John; Bauer, Florianne; Baumert, Jens; Bhangale, Tushar; Boehm, Bernhard O.; Braund, Peter S.; Burton, Paul R.; Chandrupatla, Hareesh R.; Clarke, Robert; Cooper-DeHoff, Rhonda M.; Crook, Errol D.; Davey-Smith, George; Day, Ian N.; de Boer, Anthonius; de Groot, Mark C. H.; Drenos, Fotios; Ferguson, Jane; Fox, Caroline S.; Furlong, Clement E.; Gibson, Quince; Gieger, Christian; Gilhuijs-Pederson, Lisa A.; Glessner, Joseph T.; Goel, Anuj; Gong, Yan; Grant, Struan F. A.; Kumari, Meena; van der Harst, Pim; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Wolffenbuttel, Bruce H. R.; Hofker, Marten H.; Asselbergs, Folkert W.; Wijmenga, Cisca

    2012-01-01

    To identify genetic factors contributing to type 2 diabetes (T2D), we performed large-scale meta-analyses by using a custom similar to 50,000 SNP genotyping array (the ITMAT-Broad-CARe array) with similar to 2000 candidate genes in 39 multiethnic population-based studies, case-control studies, and

  10. Chinese nuclear insurance and Chinese nuclear insurance pool

    International Nuclear Information System (INIS)

    Gong Zhiqi

    2000-01-01

    Chinese Nuclear Insurance Started with Daya Bay Nuclear Power Station, PICC issued the insurance policy. Nuclear insurance cooperation between Chinese and international pool's organizations was set up in 1989. In 1996, the Chinese Nuclear Insurance Pool was prepared. The Chinese Nuclear Insurance Pool was approved by The Chinese Insurance Regulatory Committee in May of 1999. The principal aim is to centralize maximum the insurance capacity for nuclear insurance from local individual insurers and to strengthen the reinsurance relations with international insurance pools so as to provide the high quality insurance service for Chinese nuclear industry. The Member Company of Chinese Nuclear Pool and its roles are introduced in this article

  11. Guide for decontaminating swimming pool at schools

    International Nuclear Information System (INIS)

    Matsuhashi, Shimpei; Kurikami, Hiroshi; Yasuda, Ryo; Takano, Takao; Seko, Noriaki; Naganawa, Hirochika; Kuroki, Ryota; Saegusa, Jun

    2012-07-01

    Because of TEPCO Fukushima Dai-ichi Nuclear Power Plant accident due to the Great East Japan Earthquake, a huge amount of radioactive materials was widely dispersed and precipitated into the environment. Swimming pools in Fukushima prefectures were contaminated with the radioactives. We JAEA carried out several demonstration tests to decontaminate the radioactives and discharge the pool water safely. We concluded the results obtained from the tests as 'Guide for decontaminating Swimming Pool at School' and released it quickly. Following this, we also released the guide in English. This manuscript, as an experimental report of the swimming pool water decontamination, is consisted from the guide in Japanese and English prepared. (author)

  12. Guide for decontaminating swimming pool at schools

    Energy Technology Data Exchange (ETDEWEB)

    Matsuhashi, Shimpei; Kurikami, Hiroshi; Yasuda, Ryo; Takano, Takao; Seko, Noriaki; Naganawa, Hirochika; Kuroki, Ryota; Saegusa, Jun

    2012-07-15

    Because of TEPCO Fukushima Dai-ichi Nuclear Power Plant accident due to the Great East Japan Earthquake, a huge amount of radioactive materials was widely dispersed and precipitated into the environment. Swimming pools in Fukushima prefectures were contaminated with the radioactives. We JAEA carried out several demonstration tests to decontaminate the radioactives and discharge the pool water safely. We concluded the results obtained from the tests as 'Guide for decontaminating Swimming Pool at School' and released it quickly. Following this, we also released the guide in English. This manuscript, as an experimental report of the swimming pool water decontamination, is consisted from the guide in Japanese and English prepared. (author)

  13. Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing

    NARCIS (Netherlands)

    I. Jansen (Iris); Ye, H. (Hui); Heetveld, S. (Sasja); Lechler, M.C. (Marie C.); Michels, H. (Helen); Seinstra, R.I. (Renée I.); Lubbe, S.J. (Steven J.); Drouet, V. (Valérie); S. Lesage (Suzanne); E. Majounie (Elisa); Gibbs, J.R. (J.Raphael); M.A. Nalls (Michael); M. Ryten (Mina); Botia, J.A. (Juan A.); J. Vandrovcova (Jana); J. Simón-Sánchez (Javier); Castillo-Lizardo, M. (Melissa); P. Rizzu (Patrizia); Blauwendraat, C. (Cornelis); Chouhan, A.K. (Amit K.); Li, Y. (Yarong); Yogi, P. (Puja); N. Amin (Najaf); C.M. van Duijn (Cornelia); Morris, H.R. (Huw R.); Brice, A. (Alexis); A. Singleton (Andrew); David, D.C. (Della C.); Nollen, E.A. (Ellen A.); A. Jain (Ashok); J.M. Shulman; P. Heutink (Peter); D.G. Hernandez (Dena); S. Arepalli (Sampath); J. Brooks (Janet); Price, R. (Ryan); Nicolas, A. (Aude); S. Chong (Sean); M.R. Cookson (Mark); A. Dillman (Allissa); M. Moore (Matt); B.J. Traynor (Bryan); A. Singleton (Andrew); V. Plagnol (Vincent); Nicholas W Wood,; U.-M. Sheerin (Una-Marie); Jose M Bras,; K. Charlesworth (Kate); M. Gardner (Mac); R. Guerreiro (Rita); D. Trabzuni (Danyah); Hardy, J. (John); M. Sharma; M. Saad (Mohamad); Javier Simón-Sánchez,; C. Schulte (Claudia); J.C. Corvol (Jean-Christophe); Dürr, A. (Alexandra); M. Vidailhet (M.); S. Sveinbjörnsdóttir (Sigurlaug); R.A. Barker (Roger); Caroline H Williams-Gray,; Y. Ben-Shlomo; H.W. Berendse (Henk W.); K.D. van Dijk (Karin); D. Berg (Daniela); K. Brockmann; K.D. Wurster (Kathrin); Mätzler, W. (Walter); Gasser, T. (Thomas); M. Martinez (Maria); R.M.A. de Bie (Rob); A. Biffi (Alessandro); D. Velseboer (Daan); B.R. Bloem (Bastiaan); B. Post (Bart); M. Wickremaratchi (Mirdhu); B. van de Warrenburg (Bart); Z. Bochdanovits (Zoltan); M. von Bonin (Malte); H. Pétursson (Hjörvar); O. Riess (Olaf); D.J. Burn (David); Lubbe, S. (Steven); Cooper, J.M. (J Mark); N.H. McNeill (Nathan); Schapira, A. (Anthony); Lungu, C. (Codrin); Chen, H. (Honglei); Dong, J. (Jing); Chinnery, P.F. (Patrick F.); G. Hudson (Gavin); Clarke, C.E. (Carl E.); C. Moorby (Catriona); C. Counsell (Carl); P. Damier (Philippe); J.-F. Dartigues; P. Deloukas (Panagiotis); E. Gray (Emma); T. Edkins (Ted); Hunt, S.E. (Sarah E.); S.C. Potter (Simon); A. Tashakkori-Ghanbaria (Avazeh); G. Deuschl (Günther); D. Lorenz (Delia); D.T. Dexter (David); F. Durif (Frank); J. Evans (Jonathan Mark); Langford, C. (Cordelia); T. Foltynie (Thomas); A.M. Goate (Alison); C. Harris (Clare); J.J. van Hilten (Jacobus); A. Hofman (Albert); J.R. Hollenbeck (John R.); J.L. Holton (Janice); Hu, M. (Michele); X. Huang (Xiaohong); Illig, T. (Thomas); P.V. Jónsson (Pálmi); J.-C. Lambert; S.S. O'Sullivan (Sean); T. Revesz (Tamas); K. Shaw (Karen); A.J. Lees (Andrew); P. Lichtner (Peter); P. Limousin (Patricia); G. Lopez; Escott-Price, V. (Valentina); J. Pearson (Justin); N. Williams (Nigel); E. Mudanohwo (Ese); J.S. Perlmutter (Joel); Pollak, P. (Pierre); F. Rivadeneira Ramirez (Fernando); A.G. Uitterlinden (André); S.J. Sawcer (Stephen); H. Scheffer (Hans); I. Shoulson (Ira); L. Shulman (Lee); Smith, C. (Colin); R. Walker (Robert); C.C.A. Spencer (Chris C.); A. Strange (Amy); H. Stefansson (Hreinn); F. Bettella (Francesco); J-A. Zwart (John-Anker); Stockton, J.D. (Joanna D.); D. Talbot; C.M. Tanner (Carlie); F. Tison (François); S. Winder-Rhodes (Sophie); K.P. Bhatia (Kailash)

    2017-01-01

    textabstractBackground: Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we

  14. (Important hygienic aspects for swimming pools (author's transl))

    Energy Technology Data Exchange (ETDEWEB)

    Somosi, G

    1981-01-01

    The major epidemics which occurred in Hungary and originated from water in swimming pools are reported. The difficulties encountered in producing epidemiological evidence and in monitoring infections originating from water in swimming pools are mentioned. The possibilities of controlling the water quality in swimming pools and of preventing infections are discussed. Reference is made to the existing bacteriological limit values in Hungary to be observed in the recirculation of water in swimming pools.

  15. Distinct types of primary cutaneous large B-cell lymphoma identified by gene expression profiling.

    Science.gov (United States)

    Hoefnagel, Juliette J; Dijkman, Remco; Basso, Katia; Jansen, Patty M; Hallermann, Christian; Willemze, Rein; Tensen, Cornelis P; Vermeer, Maarten H

    2005-05-01

    In the European Organization for Research and Treatment of Cancer (EORTC) classification 2 types of primary cutaneous large B-cell lymphoma (PCLBCL) are distinguished: primary cutaneous follicle center cell lymphomas (PCFCCL) and PCLBCL of the leg (PCLBCL-leg). Distinction between both groups is considered important because of differences in prognosis (5-year survival > 95% and 52%, respectively) and the first choice of treatment (radiotherapy or systemic chemotherapy, respectively), but is not generally accepted. To establish a molecular basis for this subdivision in the EORTC classification, we investigated the gene expression profiles of 21 PCLBCLs by oligonucleotide microarray analysis. Hierarchical clustering based on a B-cell signature (7450 genes) classified PCLBCL into 2 distinct subgroups consisting of, respectively, 8 PCFCCLs and 13 PCLBCLsleg. PCLBCLs-leg showed increased expression of genes associated with cell proliferation; the proto-oncogenes Pim-1, Pim-2, and c-Myc; and the transcription factors Mum1/IRF4 and Oct-2. In the group of PCFCCL high expression of SPINK2 was observed. Further analysis suggested that PCFCCLs and PCLBCLs-leg have expression profiles similar to that of germinal center B-cell-like and activated B-cell-like diffuse large B-cell lymphoma, respectively. The results of this study suggest that different pathogenetic mechanisms are involved in the development of PCFCCLs and PCLBCLs-leg and provide molecular support for the subdivision used in the EORTC classification.

  16. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

    KAUST Repository

    Wang, Yong; Yang, Jiang Ke; Lee, On On; Li, Tie Gang; Al-Suwailem, Abdulaziz M.; Danchin, Antoine; Qian, Pei-Yuan

    2011-01-01

    The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

  17. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments

    KAUST Repository

    Wang, Yong

    2011-12-21

    The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers) of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed. © 2011 Wang et al.

  18. Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments.

    Directory of Open Access Journals (Sweden)

    Yong Wang

    Full Text Available The complexity and dynamics of microbial metagenomes may be evaluated by genome size, gene duplication and the disruption rate between lineages. In this study, we pyrosequenced the metagenomes of microbes obtained from the brine and sediment of a deep-sea brine pool in the Red Sea to explore the possible genomic adaptations of the microbes in response to environmental changes. The microbes from the brine and sediments (both surface and deep layers of the Atlantis II Deep brine pool had similar communities whereas the effective genome size varied from 7.4 Mb in the brine to more than 9 Mb in the sediment. This genome expansion in the sediment samples was due to gene duplication as evidenced by enrichment of the homologs. The duplicated genes were highly disrupted, on average by 47.6% and 70% for the surface and deep layers of the Atlantis II Deep sediment samples, respectively. The disruptive effects appeared to be mainly due to point mutations and frameshifts. In contrast, the homologs from the Atlantis II Deep brine sample were highly conserved and they maintained relatively small copy numbers. Likely, the adaptation of the microbes in the sediments was coupled with pseudogenizations and possibly functional diversifications of the paralogs in the expanded genomes. The maintenance of the pseudogenes in the large genomes is discussed.

  19. Thermal analyses of solar swimming pool heating in Pakistan

    International Nuclear Information System (INIS)

    Ahmad, I.

    2011-01-01

    Hotels and swimming clubs in Pakistan pay huge gas bills for heating Swimming pools in winter. Winter days in most parts of Pakistan remain sunny and unglazed low cost solar collectors may be used to extend the swimming season. Installing the pool in a wind-protected area, which receives unobstructed solar radiation, may further reduce the size of the solar collectors required to heat the swimming pools. The pools should be covered with plastic sheet to eliminate evaporative heat losses and to prevent dust and tree leaves falling in the pool. The results of the thermal analysis show that in some parts of the country, a solar exposed pool can maintain comfortable temperature simply by using a plastic sheet on the pool surface. On the other hand, there are cities where solar collector array equal to twice the surface area of the pool is required to keep desired temperature in winter. (author)

  20. Reduction of the pool-top radiation level in HANARO

    International Nuclear Information System (INIS)

    Lee, Choong-Sung; Park, Sang-Jun; Kim, Heonil; Park, Yong-Chul; Choi, Young-San

    1999-01-01

    HANARO is an open-tank-in-pool type reactor. Pool water is the only shielding to minimize the pool top radiation level. During the power ascension test of HANARO, the measured pool top radiation level was higher than the design value because some of the activation products in the coolant reached the pool surface. In order to suppress this rising coolant, the hot water layer system (HWL) was designed and installed to maintain l.2 meter-deep hot water layer whose temperature is 5degC higher than that of the underneath pool surface. After the installation of the HWL system, however, the radiation level of the pool-top did not satisfy the design value. The operation modes of the hot water layer system and the other systems in the reactor pool, which had an effect on the formation of the hot water layer, were changed to reduce pool-top radiation level. After the above efforts, the temperature and the radioactivity distribution in the pool was measured to confirm whether this system blocked the rising coolant. The radiation level at the pool-top was significantly reduced below one tenth of that before installing the HWL and satisfied the design value. It was also confirmed by calculation that this hot water layer system would significantly reduce the release of fission gases to the reactor hall and the environment during the hypothetical accident as well. (author)

  1. 17 CFR 4.22 - Reporting to pool participants.

    Science.gov (United States)

    2010-04-01

    ..., the financial statements are not required to include consolidated information for all series. (7) For... event that the International Financial Reporting Standards require consolidated financial statements for... reporting pool's consolidated financial statements. (ii) The commodity pool operator of a pool that meets...

  2. Numerical modelling of pressure suppression pools with CFD and FEM codes

    Energy Technology Data Exchange (ETDEWEB)

    Paettikangas, T.; Niemi, J.; Timperi, A. (VTT Technical Research Centre of Finland (Finland))

    2011-06-15

    Experiments on large-break loss-of-coolant accident for BWR is modeled with computational fluid (CFD) dynamics and finite element calculations. In the CFD calculations, the direct-contact condensation in the pressure suppression pool is studied. The heat transfer in the liquid phase is modeled with the Hughes-Duffey correlation based on the surface renewal model. The heat transfer is proportional to the square root of the turbulence kinetic energy. The condensation models are implemented with user-defined functions in the Euler-Euler two-phase model of the Fluent 12.1 CFD code. The rapid collapse of a large steam bubble and the resulting pressure source is studied analytically and numerically. Pressure source obtained from simplified calculations is used for studying the structural effects and FSI in a realistic BWR containment. The collapse results in volume acceleration, which induces pressure loads on the pool walls. In the case of a spherical bubble, the velocity term of the volume acceleration is responsible of the largest pressure load. As the amount of air in the bubble is decreased, the peak pressure increases. However, when the water compressibility is accounted for, the finite speed of sound becomes a limiting factor. (Author)

  3. Behavior of spent nuclear fuel in water pool storage

    International Nuclear Information System (INIS)

    Johnson, A.B. Jr.

    1977-09-01

    Storage of irradiated nuclear fuel in water pools (basins) has been standard practice since nuclear reactors first began operation approximately 34 years ago. Pool storage is the starting point for all other fuel storage candidate processes and is a candidate for extended interim fuel storage until policy questions regarding reprocessing and ultimate disposal have been resolved. This report assesses the current performance of nuclear fuel in pool storage, the range of storage conditions, and the prospects for extending residence times. The assessment is based on visits to five U.S. and Canadian fuel storage sites, representing nine storage pools, and on discussions with operators of an additional 21 storage pools. Spent fuel storage experience from British pools at Winfrith and Windscale and from a German pool at Karlsruhe (WAK) also is summarized

  4. Design of the Demineralized Water Make-up Line to Maintain the Normal Pool Water Level of the Reactor Pool in the Research Reactor

    International Nuclear Information System (INIS)

    Yoon, Hyun Gi; Choi, Jung Woon; Yoon, Ju Hyeon; Chi, Dae Young

    2012-01-01

    In many research reactors, hot water layer system (HWLS) is used to minimize the pool top radiation level. Reactor pool divided into the hot water layer at the upper part of pool and the cold part below the hot water layer with lower temperature during normal operation. Water mixing between these layers is minimized because the hot water layer is formed above cold water. Therefore the hot water layer suppresses floatation of cold water and reduces the pool top radiation level. Pool water is evaporated form the surface to the building hall because of high temperature of the hot water layer; consequently the pool level is continuously fallen. Therefore, make-up water is necessary to maintain the normal pool level. There are two way to supply demineralized water to the pool, continuous and intermittent methods. In this system design, the continuous water make-up method is adopted to minimize the disturbance of the reactor pool flow. Also, demineralized water make-up is connected to the suction line of the hot water layer system to raise the temperature of make-up water. In conclusion, make-up demineralized water with high temperature is continuously supplied to the hot water layer in the pool

  5. Condensation in a two-phase pool

    International Nuclear Information System (INIS)

    Duffey, R.B.; Hughes, E.D.

    1991-01-01

    We consider the case of vapor condensation in a liquid pool, when the heat transfer is controlled by heat losses through the walls. The analysis is based on drift flux theory for phase separation in the pool, and determines the two-phase mixture height for the pool. To our knowledge this is the first analytical treatment of this classic problem that gives an explicit result, previous work having established the result for the evaporative case. From conservation of mass and energy in a one-dimensional steady flow, together with a void relation between the liquid and vapor fluxes, we determine the increase in the mixture level from the base level of the pool. It can be seen that the thermal and hydrodynamic influences are separable. Thus, the thermal influence of the wall heat transfer appears through its effect on the condensing length L*, so that at high condensation rates the pool is all liquid, and at low rates overflows (the level swell or foaming effect). Similarly, the phase separation effect hydrodynamically determines the height via the relative velocity of the mixture to the entering flux. We examine some practical applications of this result to level swell in condensing flows, and also examine some limits in ideal cases

  6. Identification of differentially expressed genes in cutaneous squamous cell carcinoma by microarray expression profiling

    Directory of Open Access Journals (Sweden)

    Sterry Wolfram

    2006-08-01

    Full Text Available Abstract Background Carcinogenesis is a multi-step process indicated by several genes up- or down-regulated during tumor progression. This study examined and identified differentially expressed genes in cutaneous squamous cell carcinoma (SCC. Results Three different biopsies of 5 immunosuppressed organ-transplanted recipients each normal skin (all were pooled, actinic keratosis (AK (two were pooled, and invasive SCC and additionally 5 normal skin tissues from immunocompetent patients were analyzed. Thus, total RNA of 15 specimens were used for hybridization with Affymetrix HG-U133A microarray technology containing 22,283 genes. Data analyses were performed by prediction analysis of microarrays using nearest shrunken centroids with the threshold 3.5 and ANOVA analysis was independently performed in order to identify differentially expressed genes (p vs. AK and SCC were observed for 118 genes. Conclusion The majority of identified differentially expressed genes in cutaneous SCC were previously not described.

  7. A skeleton for distributed work pools in Eden

    DEFF Research Database (Denmark)

    Dieterle, Mischa; Berthold, Jost; Loogen, Rita

    2010-01-01

    We present a flexible skeleton for implementing distributed work pools in our parallel functional language Eden. The skeleton manages a pool of tasks (work pool) in a distributed manner using a demand-driven work stealing approach for load balancing. All coordination is done locally within...

  8. Sustainability of common pool resources

    OpenAIRE

    Timilsina, Raja Rajendra; Kotani, Koji; Kamijo, Yoshio

    2017-01-01

    Sustainability has become a key issue in managing natural resources together with growing concerns for capitalism, environmental and resource problems. We hypothesize that the ongoing modernization of competitive societies, which we refer to as "capitalism," affects human nature for utilizing common pool resources, thus compromising sustainability. To test this hypothesis, we design and implement a set of dynamic common pool resource games and experiments in the following two types of Nepales...

  9. The Nuclear Insurance Pools: Operations and Covers

    International Nuclear Information System (INIS)

    Tetley, M.

    2008-01-01

    Nuclear insurance pools have provided insurance for the nuclear industry for over fifty years and it is fair to say that the development of civil nuclear power would not have been possible without the support of the commercial insurance market. The unknown risks presented by the nascent nuclear power industry in the 1950s required a leap of faith by insurers who developed specialist pooled insurance capacity to ensure adequate capacity to back up the operators' compensation obligations. Since then, nuclear insurance pools have evolved to become comprehensive suppliers of most types of insurance for nuclear plant globally. This paper will outline the structure, development, products and current operations of nuclear insurance pools.(author)

  10. Hardening Stratum, the Bitcoin Pool Mining Protocol

    Directory of Open Access Journals (Sweden)

    Recabarren Ruben

    2017-07-01

    Full Text Available Stratum, the de-facto mining communication protocol used by blockchain based cryptocurrency systems, enables miners to reliably and efficiently fetch jobs from mining pool servers. In this paper we exploit Stratum’s lack of encryption to develop passive and active attacks on Bitcoin’s mining protocol, with important implications on the privacy, security and even safety of mining equipment owners. We introduce StraTap and ISP Log attacks, that infer miner earnings if given access to miner communications, or even their logs. We develop BiteCoin, an active attack that hijacks shares submitted by miners, and their associated payouts. We build BiteCoin on WireGhost, a tool we developed to hijack and surreptitiously maintain Stratum connections. Our attacks reveal that securing Stratum through pervasive encryption is not only undesirable (due to large overheads, but also ineffective: an adversary can predict miner earnings even when given access to only packet timestamps. Instead, we devise Bedrock, a minimalistic Stratum extension that protects the privacy and security of mining participants. We introduce and leverage the mining cookie concept, a secret that each miner shares with the pool and includes in its puzzle computations, and that prevents attackers from reconstructing or hijacking the puzzles.

  11. Shedding Light on Dark Liquidity Pools

    NARCIS (Netherlands)

    Degryse, H.A.; van Achter, M.; Wuyts, G.

    2008-01-01

    This article reviews the recent developments on dark liquidity pools starting from the theoretical and empirical academic literature. The number of dark liquidity pools as well as their trading volume has grown substantially in the last couple of years. We highlight the incentives of providers as

  12. NACUBO's Guide to Unitizing Investment Pools. Second Edition

    Science.gov (United States)

    Wheeler, Mary S.

    2011-01-01

    The National Association of College and University Business Officers' (NACUBO's) "Guide to Unitizing Investment Pools" addresses the principles and concepts for administering a consolidated investment pool. Unitization is the mechanism by which investment funds are pooled to maximize investment efficiencies and provide information for donors,…

  13. Suppression pool testing at the SIET laboratory. Experimental investigation of critical phenomena expected in the Fukushima Daiichi suppression chamber

    International Nuclear Information System (INIS)

    Pellegrini, Marco; Naitoh, Masanori; Araneo, Lucio; Ninokata, Hisashi; Ricotti, Marco; Achilli, Andrea

    2016-01-01

    In the unlikely event of a nuclear power plant long duration station black-out, as in the Fukushima Daiichi (1F) severe accident (SA), it was recognized that the suppression chamber (S/C) functions of heat sink and fission product (FP) scrubbing will degrade, resulting in the S/C pressure increase, reduction of the scrubbing efficiency and subsequent necessity of venting operations. Consequently, a relatively large amount of FPs, in particular highly volatile elements (e.g. CH_3I), is likely to be dispersed into the environment. As a method to evaluate the degradation of the pool characteristics under discharge of steam and non-condensable gases through vent pipes and steam through different quencher geometries of make-up systems, an experimental campaign was recently started at the SIET research laboratory in Italy. Two different quencher geometries, representing vent pipes and the reactor core isolation cooling (RCIC) exhaust pipes in 1F2 and 1F3, were adopted. Several combinations of steam and air mass flow rates were tested to scale down the main conditions occurred during the 1F SA. Measurements of pool water temperature in different locations and visualization with high-speed camera represent the main outcome of the experimental activity. The preliminary results have demonstrated that a relatively small concentration of air in the steam flow is able to suppress the occurrence of chugging of the steam, with reduced mixing in the pool. Both RCIC quenchers adopted induced large chugging at the bottom of the pool which are effective to avoid temperature stratification, thanks to the large water recirculation and vertical mixing within the pool. At decreased subcooling, mixing in the pool ceases and the quenchers with holes disposed in the vertical direction, as in the RCIC exhaust pipe of the 1F unit 3, introduce intense stratification that drastically reduces the condensation efficiency of the S/C pool. Quencher of 1F2 RCIC does not present stratification

  14. Investigation of the condition of spent-fuel pool components

    International Nuclear Information System (INIS)

    Kustas, F.M.; Bates, S.O.; Opitz, B.E.; Johnson, A.B. Jr.; Perez, J.M. Jr.; Farnsworth, R.K.

    1981-09-01

    It is currently projected that spent nuclear fuel, which is discharged from the reactor and then stored in water pools, may remain in those pools for several decades. Other studies have addressed the expected integrity of the spent fuel during extended water storage; this study assesses the integrity of metallic spent fuel pool components. Results from metallurgical examinations of specimens taken from stainless steel and aluminum components exposed in spent fuel pools are presented. Licensee Event Reports (LERs) relating to problems with spent fuel components were assessed and are summarized to define the types of operational problems that have occurred. The major conclusions of this study are: aluminum and stainless steel spent fuel pool components have a good history of performance in both deionized and borated water pools. Although some operational problems involving pool components have occurred, these problems have had minimal impacts

  15. Investigation of the condition of spent-fuel pool components

    Energy Technology Data Exchange (ETDEWEB)

    Kustas, F.M.; Bates, S.O.; Opitz, B.E.; Johnson, A.B. Jr.; Perez, J.M. Jr.; Farnsworth, R.K.

    1981-09-01

    It is currently projected that spent nuclear fuel, which is discharged from the reactor and then stored in water pools, may remain in those pools for several decades. Other studies have addressed the expected integrity of the spent fuel during extended water storage; this study assesses the integrity of metallic spent fuel pool components. Results from metallurgical examinations of specimens taken from stainless steel and aluminum components exposed in spent fuel pools are presented. Licensee Event Reports (LERs) relating to problems with spent fuel components were assessed and are summarized to define the types of operational problems that have occurred. The major conclusions of this study are: aluminum and stainless steel spent fuel pool components have a good history of performance in both deionized and borated water pools. Although some operational problems involving pool components have occurred, these problems have had minimal impacts.

  16. When stress predicts a shrinking gene pool, trading early reproduction for longevity can increase fitness, even with lower fecundity.

    Directory of Open Access Journals (Sweden)

    William C Ratcliff

    2009-06-01

    Full Text Available Stresses like dietary restriction or various toxins increase lifespan in taxa as diverse as yeast, Caenorhabditis elegans, Drosophila and rats, by triggering physiological responses that also tend to delay reproduction. Food odors can reverse the effects of dietary restriction, showing that key mechanisms respond to information, not just resources. Such environmental cues can predict population trends, not just individual prospects for survival and reproduction. When population size is increasing, each offspring produced earlier makes a larger proportional contribution to the gene pool, but the reverse is true when population size is declining.We show mathematically that natural selection can favor facultative delay in reproduction when environmental cues predict a decrease in total population size, even if lifetime fecundity decreases with delay. We also show that increased reproduction from waiting for better conditions does not increase fitness (proportional representation when the whole population benefits similarly.We conclude that the beneficial effects of stress on longevity (hormesis in diverse taxa are a side-effect of delaying reproduction in response to environmental cues that population size is likely to decrease. The reversal by food odors of the effects of dietary restriction can be explained as a response to information that population size is less likely to decrease, reducing the chance that delaying reproduction will increase fitness.

  17. Analysis of the loss of pool cooling accident in a PWR spent fuel pool with MAAP5

    International Nuclear Information System (INIS)

    Wu, Xiaoli; Li, Wei; Zhang, Yapei; Tian, Wenxi; Su, Guanghui; Qiu, Suizheng

    2014-01-01

    Highlights: • A PWR spent fuel pool was modeled by using MAAP5. • Loss of pool cooling severe accident scenarios were studied. • Loss of pool cooling accidents with two mitigation measures were analyzed. - Abstract: The Fukushima Daiichi nuclear accident shows that it is necessary to study potential severe accidents and corresponding mitigation measures for the spent fuel pool (SFP) of a nuclear power plant (NPP). This paper presents the analysis of loss of pool cooling accident scenarios and the discussion of mitigation measures for the SFP at a pressurized water reactor (PWR) NPP with the MAAP5 code. Analysis of uncompensated loss of water due to the loss of pool cooling with different initial pool water levels of 12.2 m (designated as a reference case) and 10.7 m have been performed based on a MAAP5 input model. Scenarios of the accident such as overheating of uncovered fuel assemblies, oxidation of claddings and hydrogen generation, loss of intactness of fuel rod claddings, and release of radioactive fission products were predicted with the assumption that mitigation measures were unavailable. The results covered a broad spectrum of severe accident evaluations in the SFP. Furthermore, as important mitigation measures, the effects of recovering the SFP cooling system and makeup water in SFP on the accident progressions have also been investigated respectively based on the events of pool water boiling and spent fuels uncovery. Based upon the reference case, three cases with the recovery of SFP cooling system and three other cases with makeup water in SFP have been studied. The results showed that, severe accident might happen if SFP cooling system was not restored timely before the spent fuels started to become uncovered; spent fuels could be completely submerged and severe accident might be avoided if SFP makeup water system provided water with a mass flow rate larger than the average evaporation rate defined as the division of pool water mass above the

  18. Experiments and CFD simulations of DTBP pool fires; Experimentelle Untersuchungen und CFD-Simulationen von DTBP-Poolfeuern

    Energy Technology Data Exchange (ETDEWEB)

    Chun, Hyunjoo

    2007-07-01

    Flammable liquids are used increasingly often world-wide. Their storage, transport and chemical reactions are a considerable safety problem in industrial plants. Heat release and combustion products of big fires are a high hazard for persons, the immediate vicinity and the environment in general. Investigations of pool fires were carried out for a realistic assessment of the potential hazards to persons and plants in the immediate vicinity. Most of the available data on fire effects, safety distances and other measures relevant to fire protection are for hydrocarbons, alcohols and liquefied gases. LIttle is known on pool fires of liquid organic peroxides, which have quite different combustion characteristics with higher mass burnup rates and higher heat emissions into the vicinity. The dissertation presents experiments to characterize the combustion characteristics of organic peroxides as a function of the pool diameter. Di-tert-butylperoxide (DTBPL) was chosen for the experiments because it has a relatively high thermal stability as compared to other organic peroxides. Mass burnup rates, flame temperatures, the surface emissive power (SEP), the strength of thermal radiation and the flame length were measured as a function of the pool diameter. Further, parameters required for CFD simulations of DTBP pool fires were identified experimentally in order to ensure realistic modelling of real fires as a basis, e.g., for assessing safety distances. Experiments on large pool fires are costly and require much equipment and technical preparations so that fires are limited to pool diameters of only a few meters as a rule. CFD simulations would be capable of improving the prediction of safety-relevant parameters like flame temperature, surface emissive power, radiation strength and flame length without limiting the pool diameter or the fuel volume. Appropriate sub-models were used for modelling pool fires of organic peroxides, and the simulation results were critically

  19. Swimming-pool piles; Piles piscines

    Energy Technology Data Exchange (ETDEWEB)

    Trioulaire, M [Commissariat a l' Energie Atomique, Saclay (France).Centre d' Etudes Nucleaires

    1959-07-01

    In France two swimming-pool piles, Melusine and Triton, have just been set in operation. The swimming-pool pile is the ideal research tool for neutron fluxes of the order of 10{sup 13}. This type of pile can be of immediate interest to many research centres, but its cost must be reduced and a break with tradition should be observed in its design. It would be an advantage: - to bury the swimming-pool; - to reject the experimental channel; - to concentrate the cooling circuit in the swimming-pool; - to carry out all manipulations in the water; - to double the core. (author) [French] En France, deux piles piscines, Melusine et Triton, viennent d'entrer en service. La pile piscine est l'outil de recherche ideal pour des flux de neutrons de l'ordre de 10{sup 13}. Ce type de pile peut interesser des maintenant de nombreux centres de recherches mais il faut reduire son prix de revient et rompre avec le conformisme de sa conception. Il y a avantage: - a enterrer la piscine; - a supprimer les canaux experimentaux; - a concentrer le circuit de refrigeration dans la piscine; - a effectuer toutes les manipulations dans l'eau; - a doubler le coeur. (auteur)

  20. Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL

    Science.gov (United States)

    Dixit, Shalabh; Kumar Biswal, Akshaya; Min, Aye; Henry, Amelia; Oane, Rowena H.; Raorane, Manish L.; Longkumer, Toshisangba; Pabuayon, Isaiah M.; Mutte, Sumanth K.; Vardarajan, Adithi R.; Miro, Berta; Govindan, Ganesan; Albano-Enriquez, Blesilda; Pueffeld, Mandy; Sreenivasulu, Nese; Slamet-Loedin, Inez; Sundarvelpandian, Kalaipandian; Tsai, Yuan-Ching; Raghuvanshi, Saurabh; Hsing, Yue-Ie C.; Kumar, Arvind; Kohli, Ajay

    2015-01-01

    Sub-QTLs and multiple intra-QTL genes are hypothesized to underpin large-effect QTLs. Known QTLs over gene families, biosynthetic pathways or certain traits represent functional gene-clusters of genes of the same gene ontology (GO). Gene-clusters containing genes of different GO have not been elaborated, except in silico as coexpressed genes within QTLs. Here we demonstrate the requirement of multiple intra-QTL genes for the full impact of QTL qDTY12.1 on rice yield under drought. Multiple evidences are presented for the need of the transcription factor ‘no apical meristem’ (OsNAM12.1) and its co-localized target genes of separate GO categories for qDTY12.1 function, raising a regulon-like model of genetic architecture. The molecular underpinnings of qDTY12.1 support its effectiveness in further improving a drought tolerant genotype and for its validity in multiple genotypes/ecosystems/environments. Resolving the combinatorial value of OsNAM12.1 with individual intra-QTL genes notwithstanding, identification and analyses of qDTY12.1has fast-tracked rice improvement towards food security. PMID:26507552

  1. Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria.

    Directory of Open Access Journals (Sweden)

    Hanna Farnelid

    Full Text Available Cyanobacteria are thought to be the main N(2-fixing organisms (diazotrophs in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N(2 fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.

  2. Plant diversity associated with pools in natural and restored peatlands

    Directory of Open Access Journals (Sweden)

    N. Fontaine

    2007-06-01

    Full Text Available This study describes plant assemblages associated with the edges of peatland pools. We conducted inventories in six natural peatlands in the province of Québec (Canada in order to measure the contribution of pools to species diversity in climatic regions where peatlands are used for peat extraction. We also carried out vegetation surveys in a peatland that has been restored after peat extraction/harvesting to determine whether pool vegetation establishes along the edges of created pools when dry surface restoration techniques only are used. Pools enhanced plant species richness in natural peatlands. Around created pools, species associated with natural pools were still absent, and non-bog species were present, six years after restoration. On this basis, we emphasise the importance of preserving natural peatlands with pools. In order to restore fully the plant diversity associated with peatlands at harvested sites, it may be necessary to modify pool excavation techniques so that created pools resemble more closely those in natural peatlands. Active introduction of the plant species or communities associated with natural pools may also be needed; candidate species for North America include Andromeda glaucophylla, Cladopodiella fluitans, Carex limosa, Eriophorum virginicum, Rhynchospora alba and Sphagnum cuspidatum.

  3. Grundfoss: Chlorination of Swimming Pools

    DEFF Research Database (Denmark)

    Hjorth, Poul G.; Hogan, John; Andreassen, Viggo

    1998-01-01

    Grundfos asked for a model, describing the problem of mixing chemicals, being dosed into water systems, to be developed. The application of the model should be dedicated to dosing aqueous solution of chlorine into swimming pools.......Grundfos asked for a model, describing the problem of mixing chemicals, being dosed into water systems, to be developed. The application of the model should be dedicated to dosing aqueous solution of chlorine into swimming pools....

  4. Large scale gene expression meta-analysis reveals tissue-specific, sex-biased gene expression in humans

    Directory of Open Access Journals (Sweden)

    Benjamin Mayne

    2016-10-01

    Full Text Available The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analysed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes, followed by the heart (375 genes, kidney (224 genes, colon (218 genes and thyroid (163 genes. More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.

  5. Analysis of Phenix End-of-Life asymmetry test with multi-dimensional pool modeling of MARS-LMR code

    International Nuclear Information System (INIS)

    Jeong, H.-Y.; Ha, K.-S.; Choi, C.-W.; Park, M.-G.

    2015-01-01

    Highlights: • Pool behaviors under asymmetrical condition in an SFR were evaluated with MARS-LMR. • The Phenix asymmetry test was analyzed one-dimensionally and multi-dimensionally. • One-dimensional modeling has limitation to predict the cold pool temperature. • Multi-dimensional modeling shows improved prediction of stratification and mixing. - Abstract: The understanding of complicated pool behaviors and its modeling is essential for the design and safety analysis of a pool-type Sodium-cooled Fast Reactor. One of the remarkable recent efforts on the study of pool thermal–hydraulic behaviors is the asymmetrical test performed as a part of Phenix End-of-Life tests by the CEA. To evaluate the performance of MARS-LMR code, which is a key system analysis tool for the design of an SFR in Korea, in the prediction of thermal hydraulic behaviors during an asymmetrical condition, the Phenix asymmetry test is analyzed with MARS-LMR in the present study. Pool regions are modeled with two different approaches, one-dimensional modeling and multi-dimensional one, and the prediction results are analyzed to identify the appropriateness of each modeling method. The prediction with one-dimensional pool modeling shows a large deviation from the measured data at the early stage of the test, which suggests limitations to describe the complicated thermal–hydraulic phenomena. When the pool regions are modeled multi-dimensionally, the prediction gives improved results quite a bit. This improvement is explained by the enhanced modeling of pool mixing with the multi-dimensional modeling. On the basis of the results from the present study, it is concluded that an accurate modeling of pool thermal–hydraulics is a prerequisite for the evaluation of design performance and safety margin quantification in the future SFR developments

  6. Element Pool Changes within a Scrub-Oak Ecosystem after 11 Years of Exposure to Elevated CO2

    Science.gov (United States)

    Duval, Benjamin D.; Dijkstra, Paul; Drake, Bert G.; Johnson, Dale W.; Ketterer, Michael E.; Megonigal, J. Patrick; Hungate, Bruce A.

    2013-01-01

    The effects of elevated CO2 on ecosystem element stocks are equivocal, in part because cumulative effects of CO2 on element pools are difficult to detect. We conducted a complete above and belowground inventory of non-nitrogen macro- and micronutrient stocks in a subtropical woodland exposed to twice-ambient CO2 concentrations for 11 years. We analyzed a suite of nutrient elements and metals important for nutrient cycling in soils to a depth of ∼2 m, in leaves and stems of the dominant oaks, in fine and coarse roots, and in litter. In conjunction with large biomass stimulation, elevated CO2 increased oak stem stocks of Na, Mg, P, K, V, Zn and Mo, and the aboveground pool of K and S. Elevated CO2 increased root pools of most elements, except Zn. CO2-stimulation of plant Ca was larger than the decline in the extractable Ca pool in soils, whereas for other elements, increased plant uptake matched the decline in the extractable pool in soil. We conclude that elevated CO2 caused a net transfer of a subset of nutrients from soil to plants, suggesting that ecosystems with a positive plant growth response under high CO2 will likely cause mobilization of elements from soil pools to plant biomass. PMID:23717607

  7. The Role of Nuclear Insurance Pools

    International Nuclear Information System (INIS)

    Reitsma, S. M. S.

    2006-01-01

    Since fifty years insurers respond to the need of both governments and the electricity industry to provide financial protection to cover the perils presented by the use of nuclear energy for peaceful purposes. This paper aims at explaining what difficulties had to be solved in order to enable insurers to provide such protection, that as a solution to these difficulties Nuclear Insurance Pools were formed, how such pools operate and what security they provide. Thereby not only a number of universal principles underlying nuclear pool insurance will be explained, but also some differences in the characteristics of such insurance per group of countries. (author)

  8. Swimming Pool Safety

    Science.gov (United States)

    ... Spread the Word Shop AAP Find a Pediatrician Safety & Prevention Immunizations All Around At Home At Play ... Español Text Size Email Print Share Swimming Pool Safety Page Content ​What is the best way to ...

  9. DNA pooling base genome-wide association study identifies variants at NRXN3 associated with delayed encephalopathy after acute carbon monoxide poisoning.

    Directory of Open Access Journals (Sweden)

    Wenqiang Li

    Full Text Available Delayed encephalopathy after acute carbon monoxide poisoning (DEACMP is more characteristic of anoxic encephalopathy than of other types of anoxia. Those who have the same poisoning degree and are of similar age and gender have a greater risk of getting DEACMP. This has made it clear that there are obvious personal differences. Genetic factors may play a very important role. The authors performed a genome-wide association study involving pooling of DNA obtained from 175 patients and 244 matched acute carbon monoxide poisoning without delayed encephalopathy controls. The Illumina HumanHap 660 Chip array was used for DNA pools. Allele frequencies of all SNPs were compared between delayed encephalopathy after acute carbon monoxide poisoning and control groups and ranked. A total of 123 SNPs gave an OR >1.4. Of these, 46 mapped in or close to known genes. Forty-eight SNPs located in 19 genes were associated with DEACMP after correction for 5% FDR in the genome-wide association of pooled DNA. Two SNPs (rs11845632 and rs2196447 locate in the Neurexin 3 gene were selected for individual genotyping in all samples and another cohort consisted of 234 and 271 controls. There were significant differences in the genotype and allele frequencies of rs11845632 and rs2196447 between the DEACMP group and controls group (all P-values <0.05. This study describes a positive association between Neurexin 3 and controls in the Han Chinese population, and provides genetic evidence to support the susceptibility of DEACMP, which may be the resulting interaction of environmental and genetic factors.

  10. Nuclear Insurance Pools: World-wide Practice and Prospective

    International Nuclear Information System (INIS)

    Reitsma, S. M. S.

    2000-01-01

    The following paper explains why Nuclear Insurance Pools were established, how they operate and what insurance protection they offer to the operations of nuclear installations. It will be shown that the clear interrelationship of the Pool-insurance operations, both on a national and an international level, has resulted in a transparency of each individual Pool-Member's exposure, which enables him to make the highest possible commitment to nuclear risks. Finally, some views will be given as regards the future prospective for the long proven method of pooling this particularly sensitive class of business. (author)

  11. Gene expression analysis of flax seed development

    Science.gov (United States)

    2011-01-01

    Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise

  12. Gene expression analysis of flax seed development

    Directory of Open Access Journals (Sweden)

    Sharpe Andrew

    2011-04-01

    Full Text Available Abstract Background Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed. Results We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages seed coats (globular and torpedo stages and endosperm (pooled globular to torpedo stages and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST (GenBank accessions LIBEST_026995 to LIBEST_027011 were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152 had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development. Conclusions We have developed a foundational database of expressed sequences and collection of plasmid

  13. Environmental genomics of "Haloquadratum walsbyi" in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species

    NARCIS (Netherlands)

    Legault, Boris A.; Lopez-Lopez, Arantxa; Alba-Casado, Jose Carlos; Doolittle, W. Ford; Bolhuis, Henk; Rodriguez-Valera, Francisco; Papke, R. Thane

    2006-01-01

    Background: Mature saturated brine (crystallizers) communities are largely dominated (> 80% of cells) by the square halophilic archaeon "Haloquadratum walsbyi". The recent cultivation of the strain HBSQ001 and thesequencing of its genome allows comparison with the metagenome of this taxonomically

  14. Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution.

    Science.gov (United States)

    Clarke, Thomas H; Garb, Jessica E; Hayashi, Cheryl Y; Arensburger, Peter; Ayoub, Nadia A

    2015-06-08

    The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  15. 13 CFR 120.1708 - Pool Certificates.

    Science.gov (United States)

    2010-01-01

    ... United States. (c) SBA purchase of a Loan Interest. SBA will determine whether to purchase a Loan... reserves the right to purchase a Loan Interest from a Pool at any time. (d) Self-liquidating. A Pool... market conditions and program experience, and will publish any such change in the Federal Register. (h...

  16. Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research.

    Science.gov (United States)

    Bravo, Àlex; Piñero, Janet; Queralt-Rosinach, Núria; Rautschka, Michael; Furlong, Laura I

    2015-02-21

    Current biomedical research needs to leverage and exploit the large amount of information reported in scientific publications. Automated text mining approaches, in particular those aimed at finding relationships between entities, are key for identification of actionable knowledge from free text repositories. We present the BeFree system aimed at identifying relationships between biomedical entities with a special focus on genes and their associated diseases. By exploiting morpho-syntactic information of the text, BeFree is able to identify gene-disease, drug-disease and drug-target associations with state-of-the-art performance. The application of BeFree to real-case scenarios shows its effectiveness in extracting information relevant for translational research. We show the value of the gene-disease associations extracted by BeFree through a number of analyses and integration with other data sources. BeFree succeeds in identifying genes associated to a major cause of morbidity worldwide, depression, which are not present in other public resources. Moreover, large-scale extraction and analysis of gene-disease associations, and integration with current biomedical knowledge, provided interesting insights on the kind of information that can be found in the literature, and raised challenges regarding data prioritization and curation. We found that only a small proportion of the gene-disease associations discovered by using BeFree is collected in expert-curated databases. Thus, there is a pressing need to find alternative strategies to manual curation, in order to review, prioritize and curate text-mining data and incorporate it into domain-specific databases. We present our strategy for data prioritization and discuss its implications for supporting biomedical research and applications. BeFree is a novel text mining system that performs competitively for the identification of gene-disease, drug-disease and drug-target associations. Our analyses show that mining only a

  17. Genome-wide Association Study for Ovarian Cancer Susceptibility using Pooled DNA

    Science.gov (United States)

    Lu, Yi; Chen, Xiaoqing; Beesley, Jonathan; Johnatty, Sharon E.; deFazio, Anna; Lambrechts, Sandrina; Lambrechts, Diether; Despierre, Evelyn; Vergotes, Ignace; Chang-Claude, Jenny; Hein, Rebecca; Nickels, Stefan; Wang-Gohrke, Shan; Dörk, Thilo; Dürst, Matthias; Antonenkova, Natalia; Bogdanova, Natalia; Goodman, Marc T.; Lurie, Galina; Wilkens, Lynne R.; Carney, Michael E.; Butzow, Ralf; Nevanlinna, Heli; Heikkinen, Tuomas; Leminen, Arto; Kiemeney, Lambertus A.; Massuger, Leon F.A.G.; van Altena, Anne M.; Aben, Katja K.; Kjaer, Susanne Krüger; Høgdall, Estrid; Jensen, Allan; Brooks-Wilson, Angela; Le, Nhu; Cook, Linda; Earp, Madalene; Kelemen, Linda; Easton, Douglas; Pharoah, Paul; Song, Honglin; Tyrer, Jonathan; Ramus, Susan; Menon, Usha; Gentry-Maharaj, Alexandra; Gayther, Simon A.; Bandera, Elisa V.; Olson, Sara H.; Orlow, Irene; Rodriguez-Rodriguez, Lorna

    2013-01-01

    Recent genome-wide association studies (GWAS) have identified four low-penetrance ovarian cancer susceptibility loci. We hypothesized that further moderate or low penetrance variants exist among the subset of SNPs not well tagged by the genotyping arrays used in the previous studies which would account for some of the remaining risk. We therefore conducted a time- and cost-effective stage 1 GWAS on 342 invasive serous cases and 643 controls genotyped on pooled DNA using the high density Illumina 1M-Duo array. We followed up 20 of the most significantly associated SNPs, which are not well tagged by the lower density arrays used by the published GWAS, and genotyping them on individual DNA. Most of the top 20 SNPs were clearly validated by individually genotyping the samples used in the pools. However, none of the 20 SNPs replicated when tested for association in a much larger stage 2 set of 4,651 cases and 6,966 controls from the Ovarian Cancer Association Consortium. Given that most of the top 20 SNPs from pooling were validated in the same samples by individual genotyping, the lack of replication is likely to be due to the relatively small sample size in our stage 1 GWAS rather than due to problems with the pooling approach. We conclude that there are unlikely to be any moderate or large effects on ovarian cancer risk untagged by the less dense arrays. However our study lacked power to make clear statements on the existence of hitherto untagged small effect variants. PMID:22794196

  18. Video quality pooling adaptive to perceptual distortion severity.

    Science.gov (United States)

    Park, Jincheol; Seshadrinathan, Kalpana; Lee, Sanghoon; Bovik, Alan Conrad

    2013-02-01

    It is generally recognized that severe video distortions that are transient in space and/or time have a large effect on overall perceived video quality. In order to understand this phenomena, we study the distribution of spatio-temporally local quality scores obtained from several video quality assessment (VQA) algorithms on videos suffering from compression and lossy transmission over communication channels. We propose a content adaptive spatial and temporal pooling strategy based on the observed distribution. Our method adaptively emphasizes "worst" scores along both the spatial and temporal dimensions of a video sequence and also considers the perceptual effect of large-area cohesive motion flow such as egomotion. We demonstrate the efficacy of the method by testing it using three different VQA algorithms on the LIVE Video Quality database and the EPFL-PoliMI video quality database.

  19. ENERGY SAVING AT OPERATION OF OUTDOOR SWIMMING POOLS

    Directory of Open Access Journals (Sweden)

    V. F. Ivin

    2013-09-01

    Full Text Available Purpose. Energy saving is a major problem in modern power engineering and various energy-consuming devices. They include outdoor swimming pools. In order to maintain them in working condition, especially in winter period, it takes significant amount of thermal energy. Task of heat loss substantial decrease in open swimming pools is considered in the article (on DNURT example. Methodology. The method of determining the mass and heat loss on the basis of criteria equations of heat and mass transfer theory is used. Findings. Calculations of the actual DNURT pool heat loss for different seasons, as for natural convection both for air forced motion above the free water surface are performed. It is shown that for the adiabatic evaporation conditions of water from the pool in winter during blow-off with wind the heat loss can be up to 2 kW/m2 on surface. To reduce these losses it is offered to cover water surface in a pool with a special material with low thermal conductivity on the basis of porous polyethylene during the time when the pool is not used for other purposes. It is shown that the implementation of these standards will reduce the actual heat loss, at least 5-6 times. Originality. The solution of important environmental and energy problem thanks to reducing heat losses by the pool in different times of a year and correspondingly lower emissions of power generating enterprises. Practical value. It is shown that the coating surface of the pool with poorly heat-conducting and easy to install coating will let, at a minimum, to reduce the actual heat loss on 5-6 times and reduce the emissions of power plants generating energy for pool heating.

  20. Large scale expression changes of genes related to neuronal signaling and developmental processes found in lateral septum of postpartum outbred mice.

    Directory of Open Access Journals (Sweden)

    Brian E Eisinger

    Full Text Available Coordinated gene expression changes across the CNS are required to produce the mammalian maternal phenotype. Lateral septum (LS is a brain region critically involved with aspects of maternal care, and we recently examined gene expression of whole septum (LS and medial septum in selectively bred maternal mice. Here, we expand on the prior study by 1 conducting microarray analysis solely on LS in virgin and postpartum mice, 2 using outbred mice, and 3 evaluating the role of sensory input on gene expression changes. Large scale changes in genes related to neuronal signaling were identified, including four GABAA receptor subunits. Subunits α4 and δ were downregulated in maternal LS, likely reflecting a reduction in the extrasynaptic, neurosteroid-sensitive α4/δ containing receptor subtype. Conversely, subunits ε and θ were increased in maternal LS. Fifteen K+ channel related genes showed altered expression, as did dopamine receptors Drd1a and Drd2 (both downregulated, hypocretin receptor 1 (Hcrtr1, kappa opioid receptor 1 (Oprk1, and transient receptor potential channel 4 (Trpc4. Expression of a large number of genes linked to developmental processes or cell differentiation were also altered in postpartum LS, including chemokine (C-X-C motif ligand 12 (Cxcl12, fatty acid binding protein 7 (Fabp7, plasma membrane proteolipid (Pllp, and suppressor of cytokine signaling 2 (Socs2. Additional genes that are linked to anxiety, such as glutathione reductase (Gsr, exhibited altered expression. Pathway analysis also identified changes in genes related to cyclic nucleotide metabolism, chromatin structure, and the Ras gene family. The sensory presence of pups was found to contribute to the altered expression of a subset of genes across all categories. This study suggests that both large changes in neuronal signaling and the possible terminal differentiation of neuronal and/or glial cells play important roles in producing the maternal state.

  1. Numerical analysis of weld pool oscillation in laser welding

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Jung Ho [Chungbuk National University, Cheongju (Korea, Republic of); Farson, Dave F [The Ohio State University, Columbus (United States); Hollis, Kendall; Milewski, John O. [Los Alamos National Laboratory, Los Alamos (United States)

    2015-04-15

    Volume of fluid (VOF) numerical simulation was used to investigate melt flow and volumetric oscillation of conduction-mode pulsed laser weld pools. The result is compared to high speed video stream of titanium laser spot welding experiment. The total simulation time is 10ms with the first 5 ms being heating and melting under constant laser irradiation and the remaining 5 ms corresponding to resolidification of the weld pool. During the melting process, the liquid pool did not exhibit periodic oscillation but was continually depressed by the evaporation recoil pressure. After the laser pulse, the weld pool was excited into volumetric oscillation by the release of pressure on its surface and oscillation of the weld pool surface was analyzed. The simulation model suggested adjusting thermal diffusivity to match cooling rate and puddle diameter during solidification which is distinguishable from previous weld pool simulation. The frequency continuously increased from several thousand cycles per second to tens of thousands of cycles per second as the weld pool solidified and its diameter decreased. The result is the first trial of investigation of small weld pool oscillation in laser welding although there have been several reports about arc welding.

  2. CDC Study Finds Fecal Contamination in Pools

    Science.gov (United States)

    ... Communication (404) 639-3286 CDC study finds fecal contamination in pools A study of public pools done ... The E. coli is a marker for fecal contamination. Finding a high percentage of E. coli-positive ...

  3. Sediment transport through self-adjusting, bedrock-walled waterfall plunge pools

    Science.gov (United States)

    Scheingross, Joel S.; Lamb, Michael P.

    2016-05-01

    Many waterfalls have deep plunge pools that are often partially or fully filled with sediment. Sediment fill may control plunge-pool bedrock erosion rates, partially determine habitat availability for aquatic organisms, and affect sediment routing and debris flow initiation. Currently, there exists no mechanistic model to describe sediment transport through waterfall plunge pools. Here we develop an analytical model to predict steady-state plunge-pool depth and sediment-transport capacity by combining existing jet theory with sediment transport mechanics. Our model predicts plunge-pool sediment-transport capacity increases with increasing river discharge, flow velocity, and waterfall drop height and decreases with increasing plunge-pool depth, radius, and grain size. We tested the model using flume experiments under varying waterfall and plunge-pool geometries, flow hydraulics, and sediment size. The model and experiments show that through morphodynamic feedbacks, plunge pools aggrade to reach shallower equilibrium pool depths in response to increases in imposed sediment supply. Our theory for steady-state pool depth matches the experiments with an R2 value of 0.8, with discrepancies likely due to model simplifications of the hydraulics and sediment transport. Analysis of 75 waterfalls suggests that the water depths in natural plunge pools are strongly influenced by upstream sediment supply, and our model provides a mass-conserving framework to predict sediment and water storage in waterfall plunge pools for sediment routing, habitat assessment, and bedrock erosion modeling.

  4. Pool scrubbing and hydrodynamic experiments on jet injection regime

    International Nuclear Information System (INIS)

    Peyres, V.; Espigares, M.M.; Polo, J.; Escudero, M.J.; Herranz, L.E.; Lopez-Jimenez, J.

    1995-01-01

    Plant analyses have shown that pool scrubbing can play an important role in source term during PWR risk dominant sequences. An examination ofboundary conditions governing fission products and aerosols transport through aqueous beds revealed that most of radioactivity is discharged into the pool under jet injection regime. This fact and the lack of experimental data under such conditions pointed the need of setting out an experimental programme which provided reliable experimental data to validate code models. In this report the major results of a pool scrubbing experimental programme carried out in PECA facility are presented. One of the major findings was that a remarkable fraction of particle absorption was not a function of the residence time of bubbles rising through the pool. Such a contribution was assumed to be associated to aerosol removal mechanisms acting at the pool entrance. As a consequence, a hydrodynamic experimental plan was launched to examine the gas behaviour during the initial stages in the pool. Size and shape of gas nuclei the pool were measured and fitted to a long normal distribution. Particularly, size was found to be quite sensitive to inletgas flow and at minor extent to gas composition and pool temperature. SPARC90 and BUSCA-AUG92 were used to simulate the retention tests. Whereas SPARC90 showed a pretty good agreement with experimental data, BUSCA-AUG92 results were far away from measurements in all the cases. SPARC90consistency apparently pointed out the important role of fission products and aerosols retention at the injection zone; nonetheless, a peer examination of pool scrubbing phenomenology at the pool entrance should be carried out to test both hydrodynamic and removal models. Hence, one of the major highlights drawn from this work was the need of further research under representative severe accident conditions (i.e., saturated pools, jet injection regimes, etc.), as well as separate effect tests to validate, improve and

  5. Pool scrubbing and hydrodynamic experiment on jet injection regime

    Energy Technology Data Exchange (ETDEWEB)

    Peyres, V.; Espigares, M.M.; Polo, J.; Escudero, M.J.; Herranz, L.E.; Lopez, J.

    1995-07-01

    Plant analyses nave shown that pool scrubbing can play an important role in source term during PWR risk dominant sequences. An examination of boundary conditions governing fission products and aerosols transport through aqueous beds revealed that most of radioactivity is discharged into the pool under jet injection regime. This fact and the lack of experimental data under such conditions pointed the need of setting out an experimental programme which provided reliable experimental data to validate code models. In this report the major results of a pool scrubbing experimental programme carried out in PECA facility are presented. One of the major findings was that a remarkable fraction of particle absorption was not a function of the residence time of bubbles rising through the pool. Such a contribution was assumed to be associated to aerosol removal mechanism acting at the pool entrance. As a consequence. a hydrodynamic experimental plan was launched to examine the gas behaviour during the initial stages in the pool. Size and shape of gas nuclei in the pool were measured and fitted to a lognormal distribution. Particularly, size was found to be quite sensitive to inlet gas flow and at minor extent to gas composition and pool temperature. SPARC90 and BUSCA-AUG92 were used to simulate the retention tests. Whereas SPARC90 showed a pretty good agreement with experimental data, BUSCA-AUG92 results were far away from measurements in all the cases. SPARC90 consistency apparently pointed out the important role of fission products and aerosols retention at the injection zone; nonetheless, a peer examination of pool scrubbing phenomenology at the pool entrance should be carried out to test both hydrodynamic and removal models. Hence, one of the major high lights drawn from this work was the need of further research under representative severe accident conditions (i.e., saturated pools, jet injection regimes, etc.), as well as separate effect tests to validate, improve and

  6. Pool scrubbing and hydrodynamic experiment on jet injection regime

    International Nuclear Information System (INIS)

    Peyres, V.; Espigares, M.M.; Polo, J.; Escudero, M.J.; Herranz, L.E.; Lopez, J.

    1995-01-01

    Plant analyses nave shown that pool scrubbing can play an important role in source term during PWR risk dominant sequences. An examination of boundary conditions governing fission products and aerosols transport through aqueous beds revealed that most of radioactivity is discharged into the pool under jet injection regime. This fact and the lack of experimental data under such conditions pointed the need of setting out an experimental programme which provided reliable experimental data to validate code models. In this report the major results of a pool scrubbing experimental programme carried out in PECA facility are presented. One of the major findings was that a remarkable fraction of particle absorption was not a function of the residence time of bubbles rising through the pool. Such a contribution was assumed to be associated to aerosol removal mechanism acting at the pool entrance. As a consequence. a hydrodynamic experimental plan was launched to examine the gas behaviour during the initial stages in the pool. Size and shape of gas nuclei in the pool were measured and fitted to a lognormal distribution. Particularly, size was found to be quite sensitive to inlet gas flow and at minor extent to gas composition and pool temperature. SPARC90 and BUSCA-AUG92 were used to simulate the retention tests. Whereas SPARC90 showed a pretty good agreement with experimental data, BUSCA-AUG92 results were far away from measurements in all the cases. SPARC90 consistency apparently pointed out the important role of fission products and aerosols retention at the injection zone; nonetheless, a peer examination of pool scrubbing phenomenology at the pool entrance should be carried out to test both hydrodynamic and removal models. Hence, one of the major high lights drawn from this work was the need of further research under representative severe accident conditions (i.e., saturated pools, jet injection regimes, etc.), as well as separate effect tests to validate, improve and

  7. Turbulence model for melt pool natural convection heat transfer

    International Nuclear Information System (INIS)

    Kelkar, K.M.; Patankar, S.V.

    1994-01-01

    Under severe reactor accident scenarios, pools of molten core material may form in the reactor core or in the hemispherically shaped lower plenum of the reactor vessel. Such molten pools are internally heated due to the radioactive decay heat that gives rise to buoyant flows in the molten pool. The flow in such pools is strongly influenced by the turbulent mixing because the expected Rayleigh numbers under accidents scenarios are very high. The variation of the local heat flux over the boundaries of the molten pools are important in determining the subsequent melt progression behavior. This study reports results of an ongoing effort towards providing a well validated mathematical model for the prediction of buoyant flow and heat transfer in internally heated pool under conditions expected in severe accident scenarios

  8. Identification of a basic helix-loop-helix-type transcription regulator gene in Aspergillus oryzae by systematically deleting large chromosomal segments.

    Science.gov (United States)

    Jin, Feng Jie; Takahashi, Tadashi; Machida, Masayuki; Koyama, Yasuji

    2009-09-01

    We previously developed two methods (loop-out and replacement-type recombination) for generating large-scale chromosomal deletions that can be applied to more effective chromosomal engineering in Aspergillus oryzae. In this study, the replacement-type method is used to systematically delete large chromosomal DNA segments to identify essential and nonessential regions in chromosome 7 (2.93 Mb), which is the smallest A. oryzae chromosome and contains a large number of nonsyntenic blocks. We constructed 12 mutants harboring deletions that spanned 16- to 150-kb segments of chromosome 7 and scored phenotypic changes in the resulting mutants. Among the deletion mutants, strains designated Delta5 and Delta7 displayed clear phenotypic changes involving growth and conidiation. In particular, the Delta5 mutant exhibited vigorous growth and conidiation, potentially beneficial characteristics for certain industrial applications. Further deletion analysis allowed identification of the AO090011000215 gene as the gene responsible for the Delta5 mutant phenotype. The AO090011000215 gene was predicted to encode a helix-loop-helix binding protein belonging to the bHLH family of transcription factors. These results illustrate the potential of the approach for identifying novel functional genes.

  9. A large-scale study of the random variability of a coding sequence: a study on the CFTR gene.

    Science.gov (United States)

    Modiano, Guido; Bombieri, Cristina; Ciminelli, Bianca Maria; Belpinati, Francesca; Giorgi, Silvia; Georges, Marie des; Scotet, Virginie; Pompei, Fiorenza; Ciccacci, Cinzia; Guittard, Caroline; Audrézet, Marie Pierre; Begnini, Angela; Toepfer, Michael; Macek, Milan; Ferec, Claude; Claustres, Mireille; Pignatti, Pier Franco

    2005-02-01

    Coding single nucleotide substitutions (cSNSs) have been studied on hundreds of genes using small samples (n(g) approximately 100-150 genes). In the present investigation, a large random European population sample (average n(g) approximately 1500) was studied for a single gene, the CFTR (Cystic Fibrosis Transmembrane conductance Regulator). The nonsynonymous (NS) substitutions exhibited, in accordance with previous reports, a mean probability of being polymorphic (q > 0.005), much lower than that of the synonymous (S) substitutions, but they showed a similar rate of subpolymorphic (q < 0.005) variability. This indicates that, in autosomal genes that may have harmful recessive alleles (nonduplicated genes with important functions), genetic drift overwhelms selection in the subpolymorphic range of variability, making disadvantageous alleles behave as neutral. These results imply that the majority of the subpolymorphic nonsynonymous alleles of these genes are selectively negative or even pathogenic.

  10. (Microbiological studies of small hot-bath-pools and hot-whirl-pools (author's transl))

    Energy Technology Data Exchange (ETDEWEB)

    Exner, M; Havenith, N

    1981-01-01

    Hot small bathing pools and hot whirl-pools have the following characteristics: small watervolume, thick squeeze of swimmers, high water temperature (37-40 degrees C) and small dimension of filters. By this, the quality of bathing-water is influenced detrimentally. To elaborate the hygienic problems, bathing-water samples were taken before, during and after the visiting-hours and were tested for facultative-pathogenic microorganisms. During this investigation E. coli was isolated in 25 degrees, Coliforms and Proteus species in 37.3%, P. aeruginosa in 36%, S. aureus in 26.3%, Enterococci in 42.3 %, Candida albicans in 3.6% and yeast totally in 8.3%.

  11. Environmental controls of C, N and P biogeochemistry in peatland pools.

    Science.gov (United States)

    Arsenault, Julien; Talbot, Julie; Moore, Tim R

    2018-08-01

    Pools are common in northern peatlands but studies have seldom focused on their nutrient biogeochemistry, especially in relation to their morphological characteristics and through seasons. We determined the environmental characteristics controlling carbon (C), nitrogen (N) and phosphorus (P) biogeochemistry in pools and assessed their evolution over the course of the 2016 growing season in a subboreal ombrotrophic peatland of eastern Canada. We showed that water chemistry variations in 62 pools were significantly explained by depth (81.9%) and the surrounding vegetation type (14.8%), but not by pool area or shape. Shallow pools had larger dissolved organic carbon (DOC) and total nitrogen (TN) concentrations and lower pH than deep pools, while pools surrounded by coniferous trees had more recalcitrant DOC than pools where vegetation was dominated by mosses. The influence of depth on pool biogeochemistry was confirmed by the seasonal survey of pools of different sizes with 47.1% of the variation in pool water chemistry over time significantly explained. Of this, 67.3% was explained by the interaction between time and pool size and 32.7% by pool size alone. P concentrations were small in all pools all summer long and combined with high N:P ratios, are indicative of P-limitation. Our results show that pool biogeochemistry is influenced by internal processes and highlight the spatial and temporal heterogeneity of nutrient biogeochemistry in ombrotrophic peatlands. Copyright © 2018 Elsevier B.V. All rights reserved.

  12. Design of an actively cooled plate calorimeter for the investigation of pool fire heat fluxes

    International Nuclear Information System (INIS)

    Koski, J.A.; Keltner, N.R.; Nicolette, V.F.; Wix, S.D.

    1992-01-01

    For final qualification of shipping containers for transport of hazardous materials, thermal testing in accordance with regulations such as 10CFR71 must be completed. Such tests typically consist of 30 minute exposures with the container fully engulfed in flames from a large, open pool of JP4 jet engine fuel. Despite careful engineering analyses of the container, testing often reveals design problems that must be solved by modification and expensive retesting of the container. One source of this problem is the wide variation in surface heat flux to the container that occurs in pool fires. Average heat fluxes of 50 to 60 kW/m 2 are typical and close the values implied by the radiation model in 10CFR71, but peak fluxes up to 150 kW/m 2 are routinely observed in fires. Heat fluxes in pool fires have been shown to be a function of surface temperature of the container, height above the pool, surface orientation, wind, and other variables. If local variations in the surface heat flux to the container could be better predicted, design analyses would become more accurate, and fewer problems will be uncovered during testing. The objective of the calorimeter design described in this paper is to measure accurately pool fire heat fluxes under controlled conditions, and to provide data for calibration of improved analytical models of local flame-surface interactions

  13. A generic study of phenomena affecting two-phase mixing in BWR suppression pools during passive decay-heat removal

    International Nuclear Information System (INIS)

    Smith, B. L.; Milelli, M.; Shepel, S.; Lakehal, D.

    2003-01-01

    The paper describes some advancements made in the use of two-phase Computational Fluid Dynamics (CFD), sometimes called Computational Multi-Fluid Dynamics (CMFD), techniques in simulating the phenomena occurring in pressure suppression pools in Advanced Boiling Water Reactors which utilise passive containment cooling systems. An interface tracking procedure based on the Level-Set approach has been implemented into a commercial CFD code with the specific purpose of providing a computational environment for the development of suitable models to describe the inter-phase mass and energy transport processes which would take place when a large gas bubble is discharged into a pool. Details of the implementation and validation of the tracking algorithm are described, together with some illustrations of how the method is utilised. The paper also reports on the progress which is being made in the use of Large-Eddy Simulation (LES) to describe turbulent mixing in such plumes. The research efforts are aimed at ultimately combining the approaches to develop a mechanistic tool for fully describing the pool dynamics and steam condensation phenomena

  14. Diets high in resistent starch and arabinoxylan modulate digestion processes and SCFA pool size in the large intestine and faecal microbial composition in pigs

    DEFF Research Database (Denmark)

    Nielsen, Tina Skau; Lærke, Helle Nygaard; Theil, Peter Kappel

    2014-01-01

    The effects of a high level of dietary fibre (DF) either as arabinoxylan (AX) or resistant starch (RS) on digestion processes, SCFA concentration and pool size in various intestinal segments and on the microbial composition in the faeces were studied in a model experiment with pigs. A total...... resulted in a 3- to 5-fold higher pool size of butyrate compared with WSD feeding, with the RSD being intermediate (P microbial composition towards butyrogenic...

  15. Reserve growth in oil pools of Alberta : model and forecast

    Energy Technology Data Exchange (ETDEWEB)

    Verma, M.; Cook, T. [United States Geological Survey, Denver, CO (United States). Central Region

    2010-09-15

    This paper presented a reserve growth study that was conducted on oil pools in Alberta, Canada. Historical oil reserve data were evaluated to assess the potential for future reserve growth in both pools and fields, and reserve growth models and functions were developed to better forecast hydrocarbon volumes. The study also considered the sensitivity of reserve growth to such factors as pool size, porosity, and oil gravity. From 1960 to 2005, the reported known recoverable oil in Alberta, excluding the Athabasca oil sands and including only pools with adequate data, increased from 4.2 to 13.9 billion barrels of oil (BBO). New discoveries contributed 3.7 BBO and reserve growth added 6 BBO. Most reserve growth occurred in pools with more than 125,000 barrels of oil. Light-oil pools account for most of the total known oil volume and consequently showed the lowest growth. Pools with greater than 30 percent porosity grew more than pools with lower porosity reservoirs. Oil field growth was found to be almost twice that of pool growth, possibly because the analysis evaluated fields with two or more pools discovered in different years. The growth in oil volumes in Alberta pools is projected to be about 454 million barrels of oil in the period from 2006 to 2010. Over a 25-year period, the cumulative reserve growth in Alberta oil pools was substantially lower than other major petroleum-producing regions, but the growth at the field level compares well. 8 refs., 2 tabs., 9 figs.

  16. Numerical modelling of methanol liquid pool fires

    Science.gov (United States)

    Prasad, Kuldeep; Li, Chiping; Kailasanath, K.; Ndubizu, Chuka; Ananth, Ramagopal; Tatem, P. A.

    1999-12-01

    The focus of this paper is on numerical modelling of methanol liquid pool fires. A mathematical model is first developed to describe the evaporation and burning of a two-dimensional or axisymmetric pool containing pure liquid methanol. Then, the complete set of unsteady, compressible Navier-Stokes equations for reactive flows are solved in the gas phase to describe the convection of the fuel gases away from the pool surface, diffusion of the gases into the surrounding air and the oxidation of the fuel into product species. Heat transfer into the liquid pool and the metal container through conduction, convection and radiation are modelled by solving a modified form of the energy equation. Clausius-Clapeyron relationships are invoked to model the evaporation rate of a two-dimensional pool of pure liquid methanol. The governing equations along with appropriate boundary and interface conditions are solved using the flux-corrected transport algorithm. Numerical results exhibit a flame structure that compares well with experimental observations. Temperature profiles and burning rates were found to compare favourably with experimental data from single- and three-compartment laboratory burners. The model predicts a puffing frequency of approximately 12 Hz for a 1 cm diameter methanol pool in the absence of any air co-flow. It is also observed that increasing the air co-flow velocity helps in stabilizing the diffusion flame, by pushing the vortical structures away from the flame region.

  17. Genome-wide association study for ovarian cancer susceptibility using pooled DNA

    DEFF Research Database (Denmark)

    Lu, Yi; Chen, Xiaoqing; Beesley, Jonathan

    2012-01-01

    stage 1 GWAS rather than due to problems with the pooling approach. We conclude that there are unlikely to be any moderate or large effects on ovarian cancer risk untagged by less dense arrays. However, our study lacked power to make clear statements on the existence of hitherto untagged small......Recent Genome-Wide Association Studies (GWAS) have identified four low-penetrance ovarian cancer susceptibility loci. We hypothesized that further moderate- or low-penetrance variants exist among the subset of single-nucleotide polymorphisms (SNPs) not well tagged by the genotyping arrays used...... in the previous studies, which would account for some of the remaining risk. We therefore conducted a time- and cost-effective stage 1 GWAS on 342 invasive serous cases and 643 controls genotyped on pooled DNA using the high-density Illumina 1M-Duo array. We followed up 20 of the most significantly associated...

  18. Security cost allocation under combined bilateral-pool market dispatch

    International Nuclear Information System (INIS)

    Abdullah, M.P.; Hassan, M.Y.; Hussin, F.

    2008-01-01

    Most electricity markets around the world are a combination of bilateral and pool markets, such as NordPool and NYPOOL. In these models, market participants bid into the pool and also make bilateral contracts with each other. This paper addressed the issue of congestion management and security cost allocation in a power pool market model. The basic idea of security cost allocation is to divide the incurred security cost due to congestion relief into pool and bilateral market based on their flow contribution to the congested line. A newly proposed security cost allocation strategy of the combined bilateral-pool market was also presented along with case studies using IEEE-14 bus system that tested the proposed method. Using the proposed method, it was shown that security costs are allocated to market participants at different prices which reflect the load contribution to the security problem. This solves the problem of the uniform security cost allocation in a pure pool market system having uniform pricing, and provides a proper security signal to market participants. 11 refs., 3 tabs., 4 figs

  19. Robotic cleaning of a spent fuel pool

    International Nuclear Information System (INIS)

    Roman, H.T.; Marian, F.A.; Silverman, E.B.; Barkley, V.P.

    1987-01-01

    Spent fuel pools at nuclear power plants are not cleaned routinely, other than by purifying the water that they contain. Yet, debris can collect on the bottom of a pool and should be removed prior to fuel transfer. At Public Service Electric and Gas Company's Hope Creek Nuclear Power Plant, a submersible mobile robot - ARD Corporation's SCAVENGER - was used to clean the bottom of the spent fuel pool prior to initial fuel loading. The robotic device was operated remotely (as opposed to autonomously) with a simple forward/reverse control, and it cleaned 70-80% of the pool bottom. This paper reports that a simple cost-benefit analysis shows that the robotic device would be less expensive, on a per mission basis, than other cleaning alternatives, especially if it were used for other similar cleaning operations throughout the plant

  20. Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity.

    Science.gov (United States)

    Lee, Karen J I; Calder, Grant M; Hindle, Christopher R; Newman, Jacob L; Robinson, Simon N; Avondo, Jerome J H Y; Coen, Enrico S

    2017-01-01

    Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  1. Linking tree demography to climate change feedbacks: fire, larch forests, and carbon pools of the Siberian Arctic

    Science.gov (United States)

    Alexander, H. D.; Loranty, M. M.; Natali, S.; Pena, H., III; Ludwig, S.; Spektor, V.; Davydov, S. P.; Zimov, N.; Mack, M. C.

    2017-12-01

    Fire severity is increasing in larch forests of the Siberian Arctic as climate warms, and initial fire impacts on tree demographic processes could be an especially important determinant of long-term forest structure and carbon (C) dynamics. We hypothesized that (1) larch forest regrowth post-fire is largely determined by residual soil organic layer (SOL) depth because of the SOL's role as a seedbed and thermal regulator, and (2) changes in post-fire larch recruitment impact C accumulation through stand density impacts on understory microclimate and permafrost thaw. We tested these hypotheses by (1) experimentally creating a soil burn severity gradient in a Cajander larch (Larix cajanderi Mayr.) forest near Cherskiy, Russia and (2) quantifying C pools across a stand density gradient within a 75-year old fire scar. From 2012-2015, we added larch seeds to plots burned at different severities and monitored recruitment along with permafrost and active layer (i.e., subject to annual freeze-thaw) conditions (SOL depth, temperature, moisture, and thaw depth). Across the density gradient, we inventoried larch trees and harvested ground-layer vegetation to estimate aboveground contribution to C pools. We quantified woody debris C pools and sampled belowground C pools (soil, fine roots, and coarse roots) in the organic + upper (0-10 cm) mineral soil. Larch recruits were rare in unburned and low severity plots, but a total of 6 new germinants m-2 were tallied in moderate and high severity plots during the study. Seedling survival for > 1 year was only 40 and 25% on moderate and high severity treatments, respectively, but yielded net larch recruitment of 2 seedlings m-2, compared to 0.3 seedlings m-2 on low severity plots. Density of both total and established recruits increased with decreasing residual SOL depth, which correlated with increased soil temperature, moisture, and thaw depth. At 75-year post-fire, total C pools increased with increased larch density, largely due to

  2. The strength of intron donor splice sites in human genes displays a bell-shaped pattern

    DEFF Research Database (Denmark)

    Wang, Kai; Wernersson, Rasmus; Brunak, Søren

    2011-01-01

    introns. Interestingly, when analysing the intron containing gene pool from mouse consisting of >15 000 genes, we found the convex pattern to be conserved despite >75 million years of evolutionary divergence between the two organisms. We also analysed an interesting, novel class of chimeric genes which...

  3. Controlling pool depth during VAR of Alloy 718

    Science.gov (United States)

    Lopez, F.; Beaman, J.; Williamson, R.; Evans, D.

    2016-07-01

    A longtime goal of superalloy producers has been to control the geometry of the liquid pool in solidifying ingots. Accurate pool depth control at appropriate values is expected to result in ingots free of segregation defects. This article describes an industrial VAR experiment in which a 430mm (17 in) diameter Alloy 718 electrode was melted into a 510mm (20 in) ingot. In the experiment, the depth of the liquid pool at the mid-radius was controlled to three different set-points: 137 mm (nominal), 193 mm (deep) and 118 mm (shallow). At each level, the pool depth was marked by a power cutback of several minutes. The ingot was sectioned and longitudinal slices were cut out. Analysis of the photographed ingot revealed that accurate control was obtained for both the nominal and deep pool cases, while the third one was not conclusive.

  4. Expansion of capacity of spent fuel pools and associated problems

    International Nuclear Information System (INIS)

    Francisco, J.L. De; Lopez-Cotarelo, J.; Ramos, J.M.

    1978-01-01

    Expanding the spent fuel storage pool capacity is a good solution for utilities facing the current shortage in fuel reprocessing capacity. The problems more likely to be found when expanding a spent fuel storage facility by using high density storage racks are reviewed. Basically three types of problems arise: 1) Problems related with the characteristics of the new facility. 2) Problems related with the works of expansion. 3) Problems related with the long term storage of large quantities of spent fuel. (author)

  5. Birth order and childhood type 1 diabetes risk: a pooled analysis of 31 observational studies

    DEFF Research Database (Denmark)

    Cardwell, Chris R; Stene, Lars C; Joner, Geir

    2011-01-01

    The incidence rates of childhood onset type 1 diabetes are almost universally increasing across the globe but the aetiology of the disease remains largely unknown. We investigated whether birth order is associated with the risk of childhood diabetes by performing a pooled analysis of previous...

  6. Utility of the pooling approach as applied to whole genome association scans with high-density Affymetrix microarrays

    Directory of Open Access Journals (Sweden)

    Gray Joanna

    2010-11-01

    Full Text Available Abstract Background We report an attempt to extend the previously successful approach of combining SNP (single nucleotide polymorphism microarrays and DNA pooling (SNP-MaP employing high-density microarrays. Whereas earlier studies employed a range of Affymetrix SNP microarrays comprising from 10 K to 500 K SNPs, this most recent investigation used the 6.0 chip which displays 906,600 SNP probes and 946,000 probes for the interrogation of CNVs (copy number variations. The genotyping assay using the Affymetrix SNP 6.0 array is highly demanding on sample quality due to the small feature size, low redundancy, and lack of mismatch probes. Findings In the first study published so far using this microarray on pooled DNA, we found that pooled cheek swab DNA could not accurately predict real allele frequencies of the samples that comprised the pools. In contrast, the allele frequency estimates using blood DNA pools were reasonable, although inferior compared to those obtained with previously employed Affymetrix microarrays. However, it might be possible to improve performance by developing improved analysis methods. Conclusions Despite the decreasing costs of genome-wide individual genotyping, the pooling approach may have applications in very large-scale case-control association studies. In such cases, our study suggests that high-quality DNA preparations and lower density platforms should be preferred.

  7. Analysis of the LBLOCAs in the HANARO pool for the 3-pin fuel test loop

    International Nuclear Information System (INIS)

    Park, S. K.; Chi, D. Y.; Sim, B. S.; Park, K. N.; Ahn, S. H.; Lee, J. M.; Lee, C. Y.; Kim, Y. J.

    2004-12-01

    The Fuel Test Loop(FTL) has been developed to meet the increasing demand on fuel irradiation and burn up test required the development of new fuels in Korea. It is designed to provide the test conditions of high pressure and temperature like the commercial PWR and CANDU power plants. And also the FTL have the cooling capability to sufficiently remove the thermal power of the in-pile test section for normal operation, Anticipated Operational Occurrences(AOOs), and Design Basis Accidents(DBAs). This report deals with the Large Break Loss of Coolant Accidents (LBLOCAs) in HANARO pool for the 3-pin fuel test loop. The MARS code has been used for the prediction of the emergency core cooling capability of the FTL and the peak cladding temperature of the test fuels for the LBLOCAs. The location of the pipe break is assumed at the hill taps connecting the cold and hot legs in HANARO pool to the inlet and outlet nozzles of the In-Pile test Section (IPS). Double ended guillotine break is assumed for the large break loss of coolant accidents. The discharge coefficients of 0.1, 0.33, 0.67, 1.0 are investigated for the LBLOCAs. The test fuels for PWR and CANDU test modes are not heated up for the LBLOCAs caused by the double ended guillotine break in the HANARO pool. The reason is that the sufficient emergency cooling water to cool down the test fuels is supplied continuously to the in-pile test section. Therefore the PCTs for the LBLOCAs in the HANARO pool meet the design criterion of commercial PWR fuel that maximum PCT is lower than 1204 .deg. C

  8. Harnessing diversity towards the reconstructing of large scale gene regulatory networks.

    Directory of Open Access Journals (Sweden)

    Takeshi Hase

    Full Text Available Elucidating gene regulatory network (GRN from large scale experimental data remains a central challenge in systems biology. Recently, numerous techniques, particularly consensus driven approaches combining different algorithms, have become a potentially promising strategy to infer accurate GRNs. Here, we develop a novel consensus inference algorithm, TopkNet that can integrate multiple algorithms to infer GRNs. Comprehensive performance benchmarking on a cloud computing framework demonstrated that (i a simple strategy to combine many algorithms does not always lead to performance improvement compared to the cost of consensus and (ii TopkNet integrating only high-performance algorithms provide significant performance improvement compared to the best individual algorithms and community prediction. These results suggest that a priori determination of high-performance algorithms is a key to reconstruct an unknown regulatory network. Similarity among gene-expression datasets can be useful to determine potential optimal algorithms for reconstruction of unknown regulatory networks, i.e., if expression-data associated with known regulatory network is similar to that with unknown regulatory network, optimal algorithms determined for the known regulatory network can be repurposed to infer the unknown regulatory network. Based on this observation, we developed a quantitative measure of similarity among gene-expression datasets and demonstrated that, if similarity between the two expression datasets is high, TopkNet integrating algorithms that are optimal for known dataset perform well on the unknown dataset. The consensus framework, TopkNet, together with the similarity measure proposed in this study provides a powerful strategy towards harnessing the wisdom of the crowds in reconstruction of unknown regulatory networks.

  9. Design and computational analysis of passive siphon breaker for 49-2 swimming pool reactor

    International Nuclear Information System (INIS)

    Yue Zhiting; Song Yunpeng; Liu Xingmin; Zou Yao; Wu Yuanyuan

    2014-01-01

    Based on safety considerations, a passive siphon breaker will be added to the primary cooling system of 49-2 Swimming Pool Reactor (SPR). With the breaker location determined, the capability of siphon breakers with diameters of 1.5 cm and 2.0 cm was calculated and analyzed respectively by RELAP5/MOD3.3 code. The results show that in the condition of large break loss of coolant accident these two sizes of siphon breakers are able to break the siphon phenomena, and maintain the pool water level above the reactor core when the reactor and the pump are shutdown. In the end, to be conservative, the siphon breaker with diameter of 2.0 cm is adopted. (authors)

  10. Integrative analysis of survival-associated gene sets in breast cancer.

    Science.gov (United States)

    Varn, Frederick S; Ung, Matthew H; Lou, Shao Ke; Cheng, Chao

    2015-03-12

    Patient gene expression information has recently become a clinical feature used to evaluate breast cancer prognosis. The emergence of prognostic gene sets that take advantage of these data has led to a rich library of information that can be used to characterize the molecular nature of a patient's cancer. Identifying robust gene sets that are consistently predictive of a patient's clinical outcome has become one of the main challenges in the field. We inputted our previously established BASE algorithm with patient gene expression data and gene sets from MSigDB to develop the gene set activity score (GSAS), a metric that quantitatively assesses a gene set's activity level in a given patient. We utilized this metric, along with patient time-to-event data, to perform survival analyses to identify the gene sets that were significantly correlated with patient survival. We then performed cross-dataset analyses to identify robust prognostic gene sets and to classify patients by metastasis status. Additionally, we created a gene set network based on component gene overlap to explore the relationship between gene sets derived from MSigDB. We developed a novel gene set based on this network's topology and applied the GSAS metric to characterize its role in patient survival. Using the GSAS metric, we identified 120 gene sets that were significantly associated with patient survival in all datasets tested. The gene overlap network analysis yielded a novel gene set enriched in genes shared by the robustly predictive gene sets. This gene set was highly correlated to patient survival when used alone. Most interestingly, removal of the genes in this gene set from the gene pool on MSigDB resulted in a large reduction in the number of predictive gene sets, suggesting a prominent role for these genes in breast cancer progression. The GSAS metric provided a useful medium by which we systematically investigated how gene sets from MSigDB relate to breast cancer patient survival. We used

  11. Targeted Enrichment of Large Gene Families for Phylogenetic Inference: Phylogeny and Molecular Evolution of Photosynthesis Genes in the Portullugo Clade (Caryophyllales).

    Science.gov (United States)

    Moore, Abigail J; Vos, Jurriaan M De; Hancock, Lillian P; Goolsby, Eric; Edwards, Erika J

    2018-05-01

    Hybrid enrichment is an increasingly popular approach for obtaining hundreds of loci for phylogenetic analysis across many taxa quickly and cheaply. The genes targeted for sequencing are typically single-copy loci, which facilitate a more straightforward sequence assembly and homology assignment process. However, this approach limits the inclusion of most genes of functional interest, which often belong to multi-gene families. Here, we demonstrate the feasibility of including large gene families in hybrid enrichment protocols for phylogeny reconstruction and subsequent analyses of molecular evolution, using a new set of bait sequences designed for the "portullugo" (Caryophyllales), a moderately sized lineage of flowering plants (~ 2200 species) that includes the cacti and harbors many evolutionary transitions to C$_{\\mathrm{4}}$ and CAM photosynthesis. Including multi-gene families allowed us to simultaneously infer a robust phylogeny and construct a dense sampling of sequences for a major enzyme of C$_{\\mathrm{4}}$ and CAM photosynthesis, which revealed the accumulation of adaptive amino acid substitutions associated with C$_{\\mathrm{4}}$ and CAM origins in particular paralogs. Our final set of matrices for phylogenetic analyses included 75-218 loci across 74 taxa, with ~ 50% matrix completeness across data sets. Phylogenetic resolution was greatly improved across the tree, at both shallow and deep levels. Concatenation and coalescent-based approaches both resolve the sister lineage of the cacti with strong support: Anacampserotaceae $+$ Portulacaceae, two lineages of mostly diminutive succulent herbs of warm, arid regions. In spite of this congruence, BUCKy concordance analyses demonstrated strong and conflicting signals across gene trees. Our results add to the growing number of examples illustrating the complexity of phylogenetic signals in genomic-scale data.

  12. Sharing as risk pooling in a social dilemma experiment

    Directory of Open Access Journals (Sweden)

    Todd L. Cherry

    2015-03-01

    Full Text Available In rural economies with missing or incomplete markets, idiosyncratic risk is frequently pooled through informal networks. Idiosyncratic shocks, however, are not limited to private goods but can also restrict an individual from partaking in or benefiting from a collective activity. In these situations, a group must decide whether to provide insurance to the affected member. We describe results of a laboratory experiment designed to test whether a simple sharing institution can sustain risk pooling in a social dilemma with idiosyncratic risk. We tested whether risk could be pooled without a commitment device and, separately, whether effective risk pooling induced greater cooperation in the social dilemma. We found that even in the absence of a commitment device or reputational considerations, subjects voluntarily pooled risk, thereby reducing variance in individual earnings. In spite of effective risk pooling, however, cooperation in the social dilemma was unaffected.

  13. Sampling and Pooling Methods for Capturing Herd Level Antibiotic Resistance in Swine Feces using qPCR and CFU Approaches

    DEFF Research Database (Denmark)

    Schmidt, Gunilla Veslemøy; Mellerup, Anders; Christiansen, Lasse Engbo

    2015-01-01

    The aim of this article was to define the sampling level and method combination that captures antibiotic resistance at pig herd level utilizing qPCR antibiotic resistance gene quantification and culture-based quantification of antibiotic resistant coliform indicator bacteria. Fourteen qPCR assays...... for commonly detected antibiotic resistance genes were developed, and used to quantify antibiotic resistance genes in total DNA from swine fecal samples that were obtained using different sampling and pooling methods. In parallel, the number of antibiotic resistant coliform indicator bacteria was determined...... in the same swine fecal samples. The results showed that the qPCR assays were capable of detecting differences in antibiotic resistance levels in individual animals that the coliform bacteria colony forming units (CFU) could not. Also, the qPCR assays more accurately quantified antibiotic resistance genes...

  14. Large clusters of co-expressed genes in the Drosophila genome.

    Science.gov (United States)

    Boutanaev, Alexander M; Kalmykova, Alla I; Shevelyov, Yuri Y; Nurminsky, Dmitry I

    2002-12-12

    Clustering of co-expressed, non-homologous genes on chromosomes implies their co-regulation. In lower eukaryotes, co-expressed genes are often found in pairs. Clustering of genes that share aspects of transcriptional regulation has also been reported in higher eukaryotes. To advance our understanding of the mode of coordinated gene regulation in multicellular organisms, we performed a genome-wide analysis of the chromosomal distribution of co-expressed genes in Drosophila. We identified a total of 1,661 testes-specific genes, one-third of which are clustered on chromosomes. The number of clusters of three or more genes is much higher than expected by chance. We observed a similar trend for genes upregulated in the embryo and in the adult head, although the expression pattern of individual genes cannot be predicted on the basis of chromosomal position alone. Our data suggest that the prevalent mechanism of transcriptional co-regulation in higher eukaryotes operates with extensive chromatin domains that comprise multiple genes.

  15. Enhancing swimming pool safety by the use of range-imaging cameras

    Science.gov (United States)

    Geerardyn, D.; Boulanger, S.; Kuijk, M.

    2015-05-01

    Drowning is the cause of death of 372.000 people, each year worldwide, according to the report of November 2014 of the World Health Organization.1 Currently, most swimming pools only use lifeguards to detect drowning people. In some modern swimming pools, camera-based detection systems are nowadays being integrated. However, these systems have to be mounted underwater, mostly as a replacement of the underwater lighting. In contrast, we are interested in range imaging cameras mounted on the ceiling of the swimming pool, allowing to distinguish swimmers at the surface from drowning people underwater, while keeping the large field-of-view and minimizing occlusions. However, we have to take into account that the water surface of a swimming pool is not a flat, but mostly rippled surface, and that the water is transparent for visible light, but less transparent for infrared or ultraviolet light. We investigated the use of different types of 3D cameras to detect objects underwater at different depths and with different amplitudes of surface perturbations. Specifically, we performed measurements with a commercial Time-of-Flight camera, a commercial structured-light depth camera and our own Time-of-Flight system. Our own system uses pulsed Time-of-Flight and emits light of 785 nm. The measured distances between the camera and the object are influenced through the perturbations on the water surface. Due to the timing of our Time-of-Flight camera, our system is theoretically able to minimize the influence of the reflections of a partially-reflecting surface. The combination of a post image-acquisition filter compensating for the perturbations and the use of a light source with shorter wavelengths to enlarge the depth range can improve the current commercial cameras. As a result, we can conclude that low-cost range imagers can increase swimming pool safety, by inserting a post-processing filter and the use of another light source.

  16. Nuclear Insurance Pools: Worldwide Practice and Development

    International Nuclear Information System (INIS)

    Reitsma, S. M. S.

    1998-01-01

    The development of nuclear installations to produce electricity led to the establishment of Nuclear Insurance Pools and the introduction of international Conventions on Third Party Liability. Nuclear Pools offer both Third Party Liability insurance, reflecting the Conventions' principles, and other insurance products. They are market-wide, providing a facility for participation by insurers who could not otherwise write the insurance for the particularly sensitive nuclear risk. All acceptances are for the net retention of each Member without recourse to individual reinsurance protection. Common account reinsurance is arranged with other Nuclear Pools all over the world. Thus, a transparency is created, which ensures the highest degree of reinsurance security and imposes a known finite limit to each participating insurer's commitment. Therefore, Pool-members are prepared to make a greater commitment to nuclear risks than would be case where they felt uncertain as regards their total exposure following a significant loss. (author)

  17. Opportunities and challenges when pooling milk samples using ELISA

    DEFF Research Database (Denmark)

    Græsbøll, Kaare; Andresen, Lars Ole; Hisham Beshara Halasa, Tariq

    2017-01-01

    -positive samples by pooling. To illustrate this, the sensitivity of antibody ELISA on pooled samples of bovine milk for Salmonella Dublin, Mycobacterium avium spp. paratuberculosis, and bovine virus diarrhea was tested. For these milk assays, the analytical sensitivity decreased rapidly with increasing pool sizes...

  18. Microscopic bubble behaviour in suppression pool during wetwell venting

    Science.gov (United States)

    Zablackaite, G.; Nagasaka, H.; Kikura, H.

    2017-10-01

    During a severe accident PCV failure should be avoided and fission products inside PCV should be confined as much as possible. In order to minimize FPs release, Wetwell venting is conducted by releasing steam-non-condensable gas mixture carrying FPs from the Drywell to Suppression Pool. Steam is condensed by subcooled water in the pool, and most of FPs are retained into water. The removal of FP in the water pool is referred to as “Pool Scrubbing effect”. Hydrodynamic parameters of bubbles have impact on pool scrubbing effect. However, there is only few data available to evaluate quantitatively the bubble behaviour under depressurization and/or thermal stratification conditions. Series of experiments were conducted to evaluate the influence of temperature distribution, non-condensable gas content and pressure in the Wetwell on bubble behaviour. Bubbles were visualized using High Speed Camera and adopting shadowgraphy technique. Applying Particle Tracking Velocimetry, bubble velocity and size distribution were obtained from recorded images. Experimental results show that with increasing suppression pool temperature, bubbles reaching the pool surface decreased in size and traveling velocity became slower. In pressurized wetwell, bubble behaviour was similar to that in the heated up suppression pool case, although bubble parameters were similar to the low temperature case. Higher air content induced water surface movement and bubbles were smaller due to break up.

  19. A large and functionally diverse family of Fad2 genes in safflower (Carthamus tinctorius L.

    Directory of Open Access Journals (Sweden)

    Cao Shijiang

    2013-01-01

    Full Text Available Abstract Background The application and nutritional value of vegetable oil is highly dependent on its fatty acid composition, especially the relative proportion of its two major fatty acids, i.e oleic acid and linoleic acid. Microsomal oleoyl phosphatidylcholine desaturase encoded by FAD2 gene is known to introduce a double bond at the Δ12 position of an oleic acid on phosphatidylcholine and convert it to linoleic acid. The known plant FAD2 enzymes are encoded by small gene families consisting of 1-4 members. In addition to the classic oleate Δ12-desaturation activity, functional variants of FAD2 that are capable of undertaking additional or alternative acyl modifications have also been reported in a limited number of plant species. In this study, our objective was to identify FAD2 genes from safflower and analyse their differential expression profile and potentially diversified functionality. Results We report here the characterization and functional expression of an exceptionally large FAD2 gene family from safflower, and the temporal and spatial expression profiles of these genes as revealed through Real-Time quantitative PCR. The diversified functionalities of some of the safflower FAD2 gene family members were demonstrated by ectopic expression in yeast and transient expression in Nicotiana benthamiana leaves. CtFAD2-1 and CtFAD2-10 were demonstrated to be oleate desaturases specifically expressed in developing seeds and flower head, respectively, while CtFAD2-2 appears to have relatively low oleate desaturation activity throughout the plant. CtFAD2-5 and CtFAD2-8 are specifically expressed in root tissues, while CtFAD2-3, 4, 6, 7 are mostly expressed in the cotyledons and hypocotyls in young safflower seedlings. CtFAD2-9 was found to encode a novel desaturase operating on C16:1 substrate. CtFAD2-11 is a tri-functional enzyme able to introduce a carbon double bond in either cis or trans configuration, or a carbon triple (acetylenic bond

  20. 3D finite element simulation of TIG weld pool

    Science.gov (United States)

    Kong, X.; Asserin, O.; Gounand, S.; Gilles, P.; Bergheau, J. M.; Medale, M.

    2012-07-01

    The aim of this paper is to propose a three-dimensional weld pool model for the moving gas tungsten arc welding (GTAW) process, in order to understand the main factors that limit the weld quality and improve the productivity, especially with respect to the welding speed. Simulation is a very powerful tool to help in understanding the physical phenomena in the weld process. A 3D finite element model of heat and fluid flow in weld pool considering free surface of the pool and traveling speed has been developed for the GTAW process. Cast3M software is used to compute all the governing equations. The free surface of the weld pool is calculated by minimizing the total surface energy. The combined effects of surface tension gradient, buoyancy force, arc pressure, arc drag force to drive the fluid flow is included in our model. The deformation of the weld pool surface and the welding speed affect fluid flow, heat flow and thus temperature gradients and molten pool dimensions. Welding trials study is presented to compare our numerical results with macrograph of the molten pool.

  1. Flight-induced changes in gene expression in the Glanville fritillary butterfly.

    Science.gov (United States)

    Kvist, Jouni; Mattila, Anniina L K; Somervuo, Panu; Ahola, Virpi; Koskinen, Patrik; Paulin, Lars; Salmela, Leena; Fountain, Toby; Rastas, Pasi; Ruokolainen, Annukka; Taipale, Minna; Holm, Liisa; Auvinen, Petri; Lehtonen, Rainer; Frilander, Mikko J; Hanski, Ilkka

    2015-10-01

    Insect flight is one of the most energetically demanding activities in the animal kingdom, yet for many insects flight is necessary for reproduction and foraging. Moreover, dispersal by flight is essential for the viability of species living in fragmented landscapes. Here, working on the Glanville fritillary butterfly (Melitaea cinxia), we use transcriptome sequencing to investigate gene expression changes caused by 15 min of flight in two contrasting populations and the two sexes. Male butterflies and individuals from a large metapopulation had significantly higher peak flight metabolic rate (FMR) than female butterflies and those from a small inbred population. In the pooled data, FMR was significantly positively correlated with genome-wide heterozygosity, a surrogate of individual inbreeding. The flight experiment changed the expression level of 1513 genes, including genes related to major energy metabolism pathways, ribosome biogenesis and RNA processing, and stress and immune responses. Males and butterflies from the population with high FMR had higher basal expression of