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Sample records for core genome concept

  1. Some Core Contested Concepts

    Chomsky, Noam

    2015-01-01

    Core concepts of language are highly contested. In some cases this is legitimate: real empirical and conceptual issues arise. In other cases, it seems that controversies are based on misunderstanding. A number of crucial cases are reviewed, and an approach to language is outlined that appears to have strong conceptual and empirical motivation, and…

  2. Some core contested concepts.

    Chomsky, Noam

    2015-02-01

    Core concepts of language are highly contested. In some cases this is legitimate: real empirical and conceptual issues arise. In other cases, it seems that controversies are based on misunderstanding. A number of crucial cases are reviewed, and an approach to language is outlined that appears to have strong conceptual and empirical motivation, and to lead to conclusions about a number of significant issues that differ from some conventional beliefs.

  3. The Core Journal Concept in Black Studies

    Weissinger, Thomas

    2010-01-01

    Black Studies scholars have shown interest in the core journal concept. Indeed, the idea of core journals for the study of the Black experience has changed several times since 1940. While Black Studies scholars are citing Black Studies journals with frequency, they also cite traditional disciplinary journals a great deal of the time. However,…

  4. Core catcher concepts future PWR-Plants

    Alsmeyer, H.; Werle, H.

    1994-01-01

    Light water reactors of the next generation should have still greater passive safety, even in the most serious accidents. This includes the long term safe inclusion of the core inventory in the case of core meltdown accidents. The three concepts for cooling the liquefied core outside the reactor pressure vessel examined by KfK should remove the post-shutdown heat by direct contact of the melt with water. The geometric distribution of the melt increases its surface area, so that favourable conditions for heat removal from the poorly thermally-conducting melt are created and complete quick solidification occurs. The experiments examine both the relocation and distribution mechanisms of the melt and the reactions occurring when water enters. As strong interaction is possible on direct contact of the melt with water, an important aim is experimental determination and limitation of any resulting mechanical stresses. (orig./HP) [de

  5. Multimedia foundations core concepts for digital design

    Costello, Vic; Youngblood, Susan

    2012-01-01

    Understand the core concepts and skills of multimedia production and digital storytelling using text, graphics, photographs, sound, motion, and video. Then, put it all together using the skills that you have developed for effective project planning, collaboration, visual communication, and graphic design. Presented in full color with hundreds of vibrant illustrations, Multimedia Foundations trains you in the principles and skill sets common to all forms of digital media production, enabling you to create successful, engaging content, no matter what tools you are using. Companion website

  6. Core mechanics and configuration behavior of advanced LMFBR core restraint concepts

    Fox, J.N.; Wei, B.C.

    1978-02-01

    Core restraint systems in LMFBRs maintain control of core mechanics and configuration behavior. Core restraint design is complex due to the close spacing between adjacent components, flux and temperature gradients, and irradiation-induced material property effects. Since the core assemblies interact with each other and transmit loads directly to the core restraint structural members, the core assemblies themselves are an integral part of the core restraint system. This paper presents an assessment of several advanced core restraint system and core assembly concepts relative to the expected performance of currently accepted designs. A recommended order for the development of the advanced concepts is also presented

  7. Genomic variation in Salmonella enterica core genes for epidemiological typing

    Leekitcharoenphon, Pimlapas; Lukjancenko, Oksana; Rundsten, Carsten Friis

    2012-01-01

    Background: Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over...... genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. A consensus tree based on variation of core genes gives much better resolution than 16S and MLST; the pan-genome family tree is similar to the consensus tree, but with higher...... that there is a positive selection towards mutations leading to amino acid changes. Conclusions: Genomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. Identification of genes with different degrees of variation is important...

  8. Identifying Core Concepts of Cybersecurity: Results of Two Delphi Processes

    Parekh, Geet; DeLatte, David; Herman, Geoffrey L.; Oliva, Linda; Phatak, Dhananjay; Scheponik, Travis; Sherman, Alan T.

    2018-01-01

    This paper presents and analyzes results of two Delphi processes that polled cybersecurity experts to rate cybersecurity topics based on importance, difficulty, and timelessness. These ratings can be used to identify core concepts--cross-cutting ideas that connect knowledge in the discipline. The first Delphi process identified core concepts that…

  9. Newly discovered young CORE-SINEs in marsupial genomes.

    Munemasa, Maruo; Nikaido, Masato; Nishihara, Hidenori; Donnellan, Stephen; Austin, Christopher C; Okada, Norihiro

    2008-01-15

    Although recent mammalian genome projects have uncovered a large part of genomic component of various groups, several repetitive sequences still remain to be characterized and classified for particular groups. The short interspersed repetitive elements (SINEs) distributed among marsupial genomes are one example. We have identified and characterized two new SINEs from marsupial genomes that belong to the CORE-SINE family, characterized by a highly conserved "CORE" domain. PCR and genomic dot blot analyses revealed that the distribution of each SINE shows distinct patterns among the marsupial genomes, implying different timing of their retroposition during the evolution of marsupials. The members of Mar3 (Marsupialia 3) SINE are distributed throughout the genomes of all marsupials, whereas the Mac1 (Macropodoidea 1) SINE is distributed specifically in the genomes of kangaroos. Sequence alignment of the Mar3 SINEs revealed that they can be further divided into four subgroups, each of which has diagnostic nucleotides. The insertion patterns of each SINE at particular genomic loci, together with the distribution patterns of each SINE, suggest that the Mar3 SINEs have intensively amplified after the radiation of diprotodontians, whereas the Mac1 SINE has amplified only slightly after the divergence of hypsiprimnodons from other macropods. By compiling the information of CORE-SINEs characterized to date, we propose a comprehensive picture of how SINE evolution occurred in the genomes of marsupials.

  10. Some concept for the TRIGA core design

    Aizawa, Otohiko

    1994-01-01

    There is the research reactor called TRIGA Mark-2 of 100 kW in Atomic Energy Research Laboratory, Musashi Institute of Technology. Recently, while the various calculations on the core were carried out, the author became aware of that this TRIGA core was designed at that time with excellent consideration. The reason for that is, although fuel is arranged in simple concentric circular state at a glance, it was known that in reality, this is the modification of the hexagonal core of triangular lattice. In the examination of square lattice fuel arrangement, the reactivity was calculated by using the gap between fuel rods as the parameter and by using ENDF/B-4 library and Monte Carlo code Keno-5. It is known that the design of the lattice with maximum reactivity cannot be done by the square lattice. The similar examination was carried out on triangular lattice, and it was found that the gap between fuel rods of 4 mm is the optimal design. The average neutron energy spectra in the fuel rods of the TRIGA Mark-2 core agreed considerably well with the energy spectra at 4.16 cm fuel rod pitch in triangular hexagonal core. In the reactor of about 100 kW, even if the gap between fuel rods is less than 4 mm, heat removal is sufficiently possible. (K.I.)

  11. Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing

    Fu, Songzhe; Octavia, Sophie; Tanaka, Mark M.; Sintchenko, Vitali

    2015-01-01

    Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing foodborne infections in Australia and many other countries. Twenty-one S. Typhimurium strains from Salmonella reference collection A (SARA) were analyzed using Illumina high-throughput genome sequencing. Single nucleotide polymorphisms (SNPs) in 21 SARA strains ranged from 46 to 11,916 SNPs, with an average of 1,577 SNPs per strain. Together with 47 strains selected from publicly available S. Typhimurium genomes, the S. Typhimurium core genes (STCG) were determined. The STCG consist of 3,846 genes, a set that is much larger than that of the 2,882 Salmonella core genes (SCG) found previously. The STCG together with 1,576 core intergenic regions (IGRs) were defined as the S. Typhimurium core genome. Using 93 S. Typhimurium genomes from 13 epidemiologically confirmed community outbreaks, we demonstrated that typing based on the S. Typhimurium core genome (STCG plus core IGRs) provides superior resolution and higher discriminatory power than that based on SCG for outbreak investigation and molecular epidemiology of S. Typhimurium. STCG and STCG plus core IGR typing achieved 100% separation of all outbreaks compared to that of SCG typing, which failed to separate isolates from two outbreaks from background isolates. Defining the S. Typhimurium core genome allows standardization of genes/regions to be used for high-resolution epidemiological typing and genomic surveillance of S. Typhimurium. PMID:26019201

  12. Fast reactor core concepts to improve transmutation efficiency

    Fujimura, Koji; Kawashima, Katsuyuki; Itooka, Satoshi

    2015-01-01

    Fast Reactor (FR) core concepts to improve transmutation efficiency were conducted. A heterogeneous MA loaded core was designed based on the 1000MWe-ABR breakeven core. The heterogeneous MA loaded core with Zr-H loaded moderated targets had a better transmutation performance than the MA homogeneous loaded core. The annular pellet rod design was proposed as one of the possible design options for the MA target. It was shown that using annular pellet MA rods mitigates the self-shielding effect in the moderated target so as to enhance the transmutation rate

  13. Core design with respect to the safety concept

    Kollmar, W.

    1981-01-01

    In the present paper the following topics are dealt with: Principles of reactor core design and optimization, fuel management and safety concept for higher cycles and results of risk analyses (e.g. rod ejection, steam line break etc.) (RW)

  14. Axial heterogeneous core concept applied for super phoenix reactor

    Batista, J.L.; Renke, C.A.C.; Waintraub, M.; Santos Bastos, W. dos; Brito Aghina, L.O. de.

    1991-11-01

    Always maintaining the current design rules, this paper presents a parametric study on the type of axial heterogeneous core concept (CHA), utilizing a core of fast reactor Super Phenix type, reaching a maximum thermal burnup rate of 150000 M W d/t and being managed in single batch. (author)

  15. Evaluation of a hanging core support concept for LMR application

    Burelbach, J.P.; Cha, B.K.; Huebotter, P.R.; Kann, W.J.; Pan, Y.C.; Saiveau, J.G.; Seidensticker, R.W.; Wu, T.S.

    1985-01-01

    The paper describes an innovative design concept for a liquid metal reactor (LMR) core support structure (CSS). A hanging core support structure is described and analyzed. The design offers inherent safety features, constructability advantages, and potential cost reductions. Some safety considerations are examined which include the in-service inspection (ISI), the backup support system and the structural behavior in a hypothetical case of a broken beam in the core support structure

  16. Core concept for long operating cycle simplified BWR (LSBWR)

    Kouji, Hiraiwa; Noriyuki, Yoshida; Mikihide, Nakamaru; Hideaki, Heki; Masanori, Aritomi

    2002-01-01

    An innovative core concept for a long operating cycle simplified BWR (LSBWR) is currently being developed under a Toshiba Corporation and Tokyo Institute of Technology joint study. In this core concept, the combination of enriched uranium oxide fuels and loose-pitched lattice is adopted for an easy application of natural circulation. A combination of enriched gadolinium and 0.7-times sized small bundle with peripheral-positioned gadolinium rod is also adopted as a key design concept for 15-year cycle operation. Based on three-dimensional nuclear and thermal hydraulic calculation, a nuclear design for fuel bundle has been determined. Core performance has been evaluated based on this bundle design and shows that thermal performance and reactivity characteristics meet core design criteria. Additionally, a control rod operation plan for an extension of control rod life has been successfully determined. (author)

  17. Small ex-core heat pipe thermionic reactor concept (SEHPTR)

    Jacox, M.G.; Bennett, R.G.; Lundberg, L.B.; Miller, B.G.; Drexler, R.L.

    1991-01-01

    The Idaho National Engineering Laboratory (INEL) has developed an innovative space nuclear power concept with unique features and significant advantages for both Defense and Civilian space missions. The Small Ex-core Heat Pipe Thermionic Reactor (SEHPTR) concept was developed in response to Air Force needs for space nuclear power in the range of 10 to 40 kilowatts. This paper describes the SEHPTR concept and discusses the key technical issues and advantages of such a system

  18. Soft shell hard core concept for aircraft impact resistant design

    Chen, C.; Rieck, P.J.

    1978-01-01

    For nuclear power plants sited in the vicinity of airports, the hypothetical events of aircraft impact have to be designed for. The conventional design concept is to strengthen the exterior structure to resist the impact induced force. The stiffened structures have two (2) disadvantages; one is the high construction cost, and the other is the high reaction force induced as well as the vibrational effects on the interior equipment and piping systems. This new soft shell hard core concept can relieve the above shortcomings. In this concept, the essential equipment required for safety are installed inside the hard core area for protection and the non-essential equipment are maintained between the hard core and soft shell area. During a hypothetical impact event, the soft shell will collapse locally and absorb large amounts of kinetic energy; hence, it reduces the reaction force and the vibrational effects. The design and analysis of the soft shell concept are discussed. (Author)

  19. Core design concepts for high performance light water reactors

    Schulenberg, T.; Starflinger, J.

    2007-01-01

    Light water reactors operated under supercritical pressure conditions have been selected as one of the promising future reactor concepts to be studied by the Generation IV International Forum. Whereas the steam cycle of such reactors can be derived from modern fossil fired power plants, the reactor itself, and in particular the reactor core, still need to be developed. Different core design concepts shall be described here to outline the strategy. A first option for near future applications is a pressurized water reactor with 380 .deg. C core exit temperature, having a closed primary loop and achieving 2% pts. higher net efficiency and 24% higher specific turbine power than latest pressurized water reactors. More efficiency and turbine power can be gained from core exit temperatures around 500 .deg. C, which require a multi step heat up process in the core with intermediate coolant mixing, achieving up to 44% net efficiency. The paper summarizes different core and assembly design approaches which have been studied recently for such High Performance Light Water Reactors

  20. PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes.

    Spannagl, Manuel; Bader, Kai; Pfeifer, Matthias; Nussbaumer, Thomas; Mayer, Klaus F X

    2016-01-01

    PGSB (Plant Genome and Systems Biology; formerly MIPS-Munich Institute for Protein Sequences) has been involved in developing, implementing and maintaining plant genome databases for more than a decade. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable datasets for model plant genomes as a backbone against which experimental data, e.g., from high-throughput functional genomics, can be organized and analyzed. In addition, genomes from both model and crop plants form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny) between related species on macro- and micro-levels.The genomes of many economically important Triticeae plants such as wheat, barley, and rye present a great challenge for sequence assembly and bioinformatic analysis due to their enormous complexity and large genome size. Novel concepts and strategies have been developed to deal with these difficulties and have been applied to the genomes of wheat, barley, rye, and other cereals. This includes the GenomeZipper concept, reference-guided exome assembly, and "chromosome genomics" based on flow cytometry sorted chromosomes.

  1. Core Design Concept and Core Structural Material Development for a Prototype SFR

    Chang, Jinwook

    2013-01-01

    Core design Concept: – Initial core is Uranium metal fueled core, then it will evolve into TRU core; – Tight pressure drop constraint lowers power density; – Trade-off studies with relaxed pressure drop constraint (~0.4MPa) are on-going; – Major feature will be finalized this year. • KAERI is developing advanced cladding for high burnup fuel in Ptototype SFR: – Advanced cladding materials are now developing, which shows superior high temperature mechanical property to the conventional material; – Processing technologies related to tube making process are now developed to enhance high temperature mechanical propertyl – Preliminary HT9 cladding tube was manufactured and out-of pile mechanical properties were evaluated. Advanced cladding tube is now being developed and being prepared for irradiation test

  2. Benefits of Low Boron Core Design Concept for PWR

    Daing, Aung Tharn; Kim, Myung Hyun [Kyung Hee University, Yongin (Korea, Republic of)

    2009-10-15

    Nuclear design study was carried out to develop low boron core (LBC) based on one of current PWR concepts, OPR-1000. Most of design parameters were the same with those of Ulchin unit-5 except extensive utilization of burnable poison (BP) pins in order to compensate reactivity increase in LBC. For replacement of reduced soluble boron concentration, four different kinds of integral burnable absorbers (IBAs) such as gadolinia, integral fuel burnable absorber (IFBA), erbia and alumina boron carbide were considered in suppressing more excess reactivity. A parametric study was done to find the optimal core options from many design candidates for fuel assemblies and cores. Among them, the most feasible core design candidate was chosen in accordance with general design requirements. In this paper, the feasibility and design change benefits of the most favorable LBC design were investigated in more detail through the comparison of neutronic and thermal hydraulic design parameters of LBC with the reference plant (REF). As calculation tools, the HELIOS/MASTER code package and the MATRA code were utilized. The main purpose of research herein is to estimate feasibility and capability of LBC which was mainly designed to mitigate boron dilution accident (BDA), and for reduction of corrosion products. The LBC design concept using lower boron concentration with an elevated enrichment in {sup 10}B allows a reduction in the concentration of lithium in the primary coolant required to maintain the optimum coolant pH. All in all, LBC with operation at optimum pH is expected to achieve some benefits from radiation source reduction of reduced corrosion product, the limitation of the Axial Offset Anomaly (AOA) and fuel cladding corrosion. Additionally, several merits of LBC are closely related to fluid systems and system related aspects, reduced boron and lithium costs, equipment size reduction for boric acid systems, elimination of heat tracing, and more aggressive fuel design concepts.

  3. Benefits of Low Boron Core Design Concept for PWR

    Daing, Aung Tharn; Kim, Myung Hyun

    2009-01-01

    Nuclear design study was carried out to develop low boron core (LBC) based on one of current PWR concepts, OPR-1000. Most of design parameters were the same with those of Ulchin unit-5 except extensive utilization of burnable poison (BP) pins in order to compensate reactivity increase in LBC. For replacement of reduced soluble boron concentration, four different kinds of integral burnable absorbers (IBAs) such as gadolinia, integral fuel burnable absorber (IFBA), erbia and alumina boron carbide were considered in suppressing more excess reactivity. A parametric study was done to find the optimal core options from many design candidates for fuel assemblies and cores. Among them, the most feasible core design candidate was chosen in accordance with general design requirements. In this paper, the feasibility and design change benefits of the most favorable LBC design were investigated in more detail through the comparison of neutronic and thermal hydraulic design parameters of LBC with the reference plant (REF). As calculation tools, the HELIOS/MASTER code package and the MATRA code were utilized. The main purpose of research herein is to estimate feasibility and capability of LBC which was mainly designed to mitigate boron dilution accident (BDA), and for reduction of corrosion products. The LBC design concept using lower boron concentration with an elevated enrichment in 10 B allows a reduction in the concentration of lithium in the primary coolant required to maintain the optimum coolant pH. All in all, LBC with operation at optimum pH is expected to achieve some benefits from radiation source reduction of reduced corrosion product, the limitation of the Axial Offset Anomaly (AOA) and fuel cladding corrosion. Additionally, several merits of LBC are closely related to fluid systems and system related aspects, reduced boron and lithium costs, equipment size reduction for boric acid systems, elimination of heat tracing, and more aggressive fuel design concepts

  4. Core concepts of spatial prioritisation in systematic conservation planning.

    Kukkala, Aija S; Moilanen, Atte

    2013-05-01

    Systematic conservation planning (SCP) is a field of conservation biology concerned with delivering on-the-ground actions that achieve conservation goals. It describes a set of operational models that cover both design and implementation of conservation, with a strong focus on mobilising the collective action typically required to implement conservation. SCP, as it was originally described, was composed of six different stages: collection of data, identification of conservation goals, evaluation of the existing protected area network, design of expansions, implementation of conservation action, and long-term maintenance of biodiversity in the network. Since then, the operational model has been expanded into several different variants. Conservation actions applied inside SCP include establishment and expansion of reserve networks and allocation of habitat restoration and management. Within the broader context of SCP, there is a fundamental biogeographic-economic analysis frequently called spatial conservation prioritisation or conservation assessment, which is used for identifying where important areas for biodiversity are and how conservation goals might be achieved efficiently. Here, we review the usage and meaning of the 12 biogeographic-economic core concepts of SCP: adequacy, complementarity, comprehensiveness, effectiveness, efficiency, flexibility, irreplaceability, replacement cost, representation, representativeness, threat, and vulnerability. Some of the concepts have clear definitions whereas others may have alternative and possibly conflicting definitions. With a comprehensive literature review literature, we elucidate the historical backgrounds of these concepts, the first definitions and usages, alternative later definitions, key applications, and prior reviews. This review reduces linguistic uncertainty in the application of SCP. Since SCP is a global activity with a multitude of different stakeholders involved, it is vital that those involved can

  5. Core melt retention and cooling concept of the ERP

    Weisshaeupl, H [SIEMENS/KWU, Erlangen (Germany); Yvon, M [Nuclear Power International, Paris (France)

    1996-12-01

    For the French/German European Pressurized Water Reactor (EPR) mitigative measures to cope with the event of a severe accident with core melt down are considered already at the design stage. Following the course of a postulated severe accident with reactor pressure vessel melt through one of the most important features of a future design must be to stabilize and cool the melt within the containment by dedicated measures. This measures should - as far as possible - be passive. One very promising solution for core melt retention seems to be a large enough spreading of the melt on a high temperature resistant protection layer with water cooling from above. This is the favorite concept for the EPR. In dealing with the retention of a molten core outside of the RPV several ``steps`` from leaving the RPV to finally stabilize the melt have to gone through. These steps are: collection of the melt; transfer of the melt; distribution of the melt; confining; cooling and stabilization. The technical features for the EPR solution of a large spreading of the melt are: Dedicated spreading chamber outside the reactor pit (area about 150 m{sup 2}); high temperature resistant protection layers (e.g. Zirconia bricks) at the bottom and part of the lateral structures (thus avoiding melt concrete interaction); reactor pit and spreading compartment are connected via a discharge channel which has a slope to the spreading area and is closed by a steel plate, which will resist the core melt for a certain time in order to allow a collection of the melt; the spreading compartments is connected with the In-Containment Refuelling Water Storage Tank (IRWST) with pipes for water flooding after spreading. These pipes are closed and will only be opened by the hot melt itself. It is shown how the course of the different steps mentioned above is processed and how each of these steps is automatically and passively achieved. (Abstract Truncated)

  6. Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation.

    Inglin, Raffael C; Meile, Leo; Stevens, Marc J A

    2018-04-24

    Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events. We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20'800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species' level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class "genetic information processing" is conserved in the core-genome but that "signaling and cellular processes" is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation. Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus' evolution is directed

  7. Physicians’ Professionally Responsible Power: A Core Concept of Clinical Ethics

    McCullough, Laurence B.

    2016-01-01

    The gathering of power unto themselves by physicians, a process supported by evidence-based practice, clinical guidelines, licensure, organizational culture, and other social factors, makes the ethics of power—the legitimation of physicians’ power—a core concept of clinical ethics. In the absence of legitimation, the physician’s power over patients becomes problematic, even predatory. As has occurred in previous issues of the Journal, the papers in the 2016 clinical ethics issue bear on the professionally responsible deployment of power by physicians. This introduction explores themes of physicians’ power in papers from an international group of authors who address autonomy and trust, the virtues of perinatal hospice, conjoined twins in ethics and law, addiction and autonomy in clinical research on addicting substances, euthanasia of patients with dementia in Belgium, and a pragmatic approach to clinical futility. PMID:26671961

  8. Low void effect (CFV) core concept flexibility: from self-breeder to burner core - 15091

    Buiron, L.; Dujcikova, L.

    2015-01-01

    In the frame of the French strategy on sustainable nuclear energy, several scenarios consider fuel cycle transition toward a plutonium multi-recycling strategy in sodium cooled fast reactor (SFR). Basically, most of these scenarios consider the deployment of a 60 GWe SFR fleet in 2 steps to renew the French PWR fleet. As scenarios do investigate long term deployment configurations, some of them require tools for nuclear phase-out studies. Instead of designing new reactors, the adopted strategy does focus on adaptation of existing ones into burner configurations. This is what was done in the frame of the EFR project at the end of the 90's using the CAPRA approach (French acronym for Enhance Plutonium Consumption in Fast Reactor). The EFR burner configuration was obtained by inserting neutronic penalties inside the core (absorber material and/or diluent subassembly). Starting from the preliminary industrial image of a SFR 3600 MWth core based on Low Sodium Void concept (CFV in French), a 'CAPRA-like' approach has been studied. As the CFV self-breeding is ensured by fertile blankets, a first modification consisted in the substitution of the corresponding depleted uranium by 'inert' or absorber material leading to a 'natural burner' core with only small impacts on flux distribution. The next step forward CAPRA configuration was the substitution of 1/3 of the fuel pins by 'dummy' pins (MgO pellets). The small spectrum shift due to MgO material insertion leads to an increase Doppler constant which exceeds the value of the reference case. As the core sodium void worth value is conserved, the CFV CAPRA core 'safety' potential is quite similar to the one of the reference core. Fuel thermo-mechanical requirements are met by both nominal core power and fuel time residence reduction. However, these reduction factors are lower than those obtained for EFR core. The management of the enhanced reactivity swing is discussed

  9. An axially and radially two-zoned large liquid-metal fast breeder reactor core concept

    Kamei, T.; Arie, K.; Moriki, Y.; Suzuki, M.; Yamaoka, M.

    1985-01-01

    A new core concept that has advantages over conventional homogeneous cores in neutronics characteristics such as power peaking factor, burnup reactivity loss, and reactivity response to the movement of control rods in earthquakes has been evolved. Two options of the new core concept are feasible. One is the so-called axially heterogeneous core, with the internal blanket placed at the lower part of the core. The other concept is similar to the conventional homogeneous core, but has two different plutonium-enriched zones in the axial as well as in the radial direction, so it is a hybrid type of the conventional homogeneous core and the axially heterogeneous core. The new design concept is described and the way that the core characteristics are improved by the chosen key parameters is shown

  10. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

    Treangen, Todd J; Ondov, Brian D; Koren, Sergey; Phillippy, Adam M

    2014-01-01

    Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.

  11. The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers

    Jason W. Sahl

    2016-09-01

    Full Text Available Whole-genome sequence (WGS data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives.

  12. Analysis of pan-genome to identify the core genes and essential genes of Brucella spp.

    Yang, Xiaowen; Li, Yajie; Zang, Juan; Li, Yexia; Bie, Pengfei; Lu, Yanli; Wu, Qingmin

    2016-04-01

    Brucella spp. are facultative intracellular pathogens, that cause a contagious zoonotic disease, that can result in such outcomes as abortion or sterility in susceptible animal hosts and grave, debilitating illness in humans. For deciphering the survival mechanism of Brucella spp. in vivo, 42 Brucella complete genomes from NCBI were analyzed for the pan-genome and core genome by identification of their composition and function of Brucella genomes. The results showed that the total 132,143 protein-coding genes in these genomes were divided into 5369 clusters. Among these, 1710 clusters were associated with the core genome, 1182 clusters with strain-specific genes and 2477 clusters with dispensable genomes. COG analysis indicated that 44 % of the core genes were devoted to metabolism, which were mainly responsible for energy production and conversion (COG category C), and amino acid transport and metabolism (COG category E). Meanwhile, approximately 35 % of the core genes were in positive selection. In addition, 1252 potential essential genes were predicted in the core genome by comparison with a prokaryote database of essential genes. The results suggested that the core genes in Brucella genomes are relatively conservation, and the energy and amino acid metabolism play a more important role in the process of growth and reproduction in Brucella spp. This study might help us to better understand the mechanisms of Brucella persistent infection and provide some clues for further exploring the gene modules of the intracellular survival in Brucella spp.

  13. Weaving latino cultural concepts into Preparedness Core Competency training.

    Riley-Jacome, Mary; Parker, Blanca Angelica Gonzalez; Waltz, Edward C

    2014-01-01

    The New York • New Jersey Preparedness and Emergency Response Learning Center (NY•NJ PERLC) is one of 14 Centers funded by the Centers for Disease Control and Prevention designed to address the preparedness and response training and education needs of the public health workforce. One of the important niches, or focus areas for the Center, is training to improve the capacity of public health workers to respond with competence to the needs of vulnerable populations. During every phase of a disaster, racial and ethnic minorities, including Latinos, suffer worse outcomes than the general population. Communities with diverse cultural origins and limited English speakers often present more complex issues during public health emergencies. Training that incorporates cultural concepts into the Preparedness Core Competencies may improve the ability of public health workers to engage the Latino community in preparedness activities and ultimately improve outcomes during disasters. This article describes initiatives undertaken by the NY•NJ PERLC to improve the capacity of the public health workforce to respond competently to the needs of Latino populations. In 2012, the Center collaborated with national, state, and local partners to develop a nationwide broadcast founded on the Preparedness Core Competencies, Latinos During Emergencies: Cultural Considerations Impacting Disaster Preparedness. The widely viewed broadcast (497 sites in 47 states and 13 nations) highlighted the commonalities and differences within Latino culture that can impact emergency preparedness and response and outlined practical strategies to enhance participation. The success of the broadcast spurred a number of partner requests for training and technical assistance. Lessons learned from these experiences, including our "undercover" work at local Points of Dispensing, are incorporated into subsequent interactive trainings to improve the competency of public health workers. Participants recommended

  14. Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome

    Cornick, Jennifer E.; Chaguza, Chrispin; Yalcin, Feyruz; Harris, Simon R.; Gray, Katherine J.; Kiran, Anmol M.; Molyneux, Elizabeth; French, Neil; Faragher, Brian E.; Everett, Dean B.; Bentley, Stephen D.

    2015-01-01

    Streptococcus pneumoniae is a nasopharyngeal commensal that occasionally invades normally sterile sites to cause bloodstream infection and meningitis. Although the pneumococcal population structure and evolutionary genetics are well defined, it is not clear whether pneumococci that cause meningitis are genetically distinct from those that do not. Here, we used whole-genome sequencing of 140 isolates of S. pneumoniae recovered from bloodstream infection (n = 70) and meningitis (n = 70) to compare their genetic contents. By fitting a double-exponential decaying-function model, we show that these isolates share a core of 1,427 genes (95% confidence interval [CI], 1,425 to 1,435 genes) and that there is no difference in the core genome or accessory gene content from these disease manifestations. Gene presence/absence alone therefore does not explain the virulence behavior of pneumococci that reach the meninges. Our analysis, however, supports the requirement of a range of previously described virulence factors and vaccine candidates for both meningitis- and bacteremia-causing pneumococci. This high-resolution view suggests that, despite considerable competency for genetic exchange, all pneumococci are under considerable pressure to retain key components advantageous for colonization and transmission and that these components are essential for access to and survival in sterile sites. PMID:26259813

  15. What It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated.

    Benoît Valot

    Full Text Available Pseudomonas aeruginosa is an opportunistic bacterial pathogen able to thrive in highly diverse ecological niches and to infect compromised patients. Its genome exhibits a mosaic structure composed of a core genome into which accessory genes are inserted en bloc at specific sites. The size and the content of the core genome are open for debate as their estimation depends on the set of genomes considered and the pipeline of gene detection and clustering. Here, we redefined the size and the content of the core genome of P. aeruginosa from fully re-analyzed genomes of 17 reference strains. After the optimization of gene detection and clustering parameters, the core genome was defined at 5,233 orthologs, which represented ~ 88% of the average genome. Extrapolation indicated that our panel was suitable to estimate the core genome that will remain constant even if new genomes are added. The core genome contained resistance determinants to the major antibiotic families as well as most metabolic, respiratory, and virulence genes. Although some virulence genes were accessory, they often related to conserved biological functions. Long-standing prophage elements were subjected to a genetic drift to eventually display a G+C content as higher as that of the core genome. This contrasts with the low G+C content of highly conserved ribosomal genes. The conservation of metabolic and respiratory genes could guarantee the ability of the species to thrive on a variety of carbon sources for energy in aerobiosis and anaerobiosis. Virtually all the strains, of environmental or clinical origin, have the complete toolkit to become resistant to the major antipseudomonal compounds and possess basic pathogenic mechanisms to infect humans. The knowledge of the genes shared by the majority of the P. aeruginosa isolates is a prerequisite for designing effective therapeutics to combat the wide variety of human infections.

  16. Physicians' Professionally Responsible Power: A Core Concept of Clinical Ethics.

    McCullough, Laurence B

    2016-02-01

    The gathering of power unto themselves by physicians, a process supported by evidence-based practice, clinical guidelines, licensure, organizational culture, and other social factors, makes the ethics of power--the legitimation of physicians' power--a core concept of clinical ethics. In the absence of legitimation, the physician's power over patients becomes problematic, even predatory. As has occurred in previous issues of the Journal, the papers in the 2016 clinical ethics issue bear on the professionally responsible deployment of power by physicians. This introduction explores themes of physicians' power in papers from an international group of authors who address autonomy and trust, the virtues of perinatal hospice, conjoined twins in ethics and law, addiction and autonomy in clinical research on addicting substances, euthanasia of patients with dementia in Belgium, and a pragmatic approach to clinical futility. © The Author 2015. Published by Oxford University Press, on behalf of the Journal of Medicine and Philosophy Inc. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.

    Paul, Sandip; Bhardwaj, Archana; Bag, Sumit K; Sokurenko, Evgeni V; Chattopadhyay, Sujay

    2015-12-01

    A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing the pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen - a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for a species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars - Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. PanCoreGen – profiling, detecting, annotating protein-coding genes in microbial genomes

    Bhardwaj, Archana; Bag, Sumit K; Sokurenko, Evgeni V.

    2015-01-01

    A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen – a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars – Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study. PMID:26456591

  19. The "Core Concepts Plus" Paradigm for Creating an Electronic Textbook for Introductory Business and Economic Statistics

    Haley, M. Ryan

    2013-01-01

    This paper describes a flexible paradigm for creating an electronic "Core Concepts Plus" textbook (CCP-text) for a course in Introductory Business and Economic Statistics (IBES). In general terms, "core concepts" constitute the intersection of IBES course material taught by all IBES professors at the author's university. The…

  20. A multi-crucible core-catcher concept: Design considerations and basic results

    Szabo, I.

    1995-01-01

    A multi-crucible core-catcher concept to be implemented in new light water reactor containments has recently been proposed. This paper deals with conceptual design considerations and the various ways this type of core-catcher could be designed to meet requirements for reactor application. A systematic functional analysis of the multi-crucible core-catcher concept and the results of the preliminary design calculation are presented. Finally, the adequacy of the multi-crucible core-catcher concept for reactor application is discussed. (orig.)

  1. Full-length RNA structure prediction of the HIV-1 genome reveals a conserved core domain

    Sükösd, Zsuzsanna; Andersen, Ebbe Sloth; Seemann, Ernst Stefan

    2015-01-01

    of the HIV-1 genome is highly variable in most regions, with a limited number of stable and conserved RNA secondary structures. Most interesting, a set of long distance interactions form a core organizing structure (COS) that organize the genome into three major structural domains. Despite overlapping...

  2. Feasibility study of ultra-long life fast reactor core concept - 028

    Kim, T.K.; Taiwo, T.A.

    2010-01-01

    An ultra-long life core concept is proposed targeting capital and operational cost reductions and ultra-high discharge burnup in a fast reactor system. The core concept is achieved by de-rating the power density and adopting annular core geometry to maintain criticality for more than 40 years without refueling. The ultra-long life core has a specific power of ∼10 MW/t and an average driver fuel discharge burnup of ∼300 GWd/t. It is assumed such ultra-high burnup fuel can be developed within an advanced fuel cycle program. Several benefits are expected from the ultra-long life core concept such as capital and operational cost reductions, low proliferation risk, and effectively holding LWR spent fuel without disposal until technologies for a closed nuclear fuel cycle are developed and deployed. As future work, safety analysis, development of the advanced core cooling methods, and comparative cost analysis are expected. (authors)

  3. Preliminary concept of a zero power nuclear reactor core

    Mai, Luiz Antonio; Siqueira, Paulo de Tarso D., E-mail: lamai@ipen.b, E-mail: ptsiquei@ipen.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2011-07-01

    The purpose of this work is to define a zero power core to study the neutronic behavior of a modern research reactor as the future RMB (Brazilian Nuclear Multipurpose reactor). The platform used was the IPEN/MB-01 nuclear reactor, installed at the Nuclear and Energy Research Institute (IPEN-CNEN/SP). Equilibrium among minimal changes in the current reactor facilities and an arrangement that will be as representative as possible of a future core were taken into account. The active parts of the elements (fuel and control/safety) were determined to be exactly equal the elements of a future reactor. After several technical discussions, a basic configuration for the zero power core was defined. This reactor will validate the neutronic calculations and will allow the execution of countless future experiments aiming a real core. Of all possible alternative configurations for the zero power core representative of a future reactor - named ZPC-MRR (Zero Power Core - Modern Research Reactor), it was concluded, through technical and practical arguments, that the core will have an array of 4 x 5 positions, with 19 fuel elements, identical in its active part to a standard MTR (Material Test Reactor), 4 control/safety elements having a unique flat surface and a central position of irradiation. The specifications of the fuel elements (FEs) are the same as defined to standard MTR in its active part, but the inferior nozzles are differentiated because ZPC-MRR will be a set without heat generation. A study of reactivity was performed using MCNP code, and it was estimated that it will have around 2700 pcm reactivity excess in its 19 FEs configuration (alike the present IPEN/MB-01 reactivity). The effective change in the IPEN/MB-01 reactor will be made only in the control rods drive mechanism. It will be necessary to modify the center of this mechanism. Major modifications in the facility will not be necessary. (author)

  4. Preliminary concept of a zero power nuclear reactor core

    Mai, Luiz Antonio; Siqueira, Paulo de Tarso D.

    2011-01-01

    The purpose of this work is to define a zero power core to study the neutronic behavior of a modern research reactor as the future RMB (Brazilian Nuclear Multipurpose reactor). The platform used was the IPEN/MB-01 nuclear reactor, installed at the Nuclear and Energy Research Institute (IPEN-CNEN/SP). Equilibrium among minimal changes in the current reactor facilities and an arrangement that will be as representative as possible of a future core were taken into account. The active parts of the elements (fuel and control/safety) were determined to be exactly equal the elements of a future reactor. After several technical discussions, a basic configuration for the zero power core was defined. This reactor will validate the neutronic calculations and will allow the execution of countless future experiments aiming a real core. Of all possible alternative configurations for the zero power core representative of a future reactor - named ZPC-MRR (Zero Power Core - Modern Research Reactor), it was concluded, through technical and practical arguments, that the core will have an array of 4 x 5 positions, with 19 fuel elements, identical in its active part to a standard MTR (Material Test Reactor), 4 control/safety elements having a unique flat surface and a central position of irradiation. The specifications of the fuel elements (FEs) are the same as defined to standard MTR in its active part, but the inferior nozzles are differentiated because ZPC-MRR will be a set without heat generation. A study of reactivity was performed using MCNP code, and it was estimated that it will have around 2700 pcm reactivity excess in its 19 FEs configuration (alike the present IPEN/MB-01 reactivity). The effective change in the IPEN/MB-01 reactor will be made only in the control rods drive mechanism. It will be necessary to modify the center of this mechanism. Major modifications in the facility will not be necessary. (author)

  5. Concept of neural genoarchitecture and its genomic fundament.

    Luis ePuelles

    2012-11-01

    Full Text Available The recent concept of neural genoarchitecture (or genoarchitectonics is examined from several angles, aiming to clarify the rationale for this new approach in causal and descriptive neuroanatomy. Gene expression patterns can be used as topographic stains revealing architectonic borders that may clarify, dispute or complicate existing brain anatomical subdivisions based on other methods, while increasing our understanding of how they arise in ontogenesis and evolution. A section of the text deals with differential regulation of gene expression in an ontogenetic causal network, attending to the structure of the genome and the functional peculiarities of enhancer and repressor regulatory regions that modulate gene transcription. The emergence of regionally characteristic sets of active transcription factors represents a critical concept, molecular identity, which can be applied to discrete brain territories and neuronal populations. Gene regulation is tied to positional effects, that is, topologically invariant domains of gene expression and natural boundaries, which can be correlated with anatomic ones. The large-scale stability of these patterns among vertebrates underpins molecularly the structural brain Bauplan, and is the fundament of field homology. The study of genoarchitectonic boundaries is presented as a crucial objective of modern neuroanatomic research. At most brain regions, new neuronal populations are being detected thanks to their differential genoarchitectonic features.

  6. Development of concept and neutronic calculation method for large LMFBR core

    Shirakata, K.; Ishikawa, M.; Ikegami, T.; Sanda, T.; Kaneto, K.; Kawashima, M.; Kaise, Y.; Shirakawa, M.; Hibi, K.

    1991-01-01

    Presented in this paper is the state of the art of reactor physics R and Ds for the development of concept and neutronic calculation method for large Liquid Metal Fast Breeder Reactor (LMFBR) core. Physics characteristics of concepts for mixed oxide (MOX) fueled large FBR core were investigated by a series of benchmark critical experiments. Next, an adequacy and accuracy of the current neutronic calculation method was assessed by the experiments analyses, and then neutronic prediction accuracies by the method were evaluated for physics characteristics of the large core. Concerns on core development were discussed in terms of neutronics. (author)

  7. Improving work control systems: The core team concept

    Jorgensen, M.D.; Simpson, W.W.

    1996-01-01

    The improved work control system at the Idaho Chemical Processing Plant minimizes review and approval time, maximizes field work time, and maintains full compliance with applicable requirements. The core team method gives ownership and accountability to knowledgeable individuals, and the teams use sophisticated scheduling techniques to improve information sharing and cost control and to establish accurate roll-up master schedules

  8. Core concepts for ''zero-sodium-void-worth core'' in metal fuelled fast reactor

    Chang, Y.I.; Hill, R.N.; Fujita, E.K.; Wade, D.C.; Kumaoka, Y.; Suzuki, M.; Kawashima, M.; Nakagawa, H.

    1991-01-01

    Core design options to reduce the sodium void worth in metal fueled LMRs are investigated. Two core designs which achieve a zero sodium void worth are analyzed in detail. The first design is a ''pancaked'' and annular core with enhanced transuranic burning capabilities; the high leakage in this design yields a low breeding ratio and small void worth. The second design is an axially multilayered annular core which is fissile self-sufficient; in this design, the upper and lower core regions are neutronically decoupled for reduced void worth while fissile self-sufficiency is achieved using internal axial blankets plus external radial and axial blanket zones. The neutronic performance characteristics of these low void worth designs are assessed here; their passive safety properties are discussed in a companion paper. 16 refs., 2 figs., 3 tabs

  9. Core concepts for 'zero-sodium-void-worth core' in metal fuelled fast reactor

    Chang, Y.I.; Hill, R.N.; Fujita, E.K.; Wade, D.C.; Kumaoka, Y.; Suzuki, M.; Kawashima, M.; Nakagawa, H.

    1991-01-01

    Core design options to reduce the sodium void worth in metal fuelled LMRs are investigated. Two core designs which achieve a zero sodium void worth are analyzed in detail. The first design is a 'pancaked' and annular core with enhanced transuranic burning capabilities; the high leakage in this design yields a low breeding ratio and small void worth. The second design is an axially multilayered annular core which is fissile self-sufficient; in this design, the upper and lower core regions are neutronically decoupled for reduced void worth while fissile self-sufficiency is achieved using internal axial blankets plus external radial and axial blanket-zones. The neutronic performance characteristics of these low void worth designs are assessed here; their passive safety properties are discussed in a companion paper. (author)

  10. Flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks.

    Kang, Yu; Gu, Chaohao; Yuan, Lina; Wang, Yue; Zhu, Yanmin; Li, Xinna; Luo, Qibin; Xiao, Jingfa; Jiang, Daquan; Qian, Minping; Ahmed Khan, Aftab; Chen, Fei; Zhang, Zhang; Yu, Jun

    2014-11-25

    The prokaryotic pangenome partitions genes into core and dispensable genes. The order of core genes, albeit assumed to be stable under selection in general, is frequently interrupted by horizontal gene transfer and rearrangement, but how a core-gene-defined genome maintains its stability or flexibility remains to be investigated. Based on data from 30 species, including 425 genomes from six phyla, we grouped core genes into syntenic blocks in the context of a pangenome according to their stability across multiple isolates. A subset of the core genes, often species specific and lineage associated, formed a core-gene-defined genome organizational framework (cGOF). Such cGOFs are either single segmental (one-third of the species analyzed) or multisegmental (the rest). Multisegment cGOFs were further classified into symmetric or asymmetric according to segment orientations toward the origin-terminus axis. The cGOFs in Gram-positive species are exclusively symmetric and often reversible in orientation, as opposed to those of the Gram-negative bacteria, which are all asymmetric and irreversible. Meanwhile, all species showing strong strand-biased gene distribution contain symmetric cGOFs and often specific DnaE (α subunit of DNA polymerase III) isoforms. Furthermore, functional evaluations revealed that cGOF genes are hub associated with regard to cellular activities, and the stability of cGOF provides efficient indexes for scaffold orientation as demonstrated by assembling virtual and empirical genome drafts. cGOFs show species specificity, and the symmetry of multisegmental cGOFs is conserved among taxa and constrained by DNA polymerase-centric strand-biased gene distribution. The definition of species-specific cGOFs provides powerful guidance for genome assembly and other structure-based analysis. Prokaryotic genomes are frequently interrupted by horizontal gene transfer (HGT) and rearrangement. To know whether there is a set of genes not only conserved in position

  11. BioCore Guide: A Tool for Interpreting the Core Concepts of Vision and Change for Biology Majors

    Freeman, Scott; Wenderoth, Mary Pat; Crowe, Alison J.

    2014-01-01

    Vision and Change in Undergraduate Biology Education outlined five core concepts intended to guide undergraduate biology education: 1) evolution; 2) structure and function; 3) information flow, exchange, and storage; 4) pathways and transformations of energy and matter; and 5) systems. We have taken these general recommendations and created a Vision and Change BioCore Guide—a set of general principles and specific statements that expand upon the core concepts, creating a framework that biology departments can use to align with the goals of Vision and Change. We used a grassroots approach to generate the BioCore Guide, beginning with faculty ideas as the basis for an iterative process that incorporated feedback from more than 240 biologists and biology educators at a diverse range of academic institutions throughout the United States. The final validation step in this process demonstrated strong national consensus, with more than 90% of respondents agreeing with the importance and scientific accuracy of the statements. It is our hope that the BioCore Guide will serve as an agent of change for biology departments as we move toward transforming undergraduate biology education. PMID:26086653

  12. The Study on the Core Concepts of Contemporary Sociology of Education and Its Theoretical Construction

    Qian, Min-hui

    2006-01-01

    Within the sphere of contemporary social sciences, the terms "modernity," "post-modernity" and "globalization" have penetrated, as the core concepts, into various fields of social sciences in a logical way. In constituting the concept of "modernity," sociology of education develops the educational theory, as sociological theory does, into a "grand…

  13. Public Conceptions of Algorithms and Representations in the Common Core State Standards for Mathematics

    Nanna, Robert J.

    2016-01-01

    Algorithms and representations have been an important aspect of the work of mathematics, especially for understanding concepts and communicating ideas about concepts and mathematical relationships. They have played a key role in various mathematics standards documents, including the Common Core State Standards for Mathematics. However, there have…

  14. Development of Mycoplasma synoviae (MS) core genome multilocus sequence typing (cgMLST) scheme.

    Ghanem, Mostafa; El-Gazzar, Mohamed

    2018-05-01

    Mycoplasma synoviae (MS) is a poultry pathogen with reported increased prevalence and virulence in recent years. MS strain identification is essential for prevention, control efforts and epidemiological outbreak investigations. Multiple multilocus based sequence typing schemes have been developed for MS, yet the resolution of these schemes could be limited for outbreak investigation. The cost of whole genome sequencing became close to that of sequencing the seven MLST targets; however, there is no standardized method for typing MS strains based on whole genome sequences. In this paper, we propose a core genome multilocus sequence typing (cgMLST) scheme as a standardized and reproducible method for typing MS based whole genome sequences. A diverse set of 25 MS whole genome sequences were used to identify 302 core genome genes as cgMLST targets (35.5% of MS genome) and 44 whole genome sequences of MS isolates from six countries in four continents were used for typing applying this scheme. cgMLST based phylogenetic trees displayed a high degree of agreement with core genome SNP based analysis and available epidemiological information. cgMLST allowed evaluation of two conventional MLST schemes of MS. The high discriminatory power of cgMLST allowed differentiation between samples of the same conventional MLST type. cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation between MS isolates. Like conventional MLST, it provides stable and expandable nomenclature, allowing for comparing and sharing the typing results between different laboratories worldwide. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  15. Mammalian RNA polymerase II core promoters: insights from genome-wide studies

    Sandelin, Albin; Carninci, Piero; Lenhard, Boris

    2007-01-01

    The identification and characterization of mammalian core promoters and transcription start sites is a prerequisite to understanding how RNA polymerase II transcription is controlled. New experimental technologies have enabled genome-wide discovery and characterization of core promoters, revealing...... in the mammalian transcriptome and proteome. Promoters can be described by their start site usage distribution, which is coupled to the occurrence of cis-regulatory elements, gene function and evolutionary constraints. A comprehensive survey of mammalian promoters is a major step towards describing...

  16. Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.

    Rachel A Mann

    Full Text Available The plant pathogen Erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the Rosaceae subfamily Spiraeoideae (e.g., Malus, Pyrus, Crataegus, Sorbus and strains infecting Rubus (raspberries and blackberries. Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin of E. amylovora was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and Rubus-infecting strains (and among individual Rubus-infecting strains, the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the Rubus-infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of E. amylovora than it was to the other Rubus-infecting strains. Analysis of the accessory genomes of Spiraeoideae- and Rubus-infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1(Ea and a putative secondary metabolite pathway only present in Rubus-infecting strains.

  17. Core Thermal-Hydraulic Conceptual Design for the Advanced SFR Design Concepts

    Cho, Chung Ho; Chang, Jin Wook; Yoo, Jae Woon; Song, Hoon; Choi, Sun Rock; Park, Won Seok; Kim, Sang Ji

    2010-01-01

    The Korea Atomic Energy Research Institute (KAERI) has developed the advanced SFR design concepts from 2007 to 2009 under the National longterm Nuclear R and D Program. Two types of core designs, 1,200 MWe breakeven and 600 MWe TRU burner core have been proposed and evaluated whether they meet the design requirements for the Gen IV technology goals of sustainability, safety and reliability, economics, proliferation resistance, and physical protection. In generally, the core thermal hydraulic design is performed during the conceptual design phase to efficiently extract the core thermal power by distributing the appropriate sodium coolant flow according to the power of each assembly because the conventional SFR core is composed of hundreds of ducted assemblies with hundreds of fuel rods. In carrying out the thermal and hydraulic design, special attention has to be paid to several performance parameters in order to assure proper performance and safety of fuel and core; the coolant boiling, fuel melting, structural integrity of the components, fuel-cladding eutectic melting, etc. The overall conceptual design procedure for core thermal and hydraulic conceptual design, i.e., flow grouping and peak pin temperature calculations, pressure drop calculations, steady-state and detailed sub-channel analysis is shown Figure 1. In the conceptual design phase, results of core thermal-hydraulic design for advanced design concepts, the core flow grouping, peak pin cladding mid-wall temperature, and pressure drop calculations, are summarized in this study

  18. LMR design concepts for transuranic management in low sodium void worth cores

    Hill, R.N.

    1991-01-01

    The fuel cycle processing techniques and hard neutron spectrum of the integral Fast Reactor (IFR) metal fuel cycle have favorable characteristics for the management of transuranics; and the wide range of breeding characteristics available in metal fuelled cores provides for flexibility in transuranic management strategy. Previous studies indicate that most design options which decrease the breeding ratio also allow a decrease in sodium void worth; therefore, low void worths are achievable in transuranic burning (low breeding ratio) core designs. This paper describes numerous trade studies assessing various design options for a low void worth transuranic burner core. A flat annular core design appears to be a promising concept; the high leakage geometry yields a low breeding ratio and small sodium void worth. To allow flexibility in breeding characteristics, alternate design options which achieve fissile self-sufficiency are also evaluated. A self-sufficient core design which is interchangeable with the burner core and maintains a low sodium void worth is developed. (author)

  19. Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis

    Stata, Matt; Wang, Wei; White, Merlin M.; Moncalvo, Jean-Marc

    2018-01-01

    ABSTRACT Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects. PMID:29764946

  20. BioCore Guide: A Tool for Interpreting the Core Concepts of Vision and Change for Biology Majors.

    Brownell, Sara E; Freeman, Scott; Wenderoth, Mary Pat; Crowe, Alison J

    2014-01-01

    Vision and Change in Undergraduate Biology Education outlined five core concepts intended to guide undergraduate biology education: 1) evolution; 2) structure and function; 3) information flow, exchange, and storage; 4) pathways and transformations of energy and matter; and 5) systems. We have taken these general recommendations and created a Vision and Change BioCore Guide-a set of general principles and specific statements that expand upon the core concepts, creating a framework that biology departments can use to align with the goals of Vision and Change. We used a grassroots approach to generate the BioCore Guide, beginning with faculty ideas as the basis for an iterative process that incorporated feedback from more than 240 biologists and biology educators at a diverse range of academic institutions throughout the United States. The final validation step in this process demonstrated strong national consensus, with more than 90% of respondents agreeing with the importance and scientific accuracy of the statements. It is our hope that the BioCore Guide will serve as an agent of change for biology departments as we move toward transforming undergraduate biology education. © 2014 S. E. Brownell et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  1. Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease

    Versteeg, Bart; Bruisten, Sylvia M.; Pannekoek, Yvonne; Jolley, Keith A.; Maiden, Martin C. J.; van der Ende, Arie; Harrison, Odile B.

    2018-01-01

    Background: Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated. Results: WGS data

  2. CGUG: in silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb

    Mahadevan Padmanabhan

    2009-08-01

    Full Text Available Abstract Background Viruses and small-genome bacteria (~2 megabases and smaller comprise a considerable population in the biosphere and are of interest to many researchers. These genomes are now sequenced at an unprecedented rate and require complementary computational tools to analyze. "CoreGenesUniqueGenes" (CGUG is an in silico genome data mining tool that determines a "core" set of genes from two to five organisms with genomes in this size range. Core and unique genes may reflect similar niches and needs, and may be used in classifying organisms. Findings CGUG is available at http://binf.gmu.edu/geneorder.html as a web-based on-the-fly tool that performs iterative BLASTP analyses using a reference genome and up to four query genomes to provide a table of genes common to these genomes. The result is an in silico display of genomes and their proteomes, allowing for further analysis. CGUG can be used for "genome annotation by homology", as demonstrated with Chlamydophila and Francisella genomes. Conclusion CGUG is used to reanalyze the ICTV-based classifications of bacteriophages, to reconfirm long-standing relationships and to explore new classifications. These genomes have been problematic in the past, due largely to horizontal gene transfers. CGUG is validated as a tool for reannotating small genome bacteria using more up-to-date annotations by similarity or homology. These serve as an entry point for wet-bench experiments to confirm the functions of these "hypothetical" and "unknown" proteins.

  3. Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.

    Cabal, Adriana; Jun, Se-Ran; Jenjaroenpun, Piroon; Wanchai, Visanu; Nookaew, Intawat; Wongsurawat, Thidathip; Burgess, Mary J; Kothari, Atul; Wassenaar, Trudy M; Ussery, David W

    2018-02-14

    Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same

  4. The KALIMER-600 Reactor Core Design Concept with Varying Fuel Cladding Thickness

    Hong, Ser Gi; Jang, Jin Wook; Kim, Yeong Il

    2006-01-01

    Recently, Korea Atomic Energy Research Institute (KAERI) has developed a 600MWe sodium cooled fast reactor, the KALIMER-600 reactor core concept using single enrichment fuel. This reactor core concept is characterized by the following design targets : 1) Breakeven breeding (or fissile-self-sufficient) without any blanket, 2) Small burnup reactivity swing ( 23 n/cm 2 ). In the previous design, the single enrichment fuel concept was achieved by using the special fuel assembly designs where non-fuel rods (i.e., ZrH 1.8 , B 4 C, and dummy rods) were used. In particular, the moderator rods (ZrH 1.8 ) were used to reduce the sodium void worth and the fuel Doppler coefficient. But it has been known that this hydride moderator possesses relatively poor irradiation behavior at high temperature. In this paper, a new core design concept for use of single enrichment fuel is described. In this concept, the power flattening is achieved by using the core region wise cladding thicknesses but all non-fuel rods are removed to simplify the fuel assembly design

  5. Core concept of fast power reactor with zero sodium void reactivity

    Matveev, V.I.; Chebeskov, A.N.; Krivitsky, I.Y.

    1991-01-01

    The paper presents a core concept of BN-800 - type fast power reactor with zero sodium void reactivity (SVR). Consideration is given to the layout-and some design features of such a core. Some considerations on the determination of the required SVR value as one of the fast reactor safety criteria in accidents with coolant boiling are presented. Some methodical considerations an the development of calculation models that give a correct description of the new core features are stated. The results of the integral SVR calculation studies are included. reactivity excursions under different scenarios of sodium boiling are estimated, some corrections into the calculated SVR value are discussed. (author)

  6. Technical Meeting on Liquid Metal Reactor Concepts: Core Design and Structural Materials. Working Material

    2013-01-01

    The objective of the TM on “Liquid metal reactor concept: core design and structural materials” was to present and discuss innovative liquid metal fast reactor (LMFR) core designs with special focus on the choice, development, testing and qualification of advanced reactor core structural materials. Main results arising from national and international R&D programmes and projects in the field were reviewed, and new activities to be carried out under the IAEA aegis were identified on the basis of the analysis of current research and technology gaps

  7. Experimental and numerical thermal-hydraulics investigation of a molten salt reactor concept core

    Yamaji, Bogdan; Aszodi, Attila [Budapest Univ. of Technology and Economics (Hungary). Inst. of Nuclear Techniques

    2017-09-15

    In the paper measurement results of experimental modelling of a molten salt fast reactor concept will be presented and compared with three-dimensional computational fluid dynamics (CFD) simulation results. Purpose of this article is twofold, on one hand to introduce a geometry modification in order to avoid the disadvantages of the original geometry and discuss new measurement results. On the other hand to present an analysis in order to suggest a method of proper numerical modelling of the problem based on the comparison of calculation results and measurement data for the new, modified geometry. The investigated concept has a homogeneous cylindrical core without any internal structures. Previous measurements on the scaled and segmented plexiglas model of the concept core and simulation results have shown that this core geometry could be optimized for better thermal-hydraulics characteristics. In case of the original geometry strong undesired flow separation could develop, that could negatively affect the characteristics of the core from neutronics point of view as well. An internal flow distributor plate was designed and installed with the purpose of optimizing the flow field in the core by enhancing its uniformity. Particle image velocimetry (PIV) measurement results of the modified experimental model will be presented and compared to numerical simulation results with the purpose of CFD model validation.

  8. Learning Gains for Core Concepts in a Serious Game on Scientific Reasoning

    Forsyth, Carol; Pavlik, Philip, Jr.; Graesser, Arthur C.; Cai, Zhiqiang; Germany, Mae-lynn; Millis, Keith; Dolan, Robert P.; Butler, Heather; Halpern, Diane

    2012-01-01

    "OperationARIES!" is an Intelligent Tutoring System that teaches scientific inquiry skills in a game-like atmosphere. Students complete three different training modules, each with natural language conversations, in order to acquire deep-level knowledge of 21 core concepts of research methodology (e.g., correlation does not mean…

  9. Validating a Conceptual Framework for the Core Concept of "Cell-Cell Communication"

    Michael, Joel; Martinkova, Patricia; McFarland, Jenny; Wright, Ann; Cliff, William; Modell, Harold; Wenderoth, Mary Pat

    2017-01-01

    We have created and validated a conceptual framework for the core physiology concept of "cell-cell communication." The conceptual framework is composed of 51 items arranged in a hierarchy that is, in some instances, four levels deep. We have validated it with input from faculty who teach at a wide variety of institutional types. All…

  10. Validating a Conceptual Framework for the Core Concept of ”Cell-cell Communication”

    Michael, J.; Martinková, Patrícia; McFarland, J.L.; Wright, A.; Cliff, W.; Modell, H.; Wenderoth, M.P.

    2017-01-01

    Roč. 41, č. 2 (2017), s. 260-265 ISSN 1043-4046 R&D Projects: GA ČR GJ15-15856Y Institutional support: RVO:67985807 Keywords : conceptual framework * core concept * cell-cell communication * physiology Subject RIV: AM - Education OBOR OECD: Education , general; including training, pedagogy, didactics [and education systems] Impact factor: 1.755, year: 2016

  11. Preliminary Assessment of Two Alternative Core Design Concepts for the Special Purpose Reactor

    Sterbentz, James W. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Werner, James E. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Hummel, Andrew J. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kennedy, John C. [Idaho National Lab. (INL), Idaho Falls, ID (United States); O' Brien, Robert C. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Dion, Axel M. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Wright, Richard N. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Ananth, Krishnan P. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2017-11-01

    The Special Purpose Reactor (SPR) is a small 5 MWt, heat pipe-cooled, fast reactor based on the Los Alamos National Laboratory (LANL) Mega-Power concept. The LANL concept features a stainless steel monolithic core structure with drilled channels for UO2 pellet stacks and evaporator sections of the heat pipes. Two alternative active core designs are presented here that replace the monolithic core structure with simpler and easier to manufacture fuel elements. The two new core designs are simply referred to as Design A and Design B. In addition to ease of manufacturability, the fuel elements for both Design A and Design B can be individually fabricated, assembled, inspected, tested, and qualified prior to their installation into the reactor core leading to greater reactor system reliability and safety. Design A fuel elements will require the development of a new hexagonally-shaped UO2 fuel pellet. The Design A configuration will consist of an array of hexagonally-shaped fuel elements with each fuel element having a central heat pipe. This hexagonal fuel element configuration results in four radial gaps or thermal resistances per element. Neither the fuel element development, nor the radial gap issue are deemed to be serious and should not impact an aggressive reactor deployment schedule. Design B uses embedded arrays of heat pipes and fuel pins in a double-wall tank filled with liquid metal sodium. Sodium is used to thermally bond the heat pipes to the fuel pins, but its usage may create reactor transportation and regulatory challenges. An independent panel of U.S. manufacturing experts has preliminarily assessed the three SPR core designs and views Design A as simplest to manufacture. Herein are the results of a preliminary neutronic, thermal, mechanical, material, and manufacturing assessment of both Design A and Design B along with comparisons to the LANL concept (monolithic core structure). Despite the active core differences, all three reactor concepts behave

  12. Comparative genomics of Wolbachia and the bacterial species concept.

    Kirsten Maren Ellegaard

    2013-04-01

    Full Text Available The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally

  13. Pan-Genome Analysis of Human Gastric Pathogen H. pylori: Comparative Genomics and Pathogenomics Approaches to Identify Regions Associated with Pathogenicity and Prediction of Potential Core Therapeutic Targets

    Ali, Amjad; Naz, Anam; Soares, Siomar C.

    2015-01-01

    -genome approach; the predicted conserved gene families (1,193) constitute similar to 77% of the average H. pylori genome and 45% of the global gene repertoire of the species. Reverse vaccinology strategies have been adopted to identify and narrow down the potential core-immunogenic candidates. Total of 28 nonhost....... Pan-genome analyses of the global representative H. pylori isolates consisting of 39 complete genomes are presented in this paper. Phylogenetic analyses have revealed close relationships among geographically diverse strains of H. pylori. The conservation among these genomes was further analyzed by pan...

  14. Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile.

    Bletz, Stefan; Janezic, Sandra; Harmsen, Dag; Rupnik, Maja; Mellmann, Alexander

    2018-06-01

    Clostridium difficile , recently renamed Clostridioides difficile , is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for C. difficile Initially, we determined the breadth of the C. difficile population based on all available MLST sequence types with Bayesian inference (BAPS). The resulting BAPS partitions were used in combination with C. difficile clade information to select representative isolates that were subsequently used to define cgMLST target genes. Finally, we evaluated the novel cgMLST scheme with genomes from 3,025 isolates. BAPS grouping ( n = 6 groups) together with the clade information led to a total of 11 representative isolates that were included for cgMLST definition and resulted in 2,270 cgMLST genes that were present in all isolates. Overall, 2,184 to 2,268 cgMLST targets were detected in the genome sequences of 70 outbreak-associated and reference strains, and on average 99.3% cgMLST targets (1,116 to 2,270 targets) were present in 2,954 genomes downloaded from the NCBI database, underlining the representativeness of the cgMLST scheme. Moreover, reanalyzing different cluster scenarios with cgMLST were concordant to published single nucleotide variant analyses. In conclusion, the novel cgMLST is representative for the whole C. difficile population, is highly discriminatory in outbreak situations, and provides a unique nomenclature facilitating interlaboratory exchange. Copyright © 2018 American Society for Microbiology.

  15. KATS experiments to simulate corium spreading in the EPR core catcher concept

    Eppinger, B.; Fieg, G.; Schuetz, W.; Stegmaier, U.

    2001-01-01

    In future Light Water Reactors special devices (core catchers) might be required to prevent containment failure by basement erosion after reactor pressure vessel melt-through during a core meltdown accident. Quick freezing of the molten core masses is desirable to reduce release of radioactivity. Several concepts of core catcher de-vices have been proposed based on the spreading of corium melt onto flat surfaces with subsequent cooling by flooding with water. Therefore a series of experiments to investigate high temperature melt spreading on flat surfaces has been carried out using alumina-iron thermite melts as a simulant. The oxidic thermite melt is conditioned by adding other oxides to simulate a realistic corium melt as close as possible. Spreading of oxidic and metallic melts have been performed in one- and two-dimensional geometry. Substrates were chemically inert ceramic layers, dry concrete and concrete with a shallow water layer on top. (authors)

  16. A Metal Fuel Core Concept for 1000 MWt Advanced Burner Reactor

    Yang, W.S.; Kim, T.K.; Grandy, C.

    2007-01-01

    This paper describes the core design and performance characteristics of a metal fuel core concept for a 1000 MWt Advanced Burner Reactor. A ternary metal fuel form of U-TRU-Zr was assumed with weapons grade plutonium feed for the startup core and TRU recovered from LWR spent fuel for the recycled equilibrium core. A compact burner core was developed by trade-off between the burnup reactivity loss and TRU conversion ratio, with a fixed cycle length of one-year. In the startup core, the average TRU enrichment is 15.5%, the TRU conversion ratio is 0.81, and the burnup reactivity loss over a cycle is 3.6% Δk. The heavy metal and TRU inventories are 13.1 and 2.0 metric tons, respectively. The average discharge burnup is 93 MWd/kg, and the TRU consumption rate is 55.5 kg/year. For the recycled equilibrium core, the average TRU enrichment is 22.1 %, the TRU conversion ratio is 0.73, and the burnup reactivity loss is 2.2% Δk. The TRU inventory and consumption rate are 2.9 metric tons and 81.6 kg/year, respectively. The evaluated reactivity coefficients provide sufficient negative feedbacks. The control systems provide shutdown margins that are more than adequate. The integral reactivity parameters for quasi-static reactivity balance analysis indicate favorable passive safety features, although detailed safety analyses are required to verify passive safety behavior. (authors)

  17. Expansion of CORE-SINEs in the genome of the Tasmanian devil.

    Nilsson, Maria A; Janke, Axel; Murchison, Elizabeth P; Ning, Zemin; Hallström, Björn M

    2012-05-06

    The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species' survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons. The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago. The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.

  18. Expansion of CORE-SINEs in the genome of the Tasmanian devil

    Nilsson Maria A

    2012-05-01

    Full Text Available Abstract Background The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia, was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE retroposons. Results The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus around 14 million years ago. Conclusions The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome.

  19. Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome.

    Biju Joseph

    Full Text Available BACKGROUND: Neisseria meningitidis is a naturally transformable, facultative pathogen colonizing the human nasopharynx. Here, we analyze on a genome-wide level the impact of recombination on gene-complement diversity and virulence evolution in N. meningitidis. We combined comparative genome hybridization using microarrays (mCGH and multilocus sequence typing (MLST of 29 meningococcal isolates with computational comparison of a subset of seven meningococcal genome sequences. PRINCIPAL FINDINGS: We found that lateral gene transfer of minimal mobile elements as well as prophages are major forces shaping meningococcal population structure. Extensive gene content comparison revealed novel associations of virulence with genetic elements besides the recently discovered meningococcal disease associated (MDA island. In particular, we identified an association of virulence with a recently described canonical genomic island termed IHT-E and a differential distribution of genes encoding RTX toxin- and two-partner secretion systems among hyperinvasive and non-hyperinvasive lineages. By computationally screening also the core genome for signs of recombination, we provided evidence that about 40% of the meningococcal core genes are affected by recombination primarily within metabolic genes as well as genes involved in DNA replication and repair. By comparison with the results of previous mCGH studies, our data indicated that genetic structuring as revealed by mCGH is stable over time and highly similar for isolates from different geographic origins. CONCLUSIONS: Recombination comprising lateral transfer of entire genes as well as homologous intragenic recombination has a profound impact on meningococcal population structure and genome composition. Our data support the hypothesis that meningococcal virulence is polygenic in nature and that differences in metabolism might contribute to virulence.

  20. Development of out-of-core concepts for a supercritical-water, pressure-tube reactor

    Diamond, W.T.

    2010-01-01

    One of the Generation IV programs at Chalk River Laboratories has as its prime focus the development of out-of-core concepts for the SuperCritical Water (SCW) pressure tube reactor under development in Canada. A number of technical issues associated with the interface of out-of-core components and the pressure tubes of a SCW pressure tube reactor are being investigated. This article focuses on several aspects of out-of-core components and layouts, building upon concepts that have been developed during the past few years. The efforts are strongly focused on concepts for a fuel channel that can be fabricated with the tight lattice pitch (typically 230 to 250 mm) that may be required for some applications such as utilization of a thorium fuel cycle. It is not practical to adapt concepts with a tight lattice pitch while using the thicker materials required for the higher temperatures and pressures required for supercritical operation. A change in lattice pitch or configuration is required to accommodate the component size increases. This presentation will cover a number of new concepts developed to produce feeders and end fittings for the harsh conditions of a SCW pressure tube reactor. These components are then developed into conceptual models of a Gen IV pressure tube reactor mounted in both horizontal and vertical orientations. Full 3-D solid models of both concepts will be demonstrated as well as a 1/10th-scale model of one face of a horizontal concept that has been built from components made with a 3-D printer. (author)

  1. Business Service Outsourcing: An Evolution of Concentration on Core Business Concepts and Transaction Cost Economies

    Ahmad H. Juma'h

    2000-08-01

    Full Text Available Present and evaluate the literature with respect to business service outsourcing (BSO, with a particular concentration on a common form of BSO, information technology (IT. The review defines the issues with respect to BSO in terms of drivers and motivations, as well as internal and external implications for BSO companies and their contractors. BSO is an evolution of transaction cost theory and concentration on core business concepts. Although, there are several attempts to explain when a company should outsource, these theoretical frameworks are difficult to apply in practice since satisfaction is a function of expectation and the identification of activities are core commodity is not straightforward.

  2. Comparative study for minor actinide transmutation in various fast reactor core concepts

    Ohki, S.

    2001-01-01

    A comparative evaluation of minor actinide (MA) transmutation property was performed for various fast reactor core concepts. The differences of MA transmutation property were classified by the variations of fuel type (oxide, nitride, metal), coolant type (sodium, lead, carbon dioxide) and design philosophy. Both nitride and metal fuels bring about 10% larger MA transmutation amount compared with oxide fuel. The MA transmutation amount is almost unchanged by the difference between sodium and lead coolants, while carbon dioxide causes a reduction by about 10% compared with those. The changes of MA transmutation property by fuel and coolant types are comparatively small. The effects caused by the difference of core design are rather significant. (author)

  3. Multi-objective and multi-physics optimization methodology for SFR core: application to CFV concept

    Fabbris, Olivier

    2014-01-01

    Nuclear reactor core design is a highly multidisciplinary task where neutronics, thermal-hydraulics, fuel thermo-mechanics and fuel cycle are involved. The problem is moreover multi-objective (several performances) and highly dimensional (several tens of design parameters).As the reference deterministic calculation codes for core characterization require important computing resources, the classical design method is not well suited to investigate and optimize new innovative core concepts. To cope with these difficulties, a new methodology has been developed in this thesis. Our work is based on the development and validation of simplified neutronics and thermal-hydraulics calculation schemes allowing the full characterization of Sodium-cooled Fast Reactor core regarding both neutronics performances and behavior during thermal hydraulic dimensioning transients.The developed methodology uses surrogate models (or meta-models) able to replace the neutronics and thermal-hydraulics calculation chain. Advanced mathematical methods for the design of experiment, building and validation of meta-models allows substituting this calculation chain by regression models with high prediction capabilities.The methodology is applied on a very large design space to a challenging core called CFV (French acronym for low void effect core) with a large gain on the sodium void effect. Global sensitivity analysis leads to identify the significant design parameters on the core design and its behavior during unprotected transient which can lead to severe accidents. Multi-objective optimizations lead to alternative core configurations with significantly improved performances. Validation results demonstrate the relevance of the methodology at the pre-design stage of a Sodium-cooled Fast Reactor core. (author) [fr

  4. LMR design concepts for transuranic management in low sodium void worth cores

    Hill, R.N.

    1991-01-01

    The fuel cycle processing techniques and hard neuron spectrum of the Integral Fast Reactor (IFR) metal fuel cycle have favorable characteristics for the management of transuranics; and the wide range of breeding characteristics available in metal fuelled cores provides for flexibility in transuranic management strategy. Previous studies indicate that most design options which decrease the breeding ratio also show a decrease in sodium void worth; therefore, low void worths are achievable in transuranic burning (low breeding ratio) core designs. This paper describes numerous trade studies assessing various design options for a low void worth transuranic burner core. A flat annular core design appears to be a promising concept; the high leakage geometry yields a low breeding ratio and small sodium void worth. To allow flexibility in breeding characteristics, alternate design options which achieve fissile self-sufficiency are also evaluated. A self-sufficient core design which is interchangeable with the burner core and maintains a low sodium void worth is developed. 13 refs., 1 fig., 4 tabs

  5. Conceptual Elements: A Detailed Framework to Support and Assess Student Learning of Biology Core Concepts

    Cary, Tawnya; Branchaw, Janet

    2017-01-01

    The Vision and Change in Undergraduate Biology Education: Call to Action report has inspired and supported a nationwide movement to restructure undergraduate biology curricula to address overarching disciplinary concepts and competencies. The report outlines the concepts and competencies generally but does not provide a detailed framework to guide the development of the learning outcomes, instructional materials, and assessment instruments needed to create a reformed biology curriculum. In this essay, we present a detailed Vision and Change core concept framework that articulates key components that transcend subdisciplines and scales for each overarching biological concept, the Conceptual Elements (CE) Framework. The CE Framework was developed using a grassroots approach of iterative revision and incorporates feedback from more than 60 biologists and undergraduate biology educators from across the United States. The final validation step resulted in strong national consensus, with greater than 92% of responders agreeing that each core concept list was ready for use by the biological sciences community, as determined by scientific accuracy and completeness. In addition, we describe in detail how educators and departments can use the CE Framework to guide and document reformation of individual courses as well as entire curricula. PMID:28450444

  6. The understanding of core pharmacological concepts among health care students in their final semester.

    Aronsson, Patrik; Booth, Shirley; Hägg, Staffan; Kjellgren, Karin; Zetterqvist, Ann; Tobin, Gunnar; Reis, Margareta

    2015-12-29

    The overall aim of the study was to explore health care students´ understanding of core concepts in pharmacology. An interview study was conducted among twelve students in their final semester of the medical program (n = 4), the nursing program (n = 4), and the specialist nursing program in primary health care (n = 4) from two Swedish universities. The participants were individually presented with two pharmacological clinically relevant written patient cases, which they were to analyze and propose a solution to. Participants were allowed to use the Swedish national drug formulary. Immediately thereafter the students were interviewed about their assessments. The interviews were audio-recorded and transcribed verbatim. A thematic analysis was used to identify units of meaning in each interview. The units were organized into three clusters: pharmacodynamics, pharmacokinetics, and drug interactions. Subsequent procedure consisted of scoring the quality of students´ understanding of core concepts. Non-parametric statistics were employed. The study participants were in general able to define pharmacological concepts, but showed less ability to discuss the meaning of the concepts in depth and to implement these in a clinical context. The participants found it easier to grasp concepts related to pharmacodynamics than pharmacokinetics and drug interactions. These results indicate that education aiming to prepare future health care professionals for understanding of more complex pharmacological reasoning and decision-making needs to be more focused and effective.

  7. Ex-vessel core catcher design requirements and preliminary concepts evaluation

    Friedland, A.J.; Tilbrook, R.W.

    1974-01-01

    As part of the overall study of the consequences of a hypothetical failure to scram following loss of pumping power, design requirements and preliminary concepts evaluation of an ex-vessel core catcher (EVCC) were performed. EVCC is the term applied to a class of devices whose primary objective is to provide a stable subcritical and coolable configuration within containment following a postulated accident in which it is assumed that core debris has penetrated the Reactor Vessel and Guard Vessel. Under these assumed conditions a set of functional requirements were developed for an EVCC and several concepts were evaluated. The studies were specifically directed toward the FFTF design considering the restraints imposed by the physical design and construction of the FFTF plant

  8. Modular architecture of the T4 phage superfamily: A conserved core genome and a plastic periphery

    Comeau, Andre M.; Bertrand, Claire; Letarov, Andrei; Tetart, Francoise; Krisch, H.M.

    2007-01-01

    Among the most numerous objects in the biosphere, phages show enormous diversity in morphology and genetic content. We have sequenced 7 T4-like phages and compared their genome architecture. All seven phages share a core genome with T4 that is interrupted by several hyperplastic regions (HPRs) where most of their divergence occurs. The core primarily includes homologues of essential T4 genes, such as the virion structure and DNA replication genes. In contrast, the HPRs contain mostly novel genes of unknown function and origin. A few of the HPR genes that can be assigned putative functions, such as a series of novel Internal Proteins, are implicated in phage adaptation to the host. Thus, the T4-like genome appears to be partitioned into discrete segments that fulfil different functions and behave differently in evolution. Such partitioning may be critical for these large and complex phages to maintain their flexibility, while simultaneously allowing them to conserve their highly successful virion design and mode of replication

  9. Concepts for passive heat removal and filtration systems under core meltdown conditions

    Wilhelm, J.G.; Neitzel, H.-J.

    1993-01-01

    The objective of the new containment concept being developed by KfK is the complete passive enclosure of a power reactor after a core meltdown accident by means of a solid containment structure and passive removal of the decay heat. This is to be accomplished by cooling the containment walls with ambient air, with thermoconvection as the driving force. The concept of the containment is described. Data are given of the heat removal and the requirements for filtration of the exhaust air, which is contaminated due to the leak rate assumed for the inner containment. The concept for the filter system is described. Various solutions for reduction of the large volumetric flow to be filtered are discussed. 3 refs., 8 figs

  10. A theoretical concept for a thermal-hydraulic 3D parallel channel core model

    Hoeld, A.

    2004-01-01

    A detailed description of the theoretical concept of the 3D thermal-hydraulic single- and two-phase flow phenomena is presented. The theoretical concept is based on important development lines such as separate treatment of the mass and energy from the momentum balance eqs. The other line is the establishment of a procedure for the calculation of the mass flow distributions into different parallel channels based on the fact that the sum of pressure decrease terms over a closed loop must stay, despite of un-symmetric perturbations, zero. The concept is realized in the experimental code HERO-X3D, concentrating in a first step on an artificial BWR or PWR core which may consist of a central channel, four quadrants, and a bypass channel. (authors)

  11. 76 FR 21789 - ITS Joint Program Office; Vehicle to Infrastructure Core System Concept of Operations; Notice of...

    2011-04-18

    ... Concept of Operations; Notice of Public Meeting AGENCY: Research and Innovative Technology Administration...) Core System Concept of Operations on May 17, 2011 at the Detroit Metro Airport Marriott, 30559 Flynn... to work originally performed under the Vehicle Infrastructure Integration Proof of Concept (VII POC...

  12. Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.

    Xu, Jianping

    2006-06-01

    Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic

  13. Proposal for a advanced PWR core with adequate characteristics for passive safety concept

    Perrotta, Jose Augusto

    1999-01-01

    This work presents a discussion upon the suitable from an advanced PWR core, classified by the EPRI as 'Passive PWR' (advanced reactor with passive safety concept to power plants with less than 600 MW electrical power). The discussion upon the type of core is based on nuclear fuel engineering concepts. Discussion is made on type of fuel materials, structural materials, geometric shapes and manufacturing process that are suitable to produce fuel assemblies which give good performance for this type of reactors. The analysis is guided by the EPRI requirements for Advanced Light Water Reactor (ALWR). By means of comparison, the analysis were done to Angra 1 (old type of 600 MWe PWR class), and the design of the Westinghouse Advanced PWR-AP600. It was verified as a conclusion of this work that the modern PWR fuels are suitable for advanced PWR's Nevertheless, this work presents a technical alternative to this kind of fuel, still using UO 2 as fuel, but changing its cylindrical form of pellets and pin type fuel element to plane shape pallets and plate type fuel element. This is not a novelty fuel, since it was used in the 50's at Shippingport Reactor and as an advanced version by CEA of France in the 70's. In this work it is proposed a new mechanical assembly design for this fuel, which can give adequate safety and operational performance to the core of a 'Passive PWR'. (author)

  14. Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

    Wisniewski-Dyé, Florence; Lozano, Luis; Acosta-Cruz, Erika; Borland, Stéphanie; Drogue, Benoît; Prigent-Combaret, Claire; Rouy, Zoé; Barbe, Valérie; Mendoza Herrera, Alberto; González, Victor; Mavingui, Patrick

    2012-01-01

    Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510). The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis), and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron) are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation. PMID:24705077

  15. Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

    Victor González

    2012-09-01

    Full Text Available Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510. The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis, and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation.

  16. Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.

    Kim, Tae-Sung; He, Qiang; Kim, Kyu-Won; Yoon, Min-Young; Ra, Won-Hee; Li, Feng Peng; Tong, Wei; Yu, Jie; Oo, Win Htet; Choi, Buung; Heo, Eun-Beom; Yun, Byoung-Kook; Kwon, Soon-Jae; Kwon, Soon-Wook; Cho, Yoo-Hyun; Lee, Chang-Yong; Park, Beom-Seok; Park, Yong-Jin

    2016-05-26

    Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era.

  17. Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential

    Siragusa Gregory R

    2011-06-01

    Full Text Available Abstract Background Because biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context, we sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricultural and human pathogen. Results Phage whole-genome tetra-nucleotide signatures and proteomic tree topologies correlated closely with host phylogeny. Comparisons of our phage genomes to 26 others revealed three shared COGs; of particular interest within this core genome was an endolysin (PF01520, an N-acetylmuramoyl-L-alanine amidase and a holin (PF04531. Comparative analyses of the evolutionary history and genomic context of these common phage proteins revealed two important results: 1 strongly significant host-specific sequence variation within the endolysin, and 2 a protein domain architecture apparently unique to our phage genomes in which the endolysin is located upstream of its associated holin. Endolysin sequences from our phages were one of two very distinct genotypes distinguished by variability within the putative enzymatically-active domain. The shared or core genome was comprised of genes with multiple sequence types belonging to five pfam families, and genes belonging to 12 pfam families, including the holin genes, which were nearly identical. Conclusions Significant genomic diversity exists even among closely-related bacteriophages. Holins and endolysins represent conserved functions across divergent phage genomes and, as we demonstrate here, endolysins can have significant variability and host-specificity even among closely-related genomes. Endolysins in our phage genomes may be subject to different selective pressures than the rest of the genome. These findings may have important implications for potential biotechnological applications of phage gene products.

  18. Modeling and simulation in the systems engineering life cycle core concepts and accompanying lectures

    Loper, Margaret L

    2015-01-01

    This easy to read text/reference provides a broad introduction to the fundamental concepts of modeling and simulation (M&S) and systems engineering, highlighting how M&S is used across the entire systems engineering lifecycle. Each chapter corresponds to a short lecture covering a core topic in M&S or systems engineering.  Topics and features: reviews the full breadth of technologies, methodologies and uses of M&S, rather than just focusing on a specific aspect of the field; presents contributions from renowned specialists in each topic covered; introduces the foundational elements and proce

  19. Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly.

    Ayon Pal

    Full Text Available A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding

  20. Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly.

    Pal, Ayon; Banerjee, Rachana; Mondal, Uttam K; Mukhopadhyay, Subhasis; Bothra, Asim K

    2015-01-01

    A comprehensive in silico analysis of 71 species representing the different taxonomic classes and physiological genre of the domain Archaea was performed. These organisms differed in their physiological attributes, particularly oxygen tolerance and energy metabolism. We explored the diversity and similarity in the codon usage pattern in the genes and genomes of these organisms, emphasizing on their core cellular pathways. Our thrust was to figure out whether there is any underlying similarity in the design of core pathways within these organisms. Analyses of codon utilization pattern, construction of hierarchical linear models of codon usage, expression pattern and codon pair preference pointed to the fact that, in the archaea there is a trend towards biased use of synonymous codons in the core cellular pathways and the Nc-plots appeared to display the physiological variations present within the different species. Our analyses revealed that aerobic species of archaea possessed a larger degree of freedom in regulating expression levels than could be accounted for by codon usage bias alone. This feature might be a consequence of their enhanced metabolic activities as a result of their adaptation to the relatively O2-rich environment. Species of archaea, which are related from the taxonomical viewpoint, were found to have striking similarities in their ORF structuring pattern. In the anaerobic species of archaea, codon bias was found to be a major determinant of gene expression. We have also detected a significant difference in the codon pair usage pattern between the whole genome and the genes related to vital cellular pathways, and it was not only species-specific but pathway specific too. This hints towards the structuring of ORFs with better decoding accuracy during translation. Finally, a codon-pathway interaction in shaping the codon design of pathways was observed where the transcription pathway exhibited a significantly different coding frequency signature.

  1. Mitotic evolution of Plasmodium falciparum shows a stable core genome but recombination in antigen families.

    Selina E R Bopp

    Full Text Available Malaria parasites elude eradication attempts both within the human host and across nations. At the individual level, parasites evade the host immune responses through antigenic variation. At the global level, parasites escape drug pressure through single nucleotide variants and gene copy amplification events conferring drug resistance. Despite their importance to global health, the rates at which these genomic alterations emerge have not been determined. We studied the complete genomes of different Plasmodium falciparum clones that had been propagated asexually over one year in the presence and absence of drug pressure. A combination of whole-genome microarray analysis and next-generation deep resequencing (totaling 14 terabases revealed a stable core genome with only 38 novel single nucleotide variants appearing in seventeen evolved clones (avg. 5.4 per clone. In clones exposed to atovaquone, we found cytochrome b mutations as well as an amplification event encompassing the P. falciparum multidrug resistance associated protein (mrp1 on chromosome 1. We observed 18 large-scale (>1 kb on average deletions of telomere-proximal regions encoding multigene families, involved in immune evasion (9.5×10(-6 structural variants per base pair per generation. Six of these deletions were associated with chromosomal crossovers generated during mitosis. We found only minor differences in rates between genetically distinct strains and between parasites cultured in the presence or absence of drug. Using these derived mutation rates for P. falciparum (1.0-9.7×10(-9 mutations per base pair per generation, we can now model the frequency at which drug or immune resistance alleles will emerge under a well-defined set of assumptions. Further, the detection of mitotic recombination events in var gene families illustrates how multigene families can arise and change over time in P. falciparum. These results will help improve our understanding of how P. falciparum

  2. Mitotic Evolution of Plasmodium falciparum Shows a Stable Core Genome but Recombination in Antigen Families

    Bopp, Selina E. R.; Manary, Micah J.; Bright, A. Taylor; Johnston, Geoffrey L.; Dharia, Neekesh V.; Luna, Fabio L.; McCormack, Susan; Plouffe, David; McNamara, Case W.; Walker, John R.; Fidock, David A.; Denchi, Eros Lazzerini; Winzeler, Elizabeth A.

    2013-01-01

    Malaria parasites elude eradication attempts both within the human host and across nations. At the individual level, parasites evade the host immune responses through antigenic variation. At the global level, parasites escape drug pressure through single nucleotide variants and gene copy amplification events conferring drug resistance. Despite their importance to global health, the rates at which these genomic alterations emerge have not been determined. We studied the complete genomes of different Plasmodium falciparum clones that had been propagated asexually over one year in the presence and absence of drug pressure. A combination of whole-genome microarray analysis and next-generation deep resequencing (totaling 14 terabases) revealed a stable core genome with only 38 novel single nucleotide variants appearing in seventeen evolved clones (avg. 5.4 per clone). In clones exposed to atovaquone, we found cytochrome b mutations as well as an amplification event encompassing the P. falciparum multidrug resistance associated protein (mrp1) on chromosome 1. We observed 18 large-scale (>1 kb on average) deletions of telomere-proximal regions encoding multigene families, involved in immune evasion (9.5×10−6 structural variants per base pair per generation). Six of these deletions were associated with chromosomal crossovers generated during mitosis. We found only minor differences in rates between genetically distinct strains and between parasites cultured in the presence or absence of drug. Using these derived mutation rates for P. falciparum (1.0–9.7×10−9 mutations per base pair per generation), we can now model the frequency at which drug or immune resistance alleles will emerge under a well-defined set of assumptions. Further, the detection of mitotic recombination events in var gene families illustrates how multigene families can arise and change over time in P. falciparum. These results will help improve our understanding of how P. falciparum evolves to

  3. A Critical Review of Concepts and Methods Used in Classical Genome Analysis

    Seberg, Ole; Petersen, Gitte

    1998-01-01

    A short account of the development of classical genome analysis, the analysis of chromosome behaviour in metaphase I of meiosis, primarily in interspecific hybrids, is given. The application of the concept of homology to describe chromosome pairing between the respective chromosomes of a pair...... breeding but it has no place in systematics. With an increased knowledge and understanding of the mechanism behind meiosis, data useful in a systematic context may eventually be produced....

  4. Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak.

    Pearce, Madison E; Alikhan, Nabil-Fareed; Dallman, Timothy J; Zhou, Zhemin; Grant, Kathie; Maiden, Martin C J

    2018-06-02

    Multi-country outbreaks of foodborne bacterial disease present challenges in their detection, tracking, and notification. As food is increasingly distributed across borders, such outbreaks are becoming more common. This increases the need for high-resolution, accessible, and replicable isolate typing schemes. Here we evaluate a core genome multilocus typing (cgMLST) scheme for the high-resolution reproducible typing of Salmonella enterica (S. enterica) isolates, by its application to a large European outbreak of S. enterica serovar Enteritidis. This outbreak had been extensively characterised using single nucleotide polymorphism (SNP)-based approaches. The cgMLST analysis was congruent with the original SNP-based analysis, the epidemiological data, and whole genome MLST (wgMLST) analysis. Combination of the cgMLST and epidemiological data confirmed that the genetic diversity among the isolates predated the outbreak, and was likely present at the infection source. There was consequently no link between country of isolation and genetic diversity, but the cgMLST clusters were congruent with date of isolation. Furthermore, comparison with publicly available Enteritidis isolate data demonstrated that the cgMLST scheme presented is highly scalable, enabling outbreaks to be contextualised within the Salmonella genus. The cgMLST scheme is therefore shown to be a standardised and scalable typing method, which allows Salmonella outbreaks to be analysed and compared across laboratories and jurisdictions. Copyright © 2018. Published by Elsevier B.V.

  5. Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis.

    Cavanagh, Jorunn Pauline; Klingenberg, Claus; Hanssen, Anne-Merethe; Fredheim, Elizabeth Aarag; Francois, Patrice; Schrenzel, Jacques; Flægstad, Trond; Sollid, Johanna Ericson

    2012-06-01

    The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for S. haemolyticus using multi locus sequence typing (MLST) and multi locus variable number of tandem repeats (VNTR) analysis. Seven housekeeping genes (MLST) and five VNTR loci (MLVF) were selected for the novel typing schemes. A panel of 45 human and veterinary S. haemolyticus isolates was investigated. The collection had diverse PFGE patterns (38 PFGE types) and was sampled over a 20 year-period from eight countries. MLST resolved 17 sequence types (Simpsons index of diversity [SID]=0.877) and MLVF resolved 14 repeat types (SID=0.831). We found a low sequence diversity. Phylogenetic analysis clustered the isolates in three (MLST) and one (MLVF) clonal complexes, respectively. Taken together, neither the MLST nor the MLVF scheme was suitable to resolve the population structure of this S. haemolyticus collection. Future MLVF and MLST schemes will benefit from addition of more variable core genome sequences identified by comparing different fully sequenced S. haemolyticus genomes. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores.

    Meng, Jintao; Wang, Bingqiang; Wei, Yanjie; Feng, Shengzhong; Balaji, Pavan

    2014-01-01

    There is a widening gap between the throughput of massive parallel sequencing machines and the ability to analyze these sequencing data. Traditional assembly methods requiring long execution time and large amount of memory on a single workstation limit their use on these massive data. This paper presents a highly scalable assembler named as SWAP-Assembler for processing massive sequencing data using thousands of cores, where SWAP is an acronym for Small World Asynchronous Parallel model. In the paper, a mathematical description of multi-step bi-directed graph (MSG) is provided to resolve the computational interdependence on merging edges, and a highly scalable computational framework for SWAP is developed to automatically preform the parallel computation of all operations. Graph cleaning and contig extension are also included for generating contigs with high quality. Experimental results show that SWAP-Assembler scales up to 2048 cores on Yanhuang dataset using only 26 minutes, which is better than several other parallel assemblers, such as ABySS, Ray, and PASHA. Results also show that SWAP-Assembler can generate high quality contigs with good N50 size and low error rate, especially it generated the longest N50 contig sizes for Fish and Yanhuang datasets. In this paper, we presented a highly scalable and efficient genome assembly software, SWAP-Assembler. Compared with several other assemblers, it showed very good performance in terms of scalability and contig quality. This software is available at: https://sourceforge.net/projects/swapassembler.

  7. Testing communication strategies to convey genomic concepts using virtual reality technology.

    Kaphingst, Kimberly A; Persky, Susan; McCall, Cade; Lachance, Christina; Beall, Andrew C; Blascovich, Jim

    2009-06-01

    Health professionals need to be able to communicate information about genomic susceptibility in understandable and usable ways, but substantial challenges are involved. We developed four learning modules that varied along two factors: (1) learning mode (active learning vs. didactic learning) and (2) metaphor (risk elevator vs. bridge) and tested them using a 2 x 2 between-subjects, repeated measures design. The study used an innovative virtual reality technology experimental platform; four virtual worlds were designed to convey the concept that genetic and behavioral factors interact to affect common disease risk. The primary outcome was comprehension (recall, transfer). Study participants were 42 undergraduates aged 19-23. The results indicated that the elevator metaphor better supported learning of the concept than the bridge metaphor. Mean transfer score was significantly higher for the elevator metaphor (p health information. The findings also indicated that less complex metaphors might convey abstract concepts more effectively.

  8. Impact of the choice of reference genome on the ability of the core genome SNV methodology to distinguish strains of Salmonella enterica serovar Heidelberg.

    Usongo, Valentine; Berry, Chrystal; Yousfi, Khadidja; Doualla-Bell, Florence; Labbé, Genevieve; Johnson, Roger; Fournier, Eric; Nadon, Celine; Goodridge, Lawrence; Bekal, Sadjia

    2018-01-01

    Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. The core genome single nucleotide variant pipeline (cgSNV) is one of several whole genome based sequence typing methods used for the laboratory investigation of foodborne pathogens. SNV detection using this method requires a reference genome. The purpose of this study was to investigate the impact of the choice of the reference genome on the cgSNV-informed phylogenetic clustering and inferred isolate relationships. We found that using a draft or closed genome of S. Heidelberg as reference did not impact the ability of the cgSNV methodology to differentiate among 145 S. Heidelberg isolates involved in foodborne outbreaks. We also found that using a distantly related genome such as S. Dublin as choice of reference led to a loss in resolution since some sporadic isolates were found to cluster together with outbreak isolates. In addition, the genetic distances between outbreak isolates as well as between outbreak and sporadic isolates were overall reduced when S. Dublin was used as the reference genome as opposed to S. Heidelberg.

  9. High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform

    Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen; Rockenbauer, Eszter

    2011-01-01

    repeat units. These methods do not allow for the full resolution of STR base composition that sequencing approaches could provide. Here we present an STR profiling method based on the use of the Roche Genome Sequencer (GS) FLX to simultaneously sequence multiple core STR loci. Using this method...

  10. Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures

    Häring, Monika; Vestergaard, Gisle Alberg; Brügger, Kim

    2005-01-01

    A novel filamentous virus, AFV2, from the hyperthermophilic archaeal genus Acidianus shows structural similarity to lipothrixviruses but differs from them in its unusual terminal and core structures. The double-stranded DNA genome contains 31,787 bp and carries eight open reading frames homologous...

  11. Small Launch Vehicle Design Approaches: Clustered Cores Compared with Multi-Stage Inline Concepts

    Waters, Eric D.; Beers, Benjamin; Esther, Elizabeth; Philips, Alan; Threet, Grady E., Jr.

    2013-01-01

    In an effort to better define small launch vehicle design options two approaches were investigated from the small launch vehicle trade space. The primary focus was to evaluate a clustered common core design against a purpose built inline vehicle. Both designs focused on liquid oxygen (LOX) and rocket propellant grade kerosene (RP-1) stages with the terminal stage later evaluated as a LOX/methane (CH4) stage. A series of performance optimization runs were done in order to minimize gross liftoff weight (GLOW) including alternative thrust levels, delivery altitude for payload, vehicle length to diameter ratio, alternative engine feed systems, re-evaluation of mass growth allowances, passive versus active guidance systems, and rail and tower launch methods. Additionally manufacturability, cost, and operations also play a large role in the benefits and detriments for each design. Presented here is the Advanced Concepts Office's Earth to Orbit Launch Team methodology and high level discussion of the performance trades and trends of both small launch vehicle solutions along with design philosophies that shaped both concepts. Without putting forth a decree stating one approach is better than the other; this discussion is meant to educate the community at large and let the reader determine which architecture is truly the most economical; since each path has such a unique set of limitations and potential payoffs.

  12. Advanced core physics and thermal hydraulics analysis of boiling water reactors using innovative fuel concepts

    Winter, Dominik

    2014-01-01

    The economical operation of a boiling water reactor (BWR) is mainly achieved by the axially uniform utilization of the nuclear fuel in the assemblies which is challenging because the neutron spectrum in the active reactor core varies with the axial position. More precisely, the neutron spectrum becomes harder the higher the position is resulting in a decrease of the fuel utilization because the microscopic fission cross section is smaller by several orders of magnitude. In this work, the use of two fuel concepts based on a mixed oxide (MOX) fuel and an innovative thorium-plutonium (ThPu) fuel is investigated by a developed simulation model encompassing thermal hydraulics, neutronics, and fuel burnup. The main feature of these fuel concepts is the axially varying enrichment in plutonium which is, in this work, recycled from spent nuclear fuel and shows a high fission fraction of the absorption cross section for fast incident neutron energies. The potential of balancing the overall fuel utilization by an increase of the fission rate in the upper part of the active height with a combination of the harder spectrum and the higher fission fraction of the absorption cross section in the BWR core is studied. The three particular calculational models for thermal hydraulics, neutronics, and fuel burnup provide results at fuel assembly and/or at core level. In the former case, the main focus lies on the thermal hydraulics analysis, fuel burnup, and activity evolution after unloading from the core and, in the latter case, special attention is paid to reactivity safety coefficients (feedback effects) and the optimization of the operational behavior. At both levels (assembly and core), the isotopic buildup and depletion rates as a function of the active height are analyzed. In addition, a comparison between the use of conventional fuel types with homogeneous enrichments and the use of the innovative fuel types is made. In the framework of the simulations, the ThPu and the MOX

  13. Addressing Pre-Service Teachers' Understandings and Difficulties with Some Core Concepts in the Special Theory of Relativity

    Selcuk, Gamze Sezgin

    2011-01-01

    The aim of this study is to investigate pre-service teachers' understanding of and difficulties with some core concepts in the special theory of relativity. The pre-service teachers (n = 185) from the Departments of Physics Education and Elementary Science Education at Dokuz Eylul University (in Turkey) participated. Both quantitative and…

  14. The Curriculum-Faculty-Reinforcement Alignment and Its Effect on Learning Retention of Core Marketing Concepts of Marketing Capstone Students

    Raska, David; Keller, Eileen Weisenbach; Shaw, Doris

    2014-01-01

    Curriculum-Faculty-Reinforcement (CFR) alignment is an alignment between fundamental marketing concepts that are integral to the mastery of knowledge expected of our marketing graduates, their perceived importance by the faculty, and their level of reinforcement throughout core marketing courses required to obtain a marketing degree. This research…

  15. Technical Meeting on Liquid Metal Reactor Concepts: Core Design and Structural Materials. Presentations

    2013-01-01

    The objective of the Technical Meeting is to present and discuss innovative liquid metal fast reactor (LMFR) core designs with special focus on the choice, development, testing and qualification of advanced reactor core structural materials

  16. Science and mathematics teachers’ core teaching conceptions and their implications for engaging in cross-curricular innovations

    Hanne Møller Andersen

    2010-04-01

    Full Text Available Previous studies have found core teaching conceptions (CTCs to influence teachers’ actions, i.e. how they engage with new teaching practices (e.g. Lotter, Harwood, & Bonner, 2007. This study explores typical CTCs and their subject specific nature in a sample of teachers from physics, biology, and mathematics in Danish upper secondary school. Teachers’ CTCs were investigated through their essay responses to a set of open core questions, administered through a web-platform. Results demonstrate that teachers’ CTCs come in subject specific flavours, encompassing their purpose for teaching the subject, their conceptions of teaching and learning, and their conceptions of interdisciplinary teaching. It is argued that such differences shape teachers’ engagement with new cross-curricular innovations in the Danish context. Assessing and addressing typical and personal CTCs are found to be crucial to a successful implementation of current reform-initiatives, for teacher training, and for self-regulated professional development among teachers.

  17. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes

    Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S.; Allard, Marc W.; Strain, Errol A.; Brown, Eric W.

    2016-01-01

    ABSTRACT Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST...

  18. Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates.

    Cody, Alison J; Bray, James E; Jolley, Keith A; McCarthy, Noel D; Maiden, Martin C J

    2017-07-01

    Human campylobacteriosis, caused by Campylobacter jejuni and C. coli , remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterization methods. Whole-genome sequencing (WGS) data enable the improvement of sequence-based typing approaches, such as multilocus sequence typing (MLST), by substantially increasing the number of loci examined. A core genome MLST (cgMLST) scheme defines a comprehensive set of those loci present in most members of a bacterial group, balancing very high resolution with comparability across the diversity of the group. Here we propose a set of 1,343 loci as a human campylobacteriosis cgMLST scheme (v1.0), the allelic profiles of which can be assigned to core genome sequence types. The 1,343 loci chosen were a subset of the 1,643 loci identified in the reannotation of the genome sequence of C. jejuni isolate NCTC 11168, chosen as being present in >95% of draft genomes of 2,472 representative United Kingdom campylobacteriosis isolates, comprising 2,207 (89.3%) C. jejuni isolates and 265 (10.7%) C. coli isolates. Validation of the cgMLST scheme was undertaken with 1,478 further high-quality draft genomes, containing 150 or fewer contiguous sequences, from disease isolate collections: 99.5% of these isolates contained ≥95% of the 1,343 cgMLST loci. In addition to the rapid and effective high-resolution analysis of large numbers of diverse isolates, the cgMLST scheme enabled the efficient identification of very closely related isolates from a well-defined single-source campylobacteriosis outbreak. Copyright © 2017 Cody et al.

  19. Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes

    Jacqueline Zoe-Munn Chan

    2014-10-01

    Full Text Available Two bacteriophages, RPP1 and RLP1, infecting members of the marine Roseobacter clade were isolated from seawater. Their linear genomes are 74.7 and 74.6 kb and encode 91 and 92 coding DNA sequences, respectively. Around 30% of these are homologous to genes found in Enterobacter phage N4. Comparative genomics of these two new Roseobacter phages and twenty-three other sequenced N4-like phages (three infecting members of the Roseobacter lineage and twenty infecting other Gammaproteobacteria revealed that N4-like phages share a core genome of 14 genes responsible for control of gene expression, replication and virion proteins. Phylogenetic analysis of these genes placed the five N4-like roseophages (RN4 into a distinct subclade. Analysis of the RN4 phage genomes revealed they share a further 19 genes of which nine are found exclusively in RN4 phages and four appear to have been acquired from their bacterial hosts. Proteomic analysis of the RPP1 and RLP1 virions identified a second structural module present in the RN4 phages similar to that found in the Pseudomonas N4-like phage LIT1. Searches of various metagenomic databases, included the GOS database, using CDS sequences from RPP1 suggests these phages are widely distributed in marine environments in particular in the open ocean environment.

  20. Radiotoxicity study of a boiling water reactor core design based on a thorium-uranium fuel concept

    Nunez C, A.; Espinosa P, G.

    2007-01-01

    Full text: The innovative design of a Boiling Water Reactor (BWR) equilibrium core using the thorium-uranium (blanket-seed) concept in the same integrated fuel assembly is presented in this paper. The lattice design uses the thorium conversion capability to 233 U in a BWR spectrum. A core design was developed to achieve an equilibrium cycle of one effective full power year in a standard BWR. A comparison of the toxicity of the spent fuel showed that toxicity is lower in the thorium cycle than other commercial fuels as UO 2 and MOX (uranium and plutonium) in case of the one-through cycle for LWR. (Author)

  1. Hardware concepts for a large low-energetics LMFBR core. Final report

    Hutter, E.; Batch, R.V.

    1980-12-01

    A design study was made to identify a practical set of hardware configurations that would embody the requirements developed in the numerical study of a low-energetics core and blanket for a prototype large breeder reactor. Dimensioned drawings are presented for fuel, blanket, reflector/shield, and control rod subassemblies. A horizontal cross section drawing shows how these subassemblies are arranged in the total core/blanket assembly. A core support is illustrated showing a dual plenums arrangement

  2. Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract

    Maguin Emmanuelle

    2007-08-01

    Full Text Available Abstract Background While genes that are conserved between related bacterial species are usually thought to have evolved along with the species, phylogenetic trees reconstructed for individual genes may contradict this picture and indicate horizontal gene transfer. Individual trees are often not resolved with high confidence, however, and in that case alternative trees are generally not considered as contradicting the species tree, although not confirming it either. Here we conduct an in-depth analysis of 401 protein phylogenetic trees inferred with varying levels of confidence for three lactobacilli from the acidophilus complex. At present the relationship between these bacteria, isolated from environments as diverse as the gastrointestinal tract (Lactobacillus acidophilus and Lactobacillus johnsonii and yogurt (Lactobacillus delbrueckii ssp. bulgaricus, is ambiguous due to contradictory phenotypical and 16S rRNA based classifications. Results Among the 401 phylogenetic trees, those that could be reconstructed with high confidence support the 16S-rRNA tree or one alternative topology in an astonishing 3:2 ratio, while the third possible topology is practically absent. Lowering the confidence threshold for trees to be taken into consideration does not significantly affect this ratio, and therefore suggests that gene transfer may have affected as much as 40% of the core genome genes. Gene function bias suggests that the 16S rRNA phylogeny of the acidophilus complex, which indicates that L. acidophilus and L. delbrueckii ssp. bulgaricus are the closest related of these three species, is correct. A novel approach of comparison of interspecies protein divergence data employed in this study allowed to determine that gene transfer most likely took place between the lineages of the two species found in the gastrointestinal tract. Conclusion This case-study reports an unprecedented level of phylogenetic incongruence, presumably resulting from extensive

  3. Addressing pre-service teachers' understandings and difficulties with some core concepts in the special theory of relativity

    Selcuk, Gamze Sezgin

    2011-01-01

    The aim of this study is to investigate pre-service teachers' understanding of and difficulties with some core concepts in the special theory of relativity. The pre-service teachers (n = 185) from the Departments of Physics Education and Elementary Science Education at Dokuz Eylul University (in Turkey) participated. Both quantitative and qualitative research methods were used in this study. Students' understanding of and difficulties with core elements (time, length, mass and density) were tested using a paper-and-pencil questionnaire (including four questions) and in-depth interviews after the instruction of related modern physics topics. The analyses of the collected data were based on quantitative and qualitative techniques. The results indicate that pre-service teachers at different academic levels have specific and considerable difficulties with proper time, time dilation, proper length, mass and relativistic density concepts. In this paper, the conclusions of the study and implications for physics teaching are discussed.

  4. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes.

    Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S; Allard, Marc W; Strain, Errol A; Brown, Eric W

    2016-10-15

    Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak. Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST

  5. In-reactor testing of the closed cycle gas core reactor---the nuclear light bulb concept

    Gauntt, R.O.; Slutz, S.A.; Harms, G.A.; Latham, T.S.; Roman, W.C.; Rodgers, R.J.

    1993-01-01

    The Nuclear Light Bulb (NLB) concept is an advanced closed cycle space propulsion rocket engine design that offers unprecidented performance characteristics in terms of specific impulse (>1800 s) and thrust (>445 kN). The NLB is a gas-core nuclear reactor making use of thermal radiation from a high temperature U-plasma core to heat the hydrogen propellant to very high temperatures (∼4000 K). The following paper describes analyses performed in support of the design of in-reactor tests that are planned to be performed in the Annular Core Research Reactor (ACRR) at Sandia National Laboratories in order to demonstrate the technical feasibility of this advanced concept. The tests will examine the stability of a hydrodynamically confined fissioning U-plasma under steady and transient conditions. Testing will also involve study of propellant heating by thermal radiation from the plasma and materials performance in the nuclear environment of the NLB. The analyses presented here include neutronic performance studies and U-plasma radiation heat-transport studies of small vortex-confined fissioning U-plasma experiments that are irradiated in the ACRR. These analyses indicate that high U-plasma temperatures (4000 to 9000 K) can be sustained in the ACRR for periods of time on the order of 5 to 20 s. These testing conditions are well suited to examine the stability and performance requirements necessary to demonstrate the feasibility of this concept

  6. Dynamic behavior of homogeneous and heterogeneous LMFBR core-design concepts

    Chang, Y.I.; Henryson, H. II; Orechwa, Y.; Su, S.F.; Greenman, G.; Blomquist, R.

    1981-01-01

    The emphasis is placed on obtaining an understanding of the inherent difference between homogeneous and heterogeneous core configurations regarding neutronic characteristics related to the dynamic behavior. The space-time neutronic and thermal-hydraulic behavior was analyzed in detail for various core configurations by using the FX2-TH, a two-dimensional kinetics code with thermal-hydraulic feedback. In addition, the relationship between the flux tilt and the fundamental-to-first harmonic eigenvalue separation, and the sodium void reactivity in heterogeneous cores were also sutdied

  7. Genome-scale portrait and evolutionary significance of human-specific core promoter tri- and tetranucleotide short tandem repeats.

    Nazaripanah, N; Adelirad, F; Delbari, A; Sahaf, R; Abbasi-Asl, T; Ohadi, M

    2018-04-05

    While there is an ongoing trend to identify single nucleotide substitutions (SNSs) that are linked to inter/intra-species differences and disease phenotypes, short tandem repeats (STRs)/microsatellites may be of equal (if not more) importance in the above processes. Genes that contain STRs in their promoters have higher expression divergence compared to genes with fixed or no STRs in the gene promoters. In line with the above, recent reports indicate a role of repetitive sequences in the rise of young transcription start sites (TSSs) in human evolution. Following a comparative genomics study of all human protein-coding genes annotated in the GeneCards database, here we provide a genome-scale portrait of human-specific short- and medium-size (≥ 3-repeats) tri- and tetranucleotide STRs and STR motifs in the critical core promoter region between - 120 and + 1 to the TSS and evidence of skewing of this compartment in reference to the STRs that are not human-specific (Levene's test p human-specific transcripts was detected in the tri and tetra human-specific compartments (mid-p genome-scale skewing of STRs at a specific region of the human genome and a link between a number of these STRs and TSS selection/transcript specificity. The STRs and genes listed here may have a role in the evolution and development of characteristics and phenotypes that are unique to the human species.

  8. The Information Technology Infrastructure for the Translational Genomics Core and the Partners Biobank at Partners Personalized Medicine

    Natalie Boutin

    2016-01-01

    Full Text Available The Biobank and Translational Genomics core at Partners Personalized Medicine requires robust software and hardware. This Information Technology (IT infrastructure enables the storage and transfer of large amounts of data, drives efficiencies in the laboratory, maintains data integrity from the time of consent to the time that genomic data is distributed for research, and enables the management of complex genetic data. Here, we describe the functional components of the research IT infrastructure at Partners Personalized Medicine and how they integrate with existing clinical and research systems, review some of the ways in which this IT infrastructure maintains data integrity and security, and discuss some of the challenges inherent to building and maintaining such infrastructure.

  9. Stylized whole-core benchmark of the Integral Inherently Safe Light Water Reactor (I2S-LWR) concept

    Hon, Ryan; Kooreman, Gabriel; Rahnema, Farzad; Petrovic, Bojan

    2017-01-01

    Highlights: • A stylized benchmark specification of the I2S-LWR core. • A library of cross sections were generated in both 8 and 47 groups. • Monte Carlo solutions generated for the 8 group library using MCNP5. • Cross sections and pin fission densities provided in journal’s repository. - Abstract: The Integral, Inherently Safe Light Water Reactor (I 2 S-LWR) is a pressurized water reactor (PWR) concept under development by a multi-institutional team led by Georgia Tech. The core is similar in size to small 2-loop PWRs while having the power level of current large reactors (∼1000 MWe) but using uranium silicide fuel and advanced stainless steel cladding. A stylized benchmark specification of the I 2 S-LWR core has been developed in order to test whole-core neutronics codes and methods. For simplification the core was split into 57 distinct material regions for cross section generation. Cross sections were generated using the lattice physics code HELIOS version 1.10 in both 8 and 47 groups. Monte Carlo solutions, including eigenvalue and pin fission densities, were generated for the 8 group library using MCNP5. Due to space limitations in this paper, the full cross section library and normalized pin fission density results are provided in the journal’s electronic repository.

  10. The Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers

    2016-09-20

    Health Division, Menzies School of Health Research, Darwin , NT, 15 Australia; ePacific Biosciences; fDivision of Pediatric Infectious Diseases, 16...that a significant number of near-neighbor genomes must be 217 sequenced in order to identify a set of molecular markers that are highly 218...of potentially deadly infections. However, as our study demonstrates, 244 the genomic targets of molecular assays need to first be thoroughly

  11. Genomic potential hypothesis of evolution: a concept of biogenesis in habitable spaces of the universe.

    Schwabe, Christian

    2002-11-01

    The new hypothesis of evolution establishes a contiguity of life sciences with cosmology, physics, and chemistry, and provides a basis for the search for life on other planets. Chemistry is the sole driving force of the assembly of life, under the subtle guidance exerted by bonding orbital geometry. That phenomenon leads to multiple origins that function on the same principles but are different to the extent that their nucleic acid core varies. Thus, thoughts about the origins of life and the development of complexity have been transferred from the chance orientation of the past to the realm of atomic structures, which are subject to the laws of thermodynamics and kinetics. Evolution is a legitimate subject of basic science, and the complexity of life will submit to the laws of chemistry and physics as the problem is viewed from a new perspective. The paradigm connects life to the big events that formed every sphere of our living space and that keeps conditions fine-tuned for life to persist, perhaps a billion years or more. The "genomic potential" hypothesis leads to the prediction that life like ours is likely to exist in galaxies that are as distant from the origin of the universe as the Milky Way, and that the habitable zone of our galaxy harbors other living planets as well. Copyright 2002 Wiley-Liss, Inc.

  12. Genetic education and the challenge of genomic medicine: development of core competences to support preparation of health professionals in Europe

    Skirton, Heather; Lewis, Celine; Kent, Alastair

    2010-01-01

    in professional education and regulation between European countries, setting curricula may not be practical. Core competences are used as a basis for health professional education in many fields and settings. An Expert Group working under the auspices of the EuroGentest project and European Society of Human...... Genetics Education Committee agreed that a pragmatic solution to the need to establish common standards for education and practice in genetic health care was to agree to a set of core competences that could apply across Europe. These were agreed through an exhaustive process of consultation with relevant......The use of genetics and genomics within a wide range of health-care settings requires health professionals to develop expertise to practise appropriately. There is a need for a common minimum standard of competence in genetics for health professionals in Europe but because of differences...

  13. Advanced core concepts with enhanced proliferation resistance by transmutation of minor actinides

    Saito, Masaki

    2005-01-01

    ''Protected Plutonium Production (P 3 )'' has been proposed to establish high burn-up cores and to produce protected with high proliferation resistance due to high decay heat and large number of spontaneous fission neutron of 238 Pu by the transmutation of Minor Actinides (MAs) which is presently treated as high-level waste. The burn-up calculations have shown that the advanced fuel with UO 2 (11-13% enrichment of 235 U) by doping 237 Np to produce 238 Pu in the commercialized large LWRs burn up to 100 GWd/t with 238 Pu to Pu ratio of about 20% which means the fuel is highly protected from proliferation. It was also predicted that medium or small size LWR cores with 15-17% enrichment, liquid metal cooled cores, and gas cooled cores added by 1-2% Np could achieve 100 GWd/t burning with bearing high proliferation resistance. The 237 Np mass balance calculations have revealed that more than 20 nuclear P 3 plants of 300 MWe could be supplied with enough 237 Np from the Japanese commercial plants in equilibrium fuel cycles. From the present studies, it is confirmed that MAs are treated as burnable and fertile materials not only to extend the core life but also to improve plutonium proliferation resistance of the future nuclear energy systems instead of their geological disposal or just their burning through fission. (author)

  14. Optimization of binary breeder reactor IV - Conception of mixed fuel at central part of the core

    Dias, A.F.; Ishiguro, Y.

    1986-04-01

    Neutronic characteristics of some LMFBRs are analized for a fueling mode that is different from those reported previously. In an inner part of the core both 233 U/ 232 Th and Pu/U assemblies are placed while the outer zone is fueled with Pu/U assemblies. Both oxide metal fuels and 232 Th and 238 U blankets are considered. (Author) [pt

  15. Three core concepts for producing uranium-233 in commercial pressurized light water reactors for possible use in water-cooled breeder reactors

    Conley, G.H.; Cowell, G.K.; Detrick, C.A.; Kusenko, J.; Johnson, E.G.; Dunyak, J.; Flanery, B.K.; Shinko, M.S.; Giffen, R.H.; Rampolla, D.S.

    1979-12-01

    Selected prebreeder core concepts are described which could be backfit into a reference light water reactor similar to current commercial reactors, and produce uranium-233 for use in water-cooled breeder reactors. The prebreeder concepts were selected on the basis of minimizing fuel system development and reactor changes required to permit a backfit. The fuel assemblies for the prebreeder core concepts discussed would occupy the same space envelope as those in the reference core but contain a 19 by 19 array of fuel rods instead of the reference 17 by 17 array. An instrument well and 28 guide tubes for control rods have been allocated to each prebreeder fuel assembly in a pattern similar to that for the reference fuel assemblies. Backfit of these prebreeder concepts into the reference reactor would require changes only to the upper core support structure while providing flexibility for alternatives in the type of fuel used

  16. Production process stability - core assumption of INDUSTRY 4.0 concept

    Chromjakova, F.; Bobak, R.; Hrusecka, D.

    2017-06-01

    Today’s industrial enterprises are confronted by implementation of INDUSTRY 4.0 concept with basic problem - stabilised manufacturing and supporting processes. Through this phenomenon of stabilisation, they will achieve positive digital management of both processes and continuously throughput. There is required structural stability of horizontal (business) and vertical (digitized) manufacturing processes, supported through digitalised technologies of INDUSTRY 4.0 concept. Results presented in this paper based on the research results and survey realised in more industrial companies. Following will described basic model for structural process stabilisation in manufacturing environment.

  17. A Genome-Wide Association Study and Complex Network Identify Four Core Hub Genes in Bipolar Disorder

    Zengyan Xie

    2017-12-01

    Full Text Available Bipolar disorder is a common and severe mental illness with unsolved pathophysiology. A genome-wide association study (GWAS has been used to find a number of risk genes, but it is difficult for a GWAS to find genes indirectly associated with a disease. To find core hub genes, we introduce a network analysis after the GWAS was conducted. Six thousand four hundred fifty eight single nucleotide polymorphisms (SNPs with p < 0.01 were sifted out from Wellcome Trust Case Control Consortium (WTCCC dataset and mapped to 2045 genes, which are then compared with the protein–protein network. One hundred twelve genes with a degree >17 were chosen as hub genes from which five significant modules and four core hub genes (FBXL13, WDFY2, bFGF, and MTHFD1L were found. These core hub genes have not been reported to be directly associated with BD but may function by interacting with genes directly related to BD. Our method engenders new thoughts on finding genes indirectly associated with, but important for, complex diseases.

  18. Reduced Graphene Oxide Joins Graphene Oxide to Teach Undergraduate Students Core Chemistry and Nanotechnology Concepts

    Kondratowicz, Izabela; Nadolska, Malgorzata; Z?elechowska, Kamila

    2018-01-01

    Novel carbon nanomaterials such as reduced graphene oxide (rGO) and graphene oxide (GO) can be easily incorporated into the undergraduate curriculum to discuss basic chemistry and nanotechnology concepts. This paper describes a laboratory experiment designed to study the differences between GO and rGO regarding their physicochemical properties…

  19. The conceptual basis for interprofessional collaboration: core concepts and theoretical frameworks.

    D'Amour, Danielle; Ferrada-Videla, Marcela; San Martin Rodriguez, Leticia; Beaulieu, Marie-Dominique

    2005-05-01

    Interprofessional collaboration is a key factor in initiatives designed to increase the effectiveness of health services currently offered to the public. It is important that the concept of collaboration be well understood, because although the increasingly complex health problems faced by health professionals are creating more interdependencies among them, we still have limited knowledge of the complexity of interprofessional relationships. The goal of this literature review was to identify conceptual frameworks that could improve our understanding of this important aspect of health organizations. To this end, we have identified and taken into consideration: (A) the various definitions proposed in the literature and the various concepts associated with collaboration, and (B) the various theoretical frameworks of collaboration. Our results demonstrate that: (1) the concept of collaboration is commonly defined through five underlying concepts: sharing, partnership, power, interdependency and process; (2) the most complete models of collaboration seem to be those based on a strong theoretical background, either in organizational theory or in organizational sociology and on empirical data; (3) there is a significant amount of diversity in the way the various authors conceptualized collaboration and in the factors influencing collaboration; (4) these frameworks do not establish clear links between the elements in the models and the outputs; and (5) the literature does not provide a serious attempt to determine how patients could be integrated into the health care team, despite the fact that patients are recognized as the ultimate justification for providing collaborative care.

  20. Core Clinical Data Elements for Cancer Genomic Repositories: A Multi-stakeholder Consensus.

    Conley, Robert B; Dickson, Dane; Zenklusen, Jean Claude; Al Naber, Jennifer; Messner, Donna A; Atasoy, Ajlan; Chaihorsky, Lena; Collyar, Deborah; Compton, Carolyn; Ferguson, Martin; Khozin, Sean; Klein, Roger D; Kotte, Sri; Kurzrock, Razelle; Lin, C Jimmy; Liu, Frank; Marino, Ingrid; McDonough, Robert; McNeal, Amy; Miller, Vincent; Schilsky, Richard L; Wang, Lisa I

    2017-11-16

    The Center for Medical Technology Policy and the Molecular Evidence Development Consortium gathered a diverse group of more than 50 stakeholders to develop consensus on a core set of data elements and values essential to understanding the clinical utility of molecularly targeted therapies in oncology. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. An exploration of the extent of inclusion of spirituality and spiritual care concepts in core nursing textbooks.

    Timmins, Fiona; Murphy, Maryanne; Neill, Freda; Begley, Thelma; Sheaf, Greg

    2015-01-01

    Holistic care that encompasses a spiritual dimension is an expectation in modern healthcare (Rothman, 2009). Increasing attention is being paid to the role of nurses in providing spiritual care to patients. However nurses lack specific skills and expertise in this area (Lundmark, 2006; Timmins, 2010; RCN, 2011), and the extent to which their undergraduate education prepares them for this role is unclear. There is often an absence of clear direction about what to teach undergraduate nursing students. The extent to which core textbooks direct student studies in this area is not known. There is some evidence that some of these fundamental core textbooks provide insufficient direction (Pesut, 2008), thus gaps in knowledge and care provision in this field could be exacerbated. The aim of this study is to examine the extent to which spiritual care concepts are addressed in core nursing textbooks. Five hundred and forty three books were sampled from the Nursing and Midwifery Core Collection list (UK) (Tomlinsons, 2010) representing 94% of the total (n=580). A survey, the Spirituality Textbook Analysis Tool (STAT), was developed and used to collect data. One hundred and thirty of the books included content related to spirituality and religion. However there was little consistency in the core nursing textbooks with regard to direction for providing spiritual care. Thirty eight percent of the books defined spiritual care and 36% provided an outline of the role of the nurse in providing this. While some books advocated the assessment of patients' spiritual needs (32%) few referred specifically to assessment tools. It is essential that nurses are adequately prepared to address the spiritual needs of patients. While there are numerous spiritual care texts that deal solely with this issue for nurses, there is an argument emerging that core nursing texts used by nursing students ought to encompass spiritual care elements. Lack of specific focus on this field, by these key

  2. A concept of passive safety pressurized water reactor system with inherent matching nature of core heat generation and heat removal

    Murao, Yoshio; Araya, Fumimasa; Iwamura, Takamichi; Okumura, Keisuke

    1995-01-01

    The reduction of manpower in operation and maintenance by simplification of the system are essential to improve the safety and the economy of future light water reactors. At the Japan Atomic Energy Research Institute (JAERI), a concept of a simplified passive safety reactor system JPSR was developed for this purpose and in the concept minimization of developing work and conservation of scale-up capability in design were considered. The inherent matching nature of core heat generation and heat removal rate is introduced by the core with high reactivity coefficient for moderator density and low reactivity coefficient for fuel temperature (Doppler effect) and once-through steam generators (SGs). This nature makes the nuclear steam supply system physically-slave for the steam and energy conversion system by controlling feed water mass flow rate. The nature can be obtained by eliminating chemical shim and adopting in-vessel control rod drive mechanism (CRDM) units and a low power density core. In order to simplify the system, a large pressurizer, canned pumps, passive residual heat removal systems with air coolers as a final heat sink and passive coolant injection system are adopted and the functions of volume and boron concentration control and seal water supply are eliminated from the chemical and volume control system (CVCS). The emergency diesel generators and auxiliary component cooling system of 'safety class' for transferring heat to sea water as a final heat sink in emergency are also eliminated. All of systems are built in the containment except for the air coolers of the passive residual heat removal system. The analysis of the system revealed that the primary coolant expansion in 100% load reduction in 60 s can be mitigated in the pressurizer without actuating the pressure relief valves and the pressure in 50% load change in 30 s does not exceed the maximum allowable pressure in accidental conditions in regardless of pressure regulation. (author)

  3. Melt cooling by bottom flooding. The COMET core-catcher concept

    Foit, Jerzy Jan; Alsmeyer, Hans; Tromm, Walter; Buerger, Manfred; Journeau, Christophe

    2009-01-01

    The COMET concept has been developed to cool an ex-vessel corium melt in case of a hypothetical severe accident leading to vessel melt-through. After erosion of a sacrificial concrete layer the melt is passively flooded by bottom injection of coolant water. The open porosities and large surface that are generated during melt solidification form a porous permeable structure that is permanently filled with the evaporating water and thus allows an efficient short-term as well as long-term removal of the decay heat. The advantages of this concept are the fast cool-down and complete solidification of the melt within less than one hour typically. This stops further release of fission products from the corium. A drawback may be the fast release of steam during the quenching process. Several experimental series have been performed by FZK (Germany) to test and optimise the functionality of the different variants of the COMET concept. Thermite generated melts of iron and aluminium oxide were used. The large scale COMET-H test series with sustained inductive heating includes nine experiments performed with an array of water injection channels embedded in a sacrificial concrete layer. Variation of the water inlet pressure and melt height showed that melts up to 50 cm height can be safely cooled with an overpressure of the coolant water of 0.2 bar. The CometPC concept is based on cooling by flooding the melt from the bottom through layers of porous, water filled concrete. The third variant of the COMET design, CometPCA, uses a layer of porous, water filled concrete CometPCA from which flow channels protrude into the layer of sacrificial concrete. This modified concept combines the advantages of the original COMET concept with flow channels and the high resistance of a water-filled porous concrete layer against downward melt attack. Four large scale CometPCA experiments (FZK, Germany) have demonstrated an efficient cooling of melts up to 50 cm height using the recommended water

  4. Genetic education and the challenge of genomic medicine: development of core competences to support preparation of health professionals in Europe

    Skirton, Heather; Lewis, Celine; Kent, Alastair

    2010-01-01

    in professional education and regulation between European countries, setting curricula may not be practical. Core competences are used as a basis for health professional education in many fields and settings. An Expert Group working under the auspices of the EuroGentest project and European Society of Human...... and professions has resulted in an adaptable framework for both pre-registration and continuing professional education. This competence framework has the potential to improve the quality of genetic health care for patients globally.......The use of genetics and genomics within a wide range of health-care settings requires health professionals to develop expertise to practise appropriately. There is a need for a common minimum standard of competence in genetics for health professionals in Europe but because of differences...

  5. Using Mouse Mammary Tumor Cells to Teach Core Biology Concepts: A Simple Lab Module.

    McIlrath, Victoria; Trye, Alice; Aguanno, Ann

    2015-06-18

    Undergraduate biology students are required to learn, understand and apply a variety of cellular and molecular biology concepts and techniques in preparation for biomedical, graduate and professional programs or careers in science. To address this, a simple laboratory module was devised to teach the concepts of cell division, cellular communication and cancer through the application of animal cell culture techniques. Here the mouse mammary tumor (MMT) cell line is used to model for breast cancer. Students learn to grow and characterize these animal cells in culture and test the effects of traditional and non-traditional chemotherapy agents on cell proliferation. Specifically, students determine the optimal cell concentration for plating and growing cells, learn how to prepare and dilute drug solutions, identify the best dosage and treatment time course of the antiproliferative agents, and ascertain the rate of cell death in response to various treatments. The module employs both a standard cell counting technique using a hemocytometer and a novel cell counting method using microscopy software. The experimental procedure lends to open-ended inquiry as students can modify critical steps of the protocol, including testing homeopathic agents and over-the-counter drugs. In short, this lab module requires students to use the scientific process to apply their knowledge of the cell cycle, cellular signaling pathways, cancer and modes of treatment, all while developing an array of laboratory skills including cell culture and analysis of experimental data not routinely taught in the undergraduate classroom.

  6. A Genome-Wide Association Study Reveals Genes Associated with Fusarium Ear Rot Resistance in a Maize Core Diversity Panel

    Zila, Charles T.; Samayoa, L. Fernando; Santiago, Rogelio; Butrón, Ana; Holland, James B.

    2013-01-01

    Fusarium ear rot is a common disease of maize that affects food and feed quality globally. Resistance to the disease is highly quantitative, and maize breeders have difficulty incorporating polygenic resistance alleles from unadapted donor sources into elite breeding populations without having a negative impact on agronomic performance. Identification of specific allele variants contributing to improved resistance may be useful to breeders by allowing selection of resistance alleles in coupling phase linkage with favorable agronomic characteristics. We report the results of a genome-wide association study to detect allele variants associated with increased resistance to Fusarium ear rot in a maize core diversity panel of 267 inbred lines evaluated in two sets of environments. We performed association tests with 47,445 single-nucleotide polymorphisms (SNPs) while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments. Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0–100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets. Two of three identified SNPs colocalized with genes that have been implicated with programmed cell death. An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared with other temperate breeding pools. PMID:24048647

  7. High polyhydroxybutyrate production in Pseudomonas extremaustralis is associated with differential expression of horizontally acquired and core genome polyhydroxyalkanoate synthase genes.

    Mariela V Catone

    Full Text Available Pseudomonas extremaustralis produces mainly polyhydroxybutyrate (PHB, a short chain length polyhydroxyalkanoate (sclPHA infrequently found in Pseudomonas species. Previous studies with this strain demonstrated that PHB genes are located in a genomic island. In this work, the analysis of the genome of P. extremaustralis revealed the presence of another PHB cluster phbFPX, with high similarity to genes belonging to Burkholderiales, and also a cluster, phaC1ZC2D, coding for medium chain length PHA production (mclPHA. All mclPHA genes showed high similarity to genes from Pseudomonas species and interestingly, this cluster also showed a natural insertion of seven ORFs not related to mclPHA metabolism. Besides PHB, P. extremaustralis is able to produce mclPHA although in minor amounts. Complementation analysis demonstrated that both mclPHA synthases, PhaC1 and PhaC2, were functional. RT-qPCR analysis showed different levels of expression for the PHB synthase, phbC, and the mclPHA synthases. The expression level of phbC, was significantly higher than the obtained for phaC1 and phaC2, in late exponential phase cultures. The analysis of the proteins bound to the PHA granules showed the presence of PhbC and PhaC1, whilst PhaC2 could not be detected. In addition, two phasin like proteins (PhbP and PhaI associated with the production of scl and mcl PHAs, respectively, were detected. The results of this work show the high efficiency of a foreign gene (phbC in comparison with the mclPHA core genome genes (phaC1 and phaC2 indicating that the ability of P. extremaustralis to produce high amounts of PHB could be explained by the different expression levels of the genes encoding the scl and mcl PHA synthases.

  8. Genome-wide prediction methods in highly diverse and heterozygous species: proof-of-concept through simulation in grapevine.

    Agota Fodor

    Full Text Available Nowadays, genome-wide association studies (GWAS and genomic selection (GS methods which use genome-wide marker data for phenotype prediction are of much potential interest in plant breeding. However, to our knowledge, no studies have been performed yet on the predictive ability of these methods for structured traits when using training populations with high levels of genetic diversity. Such an example of a highly heterozygous, perennial species is grapevine. The present study compares the accuracy of models based on GWAS or GS alone, or in combination, for predicting simple or complex traits, linked or not with population structure. In order to explore the relevance of these methods in this context, we performed simulations using approx 90,000 SNPs on a population of 3,000 individuals structured into three groups and corresponding to published diversity grapevine data. To estimate the parameters of the prediction models, we defined four training populations of 1,000 individuals, corresponding to these three groups and a core collection. Finally, to estimate the accuracy of the models, we also simulated four breeding populations of 200 individuals. Although prediction accuracy was low when breeding populations were too distant from the training populations, high accuracy levels were obtained using the sole core-collection as training population. The highest prediction accuracy was obtained (up to 0.9 using the combined GWAS-GS model. We thus recommend using the combined prediction model and a core-collection as training population for grapevine breeding or for other important economic crops with the same characteristics.

  9. A map to a new treasure island: the human genome and the concept of common heritage.

    Byk, C

    1998-06-01

    While the 1970's have been called the environmental years, the 1990's could be seen as the genome years. As the challenge to map and to sequence the human genome mobilized the scientific community, risks and benefits of information and uses that would derive from this project have also raised ethical issues at the international level. The particular interest of the 1997 UNESCO Declaration relies on the fact that it emphasizes both the scientific importance of genetics and the appropriate reinforcement of human rights in this area. It considers the human genome, at least symbolically, as the common heritage of humanity.

  10. Main concepts and objectives of fuel performance modelling and core development

    Lassmann, K.; O'Carroll, C.; Van de Laar, J.; Ray, I.

    1994-01-01

    The basic concepts of the fuel rod modelling was reviewed and their limitations are discussed.Three more general modelling concepts are briefly outlined: one-dimensional models versus 2-D or 3-D models; steady-state versus transient modelling; empirical versus mechanical models. The fuel rod behaviour is determined by thermal, mechanical and physical processes such as densification, swelling, gas release, irradiation damage etc. It is shown that the macroscopic behaviour of a fuel rod is to a large extent determined by the local UO 2 microstructure. Any fuel rod model must include the solution of the heat conduction equation and the principal mechanical equations i. e. equilibrium and compatibility, together with constitutive equations. The basic limitations from the different assumptions made for the solution of the governing equations are identified. It was shown that the thermal and the mechanical analysis are strongly coupled and therefore errors are propagated. The individual correlations and processes are also not error-free and in only some cases can individual errors be estimated. There is almost for all processes a good understanding of the dominating parameters but the unsolved problem is how local quantities such as pores and grain structure, stresses etc. evolve during the irradiation. Thus the wrong input data for local processes is considered as one of the main source of uncertainty. Fission gas release and swelling could not be described by the corresponding equations without introducing some free parameters. The center line predictions of two codes for FUMEX blind exercise are given. It is stated that since the D-COM exercise in 1984, fuel rod performance codes have been improved considerably and must be now considered as mature tools for further optimisation of fuel rods. 1 tab., 12 figs., 22 refs

  11. Main concepts and objectives of fuel performance modelling and core development

    Lassmann, K; O` Carroll, C; Van de Laar, J; Ray, I [Commission of the European Communities, Karlsruhe (Germany). European Inst. for Transuranium Elements; Stefanova, S [Bylgarska Akademiya na Naukite, Sofia (Bulgaria). Inst. za Yadrena Izsledvaniya i Yadrena Energetika; Chantoin, P [International Atomic Energy Agency, Vienna (Austria)

    1994-12-31

    The basic concepts of the fuel rod modelling was reviewed and their limitations are discussed.Three more general modelling concepts are briefly outlined: one-dimensional models versus 2-D or 3-D models; steady-state versus transient modelling; empirical versus mechanical models. The fuel rod behaviour is determined by thermal, mechanical and physical processes such as densification, swelling, gas release, irradiation damage etc. It is shown that the macroscopic behaviour of a fuel rod is to a large extent determined by the local UO{sub 2} microstructure. Any fuel rod model must include the solution of the heat conduction equation and the principal mechanical equations i. e. equilibrium and compatibility, together with constitutive equations. The basic limitations from the different assumptions made for the solution of the governing equations are identified. It was shown that the thermal and the mechanical analysis are strongly coupled and therefore errors are propagated. The individual correlations and processes are also not error-free and in only some cases can individual errors be estimated. There is almost for all processes a good understanding of the dominating parameters but the unsolved problem is how local quantities such as pores and grain structure, stresses etc. evolve during the irradiation. Thus the wrong input data for local processes is considered as one of the main source of uncertainty. Fission gas release and swelling could not be described by the corresponding equations without introducing some free parameters. The center line predictions of two codes for FUMEX blind exercise are given. It is stated that since the D-COM exercise in 1984, fuel rod performance codes have been improved considerably and must be now considered as mature tools for further optimisation of fuel rods. 1 tab., 12 figs., 22 refs.

  12. ATHENA model for 4 x 350 MW(t) HTGR plant side-by-side steel vessel prismatic core concept

    Ambrosek, R.G.

    1986-01-01

    ATHENA is a computer code being developed at the Idaho National Engineering Laboratory under US Department of Energy support. The code will provide advanced best-estimate predictive capability for a wide spectrum of applications. The code has capability for modeling independent hydrodynamic systems which can currently include water, helium, Freon-II, idealgas, lithium, or lithium-lead as fluids. ATHENA was modified to allow point reactor kinetics evaluations for two nuclear reactor cores. Capability for specifying gas circulators was added and representative homologous curves were added for a helium circulator. A full system model was developed for a High Temperature Gas Reactor modular concept with a full secondary system model. The code capability to model the complete system was demonstrated and a representative transient for a circulator coastdown without reactor scram was modeled and evaluated to the point of flow stagnation

  13. The self-consistent energy system with an enhanced non-proliferated core concept for global nuclear energy utilization

    Kawashima, Masatoshi; Arie, Kazuo; Araki, Yoshio; Sato, Mitsuyoshi; Mori, Kenji; Nakayama, Yoshiyuki; Nakazono, Ryuichi; Kuroda, Yuji; Ishiguma, Kazuo; Fujii-e, Yoichi

    2008-01-01

    A sustainable nuclear energy system was developed based on the concept of Self-Consistent Nuclear Energy System (SCNES). Our study that trans-uranium (TRU) metallic fuel fast reactor cycle coupled with recycling of five long-lived fission products (LLFP) as well as actinides is the most promising system for the sustainable nuclear utilization. Efficient utilization of uranium-238 through the SCNES concept opens the doors to prolong the lifetime of nuclear energy systems towards several tens of thousand years. Recent evolution of the concept revealed compatibility of fuel sustainability, minor actinide (MA) minimization and non-proliferation aspects for peaceful use of nuclear energy systems through the discussion. As for those TRU compositions stabilized under fast neutron spectra, plutonium isotope fractions are remained in the range of reactor grade classification with high fraction of Pu240 isotope. Recent evolution of the SCNES concept has revealed that TRU recycling can cope with enhancing non-proliferation efforts in peaceful use with the 'no-blanket and multi-zoning core' concept. Therefore, the realization of SCNES is most important. In addition, along the process to the goals, a three-step approach is proposed to solve concurrent problems raised in the LWR systems. We discussed possible roles and contribution to the near future demand along worldwide expansion of LWR capacities by applying the 1st generation SCNES. MA fractions in TRU are more than 10% from LWR discharged fuels and even higher up to 20% in fuels from long interim storages. TRU recycling in the 1st generation SCNES system can reduce the MA fractions down to 4-5% in a few decades. This capability significantly releases 'MA' pressures in down-stream of LWR systems. Current efforts for enhancing capabilities for energy generation by LWR systems are efficient against the global warming crisis. In parallel to those movements, early realization of the SCNES concept can be the most viable decision

  14. O4.04‘FROM THE CORE TO BEYOND THE MARGIN’: A GENOMIC PICTURE OF GLIOBLASTOMA INTRATUMOR HETEROGENEITY

    Aubry, M.; de Tayrac, M.; Etcheverry, A.; Clavreul, A.; Saikali, S.; Menei, P.; Mosser, J.

    2014-01-01

    INTRODUCTION: Glioblastoma (GB) is a very agressive brain tumor that almost systematically recurs. This recurrence is linked to the highly invasive behavior of this tumor. Major challenges in therapy of GB are therefore associated with controlling this infiltration sustained by a strong heterogeneous biology of GB tumors. In the past decade, molecular studies of GB have been focused on inter-individual heterogeneity. These studies have identified gene mutations and molecular signatures with putative prognostic or predictive significance. However, accumulating evidence suggests that intratumor heterogeneity is the key to understanding treatment failure. MATERIAL AND METHOD: To explore GB intratumor heterogeneity we developed a surgical multisampling scheme to collect tumor fragments from 10 GB patients in four spatially distinct areas defined on 3D MRI ‘from the core to beyond the margin’: necrotic zone, tumor zone, interface, and peripheral brain zone. These samples were studied genome-wide at three molecular levels: genome, transcriptome and methylome. We used Principal Component Analysis (PCA) to classify the samples and to select genes. We constructed a co-expression network on the basis of the expression data of the most informative genes related to the data structure revealed by PCA. RESULTS AND DISCUSSION: At the genome level, we identified common GB alterations (loss/partial loss of chromosome 10, polysomy of chromosome 7, focal deletion of the CDKN2A/B and focal high-level amplifications of EGFR) and a strong inter-individual molecular heterogeneity. Transcriptome analysis highlighted a pronounced intratumor architecture reflecting the surgical sampling plan of the study and identified gene modules associated with hallmarks of cancer. We provide a master gene signature highly correlated with the intratumor gradient and associated with the tumor infiltrative behavior. In this signature, the percentage of genes presenting an anti-correlation between

  15. Large-scale boiling experiments of the flooded cavity concept for in-vessel core retention

    Chu, T.Y.; Slezak, S.E.; Bentz, J.H.; Pasedag, W.F.

    1994-01-01

    This paper presents results of ex-vessel boiling experiments performed in the CYBL (CYlindrical BoiLing) facility. CYBL is a reactor-scale facility for confirmatory research of the flooded cavity concept for accident management. CYBL has a tank-within-a-tank design; the inner tank simulates the reactor vessel and the outer tank simulates the reactor cavity. Experiments with uniform and edge-peaked heat flux distributions up to 20 W/cm 2 across the vessel bottom were performed. Boiling outside the reactor vessel was found to be subcooled nucleate boiling. The subcooling is mainly due to the gravity head which results from flooding the sides of the reactor vessel. The boiling process exhibits a cyclic pattern with four distinct phases: direct liquid/solid contact, bubble nucleation and growth, coalescence, and vapor mass dispersion (ejection). The results suggest that under prototypic heat load and heat flux distributions, the flooded cavity in a passive pressurized water reactor like the AP-600 should be capable of cooling the reactor pressure vessel in the central region of the lower head that is addressed by these tests

  16. Design of a boiling water reactor core based on an integrated blanket-seed thorium-uranium concept

    Nunez-Carrera, Alejandro; Francois, Juan Luis; Martin-del-Campo, Cecilia; Espinosa-Paredes, Gilberto

    2005-01-01

    This paper is concerned with the design of a boiling water reactor (BWR) equilibrium core using thorium as a nuclear material in an integrated blanket-seed (BS) assembly. The integrated BS concept comes from the fact that the blanket and the seed rods are located in the same assembly, and are burned out in a once-through cycle. The idea behind the lattice design is to use the thorium conversion capability in a BWR spectrum, taking advantage of the 233 U build-up. A core design was developed to achieve an equilibrium cycle of 365 effective full power days in a standard BWR with a reload of 104 fuel assemblies designed with an average 235 U enrichment of 7.5 w/o in the seed sub-lattice. The main operating parameters, like power, linear heat generation rate and void distributions were obtained as well as the shutdown margin. It was observed that the analyzed parameters behave like those obtained in a standard BWR. The shutdown margin design criterion was fulfilled by addition of a burnable poison region in the fuel assembly

  17. Concept and methodology for evaluating core damage frequency considering failure correlation at multi units and sites and its application

    Ebisawa, K.; Teragaki, T.; Nomura, S. [Former Incorporated Administrative Agency, Japan Nuclear Safety Organization (Japan); Abe, H., E-mail: Hiroshi_abe@nsr.go.jp [Former Incorporated Administrative Agency, Japan Nuclear Safety Organization (Japan); Shigemori, M.; Shimomoto, M. [Mizuho Information & Research Institute, 2-3, Kanda-Nishikicho, Chiyoda-ku, Tokyo (Japan)

    2015-07-15

    Highlights: • We develop a method to evaluate CDF considering failure correlation at multi units. • We develop a procedure to evaluate correlation coefficient between multi components. • We evaluate CDF at two different BWR units using correlation coefficients. • We confirm the validity of method and correlation coefficient through the evaluation. - Abstract: The Tohoku earthquake (Mw9.0) occurred on March 11, 2011 and caused a large tsunami. The Fukushima Daiichi Nuclear Power Plant with six units were overwhelmed by the tsunami and core damage occurred. Authors proposed the concept and method for evaluating core damage frequency (CDF) considering failure correlation at the multi units and sites. Based on the above method, one of authors developed the procedure for evaluating the failure correlation coefficient and response correlation coefficient between the multi components under the strong seismic motion. These method and failure correlation coefficients were applied to two different BWR units and their CDF was evaluated by seismic probabilistic risk assessment technology. Through this quantitative evaluation, the validity of the method and failure correlation coefficient was confirmed.

  18. Concept and methodology for evaluating core damage frequency considering failure correlation at multi units and sites and its application

    Ebisawa, K.; Teragaki, T.; Nomura, S.; Abe, H.; Shigemori, M.; Shimomoto, M.

    2015-01-01

    Highlights: • We develop a method to evaluate CDF considering failure correlation at multi units. • We develop a procedure to evaluate correlation coefficient between multi components. • We evaluate CDF at two different BWR units using correlation coefficients. • We confirm the validity of method and correlation coefficient through the evaluation. - Abstract: The Tohoku earthquake (Mw9.0) occurred on March 11, 2011 and caused a large tsunami. The Fukushima Daiichi Nuclear Power Plant with six units were overwhelmed by the tsunami and core damage occurred. Authors proposed the concept and method for evaluating core damage frequency (CDF) considering failure correlation at the multi units and sites. Based on the above method, one of authors developed the procedure for evaluating the failure correlation coefficient and response correlation coefficient between the multi components under the strong seismic motion. These method and failure correlation coefficients were applied to two different BWR units and their CDF was evaluated by seismic probabilistic risk assessment technology. Through this quantitative evaluation, the validity of the method and failure correlation coefficient was confirmed

  19. A novel concept of fault current limiter based on saturable core in high voltage DC transmission system

    Yuan, Jiaxin; Zhou, Hang; Gan, Pengcheng; Zhong, Yongheng; Gao, Yanhui; Muramatsu, Kazuhiro; Du, Zhiye; Chen, Baichao

    2018-05-01

    To develop mechanical circuit breaker in high voltage direct current (HVDC) system, a fault current limiter is required. Traditional method to limit DC fault current is to use superconducting technology or power electronic devices, which is quite difficult to be brought to practical use under high voltage circumstances. In this paper, a novel concept of high voltage DC transmission system fault current limiter (DCSFCL) based on saturable core was proposed. In the DCSFCL, the permanent magnets (PM) are added on both up and down side of the core to generate reverse magnetic flux that offset the magnetic flux generated by DC current and make the DC winding present a variable inductance to the DC system. In normal state, DCSFCL works as a smoothing reactor and its inductance is within the scope of the design requirements. When a fault occurs, the inductance of DCSFCL rises immediately and limits the steepness of the fault current. Magnetic field simulations were carried out, showing that compared with conventional smoothing reactor, DCSFCL can decrease the high steepness of DC fault current by 17% in less than 10ms, which verifies the feasibility and effectiveness of this method.

  20. Functional Genomic Screening Reveals Core Modulators of Echinocandin Stress Responses in Candida albicans

    Tavia Caplan

    2018-05-01

    Full Text Available Summary: Candida albicans is a leading cause of death due to fungal infection. Treatment of systemic candidiasis often relies on echinocandins, which disrupt cell wall synthesis. Resistance is readily acquired via mutations in the drug target gene, FKS1. Both basal tolerance and resistance to echinocandins require cellular stress responses. We performed a systematic analysis of 3,030 C. albicans mutants to define circuitry governing cellular responses to echinocandins. We identified 16 genes for which deletion or transcriptional repression enhanced echinocandin susceptibility, including components of the Pkc1-MAPK signaling cascade. We discovered that the molecular chaperone Hsp90 is required for the stability of Pkc1 and Bck1, establishing key mechanisms through which Hsp90 mediates echinocandin resistance. We also discovered that perturbation of the CCT chaperonin complex causes enhanced echinocandin sensitivity, altered cell wall architecture, and aberrant septin localization. Thus, we provide insights into the mechanisms by which cellular chaperones enable crucial responses to echinocandin-induced stress. : Caplan et al. screen 3,030 Candida albicans mutants to define circuitry governing cellular responses to echinocandins, the first-line therapy for systemic candidiasis. They reveal that the molecular chaperone Hsp90 is required for stability of Pkc1 and Bck1 and that the CCT chaperonin complex is a key modulator of echinocandin susceptibility. Keywords: fungal pathogen, Candida albicans, echinocandins, Hsp90, Pkc1, CCT complex, client protein, stress response, functional genomic screen, drug resistance

  1. Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06

    White Brian

    2010-11-01

    Full Text Available Abstract Background The genus Neisseria contains two important yet very different pathogens, N. meningitidis and N. gonorrhoeae, in addition to non-pathogenic species, of which N. lactamica is the best characterized. Genomic comparisons of these three bacteria will provide insights into the mechanisms and evolution of pathogenesis in this group of organisms, which are applicable to understanding these processes more generally. Results Non-pathogenic N. lactamica exhibits very similar population structure and levels of diversity to the meningococcus, whilst gonococci are essentially recent descendents of a single clone. All three species share a common core gene set estimated to comprise around 1190 CDSs, corresponding to about 60% of the genome. However, some of the nucleotide sequence diversity within this core genome is particular to each group, indicating that cross-species recombination is rare in this shared core gene set. Other than the meningococcal cps region, which encodes the polysaccharide capsule, relatively few members of the large accessory gene pool are exclusive to one species group, and cross-species recombination within this accessory genome is frequent. Conclusion The three Neisseria species groups represent coherent biological and genetic groupings which appear to be maintained by low rates of inter-species horizontal genetic exchange within the core genome. There is extensive evidence for exchange among positively selected genes and the accessory genome and some evidence of hitch-hiking of housekeeping genes with other loci. It is not possible to define a 'pathogenome' for this group of organisms and the disease causing phenotypes are therefore likely to be complex, polygenic, and different among the various disease-associated phenotypes observed.

  2. New concept of composite strengthening in Co-Re based alloys for high temperature applications in gas turbines

    Mukherji, D.; Roesler, J.; Fricke, T.; Schmitz, F. [Technische Univ. Braunschweig (DE). Inst. fuer Werkstoffkunde (IfW); Piegert, S. [Siemens AG, Berlin (DE). Energy Sector (F PR GT EN)

    2010-07-01

    High temperature material development is mainly driven by gas turbine needs. Today, Ni-based superalloys are the dominant material class in the hot section of turbines. Material development will continue to push the maximum service temperature of Ni-superalloys upwards. However, this approach has a fundamental limit and can not be sustained indefinitely, as the Ni-superalloys are already used very close to their melting point. Within the frame work of a DFG Forschergruppe program (FOR 727) - ''Beyond Ni-base Superalloys'' - Co-Re based alloys are being developed as a new generation of high temperature materials that can be used at +100 C above single crystal Ni-superalloys. Along with other strengthening concepts, hardening by second phase is explored to develop a two phase composite alloy. With quaternary Co-Re-Cr-Ni alloys we demonstrate this development concept, where Co{sub 2}Re{sub 3}-type {sigma} phase is used in a novel way as the hardening phase. Thermodynamic calculation was used for designing model alloy compositions. (orig.)

  3. Genomes

    Brown, T. A. (Terence A.)

    2002-01-01

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

  4. Interseasonal movements of greater sage-grouse, migratory behavior, and an assessment of the core regions concept in Wyoming

    Fedy, Bradley C.; Aldridge, Cameron L.; Doherty, Kevin E.; O'Donnell, Michael S.; Beck, Jeffrey L.; Bedrosian, Bryan; Holloran, Matthew J.; Johnson, Gregory D.; Kaczor, Nicholas W.; Kirol, Christopher P.; Mandich, Cheryl A.; Marshall, David; McKee, Gwyn; Olson, Chad; Swanson, Christopher C.; Walker, Brett L.

    2012-01-01

    Animals can require different habitat types throughout their annual cycles. When considering habitat prioritization, we need to explicitly consider habitat requirements throughout the annual cycle, particularly for species of conservation concern. Understanding annual habitat requirements begins with quantifying how far individuals move across landscapes between key life stages to access required habitats. We quantified individual interseasonal movements for greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse) using radio-telemetry spanning the majority of the species distribution in Wyoming. Sage-grouse are currently a candidate for listing under the United States Endangered Species Act and Wyoming is predicted to remain a stronghold for the species. Sage-grouse use distinct seasonal habitats throughout their annual cycle for breeding, brood rearing, and wintering. Average movement distances in Wyoming from nest sites to summer-late brood-rearing locations were 8.1 km (SE = 0.3 km; n = 828 individuals) and the average subsequent distances moved from summer sites to winter locations were 17.3 km (SE = 0.5 km; n = 607 individuals). Average nest-to-winter movements were 14.4 km (SE = 0.6 km; n = 434 individuals). We documented remarkable variation in the extent of movement distances both within and among sites across Wyoming, with some individuals remaining year-round in the same vicinity and others moving over 50 km between life stages. Our results suggest defining any of our populations as migratory or non-migratory is innappropriate as individual strategies vary widely. We compared movement distances of birds marked using Global Positioning System (GPS) and very high frequency (VHF) radio marking techniques and found no evidence that the heavier GPS radios limited movement. Furthermore, we examined the capacity of the sage-grouse core regions concept to capture seasonal locations. As expected, we found the core regions approach, which was

  5. The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions

    Andrea Cipriano

    2018-03-01

    Full Text Available The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as “junk” DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs, which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.

  6. Dual- and triple-acting agents for treating core and co-morbid symptoms of major depression: novel concepts, new drugs.

    Millan, Mark J

    2009-01-01

    The past decade of efforts to find improved treatment for major depression has been dominated by genome-driven programs of rational drug discovery directed toward highly selective ligands for nonmonoaminergic agents. Selective drugs may prove beneficial for specific symptoms, for certain patient subpopulations, or both. However, network analyses of the brain and its dysfunction suggest that agents with multiple and complementary modes of action are more likely to show broad-based efficacy against core and comorbid symptoms of depression. Strategies for improved multitarget exploitation of monoaminergic mechanisms include triple inhibitors of dopamine, serotonin (5-HT) and noradrenaline reuptake, and drugs interfering with feedback actions of monoamines at inhibitory 5-HT(1A), 5-HT(1B) and possibly 5-HT(5A) and 5-HT(7) receptors. Specific subsets of postsynaptic 5-HT receptors mediating antidepressant actions are under study (e.g., 5-HT(4) and 5-HT(6)). Association of a clinically characterized antidepressant mechanism with a nonmonoaminergic component of activity is an attractive strategy. For example, agomelatine (a melatonin agonist/5-HT(2C) antagonist) has clinically proven activity in major depression. Dual neurokinin(1) antagonists/5-HT reuptake inhibitors (SRIs) and melanocortin(4) antagonists/SRIs should display advantages over their selective counterparts, and histamine H(3) antagonists/SRIs, GABA(B) antagonists/SRIs, glutamatergic/SRIs, and cholinergic agents/SRIs may counter the compromised cognitive function of depression. Finally, drugs that suppress 5-HT reuptake and blunt hypothalamo-pituitary-adrenocorticotrophic axis overdrive, or that act at intracellular proteins such as GSK-3beta, may abrogate the negative effects of chronic stress on mood and neuronal integrity. This review discusses the discovery and development of dual- and triple-acting antidepressants, focusing on novel concepts and new drugs disclosed over the last 2 to 3 years.

  7. What can comparative genomics tell us about species concepts in the genus Aspergillus?

    Rokas, Antonis; payne, gary; Federova, Natalie D.; Baker, Scott E.; Machida, Masa; yu, Jiujiang; georgianna, D. R.; Dean, Ralph A.; Bhatnagar, Deepak; Cleveland, T. E.; Wortman, Jennifer R.; Maiti, R.; Joardar, V.; Amedeo, Paolo; Denning, David W.; Nierman, William C.

    2007-12-15

    Understanding the nature of species" boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species.

  8. MO-E-18C-04: Advanced Computer Simulation and Visualization Tools for Enhanced Understanding of Core Medical Physics Concepts

    Naqvi, S

    2014-01-01

    Purpose: Most medical physics programs emphasize proficiency in routine clinical calculations and QA. The formulaic aspect of these calculations and prescriptive nature of measurement protocols obviate the need to frequently apply basic physical principles, which, therefore, gradually decay away from memory. E.g. few students appreciate the role of electron transport in photon dose, making it difficult to understand key concepts such as dose buildup, electronic disequilibrium effects and Bragg-Gray theory. These conceptual deficiencies manifest when the physicist encounters a new system, requiring knowledge beyond routine activities. Methods: Two interactive computer simulation tools are developed to facilitate deeper learning of physical principles. One is a Monte Carlo code written with a strong educational aspect. The code can “label” regions and interactions to highlight specific aspects of the physics, e.g., certain regions can be designated as “starters” or “crossers,” and any interaction type can be turned on and off. Full 3D tracks with specific portions highlighted further enhance the visualization of radiation transport problems. The second code calculates and displays trajectories of a collection electrons under arbitrary space/time dependent Lorentz force using relativistic kinematics. Results: Using the Monte Carlo code, the student can interactively study photon and electron transport through visualization of dose components, particle tracks, and interaction types. The code can, for instance, be used to study kerma-dose relationship, explore electronic disequilibrium near interfaces, or visualize kernels by using interaction forcing. The electromagnetic simulator enables the student to explore accelerating mechanisms and particle optics in devices such as cyclotrons and linacs. Conclusion: The proposed tools are designed to enhance understanding of abstract concepts by highlighting various aspects of the physics. The simulations serve as

  9. MO-E-18C-04: Advanced Computer Simulation and Visualization Tools for Enhanced Understanding of Core Medical Physics Concepts

    Naqvi, S [Saint Agnes Cancer Institute, Department of Radiation Oncology, Baltimore, MD (United States)

    2014-06-15

    Purpose: Most medical physics programs emphasize proficiency in routine clinical calculations and QA. The formulaic aspect of these calculations and prescriptive nature of measurement protocols obviate the need to frequently apply basic physical principles, which, therefore, gradually decay away from memory. E.g. few students appreciate the role of electron transport in photon dose, making it difficult to understand key concepts such as dose buildup, electronic disequilibrium effects and Bragg-Gray theory. These conceptual deficiencies manifest when the physicist encounters a new system, requiring knowledge beyond routine activities. Methods: Two interactive computer simulation tools are developed to facilitate deeper learning of physical principles. One is a Monte Carlo code written with a strong educational aspect. The code can “label” regions and interactions to highlight specific aspects of the physics, e.g., certain regions can be designated as “starters” or “crossers,” and any interaction type can be turned on and off. Full 3D tracks with specific portions highlighted further enhance the visualization of radiation transport problems. The second code calculates and displays trajectories of a collection electrons under arbitrary space/time dependent Lorentz force using relativistic kinematics. Results: Using the Monte Carlo code, the student can interactively study photon and electron transport through visualization of dose components, particle tracks, and interaction types. The code can, for instance, be used to study kerma-dose relationship, explore electronic disequilibrium near interfaces, or visualize kernels by using interaction forcing. The electromagnetic simulator enables the student to explore accelerating mechanisms and particle optics in devices such as cyclotrons and linacs. Conclusion: The proposed tools are designed to enhance understanding of abstract concepts by highlighting various aspects of the physics. The simulations serve as

  10. A New Coupled CFD/Neutron Kinetics System for High Fidelity Simulations of LWR Core Phenomena: Proof of Concept

    Jorge Pérez Mañes

    2014-01-01

    Full Text Available The Institute for Neutron Physics and Reactor Technology (INR at the Karlsruhe Institute of Technology (KIT is investigating the application of the meso- and microscale analysis for the prediction of local safety parameters for light water reactors (LWR. By applying codes like CFD (computational fluid dynamics and SP3 (simplified transport reactor dynamics it is possible to describe the underlying phenomena in a more accurate manner than by the nodal/coarse 1D thermal hydraulic coupled codes. By coupling the transport (SP3 based neutron kinetics (NK code DYN3D with NEPTUNE-CFD, within a parallel MPI-environment, the NHESDYN platform is created. The newly developed system will allow high fidelity simulations of LWR fuel assemblies and cores. In NHESDYN, a heat conduction solver, SYRTHES, is coupled to NEPTUNE-CFD. The driver module of NHESDYN controls the sequence of execution of the solvers as well as the communication between the solvers based on MPI. In this paper, the main features of NHESDYN are discussed and the proof of the concept is done by solving a single pin problem. The prediction capability of NHESDYN is demonstrated by a code-to-code comparison with the DYNSUB code. Finally, the future developments and validation efforts are highlighted.

  11. Phylogeny of Vibrio vulnificus from the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy

    Francisco J. Roig

    2018-01-01

    Full Text Available Vibrio vulnificus (Vv is a multi-host pathogenic species currently subdivided into three biotypes (Bts. The three Bts are human-pathogens, but only Bt2 is also a fish-pathogen, an ability that is conferred by a transferable virulence-plasmid (pVvbt2. Here we present a phylogenomic analysis from the core genome of 80 Vv strains belonging to the three Bts recovered from a wide range of geographical and ecological sources. We have identified five well-supported phylogenetic groups or lineages (L. L1 comprises a mixture of clinical and environmental Bt1 strains, most of them involved in human clinical cases related to raw seafood ingestion. L2 is formed by a mixture of Bt1 and Bt2 strains from various sources, including diseased fish, and is related to the aquaculture industry. L3 is also linked to the aquaculture industry and includes Bt3 strains exclusively, mostly related to wound infections or secondary septicemia after farmed-fish handling. Lastly, L4 and L5 include a few strains of Bt1 associated with specific geographical areas. The phylogenetic trees for ChrI and II are not congruent to one another, which suggests that inter- and/or intra-chromosomal rearrangements have been produced along Vv evolution. Further, the phylogenetic trees for each chromosome and the virulence plasmid were also not congruent, which also suggests that pVvbt2 has been acquired independently by different clones, probably in fish farms. From all these clones, the one with zoonotic capabilities (Bt2-Serovar E has successfully spread worldwide. Based on these results, we propose a new updated classification of the species based on phylogenetic lineages rather than on Bts, as well as the inclusion of all Bt2 strains in a pathovar with the particular ability to cause fish vibriosis, for which we suggest the name “piscis.”

  12. Neutronic studies of the long life core concept: Part 1, Design and performance of 1000 MWe uranium oxide fueled low power density LMR cores

    Orechwa, Y.

    1987-04-01

    The parametric behavior of some key neutronic performance parameters for low power density LMR cores fueled with uranium oxide is investigated. The results are compared to reference homogeneous and heterogeneous cores with normal fuel management and Pu fueling. It can be concluded that with respect to minimizing the initial fissile mass and thereby economizing on the inventory costs and carrying charges, the superior neutron economy of the LMR fuel cycle is best exploited through normal fuel management with Pu recycling. In the once-through mode the LMR fuel cycle has disadvantages due to a higher fissile inventory and is not competitive with the LWR fuel cycle

  13. Concept and basic performance of an in-pile experimental reactor for fast breeder reactors using fast driver core

    Obara, Toru; Sekimoto, Hiroshi

    1997-01-01

    The possibility of an in-pile experimental reactor for fast breeder reactors using a fast driver core is investigated. The driver core is composed of a particle bed with diluted fuel. The results of various basic analyses show that this reactor could perform as follows: (1) power peaking at the outer boundary of test core does not take place for large test core; (2) the radial power distribution in test fuel pin is expected to be the same as a real reactor; (3) the experiments with short half width pulse is possible; (4) for the ordinary MOX core, enough heating-up is possible for core damage experiments; (5) the positive effects after power burst can be seen directly. These are difficult for conventional thermal in-pile experimental reactors in large power excursion experiments. They are very attractive advantages in the in-pile experiments for fast breeder reactors. (author)

  14. Protein sequence annotation in the genome era: the annotation concept of SWISS-PROT+TREMBL.

    Apweiler, R; Gateau, A; Contrino, S; Martin, M J; Junker, V; O'Donovan, C; Lang, F; Mitaritonna, N; Kappus, S; Bairoch, A

    1997-01-01

    SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation, a minimal level of redundancy and high level of integration with other databases. Ongoing genome sequencing projects have dramatically increased the number of protein sequences to be incorporated into SWISS-PROT. Since we do not want to dilute the quality standards of SWISS-PROT by incorporating sequences without proper sequence analysis and annotation, we cannot speed up the incorporation of new incoming data indefinitely. However, as we also want to make the sequences available as fast as possible, we introduced TREMBL (TRanslation of EMBL nucleotide sequence database), a supplement to SWISS-PROT. TREMBL consists of computer-annotated entries in SWISS-PROT format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except for CDS already included in SWISS-PROT. While TREMBL is already of immense value, its computer-generated annotation does not match the quality of SWISS-PROTs. The main difference is in the protein functional information attached to sequences. With this in mind, we are dedicating substantial effort to develop and apply computer methods to enhance the functional information attached to TREMBL entries.

  15. New conception in the theory of chemical bonding; the role of core and valence atomic orbitals in formation of chemical bonds

    Kostikova, G.P.; Kostikov, Yu.P.; Korol'kov, D.V.

    1986-01-01

    An analysis of x-ray photoelectron spectra leads to a simple and consistent conception in the theory of chemical bonding, which satisfies (unlike the simple MO-LCAO theory) the virial theorem and defines the roles of the core and valence atomic orbitals in the formation of chemical bonds. Its essence is clear from the foregoing: the exothermic effects of the formation of complexes are caused by the lowering of the energies of the core levels of the central atoms with simultaneous small changes in the energies of the core levels of the ligands despite the significant destabilization of the delocalized valence MO's in comparison to the orbital energies of the corresponding free atoms. In order to confirm these ideas, they recorded the x-ray photoelectron spectra of the valence region and the inner levels of single-crystal silicon carbide, silicon, and graphite

  16. Genetic diversity and structure of core collection of winter mushroom (Flammulina velutipes) developed by genomic SSR markers.

    Liu, Xiao Bin; Li, Jing; Yang, Zhu L

    2018-01-01

    A core collection is a subset of an entire collection that represents as much of the genetic diversity of the entire collection as possible. The establishment of a core collection for crops is practical for efficient management and use of germplasm. However, the establishment of a core collection of mushrooms is still in its infancy, and no established core collection of the economically important species Flammulina velutipes has been reported. We established the first core collection of F. velutipes , containing 32 strains based on 81 genetically different F. veltuipes strains. The allele retention proportion of the core collection for the entire collection was 100%. Moreover, the genetic diversity parameters (the effective number of alleles, Nei's expected heterozygosity, the number of observed heterozygosity, and Shannon's information index) of the core collection showed no significant differences from the entire collection ( p  > 0.01). Thus, the core collection is representative of the genetic diversity of the entire collection. Genetic structure analyses of the core collection revealed that the 32 strains could be clustered into 6 groups, among which groups 1 to 3 were cultivars and groups 4 to 6 were wild strains. The wild strains from different locations harbor their own specific alleles, and were clustered stringently in accordance with their geographic origins. Genetic diversity analyses of the core collection revealed that the wild strains possessed greater genetic diversity than the cultivars. We established the first core collection of F. velutipes in China, which is an important platform for efficient breeding of this mushroom in the future. In addition, the wild strains in the core collection possess favorable agronomic characters and produce unique bioactive compounds, adding value to the platform. More attention should be paid to wild strains in further strain breeding.

  17. Reactor core fuel management

    Silvennoinen, P.

    1976-01-01

    The subject is covered in chapters, entitled: concepts of reactor physics; neutron diffusion; core heat transfer; reactivity; reactor operation; variables of core management; computer code modules; alternative reactor concepts; methods of optimization; general system aspects. (U.K.)

  18. Asymmetric Modification of Hepatitis B Virus (HBV) Genomes by an Endogenous Cytidine Deaminase inside HBV Cores Informs a Model of Reverse Transcription.

    Nair, Smita; Zlotnick, Adam

    2018-05-15

    Cytidine deaminases inhibit replication of a broad range of DNA viruses by deaminating cytidines on single-stranded DNA (ssDNA) to generate uracil. While several lines of evidence have revealed hepatitis B virus (HBV) genome editing by deamination, it is still unclear which nucleic acid intermediate of HBV is modified. Hepatitis B virus has a relaxed circular double-stranded DNA (rcDNA) genome that is reverse transcribed within virus cores from a RNA template. The HBV genome also persists as covalently closed circular DNA (cccDNA) in the nucleus of an infected cell. In the present study, we found that in HBV-producing HepAD38 and HepG2.2.15 cell lines, endogenous cytidine deaminases edited 10 to 25% of HBV rcDNA genomes, asymmetrically with almost all mutations on the 5' half of the minus strand. This region corresponds to the last half of the minus strand to be protected by plus-strand synthesis. Within this half of the genome, the number of mutations peaks in the middle. Overexpressed APOBEC3A and APOBEC3G could be packaged in HBV capsids but did not change the amount or distribution of mutations. We found no deamination on pregenomic RNA (pgRNA), indicating that an intact genome is encapsidated and deaminated during or after reverse transcription. The deamination pattern suggests a model of rcDNA synthesis in which pgRNA and then newly synthesized minus-sense single-stranded DNA are protected from deaminase by interaction with the virus capsid; during plus-strand synthesis, when enough dsDNA has been synthesized to displace the remaining minus strand from the capsid surface, the single-stranded DNA becomes deaminase sensitive. IMPORTANCE Host-induced mutation of the HBV genome by APOBEC proteins may be a path to clearing the virus. We examined cytidine-to-thymidine mutations in the genomes of HBV particles grown in the presence or absence of overexpressed APOBEC proteins. We found that genomes were subjected to deamination activity during reverse transcription

  19. Performance Evaluation of the Concept of Hybrid Heat Pipe as Passive In-core Cooling Systems for Advanced Nuclear Power Plant

    Jeong, Yeong Shin; Kim, Kyung Mo; Kim, In Guk; Bang, In Cheol

    2015-01-01

    As an arising issue for inherent safety of nuclear power plant, the concept of hybrid heat pipe as passive in-core cooling systems was introduced. Hybrid heat pipe has unique features that it is inserted in core directly to remove decay heat from nuclear fuel without any changes of structures of existing facilities of nuclear power plant, substituting conventional control rod. Hybrid heat pipe consists of metal cladding, working fluid, wick structure, and neutron absorber. Same with working principle of the heat pipe, heat is transported by phase change of working fluid inside metal cask. Figure 1 shows the systematic design of the hybrid heat pipe cooling system. In this study, the concept of a hybrid heat pipe was introduced as a Passive IN-core Cooling Systems (PINCs) and demonstrated for internal design features of heat pipe containing neutron absorber. Using a commercial CFD code, single hybrid heat pipe model was analyzed to evaluate thermal performance in designated operating condition. Also, 1-dimensional reactor transient analysis was done by calculating temperature change of the coolant inside reactor pressure vessel using MATLAB. As a passive decay heat removal device, hybrid heat pipe was suggested with a concept of combination of heat pipe and control rod. Hybrid heat pipe has distinct feature that it can be a unique solution to cool the reactor when depressurization process is impossible so that refueling water cannot be injected into RPV by conventional ECCS. It contains neutron absorber material inside heat pipe, so it can stop the reactor and at the same time, remove decay heat in core. For evaluating the concept of hybrid heat pipe, its thermal performance was analyzed using CFD and one-dimensional transient analysis. From single hybrid heat pipe simulation, the hybrid heat pipe can transport heat from the core inside to outside about 18.20 kW, and total thermal resistance of hybrid heat pipe is 0.015 .deg. C/W. Due to unique features of long heat

  20. A core concept for the self-consistent nuclear energy system based on the promising future technology

    Arie, K.; Suzuki, M.; Kawashima, M.; Igashira, M.; Shimizu, A.; Fujii-e, Y.

    1995-01-01

    Feasibility of FP burning while maintaining fuel breeding capability for the Self-Consistent Nuclear Energy System is evaluated through neutron balance and a fast reactor core. It is shown that all radioactive FPs produced by itself can be burnt by a fast reactor while maintaining breeding capability, assuming separation of radioactive FP and stable FP isotopes. Assuming that the recovery system of fuel and FPs to be burnt is based on a pyro-chemical process, the major long-lived FPs of I, Pd, Tc, Sn, Se can be burnt with keeping breeding capability by suitability arranging materials in the fast reactor core. (Author)

  1. COMET concept

    Alsmeyer, H.; Tromm, W.

    1995-01-01

    Studies of the COMET core catcher concept developed for a future PWR have been continued. The concept is based on the spreading of a core melt on a sacrificial layer and its erosion, until a subsequent addition of water from below causes a fragmentation of the melt. A porous solidification of the melt would then admit a complete flooding within a short period. (orig.)

  2. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species.

    Dettori, Maria Teresa; Micali, Sabrina; Giovinazzi, Jessica; Scalabrin, Simone; Verde, Ignazio; Cipriani, Guido

    2015-01-01

    A wide inventory of molecular markers is nowadays available for individual fingerprinting. Microsatellites, or simple sequence repeats (SSRs), play a relevant role due to their relatively ease of use, their abundance in the plant genomes, and their co-dominant nature, together with the availability of primer sequences in many important agricultural crops. Microsatellites with long-core motifs are more easily scored and were adopted long ago in human genetics but they were developed only in few crops, and Prunus species are not among them. In the present work the peach whole-genome sequence was used to select 216 SSRs containing long-core motifs with tri-, tetra- and penta-nucleotide repeats. Microsatellite primer pairs were designed and tested for polymorphism in the five diploid Prunus species of economic relevance (almond, apricot, Japanese plum, peach and sweet cherry). A set of 26 microsatellite markers covering all the eight chromosomes, was also selected and used in the molecular characterization, population genetics and structure analyses of a representative sample of the five diploid Prunus species, assessing their transportability and effectiveness. The combined probability of identity between two random individuals for the whole set of 26 SSRs was quite low, ranging from 2.30 × 10(-7) in peach to 9.48 × 10(-10) in almond, confirming the usefulness of the proposed set for fingerprinting analyses in Prunus species.

  3. Representational coexistence in the God concept: Core knowledge intuitions of God as a person are not revised by Christian theology despite lifelong experience.

    Barlev, Michael; Mermelstein, Spencer; German, Tamsin C

    2018-01-25

    Previous research has shown that in the minds of young adult religious adherents, acquired theology about the extraordinary characteristics of God (e.g., omniscience) coexists with, rather than replaces, an initial concept of God formed by co-option of the person concept. We tested the hypothesis that representational coexistence holds even after extensive experience with Christian theology, as indexed by age. Christian religious adherents ranging in age from 18 to 87 years were asked to evaluate as true or false statements on which core knowledge intuitions about persons and Christian theology about God were consistent (both true or both false) or inconsistent (true on one and false on the other). Results showed, across adulthood, more theological errors in evaluating inconsistent versus consistent statements. Older adults also exhibited slower response times to inconsistent versus consistent statements. These findings show that despite extensive experience, indeed a lifetime of experience for some participants, the Christian theological God concept does not separate from the initial person concept from which it is formed. In fact, behavioral signatures of representational coexistence were not attenuated by experience. We discuss the broader implications of these findings to the acquisition of evolutionarily new concepts.

  4. An Advanced Sodium-Cooled Fast Reactor Core Concept Using Uranium-Free Metallic Fuels for Maximizing TRU Burning Rate

    Wuseong You

    2017-12-01

    Full Text Available In this paper, we designed and analyzed advanced sodium-cooled fast reactor cores using uranium-free metallic fuels for maximizing burning rate of transuranics (TRU nuclides from PWR spent fuels. It is well known that the removal of fertile nuclides such as 238U from fuels in liquid metal cooled fast reactor leads to the degradation of important safety parameters such as the Doppler coefficient, coolant void worth, and delayed neutron fraction. To resolve the degradation of the Doppler coefficient, we considered adding resonant nuclides to the uranium-free metallic fuels. The analysis results showed that the cores using uranium-free fuels loaded with tungsten instead of uranium have a significantly lower burnup reactivity swing and more negative Doppler coefficients than the core using uranium-free fuels without resonant nuclides. In addition, we considered the use of axially central B4C absorber region and moderator rods to further improve safety parameters such as sodium void worth, burnup reactivity swing, and the Doppler coefficient. The results of the analysis showed that the final design core can consume ~353 kg per cycle and satisfies self-controllability under unprotected accidents. The fuel cycle analysis showed that the PWR–SFR coupling fuel cycle option drastically reduces the amount of waste going to repository and the SFR burner can consume the amount of TRUs discharged from 3.72 PWRs generating the same electricity.

  5. Preservice Secondary Teachers' Conceptions from a Mathematical Modeling Activity and Connections to the Common Core State Standards

    Stohlmann, Micah; Maiorca, Cathrine; Olson, Travis A.

    2015-01-01

    Mathematical modeling is an essential integrated piece of the Common Core State Standards. However, researchers have shown that mathematical modeling activities can be difficult for teachers to implement. Teachers are more likely to implement mathematical modeling activities if they have their own successful experiences with such activities. This…

  6. Applying Mass Customization Concepts to Core Courses: Increasing Student-Centered Customization and Enabling Cross-Functional Integration

    Wilson, Darryl D.

    2011-01-01

    This conceptual paper suggests a methodology for increasing student satisfaction in core courses by applying the principle of mass customization to increase student satisfaction. It proposes that customization can be increased by increasing course flexibility along three dimensions: content flexibility, schedule flexibility, and course length…

  7. Concept Design of a Gravity Core Cooling Tank as a Passive Residual Heat Removal System for a Research Reactor

    Lee, Kwonyeong; Chi, Daeyoung; Kim, Seong Hoon; Seo, Kyoungwoo; Yoon, Juhyeon

    2014-01-01

    A core downward flow is considered to use a plate type fuel because it is benefit to install the fuel in the core. If a flow inversion from a downward to upward flow in the core by a natural circulation is introduced within a high heat flux region of residual heat, the fuel fails instantly due to zero flow. Therefore, the core downward flow should be sufficiently maintained until the residual heat is in a low heat flux region. In a small power research reactor, inertia generated by a flywheel of the PCP can maintain a downward flow shortly and resolve the problem of a flow inversion. However, a high power research reactor more than 10 MW should have an additional method to have a longer downward flow until a low heat flux. Usually, other research reactors have selected an active residual heat removal system as a safety class. But, an active safety system is difficult to design and expensive to construct. A Gravity Core Cooling Tank (GCCT) beside the reactor pool with a Residual Heat Removal Pipe connecting two pools was developed and designed preliminarily as a passive residual heat removal system for an open-pool type research reactor. It is very simple to design and cheap to construct. Additionally, a non-safety, but active residual heat removal system is applied with the GCCT. It is a Pool Water Cooling and Purification System. It can improve the usability of the research reactor by removing the thermal waves, and purify the reactor pool, the Primary Cooling System, and the GCCT. Moreover, it can reduce the pool top radiation level

  8. An exploration of the extent of inclusion of spirituality and spiritual care concepts in core nursing textbooks.

    Timmins, Fiona

    2015-01-01

    Holistic care that encompasses a spiritual dimension is an expectation in modern healthcare (Rothman, 2009). Increasing attention is being paid to the role of nurses in providing spiritual care to patients. However nurses lack specific skills and expertise in this area (Lundmark, 2006; Timmins, 2010; RCN, 2011), and the extent to which their undergraduate education prepares them for this role is unclear. There is often an absence of clear direction about what to teach undergraduate nursing students. The extent to which core textbooks direct student studies in this area is not known. There is some evidence that some of these fundamental core textbooks provide insufficient direction (Pesut, 2008), thus gaps in knowledge and care provision in this field could be exacerbated.

  9. Ex-vessel boiling experiments: laboratory- and reactor-scale testing of the flooded cavity concept for in-vessel core retention. Pt. II. Reactor-scale boiling experiments of the flooded cavity concept for in-vessel core retention

    Chu, T.Y.; Bentz, J.H.; Slezak, S.E.; Pasedag, W.F.

    1997-01-01

    For pt.I see ibid., p.77-88 (1997). This paper summarizes the results of a reactor-scale ex-vessel boiling experiment for assessing the flooded cavity design of the heavy water new production reactor. The simulated reactor vessel has a cylindrical diameter of 3.7 m and a torispherical bottom head. Boiling outside the reactor vessel was found to be subcooled nucleate boiling. The subcooling mainly results from the gravity head, which in turn results from flooding the side of the reactor vessel. The boiling process exhibits a cyclic pattern with four distinct phases: direct liquid-solid contact, bubble nucleation and growth, coalescence, and vapor mass dispersion. The results show that, under prototypic heat load and heat flux distributions, the flooded cavity will be effective for in-vessel core retention in the heavy water new production reactor. The results also demonstrate that the heat dissipation requirement for in-vessel core retention, for the central region of the lower head of an AP-600 advanced light water reactor, can be met with the flooded cavity design. (orig.)

  10. Co-diversification of Enterococcus faecium core genomes and PBP5: evidences of pbp5 horizontal transfer

    Carla Novais

    2016-10-01

    Full Text Available Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18 and ST78 in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180-280 kb chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E. faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen.

  11. Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing.

    Woksepp, Hanna; Ryberg, Anna; Berglind, Linda; Schön, Thomas; Söderman, Jan

    2017-12-01

    Enhanced precision of epidemiological typing in clinically suspected nosocomial outbreaks is crucial. Our aim was to investigate whether single nucleotide polymorphism (SNP) analysis and core genome (cg) multilocus sequence typing (MLST) of whole genome sequencing (WGS) data would more reliably identify a nosocomial outbreak, compared to earlier molecular typing methods. Sixteen isolates from a nosocomial outbreak of ESBL E. coli ST-131 in southeastern Sweden and three control strains were subjected to WGS. Sequences were explored by SNP analysis and cgMLST. cgMLST clearly differentiated between the outbreak isolates and the control isolates (>1400 differences). All clinically identified outbreak isolates showed close clustering (≥2 allele differences), except for two isolates (>50 allele differences). These data confirmed that the isolates with >50 differing genes did not belong to the nosocomial outbreak. The number of SNPs within the outbreak was ≤7, whereas the two discrepant isolates had >700 SNPs. Two of the ESBL E. coli ST-131 isolates did not belong to the clinically identified outbreak. Our results illustrate the power of WGS in terms of resolution, which may avoid overestimation of patients belonging to outbreaks as judged from epidemiological data and previously employed molecular methods with lower discriminatory ability. © 2017 APMIS. Published by John Wiley & Sons Ltd.

  12. A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group.

    Singh, Reema; Schilde, Christina; Schaap, Pauline

    2016-11-17

    Dictyostelia are a well-studied group of organisms with colonial multicellularity, which are members of the mostly unicellular Amoebozoa. A phylogeny based on SSU rDNA data subdivided all Dictyostelia into four major groups, but left the position of the root and of six group-intermediate taxa unresolved. Recent phylogenies inferred from 30 or 213 proteins from sequenced genomes, positioned the root between two branches, each containing two major groups, but lacked data to position the group-intermediate taxa. Since the positions of these early diverging taxa are crucial for understanding the evolution of phenotypic complexity in Dictyostelia, we sequenced six representative genomes of early diverging taxa. We retrieved orthologs of 47 housekeeping proteins with an average size of 890 amino acids from six newly sequenced and eight published genomes of Dictyostelia and unicellular Amoebozoa and inferred phylogenies from single and concatenated protein sequence alignments. Concatenated alignments of all 47 proteins, and four out of five subsets of nine concatenated proteins all produced the same consensus phylogeny with 100% statistical support. Trees inferred from just two out of the 47 proteins, individually reproduced the consensus phylogeny, highlighting that single gene phylogenies will rarely reflect correct species relationships. However, sets of two or three concatenated proteins again reproduced the consensus phylogeny, indicating that a small selection of genes suffices for low cost classification of as yet unincorporated or newly discovered dictyostelid and amoebozoan taxa by gene amplification. The multi-locus consensus phylogeny shows that groups 1 and 2 are sister clades in branch I, with the group-intermediate taxon D. polycarpum positioned as outgroup to group 2. Branch II consists of groups 3 and 4, with the group-intermediate taxon Polysphondylium violaceum positioned as sister to group 4, and the group-intermediate taxon Dictyostelium polycephalum

  13. Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer.

    McInnes, Tyler; Zou, Donghui; Rao, Dasari S; Munro, Francesca M; Phillips, Vicky L; McCall, John L; Black, Michael A; Reeve, Anthony E; Guilford, Parry J

    2017-03-28

    Aberrant DNA methylation profiles are a characteristic of all known cancer types, epitomized by the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). Hypermethylation has been observed at CpG islands throughout the genome, but it is unclear which factors determine whether an individual island becomes methylated in cancer. DNA methylation in CRC was analysed using the Illumina HumanMethylation450K array. Differentially methylated loci were identified using Significance Analysis of Microarrays (SAM) and the Wilcoxon Signed Rank (WSR) test. Unsupervised hierarchical clustering was used to identify methylation subtypes in CRC. In this study we characterized the DNA methylation profiles of 94 CRC tissues and their matched normal counterparts. Consistent with previous studies, unsupervized hierarchical clustering of genome-wide methylation data identified three subtypes within the tumour samples, designated CIMP-H, CIMP-L and CIMP-N, that showed high, low and very low methylation levels, respectively. Differential methylation between normal and tumour samples was analysed at the individual CpG level, and at the gene level. The distribution of hypermethylation in CIMP-N tumours showed high inter-tumour variability and appeared to be highly stochastic in nature, whereas CIMP-H tumours exhibited consistent hypermethylation at a subset of genes, in addition to a highly variable background of hypermethylated genes. EYA4, TFPI2 and TLX1 were hypermethylated in more than 90% of all tumours examined. One-hundred thirty-two genes were hypermethylated in 100% of CIMP-H tumours studied and these were highly enriched for functions relating to skeletal system development (Bonferroni adjusted p value =2.88E-15), segment specification (adjusted p value =9.62E-11), embryonic development (adjusted p value =1.52E-04), mesoderm development (adjusted p value =1.14E-20), and ectoderm development (adjusted p value =7.94E-16). Our genome-wide characterization of DNA

  14. Interim report on core physics and fuel cycle analysis of the pebble bed reactor power plant concept

    Vondy, D.R.

    1977-12-01

    Calculations were made to predict the performance of a pebble bed reactor operated in a mode to produce fissile fuel (high conversion or breeding). Both a one pebble design and a design involving large primary feed pebbles and small fertile pebbles were considered. A relatively short residence time of the primary pebbles loaded with 233 U fuel was found to be necessary to achieve a high breeding ratio, but this leads to relatively high fuel costs. A high fissile inventory is associated with a low C/Th ratio and a high thorium loading, causing the doubling time to be long, even though the breeding ratio is high, and the fuel cost of electrical product to be high. Production of 233 U fuel from 235 U feed was studied and performances of the converter and breeder reactor concepts were examined varying the key parameters

  15. Primer in Genetics and Genomics, Article 5-Further Defining the Concepts of Genotype and Phenotype and Exploring Genotype-Phenotype Associations.

    Wright, Fay; Fessele, Kristen

    2017-10-01

    As nurses begin to incorporate genetic and genomic sciences into clinical practice, education, and research, it is essential that they have a working knowledge of the terms foundational to the science. The first article in this primer series provided brief definitions of the basic terms (e.g., genetics and genomics) and introduced the concept of phenotype during the discussion of Mendelian inheritance. These terms, however, are inconsistently used in publications and conversations, and the linkage between genotype and phenotype requires clarification. The goal of this fifth article in the series is to elucidate these terms, provide an overview of the research methods used to determine genotype-phenotype associations, and discuss their significance to nursing through examples from the current nursing literature.

  16. Validation of a Computational Model for the SLS Core Stage Oxygen Tank Diffuser Concept and the Low Profile Diffuser - An Advanced Development Design for the SLS

    Brodnick, Jacob; Richardson, Brian; Ramachandran, Narayanan

    2015-01-01

    The Low Profile Diffuser (LPD) project originated as an award from the Marshall Space Flight Center (MSFC) Advanced Development (ADO) office to the Main Propulsion Systems Branch (ER22). The task was created to develop and test an LPD concept that could produce comparable performance to a larger, traditionally designed, ullage gas diffuser while occupying a smaller volume envelope. Historically, ullage gas diffusers have been large, bulky devices that occupy a significant portion of the propellant tank, decreasing the tank volume available for propellant. Ullage pressurization of spacecraft propellant tanks is required to prevent boil-off of cryogenic propellants and to provide a positive pressure for propellant extraction. To achieve this, ullage gas diffusers must slow hot, high-pressure gas entering a propellant tank from supersonic speeds to only a few meters per second. Decreasing the incoming gas velocity is typically accomplished through expansion to larger areas within the diffuser which has traditionally led to large diffuser lengths. The Fluid Dynamics Branch (ER42) developed and applied advanced Computational Fluid Dynamics (CFD) analysis methods in order to mature the LPD design from and initial concept to an optimized test prototype and to provide extremely accurate pre-test predictions of diffuser performance. Additionally, the diffuser concept for the Core Stage of the Space Launch System (SLS) was analyzed in a short amount of time to guide test data collection efforts of the qualification of the device. CFD analysis of the SLS diffuser design provided new insights into the functioning of the device and was qualitatively validated against hot wire anemometry of the exterior flow field. Rigorous data analysis of the measurements was performed on static and dynamic pressure data, data from two microphones, accelerometers and hot wire anemometry with automated traverse. Feasibility of the LPD concept and validation of the computational model were

  17. Genome-Wide Temporal Expression Profiling in Caenorhabditis elegans Identifies a Core Gene Set Related to Long-Term Memory.

    Freytag, Virginie; Probst, Sabine; Hadziselimovic, Nils; Boglari, Csaba; Hauser, Yannick; Peter, Fabian; Gabor Fenyves, Bank; Milnik, Annette; Demougin, Philippe; Vukojevic, Vanja; de Quervain, Dominique J-F; Papassotiropoulos, Andreas; Stetak, Attila

    2017-07-12

    The identification of genes related to encoding, storage, and retrieval of memories is a major interest in neuroscience. In the current study, we analyzed the temporal gene expression changes in a neuronal mRNA pool during an olfactory long-term associative memory (LTAM) in Caenorhabditis elegans hermaphrodites. Here, we identified a core set of 712 (538 upregulated and 174 downregulated) genes that follows three distinct temporal peaks demonstrating multiple gene regulation waves in LTAM. Compared with the previously published positive LTAM gene set (Lakhina et al., 2015), 50% of the identified upregulated genes here overlap with the previous dataset, possibly representing stimulus-independent memory-related genes. On the other hand, the remaining genes were not previously identified in positive associative memory and may specifically regulate aversive LTAM. Our results suggest a multistep gene activation process during the formation and retrieval of long-term memory and define general memory-implicated genes as well as conditioning-type-dependent gene sets. SIGNIFICANCE STATEMENT The identification of genes regulating different steps of memory is of major interest in neuroscience. Identification of common memory genes across different learning paradigms and the temporal activation of the genes are poorly studied. Here, we investigated the temporal aspects of Caenorhabditis elegans gene expression changes using aversive olfactory associative long-term memory (LTAM) and identified three major gene activation waves. Like in previous studies, aversive LTAM is also CREB dependent, and CREB activity is necessary immediately after training. Finally, we define a list of memory paradigm-independent core gene sets as well as conditioning-dependent genes. Copyright © 2017 the authors 0270-6474/17/376661-12$15.00/0.

  18. Development of high nickel austenitic steels for the application to fast reactor cores, (I). Alloy design with the aid of the d-electrons concept

    Murata, Yoshinori; Morinaga, Masahiko; Yukawa, Natsuo; Ukai, Shigeharu; Nomura, Shigeo; Okuda, Takanari; Harada, Makoto

    1999-01-01

    The design of high nickel austenitic steels for the core materials of the fast reactors was performed following the d-electrons concept devised on the basis of molecular orbital calculations of transition-metal based alloys. In this design two calculated parameters are mainly utilized. The one is the d-orbital energy level (Md) of alloying transition elements, and the other is the bond order (Bo) that is a measure of the covalent bond strength between atoms. Using the Md-bar - Bo-bar phase stability diagram accurate prediction become possible for the phase stability of the austenite phase and 5% swelling at 140 dpa for nickel ions. Here, Md-bar and Bo-bar are the compositional average of Md and Bo parameters, respectively. On the basis of the phase stability diagram and preliminary experiments, guidelines for the alloy design of carbo-nitrides precipitated high nickel austenitic steels were constructed. Following the guidelines several new austenitic steels were designed for the fast reactors core material. (author)

  19. A small long-cycle PWR core design concept using fully ceramic micro-encapsulated (FCM) and UO2–ThO2 fuels for burning of TRU

    Bae, Gonghoon; Hong, Ser Gi

    2015-01-01

    In this paper, a new small pressurized water reactor (PWR) core design concept using fully ceramic micro-encapsulated (FCM) particle fuels and UO 2 –ThO 2 fuels was studied for effective burning of transuranics from a view point of core neutronics. The core of this concept rate is 100 MWe. The core designs use the current PWR-proven technologies except for a mixed use of the FCM and UO 2 –ThO 2 fuel pins of low-enriched uranium. The significant burning of TRU is achieved with tri-isotropic particle fuels of FCM fuel pins, and the ThO 2 –UO 2 fuel pins are employed to achieve long-cycle length of ∼4 EFPYs (effective full-power year). Also, the effects of several candidate materials for reflector are analyzed in terms of core neutronics because the small core size leads to high sensitivity of reflector material on the cycle length. The final cores having 10 w/o SS303 and 90 w/o graphite reflector are shown to have high TRU burning rates of 33%–35% in FCM pins and significant net burning rates of 24%–25% in the total core with negative reactivity coefficients, low power peaking factors, and sufficient shutdown margins of control rods. (author)

  20. Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

    Li, Yun R.; van Setten, Jessica; Verma, Shefali S.

    2015-01-01

    genome-wide genotyping array, the 'TxArray', comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples...

  1. Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing.

    Kyung-Hwa Park

    Full Text Available Staphylococcus aureus is a leading cause of bacteremia in hospitalized patients. Whether or not S. aureus bacteremia (SAB is associated with clonality, implicating potential nosocomial transmission, has not, however, been investigated. Herein, we examined the epidemiology of SAB using whole genome sequencing (WGS. 152 SAB isolates collected over the course of 2015 at a single large Minnesota medical center were studied. Staphylococcus protein A (spa typing was performed by PCR/Sanger sequencing; multilocus sequence typing (MLST and core genome MLST (cgMLST were determined by WGS. Forty-eight isolates (32% were methicillin-resistant S. aureus (MRSA. The isolates encompassed 66 spa types, clustered into 11 spa clonal complexes (CCs and 10 singleton types. 88% of 48 MRSA isolates belonged to spa CC-002 or -008. Methicillin-susceptible S. aureus (MSSA isolates were more genotypically diverse, with 61% distributed across four spa CCs (CC-002, CC-012, CC-008 and CC-084. By MLST, there was 31 sequence types (STs, including 18 divided into 6 CCs and 13 singleton STs. Amongst MSSA isolates, the common MLST clones were CC5 (23%, CC30 (19%, CC8 (15% and CC15 (11%. Common MRSA clones were CC5 (67% and CC8 (25%; there were no MRSA isolates in CC45 or CC30. By cgMLST analysis, there were 9 allelic differences between two isolates, with the remaining 150 isolates differing from each other by over 40 alleles. The two isolates were retroactively epidemiologically linked by medical record review. Overall, cgMLST analysis resulted in higher resolution epidemiological typing than did multilocus sequence or spa typing.

  2. Genomics-based plant germplasm research (GPGR)

    Jizeng Jia; Hongjie Li; Xueyong Zhang; Zichao Li; Lijuan Qiu

    2017-01-01

    Plant germplasm underpins much of crop genetic improvement. Millions of germplasm accessions have been collected and conserved ex situ and/or in situ, and the major challenge is now how to exploit and utilize this abundant resource. Genomics-based plant germplasm research (GPGR) or "Genoplasmics" is a novel cross-disciplinary research field that seeks to apply the principles and techniques of genomics to germplasm research. We describe in this paper the concept, strategy, and approach behind GPGR, and summarize current progress in the areas of the definition and construction of core collections, enhancement of germplasm with core collections, and gene discovery from core collections. GPGR is opening a new era in germplasm research. The contribution, progress and achievements of GPGR in the future are predicted.

  3. Core Concepts of Corporate Finance

    drs. Ewoud Jansen

    2016-01-01

    Most Corporate Finance textbooks are 1,000 pages in length or more. And indeed, it is a multifaceted discipline that requires detailed coverage of many ideas and principles. However, the basics can be outlined in a much more condensed manner and there aren’t many books out there that cater to the

  4. Concept of the core for a small-to-medium-sized BWR that does not use control rods during normal operation

    Nakadozono, N.; Ikegawa, T., E-mail: naoyuki.nakadozono.st@hitachi.com [Hitachi Ltd., Hitachi Research Lab., Ibaraki (Japan); Nishida, K. [Hitachi Works, Hitachi-GE Nuclear Energy Ltd., Hitachi-shi, Ibaraki (Japan)

    2013-07-01

    A small-to-medium-sized boiling water reactor (BWR) with a natural circulation system is being developed for countries where initial investment funds for construction are limited and electricity transmission networks have not been fully constructed. To lighten operators' work load, a core that does not use control rods during normal operation (control rod-free core) was developed by using a neutronics calculation system coupled with core flow evaluation. The control rod-free core had large core power fluctuation with conventional burnable poison design. The target of core power fluctuation was set to less than 10% and was achieved by optimization of burnable poison arrangement. (author)

  5. Concept of the core for a small-to-medium-sized BWR that does not use control rods during normal operation

    Nakadozono, N.; Ikegawa, T.; Nishida, K.

    2013-01-01

    A small-to-medium-sized boiling water reactor (BWR) with a natural circulation system is being developed for countries where initial investment funds for construction are limited and electricity transmission networks have not been fully constructed. To lighten operators' work load, a core that does not use control rods during normal operation (control rod-free core) was developed by using a neutronics calculation system coupled with core flow evaluation. The control rod-free core had large core power fluctuation with conventional burnable poison design. The target of core power fluctuation was set to less than 10% and was achieved by optimization of burnable poison arrangement. (author)

  6. Evolving Ethical Concepts

    Potter, Van Rensselaer

    1977-01-01

    Discusses the role of the scientist in changing ethical concepts from simple interpersonal and theological imperatives towards "survival imperatives that must form the core of environmental bioethics." (CS)

  7. Feasibility of using tissue microarray cores of paraffin-embedded breast cancer tissue for measurement of gene expression: a proof-of-concept study.

    Drury, Suzanne; Salter, Janine; Baehner, Frederick L; Shak, Steven; Dowsett, Mitch

    2010-06-01

    To determine whether 0.6 mm cores of formalin-fixed paraffin-embedded (FFPE) tissue, as commonly used to construct immunohistochemical tissue microarrays, may be a valid alternative to tissue sections as source material for quantitative real-time PCR-based transcriptional profiling of breast cancer. Four matched 0.6 mm cores of invasive breast tumour and two 10 microm whole sections were taken from eight FFPE blocks. RNA was extracted and reverse transcribed, and TaqMan assays were performed on the 21 genes of the Oncotype DX Breast Cancer assay. Expression of the 16 recurrence-related genes was normalised to the set of five reference genes, and the recurrence score (RS) was calculated. RNA yield was lower from 0.6 mm cores than from 10 microm whole sections, but was still more than sufficient to perform the assay. RS and single gene data from cores were highly comparable with those from whole sections (RS p=0.005). Greater variability was seen between cores than between sections. FFPE sections are preferable to 0.6 mm cores for RNA profiling in order to maximise RNA yield and to allow for standard histopathological assessment. However, 0.6 mm cores are sufficient and would be appropriate to use for large cohort studies.

  8. Investigating core genetic-and-epigenetic cell cycle networks for stemness and carcinogenic mechanisms, and cancer drug design using big database mining and genome-wide next-generation sequencing data.

    Li, Cheng-Wei; Chen, Bor-Sen

    2016-10-01

    Recent studies have demonstrated that cell cycle plays a central role in development and carcinogenesis. Thus, the use of big databases and genome-wide high-throughput data to unravel the genetic and epigenetic mechanisms underlying cell cycle progression in stem cells and cancer cells is a matter of considerable interest. Real genetic-and-epigenetic cell cycle networks (GECNs) of embryonic stem cells (ESCs) and HeLa cancer cells were constructed by applying system modeling, system identification, and big database mining to genome-wide next-generation sequencing data. Real GECNs were then reduced to core GECNs of HeLa cells and ESCs by applying principal genome-wide network projection. In this study, we investigated potential carcinogenic and stemness mechanisms for systems cancer drug design by identifying common core and specific GECNs between HeLa cells and ESCs. Integrating drug database information with the specific GECNs of HeLa cells could lead to identification of multiple drugs for cervical cancer treatment with minimal side-effects on the genes in the common core. We found that dysregulation of miR-29C, miR-34A, miR-98, and miR-215; and methylation of ANKRD1, ARID5B, CDCA2, PIF1, STAMBPL1, TROAP, ZNF165, and HIST1H2AJ in HeLa cells could result in cell proliferation and anti-apoptosis through NFκB, TGF-β, and PI3K pathways. We also identified 3 drugs, methotrexate, quercetin, and mimosine, which repressed the activated cell cycle genes, ARID5B, STK17B, and CCL2, in HeLa cells with minimal side-effects.

  9. The Use of History and Philosophy of Science as a Core for a Socioconstructivist Teaching Approach of the Concept of Energy in Primary Education

    Rizaki, Aikaterini; Kokkotas, Panagiotis

    2013-01-01

    The present study should be thought as a socioconstructivist teaching approach (a teaching model) for the concept of energy in primary education. It contains important and crucial aspects of the History and Philosophy of Natural Sciences, introduces the concept of energy using the macroscopic framework of thermodynamics, takes into consideration…

  10. Governance in genomics: a conceptual challenge for public health genomics law

    Tobias Schulte in den Bäumen

    2006-12-01

    Full Text Available Increasing levels of genomic knowledge has led to awareness that new governance issues need to be taken into consideration. While some countries have created new statutory laws in the last 10 years, science supports the idea that genomic data should be treated like other medical data. In this article we discuss the three core models of governance in medical law on a conceptual level. The three models, the Medical, Public Health and Fundamental Rights Model stress different values, or in legal terms serve different principles. The Medical Model stands for expert knowledge and the standardisation of quality in healthcare. The Public Health Model fosters a social point of view as it advocates distribution justice in healthcare and an awareness of healthcare as a broader concept. The Fundamental Rights Model focuses on individual rights such as the right to privacy and autonomy. We argue that none of the models can be used in a purist fashion as governance in genomics should enable society and individuals to protect individual rights, to strive for a distribution justice and to ensure the quality of genomic services in one coherent process. Thus, genomic governance in genomics requires procedural law and a set of applicable principles. The principle which underlies all three models is the principle of medical beneficence. Therefore genomic governance should refer to it as a key principle when conflicting rights of individuals or communities need to be balanced.

  11. Concept - or no concept

    Thorsteinsson, Uffe

    1999-01-01

    Discussion about concept in industrial companies. A method for mapping of managerial concept in specific area is shown......Discussion about concept in industrial companies. A method for mapping of managerial concept in specific area is shown...

  12. Positioning genomics in biology education: content mapping of undergraduate biology textbooks.

    Wernick, Naomi L B; Ndung'u, Eric; Haughton, Dominique; Ledley, Fred D

    2014-12-01

    Biological thought increasingly recognizes the centrality of the genome in constituting and regulating processes ranging from cellular systems to ecology and evolution. In this paper, we ask whether genomics is similarly positioned as a core concept in the instructional sequence for undergraduate biology. Using quantitative methods, we analyzed the order in which core biological concepts were introduced in textbooks for first-year general and human biology. Statistical analysis was performed using self-organizing map algorithms and conventional methods to identify clusters of terms and their relative position in the books. General biology textbooks for both majors and nonmajors introduced genome-related content after text related to cell biology and biological chemistry, but before content describing higher-order biological processes. However, human biology textbooks most often introduced genomic content near the end of the books. These results suggest that genomics is not yet positioned as a core concept in commonly used textbooks for first-year biology and raises questions about whether such textbooks, or courses based on the outline of these textbooks, provide an appropriate foundation for understanding contemporary biological science.

  13. Cross-cohort analysis identifies a TEAD4 ↔ MYCN positive-feedback loop as the core regulatory element of high-risk neuroblastoma. | Office of Cancer Genomics

    High-risk neuroblastomas show a paucity of recurrent somatic mutations at diagnosis. As a result, the molecular basis for this aggressive phenotype remains elusive. Recent progress in regulatory network analysis helped us elucidate disease-driving mechanisms downstream of genomic alterations, including recurrent chromosomal alterations. Our analysis identified three molecular subtypes of high-risk neuroblastomas, consistent with chromosomal alterations, and identified subtype-specific master regulator (MR) proteins that were conserved across independent cohorts.

  14. New concept of damage evaluation method for core internal materials considering radiation induced stress relaxation (1). Experiments and modeling of radiation effects

    Miwa, Yukio; Kondo, Keietsu; Okubo, Nariaki; Kaji, Yoshiyuki; Tsukada, Takashi

    2009-01-01

    In order to build the new concept of material damage evaluation method, synergistic effect of radiation and residual stress on material degradation was estimated experimentally, and the effect of radiation induced stress relaxation on retardation of material degradation was observed. (author)

  15. Tracking of Listeria monocytogenes in meat establishment using Whole Genome Sequencing as a food safety management tool: A proof of concept.

    Nastasijevic, Ivan; Milanov, Dubravka; Velebit, Branko; Djordjevic, Vesna; Swift, Craig; Painset, Anais; Lakicevic, Brankica

    2017-09-18

    Repeated Listeria outbreaks particularly associated with Ready-To-Eat (RTE) delicatessen meat products have been reported annually at global level. The most frequent scenario that led to foodborne outbreaks was the post-thermal treatment cross-contamination of deli meat products during slicing and modified atmosphere packaging (MAP). The precondition for such cross contamination is the previous introduction of Listeria into meat processing facilities and subsequent colonization of the production environment, associated with formation of biofilms resilient to common sanitation procedures regularly applied in meat establishments. The use of Whole Genome Sequencing (WGS) can facilitate the understanding of contamination and colonization routes of pathogens within the food production environment and enable efficient pathogen tracking among different departments. This study aimed to: a) provide a proof of concept on practical use of WGS in a meat establishment to define the entry routes and spread pattern of L. monocytogenes, and b) to consider the regular use of WGS in meat processing establishments as a strong support of food safety management system. The results revealed that Listeria spp. was present in slaughter line, chilling chambers, deboning, slicing, MAP, as well as in corridors and dispatch (53 positive samples, out of 240). Eight L. monocytogenes isolates (out of 53) were identified from the slaughterhouse, chilling chambers, deboning, MAP and dispatch. L. monocytogenes isolates were of three different serotypes (1/2a, 1/2c, 4b) and correspondingly of three MLST sequence types. Overall, two pairs of L. monocytogenes isolates were genetically identical, i.e. two serotype 4b isolates (ST1), isolated from water drain at dispatch unit and two isolates obtained from slaughterhouse (floorwall junction at the carcass wash point) and MAP (water drain). These findings indicated that L. monocytogenes isolates identified in meat processing units (MAP, chilling chamber

  16. Proteomics Core

    Federal Laboratory Consortium — Proteomics Core is the central resource for mass spectrometry based proteomics within the NHLBI. The Core staff help collaborators design proteomics experiments in a...

  17. Engineering solutions for a reflector change concept in the high-temperature reactor with pebble bed core and OTTO-fueling

    Kasper, K.J.

    1975-06-01

    In the field of reactor engineering an increasing tendency is visible towards a 'repairable reactor'. In the construction of the HTR with spherical fuel elements this fact should already be taken into account at an early stage. Additionally it is possible that in connection with the OTTO-fueling load conditions for the graphite reflector could result which are locally not far away from limiting values. Therefore the removability of the reflector is included in the reactor construction as an accompanying technical step of the physical lay-out of the core. The core arrangements, realized for HTR until recently, are discussed as well as the properties of the graphites used and the operating conditions in the reactors are stated. At the example of the PR 3,000 proposals are offered for the construction of a removable side and top reflector for a pebble bed reactor. Hereby a solution was found which, on one hand allows the changing of the reflector and on the other hand requires no significant increase of the costs for the reactor assembly. Moreover the requirements of reactor operation and of repairability are satisfied in an optimal manner. (orig.) [de

  18. Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.

    So Yeon Kwon

    2016-04-01

    Full Text Available NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions.

  19. Software concepts for the build-up of complex systems - selection and realization taking as example a program system for calculation of hypothetical core meltdown accidents

    Scheuermann, W.

    1994-10-01

    Development and application of simulation systems for the analysis of complex processes require on the one hand and detailed engineering knowledge of the plant and the processes to be simulated and on the other hand a detailled knowledge about software engineering, numerics and data structures. The cooperation of specialists of both areas will become easier if it is possible to reduce the complexicity of the problems to be solved in a way that the analyses will not be disturbed and the communication between different disciplines will not become unnecessarily complicated. One solution to reduce the complexity is to consider computer science as an engineering discipline which provides mainly abstract elements and to allow engineers to build application systems based on these abstract elements. The principle of abstraction leads through the processes of modularisation and the solution of the interface problem to an almost problem independent system architecture where the elements of the system (modules, model components and models) operate only on those data assigned to them. In addition the development of abstract data types allows the formal description of the relations and interactions between system elements. This work describes how these ideas can be concretized to build complex systems which allow reliable and effective problem solutions. These ideas were applied successfully during the design, realization and application of the code system KESS, which allows the analysis of core melt down accidents in pressurized water reactors. (orig.) [de

  20. The core regulatory network of the abscisic acid pathway in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress.

    Hu, Wei; Yan, Yan; Shi, Haitao; Liu, Juhua; Miao, Hongxia; Tie, Weiwei; Ding, Zehong; Ding, XuPo; Wu, Chunlai; Liu, Yang; Wang, Jiashui; Xu, Biyu; Jin, Zhiqiang

    2017-08-29

    Abscisic acid (ABA) signaling plays a crucial role in developmental and environmental adaptation processes of plants. However, the PYL-PP2C-SnRK2 families that function as the core components of ABA signaling are not well understood in banana. In the present study, 24 PYL, 87 PP2C, and 11 SnRK2 genes were identified from banana, which was further supported by evolutionary relationships, conserved motif and gene structure analyses. The comprehensive transcriptomic analyses showed that banana PYL-PP2C-SnRK2 genes are involved in tissue development, fruit development and ripening, and response to abiotic stress in two cultivated varieties. Moreover, comparative expression analyses of PYL-PP2C-SnRK2 genes between BaXi Jiao (BX) and Fen Jiao (FJ) revealed that PYL-PP2C-SnRK2-mediated ABA signaling might positively regulate banana fruit ripening and tolerance to cold, salt, and osmotic stresses. Finally, interaction networks and co-expression assays demonstrated that the core components of ABA signaling were more active in FJ than in BX in response to abiotic stress, further supporting the crucial role of the genes in tolerance to abiotic stress in banana. This study provides new insights into the complicated transcriptional control of PYL-PP2C-SnRK2 genes, improves the understanding of PYL-PP2C-SnRK2-mediated ABA signaling in the regulation of fruit development, ripening, and response to abiotic stress, and identifies some candidate genes for genetic improvement of banana.

  1. Heterogeneous gas core reactor

    Han, K.I.

    1977-01-01

    Preliminary investigations of a heterogeneous gas core reactor (HGCR) concept suggest that this potential power reactor offers distinct advantages over other existing or conceptual reactor power plants. One of the most favorable features of the HGCR is the flexibility of the power producing system which allows it to be efficiently designed to conform to a desired optimum condition without major conceptual changes. The arrangement of bundles of moderator/coolant channels in a fissionable gas or mixture of gases makes a truly heterogeneous nuclear reactor core. It is this full heterogeneity for a gas-fueled reactor core which accounts for the novelty of the heterogeneous gas core reactor concept and leads to noted significant advantages over previous gas core systems with respect to neutron and fuel economy, power density, and heat transfer characteristics. The purpose of this work is to provide an insight into the design, operating characteristics, and safety of a heterogeneous gas core reactor system. The studies consist mainly of neutronic, energetic and kinetic analyses of the power producing and conversion systems as a preliminary assessment of the heterogeneous gas core reactor concept and basic design. The results of the conducted research indicate a high potential for the heterogeneous gas core reactor system as an electrical power generating unit (either large or small), with an overall efficiency as high as 40 to 45%. The HGCR system is found to be stable and safe, under the conditions imposed upon the analyses conducted in this work, due to the inherent safety of ann expanding gaseous fuel and the intrinsic feedback effects of the gas and water coolant

  2. REM Sleep Behavior Disorder: Updated Review of the Core Features, the RBD-Neurodegenerative Disease Association, Evolving Concepts, Controversies, and Future Directions

    Boeve, Bradley F.

    2010-01-01

    Rapid eye movement (REM) sleep behavior disorder (RBD) is a parasomnia manifested by vivid, often frightening dreams associated with simple or complex motor behavior during REM sleep. Patients appear to “act out their dreams,” in which the exhibited behaviors mirror the content of the dreams, and the dream content often involves a chasing or attacking theme. The polysomnographic features of RBD include increased electromyographic tone +/- dream enactment behavior during REM sleep. Management with counseling and pharmacologic measures is usually straight-forward and effective. In this review, the terminology, clinical and polysomnographic features, demographic and epidemiologic features, diagnostic criteria, differential diagnosis, and management strategies are discussed. Recent data on the suspected pathophysiologic mechanisms of RBD are also reviewed. The literature and our institutional experience on RBD are next discussed, with an emphasis on the RBD-neurodegenerative disease association and particularly the RBD-synucleinopathy association. Several issues relating to evolving concepts, controversies, and future directions are then reviewed, with an emphasis on idiopathic RBD representing an early feature of a neurodegenerative disease and particularly an evolving synucleinopathy. Planning for future therapies that impact patients with idiopathic RBD is reviewed in detail. PMID:20146689

  3. Conceptual study of advanced PWR core design

    Kim, Young Jin; Chang, Moon Hee; Kim, Keung Ku; Joo, Hyung Kuk; Kim, Young Il; Noh, Jae Man; Hwang, Dae Hyun; Kim, Taek Kyum; Yoo, Yon Jong.

    1997-09-01

    The purpose of this project is for developing and verifying the core design concepts with enhanced safety and economy, and associated methodologies for core analyses. From the study of the sate-of-art of foreign advanced reactor cores, we developed core concepts such as soluble boron free, high convertible and enhanced safety core loaded semi-tight lattice hexagonal fuel assemblies. To analyze this hexagonal core, we have developed and verified some neutronic and T/H analysis methodologies. HELIOS code was adopted as the assembly code and HEXFEM code was developed for hexagonal core analysis. Based on experimental data in hexagonal lattices and the COBRA-IV-I code, we developed a thermal-hydraulic analysis code for hexagonal lattices. Using the core analysis code systems developed in this project, we designed a 600 MWe core and studied the feasibility of the core concepts. Two additional scopes were performed in this project : study on the operational strategies of soluble boron free core and conceptual design of large scale passive core. By using the axial BP zoning concept and suitable design of control rods, this project showed that it was possible to design a soluble boron free core in 600 MWe PWR. The results of large scale core design showed that passive concepts and daily load follow operation could be practiced. (author). 15 refs., 52 tabs., 101 figs

  4. Conceptual study of advanced PWR core design

    Kim, Young Jin; Chang, Moon Hee; Kim, Keung Ku; Joo, Hyung Kuk; Kim, Young Il; Noh, Jae Man; Hwang, Dae Hyun; Kim, Taek Kyum; Yoo, Yon Jong

    1997-09-01

    The purpose of this project is for developing and verifying the core design concepts with enhanced safety and economy, and associated methodologies for core analyses. From the study of the sate-of-art of foreign advanced reactor cores, we developed core concepts such as soluble boron free, high convertible and enhanced safety core loaded semi-tight lattice hexagonal fuel assemblies. To analyze this hexagonal core, we have developed and verified some neutronic and T/H analysis methodologies. HELIOS code was adopted as the assembly code and HEXFEM code was developed for hexagonal core analysis. Based on experimental data in hexagonal lattices and the COBRA-IV-I code, we developed a thermal-hydraulic analysis code for hexagonal lattices. Using the core analysis code systems developed in this project, we designed a 600 MWe core and studied the feasibility of the core concepts. Two additional scopes were performed in this project : study on the operational strategies of soluble boron free core and conceptual design of large scale passive core. By using the axial BP zoning concept and suitable design of control rods, this project showed that it was possible to design a soluble boron free core in 600 MWe PWR. The results of large scale core design showed that passive concepts and daily load follow operation could be practiced. (author). 15 refs., 52 tabs., 101 figs.

  5. Genome Editing for Cancer Therapy: Delivery of Cas9 Protein/sgRNA Plasmid via a Gold Nanocluster/Lipid Core-Shell Nanocarrier.

    Wang, Peng; Zhang, Lingmin; Xie, Yangzhouyun; Wang, Nuoxin; Tang, Rongbing; Zheng, Wenfu; Jiang, Xingyu

    2017-11-01

    The type II bacterial clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 (CRISPR-associated protein) system (CRISPR-Cas9) is a powerful toolbox for gene-editing, however, the nonviral delivery of CRISPR-Cas9 to cells or tissues remains a key challenge. This paper reports a strategy to deliver Cas9 protein and single guide RNA (sgRNA) plasmid by a nanocarrier with a core of gold nanoclusters (GNs) and a shell of lipids. By modifying the GNs with HIV-1-transactivator of transcription peptide, the cargo (Cas9/sgRNA) can be delivered into cell nuclei. This strategy is utilized to treat melanoma by designing sgRNA targeting Polo-like kinase-1 ( Plk1 ) of the tumor. The nanoparticle (polyethylene glycol-lipid/GNs/Cas9 protein/sgPlk1 plasmid, LGCP) leads to >70% down-regulation of Plk1 protein expression of A375 cells in vitro. Moreover, the LGCP suppresses melanoma progress by 75% on mice. Thus, this strategy can deliver protein-nucleic acid hybrid agents for gene therapy.

  6. Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics.

    Xiao, Yinghua; van Hijum, Sacha A F T; Abee, Tjakko; Wells-Bennik, Marjon H J

    2015-01-01

    The formation of bacterial spores is a highly regulated process and the ultimate properties of the spores are determined during sporulation and subsequent maturation. A wide variety of genes that are expressed during sporulation determine spore properties such as resistance to heat and other adverse environmental conditions, dormancy and germination responses. In this study we characterized the sporulation phases of C. perfringens enterotoxic strain SM101 based on morphological characteristics, biomass accumulation (OD600), the total viable counts of cells plus spores, the viable count of heat resistant spores alone, the pH of the supernatant, enterotoxin production and dipicolinic acid accumulation. Subsequently, whole-genome expression profiling during key phases of the sporulation process was performed using DNA microarrays, and genes were clustered based on their time-course expression profiles during sporulation. The majority of previously characterized C. perfringens germination genes showed upregulated expression profiles in time during sporulation and belonged to two main clusters of genes. These clusters with up-regulated genes contained a large number of C. perfringens genes which are homologs of Bacillus genes with roles in sporulation and germination; this study therefore suggests that those homologs are functional in C. perfringens. A comprehensive homology search revealed that approximately half of the upregulated genes in the two clusters are conserved within a broad range of sporeforming Firmicutes. Another 30% of upregulated genes in the two clusters were found only in Clostridium species, while the remaining 20% appeared to be specific for C. perfringens. These newly identified genes may add to the repertoire of genes with roles in sporulation and determining spore properties including germination behavior. Their exact roles remain to be elucidated in future studies.

  7. Integral fast reactor concept

    Chang, Y.I.; Marchaterre, J.F.; Sevy, R.H.

    1984-01-01

    Key features of the IFR consist of a pool-type plant arrangement, a metal fuel-based core design, and an integral fuel cycle with colocated fuel cycle facility. Both the basic concept and the technology base have been demonstrated through actual integral cycle operation in EBR-II. This paper discusses the inherent safety characteristics of the IFR concept

  8. COMET concept; COMET-Konzept

    Alsmeyer, H.; Tromm, W.

    1995-08-01

    Studies of the COMET core catcher concept developed for a future PWR have been continued. The concept is based on the spreading of a core melt on a sacrificial layer and its erosion, until a subsequent addition of water from below causes a fragmentation of the melt. A porous solidification of the melt would then admit a complete flooding within a short period. (orig.)

  9. Participation in a Year-Long CURE Embedded into Major Core Genetics and Cellular and Molecular Biology Laboratory Courses Results in Gains in Foundational Biological Concepts and Experimental Design Skills by Novice Undergraduate Researchers†

    Peteroy-Kelly, Marcy A.; Marcello, Matthew R.; Crispo, Erika; Buraei, Zafir; Strahs, Daniel; Isaacson, Marisa; Jaworski, Leslie; Lopatto, David; Zuzga, David

    2017-01-01

    This two-year study describes the assessment of student learning gains arising from participation in a year-long curriculum consisting of a classroom undergraduate research experience (CURE) embedded into second-year, major core Genetics and Cellular and Molecular Biology (CMB) laboratory courses. For the first course in our CURE, students used micro-array or RNAseq analyses to identify genes important for environmental stress responses by Saccharomyces cerevisiae. The students were tasked with creating overexpressing mutants of their genes and designing their own original experiments to investigate the functions of those genes using the overexpression and null mutants in the second CURE course. In order to evaluate student learning gains, we employed three validated concept inventories in a pretest/posttest format and compared gains on the posttest versus the pretest with student laboratory final grades. Our results demonstrated that there was a significant correlation between students earning lower grades in the Genetics laboratory for both years of this study and gains on the Genetics Concept Assessment (GCA). We also demonstrated a correlation between students earning lower grades in the Genetics laboratory and gains on the Introductory Molecular and Cell Biology Assessment (IMCA) for year 1 of the study. Students furthermore demonstrated significant gains in identifying the variable properties of experimental subjects when assessed using the Rubric for Experimental (RED) design tool. Results from the administration of the CURE survey support these findings. Our results suggest that a year-long CURE enables lower performing students to experience greater gains in their foundational skills for success in the STEM disciplines. PMID:28904646

  10. GREEN CORE HOUSE

    NECULAI Oana

    2017-05-01

    Full Text Available The Green Core House is a construction concept with low environmental impact, having as main central element a greenhouse. The greenhouse has the innovative role to use the biomass energy provided by plants to save energy. Although it is the central piece, the greenhouse is not the most innovative part of the Green Core House, but the whole building ensemble because it integrates many other sustainable systems as "waste purification systems", "transparent photovoltaic panels" or "double skin façades".

  11. Transformer core

    Mehendale, A.; Hagedoorn, Wouter; Lötters, Joost Conrad

    2008-01-01

    A transformer core includes a stack of a plurality of planar core plates of a magnetically permeable material, which plates each consist of a first and a second sub-part that together enclose at least one opening. The sub-parts can be fitted together via contact faces that are located on either side

  12. Transformer core

    Mehendale, A.; Hagedoorn, Wouter; Lötters, Joost Conrad

    2010-01-01

    A transformer core includes a stack of a plurality of planar core plates of a magnetically permeable material, which plates each consist of a first and a second sub-part that together enclose at least one opening. The sub-parts can be fitted together via contact faces that are located on either side

  13. Information science and its core concepts

    Hjørland, Birger

    2013-01-01

    One often encounters disagreements in information science (IS) (or library and information science, LIS), even disagreements about what might seem rather trivial questions. Such disagreements range from the designation of the field to questions such as whether IS is an academic discipline or not...... terminological hygiene” may account for some of the disagreements, but basically the problem is seen as a lack of sufficient strong centripetal tendencies keeping the field together....

  14. Wire core reactor for NTP

    Harty, R.B.

    1991-01-01

    The development of the wire core system for Nuclear Thermal Propulsion (NTP) that took place from 1963 to 1965 is discussed. A wire core consists of a fuel wire with spacer wires. It's an annular flow core having a central control rod. There are actually four of these, with beryllium solid reflectors on both ends and all the way around. Much of the information on the concept is given in viewgraph form. Viewgraphs are presented on design details of the wire core, the engine design, engine weight vs. thrust, a technique used to fabricate the wire fuel element, and axial temperature distribution

  15. Microbial Genomes Multiply

    Doolittle, Russell F.

    2002-01-01

    The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

  16. Core lifter

    Pavlov, N G; Edel' man, Ya A

    1981-02-15

    A core lifter is suggested which contains a housing, core-clamping elements installed in the housing depressions in the form of semirings with projections on the outer surface restricting the rotation of the semirings in the housing depressions. In order to improve the strength and reliability of the core lifter, the semirings have a variable transverse section formed from the outside by the surface of the rotation body of the inner arc of the semiring aroung the rotation axis and from the inner a cylindrical surface which is concentric to the outer arc of the semiring. The core-clamping elements made in this manner have the possibility of freely rotating in the housing depressions under their own weight and from contact with the core sample. These semirings do not have weakened sections, have sufficient strength, are inserted into the limited ring section of the housing of the core lifter without reduction in its through opening and this improve the reliability of the core lifter in operation.

  17. Genome Variation Map: a data repository of genome variations in BIG Data Center

    Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

    2017-01-01

    Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...

  18. Review of advanced core designs for LMFBRs

    Yoshida, Kazuo

    1986-01-01

    It is a matter of great importance for the development of LMFBR to reduce its power cost to the level of the other power generating means. For this purpose, some ideas that use advanced core concepts to reduce LMFBR's power cost by improving its fuel cycle economics have recently been proposed. In this report, two hopeful ideas that use advanced core concepts: (1) Ultra Long Life Core (ULLC) - non-refueling over LMFBR power plant life; (2) Integral Fast Reactor (IFR) concept - metal fueled core and pyrometallurgical reprocessing; are picked up and their economical effect and technical probrems are investigated. (author)

  19. Reactor core

    Azekura, Kazuo; Kurihara, Kunitoshi.

    1992-01-01

    In a BWR type reactor, a great number of pipes (spectral shift pipes) are disposed in the reactor core. Moderators having a small moderating cross section (heavy water) are circulated in the spectral shift pipes to suppress the excess reactivity while increasing the conversion ratio at an initial stage of the operation cycle. After the intermediate stage of the operation cycle in which the reactor core reactivity is lowered, reactivity is increased by circulating moderators having a great moderating cross section (light water) to extend the taken up burnup degree. Further, neutron absorbers such as boron are mixed to the moderator in the spectral shift pipe to control the concentration thereof. With such a constitution, control rods and driving mechanisms are no more necessary, to simplify the structure of the reactor core. This can increase the fuel conversion ratio and control great excess reactivity. Accordingly, a nuclear reactor core of high conversion and high burnup degree can be attained. (I.N.)

  20. Ice Cores

    National Oceanic and Atmospheric Administration, Department of Commerce — Records of past temperature, precipitation, atmospheric trace gases, and other aspects of climate and environment derived from ice cores drilled on glaciers and ice...

  1. Non-invasive preimplantation genetic screening using array comparative genomic hybridization on spent culture media: a proof-of-concept pilot study.

    Feichtinger, Michael; Vaccari, Enrico; Carli, Luca; Wallner, Elisabeth; Mädel, Ulrike; Figl, Katharina; Palini, Simone; Feichtinger, Wilfried

    2017-06-01

    The aim of this pilot study was to assess if array comparative genomic hybridization (aCGH), non-invasive preimplantation genetic screening (PGS) on blastocyst culture media is feasible. Therefore, aCGH analysis was carried out on 22 spent blastocyst culture media samples after polar body PGS because of advanced maternal age. All oocytes were fertilized by intracytoplasmic sperm injection and all embryos underwent assisted hatching. Concordance of polar body analysis and culture media genetic results was assessed. Thirteen out of 18 samples (72.2%) revealed general concordance of ploidy status (euploid or aneuploid). At least one chromosomal aberration was found concordant in 10 out of 15 embryos found to be aneuploid by both polar body and culture media analysis. Overall, 17 out of 35 (48.6%) single chromosomal aneuploidies were concordant between the culture media and polar body analysis. By analysing negative controls (oocytes with fertilization failure), notable maternal contamination was observed. Therefore, non-invasive PGS could serve as a second matrix after polar body or cleavage stage PGS; however, in euploid results, maternal contamination needs to be considered and results interpreted with caution. Copyright © 2017 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

  2. Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

    Machado, Henrique; Gram, Lone

    2017-01-01

    Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

  3. Genomic taxonomy of vibrios

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  4. Genomic individuality and its biological implications.

    Zhao, J

    1996-06-01

    It is a widely accepted fundamental concept that all somatic genomes of a human individual are identical to each other. The theoretical basis of this concept is that all of these somatic genomes are the descendants of the genome of a single fertilized cell as well as the simple replicated products of asexual reproduction, thus not forming any new recombined genomes. The question here is whether such a concept might only represent one side of somatic genome biology and, even worse, whether it has perhaps already led to a very prevalent misconception that within the organism body, there exists no variability among individual somatic genomes. A hypothesis, called genomic individuality, is proposed, simply saying that every individual somatic genome, perhaps with rare exceptions, has its own unique or individual 'genetic identity' or 'fingerprint', which is characterized by its distinctive sequences or patterns of deoxyribonucleic acid molecules, or both. Thus, no two somatic genomes can be identical to each other in every or all aspects, and consequently, there must be a great deal of genomic variation present within the body of any multicellular organism. The concept or hypothesis of genomic individuality would not only provide a more complete understanding of genome biology, but also suggest a new insight into the studies of the biology of cells and organisms.

  5. Reactor core

    Matsuura, Tetsuaki; Nomura, Teiji; Tokunaga, Kensuke; Okuda, Shin-ichi

    1990-01-01

    Fuel assemblies in the portions where the gradient of fast neutron fluxes between two opposing faces of a channel box is great are kept loaded at the outermost peripheral position of the reactor core also in the second operation cycle in the order to prevent interference between a control rod and the channel box due to bending deformation of the channel box. Further, the fuel assemblies in the second row from the outer most periphery in the first operation cycle are also kept loaded at the second row in the second operation cycle. Since the gradient of the fast neutrons in the reactor core is especially great at the outer circumference of the reactor core, the channel box at the outer circumference is bent such that the surface facing to the center of the reactor core is convexed and the channel box in the second row is also bent to the identical direction, the insertion of the control rod is not interfered. Further, if the positions for the fuels at the outermost periphery and the fuels in the second row are not altered in the second operation cycle, the gaps are not reduced to prevent the interference between the control rod and the channel box. (N.H.)

  6. SCORPIO - VVER core surveillance system

    Zalesky, K.; Svarny, J.; Novak, L.; Rosol, J.; Horanes, A.

    1997-01-01

    The Halden Project has developed the core surveillance system SCORPIO which has two parallel modes of operation: the Core Follow Mode and the Predictive Mode. The main motivation behind the development of SCORPIO is to make a practical tool for reactor operators which can increase the quality and quantity of information presented on core status and dynamic behavior. This can first of all improve plant safety as undesired core conditions are detected and prevented. Secondly, more flexible and efficient plant operation is made possible. So far the system has only been implemented on western PWRs but the basic concept is applicable to a wide range of reactor including WWERs. The main differences between WWERs and typical western PWRs with respect to core surveillance requirements are outlined. The development of a WWER version of SCORPIO was initiated in cooperation with the Nuclear Research Institute at Rez and industry partners in the Czech Republic. The first system will be installed at the Dukovany NPP. (author)

  7. The EFR project: core and fuel

    Francillon, E.; Barnes, D.W.; Pay, A.; Wehmann, U.

    1991-01-01

    The draft studies on EFR has beginning, in March 1988. The first part of the summary draft has consisted in the core and fuel domains to harmonize the different approaches used in national projects (SPX2-SNR2-CDFR). Rapidly, the core First Consistent Design has been defined with references to the anterior conceptions. Since this definition, studies have been engaged on the management (mean burnup amelioration) and on the conception (breeding gain, sodium void coefficient reduction). After a presentation of the basis options and on the general conception of the fuel assemblies we make a point on the core and the interfaces with the fuel cycle [fr

  8. Challenges for proteomics core facilities.

    Lilley, Kathryn S; Deery, Michael J; Gatto, Laurent

    2011-03-01

    Many analytical techniques have been executed by core facilities established within academic, pharmaceutical and other industrial institutions. The centralization of such facilities ensures a level of expertise and hardware which often cannot be supported by individual laboratories. The establishment of a core facility thus makes the technology available for multiple researchers in the same institution. Often, the services within the core facility are also opened out to researchers from other institutions, frequently with a fee being levied for the service provided. In the 1990s, with the onset of the age of genomics, there was an abundance of DNA analysis facilities, many of which have since disappeared from institutions and are now available through commercial sources. Ten years on, as proteomics was beginning to be utilized by many researchers, this technology found itself an ideal candidate for being placed within a core facility. We discuss what in our view are the daily challenges of proteomics core facilities. We also examine the potential unmet needs of the proteomics core facility that may also be applicable to proteomics laboratories which do not function as core facilities. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Informational laws of genome structures

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-06-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

  10. Extreme genomes

    DeLong, Edward F

    2000-01-01

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

  11. Grass genomes

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

    1998-01-01

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

  12. A core performance study on an actinide recycling 'zero-sodium-void worth' core

    Kawashima, M.; Nakagawa, M.; Yamaoka, M.; Kasahara, F.

    1994-01-01

    A core performance study was made for an absorber-type parfait core (A-APC) as one of 'Zero-sodium-void-worth' core concepts. This evaluation study pursued different two aspects; one for transuranic (TRU) management strategy, and another for a loss-of-coolant anticipated transient behavior considering the unique core configuration. The results indicated that this core has a large flexibility for actinide recycling in terms of self-sufficiency and minor actinide burning. The result also showed that this core has kept a large mitigation potential for ULOF events as well as a simple flat core concept, reflecting detailed three dimensional core bowing behavior for the A-APC configuration. (author)

  13. Cancer genomics

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

    2007-01-01

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

  14. Core principles of evolutionary medicine

    Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

    2018-01-01

    Abstract Background and objectives Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. Methodology The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Results Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. Conclusions and implications This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further. PMID:29493660

  15. Whole Genome Epidemiological Typing of Salmonella

    Leekitcharoenphon, Pimlapas

    available Salmonella enterica genomes (accessed in April 2011). A consensus tree based on variation of the core genes gives better resolution than 16S rRNA and MLST that rarely provide separation between closely related strains. The performance of the pan-genome tree which is based on the presence....../absence of all genes across genomes, is similar to the consensus tree but with higher branching confidence value. The core genes can be divided into two categories: a few highly variable genes and a larger set of conserved core genes, with low variance. These core genes are useful for investigating molecular...... evolution and remain useful as candidate genes for bacterial genome typing-even if they cannot be expected to differentiate highly clonal isolates e.g. outbreak cases of Salmonella [I]. To achieve successful ‘real-time’ monitoring and identification of outbreaks, rapid and reliable sub-typing is essential...

  16. Core BPEL

    Hallwyl, Tim; Højsgaard, Espen

    The Web Services Business Process Execution Language (WS-BPEL) is a language for expressing business process behaviour based on web services. The language is intentionally not minimal but provides a rich set of constructs, allows omission of constructs by relying on defaults, and supports language......, does not allow omissions, and does not contain ignorable elements. We do so by identifying syntactic sugar, including default values, and ignorable elements in WS-BPEL. The analysis results in a translation from the full language to the core subset. Thus, we reduce the effort needed for working...

  17. Software for computing and annotating genomic ranges.

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  18. Software for computing and annotating genomic ranges.

    Lawrence, Michael; Huber, Wolfgang; Pagès, Hervé; Aboyoun, Patrick; Carlson, Marc; Gentleman, Robert; Morgan, Martin T; Carey, Vincent J

    2013-01-01

    We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  19. Genomic research perspectives in Kazakhstan

    Ainur Akilzhanova

    2014-01-01

    Full Text Available Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well

  20. Efficient Breeding by Genomic Mating.

    Akdemir, Deniz; Sánchez, Julio I

    2016-01-01

    Selection in breeding programs can be done by using phenotypes (phenotypic selection), pedigree relationship (breeding value selection) or molecular markers (marker assisted selection or genomic selection). All these methods are based on truncation selection, focusing on the best performance of parents before mating. In this article we proposed an approach to breeding, named genomic mating, which focuses on mating instead of truncation selection. Genomic mating uses information in a similar fashion to genomic selection but includes information on complementation of parents to be mated. Following the efficiency frontier surface, genomic mating uses concepts of estimated breeding values, risk (usefulness) and coefficient of ancestry to optimize mating between parents. We used a genetic algorithm to find solutions to this optimization problem and the results from our simulations comparing genomic selection, phenotypic selection and the mating approach indicate that current approach for breeding complex traits is more favorable than phenotypic and genomic selection. Genomic mating is similar to genomic selection in terms of estimating marker effects, but in genomic mating the genetic information and the estimated marker effects are used to decide which genotypes should be crossed to obtain the next breeding population.

  1. Concepts of formal concept analysis

    Žáček, Martin; Homola, Dan; Miarka, Rostislav

    2017-07-01

    The aim of this article is apply of Formal Concept Analysis on concept of world. Formal concept analysis (FCA) as a methodology of data analysis, information management and knowledge representation has potential to be applied to a verity of linguistic problems. FCA is mathematical theory for concepts and concept hierarchies that reflects an understanding of concept. Formal concept analysis explicitly formalizes extension and intension of a concept, their mutual relationships. A distinguishing feature of FCA is an inherent integration of three components of conceptual processing of data and knowledge, namely, the discovery and reasoning with concepts in data, discovery and reasoning with dependencies in data, and visualization of data, concepts, and dependencies with folding/unfolding capabilities.

  2. Comparative Genomics of Green Sulfur Bacteria

    Ussery, David; Davenport, C; Tümmler, B

    2010-01-01

    Eleven completely sequenced Chlorobi genomes were compared in oligonucleotide usage, gene contents, and synteny. The green sulfur bacteria (GSB) are equipped with a core genome that sustains their anoxygenic phototrophic lifestyle by photosynthesis, sulfur oxidation, and CO(2) fixation. Whole...... weight of 10(6), and are probably instrumental for the bacteria to generate their own intimate (micro)environment....

  3. Comparative genomics of bifidobacterium, lactobacillus and related probiotic genera

    Lukjancenko, Oksana; Ussery, David; Wassenaar, Trudy M.

    2012-01-01

    Six bacterial genera containing species commonly used as probiotics for human consumption or starter cultures for food fermentation were compared and contrasted, based on publicly available complete genome sequences. The analysis included 19 Bifidobacterium genomes, 21 Lactobacillus genomes, 4...... Lactococcus and 3 Leuconostoc genomes, as well as a selection of Enterococcus (11) and Streptococcus (23) genomes. The latter two genera included genomes from probiotic or commensal as well as pathogenic organisms to investigate if their non-pathogenic members shared more genes with the other probiotic......- and core genome of each genus were compared. In addition, it was investigated whether pathogenic genomes contain different COG classes compared to the probiotic or fermentative organisms, again comparing their pan- and core genomes. The obtained results were compared with published data from the literature...

  4. A core design study for 'zero-sodium-void-worth' cores

    Kawashima, Masatoshi; Suzuki, Masao; Hill, R.N.

    1992-01-01

    Recently, a number of low sodium-void-worth metal-fueled core design concepts have been proposed; to provide for flexibility in transuranic nuclide management strategy, core designs which exhibit a wide range of breeding characteristics have been developed. Two core concepts, a flat annular (transuranic burning) core and an absorber-type parfait (transuranic self-sufficient) core, are selected for this study. In this paper, the excess reactivity management schemes applied in the two designs are investigated in detail. In addition, the transient effect of reactivity insertions on the parfait core design is assessed. The upper and lower core regions in the parfait design are neutronically decoupled; however, the common coolant channel creates thermalhydraulic coupling. This combination of neutronic and thermalhydraulic characteristics leads to unique behavior in anticipated transient overpower events. (author)

  5. Genome plasticity and systems evolution in Streptomyces

    2012-01-01

    Background Streptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation. Results We present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication. Conclusions Our results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A

  6. The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains

    Soares, Siomar C; Silva, Artur; Trost, Eva

    2013-01-01

    , Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic...

  7. Genome Imprinting

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

  8. Baculovirus Genomics

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

    2007-01-01

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

  9. Genomic Testing

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

  10. Ancient genomes

    Hoelzel, A Rus

    2005-01-01

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

  11. Cognitive Architecture of Common and Scientific Concepts

    Tarábek, Paul

    2010-07-01

    The cognitive architecture of concept is a specific structure consisting of the concept core, concept periphery, the semantic frame as the meaning and the sense of the concept, and the relations among all components of this structure. The model of the cognitive architecture of scientific and common concepts is a conceptual meta-model built upon Vygotsky's concept theory, Fillmore's semantic frame, semantic triangle, on widespread ideas of the structuring of conceptual systems, and the Hestenes' Modeling Theory. The method of semantic mapping of concepts flowing from the model is designed.

  12. Side core lifter

    Edelman, Ya A

    1982-01-01

    A side core lifter is proposed which contains a housing with guide slits and a removable core lifter with side projections on the support section connected to the core receiver. In order to preserve the structure of the rock in the core sample by means of guaranteeing rectilinear movement of the core lifter in the rock, the support and core receiver sections are hinged. The device is equipped with a spring for angular shift in the core-reception part.

  13. Systemizing the Pedagogic Concepts

    G. N. Serikov

    2013-01-01

    Full Text Available The paper emphasizes the necessity of systemizing the pedagogic concepts to complement the pluralism principle dominating in pedagogy over the recent years. The author recommends the person oriented systematic synergetic methodology combining various research data into a holistic scientific approach. The paper regards education as the core pedagogic concept - including training, upbringing, self-education, their respective subcomponents, and generated personal resource. The elements of personal resource combine the acquired knowledge, skills and values, developed subjective attitudes and individual health data. The key pedagogic terms describing the educational process are represented by a three-level system; the first level involves the educational form concepts, the second – generated personal resource, the third – summarized notion system combining the previous levels and reflecting their binary relations. The given construct systemizes the pedagogic conceptual apparatus and clarifies the theoretical notion of personal education. 

  14. CORE annual report 2006; CORE Jahresbericht 2006

    Gut, A

    2007-04-15

    This annual report for the Swiss Federal Office of Energy (SFOE) summarises the activities of the Swiss Federal Commission on Energy Research CORE in 2006. The six main areas of work during the period 2004 - 2007 are examined, including a review of the SFOE's energy research programme, a road-map for the way towards the realisation of a 2000-watt society, the formulation of an energy research concept for 2008 - 2011, international co-operation, the dissemination of information and the assessment of existing and new instruments. International activities and Switzerland's involvement in energy research within the framework of the International Energy Agency IEA are discussed. New and existing projects are listed and the work done at the Competence Centre for Energy and Mobility noted. The Swiss Technology Award 2007 is presented. Information supplied to interested bodies to help improve knowledge on research work being done and to help make discussions on future energy supply more objective is discussed.

  15. CORE annual report 2006

    Gut, A.

    2007-04-01

    This annual report for the Swiss Federal Office of Energy (SFOE) summarises the activities of the Swiss Federal Commission on Energy Research CORE in 2006. The six main areas of work during the period 2004 - 2007 are examined, including a review of the SFOE's energy research programme, a road-map for the way towards the realisation of a 2000-watt society, the formulation of an energy research concept for 2008 - 2011, international co-operation, the dissemination of information and the assessment of existing and new instruments. International activities and Switzerland's involvement in energy research within the framework of the International Energy Agency IEA are discussed. New and existing projects are listed and the work done at the Competence Centre for Energy and Mobility noted. The Swiss Technology Award 2007 is presented. Information supplied to interested bodies to help improve knowledge on research work being done and to help make discussions on future energy supply more objective is discussed

  16. The Framatome RCVS concept and physics

    Vallee, A.; Millot, J.P.; Bruna, G.

    1986-06-01

    We have tried through this presentation to emphasize on what FRAMATOME thinks to be the most specific problems of the advanced RCVS (Reactor core with spectral shift) core concept (Spectral shift, voidage, reactivity control). Besides, FRAMATOME is analysing the most important safety related topics typically LOCA and DNBR, and has launched developments on them, in connection with CEA. The core behaviour during a loss of Coolant Accident is quite similar to PWR's, the pitch between rods being sufficiently large for clad ballooning not to cause any damage. To conclude, the core improvements developed by FRAMATOME on the RCVS concept economize the use of fissile materials

  17. Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida.

    Vincent, Antony T; Trudel, Mélanie V; Freschi, Luca; Nagar, Vandan; Gagné-Thivierge, Cynthia; Levesque, Roger C; Charette, Steve J

    2016-01-12

    Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date. We sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy. Insertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.

  18. Introductory remote sensing principles and concepts principles and concepts

    Gibson, Paul

    2013-01-01

    Introduction to Remote Sensing Principles and Concepts provides a comprehensive student introduction to both the theory and application of remote sensing. This textbook* introduces the field of remote sensing and traces its historical development and evolution* presents detailed explanations of core remote sensing principles and concepts providing the theory required for a clear understanding of remotely sensed images.* describes important remote sensing platforms - including Landsat, SPOT and NOAA * examines and illustrates many of the applications of remotely sensed images in various fields.

  19. Personalized medicine: new genomics, old lessons

    Offit, Kenneth

    2011-01-01

    Personalized medicine uses traditional, as well as emerging concepts of the genetic and environmental basis of disease to individualize prevention, diagnosis and treatment. Personalized genomics plays a vital, but not exclusive role in this evolving model of personalized medicine. The distinctions between genetic and genomic medicine are more quantitative than qualitative. Personalized genomics builds on principles established by the integration of genetics into medical practice. Principles s...

  20. Characterization of probiotic Escherichia coli isolates with a novel pan-genome microarray

    Willenbrock, Hanni; Hallin, Peter Fischer; Wassenaar, Trudy

    2007-01-01

    of the same species are rapidly becoming available, allowing for the definition and characterization of a whole species as a population of genomes - the 'pan-genome'. Results: Using 32 Escherichia coli and Shigella genome sequences we estimate the pan- and core genome of the species. We designed a high...

  1. Concept Mapping

    Technology & Learning, 2005

    2005-01-01

    Concept maps are graphical ways of working with ideas and presenting information. They reveal patterns and relationships and help students to clarify their thinking, and to process, organize and prioritize. Displaying information visually--in concept maps, word webs, or diagrams--stimulates creativity. Being able to think logically teaches…

  2. Management concepts.

    Bittner, Rhonda

    2006-01-01

    Management concepts evolve through time. Health care managers can learn new concepts by evaluating classical management strategies, as well as modern-day strategies. Focusing on quality improvement and team building can help managers align the goals of their departments with the goals of the organization, consequently improving patient care.

  3. Necrosome core machinery: MLKL.

    Zhang, Jing; Yang, Yu; He, Wenyan; Sun, Liming

    2016-06-01

    In the study of regulated cell death, the rapidly expanding field of regulated necrosis, in particular necroptosis, has been drawing much attention. The signaling of necroptosis represents a sophisticated form of a death pathway. Anti-caspase mechanisms (e.g., using inhibitors of caspases, or genetic ablation of caspase-8) switch cell fate from apoptosis to necroptosis. The initial extracellular death signals regulate RIP1 and RIP3 kinase activation. The RIP3-associated death complex assembly is necessary and sufficient to initiate necroptosis. MLKL was initially identified as an essential mediator of RIP1/RIP3 kinase-initiated necroptosis. Recent studies on the signal transduction using chemical tools and biomarkers support the idea that MLKL is able to make more functional sense for the core machinery of the necroptosis death complex, called the necrosome, to connect to the necroptosis execution. The experimental data available now have pointed that the activated MLKL forms membrane-disrupting pores causing membrane leakage, which extends the prototypical concept of morphological and biochemical events following necroptosis happening in vivo. The key role of MLKL in necroptosis signaling thus sheds light on the logic underlying this unique "membrane-explosive" cell death pathway. In this review, we provide the general concepts and strategies that underlie signal transduction of this form of cell death, and then focus specifically on the role of MLKL in necroptosis.

  4. Herbarium genomics

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

    2016-01-01

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

  5. Lateral Concepts

    Gad, Christopher; Bruun Jensen, casper

    2016-01-01

    This essay discusses the complex relation between the knowledges and practices of the researcher and his/her informants in terms of lateral concepts. The starting point is that it is not the prerogative of the (STS) scholar to conceptualize the world; all our “informants” do it too. This creates...... the possibility of enriching our own conceptual repertoires by letting them be inflected by the concepts of those we study. In a broad sense, the lateral means that there is a many-to-many relation between domains of knowledge and practice. However, each specific case of the lateral is necessarily immanent...... to a particular empirical setting and form of inquiry. In this sense lateral concepts are radically empirical since it locates concepts within the field. To clarify the meaning and stakes of lateral concepts, we first make a contrast between lateral anthropology and Latour’s notion of infra-reflexivity. We end...

  6. Concept theory

    Hjørland, Birger

    2009-01-01

      Concept theory is an extremely broad, interdisciplinary and complex field of research related to many deep fields with very long historical traditions without much consensus. However, information science and knowledge organization cannot avoid relating to theories of concepts. Knowledge...... organizing systems (e.g. classification systems, thesauri and ontologies) should be understood as systems basically organizing concepts and their semantic relations. The same is the case with information retrieval systems. Different theories of concepts have different implications for how to construe......, evaluate and use such systems. Based on "a post-Kuhnian view" of paradigms this paper put forward arguments that the best understanding and classification of theories of concepts is to view and classify them in accordance with epistemological theories (empiricism, rationalism, historicism and pragmatism...

  7. Advantages of iron core in a tokamak

    Bettis, E.S.; Ballou, J.K.; Becraft, W.R.; Peng, Y.K.M.; Watts, H.L.

    1977-01-01

    A quantitative comparison of the iron core vs air core concepts was carried out on a preliminary basis by using a representative tokamak reactor design with the following self-consistent reference parameters. In the area of plasma engineering, poloidal field and MHD equilibrium considerations with an unsaturated iron core is discussed. The question of proper poloidal field coils to maintain D-shaped plasmas of relatively high anti β (7%) with a saturated iron core is also discussed. Estimates of the required iron core size, volt seconds, magnetic flux and its influence on force loading on the superconducting toroidal field coils are shown. Conceptual designs of the mechanical structure of an iron core device are presented. Favorable impacts on the OH power supply cost and complexity are indicated

  8. Development of high performance core for large fast breeder reactors

    Inoue, Kotaro; Kawashima, Katsuyuki; Watari, Yoshio.

    1982-01-01

    Subsequently to the fast breeder prototype reactor ''Monju'', the construction of a demonstration reactor with 1000 MWe output is planned. This research aims at the establishment of the concept of a large core with excellent fuel breeding property and safety for a demonstration and commercial reactors. For the purpose, the optimum specification of fuel design as a large core was clarified, and the new construction of a core was examined, in which a disk-shaped blanket with thin peripheral edge is introduced at the center of a core. As the result, such prospect was obtained that the time for fuel doubling would be 1/2, and the energy generated in a core collapse accident would be about 1/5 as compared with a large core using the same fuel as ''Monju''. Generally, as a core is enlarged, the rate of breeding lowers. If a worst core collapse accident occurs, the scale of accident will be very large in the case of a ''Monju'' type large core. In an unhomogeneous core, an internal blanket is provided in the core for the purpose of improving the breeding property and safety. Hitachi Ltd. developed the concept of a large core unhomogeneous in axial direction and proposed it. The research on the fuel design for a large core, an unhomogeneous core and its core collapse accident is reported. (Kako, I.)

  9. Animal MRI Core

    Federal Laboratory Consortium — The Animal Magnetic Resonance Imaging (MRI) Core develops and optimizes MRI methods for cardiovascular imaging of mice and rats. The Core provides imaging expertise,...

  10. SCORPIO - WWER core surveillance system

    Hornaes, Arne; Bodal, Terje; Sunde, Svein; Zalesky, K.; Lehman, M.; Pecka, M.; Svarny, J.; Krysl, V.; Juzova, Z.; Sedlak, A.; Semmler, M.

    1998-01-01

    The Institut for energiteknikk has developed the core surveillance system SCORPIO, which has two parallel modes of operation: the Core Follow Mode and the Predictive Mode. The main motivation behind the development of SCORPIO is to make a practical tool for reactor operators which can increase the quality and quantity of information presented on core status and dynamic behavior. This can first of all improve plant safety, as undesired core conditions are detected and prevented. Secondly, more flexible and efficient plant operation is made possible. The system has been implemented on western PWRs, but the basic concept is applicable to a wide range of reactors including WWERs. The main differences between WWERs and typical western PWRs with respect to core surveillance requirements are outlined. The development of a WWER version of SCORPIO has been done in co-operation with the Nuclear Research Institute Rez, and industry partners in the Czech Republic. The first system is installed at Dukovany NPP, where the Site Acceptance Test was completed 6. March 1998.(Authors)

  11. SCORPIO - VVER core surveillance system

    Hornaes, A.; Bodal, T.; Sunde, S.

    1998-01-01

    The Institutt for energiteknikk has developed the core surveillance system SCORPIO, which has two parallel modes of operation: the Core Follow Mode and the Predictive Mode. The main motivation behind the development of SCORPIO is to make a practical tool for reactor operators, which can increase the quality and quantity of information presented on core status and dynamic behavior. This can first of all improve plant safety, as undesired core conditions are detected and prevented. Secondly, more flexible and efficient plant operation is made possible. The system has been implemented on western PWRs, but the basic concept is applicable to a wide range of reactors including VVERs. The main differences between VVERs and typical western PWRs with respect to core surveillance requirements are outlined. The development of a VVER version of SCORPIO has been done in co-operation with the Nuclear Research Institute Rez, and industry partners in the Czech Republic. The first system is installed at Dukovany NPP, where the Site Acceptance Test was completed 6. March 1998.(author)

  12. Extreme-Scale De Novo Genome Assembly

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

    2017-09-26

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

  13. Travelling Concepts

    Simonsen, Karen-Margrethe

    2013-01-01

    Review of "Travelling Concepts, Metaphors, and Narratives: Literary and Cultural Studies in an Age of Interdisciplinary Research" ed. by Sibylle Baumgarten, Beatrice Michaelis and Ansagar Nünning, Trier; Wissenschaftlicher Verlag Trier, 2012......Review of "Travelling Concepts, Metaphors, and Narratives: Literary and Cultural Studies in an Age of Interdisciplinary Research" ed. by Sibylle Baumgarten, Beatrice Michaelis and Ansagar Nünning, Trier; Wissenschaftlicher Verlag Trier, 2012...

  14. SCWR Concepts in Japan

    NONE

    2014-08-15

    Two SCWR concepts are being developed in Japan, one corresponding to the thermal spectrum reactor and the other to the fast spectrum reactor. Yamada et al. described the thermal-spectrum reactor concept referred to as the Japan SCWR (or JSCWR). This concept was developed under the financial support of the Ministry of Economy, Trade and Industry (METI). The basic philosophy of the JSCWR development is to utilize proven light water reactor and supercritical fossil-fired power plant technologies as much as possible to minimize the R&D cost, time and risks. Therefore, the JSCWR is designed as a thermal neutron spectrum reactor using light water as moderator and reactor coolant. The JSCWR plant consists of a pressure-vessel type, once-through reactor and a direct Rankine cycle system. Reactor coolant fed through inlet nozzles is heated up in the core and flows through outlet nozzles with no recirculation in the vessel. Other options to the JSCWR core design are being investigated at the University of Tokyo. The electric output of the JSCWR is assumed to range from 600 MWe to 1700 MWe class to fulfill user’s requirements as much as possible. In this section, the reference value is selected to 1725 MWe, which corresponds to a reactor thermal output of 4039 MWth. Nakatsuka et al. described the core design for the fast-spectrum reactor, which is based on a similar plant system compared to that of the thermal-spectrum reactor. The fast-spectrum reactor, however, would produce higher power rating than the thermal-spectrum one of the same reactor pressure-vessel size. Since the fast-spectrum reactor does not require the moderator, its unit capital cost would be lower than the thermal-spectrum reactor.

  15. Cephalopod genomics

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

    2012-01-01

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

  16. Genome Sequencing

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

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

  17. Developments in gaseous core reactor technology

    Diaz, N.J.; Dugan, E.T.

    1979-01-01

    An effort to characterize the most promising concepts for large, central-station electrical generation was done under the auspices of the Nonproliferation Alternative Systems Assessment Program (NASAP). The two leading candidates were identified from this effort: The Mixed-Flow Gaseous Core Reactor (MFGCR) and the Heterogeneous Gas Core Reactor (HGCR). Key advantages over other nuclear concepts are weighed against the disadvantages of an unproven technology and the cost-time for deployment to make a sound decision on RandD support for these promising reactor alternatives. 38 refs

  18. The Salmonella enterica Pan-genome

    Jacobsen, Annika; Hendriksen, Rene S.; Aarestrup, Frank Møller

    2011-01-01

    Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22......, and the core and pan-genome of Salmonella were estimated to be around 2,800 and 10,000 gene families, respectively. The constructed pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype. Any given Salmonella strain has a large stable core, whilst...... there is an abundance of accessory genes, including the Salmonella pathogenicity islands (SPIs), transposable elements, phages, and plasmid DNA. We visualize conservation in the genomes in relation to chromosomal location and DNA structural features and find that variation in gene content is localized in a selection...

  19. Development of core design and analyses technology for integral reactor

    Zee, Sung Quun; Lee, C. C.; Song, J. S. and others

    1999-03-01

    Integral reactors are developed for the applications such as sea water desalination, heat energy for various industries, and power sources for large container ships. In order to enhance the inherent and passive safety features, low power density concept is chosen for the integral reactor SMART. Moreover, ultra-longer cycle and boron-free operation concepts are reviewed for better plant economy and simple design of reactor system. Especially, boron-free operation concept brings about large difference in core configurations and reactivity controls from those of the existing large size commercial nuclear power plants and also causes many differences in the safety aspects. The ultimate objectives of this study include detailed core design of a integral reactor, development of the core design system and technology, and finally acquisition of the system design certificate. The goal of the first stage is the conceptual core design, that is, to establish the design bases and requirements suitable for the boron-free concept, to develop a core loading pattern, to analyze the nuclear, thermal and hydraulic characteristics of the core and to perform the core shielding design. Interface data for safety and performance analyses including fuel design data are produced for the relevant design analysis groups. Nuclear, thermal and hydraulic, shielding design and analysis code systems necessary for the core conceptual design are established through modification of the existing design tools and newly developed methodology and code modules. Core safety and performance can be improved by the technology development such as boron-free core optimization, advaned core monitoring and operational aid system. Feasiblity study on the improvement of the core protection and monitoring system will also contribute toward core safety and performance. Both the conceptual core design study and the related technology will provide concrete basis for the next design phase. This study will also

  20. Development of core design and analyses technology for integral reactor

    Zee, Sung Quun; Lee, C. C.; Song, J. S. and others

    1999-03-01

    Integral reactors are developed for the applications such as sea water desalination, heat energy for various industries, and power sources for large container ships. In order to enhance the inherent and passive safety features, low power density concept is chosen for the integral reactor SMART. Moreover, ultra-longer cycle and boron-free operation concepts are reviewed for better plant economy and simple design of reactor system. Especially, boron-free operation concept brings about large difference in core configurations and reactivity controls from those of the existing large size commercial nuclear power plants and also causes many differences in the safety aspects. The ultimate objectives of this study include detailed core design of a integral reactor, development of the core design system and technology, and finally acquisition of the system design certificate. The goal of the first stage is the conceptual core design, that is, to establish the design bases and requirements suitable for the boron-free concept, to develop a core loading pattern, to analyze the nuclear, thermal and hydraulic characteristics of the core and to perform the core shielding design. Interface data for safety and performance analyses including fuel design data are produced for the relevant design analysis groups. Nuclear, thermal and hydraulic, shielding design and analysis code systems necessary for the core conceptual design are established through modification of the existing design tools and newly developed methodology and code modules. Core safety and performance can be improved by the technology development such as boron-free core optimization, advaned core monitoring and operational aid system. Feasiblity study on the improvement of the core protection and monitoring system will also contribute toward core safety and performance. Both the conceptual core design study and the related technology will provide concrete basis for the next design phase. This study will also

  1. An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli.

    Bohlin, Jon; Brynildsrud, Ola B; Sekse, Camilla; Snipen, Lars

    2014-10-09

    There are several studies describing loss of genes through reductive evolution in microbes, but how selective forces are associated with genome expansion due to horizontal gene transfer (HGT) has not received similar attention. The aim of this study was therefore to examine how selective pressures influence genome expansion in 53 fully sequenced and assembled Escherichia coli strains. We also explored potential connections between genome expansion and the attainment of virulence factors. This was performed using estimations of several genomic parameters such as AT content, genomic drift (measured using relative entropy), genome size and estimated HGT size, which were subsequently compared to analogous parameters computed from the core genome consisting of 1729 genes common to the 53 E. coli strains. Moreover, we analyzed how selective pressures (quantified using relative entropy and dN/dS), acting on the E. coli core genome, influenced lineage and phylogroup formation. Hierarchical clustering of dS and dN estimations from the E. coli core genome resulted in phylogenetic trees with topologies in agreement with known E. coli taxonomy and phylogroups. High values of dS, compared to dN, indicate that the E. coli core genome has been subjected to substantial purifying selection over time; significantly more than the non-core part of the genome (pcoli genome size correlated with estimated HGT size (pcoli are largely attained through HGT. No associations were found between selective pressures operating on the E. coli core genome, as estimated using relative entropy, and genome size (p~0.98). On a larger time frame, genome expansion in E. coli, which is significantly associated with the acquisition of virulence factors, appears to be independent of selective forces operating on the core genome.

  2. Core Hunter 3: flexible core subset selection.

    De Beukelaer, Herman; Davenport, Guy F; Fack, Veerle

    2018-05-31

    Core collections provide genebank curators and plant breeders a way to reduce size of their collections and populations, while minimizing impact on genetic diversity and allele frequency. Many methods have been proposed to generate core collections, often using distance metrics to quantify the similarity of two accessions, based on genetic marker data or phenotypic traits. Core Hunter is a multi-purpose core subset selection tool that uses local search algorithms to generate subsets relying on one or more metrics, including several distance metrics and allelic richness. In version 3 of Core Hunter (CH3) we have incorporated two new, improved methods for summarizing distances to quantify diversity or representativeness of the core collection. A comparison of CH3 and Core Hunter 2 (CH2) showed that these new metrics can be effectively optimized with less complex algorithms, as compared to those used in CH2. CH3 is more effective at maximizing the improved diversity metric than CH2, still ensures a high average and minimum distance, and is faster for large datasets. Using CH3, a simple stochastic hill-climber is able to find highly diverse core collections, and the more advanced parallel tempering algorithm further increases the quality of the core and further reduces variability across independent samples. We also evaluate the ability of CH3 to simultaneously maximize diversity, and either representativeness or allelic richness, and compare the results with those of the GDOpt and SimEli methods. CH3 can sample equally representative cores as GDOpt, which was specifically designed for this purpose, and is able to construct cores that are simultaneously more diverse, and either are more representative or have higher allelic richness, than those obtained by SimEli. In version 3, Core Hunter has been updated to include two new core subset selection metrics that construct cores for representativeness or diversity, with improved performance. It combines and outperforms the

  3. Comparative Genomics

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

  4. Tuned Chamber Core Panel Acoustic Test Results

    Schiller, Noah H.; Allen, Albert R.

    2016-01-01

    This report documents acoustic testing of tuned chamber core panels, which can be used to supplement the low-frequency performance of conventional acoustic treatment. The tuned chamber core concept incorporates low-frequency noise control directly within the primary structure and is applicable to sandwich constructions with a directional core, including corrugated-, truss-, and fluted-core designs. These types of sandwich structures have long, hollow channels (or chambers) in the core. By adding small holes through one of the facesheets, the hollow chambers can be utilized as an array of low-frequency acoustic resonators. These resonators can then be used to attenuate low-frequency noise (below 400 Hz) inside a vehicle compartment without increasing the weight or size of the structure. The results of this test program demonstrate that the tuned chamber core concept is effective when used in isolation or combined with acoustic foam treatments. Specifically, an array of acoustic resonators integrated within the core of the panels was shown to improve both the low-frequency absorption and transmission loss of the structure in targeted one-third octave bands.

  5. Human Adenovirus Core Protein V Is Targeted by the Host SUMOylation Machinery To Limit Essential Viral Functions.

    Freudenberger, Nora; Meyer, Tina; Groitl, Peter; Dobner, Thomas; Schreiner, Sabrina

    2018-02-15

    Human adenoviruses (HAdV) are nonenveloped viruses containing a linear, double-stranded DNA genome surrounded by an icosahedral capsid. To allow proper viral replication, the genome is imported through the nuclear pore complex associated with viral core proteins. Until now, the role of these incoming virion proteins during the early phase of infection was poorly understood. The core protein V is speculated to bridge the core and the surrounding capsid. It binds the genome in a sequence-independent manner and localizes in the nucleus of infected cells, accumulating at nucleoli. Here, we show that protein V contains conserved SUMO conjugation motifs (SCMs). Mutation of these consensus motifs resulted in reduced SUMOylation of the protein; thus, protein V represents a novel target of the host SUMOylation machinery. To understand the role of protein V SUMO posttranslational modification during productive HAdV infection, we generated a replication-competent HAdV with SCM mutations within the protein V coding sequence. Phenotypic analyses revealed that these SCM mutations are beneficial for adenoviral replication. Blocking protein V SUMOylation at specific sites shifts the onset of viral DNA replication to earlier time points during infection and promotes viral gene expression. Simultaneously, the altered kinetics within the viral life cycle are accompanied by more efficient proteasomal degradation of host determinants and increased virus progeny production than that observed during wild-type infection. Taken together, our studies show that protein V SUMOylation reduces virus growth; hence, protein V SUMOylation represents an important novel aspect of the host antiviral strategy to limit virus replication and thereby points to potential intervention strategies. IMPORTANCE Many decades of research have revealed that HAdV structural proteins promote viral entry and mainly physical stability of the viral genome in the capsid. Our work over the last years showed that this

  6. k-core covers and the core

    Sanchez-Rodriguez, E.; Borm, Peter; Estevez-Fernandez, A.; Fiestras-Janeiro, G.; Mosquera, M.A.

    This paper extends the notion of individual minimal rights for a transferable utility game (TU-game) to coalitional minimal rights using minimal balanced families of a specific type, thus defining a corresponding minimal rights game. It is shown that the core of a TU-game coincides with the core of

  7. REGEN: Ancestral Genome Reconstruction for Bacteria

    João C. Setubal

    2012-07-01

    Full Text Available Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.

  8. The characterization of twenty sequenced human genomes.

    Kimberly Pelak

    2010-09-01

    Full Text Available We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten "case" genomes from individuals with severe hemophilia A and ten "control" genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways.

  9. REGEN: Ancestral Genome Reconstruction for Bacteria.

    Yang, Kuan; Heath, Lenwood S; Setubal, João C

    2012-07-18

    Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.

  10. Conceptual core designs for a 1200 MWe sodium cooled fast reactor

    Joo, H. K.; Lee, K. B.; Yoo, J. W.; Kim, Y. I.

    2008-01-01

    The conceptual core design for a 1200 MWe sodium cooled fast reactor is being developed under the framework of the Gen-IV SFR development program. To this end, three core concepts have been tested during the development of a core concept: a core with an enrichment split fuel, a core with a single-enrichment fuel with a region-wise varying clad thickness, and a core with a single-enrichment fuel with non-fuel rods. In order to optimize a conceptual core configuration which satisfies the design targets, a sensitivity study of the core design parameters has been performed. Two core concepts, the core with an enrichment-split fuel and the core with a single-enrichment fuel with a region-wise varying clad thickness, have been proposed as the candidates of the conceptual core for a 1200 MWe sodium cooled fast reactor. The detailed core neutronic, fuel behavior, thermal, and safety analyses will be performed for the proposed candidate core concepts to finalize the core design concept. (authors)

  11. Computer Science Concept Inventories: Past and Future

    Taylor, C.; Zingaro, D.; Porter, L.; Webb, K. C.; Lee, C. B.; Clancy, M.

    2014-01-01

    Concept Inventories (CIs) are assessments designed to measure student learning of core concepts. CIs have become well known for their major impact on pedagogical techniques in other sciences, especially physics. Presently, there are no widely used, validated CIs for computer science. However, considerable groundwork has been performed in the form…

  12. Genomic technologies in neonatology

    L. N. Chernova

    2017-01-01

    Full Text Available In recent years, there has been a tremendous trend toward personalized medicine. Advances in the field forced clinicians, including neonatologists, to take a fresh look at prevention, tactics of management and therapy of various diseases. In the center of attention of foreign, and increasingly Russian, researchers and doctors, there are individual genomic data that allow not only to assess the risks of some form of pathology, but also to successfully apply personalized strategies of prediction, prevention and targeted treatment. This article provides a brief review of the latest achievements of genomic technologies in newborns, examines the problems and potential applications of genomics in promoting the concept of personalized medicine in neonatology. The increasing amount of personalized data simply impossible to analyze only by the human mind. In this connection, the need of computers and bioinformatics is obvious. The article reveals the role of translational bioinformatics in the analysis and integration of the results of the accumulated fundamental research into complete clinical decisions. The latest advances in neonatal translational bioinformatics such as clinical decision support systems are considered. It helps to monitor vital parameters of newborns influencing the course of a particular disease, to calculate the increased risks of the development of various pathologies and to select the drugs.

  13. Comparing Mycobacterium tuberculosis genomes using genome topology networks.

    Jiang, Jianping; Gu, Jianlei; Zhang, Liang; Zhang, Chenyi; Deng, Xiao; Dou, Tonghai; Zhao, Guoping; Zhou, Yan

    2015-02-14

    Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/ , and allows re-annotating the 'lost' genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes

  14. Basic concepts

    Dorner, B.

    1999-01-01

    The basic concepts of neutron scattering as a tool for studying the structure and the dynamics of condensed matter. Theoretical aspects are outlined, the two different cases of coherent and incoherent scattering are presented. The issue of resolution, coherence volume and the role of monochromators are also discussed. (K.A.)

  15. Simple Concepts

    Materna, Pavel

    2013-01-01

    Roč. 28, č. 3 (2013), s. 295-319 ISSN 0353-5150 R&D Projects: GA ČR(CZ) GAP401/10/0792 Institutional support: RVO:67985955 Keywords : concept * constructions * set-theoretical paradigm Subject RIV: AA - Philosophy ; Religion

  16. Evaluating Community Health Advisor (CHA) Core Competencies: The CHA Core Competency Retrospective Pretest/Posttest (CCCRP).

    Story, Lachel; To, Yen M

    2016-05-01

    Health care and academic systems are increasingly collaborating with community health advisors (CHAs) to provide culturally relevant health interventions that promote sustained community transformation. Little attention has been placed on CHA training evaluation, including core competency attainment. This study identified common CHA core competencies, generated a theoretically based measure of those competencies, and explored psychometric properties of that measure. A concept synthesis revealed five CHA core competencies (leadership, translation, guidance, advocacy, and caring). The CHA Core Competency Retrospective Pretest/Posttest (CCCRP) resulted from that synthesis, which was administered using multiple approaches to individuals who previously received CHA training (N= 142). Exploratory factor analyses revealed a two-factor structure underlying the posttraining data, and Cronbach's alpha indicated high internal consistency. This study suggested some CHA core competencies might be more interrelated than previously thought, and two major competencies exist rather than five and supported the CCCRP's use to evaluate core competency attainment resulting from training. © The Author(s) 2014.

  17. Personal genomics services: whose genomes?

    Gurwitz, David; Bregman-Eschet, Yael

    2009-07-01

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

  18. Nuclear reactor core catcher

    1977-01-01

    A nuclear reactor core catcher is described for containing debris resulting from an accident causing core meltdown and which incorporates a method of cooling the debris by the circulation of a liquid coolant. (U.K.)

  19. New approach to the design of core support structures for large LMFBR plants

    Burelbach, J.P.; Kann, W.J.; Pan, Y.C.; Saiveau, J.G.; Seidensticker, R.W.

    1984-01-01

    The paper describes an innovative design concept for a LMFBR Core Support Structure. A hanging Core Support Structure is described and analyzed. The design offers inherent safety features, constructibility advantages, and potential cost reductions

  20. Seismic core shroud

    Puri, A.; Mullooly, J.F.

    1981-01-01

    A core shroud is provided, comprising: a coolant boundary, following the shape of the core boundary, for channeling the coolant through the fuel assemblies; a cylindrical band positioned inside the core barrel and surrounding the coolant boundary; and support members extending from the coolant boundary to the band, for transferring load from the coolant boundary to the band. The shroud may be assembled in parts using automated welding techniques, and it may be adjusted to fit the reactor core easily

  1. Investigation of genome sequences within the family Pasteurellaceae

    Angen, Øystein; Ussery, David

    Introduction The bacterial genome sequences are now available for an increasing number of strains within the family Pasteurellaceae. At present, 24 Pasteurellaceae genomes are publicly available through internet databases, and another 40 genomes are being sequenced. This investigation will describe...... the core genome for both the family Pasteurellaceae and for the species Haemophilus influenzae. Methods Twenty genome sequences from the following species were included: Haemophilus influenzae (11 strains), Haemophilus ducreyi (1 strain), Histophilus somni (2 strains), Haemophilus parasuis (1 strain......), Actinobacillus pleuropneumoniae (2 strains), Actinobacillus succinogenes (1 strain), Mannheimia succiniciproducens (1 strain), and Pasteurella multocida (1 strain). The predicted proteins for each genome were BLASTed against each other, and a set of conserved core gene families was determined as described...

  2. Astrophysical Concepts

    Harwit, Martin

    2006-01-01

    This classic text, aimed at senior undergraduates and beginning graduate students in physics and astronomy, presents a wide range of astrophysical concepts in sufficient depth to give the reader a quantitative understanding of the subject. Emphasizing physical concepts, the book outlines cosmic events but does not portray them in detail: it provides a series of astrophysical sketches. For this fourth edition, nearly every part of the text has been reconsidered and rewritten, new sections have been added to cover recent developments, and others have been extensively revised and brought up to date. The book begins with an outline of the scope of modern astrophysics and enumerates some of the outstanding problems faced in the field today. The basic physics needed to tackle these questions are developed in the next few chapters using specific astronomical processes as examples. The second half of the book enlarges on these topics and shows how we can obtain quantitative insight into the structure and evolution of...

  3. Visualization for genomics: the Microbial Genome Viewer.

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

    2004-01-01

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

  4. Core Ideas of Engineering and Technology

    Sneider, Cary

    2012-01-01

    Last month, Rodger Bybee's article, "Scientific and Engineering Practices in K-12 Classrooms," provided an overview of Chapter 3 in "A Framework for K-12 Science Education: Practices, Crosscutting Concepts, and Core Ideas" (NRC 2011). Chapter 3 describes the practices of science and engineering that students are expected to develop during 13 years…

  5. Core Values | NREL

    Core Values Core Values NREL's core values are rooted in a safe and supportive work environment guide our everyday actions and efforts: Safe and supportive work environment Respect for the rights physical and social environment Integrity Maintain the highest standard of ethics, honesty, and integrity

  6. Sidewall coring shell

    Edelman, Ya A; Konstantinov, L P; Martyshin, A N

    1966-12-12

    A sidewall coring shell consists of a housing and a detachable core catcher. The core lifter is provided with projections, the ends of which are situated in another plane, along the longitudinal axis of the lifter. The chamber has corresponding projections.

  7. Design study on metal fuel FBR cores

    Yokoo, T.; Tanaka, Y.; Ogata, T.

    1991-01-01

    A design approach for metal fuel FBR core to maintain fuel integrity during transient events by limiting eutectic/liquid phase formation is proposed based on the current status of metallic fuel development. Its impact as the limitation on the core outlet temperature is assessed through its application to two of CRIEPI's core concepts, high linear power 1000 MWe homogeneous design and medium linear power 300 MWe radially heterogeneous design. SESAME/SALT code is used in this study to analyze steady state and transient fuel behavior. SE2-FA code is developed based on SUPERENERGY-2 and used to analyze core thermal-hydraulics with uncertainties. As the result, the core outlet temperatures of both designs are found to be limited to ≤500degC if it is required to prevent eutectic/liquid phase formation during operational transients in order to guarantee the fuel integrity. Additional assessment is made assuming an advanced limiting condition that allows small liquid phase formation based on the liquid phase penetration rate derived from existing experimental results. The result indicates possibility of raising core outlet temperature to ∼ 530degC. Also, it is found that core design technology improvements such as hot spot factors reduction can contribute to the core outlet temperature extension by 10 ∼ 20degC. (author)

  8. Development of core design technology for LMR

    Kim, Young Jin; In, Kim Young; Kim, Young Il; Kim, Y G; Kim, S J; Song, H; Kim, T K; Kim, W S; Hwang, W; Lee, B O; Park, C K; Joo, H K; Yoo, J W; Kang, H Y; Park, W S

    2000-05-01

    For the development of KALIMER (150 MWe) core conceptual design, design evolution and optimization for improved economics and safety enhancement was performed in the uranium metallic fueled equilibrium core design which uses U-Zr binary fuel not in excess of 20 percent enrichment. Utilizing results of the uranium ,metallic fueled core design, the breeder equilibrium core design with breeding ratio being over 1.1 was developed. In addition, utilizing LMR's excellent neutron economy, various core concepts for minor actinide burnup, inherent safety, economics and non-proliferation were realized and its optimization studies were performed. A code system for the LMR core conceptual design has been established through the implementation of needed functions into the existing codes and development of codes. To improve the accuracy of the core design, a multi-dimensional nodal transport code SOLTRAN, a three-dimensional transient code analysis code STEP, MATRA-LMR and ASSY-P for T/H analysis are under development. Through the automation of design calculations for efficient core design, an input generator and several interface codes have been developed. (author)

  9. Development of core design technology for LMR

    Kim, Young Jin; Kim Young In; Kim, Young Il; Kim, Y. G.; Kim, S. J.; Song, H.; Kim, T. K.; Kim, W. S.; Hwang, W.; Lee, B. O.; Park, C. K.; Joo, H. K.; Yoo, J. W.; Kang, H. Y.; Park, W. S

    2000-05-01

    For the development of KALIMER (150 MWe) core conceptual design, design evolution and optimization for improved economics and safety enhancement was performed in the uranium metallic fueled equilibrium core design which uses U-Zr binary fuel not in excess of 20 percent enrichment. Utilizing results of the uranium ,metallic fueled core design, the breeder equilibrium core design with breeding ratio being over 1.1 was developed. In addition, utilizing LMR's excellent neutron economy, various core concepts for minor actinide burnup, inherent safety, economics and non-proliferation were realized and its optimization studies were performed. A code system for the LMR core conceptual design has been established through the implementation of needed functions into the existing codes and development of codes. To improve the accuracy of the core design, a multi-dimensional nodal transport code SOLTRAN, a three-dimensional transient code analysis code STEP, MATRA-LMR and ASSY-P for T/H analysis are under development. Through the automation of design calculations for efficient core design, an input generator and several interface codes have been developed. (author)

  10. Comparative RNA genomics

    Backofen, Rolf; Gorodkin, Jan; Hofacker, Ivo L.

    2018-01-01

    Over the last two decades it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly...... small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs...... that exert a vastly diverse array of molecule functions. In this chapter we provide a—necessarily incomplete—overview of the current state of comparative analysis of noncoding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world....

  11. Introductory concepts

    Barnes, W.E.

    1983-01-01

    Physical theories are commonly classified as being either ''classical'' or ''modern''. The reasons for this distinction are both historical and substantive. Limited in the sophistication of their measuring instruments, early scientists proposed theories appropriate for the description of the simplest and most accessible physical phenomena, e.g., the trajectories of the planets. Because of the class of phenomena observed, certain beliefs came to underlie all classical theories with regard to the nature of time, space, matter, etc. For example, the idea was undisputed that an object has at all times both a definite position and velocity. Not until the interior of the atom and the nature of electromagnetic radiation were explored was it discovered that the concepts of classical physics are inadequate to deal with many phenomena. A reassessment of fundamental postulates led to the formulation of modern physics which, it is believed, successfully treats the behavior of all physical systems. To gain an understanding of the rudiments of modern physics, one proceeds as the early scientists did by first mastering the classical concepts that emerge from their intuitive picture of the world. Modifications of these concepts are subsequently introduced which allow a more accurate treatment of physical phenomena, particularly atomic and nuclear systems

  12. Innovative reactor core: potentialities and design

    Artioli, C.; Petrovich, Carlo; Grasso, Giacomo

    2010-01-01

    Gen IV nuclear reactors are considered a very attractive answer for the demand of energy. Because public acceptance they have to fulfil very clearly the requirement of sustainable development. In this sense a reactor concept, having by itself a rather no significant interaction with the environment both on the front and back end ('adiabatic concept'), is vital. This goal in mind, a new way of designing such a core has to be assumed. The starting point must be the 'zero impact'. Therefore the core will be designed having as basic constraints: a) fed with only natural or depleted Uranium, and b) discharges only fission products. Meantime its potentiality as a net burner of Minor Actinide has to be carefully estimated. This activity, referred to the ELSY reactor, shows how to design such an 'adiabatic' core and states its reasonable capability of burning MA legacy in the order of 25-50 kg/GW e y. (authors)

  13. Molten salt reactor concept

    Sood, D.D.

    1980-01-01

    Molten salt reactor is an advanced breeder concept which is suited for the utilization of thorium for nuclear power production. This reactor is based on the use of solutions of uranium or plutonium fluorides in LiF-BeF 2 -ThF 4 as fuel. Unlike the conventional reactors, no external coolant is used in the reactor core and the fuel salt itself is circulated through heat exchangers to transfer the fission produced heat to a secondary salt (NaF-NaBF 4 ) for steam generation. A part of the fuel stream is continuously processed to isolate 233 Pa, so that it can decay to fissile 233 U without getting converted to 234 Pa, and for the removal of neutron absorbing fission products. This on-line processing scheme makes this reactor concept to achieve a breeding ratio of 1.07 which is the highest for any thermal breeder reactor. Experimental studies at the Bhabha Atomic Research Centre, Bombay, have established the use of plutonium as fuel for this reactor. This molten salt reactor concept is described and the work conducted at the Bhabha Atomic Research Centre is summarised. (auth.)

  14. SCWR Concept in Korea

    NONE

    2014-08-15

    One of the major difficulties in the design of an SCWR is the additional neutron moderation in order to compensate the low coolant density in the later stage of coolant heat-up. The water rod concept was introduced as a simple method to provide additional moderation, however it may result in an inevitable complexity in the design of the reactor upper part. A solid moderator concept was introduced in the Korean SCWR to avoid this difficulty. A conceptual design of a 1400 MWe SCWR core with a cruciform type of U/ZrH{sub 2} solid moderator has been studied. The design features include a solid moderator design, an axial zoning of the burnable poison and fuel rod, a flow rate control by adjusting the orifice design, and a control rod design for an excess reactivity control. The maximum power peaking is 2.48 and the maximum coolant temperature is 577°C. Reactivity coefficients such as the moderator temperature coefficient and fuel temperature coefficient are negative for the whole burn-up period. At a cold zero power condition, the minimum shutdown margin is 1.16%Δρ at the beginning of a cycle, which satisfies the required shutdown margin limit. The concept described here should not be considered as a complete one, but a preliminary idea. It is solely based on information frozen at the time, and is subject to further improvement.

  15. Passage relevance models for genomics search

    Frieder Ophir

    2009-03-01

    Full Text Available Abstract We present a passage relevance model for integrating syntactic and semantic evidence of biomedical concepts and topics using a probabilistic graphical model. Component models of topics, concepts, terms, and document are represented as potential functions within a Markov Random Field. The probability of a passage being relevant to a biologist's information need is represented as the joint distribution across all potential functions. Relevance model feedback of top ranked passages is used to improve distributional estimates of query concepts and topics in context, and a dimensional indexing strategy is used for efficient aggregation of concept and term statistics. By integrating multiple sources of evidence including dependencies between topics, concepts, and terms, we seek to improve genomics literature passage retrieval precision. Using this model, we are able to demonstrate statistically significant improvements in retrieval precision using a large genomics literature corpus.

  16. RUCS: Rapid identification of PCR primers for unique core sequences

    Thomsen, Martin Christen Frølund; Hasman, Henrik; Westh, Henrik

    2017-01-01

    Designing PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous, and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs...... for the targets in silico . Here we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex...... in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin...

  17. Rotary core drills

    1967-11-30

    The design of a rotary core drill is described. Primary consideration is given to the following component parts of the drill: the inner and outer tube, the core bit, an adapter, and the core lifter. The adapter has the form of a downward-converging sleeve and is mounted to the lower end of the inner tube. The lifter, extending from the adapter, is split along each side so that it can be held open to permit movement of a core. It is possible to grip a core by allowing the lifter to assume a closed position.

  18. GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

    Yuan, Lina; Yu, Yang; Zhu, Yanmin; Li, Yulai; Li, Changqing; Li, Rujiao; Ma, Qin; Siu, Gilman Kit-Hang; Yu, Jun; Jiang, Taijiao; Xiao, Jingfa; Kang, Yu

    2017-01-25

    Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.

  19. Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups

    Guillermo Nourdin-Galindo

    2017-10-01

    Full Text Available Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these

  20. HYDRATE CORE DRILLING TESTS

    John H. Cohen; Thomas E. Williams; Ali G. Kadaster; Bill V. Liddell

    2002-11-01

    The ''Methane Hydrate Production from Alaskan Permafrost'' project is a three-year endeavor being conducted by Maurer Technology Inc. (MTI), Noble, and Anadarko Petroleum, in partnership with the U.S. DOE National Energy Technology Laboratory (NETL). The project's goal is to build on previous and ongoing R&D in the area of onshore hydrate deposition. The project team plans to design and implement a program to safely and economically drill, core and produce gas from arctic hydrates. The current work scope includes drilling and coring one well on Anadarko leases in FY 2003 during the winter drilling season. A specially built on-site core analysis laboratory will be used to determine some of the physical characteristics of the hydrates and surrounding rock. Prior to going to the field, the project team designed and conducted a controlled series of coring tests for simulating coring of hydrate formations. A variety of equipment and procedures were tested and modified to develop a practical solution for this special application. This Topical Report summarizes these coring tests. A special facility was designed and installed at MTI's Drilling Research Center (DRC) in Houston and used to conduct coring tests. Equipment and procedures were tested by cutting cores from frozen mixtures of sand and water supported by casing and designed to simulate hydrate formations. Tests were conducted with chilled drilling fluids. Tests showed that frozen core can be washed out and reduced in size by the action of the drilling fluid. Washing of the core by the drilling fluid caused a reduction in core diameter, making core recovery very difficult (if not impossible). One successful solution was to drill the last 6 inches of core dry (without fluid circulation). These tests demonstrated that it will be difficult to capture core when drilling in permafrost or hydrates without implementing certain safeguards. Among the coring tests was a simulated hydrate

  1. Ancient genomics

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

    2015-01-01

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

  2. Marine genomics

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

    2017-01-01

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

  3. Core Pedagogy: Individual Uncertainty, Shared Practice, Formative Ethos

    Dotger, Benjamin H.

    2015-01-01

    Attention to the core practices of teaching necessitates core pedagogies in teacher preparation. This article outlines the diffusion of one such pedagogy from medical to teacher education. The concept of clinical simulations is outlined through the lens of "signature pedagogies" and their uncertain, engaging, formative qualities.…

  4. Product Image to Build the Core Competitiveness of Enterprises

    Shi Yan

    2017-01-01

    Full Text Available As a new specialty research field, Product Image is being paid more attention. This article introduced the concept of Product Image and Core-competition, and illustrated how to conduct Core-competition of enterprise from two aspects of the foundation of Product Image and the communication of Product Image.

  5. Simulation and Representation of Body, Emotion, and Core Consciousness

    Bosse, T.; Jonker, C.M.; Treur, J.; Henderson-Sellers, B.; Winikoff, M.

    2005-01-01

    This paper contributes an analysis and formalisation of Damasio's theory on core consciousness. Three important concepts in this theory are 'emotion', 'feeling', and 'feeling a feeling' (or core consciousness). In particular, a simulation model is described of the neural dynamics leading via emotion

  6. Common Core Science Standards: Implications for Students with Learning Disabilities

    Scruggs, Thomas E.; Brigham, Frederick J.; Mastropieri, Margo A.

    2013-01-01

    The Common Core Science Standards represent a new effort to increase science learning for all students. These standards include a focus on English and language arts aspects of science learning, and three dimensions of science standards, including practices of science, crosscutting concepts of science, and disciplinary core ideas in the various…

  7. Sensitivity of reactivity feedback due to core bowing in a metallic-fueled core

    Nakagawa, Masatoshi; Kawashima, Masatoshi; Endo, Hiroshi; Nishimura, Tomohiro

    1991-01-01

    A sensitivity study has been carried out on negative reactivity feedback caused by core bowing to assess the potential effectiveness of FBR passive safety features in regard to withstanding an anticipated transient without scram (ATWS). In the present study, an analysis has been carried to obtain the best material and geometrical conditions concerning the core restraint system out for several power to flow rates (P/F), up to 2.0 for a 300 MWe metallic-fueled core. From this study, it was clarified that the pad stiffness at an above core loading pads (ACLP) needs to be large enough to ensure negative reactivity feedback against ATWS. It was also clarified that there is an upper limit for the clearances between ducts at ACLP. A new concept, in regard to increasing the absolute value for negative reactivity feedback due to core bowing at ATWS, is proposed and discussed. (author)

  8. Analysis the Response Function of the HTR Ex-core Neutron Detectors in Different Core Status

    Fan Kai; Li Fu; Zhou Xuhua

    2014-01-01

    Modular high temperature gas cooled reactor HTR-PM demonstration plant, designed by INET, Tsinghua University, is being built in Shidao Bay, Shandong province, China. HTR-PM adopts pebble bed concept. The harmonic synthesis method has been developed to reconstruct the power distributions on HTR-PM. The method based on the assumption that the neutron detector readings are mainly determined by the status of the core through the power distribution, and the response functions changed little when the status of the core changed. To verify the assumption, the influence factors to the ex-core neutron detectors are calculated in this paper, including the control rod position and the temperature of the core. The results shows that when the status of the core changed, the power distribution changed more remarkable than the response function, but the detector readings could change about 5% because of the response function changing. (author)

  9. Conceptual design study of LMFBR core with carbide fuel

    Tezuka, H.; Hojuyama, T.; Osada, H.; Ishii, T.; Hattori, S.; Nishimura, T.

    1987-01-01

    Carbide fuel is a hopeful candidate for demonstration FBR(DFBR) fuel from the plant cost reduction point of view. High thermal conductivity and high heavy metal content of carbide fuel lead to high linear heat rate and high breeding ratio. We have analyzed carbide fuel core characteristics and have clarified the concept of carbide fuel core. By survey calculation, we have obtained a correlation map between core parameters and core characteristics. From the map, we have selected a high efficiency core whose features are better than those of an oxide core, and have obtained reactivity coefficients. The core volume and the reactor fuel inventory are approximately 20% smaller, and the burn-up reactivity loss is 50% smaller compared with the oxide fuel core. These results will reduce the capital cost. The core reactivity coefficients are similar to the conventional oxide DFBR's. Therefore the carbide fuel core is regarded as safe as the oxide core. Except neutron fluence, the carbide fuel core has better nuclear features than the oxide core

  10. The core paradox.

    Kennedy, G. C.; Higgins, G. H.

    1973-01-01

    Rebuttal of suggestions from various critics attempting to provide an escape from the seeming paradox originated by Higgins and Kennedy's (1971) proposed possibility that the liquid in the outer core was thermally stably stratified and that this stratification might prove a powerful inhibitor to circulation of the outer core fluid of the kind postulated for the generation of the earth's magnetic field. These suggestions are examined and shown to provide no reasonable escape from the core paradox.

  11. Nuclear reactor core flow baffling

    Berringer, R.T.

    1979-01-01

    A flow baffling arrangement is disclosed for the core of a nuclear reactor. A plurality of core formers are aligned with the grids of the core fuel assemblies such that the high pressure drop areas in the core are at the same elevations as the high pressure drop areas about the core periphery. The arrangement minimizes core bypass flow, maintains cooling of the structure surrounding the core, and allows the utilization of alternative beneficial components such as neutron reflectors positioned near the core

  12. Genomic evolution of 11 type strains within family Planctomycetaceae.

    Min Guo

    Full Text Available The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes orthology system. Subsequently, we identified genomic islands (GIs and structural variations (SVs among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.

  13. Sediment Core Laboratory

    Federal Laboratory Consortium — FUNCTION: Provides instrumentation and expertise for physical and geoacoustic characterization of marine sediments.DESCRIPTION: The multisensor core logger measures...

  14. Provincializing and Localizing Core-Periphery Relations

    Cilja Harders

    2015-11-01

    Full Text Available The paper engages engages with core-periphery conceptions because they are a useful "Denkfigur" in a time of increasing global interconnectedness. I argue that the core-periphery metaphor is a useful one because it provides us (1 with a relational tool of analysis and (2 with a focus on asymmetric power-relations. But it also has some serious limitations such as a tendency to be over-deterministic and to be too global in scale. In order to meet these limitations, I suggest to re-scale Prebisch, Amin and Wallersteins global conception of core and periphery to the local scale. I hold that we need to “provincialise” the core-periphery metaphor to borrow Chakrabarty’s (2000 famous term and to make the agency of local actors more relevant to our understanding of political dynamics in the Maghreb, Mashreq and Gulf region. I sketch how “provincialized” and “localized” ways of using the core-periphery metaphor could look like. This part builds on the main ideas Malika Bouziane, Anja Hoffmann and I developed in the introduction to our volume on “Local Politics and Contemporary Transformations in the Arab World” as well as my approach of a “state analysis from below”.

  15. Can Psychiatric Rehabilitation Be Core to CORE?

    Olney, Marjorie F.; Gill, Kenneth J.

    2016-01-01

    Purpose: In this article, we seek to determine whether psychiatric rehabilitation principles and practices have been more fully incorporated into the Council on Rehabilitation Education (CORE) standards, the extent to which they are covered in four rehabilitation counseling "foundations" textbooks, and how they are reflected in the…

  16. Thermal neutrons core concepts for minor actinides inventory reduction

    Huang, Shio-Ling

    1996-01-01

    The goal of this thesis is to propose a solution to the problem of reducing the inventory of Minor Actinides, discharged from PWR spent fuel, in the framework of a Separation/ Transmutation strategy. The solution envisaged is based on the utilisation of Pressurised Water Reactors (PWR), of the same type as those used to produce energy. The suggested solution is original and based on a special Assembly ANDIAMO dedicated to transmutation, where Actinide incineration is performed with the help of a fissile support in a once-through strategy. During this study, we have also tackled the impact of some parameters which so far have been less carefully studied (like the unavoidable presence of Lanthanides in fuel containing Am and Cm and the consequences on the cycle parameters with Actinide recycle). Moreover, we have carried out a sensitivity study in order to analysis the impact of nuclear data uncertainties on some important parameters of the reactor (reactivity coefficients) and on the isotopic concentration. This original study allows us to assess the accuracy of the results, of the presented tendencies and of the propositions made in the present thesis. (author) [fr

  17. Progress of full MOX core design in ABWR

    Izutsu, S.; Sasagawa, M.; Aoyama, M.; Maruyama, H.; Suzuki, T.

    2000-01-01

    Full MOX ABWR core design has been made, based on the MOX design concept of 8x8 bundle configuration with a large central water rod, 40 GWd/t maximum bundle exposure, and the compatibility with 9x9 high-burnup UO 2 bundles. Core performance on shutdown margin and thermal margin of the MOX-loaded core is similar to that of UO 2 cores for the range from full UO 2 core to full MOX core. Safety analyses based on its safety parameters and MOX property have shown its conformity to the design criteria in Japan. In order to confirm the applicability of the nuclear design method to full MOX cores, Tank-type Critical Assembly (TCA) experiment data have been analyzed on criticality, power distribution and β eff /l measurements. (author)

  18. [A concept analysis of assertiveness].

    Park, Hyoung-Sook; Yang, Young-Ok

    2006-06-01

    The purpose of this study was to analyze and clarify the meaning of the concept, assertiveness. This study used Walker and Avant's process of concept analysis. 1. Attributes of assertiveness were defined as 1) Self-esteem 2) Comprehension to others 3) Clarification of the subject 4) Verbal communication 5) Non-verbal communication. 2. The antecedents of assertiveness consist of these facts 1) The occurrence of a conflict situation 2) The occurrence of will to stick to one's opinions. 3. There are consequences occurring as a result of assertiveness 1) Positive self-confidence 2) Increased comprehension or consideration to others 3) Expand of mutual respect 4) Maintenance of continuously cooperative relationship with each other 5) Output of acceptable results to each other. Assertiveness is a core human behavior and is key to interpersonal relationships. Using the components of the concept of assertiveness, many conflicts in a nursing situation can be effectively prevented.

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

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

    2016-01-04

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

  20. Rodent malaria parasites : genome organization & comparative genomics

    Kooij, Taco W.A.

    2006-01-01

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

  1. The concept of collaborative health.

    Sandberg, Håkan

    2010-11-01

    Based on empirical research about teamwork in human service organizations in Sweden, the concept of collaborative health (CH) encapsulates the physical, psychological and social health resources the individual uses in teamwork; resources which at the same time are influenced by the teamwork. My argument built on empirical research leading up to identifying and defining the core concept in this article, is that teamwork affects team members' health and this in turn affects the teamwork and its outcome. In this paper collaborative health is viewed from a social constructionism perspective and discussed in relation to earlier concepts developed in social psychology and working life research, including psychosocial stress and burnout. The paper also introduces the concept of functional synergy, which in this context is defined as the simultaneous presence of sharp goal-orientation and synergy in teamwork. The need for a holistic team theory is emphasized as a tool in research on teamwork. Such a theory relies on identifying sound and illuminating constituent concepts. I suggest that collaborative health could be a useful concept for better understanding the complex collaborative and co-operative teamwork of human service organizations of today.

  2. Mathematical concepts

    Jost, Jürgen

    2015-01-01

    The main intention of this book is to describe and develop the conceptual, structural and abstract thinking of mathematics. Specific mathematical structures are used to illustrate the conceptual approach; providing a deeper insight into mutual relationships and abstract common features. These ideas are carefully motivated, explained and illustrated by examples so that many of the more technical proofs can be omitted. The book can therefore be used: ·         simply as an overview of the panorama of mathematical structures and the relations between them, to be supplemented by more detailed texts whenever you want to acquire a working knowledge of some structure ·         by itself as a first introduction to abstract mathematics ·         together with existing textbooks, to put their results into a more general perspective ·         to gain a new and hopefully deeper perspective after having studied such textbooks Mathematical Concepts has a broader scope and is less detaile...

  3. PWR core design calculations

    Trkov, A.; Ravnik, M.; Zeleznik, N.

    1992-01-01

    Functional description of the programme package Cord-2 for PWR core design calculations is presented. Programme package is briefly described. Use of the package and calculational procedures for typical core design problems are treated. Comparison of main results with experimental values is presented as part of the verification process. (author) [sl

  4. HGVA: the Human Genome Variation Archive.

    Lopez, Javier; Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gräf, Stefan; Rendon, Augusto; Dopazo, Joaquin; Medina, Ignacio

    2017-07-03

    High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK's 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Replaceable LMFBR core components

    Evans, E.A.; Cunningham, G.W.

    1976-01-01

    Much progress has been made in understanding material and component performance in the high temperature, fast neutron environment of the LMFBR. Current data have provided strong assurance that the initial core component lifetime objectives of FFTF and CRBR can be met. At the same time, this knowledge translates directly into the need for improved core designs that utilize improved materials and advanced fuels required to meet objectives of low doubling times and extended core component lifetimes. An industrial base for the manufacture of quality core components has been developed in the US, and all procurements for the first two core equivalents for FFTF will be completed this year. However, the problem of fabricating recycled plutonium while dramatically reducing fabrication costs, minimizing personnel exposure, and protecting public health and safety must be addressed

  6. Lunar Core and Tides

    Williams, J. G.; Boggs, D. H.; Ratcliff, J. T.

    2004-01-01

    Variations in rotation and orientation of the Moon are sensitive to solid-body tidal dissipation, dissipation due to relative motion at the fluid-core/solid-mantle boundary, and tidal Love number k2 [1,2]. There is weaker sensitivity to flattening of the core-mantle boundary (CMB) [2,3,4] and fluid core moment of inertia [1]. Accurate Lunar Laser Ranging (LLR) measurements of the distance from observatories on the Earth to four retroreflector arrays on the Moon are sensitive to lunar rotation and orientation variations and tidal displacements. Past solutions using the LLR data have given results for dissipation due to solid-body tides and fluid core [1] plus Love number [1-5]. Detection of CMB flattening, which in the past has been marginal but improving [3,4,5], now seems significant. Direct detection of the core moment has not yet been achieved.

  7. Internal core tightener

    Brynsvold, G.V.; Snyder, H.J. Jr.

    1976-01-01

    An internal core tightener is disclosed which is a linear actuated (vertical actuation motion) expanding device utilizing a minimum of moving parts to perform the lateral tightening function. The key features are: (1) large contact areas to transmit loads during reactor operation; (2) actuation cam surfaces loaded only during clamping and unclamping operation; (3) separation of the parts and internal operation involved in the holding function from those involved in the actuation function; and (4) preloaded pads with compliant travel at each face of the hexagonal assembly at the two clamping planes to accommodate thermal expansion and irradiation induced swelling. The latter feature enables use of a ''fixed'' outer core boundary, and thus eliminates the uncertainty in gross core dimensions, and potential for rapid core reactivity changes as a result of core dimensional change. 5 claims, 12 drawing figures

  8. LMFBR design and its evolution. (2) Core design of LMFBR

    Uto, Nariaki; Mizuno, Tomoyasu

    2003-01-01

    Sodium-cooled core design studies are performed. MOX fuel core with axial blanket partial elimination subassembly due to safety consideration is studied. This type of core with high internal conversion ratio possesses capability of achieving 26 months of operation cycle length and 100 GWd/t of burnup averaged over core and blanket, which are superior characteristics in view of reducing cost of power generation. Metal fuel core is also studied, and its higher breeding capability reveals a potential of better core performance such as longer operation cycle length for the same level of electricity generation, though core outlet temperature is limited to lower level due to steel cladding-metal fuel compatibility concerns. Another metal fuel core concept using single Pu enrichment and two radial regions with individual fuel pin diameters achieves 550degC of core outlet temperature identical to that of MOX fuel core, keeping operation cycle length comparable with that of MOX fuel core. This series of study results show that sodium-cooled MOX and metal fuel cores have a high flexibility in satisfying various needs including fuel cycle cost and breeding capability, depending on the stage of introducing commercialized fast reactor cycle system. (author)

  9. Funding Opportunity: Genomic Data Centers

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

  10. Comparative Genome Analysis of Enterobacter cloacae

    Liu, Wing-Yee; Wong, Chi-Fat; Chung, Karl Ming-Kar; Jiang, Jing-Wei; Leung, Frederick Chi-Ching

    2013-01-01

    The Enterobacter cloacae species includes an extremely diverse group of bacteria that are associated with plants, soil and humans. Publication of the complete genome sequence of the plant growth-promoting endophytic E. cloacae subsp. cloacae ENHKU01 provided an opportunity to perform the first comparative genome analysis between strains of this dynamic species. Examination of the pan-genome of E. cloacae showed that the conserved core genome retains the general physiological and survival genes of the species, while genomic factors in plasmids and variable regions determine the virulence of the human pathogenic E. cloacae strain; additionally, the diversity of fimbriae contributes to variation in colonization and host determination of different E. cloacae strains. Comparative genome analysis further illustrated that E. cloacae strains possess multiple mechanisms for antagonistic action against other microorganisms, which involve the production of siderophores and various antimicrobial compounds, such as bacteriocins, chitinases and antibiotic resistance proteins. The presence of Type VI secretion systems is expected to provide further fitness advantages for E. cloacae in microbial competition, thus allowing it to survive in different environments. Competition assays were performed to support our observations in genomic analysis, where E. cloacae subsp. cloacae ENHKU01 demonstrated antagonistic activities against a wide range of plant pathogenic fungal and bacterial species. PMID:24069314

  11. Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization.

    Nair, Govind; Jungreuthmayer, Christian; Zanghellini, Jürgen

    2017-02-01

    Knockout strategies, particularly the concept of constrained minimal cut sets (cMCSs), are an important part of the arsenal of tools used in manipulating metabolic networks. Given a specific design, cMCSs can be calculated even in genome-scale networks. We would however like to find not only the optimal intervention strategy for a given design but the best possible design too. Our solution (PSOMCS) is to use particle swarm optimization (PSO) along with the direct calculation of cMCSs from the stoichiometric matrix to obtain optimal designs satisfying multiple objectives. To illustrate the working of PSOMCS, we apply it to a toy network. Next we show its superiority by comparing its performance against other comparable methods on a medium sized E. coli core metabolic network. PSOMCS not only finds solutions comparable to previously published results but also it is orders of magnitude faster. Finally, we use PSOMCS to predict knockouts satisfying multiple objectives in a genome-scale metabolic model of E. coli and compare it with OptKnock and RobustKnock. PSOMCS finds competitive knockout strategies and designs compared to other current methods and is in some cases significantly faster. It can be used in identifying knockouts which will force optimal desired behaviors in large and genome scale metabolic networks. It will be even more useful as larger metabolic models of industrially relevant organisms become available.

  12. The 2nd reactor core of the NS Otto Hahn

    Manthey, H.J.; Kracht, H.

    1979-01-01

    Details of the design of the 2nd reactor core are given, followed by a brief report summarising the operating experience gained with this 2nd core, as well as by an evaluation of measured data and statements concerning the usefulness of the knowledge gained for the development of future reactor cores. Quite a number of these data have been used to improve the concept and thus the specifications for the fuel elements of the 3rd core of the reactor of the NS Otto Hahn. (orig./HP) [de

  13. Gas core nuclear thermal rocket engine research and development in the former USSR

    Koehlinger, M.W.; Bennett, R.G.; Motloch, C.G.; Gurfink, M.M.

    1992-09-01

    Beginning in 1957 and continuing into the mid 1970s, the USSR conducted an extensive investigation into the use of both solid and gas core nuclear thermal rocket engines for space missions. During this time the scientific and engineering. problems associated with the development of a solid core engine were resolved. At the same time research was undertaken on a gas core engine, and some of the basic engineering problems associated with the concept were investigated. At the conclusion of the program, the basic principles of the solid core concept were established. However, a prototype solid core engine was not built because no established mission required such an engine. For the gas core concept, some of the basic physical processes involved were studied both theoretically and experimentally. However, no simple method of conducting proof-of-principle tests in a neutron flux was devised. This report focuses primarily on the development of the. gas core concept in the former USSR. A variety of gas core engine system parameters and designs are presented, along with a summary discussion of the basic physical principles and limitations involved in their design. The parallel development of the solid core concept is briefly described to provide an overall perspective of the magnitude of the nuclear thermal propulsion program and a technical comparison with the gas core concept

  14. Earth's inner core: Innermost inner core or hemispherical variations?

    Lythgoe, K. H.; Deuss, A.|info:eu-repo/dai/nl/412396610; Rudge, J. F.; Neufeld, J. A.

    2014-01-01

    The structure of Earth's deep inner core has important implications for core evolution, since it is thought to be related to the early stages of core formation. Previous studies have suggested that there exists an innermost inner core with distinct anisotropy relative to the rest of the inner core.

  15. Dependence of Core and Extended Flux on Core Dominance ...

    Abstract. Based on two extragalactic radio source samples, the core dominance parameter is calculated, and the correlations between the core/extended flux density and core dominance parameter are investi- gated. When the core dominance parameter is lower than unity, it is linearly correlated with the core flux density, ...

  16. Korrelasjon mellom core styrke, core stabilitet og utholdende styrke i core

    Berg-Olsen, Andrea Marie; Fugelsøy, Eivor; Maurstad, Ann-Louise

    2010-01-01

    Formålet med studien var å se hvilke korrelasjon det er mellom core styrke, core stabilitet og utholdende styrke i core. Testingen bestod av tre hoveddeler hvor vi testet core styrke, core stabilitet og utholdende styrke i core. Innenfor core styrke og utholdende styrke i core ble tre ulike tester utført. Ved måling av core stabilitet ble det gjennomført kun en test. I core styrke ble isometrisk abdominal fleksjon, isometrisk rygg ekstensjon og isometrisk lateral fleksjon testet. Sit-ups p...

  17. Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate

    Andersson Jan O

    2010-10-01

    Full Text Available Abstract Background Giardia intestinalis is a protozoan parasite that causes diarrhea in a wide range of mammalian species. To further understand the genetic diversity between the Giardia intestinalis species, we have performed genome sequencing and analysis of a wild-type Giardia intestinalis sample from the assemblage E group, isolated from a pig. Results We identified 5012 protein coding genes, the majority of which are conserved compared to the previously sequenced genomes of the WB and GS strains in terms of microsynteny and sequence identity. Despite this, there is an unexpectedly large number of chromosomal rearrangements and several smaller structural changes that are present in all chromosomes. Novel members of the VSP, NEK Kinase and HCMP gene families were identified, which may reveal possible mechanisms for host specificity and new avenues for antigenic variation. We used comparative genomics of the three diverse Giardia intestinalis isolates P15, GS and WB to define a core proteome for this species complex and to identify lineage-specific genes. Extensive analyses of polymorphisms in the core proteome of Giardia revealed differential rates of divergence among cellular processes. Conclusions Our results indicate that despite a well conserved core of genes there is significant genome variation between Giardia isolates, both in terms of gene content, gene polymorphisms, structural chromosomal variations and surface molecule repertoires. This study improves the annotation of the Giardia genomes and enables the identification of functionally important variation.

  18. Exploring Other Genomes: Bacteria.

    Flannery, Maura C.

    2001-01-01

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

  19. Windscale pile core surveys

    Curtis, R.F.; Mathews, R.F.

    1996-01-01

    The two Windscale Piles were closed down, defueled as far as possible and mothballed for thirty years following a fire in the core of Pile 1 in 1957 resulting from the spontaneous release of stored Wigner energy in the graphite moderator. Decommissioning of the reactors commenced in 1987 and has reached the stage where the condition of both cores needs to be determined. To this end, non-intrusive and intrusive surveys and sampling of the cores have been planned and partly implemented. The objectives for each Pile differ slightly. The location and quantity of fuel remaining in the damaged core of Pile 1 needed to be established, whereas the removal of all fuel from Pile 2 needed to be confirmed. In Pile 1, the possible existence of a void in the core is to be explored and in Pile 2, the level of Wigner energy remaining required to be quantified. Levels of radioactivity in both cores needed to be measured. The planning of the surveys is described including strategy, design, safety case preparation and the remote handling and viewing equipment required to carry out the inspection, sampling and monitoring work. The results from the completed non-intrusive survey of Pile 2 are summarised. They confirm that the core is empty and the graphite is in good condition. The survey of Pile 1 has just started. (UK)

  20. The niche party concept and its measurement

    Meyer, Thomas M; Miller, Bernhard

    2015-01-01

    The concept of the niche party has become increasingly popular in analyses of party competition. Yet, existing approaches vary in their definitions and their measurement approaches. We propose using a minimal definition that allows us to compare political parties in terms of their ?nicheness?. We argue that the conceptual core of the niche party concept is based on issue emphasis and that a niche party emphasizes policy areas neglected by its rivals. Based on this definition, we propose a con...

  1. Preliminary study on flexible core design of super FBR with multi-axial fuel shuffling

    Sukarman; Yamaji, Akifumi; Someya, Takayuki; Noda, Shogo

    2017-01-01

    Preliminary study has been conducted on developing a new flexible core design concept for the Supercritical water-cooled Fast Breeder Reactor (Super FBR) with multi-axial fuel shuffling. The proposed new concept focuses on the characteristic large axial coolant density change in supercritical water cooled reactors (SCWRs) when the coolant inlet temperature is below the pseudocritical point and large coolant enthalpy rise is taken in the core for achieving high thermal efficiency. The aim of the concept is to attain both the high breeding performance and good thermal-hydraulic performance at the same time. That is, short Compound System Doubling Time (CSDT) for high breeding, large coolant enthalpy rise for high thermal efficiency, and large core power. The proposed core concept consists of horizontal layers of mixed oxide (MOX) fuels and depleted uranium (DU) blanket layers at different elevation levels. Furthermore, the upper core and the lower core are separated and independent fuel shuffling schemes in these two core regions are considered. The number of fuel batches and fuel shuffling scheme of the upper core were changed to investigate influence of multi-axial fuel shuffling on the core characteristics. The core characteristics are evaluated with-three-dimensional diffusion calculations, which are fully-coupled with thermal-hydraulics calculations based on single channel analysis model. The results indicate that the proposed multi-axial fuel shuffling scheme does have a large influence on CSDT. Further investigations are necessary to develop the core concept. (author)

  2. Study of an amorphous alloy core transformer

    Nafalski, A.; Frost, D. C.

    1994-05-01

    Amorphous core transformers (ACT) have become a technological and commercial reality and there are an estimated 400,000 units installed worldwide [1]. Their applications reflect changes in buying practices, where the efficiency evaluation is an important factor in the purchasing decision for distribution transformers. Use of the total ownership cost (TOC) concept facilities the selection of a transformer on the basis of its performance. This concept is used in this paper to investigate the feasibility of applying a distribution ACT in Western Australian (WA). A 10 kVA ACT, evaluated by the TOC method, was compared with a traditional silicon iron core transformer of the same rating. The cost of amorphous metal (relative to alternative materials), the distribution load profile, and the values of capitalised loss costs are factors which affect the cost effectiveness of ACTs.

  3. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.

    Tamara Smokvina

    Full Text Available Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis

  4. Core shroud corner joints

    Gilmore, Charles B.; Forsyth, David R.

    2013-09-10

    A core shroud is provided, which includes a number of planar members, a number of unitary corners, and a number of subassemblies each comprising a combination of the planar members and the unitary corners. Each unitary corner comprises a unitary extrusion including a first planar portion and a second planar portion disposed perpendicularly with respect to the first planar portion. At least one of the subassemblies comprises a plurality of the unitary corners disposed side-by-side in an alternating opposing relationship. A plurality of the subassemblies can be combined to form a quarter perimeter segment of the core shroud. Four quarter perimeter segments join together to form the core shroud.

  5. IGCSE core mathematics

    Wall, Terry

    2013-01-01

    Give your core level students the support and framework they require to get their best grades with this book dedicated to the core level content of the revised syllabus and written specifically to ensure a more appropriate pace. This title has been written for Core content of the revised Cambridge IGCSE Mathematics (0580) syllabus for first teaching from 2013. ? Gives students the practice they require to deepen their understanding through plenty of practice questions. ? Consolidates learning with unique digital resources on the CD, included free with every book. We are working with Cambridge

  6. Development of Core Design Technology for LMR

    Kim, Yeong Il; Hong, S. G.; Jang, J. W. (and others)

    2007-06-15

    developed and programmed. The 1st order and exact perturbation theory calculation module to use in the TRI-Z geometry model was developed. The SFR inter-assembly core thermal flow analysis code MATCOM has been developed using the sub-channel code MATRA-LMR and the porous media code COMMIX-1AR/P. The analysis model for thermal creep, irradiation creep and the creep rupture strength characteristics for the Mod. HT9 were developed based on the available experiment data. To analyze the pin power distributions considering the influence of non-fuel pin inside fuel assembly, the form function concept was introduced and the program for the pin power calculation was develop.

  7. Genomics With Cloud Computing

    Sukhamrit Kaur; Sandeep Kaur

    2015-01-01

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

  8. Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes.

    Jinhui Wang

    Full Text Available Haplotypes A and B of 'Candidatus Liberibacter solanacearum' (CLso are associated with diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, D and E are associated with symptoms on apiaceous plants. To date, one complete genome of haplotype B and two high quality draft genomes of haplotype A have been obtained for these unculturable bacteria using metagenomics from the psyllid vector Bactericera cockerelli. Here, we present the first genomic sequences obtained for the carrot-associated CLso. These two genomic sequences of haplotype C, FIN114 (1.24 Mbp and FIN111 (1.20 Mbp, were obtained from carrot psyllids (Trioza apicalis harboring CLso. Genomic comparisons between the haplotypes A, B and C revealed that the genome organization differs between these haplotypes, due to large inversions and other recombinations. Comparison of protein-coding genes indicated that the core genome of CLso consists of 885 ortholog groups, with the pan-genome consisting of 1327 ortholog groups. Twenty-seven ortholog groups are unique to CLso haplotype C, whilst 11 ortholog groups shared by the haplotypes A and B, are not found in the haplotype C. Some of these ortholog groups that are not part of the core genome may encode functions related to interactions with the different host plant and psyllid species.

  9. Core principles of evolutionary medicine: A Delphi study.

    Grunspan, Daniel Z; Nesse, Randolph M; Barnes, M Elizabeth; Brownell, Sara E

    2018-01-01

    Evolutionary medicine is a rapidly growing field that uses the principles of evolutionary biology to better understand, prevent and treat disease, and that uses studies of disease to advance basic knowledge in evolutionary biology. Over-arching principles of evolutionary medicine have been described in publications, but our study is the first to systematically elicit core principles from a diverse panel of experts in evolutionary medicine. These principles should be useful to advance recent recommendations made by The Association of American Medical Colleges and the Howard Hughes Medical Institute to make evolutionary thinking a core competency for pre-medical education. The Delphi method was used to elicit and validate a list of core principles for evolutionary medicine. The study included four surveys administered in sequence to 56 expert panelists. The initial open-ended survey created a list of possible core principles; the three subsequent surveys winnowed the list and assessed the accuracy and importance of each principle. Fourteen core principles elicited at least 80% of the panelists to agree or strongly agree that they were important core principles for evolutionary medicine. These principles over-lapped with concepts discussed in other articles discussing key concepts in evolutionary medicine. This set of core principles will be helpful for researchers and instructors in evolutionary medicine. We recommend that evolutionary medicine instructors use the list of core principles to construct learning goals. Evolutionary medicine is a young field, so this list of core principles will likely change as the field develops further.

  10. CONSUL code package application for LMFR core calculations

    Chibinyaev, A.V.; Teplov, P.S.; Frolova, M.V. [RNC ' Kurchatovskiy institute' , Kurchatov sq.1, Moscow (Russian Federation)

    2008-07-01

    CONSUL code package designed for the calculation of reactor core characteristics has been developed at the beginning of 90's. The calculation of nuclear reactor core characteristics is carried out on the basis of correlated neutron, isotope and temperature distributions. The code package has been generally used for LWR core characteristics calculations. At present CONSUL code package was adapted to calculate liquid metal fast reactors (LMFR). The comparisons with IAEA computational test 'Evaluation of benchmark calculations on a fast power reactor core with near zero sodium void effect' and BN-1800 testing calculations are presented in the paper. The IAEA benchmark core is based on the innovative core concept with sodium plenum above the core BN-800. BN-1800 core is the next development step which is foreseen for the Russian fast reactor concept. The comparison of the operational parameters has shown good agreement and confirms the possibility of CONSUL code package application for LMFR core calculation. (authors)

  11. Fast Flux Test Facility core system

    Ethridge, J.L.; Baker, R.B.; Leggett, R.D.; Pitner, A.L.; Waltar, A.E.

    1990-11-01

    A review of Liquid Metal Reactor (LMR) core system accomplishments provides an excellent road map through the maze of issues that faced reactor designers 10 years ago. At that time relatively large uncertainties were associated with fuel pin and fuel assembly performance, irradiation of structural materials, and performance of absorber assemblies. The extensive core systems irradiation program at the US Department of Energy's Fast Flux Test Facility (FFTF) has addressed each of these principal issues. As a result of the progress made, the attention of long-range LMR planners and designers can shift away from improving core systems and focus on reducing capital costs to ensure the LMR can compete economically in the 21st century with other nuclear reactor concepts. 3 refs., 6 figs., 1 tab

  12. ESFR core optimization and uncertainty studies

    Rineiski, A.; Vezzoni, B.; Zhang, D.; Marchetti, M.; Gabrielli, F.; Maschek, W.; Chen, X.-N.; Buiron, L.; Krepel, J.; Sun, K.; Mikityuk, K.; Polidoro, F.; Rochman, D.; Koning, A.J.; DaCruz, D.F.; Tsige-Tamirat, H.; Sunderland, R.

    2015-01-01

    In the European Sodium Fast Reactor (ESFR) project supported by EURATOM in 2008-2012, a concept for a large 3600 MWth sodium-cooled fast reactor design was investigated. In particular, reference core designs with oxide and carbide fuel were optimized to improve their safety parameters. Uncertainties in these parameters were evaluated for the oxide option. Core modifications were performed first to reduce the sodium void reactivity effect. Introduction of a large sodium plenum with an absorber layer above the core and a lower axial fertile blanket improve the total sodium void effect appreciably, bringing it close to zero for a core with fresh fuel, in line with results obtained worldwide, while not influencing substantially other core physics parameters. Therefore an optimized configuration, CONF2, with a sodium plenum and a lower blanket was established first and used as a basis for further studies in view of deterioration of safety parameters during reactor operation. Further options to study were an inner fertile blanket, introduction of moderator pins, a smaller core height, special designs for pins, such as 'empty' pins, and subassemblies. These special designs were proposed to facilitate melted fuel relocation in order to avoid core re-criticality under severe accident conditions. In the paper further CONF2 modifications are compared in terms of safety and fuel balance. They may bring further improvements in safety, but their accurate assessment requires additional studies, including transient analyses. Uncertainty studies were performed by employing a so-called Total Monte-Carlo method, for which a large number of nuclear data files is produced for single isotopes and then used in Monte-Carlo calculations. The uncertainties for the criticality, sodium void and Doppler effects, effective delayed neutron fraction due to uncertainties in basic nuclear data were assessed for an ESFR core. They prove applicability of the available nuclear data for ESFR

  13. Engineered inorganic core/shell nanoparticles

    Mélinon, Patrice, E-mail: patrice.melinon@univ-lyon1.fr [Institut Lumière matière Université Claude Bernard Lyon 1 et CNRS et OMNT, Domaine Scientifique de la Doua, Bâtiment Léon Brillouin, 43 Boulevard du 11 Novembre 1918, F 69622 Villeurbanne (France); Begin-Colin, Sylvie [IPCMS et OMNT, 23 rue du Loess BP 43, 67034 STRASBOURG Cedex 2 (France); Duvail, Jean Luc [IMN UMR 6502 et OMNT Campus Sciences : 2 rue de la Houssinire, BP32229, 44322 Nantes Cedex3 (France); Gauffre, Fabienne [SPM et OMNT : Institut des sciences chimiques de Rennes - UMR 6226, 263 Avenue du General Leclerc, CS 74205, 35042 RENNES Cedex (France); Boime, Nathalie Herlin [IRAMIS-NIMBE, Laboratoire Francis Perrin (CEA CNRS URA 2453) et OMNT, Bat 522, CEA Saclay, 91191 Gif sur Yvette Cedex (France); Ledoux, Gilles [Institut Lumière Matière Université Claude Bernard Lyon 1 et CNRS et OMNT, Domaine Scientifique de la Doua, Bâtiment Alfred Kastler 43 Boulevard du 11 Novembre 1918 F 69622 Villeurbanne (France); Plain, Jérôme [Universit de technologie de Troyes LNIO-ICD, CNRS et OMNT 12 rue Marie Curie - CS 42060 - 10004 Troyes cedex (France); Reiss, Peter [CEA Grenoble, INAC-SPrAM, UMR 5819 CEA-CNRS-UJF et OMNT, Grenoble cedex 9 (France); Silly, Fabien [CEA, IRAMIS, SPEC, TITANS, CNRS 2464 et OMNT, F-91191 Gif sur Yvette (France); Warot-Fonrose, Bénédicte [CEMES-CNRS, Université de Toulouse et OMNT, 29 rue Jeanne Marvig F 31055 Toulouse (France)

    2014-10-20

    It has been for a long time recognized that nanoparticles are of great scientific interest as they are effectively a bridge between bulk materials and atomic structures. At first, size effects occurring in single elements have been studied. More recently, progress in chemical and physical synthesis routes permitted the preparation of more complex structures. Such structures take advantages of new adjustable parameters including stoichiometry, chemical ordering, shape and segregation opening new fields with tailored materials for biology, mechanics, optics magnetism, chemistry catalysis, solar cells and microelectronics. Among them, core/shell structures are a particular class of nanoparticles made with an inorganic core and one or several inorganic shell layer(s). In earlier work, the shell was merely used as a protective coating for the core. More recently, it has been shown that it is possible to tune the physical properties in a larger range than that of each material taken separately. The goal of the present review is to discuss the basic properties of the different types of core/shell nanoparticles including a large variety of heterostructures. We restrict ourselves on all inorganic (on inorganic/inorganic) core/shell structures. In the light of recent developments, the applications of inorganic core/shell particles are found in many fields including biology, chemistry, physics and engineering. In addition to a representative overview of the properties, general concepts based on solid state physics are considered for material selection and for identifying criteria linking the core/shell structure and its resulting properties. Chemical and physical routes for the synthesis and specific methods for the study of core/shell nanoparticle are briefly discussed.

  14. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

    Yang, Laurence; Tan, Justin; O'Brien, Edward J.

    2015-01-01

    based on proteomics data. This systems biology core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has 78% gene function overlap with minimal genomes (Buchnera aphidicola and Mycoplasma......Finding the minimal set of gene functions needed to sustain life is of both fundamental and practical importance. Minimal gene lists have been proposed by using comparative genomics-based core proteome definitions. A definition of a core proteome that is supported by empirical data, is understood...... at the systems-level, and provides a basis for computing essential cell functions is lacking. Here, we use a systems biology-based genome-scale model of metabolism and expression to define a functional core proteome consisting of 356 gene products, accounting for 44% of the Escherichia coli proteome by mass...

  15. The Importance of Sensory-Motor Control in Providing Core Stability Implications for Measurement and Training

    Borghuis, Jan; Hof, At L.; Lemmink, Koen A. P. M.

    2008-01-01

    Although the hip musculature is found to be very important in connecting the core to the lower extremities and in transferring forces from and to the core, it is proposed to leave the hip musculature out of consideration when talking about the concept of core stability. A low level of co-contraction

  16. Genome Maps, a new generation genome browser.

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

    2013-07-01

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

  17. Compound process fuel cycle concept

    Ikegami, Tetsuo

    2005-01-01

    Mass flow of light water reactor spent fuel for a newly proposed nuclear fuel cycle concept 'Compound Process Fuel Cycle' has been studied in order to assess the capacity of the concept for accepting light water reactor spent fuels, taking an example for boiling water reactor mixed oxide spent fuel of 60 GWd/t burn-up and for a fast reactor core of 3 GW thermal output. The acceptable heavy metal of boiling water reactor mixed oxide spent fuel is about 3.7 t/y/reactor while the burn-up of the recycled fuel is about 160 GWd/t and about 1.6 t/y reactor with the recycled fuel burn-up of about 300 GWd/t, in the case of 2 times recycle and 4 times recycle respectively. The compound process fuel cycle concept has such flexibility that it can accept so much light water reactor spent fuels as to suppress the light water reactor spent fuel pile-up if not so high fuel burn-up is expected, and can aim at high fuel burn-up if the light water reactor spent fuel pile-up is not so much. Following distinctive features of the concept have also been revealed. A sort of ideal utilization of boiling water reactor mixed oxide spent fuel might be achieved through this concept, since both plutonium and minor actinide reach equilibrium state beyond 2 times recycle. Changes of the reactivity coefficients during recycles are mild, giving roughly same level of reactivity coefficients as the conventional large scale fast breeder core. Both the radio-activity and the heat generation after 4 year cooling and after 4 times recycle are less than 2.5 times of those of the pre recycle fuel. (author)

  18. Heterogeneous gas core reactor

    Diaz, N.J.; Dugan, E.T.

    1983-01-01

    A heterogeneous gas core nuclear reactor is disclosed comprising a core barrel provided interiorly with an array of moderator-containing tubes and being otherwise filled with a fissile and/or fertile gaseous fuel medium. The fuel medium may be flowed through the chamber and through an external circuit in which heat is extracted. The moderator may be a fluid which is flowed through the tubes and through an external circuit in which heat is extracted. The moderator may be a solid which may be cooled by a fluid flowing within the tubes and through an external heat extraction circuit. The core barrel is surrounded by moderator/coolant material. Fissionable blanket material may be disposed inwardly or outwardly of the core barrel

  19. iPSC Core

    Federal Laboratory Consortium — The induced Pluripotent Stem Cells (iPSC) Core was created in 2011 to accelerate stem cell research in the NHLBI by providing investigators consultation, technical...

  20. Core Flight Software

    National Aeronautics and Space Administration — The AES Core Flight Software (CFS) project purpose is to analyze applicability, and evolve and extend the reusability of the CFS system originally developed by...

  1. PWR degraded core analysis

    Gittus, J.H.

    1982-04-01

    A review is presented of the various phenomena involved in degraded core accidents and the ensuing transport of fission products from the fuel to the primary circuit and the containment. The dominant accident sequences found in the PWR risk studies published to date are briefly described. Then chapters deal with the following topics: the condition and behaviour of water reactor fuel during normal operation and at the commencement of degraded core accidents; the generation of hydrogen from the Zircaloy-steam and the steel-steam reactions; the way in which the core deforms and finally melts following loss of coolant; debris relocation analysis; containment integrity; fission product behaviour during a degraded core accident. (U.K.)

  2. Genomic sovereignty and the African promise: mining the African genome for the benefit of Africa.

    de Vries, Jantina; Pepper, Michael

    2012-08-01

    Scientific interest in genomics in Africa is on the rise with a number of funding initiatives aimed specifically at supporting research in this area. Genomics research on material of African origin raises a number of important ethical issues. A prominent concern relates to sample export, which is increasingly seen by researchers and ethics committees across the continent as being problematic. The concept of genomic sovereignty proposes that unique patterns of genomic variation can be found in human populations, and that these are commercially, scientifically or symbolically valuable and in need of protection against exploitation. Although it is appealing as a response to increasing concerns regarding sample export, there are a number of important conceptual problems relating to the term. It is not clear, for instance, whether it is appropriate that ownership over human genomic samples should rest with national governments. Furthermore, ethnic groups in Africa are frequently spread across multiple nation states, and protection offered in one state may not prevent researchers from accessing the same group elsewhere. Lastly, scientific evidence suggests that the assumption that genomic data is unique for population groups is false. Although the frequency with which particular variants are found can differ between groups, such genes or variants per se are not unique to any population group. In this paper, the authors describe these concerns in detail and argue that the concept of genomic sovereignty alone may not be adequate to protect the genetic resources of people of African descent.

  3. Comfort measures: a concept analysis.

    Oliveira, Irene

    2013-01-01

    Reference to the concept of comfort measures is growing in the nursing and medical literature; however, the concept of comfort measures is rarely defined. For the comfort work of nurses to be recognized, nurses must be able to identify and delineate the key attributes of comfort measures. A concept analysis using Rodgers' evolutionary method (2000) was undertaken with the goal of identifying the core attributes of comfort measures and thereby clarifying this concept. Health care literature was accessed from the CINAHL and PubMed databases. No restrictions were placed on publication dates. Four main themes of attributes for comfort measures were identified during the analysis. Comfort measures involve an active, strategic process including elements of "stepping in" and "stepping back," are both simple and complex, move from a physical to a holistic perspective and are a part of supportive care. The antecedents to comfort measures are comfort needs and the most common consequence of comfort measures is enhanced comfort. Although the concept of comfort measures is often associated with end-of-life care, this analysis suggests that comfort measures are appropriate for nursing care in all settings and should be increasingly considered in the clinical management of patients who are living with multiple, chronic comorbidities.

  4. Restraint system for core elements of a reactor core

    Class, G.

    1975-01-01

    In a nuclear reactor, a core element bundle formed of a plurality of side-by-side arranged core elements is surrounded by restraining elements that exert a radially inwardly directly restraining force generating friction forces between the core elements in a restraining plane that is transverse to the core element axes. The adjoining core elements are in rolling contact with one another in the restraining plane by virtue of rolling-type bearing elements supported in the core elements. (Official Gazette)

  5. Convergent functional genomics of psychiatric disorders.

    Niculescu, Alexander B

    2013-10-01

    Genetic and gene expression studies, in humans and animal models of psychiatric and other medical disorders, are becoming increasingly integrated. Particularly for genomics, the convergence and integration of data across species, experimental modalities and technical platforms is providing a fit-to-disease way of extracting reproducible and biologically important signal, in contrast to the fit-to-cohort effect and limited reproducibility of human genetic analyses alone. With the advent of whole-genome sequencing and the realization that a major portion of the non-coding genome may contain regulatory variants, Convergent Functional Genomics (CFG) approaches are going to be essential to identify disease-relevant signal from the tremendous polymorphic variation present in the general population. Such work in psychiatry can provide an example of how to address other genetically complex disorders, and in turn will benefit by incorporating concepts from other areas, such as cancer, cardiovascular diseases, and diabetes. © 2013 Wiley Periodicals, Inc.

  6. Holistic Nursing in the Genetic/Genomic Era.

    Sharoff, Leighsa

    2016-06-01

    Holistic nursing practice is an ever-evolving transformative process with core values that require continued growth, professional leadership, and advocacy. Holistic nurses are required to stay current with all new required competencies, such as the Core Competencies in Genetics for Health Professional, and, as such, be adept at translating scientific evidence relating to genetics/genomics in the clinical setting. Knowledge of genetics/genomics in relation to nursing practice, policy, utilization, and research influence nurses' responsibilities. In addition to holistic nursing competencies, the holistic nurse must have basic knowledge and skills to integrate genetics/genomics aspects. It is important for holistic nurses to enhance their overall knowledge foundation, skills, and attitudes about genetics to prepare for the transformation in health care that is already underway. Holistic nurses can provide an important perspective to the application of genetics and genomics, focusing on health promotion, caring, and understanding the relationship between caring and families, community, and society. Yet there may be a lack of genetic and genomic knowledge to fully participate in the current genomic era. This article will explore the required core competencies for all health care professionals, share linkage of holistic nurses in practice with genetic/genomic conditions, and provide resources to further one's knowledge base. © The Author(s) 2015.

  7. FBR type reactor core

    Tamiya, Tadashi; Kawashima, Katsuyuki; Fujimura, Koji; Murakami, Tomoko.

    1995-01-01

    Neutron reflectors are disposed at the periphery of a reactor core fuel region and a blanket region, and a neutron shielding region is disposed at the periphery of them. The neutron reflector has a hollow duct structure having a sealed upper portion, a lower portion opened to cooling water, in which a gas and coolants separately sealed in the inside thereof. A driving pressure of a primary recycling pump is lowered upon reduction of coolant flow rate, then the liquid level of coolants in the neutron reflector is lowered due to imbalance between the driving pressure and a gas pressure, so that coolants having an effect as a reflector are eliminated from the outer circumference of the reactor core. Therefore, the amount of neutrons leaking from the reactor core is increased, and negative reactivity is charged to the reactor core. The negative reactivity of the neutron reflector is made greater than a power compensation reactivity. Since this enables reactor scram by using an inherent performance of the reactor core, the reactor core safety of an LMFBR-type reactor can be improved. (I.N.)

  8. The earths innermost core

    Nanda, J.N.

    1989-01-01

    A new earth model is advanced with a solid innermost core at the centre of the Earth where elements heavier than iron, over and above what can be retained in solution in the iron core, are collected. The innermost core is separated from the solid iron-nickel core by a shell of liquid copper. The innermost core has a natural vibration measured on the earth's surface as the long period 26 seconds microseisms. The earth was formed initially as a liquid sphere with a relatively thin solid crust above the Byerly discontinuity. The trace elements that entered the innermost core amounted to only 0.925 ppm of the molten mass. Gravitational differentiation must have led to the separation of an explosive thickness of pure 235 U causing a fission explosion that could expel beyond the Roche limit a crustal scab which would form the centre piece of the moon. A reservoir of helium floats on the liquid copper. A small proportion of helium-3, a relic of the ancient fission explosion present there will spell the exciting magnetic field. The field is stable for thousands of years because of the presence of large quantity of helium-4 which accounts for most of the gaseous collisions that will not disturb the atomic spin of helium-3 atoms. This field is prone to sudden reversals after long periods of stability. (author). 14 refs

  9. A new concept of equivalent homogenization method

    Kim, Young Jin; Pogoskekyan, Leonid; Kim, Young Il; Ju, Hyung Kook; Chang, Moon Hee [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1996-07-01

    A new concept of equivalent homogenization is proposed. The concept employs new set of homogenized parameters: homogenized cross sections (XS) and interface matrix (IM), which relates partial currents at the cell interfaces. The idea of interface matrix generalizes the idea of discontinuity factors (DFs), proposed and developed by K. Koebke and K. Smith. The offered concept covers both those of K. Koebke and K. Smith; both of them can be simulated within framework of new concept. Also, the offered concept covers Siemens KWU approach for baffle/reflector simulation, where the equivalent homogenized reflector XS are derived from the conservation of response matrix at the interface in 1D simi-infinite slab geometry. The IM and XS of new concept satisfy the same assumption about response matrix conservation in 1D semi-infinite slab geometry. It is expected that the new concept provides more accurate approximation of heterogeneous cell, especially in case of the steep flux gradients at the cell interfaces. The attractive shapes of new concept are: improved accuracy, simplicity of incorporation in the existing codes, equal numerical expenses in comparison to the K. Smith`s approach. The new concept is useful for: (a) explicit reflector/baffle simulation; (b) control blades simulation; (c) mixed UO{sub 2}/MOX core simulation. The offered model has been incorporated in the finite difference code and in the nodal code PANDOX. The numerical results show good accuracy of core calculations and insensitivity of homogenized parameters with respect to in-core conditions. 9 figs., 7 refs. (Author).

  10. Genome organization, instabilities, stem cells, and cancer

    Senthil Kumar Pazhanisamy

    2009-01-01

    Full Text Available It is now widely recognized that advances in exploring genome organization provide remarkable insights on the induction and progression of chromosome abnormalities. Much of what we know about how mutations evolve and consequently transform into genome instabilities has been characterized in the spatial organization context of chromatin. Nevertheless, many underlying concepts of impact of the chromatin organization on perpetuation of multiple mutations and on propagation of chromosomal aberrations remain to be investigated in detail. Genesis of genome instabilities from accumulation of multiple mutations that drive tumorigenesis is increasingly becoming a focal theme in cancer studies. This review focuses on structural alterations evolve to raise a variety of genome instabilities that are manifested at the nucleotide, gene or sub-chromosomal, and whole chromosome level of genome. Here we explore an underlying connection between genome instability and cancer in the light of genome architecture. This review is limited to studies directed towards spatial organizational aspects of origin and propagation of aberrations into genetically unstable tumors.

  11. JGI Fungal Genomics Program

    Grigoriev, Igor V.

    2011-03-14

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

  12. Genomic Encyclopedia of Fungi

    Grigoriev, Igor

    2012-08-10

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

  13. Genetic Competence Drives Genome Diversity in Bacillus subtilis

    Chevreux, Bastien; Serra, Cláudia R; Schyns, Ghislain; Henriques, Adriano O

    2018-01-01

    Abstract Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1,659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them. PMID:29272410

  14. Faustoviruses: Comparative genomics of new Megavirales family members

    Samia eBenamar

    2016-02-01

    Full Text Available An emerging interest for the giant virus discovery process, genome sequencing and analysis has allowed an expansion of the number of known Megavirales members. Using the protist Vermamoeba sp. as cell support, a new giant virus named Faustovirus has been isolated. In this study, we describe the genome sequences of nine Faustoviruses and build a genomic comparison in order to have a comprehensive overview of genomic composition and diversity among this new virus family. The average sequence length of these viruses is 467,592.44 bp (ranging from 455,803 bp to 491,024 bp, making them the fourth largest Megavirales genome after Mimiviruses, Pandoraviruses and Pithovirus sibericum. Faustovirus genomes displayed an average G+C content of 37.14 % (ranging from 36.22% to 39.59% which is close to the G+C content range of the Asfarviridae genomes (38%. The proportion of best matches and the phylogenetic analysis suggest a shared origin with Asfarviridae without belonging to the same family. The core-gene-based phylogeny of Faustoviruses study has identified four lineages. These results were confirmed by the analysis of amino acids and COGs category distribution. The diversity of the gene composition of these lineages is mainly explained by gene deletion or acquisition and some exceptions for gene duplications. The high proportion of best matches from Bacteria and Phycodnaviridae on the pan-genome and unique genes may be explained by an interaction occurring after the separation of the lineages. The Faustovirus core-genome appears to consolidate the surrounding of 207 genes whereas the pan-genome is described as an open pan-genome, its enrichment via the discovery of new Faustoviruses is required to better seize all the genomic diversity of this family.

  15. Cost Concept Model and Gateway Specification

    Kejser, Ulla Bøgvad

    2014-01-01

    This document introduces a Framework supporting the implementation of a cost concept model against which current and future cost models for curating digital assets can be benchmarked. The value built into this cost concept model leverages the comprehensive engagement by the 4C project with various...... to promote interoperability; • A Nested Model for Digital Curation—that visualises the core concepts, demonstrates how they interact and places them into context visually by linking them to A Cost and Benefit Model for Curation; This Framework provides guidance for data collection and associated calculations...

  16. Teachers' Conceptions of Mathematical Modeling

    Gould, Heather

    2013-01-01

    The release of the "Common Core State Standards for Mathematics" in 2010 resulted in a new focus on mathematical modeling in United States curricula. Mathematical modeling represents a way of doing and understanding mathematics new to most teachers. The purpose of this study was to determine the conceptions and misconceptions held by…

  17. Genomics With Cloud Computing

    Sukhamrit Kaur

    2015-04-01

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

  18. The advanced MAPLE reactor concept

    Lidstone, R.F.; Lee, A.G.; Gillespie, G.E.; Smith, H.J.

    1989-01-01

    During the past several years, Atomic Energy of Canada Limited (AECL) has been developing the new MAPLE multipurpose reactor concept, which is capable of generating peak thermal neutron fluxes of up to 3 x 10 18 n/m 2 s in its heavy water reflector at a nominal thermal power level of 15MW. An assessment of the MAPLE-D 2 O reactor has shown that it could also be used as a high-flux neutron source. it could be developed to be used for several applications if a 12-site annular core is used. Thermal fluxes several times greater than in existing facilities would be available (author)

  19. NASA's Gravitational - Wave Mission Concept Study

    Stebbins, Robin; Jennrich, Oliver; McNamara, Paul

    2012-01-01

    With the conclusion of the NASA/ESA partnership on the Laser Interferometer Space Antenna (LISA) Project, NASA initiated a study to explore mission concepts that will accomplish some or all of the LISA science objectives at lower cost. The Gravitational-Wave Mission Concept Study consisted of a public Request for Information (RFI), a Core Team of NASA engineers and scientists, a Community Science Team, a Science Task Force, and an open workshop. The RFI yielded were 12 mission concepts, 3 instrument concepts and 2 technologies. The responses ranged from concepts that eliminated the drag-free test mass of LISA to concepts that replace the test mass with an atom interferometer. The Core Team reviewed the noise budgets and sensitivity curves, the payload and spacecraft designs and requirements, orbits and trajectories and technical readiness and risk. The Science Task Force assessed the science performance by calculating the horizons. the detection rates and the accuracy of astrophysical parameter estimation for massive black hole mergers, stellar-mass compact objects inspiraling into central engines. and close compact binary systems. Three mission concepts have been studied by Team-X, JPL's concurrent design facility. to define a conceptual design evaluate kt,y performance parameters. assess risk and estimate cost and schedule. The Study results are summarized.

  20. Development of inherent core technologies for advanced reactor

    Kim, Keung Koo; Noh, J.M.; Hwang, D.H.

    1999-03-01

    Recently, the developed countries made their effort on developing the advanced reactor which will result in significantly enhanced safety and economy. However, they will protect the advanced reactor and its design technology with patent and proprietary right. Therefore, it is very important to develop our own key core concepts and inherent core design technologies which can form a foundation of indigenous technologies for development of the domestic advanced reactor in order to keep the superiority in the nuclear plant building market among the developing countries. In order to provide the basic technology for the core design of advanced reactor, this project is for developing the inherent core design concepts with enhanced safety and economy, and associated methodologies and technologies for core analyses. The feasibility study of constructing domestic critical facilities are performed by surveying the status and utilization of foreign facilities and by investigating the demand for domestic facilities. The research results developed in this project, such as core analysis methodologies for hexagonal core, conceptual core design based on hexagonal fuel assemblies and soluble boron core design and control strategies, will provide a technical foundation in developing core design of domestic advanced reactor. Furthermore, they will strengthen the competitiveness of Korean nuclear technology. We also expect that some of the design concepts developed in this project to improve the reactor safety and economy can be applicable to the design of advanced reactor. This will significantly reduce the public anxiety on the nuclear power plant, and will contribute to the economy of construction and operation for the future domestic reactors. Even though the critical facility will not be constructed right now, the investigation of the status and utilization of foreign critical facility will contribute to the future critical facility construction. (author). 150 refs., 34 tabs., 103

  1. Development of inherent core technologies for advanced reactor

    Kim, Keung Koo; Noh, J.M.; Hwang, D.H. [and others

    1999-03-01

    Recently, the developed countries made their effort on developing the advanced reactor which will result in significantly enhanced safety and economy. However, they will protect the advanced reactor and its design technology with patent and proprietary right. Therefore, it is very important to develop our own key core concepts and inherent core design technologies which can form a foundation of indigenous technologies for development of the domestic advanced reactor in order to keep the superiority in the nuclear plant building market among the developing countries. In order to provide the basic technology for the core design of advanced reactor, this project is for developing the inherent core design concepts with enhanced safety and economy, and associated methodologies and technologies for core analyses. The feasibility study of constructing domestic critical facilities are performed by surveying the status and utilization of foreign facilities and by investigating the demand for domestic facilities. The research results developed in this project, such as core analysis methodologies for hexagonal core, conceptual core design based on hexagonal fuel assemblies and soluble boron core design and control strategies, will provide a technical foundation in developing core design of domestic advanced reactor. Furthermore, they will strengthen the competitiveness of Korean nuclear technology. We also expect that some of the design concepts developed in this project to improve the reactor safety and economy can be applicable to the design of advanced reactor. This will significantly reduce the public anxiety on the nuclear power plant, and will contribute to the economy of construction and operation for the future domestic reactors. Even though the critical facility will not be constructed right now, the investigation of the status and utilization of foreign critical facility will contribute to the future critical facility construction. (author). 150 refs., 34 tabs., 103

  2. Ecophysiology of novel core phylotypes in activated sludge wastewater treatment plants with nutrient removal

    McIlroy, Simon Jon; Awata, Takanori; Nierychlo, Marta

    limited to no information is available for their ecophysiology in activated sludge. A combination of MAR-FISH and SIP was applied to identify members of the genera Rhodoferax, Dechloromonas and Sulfuritalea, all within the class Betaproteobacteria, to be core denitrifiers in these systems. Similar...... may explain why many of these core organisms have not attracted attention during the many years of research into the ecology of these systems. The future goal will be to obtain genome sequences for members of these core genera, applying recently developed protocols for the assembly of genomes from...

  3. Reactor core control device

    Sano, Hiroki

    1998-01-01

    The present invention provides a reactor core control device, in which switching from a manual operation to an automatic operation, and the control for the parameter of an automatic operation device are facilitated. Namely, the hysteresis of the control for the operation parameter by an manual operation input means is stored. The hysteresis of the control for the operation parameter is collected. The state of the reactor core simulated by an operation control to which the collected operation parameters are manually inputted is determined as an input of the reactor core state to the automatic input means. The record of operation upon manual operation is stored as a hysteresis of control for the operation parameter, but the hysteresis information is not only the result of manual operation of the operation parameter. This is results of operation conducted by a skilled operator who judge the state of the reactor core to be optimum. Accordingly, it involves information relevant to the reactor core state. Then, it is considered that the optimum automatic operation is not deviated greatly from the manual operation. (I.S.)

  4. Microbial comparative pan-genomics using binomial mixture models

    Ussery, David; Snipen, L; Almøy, T

    2009-01-01

    The size of the core- and pan-genome of bacterial species is a topic of increasing interest due to the growing number of sequenced prokaryote genomes, many from the same species. Attempts to estimate these quantities have been made, using regression methods or mixture models. We extend the latter...... approach by using statistical ideas developed for capture-recapture problems in ecology and epidemiology. RESULTS: We estimate core- and pan-genome sizes for 16 different bacterial species. The results reveal a complex dependency structure for most species, manifested as heterogeneous detection...... probabilities. Estimated pan-genome sizes range from small (around 2600 gene families) in Buchnera aphidicola to large (around 43000 gene families) in Escherichia coli. Results for Echerichia coli show that as more data become available, a larger diversity is estimated, indicating an extensive pool of rarely...

  5. Function Concepts for Machine Parts

    Mortensen, Niels Henrik

    1999-01-01

    The majority of resources, like time and costs, consumed in industrial product development can be related to detailed design, i.e. the materialisation of machine parts (German Maschinenteile). Existing design theories based on a systems approach, e.g. Haberfellner [5] all have function, i.......e. transformation from input to output or ability to deliver purposeful effects as the core concept. The units in a product which posses functions are the organs (German: Funktionsträgern). Because individual parts do not posses functions, one could argue that the design theories based on a systems approach...... to be identification of a purposeful behaviour concept, i.e. function for a machine part. The contribution is based on the theory of technical systems, Hubka and the domain theory, Andreasen....

  6. Selection of core animals in the Algorithm for Proven and Young using a simulation model.

    Bradford, H L; Pocrnić, I; Fragomeni, B O; Lourenco, D A L; Misztal, I

    2017-12-01

    The Algorithm for Proven and Young (APY) enables the implementation of single-step genomic BLUP (ssGBLUP) in large, genotyped populations by separating genotyped animals into core and non-core subsets and creating a computationally efficient inverse for the genomic relationship matrix (G). As APY became the choice for large-scale genomic evaluations in BLUP-based methods, a common question is how to choose the animals in the core subset. We compared several core definitions to answer this question. Simulations comprised a moderately heritable trait for 95,010 animals and 50,000 genotypes for animals across five generations. Genotypes consisted of 25,500 SNP distributed across 15 chromosomes. Genotyping errors and missing pedigree were also mimicked. Core animals were defined based on individual generations, equal representation across generations, and at random. For a sufficiently large core size, core definitions had the same accuracies and biases, even if the core animals had imperfect genotypes. When genotyped animals had unknown parents, accuracy and bias were significantly better (p ≤ .05) for random and across generation core definitions. © 2017 The Authors. Journal of Animal Breeding and Genetics Published by Blackwell Verlag GmbH.

  7. Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes

    Charu Tripathi

    2017-07-01

    Full Text Available Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C using PacBio RSII SMRT technique. The small genome (2.01 Mbp comprises a chromosome (1.87 Mbp and a plasmid (143 Kbp, designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%. We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI, conserved marker genes (31 and 400, pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5 by recruiting raw metagenomic data (from the same niche against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.

  8. Evidence that personal genome testing enhances student learning in a course on genomics and personalized medicine.

    Keyan Salari

    Full Text Available An emerging debate in academic medical centers is not about the need for providing trainees with fundamental education on genomics, but rather the most effective educational models that should be deployed. At Stanford School of Medicine, a novel hands-on genomics course was developed in 2010 that provided students the option to undergo personal genome testing as part of the course curriculum. We hypothesized that use of personal genome testing in the classroom would enhance the learning experience of students. No data currently exist on how such methods impact student learning; thus, we surveyed students before and after the course to determine its impact. We analyzed responses using paired statistics from the 31 medical and graduate students who completed both pre-course and post-course surveys. Participants were stratified by those who did (N = 23 or did not (N = 8 undergo personal genome testing. In reflecting on the experience, 83% of students who underwent testing stated that they were pleased with their decision compared to 12.5% of students who decided against testing (P = 0.00058. Seventy percent of those who underwent personal genome testing self-reported a better understanding of human genetics on the basis of having undergone testing. Further, students who underwent personal genome testing demonstrated an average 31% increase in pre- to post-course scores on knowledge questions (P = 3.5×10(-6; this was significantly higher (P = 0.003 than students who did not undergo testing, who showed a non-significant improvement. Undergoing personal genome testing and using personal genotype data in the classroom enhanced students' self-reported and assessed knowledge of genomics, and did not appear to cause significant anxiety. At least for self-selected students, the incorporation of personal genome testing can be an effective educational tool to teach important concepts of clinical genomic testing.

  9. The PWR cores management

    Barral, J.C.; Rippert, D.; Johner, J.

    2000-01-01

    During the meeting of the 25 january 2000, organized by the SFEN, scientists and plant operators in the domain of the PWR debated on the PWR cores management. The five first papers propose general and economic information on the PWR and also the fast neutron reactors chains in the electric power market: statistics on the electric power industry, nuclear plant unit management, the ITER project and the future of the thermonuclear fusion, the treasurer's and chairman's reports. A second part offers more technical papers concerning the PWR cores management: performance and optimization, in service load planning, the cores management in the other countries, impacts on the research and development programs. (A.L.B.)

  10. Molten core retention assembly

    Lampe, R.F.

    1976-01-01

    Molten fuel produced in a core overheating accident is caught by a molten core retention assembly consisting of a horizontal baffle plate having a plurality of openings therein, heat exchange tubes having flow holes near the top thereof mounted in the openings, and a cylindrical imperforate baffle attached to the plate and surrounding the tubes. The baffle assembly is supported from the core support plate of the reactor by a plurality of hanger rods which are welded to radial beams passing under the baffle plate and intermittently welded thereto. Preferably the upper end of the cylindrical baffle terminates in an outwardly facing lip to which are welded a plurality of bearings having slots therein adapted to accept the hanger rods

  11. Core status computing system

    Yoshida, Hiroyuki.

    1982-01-01

    Purpose: To calculate power distribution, flow rate and the like in the reactor core with high accuracy in a BWR type reactor. Constitution: Total flow rate signals, traverse incore probe (TIP) signals as the neutron detector signals, thermal power signals and pressure signals are inputted into a process computer, where the power distribution and the flow rate distribution in the reactor core are calculated. A function generator connected to the process computer calculates the absolute flow rate passing through optional fuel assemblies using, as variables, flow rate signals from the introduction part for fuel assembly flow rate signals, data signals from the introduction part for the geometrical configuration data at the flow rate measuring site of fuel assemblies, total flow rate signals for the reactor core and the signals from the process computer. Numerical values thus obtained are given to the process computer as correction signals to perform correction for the experimental data. (Moriyama, K.)

  12. Comparative Genome Analysis and Genome Evolution

    Snel, Berend

    2002-01-01

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

  13. A decade of human genome project conclusion: Scientific diffusion about our genome knowledge.

    Moraes, Fernanda; Góes, Andréa

    2016-05-06

    The Human Genome Project (HGP) was initiated in 1990 and completed in 2003. It aimed to sequence the whole human genome. Although it represented an advance in understanding the human genome and its complexity, many questions remained unanswered. Other projects were launched in order to unravel the mysteries of our genome, including the ENCyclopedia of DNA Elements (ENCODE). This review aims to analyze the evolution of scientific knowledge related to both the HGP and ENCODE projects. Data were retrieved from scientific articles published in 1990-2014, a period comprising the development and the 10 years following the HGP completion. The fact that only 20,000 genes are protein and RNA-coding is one of the most striking HGP results. A new concept about the organization of genome arose. The ENCODE project was initiated in 2003 and targeted to map the functional elements of the human genome. This project revealed that the human genome is pervasively transcribed. Therefore, it was determined that a large part of the non-protein coding regions are functional. Finally, a more sophisticated view of chromatin structure emerged. The mechanistic functioning of the genome has been redrafted, revealing a much more complex picture. Besides, a gene-centric conception of the organism has to be reviewed. A number of criticisms have emerged against the ENCODE project approaches, raising the question of whether non-conserved but biochemically active regions are truly functional. Thus, HGP and ENCODE projects accomplished a great map of the human genome, but the data generated still requires further in depth analysis. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:215-223, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

  14. Genome Variation Map: a data repository of genome variations in BIG Data Center.

    Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

    2018-01-04

    The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Genome Variation Map: a data repository of genome variations in BIG Data Center

    Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

    2018-01-01

    Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

  16. Genomic Data Commons launches

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

  17. Rat Genome Database (RGD)

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

  18. Data on genome analysis of Bacillus velezensis LS69.

    Liu, Guoqiang; Kong, Yingying; Fan, Yajing; Geng, Ce; Peng, Donghai; Sun, Ming

    2017-08-01

    The data presented in this article are related to the published entitled "Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria" (Liu et al., 2017) [1]. Genome analysis revealed B. velezensis LS69 has a good potential for biocontrol and plant growth promotion. This article provides an extended analysis of the genetic islands, core genes and amylolysin loci of B. velezensis LS69.

  19. Data on genome analysis of Bacillus velezensis LS69

    Liu, Guoqiang; Kong, Yingying; Fan, Yajing; Geng, Ce; Peng, Donghai; Sun, Ming

    2017-01-01

    The data presented in this article are related to the published entitled “Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria” (Liu et al., 2017) [1]. Genome analysis revealed B. velezensis LS69 has a good potential for biocontrol and plant growth promotion. This article provides an extended analysis of the genetic islands, core genes and amylolysin loci of B. velezensis LS69.

  20. Data on genome analysis of Bacillus velezensis LS69

    Guoqiang Liu

    2017-08-01

    Full Text Available The data presented in this article are related to the published entitled “Whole-genome sequencing of Bacillus velezensis LS69, a strain with a broad inhibitory spectrum against pathogenic bacteria” (Liu et al., 2017 [1]. Genome analysis revealed B. velezensis LS69 has a good potential for biocontrol and plant growth promotion. This article provides an extended analysis of the genetic islands, core genes and amylolysin loci of B. velezensis LS69.

  1. Genome Sequence of the Biocontrol Strain Pseudomonas fluorescens F113

    Redondo-Nieto, Miguel; Barret, Matthieu; Morrisey, John P.; Germaine, Kieran; Martínez-Granero, Francisco; Barahona, Emma; Navazo, Ana; Sánchez-Contreras, María; Moynihan, Jennifer A.; Giddens, Stephen R.; Coppoolse, Eric R.; Muriel, Candela; Stiekema, Willem J.; Rainey, Paul B.; Dowling, David; O'Gara, Fergal; Martín, Marta

    2012-01-01

    Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) that has biocontrol activity against fungal plant pathogens and is a model for rhizosphere colonization. Here, we present its complete genome sequence, which shows that besides a core genome very similar to those of other strains sequenced within this species, F113 possesses a wide array of genes encoding specialized functions for thriving in the rhizosphere and interacting with eukaryotic organisms. PMID:22328765

  2. Skate Genome Project: Cyber-Enabled Bioinformatics Collaboration

    Vincent, J.

    2011-01-01

    The Skate Genome Project, a pilot project of the North East Cyber infrastructure Consortium, aims to produce a draft genome sequence of Leucoraja erinacea, the Little Skate. The pilot project was designed to also develop expertise in large scale collaborations across the NECC region. An overview of the bioinformatics and infrastructure challenges faced during the first year of the project will be presented. Results to date and lessons learned from the perspective of a bioinformatics core will be highlighted.

  3. TMI-2 core examination

    Hobbins, R.R.; MacDonald, P.E.; Owen, D.E.

    1983-01-01

    The examination of the damaged core at the Three Mile Island Unit 2 (TMI-2) reactor is structured to address the following safety issues: fission product release, transport, and deposition; core coolability; containment integrity; and recriticality during severe accidents; as well as zircaloy cladding ballooning and oxidation during so-called design basis accidents. The numbers of TMI-2 components or samples to be examined, the priority of each examination, the safety issue addressed by each examination, the principal examination techniques to be employed, and the data to be obtained and the principal uses of the data are discussed in this paper

  4. Superconducting tin core fiber

    Homa, Daniel; Liang, Yongxuan; Hill, Cary; Kaur, Gurbinder; Pickrell, Gary

    2015-01-01

    In this study, we demonstrated superconductivity in a fiber with a tin core and fused silica cladding. The fibers were fabricated via a modified melt-draw technique and maintained core diameters ranging from 50-300 microns and overall diameters of 125-800 microns. Superconductivity of this fiber design was validated via the traditional four-probe test method in a bath of liquid helium at temperatures on the order of 3.8 K. The synthesis route and fiber design are perquisites to ongoing research dedicated all-fiber optoelectronics and the relationships between superconductivity and the material structures, as well as corresponding fabrication techniques. (orig.)

  5. LMFBR core design analysis

    Cho, M.; Yang, J.C.; Yoh, K.C.; Suk, S.D.; Soh, D.S.; Kim, Y.M.

    1980-01-01

    The design parameters of a commercial-scale fast breeder reactor which is currently under construction by regeneration of these data is preliminary analyzed. The analysis of nuclear and thermal characteristics as well as safety features of this reactor is emphasized. And the evaluation of the initial core mentioned in the system description is carried out in the areas of its kinetics and control system, and, at the same time, the flow distribution of sodium and temperature distribution of the initial FBR core system are calculated. (KAERI INIS Section)

  6. Nuclear core catchers

    Golden, M.P.; Tilbrook, R.W.; Heylmun, N.F.

    1976-01-01

    A receptacle is described for taking the molten fragments of a nuclear reactor during a reactor core fusion accident. The receptacle is placed under the reactor. It includes at least one receptacle for the reactor core fragments, with a dome shaped part to distribute the molten fragments and at least one outside layer of alumina bricks around the dome. The characteristic of this receptacle is that the outer layer of bricks contains neutron poison rods which pass through the bricks and protrude in relation to them [fr

  7. Organizing Core Tasks

    Boll, Karen

    has remained much the same within the last 10 years. However, how the core task has been organized has changed considerable under the influence of various “organizing devices”. The paper focusses on how organizing devices such as risk assessment, output-focus, effect orientation, and treatment...... projects influence the organization of core tasks within the tax administration. The paper shows that the organizational transformations based on the use of these devices have had consequences both for the overall collection of revenue and for the employees’ feeling of “making a difference”. All in all...

  8. PWR core design calculations

    Trkov, A; Ravnik, M; Zeleznik, N [Inst. Jozef Stefan, Ljubljana (Slovenia)

    1992-07-01

    Functional description of the programme package Cord-2 for PWR core design calculations is presented. Programme package is briefly described. Use of the package and calculational procedures for typical core design problems are treated. Comparison of main results with experimental values is presented as part of the verification process. (author) [Slovenian] Opisali smo programski paket CORD-2, ki se uporablja pri projektnih izracunih sredice pri upravljanju tlacnovodnega reaktorja. Prikazana je uporaba paketa in racunskih postopkov za tipicne probleme, ki nastopajo pri projektiranju sredice. Primerjava glavnih rezultatov z eksperimentalnimi vrednostmi je predstavljena kot del preveritvenega procesa. (author)

  9. Visualization for genomics: the Microbial Genome Viewer.

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

    2004-07-22

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

  10. Genomic prediction using subsampling

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

    2017-01-01

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

  11. A comparative design study of PB-BI cooled reactor cores with forced and natural convection cooling

    Mizuno, Tomoyasu; Enuma, Yasuhiro; Tanji, Mikio

    2003-01-01

    A comparative core design study is performed on Pb-Bi cooled reactors with forced and natural convection (FC and NC) cooling. Major interests of the study are core performance and core safety features. The designed core concepts with nitride fuel achieve reasonable breeding capability. The results of unprotected event analyses such as UTOP and ULOF show that both of concepts have possible features to withstand unprotected events due to negative reactivity feedback by Doppler effect, control rod drive line expansion, etc. These results lead to a conclusion that both of concepts have possible capability as one of future promising core concepts. A FC cooling core concept has more advantage if fuel recycle viewpoint is emphasized. (author)

  12. Draft genome of the gayal, Bos frontalis

    Wang, Ming-Shan; Zeng, Yan; Wang, Xiao; Nie, Wen-Hui; Wang, Jin-Huan; Su, Wei-Ting; Xiong, Zi-Jun; Wang, Sheng; Qu, Kai-Xing; Yan, Shou-Qing; Yang, Min-Min; Wang, Wen; Dong, Yang; Zhang, Ya-Ping

    2017-01-01

    Abstract Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history, and genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome. Based on the Illumina genomic sequencing platform, we have generated 350.38 Gb of raw data from 16 different insert-size libraries. A total of 276.86 Gb of clean data is retained after quality control. The assembled genome is about 2.85 Gb with scaffold and contig N50 sizes of 2.74 Mb and 14.41 kb, respectively. Repetitive elements account for 48.13% of the genome. Gene annotation has yielded 26 667 protein-coding genes, of which 97.18% have been functionally annotated. BUSCO assessment shows that our assembly captures 93% (3183 of 4104) of the core eukaryotic genes and 83.1% of vertebrate universal single-copy orthologs. We provide the first comprehensive de novo genome of the gayal. This genetic resource is integral for investigating the origin of the gayal and performing comparative genomic studies to improve understanding of the speciation and divergence of bovine species. The assembled genome could be used as reference in future population genetic studies of gayal. PMID:29048483

  13. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

    Daniel Garrido-Sanz

    Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

  14. Human genes and genomes: science, health, society

    Rosenberg, Leon E; Rosenberg, Diane Drobnis

    2012-01-01

    .... With the use of core concepts and the integration of extensive references, this book provides students and professionals alike with the most in-depth view of the current state of the science and its relevance across disciplines."--Publisher's website.

  15. Maximum stellar iron core mass

    An analytical method of estimating the mass of a stellar iron core, just prior to core collapse, is described in this paper. The method employed depends, in part, upon an estimate of the true relativistic mass increase experienced by electrons within a highly compressed iron core, just prior to core collapse, and is significantly ...

  16. Comparative genomic hybridization.

    Pinkel, Daniel; Albertson, Donna G

    2005-01-01

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

  17. Ebolavirus comparative genomics

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

    2015-01-01

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

  18. Conceptions of Parents, Conceptions of Self, and Conceptions of God.

    Buri, John R.; Mueller, Rebecca A.

    Different theorists have suggested that an individual's view of God may be related to one's view of one's father, one's mother, or one's self. A study was conducted to examine the relationship of college students' conceptions of the wrathfulness-kindliness of God to their conceptions of their father's and mother's permissiveness, authoritarianism,…

  19. Nuclear core baffling apparatus

    Cooper, F.W. Jr.; Silverblatt, B.L.; Knight, C.B.; Berringer, R.T.

    1979-01-01

    An apparatus for baffling the flow of reactor coolant fluid into and about the core of a nuclear reactor is described. The apparatus includes a plurality of longitudinally aligned baffle plates with mating surfaces that allow longitudinal growth with temperature increases while alleviating both leakage through the aligned plates and stresses on the components supporting the plates

  20. The Uncommon Core

    Ohler, Jason

    2013-01-01

    This author contends that the United States neglects creativity in its education system. To see this, he states, one may look at the Common Core State Standards. If one searches the English Language Arts and Literacy standards for the words "creative," "innovative," and "original"--and any associated terms, one will…

  1. Utah's New Mathematics Core

    Utah State Office of Education, 2011

    2011-01-01

    Utah has adopted more rigorous mathematics standards known as the Utah Mathematics Core Standards. They are the foundation of the mathematics curriculum for the State of Utah. The standards include the skills and understanding students need to succeed in college and careers. They include rigorous content and application of knowledge and reflect…

  2. Reactor core structure

    Higashinakagawa, Emiko; Sato, Kanemitsu.

    1992-01-01

    Taking notice on the fact that Fe based alloys and Ni based alloys are corrosion resistant in a special atmosphere of a nuclear reactor, Fe or Ni based alloys are applied to reactor core structural components such as fuel cladding tubes, fuel channels, spacers, etc. On the other hand, the neutron absorption cross section of zirconium is 0.18 barn while that of iron is 2.52 barn and that of nickel is 4.6 barn, which amounts to 14 to 25 times compared with that of zirconium. Accordingly, if the reactor core structural components are constituted by the Fe or Ni based alloys, neutron economy is lowered. Since it is desirable that neutrons contribute to uranium fission with least absorption to the reactor core structural components, the reactor core structural components are constituted with the Fe or Ni based alloys of good corrosion resistance only at a portion in contact with reactor water, that is, at a surface portion, while the main body is constituted with zircalloy in the present invention. Accordingly, corrosion resistnace can be kept while keeping small neutron absorption cross section. (T.M.)

  3. Investigation of EAS cores

    Shaulov S.B.

    2017-01-01

    Full Text Available The development of nuclear-electromagnetic cascade models in air in the late forties have shown informational content of the study of cores of extensive air showers (EAS. These investigations were the main goal in different experiments which were carried out over many years by a variety of methods. Outcomes of such investigations obtained in the HADRON experiment using an X-ray emulsion chamber (XREC as a core detector are considered. The Ne spectrum of EAS associated with γ-ray families, spectra of γ-rays (hadrons in EAS cores and the Ne dependence of the muon number, ⟨Nμ⟩, in EAS with γ-ray families are obtained for the first time at energies of 1015–1017 eV with this method. A number of new effects were observed, namely, an abnormal scaling violation in hadron spectra which are fundamentally different from model predictions, an excess of muon number in EAS associated with γ-ray families, and the penetrating component in EAS cores. It is supposed that the abnormal behavior of γ-ray spectra and Ne dependence of the muon number are explained by the emergence of a penetrating component in the 1st PCR spectrum ‘knee’ range. Nuclear and astrophysical explanations of the origin of the penetrating component are discussed. The necessity of considering the contribution of a single close cosmic-ray source to explain the PCR spectrum in the knee range is noted.

  4. Plutonium cores of zenith

    Barclay, F R; Cameron, I R; Drageset, A; Freemantle, R G; Wilson, D J

    1965-03-15

    The report describes a series of experiments carried out with plutonium fuel in the heated zero power reactor ZENITH, with the aim of testing current theoretical methods, with particular reference to excess reactivity, temperature coefficients, differential spectrum and reaction rate distributions. Two cores of widely different fissile/moderator atom ratios were loaded in order to test the theory under significantly varied spectrum conditions.

  5. Core damage risk indicators

    Szikszai, T.

    1994-01-01

    The purpose of this document is to show a method for the fast recalculation of the PSA. To avoid the information loose, it is necessary to simplify the PSA models, or at least reorganize them. The method, introduced in this document, require that preparation, so we try to show, how to do that. This document is an introduction. This is the starting point of the work related to the development of the risk indicators. In the future, with the application of this method, we are going to show an everyday use of the PSA results to produce the indicators of the core damage risk. There are two different indicators of the plant safety performance, related to the core damage risk. The first is the core damage frequency indicator (CDFI), and the second is the core damage probability indicator (CDPI). Of course, we cannot describe all of the possible ways to use these indicators, rather we will try to introduce the requirements to establish such an indicator system and the calculation process

  6. Core calculations of JMTR

    Nagao, Yoshiharu [Japan Atomic Energy Research Inst., Oarai, Ibaraki (Japan). Oarai Research Establishment

    1998-03-01

    In material testing reactors like the JMTR (Japan Material Testing Reactor) of 50 MW in Japan Atomic Energy Research Institute, the neutron flux and neutron energy spectra of irradiated samples show complex distributions. It is necessary to assess the neutron flux and neutron energy spectra of an irradiation field by carrying out the nuclear calculation of the core for every operation cycle. In order to advance core calculation, in the JMTR, the application of MCNP to the assessment of core reactivity and neutron flux and spectra has been investigated. In this study, in order to reduce the time for calculation and variance, the comparison of the results of the calculations by the use of K code and fixed source and the use of Weight Window were investigated. As to the calculation method, the modeling of the total JMTR core, the conditions for calculation and the adopted variance reduction technique are explained. The results of calculation are shown. Significant difference was not observed in the results of neutron flux calculations according to the difference of the modeling of fuel region in the calculations by K code and fixed source. The method of assessing the results of neutron flux calculation is described. (K.I.)

  7. Emergency core cooling system

    Kato, Ken.

    1989-01-01

    In PWR type reactors, a cooling water spray portion of emergency core cooling pipelines incorporated into pipelines on high temperature side is protruded to the inside of an upper plenum. Upon rupture of primary pipelines, pressure in a pressure vessel is abruptly reduced to generate a great amount of steams in the reactor core, which are discharged at a high flow rate into the primary pipelines on high temperature side. However, since the inside of the upper plenum has a larger area and the steam flow is slow, as compared with that of the pipelines on the high temperature side, ECCS water can surely be supplied into the reactor core to promote the re-flooding of the reactor core and effectively cool the reactor. Since the nuclear reactor can effectively be cooled to enable the promotion of pressure reduction and effective supply of coolants during the period of pressure reduction upon LOCA, the capacity of the pressure accumulation vessel can be decreased. Further, the re-flooding time for the reactor is shortened to provide an effect contributing to the improvement of the safety and the reduction of the cost. (N.H.)

  8. Concept relation discovery and innovation enabling technology (CORDIET)

    Poelmans, J.; Elzinga, P.; Neznanov, A.; Viaene, S.; Kuznetsov, S.O.; Ignatov, D.; Dedene, G.

    2011-01-01

    Concept Relation Discovery and Innovation Enabling Technology (CORDIET), is a toolbox for gaining new knowledge from unstructured text data. At the core of CORDIET is the C-K theory which captures the essential elements of innovation. The tool uses Formal Concept Analysis (FCA), Emergent Self

  9. Using "Monopoly" to Introduce Concepts of Race and Ethnic Relations

    Waren, Warren

    2011-01-01

    In this paper I suggest a technique which uses the familiar Parker Brother's game "Monopoly" to introduce core concepts of race and ethnic relations. I offer anecdotes from my classes where an abbreviated version of the game is used as an analog to highlight the sociological concepts of direct institutional discrimination, the legacy of…

  10. Neutronics of a mixed-flow gas-core reactor

    Soran, P.D.; Hansen, G.E.

    1977-11-01

    The study was made to investigate the neutronic feasibility of a mixed-flow gas-core reactor. Three reactor concepts were studied: four- and seven-cell radial reactors and a seven-cell scallop reactor. The reactors were fueled with UF 6 (either U-233 or U-235) and various parameters were varied. A four-cell reactor is not practical nor is the U-235 fueled seven-cell radial reactor; however, the 7-cell U-233 radial and scallop reactors can satisfy all design criteria. The mixed flow gas core reactor is a very attractive reactor concept and warrants further investigation

  11. Core design studies on various forms of coolants and fuel materials. 2. Studies on liquid heavy metal and gas cooled cores, small cores and evaluation of 4-type cores

    Hayashi, Hideyuki; Sakashita, Yoshiyuki; Naganuma, Masayuki; Takaki, Naoyuki; Mizuno, Tomoyasu; Ikegami, Tetsuo

    2001-01-01

    Alternative concepts to sodium cooled fast reactors, such as heavy metal liquid cooled reactors and gas cooled fast reactors were studied in Phase-1 of the feasibility studies, aiming at simplification of the system, high thermal efficiency and enhancing safety. Fuel and core specifications and nuclear characteristics were surveyed to meet the targets for commercialization of fast reactor cycle. Nuclear characteristics of small fast reactor cores were also surveyed from the perspective of the possibility of multi-purpose use and dispersed power stations. The key points of the design study for each concept in Phase-2 were summarized from the aspect of the screening of the candidates for FR commercialization. (author)

  12. Inflation targeting and core inflation

    Julie Smith

    2005-01-01

    This paper examines the interaction of core inflation and inflation targeting as a monetary policy regime. Interest in core inflation has grown because of inflation targeting. Core inflation is defined in numerous ways giving rise to many potential measures; this paper defines core inflation as the best forecaster of inflation. A cross-country study finds before the start of inflation targeting, but not after, core inflation differs between non-inflation targeters and inflation targeters. Thr...

  13. Information professionals: core competencies and professional development

    Flávia Ferreira

    2007-01-01

    Full Text Available Introduction. We discuss the concept of core competencies applied to policies for teaching and training information professionals, particularly librarians. Method. Sixty graduates of the Institute were employed as information professionals. These sixty were asked to attribute degrees of importance to specific items associated with knowledge and skills that, within the scope of this research, were considered core competencies for meeting the demands of their jobs. Participants were also asked to cite knowledge they acquired in school and knowledge they use in exercising their profession, the skills that they consider necessary but that they did not gain in school, and the difficulties they encounter in exercising their profession and for which they were not sufficiently well prepared. Analysis. Both quantitative and qualitative data analyses were performed. The data were tabulated using Access and several reports and cross-tabulations were generated. Results. The results suggest a gulf between knowledge and skills acquired in library school and those that are required by the job market. In particular, participants lacked the skills they needed to work with information and communication technologies. Conclusion. The concept of core competencies is increasingly taken into account by the productive sector of the economy. The educational system ought to keep up with this change. The empirical research described shows that there is a need to establish advanced and modern policies for the education of librarians, participants in the market for information professionals.

  14. The Sequenced Angiosperm Genomes and Genome Databases.

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

    2018-01-01

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

  15. Human genomics projects and precision medicine.

    Carrasco-Ramiro, F; Peiró-Pastor, R; Aguado, B

    2017-09-01

    The completion of the Human Genome Project (HGP) in 2001 opened the floodgates to a deeper understanding of medicine. There are dozens of HGP-like projects which involve from a few tens to several million genomes currently in progress, which vary from having specialized goals or a more general approach. However, data generation, storage, management and analysis in public and private cloud computing platforms have raised concerns about privacy and security. The knowledge gained from further research has changed the field of genomics and is now slowly permeating into clinical medicine. The new precision (personalized) medicine, where genome sequencing and data analysis are essential components, allows tailored diagnosis and treatment according to the information from the patient's own genome and specific environmental factors. P4 (predictive, preventive, personalized and participatory) medicine is introducing new concepts, challenges and opportunities. This review summarizes current sequencing technologies, concentrates on ongoing human genomics projects, and provides some examples in which precision medicine has already demonstrated clinical impact in diagnosis and/or treatment.

  16. Behavioral Economics: A New Lens for Understanding Genomic Decision Making.

    Moore, Scott Emory; Ulbrich, Holley H; Hepburn, Kenneth; Holaday, Bonnie; Mayo, Rachel; Sharp, Julia; Pruitt, Rosanne H

    2018-05-01

    This article seeks to take the next step in examining the insights that nurses and other healthcare providers can derive from applying behavioral economic concepts to support genomic decision making. As genomic science continues to permeate clinical practice, nurses must continue to adapt practice to meet new challenges. Decisions associated with genomics are often not simple and dichotomous in nature. They can be complex and challenging for all involved. This article offers an introduction to behavioral economics as a possible tool to help support patients', families', and caregivers' decision making related to genomics. Using current writings from nursing, ethics, behavioral economic, and other healthcare scholars, we review key concepts of behavioral economics and discuss their relevance to supporting genomic decision making. Behavioral economic concepts-particularly relativity, deliberation, and choice architecture-are specifically examined as new ways to view the complexities of genomic decision making. Each concept is explored through patient decision making and clinical practice examples. This article also discusses next steps and practice implications for further development of the behavioral economic lens in nursing. Behavioral economics provides valuable insight into the unique nature of genetic decision-making practices. Nurses are often a source of information and support for patients during clinical decision making. This article seeks to offer behavioral economic concepts as a framework for understanding and examining the unique nature of genomic decision making. As genetic and genomic testing become more common in practice, it will continue to grow in importance for nurses to be able to support the autonomous decision making of patients, their families, and caregivers. © 2018 Sigma Theta Tau International.

  17. Feasibility study of full-reactor gas core demonstration test

    Kunze, J. F.; Lofthouse, J. H.; Shaffer, C. J.; Macbeth, P. J.

    1973-01-01

    Separate studies of nuclear criticality, flow patterns, and thermodynamics for the gas core reactor concept have all given positive indications of its feasibility. However, before serious design for a full scale gas core application can be made, feasibility must be shown for operation with full interaction of the nuclear, thermal, and hydraulic effects. A minimum sized, and hence minimum expense, test arrangement is considered for a full gas core configuration. It is shown that the hydrogen coolant scattering effects dominate the nuclear considerations at elevated temperatures. A cavity diameter of somewhat larger than 4 ft (122 cm) will be needed if temperatures high enough to vaporize uranium are to be achieved.

  18. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

    Wolf Yuri I

    2007-11-01

    Full Text Available Abstract Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs. Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. Results New Archaeal Clusters of Orthologous Genes (arCOGs were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover ~88% of the genes in a genome compared to a ~76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; ~40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile

  19. Analytical Chemistry Core Capability Assessment - Preliminary Report

    Barr, Mary E.; Farish, Thomas J.

    2012-01-01

    The concept of 'core capability' can be nebulous one. Even at a fairly specific level, where core capability equals maintaining essential services, it is highly dependent upon the perspective of the requestor. Samples are submitted to analytical services because the requesters do not have the capability to conduct adequate analyses themselves. Some requests are for general chemical information in support of R and D, process control, or process improvement. Many analyses, however, are part of a product certification package and must comply with higher-level customer quality assurance requirements. So which services are essential to that customer - just those for product certification? Does the customer also (indirectly) need services that support process control and improvement? And what is the timeframe? Capability is often expressed in terms of the currently utilized procedures, and most programmatic customers can only plan a few years out, at best. But should core capability consider the long term where new technologies, aging facilities, and personnel replacements must be considered? These questions, and a multitude of others, explain why attempts to gain long-term consensus on the definition of core capability have consistently failed. This preliminary report will not try to define core capability for any specific program or set of programs. Instead, it will try to address the underlying concerns that drive the desire to determine core capability. Essentially, programmatic customers want to be able to call upon analytical chemistry services to provide all the assays they need, and they don't want to pay for analytical chemistry services they don't currently use (or use infrequently). This report will focus on explaining how the current analytical capabilities and methods evolved to serve a variety of needs with a focus on why some analytes have multiple analytical techniques, and what determines the infrastructure for these analyses. This information will be

  20. Study on core design for reduced-moderation water reactors

    Okubo, Tsutomu

    2002-01-01

    The Reduced-Moderation Water Reactor (RMWR) is a water-cooled reactor with the harder neutron spectrum comparing with the LWR, resulting from low neutron moderation due to reduced water volume fraction. Based on the difference from the spectrum from the LWR, the conversion from U-238 to Pu-239 is promoted and the new cores preferable to effective utilization of uranium resource can be possible Design study of the RMWR core started in 1997 and new four core concepts (three BWR cores and one PWR core) are recently evaluated in terms of control rod worths, plutonium multiple recycle, high burnup and void coefficient. Comparative evaluations show needed incorporation of control rod programming and simplified PUREX process as well as development of new fuel cans for high burnup of 100 GW-d/t. Final choice of design specifications will be made at the next step aiming at realization of the RMWR. (T. Tanaka)

  1. Study on core design for reduced-moderation water reactors

    Okubo, Tsutomu [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    2002-12-01

    The Reduced-Moderation Water Reactor (RMWR) is a water-cooled reactor with the harder neutron spectrum comparing with the LWR, resulting from low neutron moderation due to reduced water volume fraction. Based on the difference from the spectrum from the LWR, the conversion from U-238 to Pu-239 is promoted and the new cores preferable to effective utilization of uranium resource can be possible Design study of the RMWR core started in 1997 and new four core concepts (three BWR cores and one PWR core) are recently evaluated in terms of control rod worths, plutonium multiple recycle, high burnup and void coefficient. Comparative evaluations show needed incorporation of control rod programming and simplified PUREX process as well as development of new fuel cans for high burnup of 100 GW-d/t. Final choice of design specifications will be made at the next step aiming at realization of the RMWR. (T. Tanaka)

  2. Thermal-hydraulic characteristics of double flat core HCLWR

    Sugimoto, Jun; Iwamura, Takamichi; Okubo, Tsutomu; Murao, Yoshio

    1989-02-01

    A thermal-hydraulic characteristics of double flat core high conversion light water reactor (HCLWR) is described. The concept of flat core proposed by Ishiguro et al. is to achieve negative void reactivity coefficient in tight lattice core, and at the same time, high conversion ratio and high burnup can be obtainable. The proposed double flat core HCLWR, based on these physical advantages and the consideration of safety assurance, aims at efficient use of the pressure vessel space to produce comparable thermal output as current 3-loop PWRs. The present work revealed the following items concerning the thermalhydraulic feasibility of the double flat core HCLWR: (1) Main thermal-hydraulic parameters of the plant can be almost the same as current PWRs, showing the use of PWR standard components without major modifications except in core region. (2) Heat removal from the fuel rod in a steady operational condition has enough margin to the critical heat flux (CHF) limit, which is evaluated with the existing CHF correlations. (3) The calculation by REFLA code shows that the maximum cladding temperature in LOCA-reflood is estimated to be far lower than the licensing criteria. It is therefore considered that the proposed double flat core HCLWR is feasible from the point of thermal-hydraulics. Since the available data base has certain applicational limit to the very short core as the present double flat core HCLWR, further detailed assessment is required. (author)

  3. The plastid genome of the red macroalga Grateloupia taiwanensis (Halymeniaceae.

    Michael S DePriest

    Full Text Available The complete plastid genome sequence of the red macroalga Grateloupia taiwanensis S.-M.Lin & H.-Y.Liang (Halymeniaceae, Rhodophyta is presented here. Comprising 191,270 bp, the circular DNA contains 233 protein-coding genes and 29 tRNA sequences. In addition, several genes previously unknown to red algal plastids are present in the genome of G. taiwanensis. The plastid genomes from G. taiwanensis and another florideophyte, Gracilaria tenuistipitata var. liui, are very similar in sequence and share significant synteny. In contrast, less synteny is shared between G. taiwanensis and the plastid genome representatives of Bangiophyceae and Cyanidiophyceae. Nevertheless, the gene content of all six red algal plastid genomes here studied is highly conserved, and a large core repertoire of plastid genes can be discerned in Rhodophyta.

  4. The Plastid Genome of the Red Macroalga Grateloupia taiwanensis (Halymeniaceae)

    DePriest, Michael S.; Bhattacharya, Debashish; López-Bautista, Juan M.

    2013-01-01

    The complete plastid genome sequence of the red macroalga Grateloupia taiwanensis S.-M.Lin & H.-Y.Liang (Halymeniaceae, Rhodophyta) is presented here. Comprising 191,270 bp, the circular DNA contains 233 protein-coding genes and 29 tRNA sequences. In addition, several genes previously unknown to red algal plastids are present in the genome of G. taiwanensis. The plastid genomes from G. taiwanensis and another florideophyte, Gracilaria tenuistipitata var. liui, are very similar in sequence and share significant synteny. In contrast, less synteny is shared between G. taiwanensis and the plastid genome representatives of Bangiophyceae and Cyanidiophyceae. Nevertheless, the gene content of all six red algal plastid genomes here studied is highly conserved, and a large core repertoire of plastid genes can be discerned in Rhodophyta. PMID:23894297

  5. Ice cores and palaeoclimate

    Krogh Andersen, K.; Ditlevsen, P.; Steffensen, J.P.

    2001-01-01

    Ice cores from Greenland give testimony of a highly variable climate during the last glacial period. Dramatic climate warmings of 15 to 25 deg. C for the annual average temperature in less than a human lifetime have been documented. Several questions arise: Why is the Holocene so stable? Is climatic instability only a property of glacial periods? What is the mechanism behind the sudden climate changes? Are the increased temperatures in the past century man-made? And what happens in the future? The ice core community tries to attack some of these problems. The NGRIP ice core currently being drilled is analysed in very high detail, allowing for a very precise dating of climate events. It will be possible to study some of the fast changes on a year by year basis and from this we expect to find clues to the sequence of events during rapid changes. New techniques are hoped to allow for detection of annual layers as far back as 100,000 years and thus a much improved time scale over past climate changes. It is also hoped to find ice from the Eemian period. If the Eemian layers confirm the GRIP sequence, the Eemian was actually climatically unstable just as the glacial period. This would mean that the stability of the Holocene is unique. It would also mean, that if human made global warming indeed occurs, we could jeopardize the Holocene stability and create an unstable 'Eemian situation' which ultimately could start an ice age. Currenlty mankind is changing the composition of the atmosphere. Ice cores document significant increases in greenhouse gases, and due to increased emissions of sulfuric and nitric acid from fossil fuel burning, combustion engines and agriculture, modern Greenland snow is 3 - 5 times more acidic than pre-industrial snow (Mayewski et al., 1986). However, the magnitude and abruptness of the temperature changes of the past century do not exceed the magnitude of natural variability. It is from the ice core perspective thus not possible to attribute the

  6. The core proteome and pan proteome of Salmonella Paratyphi A epidemic strains.

    Li Zhang

    Full Text Available Comparative proteomics of the multiple strains within the same species can reveal the genetic variation and relationships among strains without the need to assess the genomic data. Similar to comparative genomics, core proteome and pan proteome can also be obtained within multiple strains under the same culture conditions. In this study we present the core proteome and pan proteome of four epidemic Salmonella Paratyphi A strains cultured under laboratory culture conditions. The proteomic information was obtained using a Two-dimensional gel electrophoresis (2-DE technique. The expression profiles of these strains were conservative, similar to the monomorphic genome of S. Paratyphi A. Few strain-specific proteins were found in these strains. Interestingly, non-core proteins were found in similar categories as core proteins. However, significant fluctuations in the abundance of some core proteins were also observed, suggesting that there is elaborate regulation of core proteins in the different strains even when they are cultured in the same environment. Therefore, core proteome and pan proteome analysis of the multiple strains can demonstrate the core pathways of metabolism of the species under specific culture conditions, and further the specific responses and adaptations of the strains to the growth environment.

  7. Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.

    I-Hsuan Lin

    Full Text Available Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I and S. pasteurianus ATCC 43144 (biotype II.2. The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92% and 1607 (86% of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS and substantial evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to contribute to the fitness and virulence of each of the two subspecies. We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans. This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops.

  8. Species concept and speciation

    Amal Y. Aldhebiani

    2018-03-01

    Full Text Available Defining and recognizing a species has been a controversial issue for a long time. To determine the variation and the limitation between species, many concepts have been proposed. When a taxonomist study a particular taxa, he/she must adopted a species concept and provide a species limitation to define this taxa. In this paper some of species concepts are discussed starting from the typological species concepts to the phylogenetic concept. Positive and negative aspects of these concepts are represented in addition to their application. Keywords: Species concept, Species limitation, Species, Taxonomy, Classification

  9. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes

    Kaas, Rolf Sommer; Rundsten, Carsten Friis; Ussery, David

    2012-01-01

    Background Escherichia coli exists in commensal and pathogenic forms. By measuring the variation of individual genes across more than a hundred sequenced genomes, gene variation can be studied in detail, including the number of mutations found for any given gene. This knowledge will be useful...... for creating better phylogenies, for determination of molecular clocks and for improved typing techniques. Results We find 3,051 gene clusters/families present in at least 95% of the genomes and 1,702 gene clusters present in 100% of the genomes. The former 'soft core' of about 3,000 gene families is perhaps...... more biologically relevant, especially considering that many of these genome sequences are draft quality. The E. coli pan-genome for this set of isolates contains 16,373 gene clusters. A core-gene tree, based on alignment and a pan-genome tree based on gene presence/absence, maps the relatedness...

  10. Emergency core cooling device

    Suzaki, Kiyoshi; Inoue, Akihiro.

    1979-01-01

    Purpose: To improve core cooling effect by making the operation region for a plurality of water injection pumps more broader. Constitution: An emergency reactor core cooling device actuated upon failure of recycling pipe ways is adapted to be fed with cooling water through a thermal sleeve by way of a plurality of water injection pump from pool water in a condensate storage tank and a pressure suppression chamber as water feed source. Exhaust pipes and suction pipes of each of the pumps are connected by way of switching valves and the valves are switched so that the pumps are set to a series operation if the pressure in the pressure vessel is high and the pumps are set to a parallel operation if the pressure in the pressure vessel is low. (Furukawa, Y.)

  11. Birefringent hollow core fibers

    Roberts, John

    2007-01-01

    Hollow core photonic crystal fiber (HC-PCF), fabricated according to a nominally non-birefringent design, shows a degree of un-controlled birefringence or polarization mode dispersion far in excess of conventional non polarization maintaining fibers. This can degrade the output pulse in many...... applications, and places emphasis on the development of polarization maintaining (PM) HC-PCF. The polarization cross-coupling characteristics of PM HC-PCF are very different from those of conventional PM fibers. The former fibers have the advantage of suffering far less from stress-field fluctuations...... and an increased overlap between the polarization modes at the glass interfaces. The interplay between these effects leads to a wavelength for optimum polarization maintenance, lambda(PM), which is detuned from the wavelength of highest birefringence. By a suitable fiber design involving antiresonance of the core...

  12. Plasma core reactor applications

    Latham, T.S.; Rodgers, R.J.

    1976-01-01

    Analytical and experimental investigations are being conducted to demonstrate the feasibility of fissioning uranium plasma core reactors and to characterize space and terrestrial applications for such reactors. Uranium hexafluoride (UF 6 ) fuel is injected into core cavities and confined away from the surface by argon buffer gas injected tangentially from the peripheral walls. Power, in the form of thermal radiation emitted from the high-temperature nuclear fuel, is transmitted through fused-silica transparent walls to working fluids which flow in axial channels embedded in segments of the cavity walls. Radiant heat transfer calculations were performed for a six-cavity reactor configuration; each cavity is approximately 1 m in diameter by 4.35 m in length. Axial working fluid channels are located along a fraction of each cavity peripheral wall

  13. Reactor core cooling device

    Kobayashi, Masahiro.

    1986-01-01

    Purpose: To safely and effectively cool down the reactor core after it has been shut down but is still hot due to after-heat. Constitution: Since the coolant extraction nozzle is situated at a location higher than the coolant injection nozzle, the coolant sprayed from the nozzle, is free from sucking immediately from the extraction nozzle and is therefore used effectively to cool the reactor core. As all the portions from the top to the bottom of the reactor are cooled simultaneously, the efficiency of the reactor cooling process is increased. Since the coolant extraction nozzle can be installed at a point considerably higher than the coolant injection nozzle, the distance from the coolant surface to the point of the coolant extraction nozzle can be made large, preventing cavitation near the coolant extraction nozzle. Therefore, without increasing the capacity of the heat exchanger, the reactor can be cooled down after a shutdown safely and efficiently. (Kawakami, Y.)

  14. Portero versus portador: Spanish interpretation of genomic terminology during whole exome sequencing results disclosure.

    Gutierrez, Amanda M; Robinson, Jill O; Statham, Emily E; Scollon, Sarah; Bergstrom, Katie L; Slashinski, Melody J; Parsons, Donald W; Plon, Sharon E; McGuire, Amy L; Street, Richard L

    2017-11-01

    Describe modifications to technical genomic terminology made by interpreters during disclosure of whole exome sequencing (WES) results. Using discourse analysis, we identified and categorized interpretations of genomic terminology in 42 disclosure sessions where Spanish-speaking parents received their child's WES results either from a clinician using a medical interpreter, or directly from a bilingual physician. Overall, 76% of genomic terms were interpreted accordantly, 11% were misinterpreted and 13% were omitted. Misinterpretations made by interpreters and bilingual physicians included using literal and nonmedical terminology to interpret genomic concepts. Modifications to genomic terminology made during interpretation highlight the need to standardize bilingual genomic lexicons. We recommend Spanish terms that can be used to refer to genomic concepts.

  15. The SAFR liquid metal concept

    Baumeister, E.B.

    1987-01-01

    The Sodium Advanced Fast Reactor (SAFR) modular reactor concept is being developed by the team of Rockwell International, Combustion Engineering, and Bechtel under the U.S. Department of Energy's (DOE's) Advanced Liquid Metal Reactor (LMR) program. The SAFR plant would provide a viable alternate to light water reactors, especially for applications favoring small incremental capacity additions. SAFR is also a logical step to facilitate the later transition to LMFBRs. The SAFR plant concept employs multiple 350-MWe LMR Power Pak modules. Each Power Pak is a standardized, shop-fabricated unit that can be barge-shipped to the plant site for installation. The 350-MWe size allows SAFR to capitalize on all the inherent safety features provided by small reactors and factory fabrication, while still preserving some economy of scale. Shop fabrication minimizes nuclear-grade field fabrication and minimizes the overall plant construction schedule and capital cost. Each Power Pak consists of one reactor assembly and associated heat transfer equipment coupled to a single turbine generator. The reactor core employs mixed uranium-plutonium zirconium alloy metal fuel. The metal-alloy fuel (which has been used in EBR-II) has cost, safety, and safeguard advantages. The intrinsic properties of the sodium coolant (e.g., high boiling point, low vapor pressure, and strong natural convection), blended together with the pool-type LMR concept and the metal fuel, result in an inherently safe plant. Passive inherent features provide both public safety and plant investment protection. Refueling is carried out annually on each Power Pak, replacing one-fourth of the core over a 6-day refueling outage. A colocated pyroprocessing fuel cycle facility can be accommodated at the site such that no off-site shipments are required. (J.P.N.)

  16. Selection of JAERI'S HTGR-GT concept

    Muto, Y.; Ishiyama, S.; Shiozawa, S.

    2001-01-01

    In JAERI, a feasibility study of HTGR-GT has been conducted as an assigned work from STA in Japan since January 1996. So far, the conceptual or preliminary designs of 600, 400 and 300 MW(t) power plants have been completed. The block type core and pebble-bed core have been selected in 600 MW(t) and 400/300 MW(t), respectively. The gas-turbine system adopts a horizontal single shaft rotor and then the power conversion vessel is separated into a turbine vessel and a heat exchanger vessel. In this paper, the issues related to the selection of these concepts are technically discussed. (author)

  17. Gas core reactors for coal gasification

    Weinstein, H.

    1976-01-01

    The concept of using a gas core reactor to produce hydrogen directly from coal and water is presented. It is shown that the chemical equilibrium of the process is strongly in favor of the production of H 2 and CO in the reactor cavity, indicating a 98 percent conversion of water and coal at only 1500 0 K. At lower temperatures in the moderator-reflector cooling channels the equilibrium strongly favors the conversion of CO and additional H 2 O to CO 2 and H 2 . Furthermore, it is shown the H 2 obtained per pound of carbon has 23 percent greater heating value than the carbon so that some nuclear energy is also fixed. Finally, a gas core reactor plant floating in the ocean is conceptualized which produces H 2 , fresh water and sea salts from coal

  18. .net core application lifecycle on Openshift

    CERN. Geneva

    2017-01-01

    # .net core application lifecycle on Openshift I will show an example of a lifecycle of an OpenShift application with an emphasis on the continuous integration and deployment. The application compatible with [.net Standard](https://docs.microsoft.com/en-us/dotnet/standard/net-standard) can be easily deployed on OpenShift using [Source2Image](https://docs.openshift.com/enterprise/3.0/architecture/core_concepts/builds_and_image_streams.html#source-build) functionality, which doesn't require developers to maintain docker images of the application. I will also present how to efficiently integrate this feature into GitLab pipelines with an automated deployment of the "review" environment, as one its parts.

  19. Schumpeter's core works revisited

    Andersen, Esben Sloth

    2012-01-01

    This paper organises Schumpeter’s core books in three groups: the programmatic duology,the evolutionaryeconomic duology,and the socioeconomic synthesis. By analysing these groups and their interconnections from the viewpoint of modern evolutionaryeconomics,the paper summarises resolved problems a...... and points at remaining challenges. Its analyses are based on distinctions between microevolution and macroevolution, between economic evolution and socioeconomic coevolution, and between Schumpeter’s three major evolutionary models (called Mark I, Mark II and Mark III)....

  20. Self-care Concept Analysis in Cancer Patients: An Evolutionary Concept Analysis

    Hasanpour-Dehkordi, Ali

    2016-01-01

    Background: Self-care is a frequently used concept in both the theory and the clinical practice of nursing and is considered an element of nursing theory by Orem. The aim of this paper is to identify the core attributes of the self-care concept in cancer patients. Materials and Methods: We used Rodgers? evolutionary method of concept analysis. The articles published in English language from 1980 to 2015 on nursing and non-nursing disciplines were analyzed. Finally, 85 articles, an MSc thesis,...